Live recombinant measles-M2 virus - its use in eliciting immunity against influenza viruses

[001] The invention relates to the field of immunity against influenza A virus. In this respect, the invention provides vectorized antigens derived from influenza viruses that trigger an immune response against influenza A viruses. The invention accordingly relates to an active ingredient which is a live attenuated recombinant measles virus expressing influenza A virus antigen(s) and to its use in the elicitation of immunity, in particular protective immunity and advantageously broad-spectrum protective immunity against influenza A virus.

[002] Influenza is caused by Influenza virus which typically infects people around the world during seasonal epidemics resulting in severe illness or death for a large number of the infected human hosts. In addition to seasonal epidemics, influenza viruses may emerge as novel strains that may cause pandemics.

[003] Influenza virus classifies as influenza A, influenza B and influenza C types and influenza A strains are considered to be the primary pathogens responsible for seasonal illness and also pandemic influenza outbreak. The influenza A virus is classified by reference to surface antigens which are the hemagglutinin antigen (HA) of which 18 subtypes have been identified and the neuraminidase antigen (NA) which defines 11 subtypes. A virus strain thus qualifies as A HxNy wherein "x" qualifies the subtype of HA and "y" qualifies the subtype of NA antigens. These surface antigens are known to constitute targets of the immune response. Among the various subtypes, A H1 N1 and A H3N2 are virus subtypes that have been circulating in the human population since 1918 and 1968 respectively; they are thus considered to derive antigens suitable for the design of seasonal vaccine and their HA and NA antigens are accordingly encompassed within vaccine compositions against seasonal flu. However, as the HA and NA antigens continuously evolve in the virus strains under the selective pressure of the immune system of their hosts, vaccines that make use of these antigens have to be redesigned every year and updated. HA and NA undergo two types of antigenic evolution. The first type is antigenic drift, which corresponds to accumulation of point mutations overtime and results in viruses that are antigenically different. The second type is antigenic shift, an abrupt and major change in the influenza A viruses infecting humans resulting in new hemagglutinin and/or new hemagglutinin and neuraminidase proteins. Shift results from the introduction in the human population of a new influenza A subtype or a virus with a hemagglutinin or a hemagglutinin / neuraminidase combination that is so different from the same subtype in humans that most people do not have immunity to the new virus. Such a "shift" occurred in 2009 when a new H1 N1 strain (called H1 N1 pdm or H1 N1v) emerged and quickly spread, causing a pandemic and ultimately replacing the seasonal H1 N1.

[004] It remains accordingly necessary to propose alternative vaccine candidates that would escape the drawbacks associated with the high variation of the antigens of influenza A viruses and, in addition, would be capable of providing protection against a broad range of influenza A strains, especially epidemic influenza A strains and advantageously pandemic influenza A strains. Difficulties however have been encountered in the developed and disclosed strategies even when such strategies aimed at targeting the conserved influenza antigenic motifs among different strains of influenza virus, in particular conserved motifs in nucleoprotein (NP), matrix (M1 and M2) proteins or HA glycoprotein.

[005] M2-based influenza vaccines have been proposed as a promising target for the elicitation of an immune response against influenza virus, because of its conserved amino acid sequence. In particular various vaccine candidates have been disclosed using the extracellular domain of the protein (M2e). However the various attempts using the M2 or the M2e antigens have not proved to elicit antibodies or T-cell response that would be strong enough and long lasting to efficiently and broadly protect human against influenza virus, be it against a seasonal virus or a pandemic one and these results have been correlated with poor immunity observed with this antigen during infection (Deng L. et al 2015).

[006] The M2e ectodomain of the M2 protein has also been subject of various studies attempting to determine its interest in the design of a vaccine as M2e appears to be highly conserved among human epidemic virus strains whatever the subtype, and does not appear to take part in the drift/shift phenomena impacting the immunity competition (that is seen for example with the HA antigen) thus making this M2e antigen an attractive antigen for the elicitation of a protective response against infection with influenza virus when defining a broad-spectrum influenza A vaccine enabling elicitation of a long-lasting response. However this domain is also only minimally immunogenic during infection and conventional vaccination, possibly due to low abundance of M2 in virions. It has nevertheless been observed that the B cell repertoire is capable of generating a specific anti-M2e antibody response when a mammalian host primed with a first virus infection is then boosted by re-infection with an influenza virus including a heterosubtypic one (Deng L. et al 2015).

[007] The inventors have thus assumed that the interest of the M2 antigen, and in particular of portions of the M2 antigen that contain the M2e domain, needed further thoughts to improve their potential and possibly required the development of an appropriate vector molecule or system. [008] With the aim of developing a vaccine against seasonal or emerging or pandemic influenza viruses that could be used in children (in particular in young children or babies) or in adult population, the inventors designed a strategy based on the expression of the M2 influenza antigen (or a suitable portion thereof) by a measles virus vector, wherein in particular the measles virus is selected among live attenuated measles viruses such as vaccine measles viruses.

[009] The invention accordingly proposes a new approach to vectorize influenza antigens including M2 derived antigens wherein this approach takes benefits from the carrier properties and possibly of the immune properties of the vector and show improved immunogenicity. They hence provide a recombinant live attenuated measles virus capable of eliciting an immune response in human individuals that would be effective and long lasting against illness resulting from influenza A virus infection.

[0010] The invention relates to the use of the measles virus as a vector to express influenza A virus immunogens or epitopes wherein said immunogens or epitopes encompass polypeptides derived from an M2 protein (including the M2 protein), in particular the ectodomain of an M2 protein, wherein the M2 protein is advantageously a protein expressed from a consensus amino acid sequence derived from the amino acid sequences from multiple M2 proteins of influenza A virus strains.

[0011] Accordingly, the invention relates to a recombinant measles virus (MV) expressing at least a first antigen comprising or consisting in (i) a M2 antigen whose amino acid sequence is a consensus amino acid sequence representative of the M2 sequences of a selection of various subtypes of Influenza A viruses including circulating seasonal human viruses and optionally one or many pandemic human virus(es) and/or of a selection of various subtypes of Influenza A viruses including animal viruses, in particular endemic animal viruses and optionally animal virus(es) reported to have infected human subjects and considered to pose a pandemic risk, (ii) a portion comprising the ectodomain of said M2 antigen of (i) or consisting in said ectodomain.

[0012] The recombinant measles virus prepared according to the invention is derived from a measles virus which is advantageously a live attenuated measles virus, such as a virus authorized as a vaccine strain. The vaccine strain of measles virus can be distinguished from wild-type viruses by determination of the genotype from clinical samples or virus isolates. (See Specimens for Detection of Measles RNA by RT-PCR or Virus Isolation Lab Tools - Center of disease Control and Prevention.)

[0013] A measles virus suitable to carry out the invention may thus be a Schwarz strain known to be a live-attenuated vaccine strain (Rouvax® by Aventis Pasteur-France or Priorix® from GalxoSmithkline Pharma GmbH-Austria) or a Moraten strain that was shown to have the same nucleotide sequence as the Schwarz strain, or an AIK-C strain, a Zagreb strain (vaccine strains of the Edmonston lineage), or a TD97 strain, a CAM70 strain, a Leningrad-16 strain, a Shanghai-191 strain, a Changchun-47 strain (derived from different wild-type isolates) (Bankamp B. et al 2011 ). In a particular embodiment, the Schwarz strain or the Moraten strain is used.

[0014] In a particular embodiment of the invention, the recombinant measles virus is obtained starting from a cDNA corresponding to the full-length antigenomic RNA of the virus strain and cloned from virus particles of the live attenuated MV strain, in particular of the Schwarz or Moraten strain according to a process which is fully disclosed in WO 04/000876 (incorporated by reference) and the recombinant virus is rescued according to the process disclosed in WO04/000876 application for the rescue of measles virus particles starting from the preparation of a cDNA encoding the full length antigenomic (+)RNA of the virus. Regarding MV cDNA preparation and rescue of a cloned Schwarz strain of MV reference is made also to Combredet C et al (2003). The same rescue process may be used for other strains among the above cited ones using a molecular clone of the virus RNA. The recombinant Measles virus according to the invention may be grown on Vero cells. The recombinant MV may be presented for use in a liquid formulation. The Examples section provides also relevant indications in this regard for the preparation of the recombinant measles virus particles.

[0015] A "consensus sequence" according to the invention, in particular a consensus amino acid sequence is a sequence, respectively an amino acid sequence, which is the result of one of the following conception or selection methods:

a) it is derived from (i.e., defined) the alignment of multiple sequences of a determined protein identified for selected virus strains (especially influenza A strains) and in which each residue, in particular each amino acid residue, is the one which is the most frequent at the aligned positions in the different selected sequences occurring in known or in particular published virus strains that have been isolated. Accordingly, the residues which are shared at a given site among all selected sequences are present in the consensus sequence at said site and when a residue is variable at a given position among the selected sequences the most frequently found residue is retained in the consensus sequence at this position. When a considered residue is different in all the sequences selected for the definition of the consensus, the identity of this residue may be chosen to correspond to the residue in the sequence of the most predominant virus either in a relevant period of time or in terms of impact on health or

b) it is a sequence of (i) a particular influenza virus, especially influenza A virus, which is selected for its capability to elicit an immune response which is sufficiently broad to protect against other viruses, including viruses from a different subtype or lineage or (ii) it is a sequence of a particular virus cluster which cluster does not show sequence diversity and against which an immune response is sought, such cluster being illustrated by pandemic viruses.

Accordingly, a consensus sequence according to the invention is a representative sequence as a result of steps carried out to conceive it or based on existing viral sequences ; in particular but not necessarily it is a theoretical representative sequence of a group of determined actual sequences. Alternatively a consensus sequence is a sequence of an actual virus which is however essentially shared by a sufficient number of viruses within at least one lineage or subtype or cluster and accordingly does not show divergence (i.e., the comparison of the considered sequence within the group of interest shows less than 10% differences) in the sequence of amino acid residues of at least the protein(s)/antigens of interest (such a M2 or M2e or NP or M1 polypeptides of influenza A viruses) to present relevancy for the definition of an immunogenic product with a view to design a vaccine. A consensus sequence is used according to the invention to express a molecule which is a nucleic acid molecule or a polypeptide.

When reference is made to a consensus sequence in the present disclosure, each of these alternatives may be contemplated except where specified differently or technically inappropriate according to the understanding of the person skilled in the art. In a particular embodiment of the invention, the consensus sequence is the sequence as obtained under a).

[0016] The "M2 antigen" according to the invention is a structural tetrameric type III transmembrane protein of influenza A virus and is highly conserved among human influenza A subtypes. M2 protein is abundantly expressed on the surface of virus-infected cells. Antibodies against M2 are found in the serum of convalescent individuals after they have been infected with influenza A virus. The M2 protein contains 97 amino acids and is expressed from spliced mRNA derived from influenza gene segment 7 which also encodes the matrix M1. M2 mainly acts as a viroporin having a ion-channel activity. According to the invention, the amino acid sequence of the M2 antigen is a native viral sequence or is a consensus sequence derived from various viruses as disclosed herein.

[0017] The "ectodomain" of the M2 antigen (designated M2e) according to the invention is the external domain of the M2-protein in influenza A virus located on the N- terminal portion of the M2 protein (starting with residue 2 of the M2 protein). This domain is 23 amino acids in length (among which 9 residues are also present in the M1 protein and are the most conserved residues).

[0018] In a particular embodiment of the invention, the consensus sequence for the M2 protein is used to define the M2e antigen. In an embodiment, the consensus sequence of the M2 antigen (especially suitable for the design of the M2e antigen) encompasses alignment of the sequences of these polypeptides from the seasonal A/H1 N1 and A H3N2 virus subtypes and optionally A H9N2. In another embodiment, the consensus sequence is obtained by alignment of the sequences of this antigen from these strains together with the corresponding sequence from the pandemic strain pdmH1 N1 (also designated H1 N1v) found in 2009. In another embodiment, the consensus sequence of the M2 antigen (especially suitable for the design of the M2e antigen) also encompasses alignment of the sequences of these polypeptides from the avian A/H5N1 , A H9N2 and A H7N9 virus subtypes. In another embodiment, the consensus sequence of the M2 antigen (especially suitable for the design of the M2e antigen) also encompasses alignment of the sequences of these polypeptides from the avian A/H5N1 , A H9N2 and A H7N9 virus subtypes and further encompasses the alignement of the sequences of these polypeptides from the H5N6 and H10N8 virus subtypes detected in human. In another embodiment, the consensus sequence is obtained by alignment of the sequences of this antigen from these strains (according in particular to the various above groups) together with the corresponding sequence from the pandemic strain pdmH1 N1 (also designated H1 N1v) In another embodiment, the alignment may further encompass the corresponding sequence of the influenza A strain newly emerged as an epidemic strain or as a pandemic strain, or of an influenza animal strains reported to have infected human subjects and considered to pose a pandemic threat. In a particular embodiment the M2 or M2e consensus amino acid sequence is a human-type or an avian-type consensus sequence.

[0019] A "portion" of an antigen according to the invention is a molecule that consists in a fragment of the antigen wherein the amino acid sequence of this fragment is accordingly shorter than the amino acid sequence of the antigen and contains a segment of contiguous residues of the full-length sequence of the antigen. An amino acid sequence of such portion has at least 6 contiguous amino acid residues of the sequence of the antigen and advantageously consists or comprises one or a plurality of epitopes of the antigen, B and/or T cell epitopes. It may be less or equal to 25 amino acid residues long.

[0020] In an embodiment of the invention, the influenza A viruses referred to for the design of the consensus sequence of the M2 antigen encompass seasonal viruses that originate from distinct virus lineages or from distinct virus subtypes or from distinct virus clusters. Optionally, these viruses further encompass pandemic strains or animal strains reported to have infected human subjects and considered to pose a pandemic threat. In one virus lineage, one or many viruses may be used as reference. Among influenza A virus lineages, the following are especially considered: the human H1 N1 lineage since its reemergence in 1977, the human H3N2 lineage since its emergence in 1968, the human H1 N1 v lineage since its recent emergence in 2009, and lineages of avian H5N1 , H9N2 or H7N9 viruses which may emerge in the human population and pose a pandemic threat (WHO). Other animal virus subtypes including avian H2 and H9 viruses and swine H1 and H3 viruses may also pose a pandemic threat and are especially considered. The sequences of the influenza viruses and of their polypeptides are available in database such as NCBI where they are updated as soon as new viruses or isolates are characterized. The selection of the viruses for the design of the consensus sequence for the M2 antigen or the M2e portion thereof may take into account the diversity of strains in a lineage over time, or the overall diversity of strains within a given subtype. If alignment is performed to achieve the consensus sequence, before alignment is performed between the amino acid sequences of an antigen of various subtypes or various lineages or various clusters, a step of alignment may be carried out within each subtype or lineage (within a cluster no significant divergence is observed, in particular less than 3% or not more than 2% differences) to design a consensus sequence reflecting the diversity of strains for each subtype or lineage of virus. Illustration of the steps carried out to design a consensus sequence is provided in the Examples section and the method proposed may be applied similarly to other selections of virus lineages than those characterizing the spectrum of H1 N1 , H3N2 and pandemic H1 N1v.

[0021] The inventors have observed that the recombinant measles virus of the invention expressing the influenza M2 antigen or M2e-based antigen elicits an antibody response against the influenza antigen in mice susceptible to infection by measles virus which response is stronger than the response observed after natural infection with the homotypic influenza strain. In addition, the inventors have shown that the response may be increased by a boost administration of the recombinant measles virus expressing the influenza M2 antigen or M2e-based antigen.

[0022] Surprisingly, the inventors have shown in addition that mice (restricted for CMH H2b) immunized with the recombinant measles virus of the invention developed an immune response against the M2e or the M2 antigen of influenza A virus although these mice were known to have a restricted haplotype that would hardly elicit a response as seen in the past using a composition comprising DNA encoding the M2 antigen or a composition comprising synthetic peptides derived from the M2e sequence that was intended for the induction of an immune response against the M2 antigen (Misplon et al., 2010; Wolf et al., 2011 ). The recombinant measles virus takes part in the observed phenomenon by its capacity to help overcoming the failure of the immunized host to possibly recognize the epitope of the influenza A virus antigen in the proper CMH context, by supplying a T helper response against the MV that proves to be appropriate in helping the elicitation of the response of the host against said influenza A virus antigen.

[0023] In an embodiment, the invention relates to a recombinant measles virus as disclosed herein wherein the M2 antigen has a consensus amino acid sequence derived from the M2 sequences of viruses comprising A/H1 N1 and A H3N2 seasonal strains and

A/H1 N1 pandemic variant strain. In another embodiment, the recombinant measles virus as disclosed herein is such that the M2 antigen has a consensus amino acid sequence derived from the M2 sequences of viruses comprising A/H5N1 , A H9N2 and A H7N9 avian strains and optionally A/H1 N1 pandemic variant strain. Using as a first antigen the M2 antigen or a portion thereof comprising the ectodomain of M2 originating from many seasonal viruses and a pandemic variant strain may provide a broad-spectrum vaccine of the type of universal vaccine sought against influenza A.

[0024] In an embodiment of the invention, the recombinant measles virus expresses the M2 ectodomain (M2e) the amino acid sequence of which is SEQ ID No. 21.

[0025] In another embodiment, the recombinant measles virus expresses an M2e- based antigen that comprises the above sequence. In particular, this M2e-based antigen is the M2 antigen that has the sequence of SEQ ID No.19.

[0026] The thus defined sequence of the ectodomain of M2 is a consensus sequence. After being defined as a consensus the M2e domain may be comprised within a M2e-based antigen which is an antigen modified with respect to the M2e domain. Such modification may result by the addition of terminal amino acid residues, in particular 1 , 2, 3, 4 or 5 additional amino acid residues which are or are not amino acids encompassed within an actual M2 protein such as residues naturally framing the M2e domain in the consensus sequence or in an actual sequence, i.e., the sequence of the antigen of an identified virus or virus strain. The M2 antigen may alternatively or further be modified to give rise to a M2e-based antigen by the addition of a linker sequence such as a glycin- rich sequence e.g. an SGGSGG sequence (SEQ ID No.38) which provides flexibility or by the addition of a spacer sequence such as a glycine-rich sequence of the GGG type or an alanine-rich sequence with 2 to 6 consecutive alanine residues. An M2e-based antigen may also encompass an antigen consisting of or comprising multiple copies of

M2e domain(s) or multiple copies of such M2e domain(s) comprising the above disclosed specific modifications consisting in addition of terminal amino acid residues and/or linker or spacer sequences. The M2e-based antigen may accordingly be a chimeric antigen through the combination of multiple M2E domains.

[0027] According to these embodiments of the invention, the recombinant measles virus comprises, inserted in its genome, a polynucleotide encoding the M2 consensus antigen of the influenza A virus or encoding the M2e consensus domain. Preferably, the polynucleotide is inserted in an additional transcription unit (ATU) cloned into an intergenic region of the cDNA corresponding to the full-length antigenomic RNA of the measles virus. Nucleic acid constructs suitable for the expression of the M2 antigen or the M2e-based antigen are in particular illustrated in the Examples section. In particular the transgene encoding one or multiple polypeptides characteristic of the influenza virus as disclosed herein, may be introduced in the ATU1 , ATU2 or ATU3 as provided in the plasmids designated pTM-MVSchw-ATU1 having the sequence of SEQ ID No.14, or pTM-MVSchw-ATU2 having the sequence of SEQ ID No.15 or pTM-MVSchw-ATU3 having the sequence of SEQ ID No.16, wherein they would replace the sequence encoding the eGFP. In a particular embodiment, the transgene is inserted in ATU2

(between the P and M genes of the measles genome) or even upstream such as in ATU1 in order to increase the expression of influenza polypeptide based on the expression gradient of the measles genome. According to a preferred embodiment an M2e-based antigen, in particular an antigen encompassing multiple copies of M2e as disclosed herein or a fusion of such an M2e-based antigen (such as N-M2e wherein N is the measles antigen) is inserted in said ATU3 or in said ATU2. When double recombinant measles virus is prepared such as a measles virus recombined with the M2e-based antigen as disclosed above and with an additional antigen of the influenza virus (such as M1 or NP), the nucleotide sequence of the latter may be inserted in ATU2 and the sequence of the M2e-based antigen may be inserted in another ATU, in particular in ATU3 or in ATU1.

[0028] In an embodiment of the invention, the genome of the recombinant measles virus of the invention comprises multiple copies of polynucleotide(s) encoding the ectodomain of the M2 antigen.

[0029] The feature "multiple copies of polynucleotide(s) encoding the M2e domain" means that more than one copy of a polynucleotide encoding this domain is present in the MV vector genome, therefore enabling the expression of "multiple copies encoding the M2e domain" in a thus formed chimeric M2e-based antigen. In particular 2, 3, 4, or 5 or more copies of an identical M2e domain or of distinct M2e domains are encompassed within a chimeric antigen. Domains are considered distinct when they have sequences that have diverging amino acid residues at one or more than one site when compared to the determined consensus sequence of M2 or of M2e. Domains may be distinct but nevertheless similar when the diverging positions do not exceed 10 % (90 % identity) or preferably do not exceed 5% (95% identity) of the number of amino acid residues in the compared sequences (the diverging sequence compared to the consensus sequence and the consensus sequence determining the number of amino acid residues). Distinct M2e domains may be those of different consensus sequences or may originate from different clusters, different lineages or different subtypes. The multiple copies of the M2e domain may be directly fused to the adjacent copy(ies) or separated from the adjacent copy(ies) by a linker (a particular linker is illustrated in the constructs provided as examples and as SEQ ID No.38). Multiple copies of the M2e antigen may be connected by linker or spacer sequences as disclosed herein. The expression by the recombinant measles virus of the invention, of multiple copies of the M2 antigen or the M2e-based antigen may favor the elicitation of a stronger and broader immune response resulting from an increased abundance of the influenza antigen and/or more favorable exposure to the immune system of the host. Examples of multiple copies of M2e domain that may advantageously be expressed by the live recombinant measles virus of the invention consist of chimeric polypeptides comprising or consisting of the consensus sequence of M2e for the A/H1 N1 and the A/H3N2 lineages (SEQ ID No.21 ) and the consensus sequence of M2e for the A/H1 N1 v pandemic strain (SEQ ID No.32). These sequences of various M2e show 4 amino acid residues of difference (17%). As an alternative combination of sequences for a M2e domain, the consensus sequence for the A/H1 N1 and the A H3N2 lineages may be associated with the sequence of the M2e domain of A/H5N1 (SLLTEVETPT RNEWECRCSD SSD SEQ ID No.40 ). These sequences are different at 3 amino acid residue positions (13%). Multiple copies of M2e domain constitute a M2e containing antigen (or M2e-based antigen) according to the invention.

[0030] In a particular embodiment of the invention, the M2 antigen or the M2e containing antigen (M2e-based antigen) when expressed by the recombinant measles virus is borne by a carrier molecule, in particular fused to an extremity (N- or C-terminal) of a carrier protein. Such a carrier molecule may be chosen for its ability to help presenting the M2 or M2e-containing antigen by the recombinant measles virus when it is produced and replicates in the immunized host. It may additionally or alternatively consist in an immunogenic molecule involved in the elicitation of an immune response against influenza A virus, including the NP protein of the influenza virus or a consensus sequence of said protein such as NPflu protein having the sequence of SEQ ID No. 31.

[0031] The invention thus relates in particular to a recombinant measles virus wherein in its genome, the polynucleotide encoding the ectodomain(s) of the M2 antigen or one of the polynucleotides encoding the multiple ectodomain(s) of the M2 antigen (including when such ectodomain(s) is (are) encompassed in an M2e-based antigen) is genetically fused with a polynucleotide encoding a carrier protein, optionally an immunogenic carrier protein. The genetic fusion is advantageously carried out at the extremity of the DNA encoding the carrier protein. Accordingly when a feature is disclosed herein by reference to the M2e domain the feature applies either to the M2e domain in the strict sense of it or to the M2e encompassed in more complex sequence such as those disclosed herein for the M2e-based antigen.

[0032] In a particular embodiment of the invention, the carrier molecule is a protein of the measles virus, in particular a structural protein of the virus. In an advantageous embodiment, the protein is the Nucleoprotein (N) of a measles virus, especially a N protein of the strain used to rescue recombinant measles virus particles of the invention, such as the Schwarz strain. In another advantageous embodiment, the protein is the Nucleoprotein (NP) of one of influenza virus strains cited herein, including the NP protein of an influenza virus or a consensus sequence of said protein such as NPflu protein having the sequence of SEQ ID No. 31. It may be alternatively a variant thereof such as a portion, in particular an immunogenic portion of this protein, in particular an immunogenic portion of the protein the amino acid sequence of which is SEQ ID No. 31. Preferably, the polynucleotide encoding the M2 or the M2e-based antigen of the influenza virus and, when present, the polynucleotides encoding the carrier protein globally fulfill the "rule of six" or are adapted to fulfill said rule. Examples of M2e-based antigen borne by a carrier according to the invention are NPflu-M2e, or NPflu-3xM2e having the sequence of SEQ ID No. 25.

[0033] In a particular embodiment of the invention, the recombinant measles virus expresses a fusion of the measles N protein with one or multiple copies of the M2e domain. As an example a fusion of N with 3 copies of the M2e domain fused at the C- or N-terminal part of the N is expressed.

[0034] In a particular embodiment the M2 antigen or the M2e-based antigen is fused to the C-terminal end of the N protein or to the C-terminal end of a portion of the N protein that comprises the Ncore domain. Examples of the fusion protein between the MV N protein and the M2 antigen or the M2e-based antigen are illustrated as SEQ ID No.

28 (N _M v-M2e fusion protein) and SEQ ID No. 29 (N _M v-3xM2e fusion protein) . In these particular embodiments, the N _M v and the M2e antigens are separated by a linker and when multiple M2e peptides are included in the fusion protein they are also separated by linker sequences.

[0035] Preferably the fusion protein leads to the expression of additional N proteins of

MV rather than to the substitution of the native N protein by the fusion protein. Hence, the fusion protein comprising the MV N protein is expressed in addition to the native N protein.

[0036] In a particular embodiment, in order to express the chimeric antigen consisting of the carrier-M2e or the carrier-nxM2e fusion (wherein "n" represents the number of M2e copies) a polynucleotide encoding said fusion is inserted in the cDNA of the MV vector in an ATU (an additional transcription unit which is a multiple-cloning-site cassette) provided in the vector at a position located in the intergenic region between the P and the M genes of MV or at position located between the H and the L genes. This enables the recombinant virus to express both the native and the fused chimeric N-M2e or N-nxM2e proteins. Accordingly, in the RNPs (Ribonucleoproteins) which are produced by the recombinant measles virus, the chimeric N-M2e or N-nxM2e proteins are displayed on the RNPs. Constructs encompassing the ATU in the vector backbone are illustrated in the Examples section. In particular the transfer vector used to derive a construct of the invention suitable to express a live recombinant measles virus may be one of the following plasmids: pTM-MVSchw-ATU1 having the sequence of SEQ ID No.14, or pTM- MVSchw-ATU2 having the sequence of SEQ ID No.15 or pTM-MVSchw-ATU3 having the sequence of SEQ ID No.16. All these plasmids contain the sequence encoding the eGFP marker that may be deleted.

[0037] In another embodiment of the invention, alternatively to a protein of measles virus, wherein the carrier protein is an antigen of Influenza A virus, in particular is the nucleoprotein NP or an immunogenic portion thereof.

[0038] As examples of such carrier originating from an influenza virus or from a consensus sequence of a protein of an influenza virus, the nucleoprotein (NP protein) is suitable to provide a T epitope of influenza virus, which epitope can be boosted in a host who would become infected by an influenza A virus after receiving the recombinant measles virus of the invention and the presence of which would thus elicit or improve the immune reaction.

[0039] The carrier may be an immunogenic portion of a protein rather than the whole protein if the immunogenicity of the carrier is sought. The skilled person would be able to determine an immunogenic portion of a protein by simple tests carried out on fragments of the protein determining whether the fragment elicit an antibody response or a cellular response. An immunogenic portion of a protein may in particular consist of a truncated protein or a deletion variant of the protein such as a fragment consisting of more than 50% of the native protein or in particular 90% or more or 95% or more in length of the whole protein.

[0040] The NP protein of an influenza A virus may be the expression product of a consensus sequence wherein the consensus is designed in the same way as the consensus for the M2 antigen. It may alternatively be an actual (i.e., native) sequence of a particular viral strain. The NP protein of influenza A virus is the nucleocapsid protein having 498 amino acid residues. According to the invention the NP protein is the full- length protein or a portion suitable to act as a carrier and optionally as an immunogen. An example of the NP protein suitable for use according to the invention corresponds to the sequence of SEQ ID No.31 encoded by the polynucleotide of sequence SEQ ID No. 30. In a particular embodiment, the NP protein is used in a fusion protein with 3 copies of the M2e domain such as illustrated by the protein whose sequence is SEQ ID No.25. encoded by the transgene consisting of SEQ ID No.24.

[0041] As stated above, the recombinant measles virus expresses at least a first antigen of influenza A virus. Accordingly, in further embodiments of the invention, wherein such embodiments may also encompass any of the features recited above or their combinations, the recombinant measles virus may express additional antigens (wherein the term antigen is used interchangeably with protein or polypeptide and encompasses immunogenic portions of native proteins), including additional influenza A antigen(s) (e.g. NP or M1 antigens) that may be expressed by consensus amino acid sequences or sequences of actual strains or isolates. Alternatively or in addition, the recombinant measles virus may express antigens of other viruses, including of other influenza types or subtypes than those used in the design of the consensus sequence of the M2 antigen, such as antigens, in particular M2 antigen, of influenza B virus type. Such distinct antigen may be designated as a second or a further antigen when more than one additional antigen is present. According to the invention, when reference is made to the M2 antigen or to an antigen comprising the M2e domain (M2e-based antigen), reference is primarily made to the antigen with a consensus amino acid sequence. Similarly, said further antigens of influenza A virus may optionally be a consensus sequence built using analogous steps to those defined herein and illustrated in the Example section.

[0042] Independently of the carrier molecule, as stated above, the recombinant measles virus may express further antigen(s) of the influenza A virus. Such further antigens may be selected for their ability to elicit, in particular to prime or to boost an immune response in a host or to take part in the response elicited by other antigens. They may be expressed as a consensus antigen having a consensus sequence defined as explained herein for the consensus of the M2 protein, in particular using the alignment of the sequences of the antigens of the same influenza viruses as those involved in the design of the consensus sequence of the M2 protein.

[0043] Accordingly, the invention is directed to a live recombinant measles virus which also expresses one or multiple further antigen(s) of an influenza A virus or one or multiple further antigen(s) the amino sequence of which is a consensus sequence representative of the sequence of a determined antigen of viruses from a selection of various subtypes of Influenza A viruses wherein the selection includes circulating seasonal human virus(es) and optionally pandemic human virus(es) and/or animal virus(es) reported to have infected people and considered to pose a pandemic threat. [0044] Among suitable proteins of influenza A virus for the constitution of the further antigen(s) M1 (matrix protein), NP and/or NA (Neuraminidase) proteins or immunogenic portions thereof are preferred. In particular, both M1 and NP proteins may be suitable as they are highly conserved and are the target of cellular responses in individuals infected by influenza virus. The M1 protein may also promote the budding of influenza VLPs from cells. The NA protein may also be suitable as it is a known immunogen and because it may enhance the budding for the release of viral particles or of influenza VLPs from cells. The NA protein is also less susceptible to antigenic drift than the hemagglutinin protein (HA). It may therefore interestingly complete the M2 protein or the M2e-based protein for the induction of a broad immune response. Accordingly, a recombinant measles virus expressing the M2 antigen or the M2e-based antigen and the NA antigen of a particular subtype may provide a semi-universal vaccine able to induce wide coverage against influenza A of the corresponding subtype(s).

[0045] In a particular embodiment of the invention, the recombinant measles virus expresses a further antigen which is the M1 protein having the sequence of SEQ ID

No.23 which is a consensus sequence encoded by the polynucleotide whose sequence is SEQ ID N0.22 and/or the NP protein having the sequence of SEQ ID No.31.

[0046] In an embodiment of the invention, the influenza A antigens expressed by the recombinant measles virus are M1 and M2 or M1 and M2e-based proteins either as a M1-M2 fusion protein, as a M2-M1 fusion protein or as M1-M2e-based fusion protein, as a M2e-based-M1 fusion protein . These fusion proteins may be designed using the polynucleotides disclosed as SEQ ID No. 17, SEQ ID No.18 (for M2) or SEQ ID No.20 (for M2e) and SEQ ID No. 22 for M1. In order to be expressed by the genome of the recombinant MV, the polynucleotide encoding said fusion protein is advantageously inserted in the ATU2 at position between the P and the M genes of MV. In another embodiment, the antigens of influenza A virus (for example M2 (or M2e-based antigen) and M1 or, M2 (or M2e-based antigen) and NP, or even the three antigens M1 , M2 (or M2e-based antigen) and NP) expressed by the recombinant MV are inserted in different ATUs. For example if influenza A M2 (or M2e-based antigen) NP and M1 are used one is expressed from a polynucleotide inserted in an ATU located before the N gene of MV, one is expressed from a polynucleotide inserted in an ATU located between the P and the M genes and the third one is expressed from a polynucleotide inserted in an ATU located between the H and the L genes of MV. Alternatively, the M1 and NP proteins of influenza may be expressed as a fusion protein. The use of multiple influenza A virus antigens may enable to improve protection with the induction of both humoral and cellular responses. [0047] In another aspect, the invention relates to nucleic acid constructs required for the rescue of a recombinant measles virus as defined herein. These constructs encompass a nucleic acid construct which comprises or consist in a cDNA whose nucleotide sequence comprises (i) a nucleotide sequence that encodes the sequence of a full-length antigenomic RNA of MV (i.e., corresponds to the RNA except for the change of the U nucleotides into T) and wherein one or multiple Additional Transcription Unit(s) (ATU) has (have) been inserted upstream of the N gene (ATU1 ) and/or in the intergenic region(s) between the P and M genes (ATU2) and/or between the H and L genes (ATU3) of MV and, (ii) operably linked into said ATU or ATUs (in frame), a heterologous nucleotide sequence encompassing an open reading frame that encodes one or multiple antigen(s) of influenza A virus as defined herein and in particular in the Examples and by reference to the sequences of the sequence listing. In order to be cloned into the ATU, the polynucleotide encoding the amino acid sequence of the influenza A antigen(s) (and if present of the carrier) may be flanked by added restriction sites.

[0048] In a particular embodiment, if necessary or suitable, the nucleic acid molecule is such that the polynucleotide encoding the consensus sequence of the influenza A virus may encompass modifications such as editing modifications to remove MV editing (A ₅ G ₃ )- and core gene end (A ₄ CKT)-like sequences on both strands of the nucleic acid. Additional modifications may concern cis-acting sequence motifs such as internal TATA- boxes, chi-sites, ribosomal entry sites, ARE, INS and CRS sequence elements, or repetitive sequences, RNA secondary structures and splice donor and acceptor sites.

[0049] In an embodiment, the nucleic acid construct may be codon optimized to improve expression in mammalian cells, in particular in human cells. Codon optimization may be carried out on the sequence encoding the influenza A virus antigens or may be carried out both on the sequence encoding the influenza A antigens and if appropriate their carrier protein. Codon optimization is known from the skilled person and is illustrated in the Examples provided herein.

[0050] The polynucleotides encoding the influenza A antigen(s) possibly linked with a carrier may be prepared according to techniques available to the person skilled in the art such as by chemical synthesis.

[0051] The nucleic acid of the invention encompassing the cDNA encoding the full- length antigenomic (+)RNA of the measles virus and the other antigens in particular the influenza A virus antigen(s), including the optional sequence of the carrier, may advantageously fulfill the "rule of six" which is known to take place in the sequence of natural MV genomes and to enable recovery of high yield of live recombinant measles virus. Accordingly this nucleic acid should have a number of nucleotides on each strand which is a multiple of six. Alternatively, the rule of six is not fulfilled by the construct of the recombinant viral genome and the yield of recombinant virus in the rescue is altered, possibly after repair of the error relating to the compliance with the rule of six.

[0052] Among the nucleic acid constructs, the invention concerns in particular vectors (transfer vectors) suitable for the rescue of the recombinant measles virus of the invention. Vectors are said to be suitable for the rescue when they provide functional polynucleotides encoding the full-length measles virus antigenomic (+)RNA together with the nucleic acid constructs encoding the influenza A antigen(s) and are thus able to provide the genome of viral particles and their proteins when they are used for transformation of a cell, in particular a mammalian cell, especially a human cell, chosen for the rescue wherein said cell expresses measles virus proteins necessary for transcomplementation in particular when the cell is transcomplemented with vector(s) providing sequences of the P, N and L proteins of the MV. Such constructs have been amply disclosed in Combredet C. et al (2003) and in WO 04/000876.

[0053] Accordingly, the invention concerns a transfer vector, in particular a plasmid vector, suitable for the rescue of a recombinant measles virus as defined herein which comprises as an insert operably linked in the vector backbone, cloned into the cDNA encoding the full-length antigenomic RNA of the measles virus, a polynucleotide encoding one or many antigens as defined herein.

[0054] A particular transfer vector suitable for the expression of the recombinant measles virus according to the invention is a recombinant plasmid carrying a cDNA whose nucleotide sequence comprises (i) a nucleotide sequence that encodes the sequence of the full-length antigenomic RNA of MV wherein one or multiple Additional Transcription Unit (ATU) has (have) been inserted upstream of the N gene and/or in intergenic regions and, (ii) inserted in said ATU or ATUs a heterologous polynucleotide the sequence of which encompasses an open reading frame that encodes one or many antigen(s) as defined herein. These vectors are advantageously derived from the plasmids designated pTM-MVSchw-ATU1 having the sequence of SEQ ID No.14, or pTM-MVSchw-ATU2 having the sequence of SEQ ID No.15 or pTM-MVSchw-ATU3 having the sequence of SEQ ID No.16, wherein the sequence encoding the eGFP would be replaced by inserts encoding the influenza virus protein(s) and optionally carrier protein(s) of different origin..

[0055] In a particular aspect, the transfer vector is a pTM plasmid derived from a pBluescript plasmid is selected from the group of:

- pTM-MVSchw-ATU1 or pTM-MVSchw-ATU2 or pTM-MVSchw-ATU3wherein the sequence encoding an M2 antigen is inserted in ATU1 or ATU2 or in ATU3, pTM-MVSchw-ATU3 wherein the sequence encoding the fusion of the C-terminal end of the Nucleoprotein of the MV virus and the sequence encoding one or multiple ectodomain(s) of an M2 protein (M2e) is inserted in ATU3;

- pTM-MV-ATU1-M2raw having the sequence of SEQ ID No.1 , pTM-MV-ATU2- M2raw having the sequence of SEQ ID No.3, pTM-MV-ATU1-M2opt having the sequence of SEQ ID No.2, pTM-MV-ATU2-M2opt having the sequence of SEQ ID No.4, pTM-MV-ATU3-M2opt having the sequence of SEQ ID No.8

- pTM-MV-ATU3-N-1xM2e having the sequence of SEQ ID No.5, pTM-MV-ATU3- N-3xM2e having the sequence of SEQ ID No.6 (N is the measles virus N protein)

- pTM-MV-M1 &M2 having the sequence of SEQ ID No.9

- pTM-MV-NPflu&M2 having the sequence of SEQ ID No.10 and pTM-MV-ATU2- NPflu having the sequence of SEQ ID No.11 which is the parental construct for pTM-MV-NPflu&M2 ,

- pTM-MV-ATU2-NPflu-3xM2e having the sequence of SEQ ID No.13

- pTM-MV-ATU2-M1 opt having the sequence of SEQ ID No.7.

- pTM-MV-ATU2-N-3xM2e having the sequence of SEQ ID No.12, where N is the measles protein.

[0056] The invention also concerns the polynucleotides consisting in the inserts included in the measles virus genome of said plasmids as they are indicated in the provided sequences. In particular, the invention relates to the polynucleotides whose sequences are the following:

- SEQ ID No.17 for M2raw synthetic gene wherein the sequence encoding M2 is a sequence encoding a consensus protein , SEQ ID No.18 for M2opt synthetic gene wherein the sequence is optimized, in particular codon optimized with respect to the raw sequence,

- SEQ ID No.20 for sequence encoding the consensus M2e polypeptide, which sequence is optimized,

- SEQ ID No.22 for the optimized sequence encoding the M1 consensus protein,

- SEQ ID No.24 for the fusion polynucleotide encoding NPflu-3xM2e fusion protein,

- SEQ ID No.26 for the fusion polynucleotide encoding N-1xM2e fusion protein where N is from the measles virus and wherein a linker links the N and the M2e sequences,

- SEQ ID No.27 for the fusion polynucleotide encoding N-3xM2e fusion protein wherein a linker links the N and the M2e sequences and links the multiple M2e sequences

- SEQ ID No. 30 for the synthetic gene encoding the consensus NPflu protein.

- a polynucleotide encoding any of the polypeptide the sequence of which consists of a sequence selected in the following group: SEQ ID No.19, SEQ ID No.21 , SEQ ID No.23, SEQ ID No.25, SEQ ID No.28, SEQ ID No.29, SEQ ID No.31 , SEQ ID No.32 and SEQ ID No.40.

[0057] The invention also relates to the use of a transfer vector as described herein for the preparation of a recombinant measles virus as defined in the present invention.

[0058] The invention thus also concerns a rescue system for the assembly of infectious recombinant measles virus particles and optionally influenza A VLPs, comprising a cell, preferably a mammalian cell or cell line, transformed, in particular transfected, with vectors, in particular plasmid vectors, suitable for the expression of a polymerase such as a T7 polymerase, and for the expression of the N, P and L proteins of a measles virus, wherein said cell is further transfected with a vector according to the invention.

[0059] In particular the cells used for the rescue are selected among a 293-T7-NP cell line deposited on June 14, 2006 with the CNCM (Paris, France) under number 1-3618 or a 293-Tnls7-NP deposited on August 4, 2006 with the CNCM (Paris, France) under number 1-3662.

[0060] For the preparation of the recombinant measles virus of the invention, the cDNA cloned as the insert into the transfer vector may be obtained after a step of purifying the genomic RNA of measles virus from particles of the virus, in particular from particles of a live-attenuated strain or a vaccine strain such as the Schwarz strain.

[0061] The invention also concerns an immunogenic composition comprising a recombinant measles virus of the invention as defined herein according to any of the embodiments disclosed, a pharmaceutical vehicle suitable for administration to a host and optionally an adjuvant of the immune response.

[0062] In addition to the recombinant measles virus of the invention, the immunogenic composition may comprise influenza virus-like particles (VLPs) that form during the rescue and production of the recombinant measles virus. The invention also concerns said influenza virus-like particles (VLPs) and their use as active ingredient for the elicitation of the immune response against influenza A virus or improvement of the response elicited by the live recombinant measles virus of the invention. The immunogenic composition may be, may comprise or may be derived from a supernatant or a lysate of cells producing the recombinant measles virus of the invention.

[0063] An immunogenic composition according to the invention may be formulated using additional substances such as salts, preservation substances, buffers, texture agents...

[0064] The immune response may be an antibody response and/or a cellular response including a T cell response. The response thus elicited is protective, advantageously confers a broad and long lasting protection. [0065] The invention also concerns a recombinant measles virus as defined herein, for use as active ingredient in the elicitation of an immune response for prophylactic protection against a condition or a disease resulting from the infection by an influenza virus A in a human host.

[0066] In particular, the invention relates to a recombinant measles virus as defined herein, for use as active ingredient in the elicitation of an immune response for prophylactic protection against a condition resulting from the infection by an influenza virus A, wherein the influenza A virus is one of the A/H1 N1 , A/H3N2, A/H5N1 or A/H7N9 or A/H9N2 or H1 N1v virus.

[0067] The invention also relates to a recombinant measles virus as defined herein, for use as active ingredient in the elicitation of an immune response for prophylactic protection against flu in a human host, in particular in children.

[0068] In a particular embodiment, the invention relates to a recombinant measles virus as defined herein, optionally in combination with Influenza VLPs for the elicitation of antibodies against the influenza A virus and/or for the elicitation of a cellular response against the infection by the influenza A virus in a human host.

[0069] In an embodiment of the invention, the recombinant measles virus optionally in combination with Influenza VLPs, is used for protection, in particular for prophylactic protection, against a condition or a disease resulting from the infection by an influenza virus A in a human host.

[0070] The invention also concerns a method to prevent the onset of flu or the onset of a condition resulting from infection by an influenza A virus in a human host, comprising administering to said human host, in particular in a child, one or multiple doses of a composition comprising a recombinant measles virus as defined herein, optionally in a prime-boost administration regimen.

[0071] According to a particular aspect of the invention, the immunogenic composition is formulated for administration to children.

[0072] The administration of the immunogenic composition of the invention may be performed by known administration routes including systemic or peripheral administration.

[0073] The invention also relates to the use of a recombinant measles virus according to any one of the herein described embodiments, optionally in combination of Influenza VLPs in the preparation of active ingredients for the prevention of the infection by an influenza A virus or the prevention of the outcome of the infection by an influenza A virus, in a multivalent vaccine for a human host, such as a combined measles, mumps, rubella and influenza multivalent vaccine or a measles, mumps, rubella, varicella and influenza multivalent vaccine. [0074] According to a particular embodiment of such preparation of active ingredients, the recombinant measles virus of the invention is also used as active ingredient for the prevention of an infection by measles virus or for the prevention of the outcome of an infection by the measles virus.

[0075] The invention also concerns a cell transformed, in particular transfected with the vectors, especially the plasmid vectors, suitable to carry out the rescue of recombinant measles virus according to the invention and comprising nucleotide sequences expressing a polymerase such as a T7 polymerase, and nucleotide sequences expressing the N, P and L proteins of a measles virus, wherein said cell is further transfected with a transfer vector as defined herein in conditions enabling production of recombinant measles virus.

[0076] The invention also relates to the products recovered from the thus defined cell used to rescue or from cells used to amplify the rescued virus such as Vero cells. The invention thus concerns in particular the supernatant of such cells or the lysate prepared from such cells expressing the rescued recombinant measles virus of the invention. These products, in particular the supernatant or lysate of cells used for the production of the recombinant measles virus of the invention, may be used in the preparation of active ingredients for an immunogenic composition of the invention.

[0077] Additional features may be derived from the examples which follow and from the figures.

[0078] FIGURE LEGENDS

Figure 1 : Characterization of MV-M2 recombinant viruses expressing the full-length transmembrane M2 protein.

A. Schematic representation of the pTM-MVSchw-ATU2 vector containing the Schwarz MV cDNA with a green fluorescent protein (eGFP) gene as an additional transcription unit

(ATU) between the P and the M genes (ATU2). Wild-type (M2raw) and codon-optimized (M2opt) synthetic genes coding for the full-length M2 consensus protein were inserted into pTM-MVSchw-ATU2 between the BsiWI and BssHII sites of the ATU, in place of the eGFP gene. Both M2raw and M2opt genes were also inserted into pTM-MVSchw-ATU1 as an additional ATU upstream of the N gene (not shown).

MV genes are indicated: N (nucleoprotein), P (phosphoprotein) and V/C (accessory proteins), M (matrix), F (fusion), H (hemaglutinin), L (polymerase). T7: T7 RNA polymerase promoter. hhR: hammerhead ribozyme. T7t: T7 RNA polymerase terminator. h3vR: hepatitis delta virus (HDV) ribozyme.

B. Growth kinetics of recombinant MV-M2 viruses. Vero NK cells were infected with parental MVSchw or recombinant MV-ATU2-M2raw or MV-ATU2-M2opt viruses at an MOI of 0.1. The cells were collected at the indicated time points, and the cell-associated virus titers were determined as described in Materials and Methods.

C. Immunofluorescence staining of M2 polypeptides in syncytia of MV-M2-infected Vero NK cells. Cells were fixed 30-36 hours after infection with the indicated viruses and stained with mouse monoclonal anti-M2 antibody (14C2) and AF555-conjugated anti- mouse IgG antibodies. Magnification: x40.

D. and E. Western blot analysis of M2 polypeptides expression. M2 was detected in lysates of Vero-NK cells infected with the indicated MV-M2 or parental MVSchw viruses using mouse monoclonal anti-M2 antibody (14C2). Lysates of MV-infected cells were diluted 1 in 4 (D) or 1 in 10 (E) before being assayed. Lysates prepared from MDCK cells infected with A/Scotland/20/74 (SCOT) or A/PuertoRico/8/34 (PR8) influenza viruses at a MOI of 5 were used as positive controls. The positions of molecular weight markers (size in kDa) are indicated. D. Two viral clones (1 , 2) of MV-M2raw and MV-M2opt were assayed as indicated. E. Lysates were harvested 24 or 36 hours post-infection as indicated.

Figure 2: Characterization of MV-NM2e recombinant viruses expressing N-M2e fusion proteins.

A. Schematic representation of the pTM-MVSchw-ATU3 vector containing the Schwarz MV cDNA with a green fluorescent protein (eGFP) gene as an ATU between the H and the L genes (ATU3). Genes encoding the MV N protein fused to a single copy of M2 ectodomain consensus sequence (N-1xM2e) or to three tandem copies of M2e (N- 3xM2e) were inserted into pTM-MVSchw-ATU3 between the BsiWI and BssHII sites of the ATU, in place of the eGFP gene.

MV genes are indicated as in figure 1.

B. Immunofluorescence staining in syncytia of MV-NM2e-infected Vero NK cells. Cells were fixed 30-36 hours after infection with the indicated viruses and stained with mouse monoclonal anti-M2 antibody (14C2) and AF555-conjugated anti-mouse IgG antibodies, and with rabbit polyclonal anti-MV-N and AF488-conjugated anti-rabbit IgG antibodies. Single-color and merged images are shown. Magnification: x20.

C. and D. Western blot analysis of N-M2e fusion polypeptides expression. N-M2e fusion proteins were detected in lysates of Vero-NK cells infected with the indicated MV-NM2e or parental MVSchw viruses using mouse monoclonal anti-M2 antibody (14C2, panel C) or rabbit polyclonal anti-MV-N (panel D). Two viral clones (1 , 2) of MV-N-1xM2e and MV- N-3xM2e were assayed as indicated. Lysates prepared from Vero NK cells infected with

MV-ATU1-M2opt or MV-ATU2-M2opt were used as positive controls. The positions of MV N protein and N-M2e fusion proteins as well as molecular weight markers (size in kDa) are indicated.

Figure 3: Antibody response in CD46-IFNAR mice immunized with MV-M2 recombinant viruses.

Groups of 6 or 12 CD46-IFNAR mice were injected twice intraperitoneally at four-week interval with 10 ⁵ TCID ₅₀ of the indicated recombinant MV-M2 measles viruses or with parental MVSchw, as control. Another group of mice was immunized with two intranasal administration of 0.1 LD50 of mouse-adapted A Scotland/20/74 (SCOT) influenza virus. Sera were collected 3 weeks after each injection (IS1 and IS2, respectively). M2e-specific (A, C) or MV-specific (B, D) IgG antibody titers were determined by indirect ELISA, as described in Material and Methods. A-D. Each symbol represents an individual mouse, and the short horizontal line indicates the mean value of the group. Detection limits of the assays are indicated by dotted lines.

D-E. Survival curves for 5-6 mice per group were recorded for 22 days after intranasal challenge with 10 LD50 of mouse-adapted A/Scotl and/20/74 (H3N2) or A/Paris/2590/09 (H 1 N 1 v) influenza viruses.

Figure 4: Antibody response in CD46-IFNAR mice immunized with MV-NM2e recombinant viruses.

Groups of CD46-IFNAR mice were injected twice intraperitoneally at four-week interval with 10 ⁵ TCID ₅₀ of the indicated recombinant MV-NM2e measles viruses or with parental MVSchw, as control. Another group of mice was immunized with MV-ATU2-M2opt. Sera were collected 3 weeks after each injection (IS1 and IS2, respectively). M2e-specific (A) or MV-specific (B) IgG antibody titers were determined by indirect ELISA.

C. M2e-specific, lgG1 (filled circles) and lgG2a (open circles) isotype titers were determined for IS2 sera by indirect ELISA.

D. Specific antibodies against the native form of the M2 protein were measured using a cell-based ELISA, as described in Material and Methods.

A-D. Each symbol represents an individual mouse, and the short horizontal line indicates the mean value of the group. Detection limits of the assays are indicated by dotted lines.

E. Survival curves were recorded for 21 days after intranasal challenge with 10 LD50 of mouse-adapted A/Scotland/20/74 (H3N2) influenza virus. Figure 5: Contribution of humoral response to protection

Survival of C57BL/6 mice (6 mice/group) lethally challenged with 10 LD50 of mouse- adapted A/Scotland/20/74 (H3N2) influenza virus after passive transfer of pooled sera from CD46-IFNAR mice immunized with MV-ATU1-M2opt or MV-ATU2-M2opt recombinant virus. Control mice received sera from CD46-IFNAR mice immunized with empty parental MVSchw. Figure 6: Characterization of double recombinant measles viruses expressing both M1 and M2 proteins.

A. Schematic representation of the pTM-MV-ATU2-M1 vector containing the Schwarz MV cDNA with the M1 codon-optimized consensus gene as an ATU between the P and the M genes (ATU2), of the pTM-MV-ATU3-M2 vector with the M2 codon-optimized consensus gene as an ATU between the H and the L genes (ATU3), and of the double recombinant pTM-MV-M1 &M2 vector.

MV genes are indicated as in figure 1.

B. and C. Western blot analysis of M1 and M2 polypeptide expression. M1 and M2 were detected in lysates of Vero-NK cells infected with the indicated recombinant or parental measles viruses using mouse monoclonal anti-M1 (GA2B, panel B) or anti-M2 antibody

(14C2, panel C). Three viral clones (1 , 2, 3) of each viral construct were assayed as indicated. Lysates prepared from MDCK cells infected with A Scotland/20/74 (SCOT) influenza virus were used as positive controls. The positions of M1 and M2 proteins as well as molecular weight markers (size in kDa) are indicated.

Figure 7: examples of sequences of polynucleotides or proteins used in the invention

Figure 8: Antibody response in CD46-IFNAR mice immunized with dual recombinant measles viruses expressing both M1 and M2 proteins.

Groups of 12 CD46-IFNAR mice were injected twice intraperitoneally at four-week interval with 10 ⁵ TCID50 of the indicated single recombinant MV-ATU3-M2opt and MV-

ATU2-M1 opt viruses, with the dual recombinant MV-M1&M2 virus or with parental MVSchw, as control. Another group of mice was immunized with the former MV-ATU2- M2opt. Sera were collected 3 weeks after each injection (IS1 and IS2, respectively). M2e- specific (A) or MV-specific (B) IgG antibody titers were determined by indirect ELISA, as described in Materials and Methods. A-B. Each symbol represents an individual mouse, and the short horizontal line indicates the mean value of the group. Detection limits of the assays are indicated by dotted lines.

C. Survival curves were recorded for 21 days after intranasal challenge with 10 LD50 of mouse-adapted A Scotland/20/74 (H3N2) influenza virus.

D. Weight curves of infected mice were recorded. Values represent the mean weight of surviving mice, expressed as the percentage of initial weight at day of infection. SD are represented by one-sided vertical bars. For clarity, filled symbols indicate that all mice of the group were alive on the day of monitoring, half-filled symbols that at least one mouse died previously and open symbols that a single mouse remained alive in the group.

Figure 9: Characterization of dual recombinant measles viruses expressing both NP and M2 full-length influenza proteins, or a fusion protein between the NP protein and 3 copies of the M2e ectodomain.

A. Schematic representation of the pTM-MV-ATU2-NPflu vector containing the Schwarz MV cDNA with the NP codon-optimized consensus gene as an ATU between the P and the M genes (ATU2), of the pTM-MV-ATU3-M2 vector with the M2 codon-optimized consensus gene as an ATU between the H and the L genes (ATU3), and of the dual recombinant pTM-MV-NPflu&M2 vector. MV genes are indicated as in figure 1.

B. Schematic representation of the pTM-MVSchw-ATU2 vector as described in figure 1. The gene encoding the consensus influenza type A nucleoprotein (NPflu) fused to three tandem copies of M2e (NPflu-3xM2e) was inserted into pTM-MVSchw-ATU2 between the BsiWI and BssHII sites of the ATU, in place of the eGFP gene.

C. and D. Western blot analysis of NP and M2 polypeptide expression. NP and M2 (or M2e) were detected in lysates of Vero-NK cells infected with the indicated recombinant or parental measles viruses using rabbit polyclonal anti-influenza virion antibodies (panel C) or mouse monoclonal anti-M2 antibody (14C2, panel D). Three or four viral clones (1 , 2, 3, 4) of each viral construct were assayed as indicated. Lysates prepared from MDCK cells infected with A Scotland/20/74 (SCOT) influenza virus were used as positive controls. The positions of NPflu, M2 and NPflu-3xM2e proteins as well as molecular weight markers (size in kDa) are indicated. Figure 10: Antibody and cellular responses in CD46-IFNAR mice immunized with dual recombinant measles viruses expressing both NP and M2 proteins.

Groups of CD46-IFNAR mice were injected twice intraperitoneally at four-week interval with 10 ⁵ TCID50 of the indicated single recombinant MV-ATU2-NPflu and MV-ATU3- M2opt viruses, with the dual recombinant MV-NPflu&M2 virus or with parental MVSchw, as control. Sera were collected 3 weeks after each injection (IS1 and IS2, respectively).

M2e-specific (A) or MV-specific (B) IgG antibody titers were determined by indirect ELISA.

C. Frequency of influenza-specific IFN-y-producing T cells in the spleens of immunized mice was quantified by ELISPOT 7 to 10 days after a single injection of the indicated recombinant measles viruses. ELISPOT was performed as described in Materials and Methods, in response to the NP366 (H3N2) consensus peptide (class I), the NP366 (SCOT) peptide of the A/Scotland/20/74 challenge virus (class I) and the NP260-273 conserved peptide (class II).

A-C. Each symbol represents an individual mouse, and the short horizontal line indicates the mean value of the group. Detection limits of the assays are indicated by dotted lines. D. Survival curves were recorded for 21 days after intranasal challenge with 10 LD50 of mouse-adapted A/Scotland/20/74 (H3N2) influenza virus.

E. Weight curves of infected mice were recorded. Values represent the mean weight of surviving mice, expressed as the percentage of initial weight at day of infection. SD are represented by one-sided vertical bars. For clarity, filled symbols indicate that all mice of the group were alive on the day of monitoring and half-filled symbols that at least one mouse died previously.

Figure 11 : Characterization of a MV-N-3xM2e recombinant virus expressing a N- M2e fusion protein from ATU2.

A. Schematic representation of the pTM-MVSchw-ATU2 vector containing the Schwarz

MV cDNA with a green fluorescent protein (eGFP) gene as an ATU between the P and the M genes (ATU2). The gene encoding the MV N protein fused to three tandem copies of M2e (N-3xM2e) was inserted into pTM-MVSchw-ATU2 between the BsiWI and BssHII sites of the ATU, in place of the eGFP gene.

MV genes are indicated as in figure 1.

B. and C. Western blot analysis of N-M2e fusion polypeptide expression. N-3xM2e fusion protein was detected in lysates of Vero-NK cells infected with the indicated virus using mouse monoclonal anti-M2 antibody (14C2, panel B) or rabbit polyclonal anti-MV-N (panel C). Two viral clones (1 , 2) of MV-ATU2-N-3xM2e were assayed as indicated. Lysates prepared from Vero NK cells infected with MV-ATU3-N-3xM2e or MVSchw were used as positive controls. The positions of MV N protein and N-3xM2e fusion protein as well as molecular weight markers (size in kDa) are indicated.

Examples

MATERIALS AND METHODS

Cell lines and viruses

Vero-NK (African Green Monkey Kidney) cells were grown at 37°C under 5% C0 ₂ in complete DMEM (Dulbecco's modified Eagle medium with 4.5 mg/ml L-glucose, 100 U/ml penicillin and 100 μg ml streptomycin), supplemented with 5% heat-inactivated fetal bovine serum (FBS). Helper 293-T7-MV cells stably expressing T7 RNA polymerase and N and P genes from Schwarz MV were grown in complete DMEM supplemented with 10% FBS.

MDCK (Madin-Darby canine kidney) cells were grown at 37°C under 5% C0 ₂ in MEM (Minimum Essential Media), supplemented with penicillin, streptomycin and 10% FBS (MEM- 10). MDCK-M2 cells that constitutively express the full-length M2 consensus sequence were generated by repeated transduction with a lentiviral TRIP-M2opt vector. Cells expressing high-levels of M2 on the cell surface were selected by fluorescence-activated cell sorting and stably maintained in culture in MEM-10 supplemented with 20 μg ml of rimantadine, an M2 proton channel inhibitor (Sigma-Aldrich).

The mouse-adapted influenza A Scotland/20/74 (H3N2) virus was previously described (Ramisse et al., 1998). Working stocks were prepared from lung homogenates by two successive amplifications in MDCK cells at a multiplicity of infection (MOI) of 10 ^"3 for 3 days at 35°C in completed MEM supplemented with 1 μg ml TPCK-treated trypsin. Virus titers were determined on MDCK cells by a standard plaque assay under Avicel® overlays and are expressed as plaque forming unit per ml (pfu/ml).

The A Paris/2590/09 virus (Jonges M. et al 2010) was isolated by the National Influenza Center (Northern-France) at the Institut Pasteur in Paris (France) from nasal swab collected in Paris during the 2009 pandemic, and passaged twice in MDCK cells. The eight genomic segments were cloned from viral RNA into a bidirectional transcription plasmid derived from pHW2000 (Hoffmann et al., 2002) to generate recombinant viruses. The rescued virus was adapted to mice by serial passage of pulmonary homogenates of infected to naive mice, and further amplified in MDCK cells as described above to constitute working stocks.

Plasmid constructs

The MVSchw recombinant plasmid constructs were derived from the previously described pTM-MVSchw-ATU1 , -ATU2 and -ATU3 plasmid vectors (Combredet et al., 2003). These vectors were cloned from a commercial batch of the licensed vaccine Rouvax (kindly provided by Sanofi Pasteur MSD, Marcy I'Etoile, France). They carry an infectious cDNA corresponding to the anti-genome of the Schwarz MV vaccine strain and an additional transcription unit containing unique BsiWI and BssHII restriction sites for the insertion of foreign open reading frames upstream from the N gene (ATU1 ), between the P and M genes (ATU2) and between the H and L genes (ATU3).

A full-length M2 consensus sequence, reflecting circulating human influenza lineages (seasonal A H3N2 and A H1 N1 strains, as well as the 2009 pandemic A H1 N1 variants i.e., H1 N1 v), was generated from complete M2 coding sequences available at the NCBI Influenza Virus Sequence Database, accessed in October 2011 (Bao et al., 2008). Briefly, a total of 1148 complete M2 coding sequences, representing the spectrum of H3N2 (540 sequences), H1 N1 (386 sequences) and H1 N1v (222 sequences) influenza A diversity in humans from 1918 to 2011 , were selected and downloaded. From these data, sequence alignments and consensus sequences were computed for each of the three subtypes on the CLC Main Workbench platform (version 6.1.1 ) using the default settings. Next, a global consensus was generated by giving the same weight to each of H3N2, H1 N1 and H1 N1v M2 consensus and following the majority rule whenever applicable. When the three consensus differed at a given position, the H3N2 value was chosen to reflect the predominance of this subtype during the 2011-2012 flu season in the northern hemisphere at the time of design. The global consensus sequence was further edited to remove MV editing (A ₅ G ₃ )- and core gene end (A ₄ CKT)-like sequences on both strands. This consensus sequence was named M2raw and has the sequence of SEQ ID No. 17.

The full-length M2raw consensus sequence was chemically synthesized by Geneart (Life Technologies) with additional BsiWI and BssHII restriction sites at the 5' and 3' ends, respectively. The sequence respects the "rule of six", which stipulates that the number of nucleotides of the MV genome must be a multiple of 6 (Calain and Roux, 1993; Schneider et al., 1997). A human codon-optimized version of the consensus (M2opt) was also synthesized and has the sequence of SEQ ID No. 18. In addition to codon bias optimization for high expression in mammalian cells, MV editing (A ₅ G ₃ )- and core gene end (A ₄ CKT)-like sequences, and regions of very high (>80%) or low (<30%) GC content were avoided whenever possible. Furthermore, cis-acting sequence motifs such as internal TATA-boxes, chi-sites, ribosomal entry sites, ARE, INS, and CRS sequence elements, as well as repetitive sequences, RNA secondary structures and splice donor and acceptor sites, were avoided. Both M2raw and M2opt cDNAs were inserted into BsiWI/BssHII-digested pTM-MVSchw- ATUI (eGFP) vector, resulting in pTM-MV-ATU1-M2raw and pTM-MV-ATU1-M2opt plasmids. Similarly, pTM-MV-ATU2-M2raw and pTM-MV-ATU2-M2opt were generated by inserting both cDNAs into pTM-MVSchw-ATU2(eGFP).

A construct encoding the MV N protein fused to a single copy of M2 ectodomain (M2e) derived from the consensus sequence was chemically synthesized by Geneart. This construct encompassed the 5' extremity of the MV rescue plasmid from the T7 and hammerhead ribozyme sequence up to nt 2042 of MV antigenome. It contains unique BspE1 and BstB1 restriction enzyme sites in order to permit subsequent exchange of the M2e ectodomain sequence. In this synthetic gene, the M2e peptide (SLLTEVETPI RNEWGCRCND SSD SEQ ID No.21 ) is connected to the C-terminus of MV nucleoprotein through a flexible SGGSGG linker (N-1xM2e fusion protein). A second construct was obtained by exchange of the BspE1-BstB1 fragment with a synthetic and codon-optimized sequence encoding three tandem copies of M2e consensus connected by GGG spacers. A restriction enzyme site was also included after the third copy of M2e sequence for further subcloning. Next, the construct encoding the N-3xM2e fusion protein was used as a template for PCR amplification using the forward primer 5'- AGTCGTACG G AG ATG G CCACACTTTTAAG G-3 ' (SEQ ID No.33) containing BsiWI restriction site (underlined) and the reverse primer 5'-GGCCTTGAGAGCCCGGATG-3' (SEQ ID No.34). The N-1xM2e coding sequence was amplified by PCR using the same forward primer and the reverse primer 5'-GTTGCGCGCTCGTTATCAATCAGAGCTGTCGTTGCAC- 3' (SEQ ID No.35) containing BssHII restriction site. After digestion with BsiWI and BssHII restriction enzymes, the resulting DNA fragments were inserted into the corresponding sites of pTM-MVSchw-ATU3(eGFP) plasmid and both pTM-MV-ATU3-N-1xM2e and pTM-MV- ATU3-N-3xM2e constructs were checked by sequencing of the insert.

Rescue of recombinant MV-M2 and MV-NM2e viruses

The pTM recombinant plasmids were used to rescue recombinant viruses using a helper-cell- based system as previously described (Combredet et al., 2003). Single viral clones were amplified on Vero-NK cells. All viral stocks were produced after infection at a MOI of 0.1 , stored at -80°C and titrated by an endpoint limiting dilution assay on Vero-NK cell monolayers. Infectious titers were determined as 50% tissue culture infectious doses (TCID ₅₀ ) according to the Reed and Muench method (Reed and Muench, 1938). Growth curves of recombinant and parental viruses were determined on Vero-NK cells infected at a MOI of 0.1 , as described (Combredet et al., 2003).

Immunofluorescence assays

Monolayers of Vero-NK cells plated on 20 mm glass coverslips in a 12-well plate were infected with the recombinant or parental MVSchw viruses at a MOI of 0.01. When syncytia were clearly visible but not yet confluent (30-36 hours post-infection), cells were washed in Dulbecco's PBS and fixed with PBS-4% paraformaldehyde for 20 minutes. In order to analyze the expression of N-M2e fusion proteins, cells were further permeabilized with PBS- 0.2% triton X-100 for 10 minutes at 4°C. Coverslips were then incubated with 0.5 μg/ml of 14C2 mouse anti-M2e monoclonal antibody (Santa Cruz Biotechnology) or with rabbit polyclonal anti-MV-N (Covalab) diluted 1/1500 in PBS-1% donkey serum (DKS). After subsequent incubation with Alexa Fluor-labeled donkey anti-mouse or anti-rabbit IgG conjugates (Life Technologies, 1/500 dilution), the coverslips were mounted on slides with DAPI-containing Prolong Gold Antifade Reagent (Life Technologies) and analyzed under a DM IRB fluorescence microscope (Leica) using a 20x objective or 40x oil immersion objective. Pictures were acquired with a QICAM Fast 1394 camera (Qlmaging) and processed with the Qcapture Pro software (version 6.0.0.412, Qlmaging). Western blots

Monolayers of Vero-NK cells were infected at a MOI of 0.05 with the recombinant MV-M2, MV-NM2e or parental MVSchw viruses. 24 or 36 h post-infection, cell extracts were harvested in Laemmli sample buffer and denatured by heating at 95°C for 10 min. Proteins were separated by 4-12% SDS Bis-Tris polyacrylamide gels (Life Technologies) and transferred onto a PVDF membrane prior to immunoblotting with 14C2 anti-M2e antibody (Santa Cruz Biotechnology, 0.2 g/ml) or with anti-MV-N antibody (Covalab, 1/10000 dilution). Following incubation with Alexa Fluor 680-labeled donkey anti-mouse or anti-rabbit IgG conjugates (Life Technologies, 1/40000 dilution), fluorescence was captured with an Odyssey Infrared Imaging system (Li-Cor Biosciences).

Mice experiments and characterization of humoral immune responses

All experiments were approved and conducted in accordance to the Pasteur Institute guidelines in compliance with European animal welfare regulations (http:// ec.europa.eu/ environment/ chemicals/ lab_animals/ home_en.htm). The protocol was approved by the Institut Pasteur animal care and use committee. All experiments were conducted under enhanced biosafety level 2 conditions. To obtain CD46 ^+/" IFNa^R ^" ' ^" mice permissive for measles vaccine (Mrkic et al., 1998), FVB mice heterozygous for the measles vaccine CD46 receptor transgene were backcrossed to 129/Sv mice lacking the type IFN (Combredet et al., 2003). After more than 10 generations of backcrossing in our breeding colony, the resulting CD46-IFNAR line acquired a uniform 129/Sv background.

Six- to nine-week-old CD46-IFNAR mice were used to assess the immune response induced by recombinant MV-M2 and MV-NM2e viruses. Unless otherwise stated, groups of 6 mice were injected intraperitoneally (i.p.) with 10 ⁵ TCID ₅₀ of recombinant or parental MVSchw or with PBS as a control. Booster injections were administered four weeks thereafter. Serum samples were collected three weeks after each injection (IS1 and IS2 sera, respectively).

Antibody response to the M2 protein in immunized mice was measured by indirect ELISA. Briefly, biotinylated M2e peptide corresponding to the consensus M2e sequence

(SLLTEVETPIRNEWGCRCNDSSDK-biotin - SEQ ID No. 39, Eurogentec) was immobilized on streptavidine-coupled microtiter plates (Nunc) at a concentration of 1 μg/ml in 50 μΙ PBS.

The M2e-coupled plates were subsequently incubated with serial dilutions of the test sera.

Bound antibodies were revealed with mouse-specific anti-lgG secondary antibody conjugated to horseradish peroxidase (Southern Biotech, 1/8000) and TMB (3,3'-5,5'- tetramethylbenzidine, KPL). The isotype determination of the antibody responses was performed using isotype-specific (lgG1 and lgG2a) secondary antibodies coupled to horseradish peroxidase (Southern Biotech). The reaction was stopped by addition of an equal volume of H ₃ P0 ₄ (1 M) and absorbance of each well was read at 450 nm/620 nm. The M2e-specific antibody titers were calculated as the reciprocal of the highest dilution of individual serum, giving an absorbance of 0.5 over blank value. MV-specific antibodies were similarly measured using ELISA plates (Maxisorp, Nunc) coated with 50 ng/well of purified measles antigens (Jena Bioscience, Germany).

Specific antibodies against the native form of the M2 protein were measured using a cell- based ELISA. Brieftly, monolayers of MDCK and MDCK-M2 cells in 96-well microtiter plates were incubated with serial dilutions of the test sera. Bound antibodies were revealed with anti-mouse IgG secondary antibody and TMB substrate as described above. Readings from wells seeded with MDCK cells were substracted from wells with MDCK-M2 cells and the M2- specific IgG titers were calculated as the reciprocal of the highest dilution of individual serum, giving an absorbance of 0.2. Challenge infection of animals with influenza virus

Four weeks after the second immunization, animals were lightly anesthetized with ketamine/xylazine solution (50 mg/kg and 10 mg/kg respectively) and, unless otherwise stated, inoculated intranasally with 10 Lethal Dose 50 (LD50) of virus in 30 μΙ PBS. Mice were weighed every other day and monitored daily for signs of morbidity and mortality over 21 days. Animals that lost more than 30% of their initial weight were euthanized by cervical dislocation.

Passive immunization and virus challenge

Immune sera were prepared from CD46-IFNAR mice previously immunized with MV-M2 recombinant viruses and control MVSchw virus. Blood was collected 3 and 4 weeks after the second administration of virus, and serum was prepared by clotting the blood at room temperature for 2 to 4 hours, followed by 2 hours incubation at 4°C and centrifugation Sera were pooled per immunization group, filter-sterilized and kept at -20°C.

Eight-week-old C57BL/6 mice (Charles River) were injected by the i.p. route with 400 μΙ of pooled immune serum, diluted in PBS up to 500 μΙ, or with 500 μΙ PBS alone as a control. The day after, the passively immunized mice were challenged with 10 LD50 of the mouse- adapted A Scotland/20/74 (H3N2) strain and monitored, as described above.

Supplementary Materials and Methods for the construction and characterization of recombinant MV-M1 and MV-M1&M2 viruses

A full-length M1 consensus sequence, reflecting circulating human influenza lineages (seasonal A H3N2 and A H1 N1 strains, as well as the 2009 pandemic A H1 N1 variants), was generated from complete M1 protein sequences available at the NCBI Influenza Virus Sequence Database, accessed in January 2013. Briefly, a total of 4686 complete M1 protein sequences, representing the spectrum of H3N2 (1480 sequences from the period of 2007- 2012), H1 N1 (1740 sequences from the period of 1977-2012) and H1 N1v (1466 sequences) influenza A diversity in humans from 1977 or 2007 to 2012, were selected and downloaded. From these data, sequence alignments and consensus sequences were computed for each of the three subtypes on the CLC Main Workbench platform (version 6.7.1 ) using the default settings. Next, a global consensus was generated by giving the same weight to each of H3N2, H1 N1 and H1 N1v M1 consensus and following the majority rule whenever applicable. When the three consensus differed on a given position, the H3N2 value was chosen to reflect the overall predominance of this subtype during the 2011-2012 and 2012-2013 flu seasons in the northern hemisphere preceeding the time of design. The amino acid sequence of the M1 global consensus was then processed to generate a codon-optimized nucleotide sequence for high expression in mammalian cells. This coding sequence was further edited to inhibit alternative splicing and prevent synthesis of truncated M2-like polypeptide, and to avoid MV editing (A ₅ G ₃ )- and core gene end (A ₄ CKT)-like sequences, and regions of very high (>80%) or low (<30%) GC content whenever possible. Furthermore, cis-acting sequence motifs such as internal TATA-boxes, chi-sites, ribosomal entry sites, ARE, INS, and CRS sequence elements, as well as repetitive sequences, RNA secondary structures and other cryptic splice donor and acceptor sites, were avoided. The optimized nucleotide sequence of the M1 global consensus (M1opt) was chemically synthesized (Geneart, Life Technologies) with additional BsiWI and BssHII restriction sites at the 5' and 3' ends, respectively. The sequence respects the "rule of six", which stipulates that the number of nucleotides of the MV genome must be a multiple of 6.

Insertion of M1 opt and M2opt cDNAs in BsiWI/BssHII-digested pTM-MVSchw-ATU2(eGFP) and pTM-MVSchw-ATU3(eGFP) vectors resulted in pTM-MV-ATU2-M1 and pTM-MV-ATU3- M2 plasmids, respectively. These two plasmids were then digested with Sail restriction enzyme and ligated to produce the double recombinant pTM-MV-M1 &M2 plasmid.

Rescue and characterization of MV-ATU2-M1 , MV-ATU3-M2 and MV-M1&M2 recombinant viruses were performed as described above. The GA2B anti-M1 mAb (Thermo Scientific, 0.2 μg ml) was used for immunofluorescence and western blot assays of M1 expression.

Supplementary Materials and Methods for the design of a consensus nucleoprotein (NP) gene and of a construct encoding the NP consensus protein fused to 3 copies of M2e (NPflu-3xM2e) A full-length nucleoprotein (NP) consensus sequence, reflecting circulating human influenza lineages (seasonal A H3N2 and A/H1 N1 strains, as well as the 2009 pandemic A/H1 N1 variants), was generated from complete NP protein sequences available at the NCBI Influenza Virus Sequence Database, accessed in May 2015. Briefly, a total of 1494 complete NP protein sequences, representing the spectrum of H3N2 (746 sequences from the period of 1968-2015), H1 N1 (249 sequences from the period of 1977-2015) and H1 N1v (499 sequences) influenza A diversity in humans from 1968 to 2015, were selected (after collapsing identical sequences) and downloaded. From these data, sequence alignments and consensus protein sequences were computed for each of the three subtypes on the CLC Main Workbench platform (version 6.8.4) using the default settings. Next, a global consensus was generated by giving the same weight to each of H3N2, H1 N1 and H1 N1 v NP consensus and following the majority rule whenever applicable. When the three protein consensus sequence differed on a given position, the H3N2 value was chosen to reflect the overall predominance of this subtype during the 2011-2012, 2012-2013, and 2014-2015 flu seasons in the northern hemisphere preceding the time of design. The amino acid sequence of the NP global consensus was then processed to generate a codon-optimized nucleotide sequence for high expression in mammalian cells. Regions of very high (>80%) or low (<30%) GC content were avoided whenever possible, and cis-acting sequence motifs like internal TATA-boxes, chi-sites, ribosomal entry sites, ARE, INS, and CRS sequence elements, as well as repetitive sequences, RNA secondary structures and splice donor and acceptor sites, were avoided. The sequence was further edited to remove MV editing (A ₅ G ₃ )- and core gene end (A ₄ CKT)-like sequences on both strands. BsiWI and BssHII restriction sites were then added at the 5' and 3' ends, respectively, of the nucleotide sequence (NPflu) of the NP global consensus. The sequence respects the "rule of six", which stipulates that the number of nucleotides of the MV genome must be a multiple of 6 and has the sequence of SEQ ID No. 30..

A further construct encoding the NP consensus protein fused to three copies of M2e (NPflu- 3xM2e) was generated by PCR amplification using the NPflu consensus gene as a template and the forward primer 5'-AGTCGTACGG CCACCATGGC CTCTC-3' 5seq id No;36) containing BsiWI restriction site (underlined) and the reverse primer 5'- TCGGCGCGCG ATCCTCCGGA GTTGTCGTAC TCTTCGGCGT TG -3' (SEQ ID No.37) containing BspE1 and BssHII restriction enzyme sites (underlined). The resulting cDNA was cloned into the PCR4Blunt-TOPO plasmid. It contained unique BspE1 and BssHII restriction enzyme sites at the 3' extremity of the NPflu coding sequence which permitted subsequent insertion of the synthetic and codon-optimized 3xM2e sequence described above. Supplementary Materials and Methods for the construction and characterization of recombinant MV-NPflu&M2 and MV-NPflu-3xM2e viruses

Both NPflu and NPflu-3xM2e cDNAs were inserted into BsiWI/BssHII-digested pTM- MVSchw-ATU2(eGFP) vector, resulting in pTM-MV-ATU2-NPflu (SEQ ID No.11 ) and pTM- MV-ATU2-NPflu-3xM2e plasmids. (SEQ ID No.13) The plasmids pTM-MV-ATU2-NPflu and pTM-MV-ATU3-M2 were then digested with Sail restriction enzyme and ligated to produce the double recombinant pTM-MV-NPflu&M2 (SEQ ID No.10) plasmid.

Rescue of MV-ATU2-NPflu, MV-NPflu&M2 and MV-ATU2-NPflu-3xM2e recombinant viruses was performed in 293T-T7-MV helper cells as described above. The viruses were characterized by sequencing of their genome and by western blot assay of influenza NP and M2 (or M2e) expression (Figure 9).

Supplementary Materials and Methods for the construction and characterization of recombinant MV-ATU2-N-3xM2e virus

The N-3xM2e coding sequence was obtained by digestion with BsiWI and BssHII restriction enzymes of the pTM-MV-ATU3-N-3xM2e plasmid. The resulting DNA fragment was then inserted into the corresponding sites of pTM-MVSchw-ATU2(eGFP) vector and the resulting pTM-MV-ATU2-N-3xM2e construct (SEQ ID No.12) was checked by sequencing of the insert.

Rescue of MV-ATU2-N-3xM2e recombinant virus was performed in 293T-T7-MV helper cells as described above. The virus was characterized by sequencing of its genome and by western blot analysis of infected cell lysates. High level of expression of the N-3xM2e fusion protein was evidenced with anti-MV N antibodies and with the 14C2 anti-M2e monoclonal antibody, demonstrating that such fusion protein can be expressed either from ATU2 (figure 11 ) or from ATU3 (Figure 2).

Supplementary Materials and Methods for the characterization of cellular immune responses

Spleen cells were collected 7 to 10 days after a single administration of recombinant or parental measles virus and the frequency of influenza virus-specific IFN-v-producing T cells was quantified in a standard ELISPOT assay. Briefly, 96-wells Multi-screen PVDF plates (Millipore) were coated with 10 μg ml rat anti-mouse IFN-γ antibodies (R4-6A2, Becton- Dickinson) in PBS. Plates were washed and blocked with complete RPMI medium (RPMI 1640 supplemented with 10% FCS, 10mM Hepes, 5x10 ^"5 M β-mercaptoethanol, non- essential amino acids, Sodium Pyruvate, 100 U/ml penicillin and 100 g/ml styreptomycin) for 2 h. Various numbers of splenocytes (typically 4x10 ⁵ , 2x10 ⁵ and 1x10 ⁵ ) from immunized and control mice were then plated in triplicate in the presence or absence of the appropriate peptide (10μΜ) and IL2 (10 U/ml). The cells were incubated for 20 h at 37°C, and after extensive washes, the spots were revealed by successive incubations with biotinylated rat anti-mouse IFNy antibodies (XMG1.2, Becton-Dickinson), alkaline phosphatase-conjugated streptavidin (Becton-Dickinson) and 5-bromo-4-chloro-3-indolylphosphate/ nitroblue tetrazolium (BCIP/NBT, Sigma) as the substrate. The spots were counted using the automated S6 Ultimate-V analyzer and associated Immunosoft software (CTL Analyzer). For each mouse, the number of peptide-specific IFNy-producing cells was determined by calculating the difference between the number of spots generated in the absence and in the presence of the peptide. Results were expressed as the number of spot-forming cells (SFCs) per 10 ⁶ splenocytes.

The NP366 (H3N2) consensus peptide (ASNENMDNM - SEQ ID No.41 ), the NP366 (Scotland ) peptide (ASNENMDTM - SEQ ID No.42) and the NP263-276 conserved peptide (ALILRGSVAH KSCL - SEQ ID No.43) were synthesized by Eurogentec and used to measure the frequency of influenza-specific T cells. The measles H22-30 (RIVINREHL - SEQ ID No.44) and H446-454 (SNHNNVYWL - SEQ ID No.45) peptides and the LCMV NP396-404 (FQPQNGQFI - SEQ ID No.46) peptide were used as positive and negative control peptides, respectively.

RESULTS Recombinant MVSchw express the full-length M2 consensus protein and replicate efficiently

A full-length M2 consensus sequence was designed by the inventors, reflecting circulating human influenza lineages, seasonal A/H3N2 and A/H1 N1 strains, as well as the 2009 pandemic A/H1 N1 variant strain, from complete coding sequences available at the NCBI in november 2011. This global consensus (M2raw) was generated from separate H3N2, H1 N1 and H1 N1v consensus, as described in materials and methods and was edited to remove potential MV editing- and polyadenylation sites. The global consensus amino acid sequence is identical to the H3N2 consensus with the exception of a single conservative substitution (Val51 lle) in the cytoplasmic domain, but different from the H1 N1 (7 substitutions) and the H1 N1v consensus (15 substitutions). When the M2 ectodomain (M2e) region only is considered, the global M2e consensus is identical to both H1 N1 and H3N2 consensus, and differs at 4 positions from the H1 N1v consensus (Table 1 ). Both M2raw and a human codon-optimized version (M2opt) of the consensus gene were inserted as an additional transcription unit (ATU) into MV vector, either in position 3 (ATU2, Figure 1A) or in position 1 (ATU1 , not shown) of the genome. All four corresponding recombinant viruses were successfully rescued in helper 293-T7-MV, as indicated by the formation of syncytia in MV-infected Vero-NK cells (Figure 1 C for ATU2 viruses, not shown for ATU1 viruses) and by the sequencing of the ATU on the rescued virus genomes.

The growth of recombinant MV-ATU2 viruses was next analyzed in Vero-NK cells. Growth kinetics of both recombinant MV-ATU2-M2raw and MV-ATU2-M2opt were slightly delayed compared to that of parental MVSchw (Figure 1 B). Furthermore, the yields of recombinant viruses were 10 times lower than for the parental virus, with a maximum titer of 10 ⁶⁴ TCID ₅₀ /ml. This may be due to the toxicity of the M2 ion channel for mammalian cells (llyinskii et al., 2007) and the high levels of M2 expression at the surface of MV-M2 infected cells.

Indeed, expression of M2 consensus protein at the surface of infected cells was evidenced by immunofluorescence analysis of non-permeabilized cells with the 14C2 mouse monoclonal antibody directed against the extracellular M2 ectodomain (Figure 1 C). Furthermore, expression levels of M2 in Vero-NK cells infected by the recombinant MV-M2 viruses were analyzed by fluorescent western blotting of cell lysates and were shown to be much higher than expression levels in MDCK cells infected with A PR/8/34 (PR8) or A/Scotl and/20/74 (SCOT) influenza viruses (Figure 1 D-E). More precisely, lysates from MV- M2-infected Vero NK cells had to be diluted more than 1 in 4 (Figure 1 D) or up to 1 in 10 (Figure 1 E) to match band intensity of lysates from influenza-infected MDCK cells.

Recombinant MVSchw express an additional N protein fused to M2e ectodomain and replicate efficiently

To enhance M2e immunogenicity, we sought to express M2e as a fusion protein with measles nucleoprotein (N), thereby achieving multimerization and display of M2e on the viral nucleoprotein. To that end, one or three tandem copies of the 23 aa-consensus M2e sequence was genetically linked to the measles N C-terminus through a flexible SGGSGG linker (SEQ ID No.38), and the resulting protein was expressed from the ATU located in position 6 of the pTM-MVSchw-ATU3 vector (Figure 2). In this approach, the measles N protein serves as a carrier to incorporate M2e into measles ribonucleoprotein (RNP) complexes.

Both recombinant MV-N-1xM2e and MV-N-3xM2e viruses were successfully rescued in helper 293-T7-MV, as indicated by the formation of syncytia in MV-infected Vero-NK cells (Figure 2B) and by the sequencing of the ATU on the rescued virus genomes. Both recombinant viruses grew to titers in the 10 ⁷ -10 ⁸ TCID ₅₀ /ml range, which are similar to those achieved by parental MVSchwarz. This indicates that the expression of the hybrid N proteins from an additional gene in position 6 of the genome does not affect viral propagation in vitro. Expression of the N-M2e fusion proteins was analyzed by immunofluorescence of infected cells and western blotting of infected cell lysates. In addition to the authentic N band, an additional band was observed by western blotting with anti-MV N antibodies for each fusion protein at the expected size (Figure 2D). These bands also reacted with the 14C2 anti-M2e monoclonal antibody (Figure 2C), validating the correct expression of the M2e epitopes on its N carrier. It is noteworthy that several minor additional bands are visible on the blots, indicating degradation of authentic and fusion N proteins and susceptibility of measles N to proteolysis, as already evidenced by others (Rima, 1983). Intensity of the N-M2e bands was lower than that of the authentic N, indicating reduced expression levels of the N-M2e genes from the ATU located in the distal position 6 when compared to those of the authentic N gene located in the proximal position 1 of the antigenome. This was expected, since viral mRNAs are produced in decreasing amounts from the 3' to the 5' end of MV genomic RNA (Plumet et al., 2005). As illustrated in figure 2B, immunostaining with anti-MV N antibodies showed that N is mainly contained in large cytoplasmic inclusion bodies, as already described by others (Griffin, 2013). The role of these inclusion bodies in MV life cycle has not been extensively studied, but are likely the sites of viral genome transcription and replication as evidenced recently for other paramyxoviruses and rhabdoviruses (reviewed in Zhang et al., 2013). Interestingly, immunostaining with the 14C2 anti-M2e monoclonal antibody showed a similar localization of both N-M2e fusion proteins, indicating that their measles N region directed the fusion proteins to the sites of viral replication and likewise promoted their incorporation and multimerization into the active RNP complexes. MV-M2 and MV-N-M2e induce Th1 -type immune response

The immunogenicity of the recombinant MV-M2 viruses was investigated in genetically modified CD46-IFNAR mice susceptible to MV infection (Mrkic et al., 1998) and compared to the immunogenicity of M2 expressed during experimental influenza infection with the mouse- adapted A/Scotland/20/74 strain (Figure 3).

M2e- and measles-specific antibody responses were evaluated for each individual mouse by indirect ELISA against M2e peptide and MV antigens, respectively. M2e peptide was biotinylated at its C-terminus and immobilized on streptavidine-coupled microtiter plates in order to ensure that the peptide was displayed onto the polystyrene wells in a conformation as close as possible to its natural conformation, where it is C-terminally linked to M2 transmembrane region and displayed on the cell surface. Indeed, preliminary experiments showed that recognition of the M2e peptide by the 14C2 monoclonal antibody as well as by polyclonal antibodies induced in mice by experimental influenza infection was much more efficient when the M2e peptide was biotinylated and immobilized, rather than adsorbed on the plastic surface of ELISA plates (not shown).

High titers of anti-M2e IgG were raised in all mice to similar levels after the first injection of recombinant MV-ATU2-M2 viruses (Figure 3A) and MV-ATU1-M2 viruses (not shown), whereas preimmune sera (not shown) and sera from control animals that received empty MVSchw remained negative. These titers were higher for both MV-ATU2-M2raw and MV- ATU2-M2opt injected animals (average titer of 3.7 ± 0.3 and 3.7 ± 0.2 Iog10, respectively) than for animals infected with the A/Scotland/20/74 virus (2.9 ± 0.3 Iog10 titer, p<10 ^"3 ). After the second injection, titers were boosted 10 to 20 times for animals immunized with MV vectors. Tallying with the results observed after the first injection, the four MV-M2 recombinant viruses induced similar high IgG titers, which felt in the 10 ⁴ -10 ⁵ range (Figures 3A and 3C). Noticeably, the second inoculation of A Scotland/20/74 virus did not amplify the anti-M2 IgG response (2.9 ± 0.8 Iog10).

Next, the immunogenicity of the recombinant MV-N-M2e viruses was compared to that of the MV-ATU2-M2opt virus. Significant titers of anti-M2e IgG were raised in all mice after the first injection of recombinant MV-N-3xM2e virus (2.7 ± 0.2 Iog10 titer), whereas sera from control animals and sera from animals that received the MV-N-1xM2e remained negative (Iog10 titers < 1.7, Figure 4A). After the second injection, titers were boosted up to 3.5 ± 0.4 Iog10 for animals immunized with the MV-3xM2e virus and an anti-M2 response was detected at low titers in 2 out of 6 mice immunized with the MV-N-1xM2e virus (2.0 and 2.7 log 10 titers). In contrast, a single injection of MV-ATU2-M2opt induced a high IgG titer (3.9 ± 0.2 Iog10 titer) that further increased after a second injection (4.3 ± 0.3 Iog10 titer).

To analyze the polarization of the immune response induced by the recombinant MV vaccines, we next measured the level of lgG1 and lgG2a isotypes three weeks after the second injection (Figure 4C). Immunization with two doses of MV-ATU2-M2 or MV-N-3xM2e induced higher titers of lgG2a than lgG1 antibodies (average ratio lgG2a over lgG1 of 60 and 79 respectively), suggesting that the immune response was skewed towards a Th1-type response.

Interestingly, antibodies to MV were raised at similar levels in all mice that received either MVSchw, MV-M2 viruses (Figure 3B and 3D) or MV-N-M2e viruses (Figure 4B). This indicates that expression of the full-length M2 protein by the recombinant viruses did not alter their replication in vivo nor modify their measles-specific immunogenicity, despite their delayed growth curve and reduced titers in in vitro experiments. This also indicates that the expression of the hybrid N-M2e proteins from an additional nucleoprotein gene did not affect replication and immunogenicity of measles virus in mice.

Altogether, these results demonstrated that the measles vector is capable of inducing very high levels of anti-M2e antibodies in CD46-IFNAR mice (H-2b 129/Sv background) whether the full-length M2 gene is expressed from an ATU or 3 tandem copies of the short 23-aa M2e sequence are fused to an extra copy of the N gene. Most interestingly, both vectorization strategy allowed to bypass the H-2 restriction of anti-M2e responses, which was described recently for DNA immunization, adenovirus vectorization and M2e-multiple antigenic peptides (MAP) immunization, and which evidenced very poor responsiveness in mice of the H2 ^b haplotype (Misplon et al., 2010; Wolf et al., 2011 ). In addition, anti-M2e responses are likely Th1 -skewed, a hallmark of live attenuated viruses and a highly desirable feature for an antiviral vaccine. Protection of mice after homologous and heterologous challenge

To determine the protective efficacy of MV-ATU1-M2opt and MV-ATU2-M2opt, we examined the survival of CD46-IFNAR mice after intranasal lethal challenge with 10 LD50 of the homologous A/Scotland/20/74 (H3N2) strain or the heterologous A/Paris/2590/09 (H1 N1v) strain. Mice were also monitored for weight change as a measure of illness. All mice immunized as a control with the parental MVSchw died within 10 days after challenge with A Paris/2590/09 (H1 N1v) (Figure 3F). All but one control mice immunized with the parental MVSchw died within 10 days after challenge with the A/Scotland/20/74 (H3N2) (Figure 3E). In contrast, mice immunized with MV-ATU1-M2 or MV-ATU2-M2 were partially protected against challenge, with a reduction in global mortality and delayed death time. Survival rates ranged from 17 to 83% and mice that survived the challenge, presented weight loss up to 25% of their initial body weight and began to recover on day 8-10 post challenge (not shown).

To confirm that the antibodies induced by vaccination with MV-M2 recombinant viruses were responsible for the observed protection, serum was prepared from CD46-IFNAR mice immunized with MV-ATU1-M2 or MV-ATU2-M2 and transferred to naive C57BL/6 recipient mice. Each mouse received 400 μΙ of pooled immune serum by intraperitoneal injection, a dose sufficient to obtain anti-M2e circulating antibody titers in the recipient mice at approximately 1/10 ^th the levels present in the donor mice (preliminary experiments, not shown). The day after transfer, mice were challenged with homologous A/Scotland/20/74 (H3N2) and survival curves were recorded (figure 5). As was observed for donor immunized mice (figure 3E), mice transferred with either immune sera were partially protected against challenge, with a reduction in global mortality and delayed death time, whereas all mice transferred with control serum died within 11 days.

Together, these results indicate that recombinant MV-M2 viruses induced protective immunity against homologous H3N2 and heterologous H1 N1v influenza in CD46-IFNAR mice, and that circulating antibodies against M2 present in the immunized animals contribute to the observed protection. Antibodies induced by N-M2e fusion proteins recognize native tetrameric M2 and protect mice against homologous challenge

Although the mechanism of protection by anti-M2e antibodies remains poorly understood, it relies largely on Fc receptor-dependent elimination of influenza virus-infected cells, ADCC and Ab-dependant cell-mediated phagocytosis (El Bakkouri et al., 2011 ; Jegerlehner et al., 2004). Therefore, it is critical that anti-M2e antibodies raised by immunization are capable of recognizing native M2e, which is presented as a tetrameric complex at the surface of influenza-infected cells as on influenza virions. To investigate this point, we produced MDCK cells constitutively expressing the full-length consensus M2 protein at the cell surface, as described in materials and methods. We used these MDCK-M2 cells in a cell-based indirect ELISA to analyze binding of sera from MV-N-1xMe- and MV-N-3xM2e-immunized mice (Figure 4D).

MV-N-3xM2e recombinant virus induced high levels of antibodies able to bind to MDCK-M2 cells (2.8 ± 0.4 Iog10 titer). The titers of anti-MDCK-M2 antibodies induced by N-displayed M2e in these MV-N-3xM2e-immunized mice were 20 times lower than those of antibodies induced by the native M2 consensus protein in MV-ATU2-M2-immunized mice (4.2 ± 0.2 Iog10 titer, p<10 ^"3 ). Sera from mice immunized with MV-N-1xM2e remained negative (Iog10 titer < 1.7). The hierarchy of binding titers was indeed comparable to that observed with the peptide ELISA (Figure 4A) and confirmed that the N-1xM2e construct with a single copy of M2e is less immunogenic than the N-3xM2e construct expressing 3 tandem copies of the M2.

Altogether, these results demonstrated that the M2e peptide, displayed and multimerized on measles RNP complexes is able to induce antibodies recognizing the native tetrameric M2 protein expressed at the cell surface of MDCK-M2 cells.

To investigate the protective efficacy of MV-N-1xM2e and MV-N-3xM2e, we examined the survival of CD46-IFNAR mice after intranasal lethal challenge with the homologous A Scotl and/20/74 (H3N2) virus. All mice immunized with the parental MVSchw died within 9 days (Figure 4E). In contrast, 2 and 3 out of 6 mice immunized with MV-N-1xM2e and MV-N- 3xM2e respectively, survived up to 21 days after challenge. Noticeably, immunization with MV-N-3xM2e resulted in a delayed death time for mice that eventually succumbed to infection, and immunization with MV-ATU2-M2opt induced better protection, in agreement with the induction of higher anti-M2e and anti-native M2 antibody titers. Together, these results suggested that recombinant MV-N-3xM2e and, to a lesser extent, MV-N-1xM2e induces significant protective immunity against influenza in CD46-IFNAR mice. Supplementary Results for the construction and characterization of recombinant MV- M1 and MV-M1&M2 viruses

Recombinant MVSchw can be engineered to express full-length M1 and M2 consensus proteins from two ATUs

We designed a full-length M1 consensus sequence, reflecting circulating human influenza lineages, seasonal A/H3N2 and A/H1 N1 strains, as well as the 2009 pandemic A/H1 N1v strain, from complete protein sequences available at the NCBI in January 2013. This global consensus was generated from separate H3N2, H1 N1 and H1 N1v consensus, as described in materials and methods. The corresponding nucleotide coding sequence was then generated, codon-optimized for high expression in mammalian cells, and further edited to remove influenza splice sites and prevent synthesis of truncated M2-like polypeptides. It was also edited to remove potential MV editing- and polyadenylation sites. Taking advantage of the gradient of gene expression generated by MV replication (Plumet et al., 2005), the resulting M1 opt consensus gene was inserted as an ATU in position 3 (ATU2, Figure 6A) of the MV vector and the M2opt consensus gene was inserted in position 6 (ATU3). This choice was made in an attempt to reduce M2 expression and negative impact on measles vector replication, which we observed previously when M2 was inserted in the more proximal ATU2 (Figure 1 ).

Then, a measles vector with M1 opt and M2opt consensus genes inserted in two distinct ATUs was produced by Sail restriction and ligation. The single and double recombinant viruses were successfully rescued in helper 293-T7-MV, as indicated by the formation of syncytia in MV-infected Vero-NK cells and by the sequencing of the ATUs on the rescued virus genomes. All recombinant viruses grew to titers in the 10 ⁷ -10 ⁸ TCID ₅₀ /ml range, which are similar to those achieved by parental MVSchwarz. Interestingly, M2 toxicity for mammalian cells did not impair growth of MV-ATU3-M2opt and MV-M1 &M2 viruses, as it did for MV-ATU2-M2opt, suggesting that M2 expression levels from the distal ATU3 were reduced below toxicity levels, as expected.

Expression of M1 and M2 in Vero-NK cells infected by either the single and double recombinant virus was analyzed by fluorescent western blotting of cell lysates. M2 expression levels were shown to be higher than expression levels in MDCK cells infected with A.Scotland/20/74 influenza virus (Figure 6C), whereas M1 expression levels were shown to be somewhat lower (Figure 6B). M1 and M2 expression levels of the double MV- M1&M2 recombinant virus were similar to those of the single recombinant viruses, MV- ATU2-M1 opt and MV-ATU3-M2opt respectively.

Altogether, these data indicate that measles virus vector may be engineered in order to simultaneously express consensus genes coding for both M1 matrix and M2 ion channel from circulating influenza lineages. This double recombinant virus should drive the production of influenza virus-like particles (VLPs) covered with the M2 protein from infected cells and induce enhanced immune responses in immunized animals against both M1 and M2 influenza antigens.

Dual recombinant measles virus expressing both M1 and M2 consensus proteins exhibit higher protection efficiency in mice than single recombinant viruses.

Immunogenicity of the dual recombinant MV-M1&M2 virus was investigated in CD46-IFNAR mice and compared to the immunogenicity of the single recombinant MV-ATU2-M2opt and MV-ATU3-M2opt viruses. High titers of anti-M2e IgG were raised in all mice after the first injection of either of the 3 recombinant viruses, whereas sera from control animals that received empty MVSchw or MV-ATU2-M1 opt remained negative (Figure 8A). After the second injection, titers were boosted up to similar levels for animals immunized with either MV-ATU2-M2opt or MV-ATU3-M2opt viruses (3.9±0.4 and 3.8± 0.3 log 10 titers, respectively). Remarkably, significantly higher anti-M2e responses were detected in mice immunized with the dual recombinant MV-M1 &M2 virus (4.1±0.3 log 10 titers) than in mice immunized with parental MV-ATU3-M2opt (p<0.01 ) or former MV-ATU2-M2opt (p<0.1 ) viruses.

Interestingly, antibodies to MV were raised at similar levels in all mice that received either MVSchw or MV-M1 &M2 virus (Figure 8B), indicating that the simultaneous expression of two foreign proteins by the dual recombinant virus did not alter its replication in vivo nor modify its measles-specific immunogenicity, as already observed for single recombinant viruses.

To investigate the protective efficacy of the dual recombinant MV-M1 &M2 virus, we examined the survival of CD46-IFNAR mice after intranasal lethal challenge with the homologous A/Scotland/20/74 (H3N2) virus. Mice immunized with MV-ATU2-M1 opt or the parental MVSchw presented a massive and rapid weight loss from day 3 post-challenge and most died within 12 days (Figure 8C). Mice immunized with either MV-ATU2-M2opt or MV- ATU3-M2opt single recombinant viruses were partially protected against challenge, with a good reduction in global mortality. Survival rates were 75% and 70% respectively, and mice that survived the challenge, presented weight loss up to 25% of their initial body weight (Figure 8D). In sharp contrast, all mice immunized with the dual recombinant MV-M1 &M2 virus survived after challenge with reduced clinical symptoms and limited weight loss.

Together, these results indicated that the dual recombinant MV-M1&M2 virus induces significantly better protective immunity against influenza in CD46-IFNAR mice than either of its parental MV-ATU2-M1 opt or MV-ATU3-M2opt. Recombinant MVSchw can be engineered to simultaneously express full-length NP consensus and M2 or M2e consensus

We designed a full-length NP consensus sequence, reflecting circulating human influenza lineages, seasonal A H3N2 and A/H1 N1 strains, as well as the 2009 pandemic A/H1 N1v strain, from complete protein sequences available at the NCBI in May 2015. This global consensus was generated from separate H3N2, H1 N1 and H1 N1v consensus, as described in materials and methods. The corresponding nucleotide coding sequence was then generated, codon-optimized for high expression in mammalian cells, and further edited to remove potential MV editing- and polyadenylation sites.

Two alternative strategies were then explored for simultaneous expression of NP and M2 consensus sequences.

First, similarly to the strategy used to express M1 and M2 sequences (see above), the resulting NPflu consensus gene was inserted as an ATU in position 3 (ATU2, Figure 9A) of the MV vector and the M2opt consensus gene was inserted in position 6 (ATU3). Then, a measles vector with NPflu and M2opt consensus genes inserted in two distinct ATUs was produced by Sail restriction and ligation. The single MV-NPflu and double MV-NPflu&M2 recombinant viruses were successfully rescued in helper 293-T7-MV, as indicated by the formation of syncytia in MV-infected Vero-NK cells and by the sequencing of the ATUs on the rescued virus genomes. Both recombinant viruses grew with a delayed kinetic up to titers in the 10 ⁷ TCID ₅₀ /ml range, which are slightly lower to those achieved by parental MVSchwarz, indicating that expression of NPflu interferes to some extent with replication of the Measles virus genome and/or dissemination of the virus.

Second, NP and M2e were expressed as a chimeric NPflu-3xM2e antigen from the ATU located in position 3 of the pTM-MVSchw-ATU2 vector (Figure 9B). In this approach, the NPflu consensus protein acted as a carrier and displayed 3 copies of the 23 aa-consensus M2e polypeptide at its C-terminus. It its most likely that the chimeric antigen will multimerize as authentic influenza NP does, thus enhancing immunogenicity of the M2e polypeptide. The recombinant MV-NPflu-3xM2e virus was successfully rescued in helper 293-T7-MV and was propagated in Vero-NK cells up to titers in the 10 ⁷ TCID ₅₀ /ml range which are similar to those achieved by parental MV-ATU2-NPflu although lower than those achieved by empty MVSchwarz vector.

Expression of NPflu and M2 / M2e in Vero-NK cells infected by either single or double recombinant virus was analyzed by fluorescent western blotting of cell lysates. NPflu expressions levels were shown to be similar than expression levels in MDCK cells infected with A Scotland/20/74 influenza virus (Figure 9C), whereas M2 expression levels had already been shown to be higher (Figure 6C). M2 expression levels of the double MV-NPflu&M2 recombinant virus were somewhat lower than those of the single MV-ATU3-M2opt recombinant virus (Figure 9D), in accordance with the observed delayed growth of the former. NP expression levels of the double MV-NPflu&M2 recombinant virus were similar to those of the single MV-ATU2-NPflu recombinant virus.

Expression of the NPflu-M2e fusion protein was demonstrated by the presence of a band of higher molecular weight and expected size (64.6 kDa) than that of authentic NP (56 kDa). This band reacted with both anti-influenza virion antibodies and 14C2 anti-M2e monoclonal antibody (Figures 9C and 9D), validating the correct expression of the M2e epitopes on the NP carrier.

Altogether, these data indicate that measles virus vector may also be engineered in order to simultaneously express consensus genes coding for both NP nucleoprotein and M2 ion channel from circulating influenza lineages. M2 can be expressed either as a full length integral protein from a dedicated ATU, such as in the dual MV-NPflu&M2 recombinant virus, or as a fusion protein between its 23 aa-core M2e ectodomain and NPflu, such as in the single MV-NPflu-3xM2e recombinant virus.

Dual recombinant measles virus expressing both NPflu and M2 consensus proteins exhibit higher protection efficiency in mice than single recombinant viruses.

Immunogenicity of the dual recombinant MV-NPflu&M2 virus was investigated in CD46- IFNAR mice and compared to the immunogenicity of the single recombinant MV-ATU3- M2opt viruses.

High titers of anti-M2e IgG were raised in all mice after the first injection of either of the recombinant viruses, whereas sera from control animals that received empty MVSchw or MV-ATU2-NPflu remained negative (Figure 10A). After the second injection, titers were boosted up to lower levels for animals immunized with MV-NPflu&M2 (3.6±0.5 Iog10 titers) than for animal immunized with MV-ATU3-M2opt viruses (4.2±0.4 log 10 titers, p<0.1 ), in accordance with the delayed growth curve and reduced yields in vitro of the former.

Induction of an heterospecific cellular response was examined in mice that had been immunized with the dual MV-NPflu&M2 virus. Frequencies of influenza virus-specific IFN-γ- producing T cells in the spleens of immunized mice were quantified by ELISPOT, using the influenza virus NP366 immunodominant class I peptide and the NP260-273 class II peptide. IFNy-producing CD8+ T cells were detected in response to the NP366 (H3N2) consensus class I peptide (SEQ ID No.41 ) when splenocytes were isolated from 5 out of 6 MV- NPflu&M2 immunized mice but not from control MVSchw and MV-ATU3-M2opt immunized mice (Fig. 10C). Influenza-specific T cell precursor frequencies ranging between 670 and 2000 per 10 ⁶ splenocytes (average 1300 ± 510) were observed, demonstrating that a very strong heterospecific CD8+ T cell response was induced upon immunization with the dual MV-NPflu&M2 recombinant virus. These NP366 specific T cells were cross-reactive and able to recognize the NP366 (Scotland)- SEQ ID No.42) peptide corresponding to the A/Scotland/20/74 virus with similar efficiencies (860±340 SFC/10 ⁶ splenocytes). IFNy- producing CD4+ T cells were detected in response to the NP260-273 conserved class II peptide (SEQ ID No.43), albeit at slightly lower frequencies (520±150 SFC/10 ⁶ splenocytes). To investigate the protective efficacy of the dual recombinant MV-NPflu&M2 virus, we examined the survival of CD46-IFNAR mice after intranasal lethal challenge with the homologous A/Scotland/20/74 (H3N2) virus. Mice immunized with the control parental MVSchw presented a massive and rapid weight loss from day 3 post-challenge (Figure 10D) and 4 out of 6 mice died within 12 days (Figure 10E). Mice immunized with either MV-ATU2- NPflu or MV-ATU3-M2opt single recombinant viruses were partially protected against challenge, with a reduction in global mortality and weight loss. Most mice survived the challenge and presented maximal weight loss of 16.5±2.9% (day 8) and 19.2±4.4% (day9) of their initial body weight, respectively (Figure 10E). In contrast, all mice immunized with the dual recombinant MV-NPflu&M2 virus survived after challenge with a net reduction of clinical symptoms (not shown) and a more transient weight loss: they presented a maximal weight loss of 11.0±3.7% at day 7 and quickly recovered thereafter.

Together, these results indicated that the dual recombinant MV-NPflu&M2 virus induces significantly better protective immunity against influenza in CD46-IFNAR mice than either of its parental MV-ATU2-NPflu or MV-ATU3-M2opt. Higher protective efficiency was correlated to the induction of both anti-M2e antibodies and anti-NP cellular responses.

TABLES

Table 1 : Alignment of the M2e consensus amino acid sequences

global consensus ¹ SLLTEVETPI RNEWGCRCND SSD (SEQ ID No

H1N1 consensus

HINlv consensus T -S—E S- (SEQ ID No

H3N2 consensus

^† used as immunogen in the reported experiments.

- indicates matching residues.

Conclusion

The objective of this preclinical study was to evaluate the proof-of-concept of a new universal influenza vaccine strategy based on a standard measles vaccine engineered to express a M2 consensus protein. The inventors found that the vaccines induced high titers of anti-M2e antibodies and protected mice from an intranasal lethal challenge with homologous or heterologous influenza viruses.

After two successive immunizations with recombinant MV-M2 or MV-NM2e viruses, mice were partially protected from intranasal infectious challenge with mouse-adapted A/Scotland/20/74 (H3N2) and A/Paris/2590/09 (H1 N1v) viruses and passive transfer experiments demonstrated that anti-M2 antibodies contributed to the protection. The anti- M2e responses are likely Th1 -skewed, a hallmark of live attenuated viruses and a highly desirable feature for an antiviral vaccine.

Interestingly, as already mentioned above, both vectorization strategy allowed to bypass the H-2 restriction of anti-M2e responses, which was evidenced recently and predicted very poor responsiveness of all mice of the H-2 ^b MHC haplotype such as the CD46-IFNAR mice used in the study. This indicates that T cell responses induced against the measles vector likely supplied the T helper cellular response, which is needed to trigger B cells to produce anti- M2e antibodies. Remarkably, help was supplied whether M2 epitopes were linked to measles N within the N-M2e hybrid protein (like in a hapten-carrier conjugate) or co-expressed with MV proteins in the case of the MV-ATU1-M2 or MV-ATU2-M2 viruses.

Most interestingly, protection was conferred against challenge with the A Scotland/20/74 virus but also with the pandemic A/Paris/2590/09 H1 N1v strain, whose M2e sequence has an avian origin and differs at 4 positions from the global consensus sequence used for immunization. This result may be predictive of broad protection against a variety of subtypes, since, as an example, avian H5N1 viruses differs only at 3 of the 4 above mentioned positions.

Partial protection suggests that the recombinant vaccine might be improved. In that respect, expression of the hybrid N-M2e proteins as an additional nucleoprotein gene placed in position 6 of the genome (ATU3) did not affect replication in vitro and immunogenicity in mice. This gave the inventors the opportunity for further refinement of this strategy by placing the additional hybrid N-M2e genes upstream in the genome, such as in position 3 (ATU2) between the P and the M genes, thus increasing N-M2e expression and possibly immunogenicity and levels of protection. Levels of protection may also be improved by the co-expression of a second influenza consensus protein, such as an M1 or NP consensus, in a double recombinant measles vaccine. This approach would advantageously complete the induction of broad anti-M2 antibody responses by cellular responses targeting conserved influenza structural proteins. Indeed, the inventors showed that the measles vaccine can be further engineered to express either M1 and M2 consensus proteins, or NP and M2 / M2e consensus proteins and that such double recombinant viruses provide enhanced protection against influenza in the IFNAR-CD46 mouse model than any single recombinant virus. Higher protection efficiency of the double MV-NP&M2 recombinant virus correlated to the induction of cross-reactive cellular responses against the NP protein. Interestingly, better protection efficiency of the double MV-M1&M2 recombinant virus correlated to the induction of higher anti-M2e antibody levels, strongly advocating in favor of the production of influenza VLP in cells infected by the double MV-M1 &M2 recombinant virus.

Alternatively, partial protection might be indicative of the stringency of the mouse model. The inventors used mouse-adapted viruses for challenge, and relied on stocks prepared after a limited number of passages (less than 2) in cell culture. At the challenge doses used (10 LD50 and less than 10 ³ PFU), most control mice died quickly, CD46-IFNAR mice within 8 days (figure 3 and 4) and immunocompetent C57BL/6 mice (figure 5) within 10 days. This match previous observation of the inventors in other mouse strains and is strongly indicative of the high virulence of the adapted viruses in laboratory strains of mice. In addition, CD46- IFNAR mice were established by backcrossing CD46-transgenic mice against IFNAR mice lacking the type 1 IFN receptor (IFNa^R ^" ' ^" ) and are expected to exhibit increased mortality and morbidity after influenza challenge as their IFNAR parents (Arimori et al., 2013).

Because recombinant MV-influenza vaccine can be easily and rapidly produced in large quantities and at low cost in most countries, recombinant MV-influenza vaccines might be used instead of the standard MV vaccine routinely used for infants worldwide, notably through the Expanded Program of Immunization of WHO. Interestingly, the induction of measles-specific immunity was not altered in the mouse preclinical model by the expression of any of the M1 , M2 and NP transgenes, suggesting that MV-influenza vaccine might even replace the MV Schwarz strain in the combined measles, mumps, rubella vaccine or the measles, mumps, rubella, varicella vaccines.

In conclusion, the inventors have produced new recombinant MV-influenza viruses able to induce high levels of anti-M2 antibodies and cellular responses to influenza and broad protection from intranasal challenge, thus making the proof-of-concept of this strategy for universal influenza vaccine development. It could also help achieve wide vaccine coverage in both children and adults against zoonotic influenza viruses, such as avian H5N1 , H9N2 and H7N9 viruses, in the regions that are affected by cases of animal to human transmission. These characterized universal influenza vaccine candidates deserve to be evaluated in a more adapted, non-immuno-compromised and genetically diverse, non-human-primate model, in which the protective potential of the induced immune responses against field isolates of seasonal and zoonotic influenza strains could be addressed. REFERENCES

Arimori, Y., Nakamura, R., Yamada, H., Shibata, K., Maeda, N., Kase, T., Yoshikai, Y., 2013. Type I interferon limits influenza virus-induced acute lung injury by regulation of excessive inflammation in mice. Antiviral Res 99, 230-237

Bankamp B et al Genetic characterization of Measles Vaccine Strains - The Journal of Infectious Diseases 2011 ;204:S533-S548

Deng L. et al Vaccines 2015, 3, 105-136

Bao, Y., Bolotov, P., Dernovoy, D., Kiryutin, B., Zaslavsky, L, Tatusova, T., Ostell, J., Lipman, D., 2008. The influenza virus resource at the National Center for Biotechnology Information. J Virol 82, 596-601.

Calain, P., Roux, L, 1993. The rule of six, a basic feature for efficient replication of Sendai virus defective interfering RNA. J Virol 67, 4822-4830.

Combredet, C, Labrousse, V., Mollet, L, Lorin, C, Delebecque, F., Hurtrel, B., McClure, H., Feinberg, M.B., Brahic, M., Tangy, F., 2003. A molecularly cloned Schwarz strain of measles virus vaccine induces strong immune responses in macaques and transgenic mice. J Virol 77, 11546-11554.

El Bakkouri, K., Descamps, F., De Filette, M., Smet, A., Festjens, E., Birkett, A., Van Rooijen, N., Verbeek, S., Fiers, W., Saelens, X., 2011. Universal vaccine based on ectodomain of matrix protein 2 of influenza A: Fc receptors and alveolar macrophages mediate protection. J Immunol 186, 1022-1031.

Griffin, D.E., 2013. Measles virus, in: Knipe, D.M., Howley, P.M. (Eds.), Fields Virology, 6th ed. Lippincott Williams & Wilkins, Philadelphia, PA.

Hoffmann, E., Krauss, S., Perez, D., Webby, R., Webster, R.G., 2002. Eight-plasmid system for rapid generation of influenza virus vaccines. Vaccine 20, 3165-3170.

Ilyinskii, P.O., Gabai, V.L., Sunyaev, S.R., Thoidis, G., Shneider, A.M., 2007. Toxicity of influenza A virus matrix protein 2 for mammalian cells is associated with its intrinsic proton- channeling activity. Cell cycle 6, 2043-2047.

Jegerlehner, A., Schmitz, N., Storni, T., Bachmann, M.F., 2004. Influenza A vaccine based on the extracellular domain of M2: weak protection mediated via antibody-dependent NK cell activity. J Immunol 172, 5598-5605.

Marcel Jonges et a\.J. Clin. Microbiol. March 2010 vol. 48 no. 3 928-940

Misplon, J.A., Lo, C.Y., Gabbard, J.D., Tompkins, S.M., Epstein, S.L., 2010. Genetic control of immune responses to influenza A matrix 2 protein (M2). Vaccine 28, 5817-5827.

Mrkic, B., Pavlovic, J., Rulicke, T., Volpe, P., Buchholz, C.J., Hourcade, D., Atkinson, J. P., Aguzzi, A., Cattaneo, R., 1998. Measles virus spread and pathogenesis in genetically modified mice. J Virol 72, 7420-7427.

Plumet, S., Duprex, W.P., Gerlier, D., 2005. Dynamics of viral RNA synthesis during measles virus infection. J Virol 79, 6900-6908.

Ramisse, F., Deramoudt, F.X., Szatanik, M., Bianchi, A., Binder, P., Hannoun, C, Alonso, J.M., 1998. Effective prophylaxis of influenza A virus pneumonia in mice by topical passive immunotherapy with polyvalent human immunoglobulins or F(ab')2 fragments. Clinical and experimental immunology 111 , 583-587.

Reed, L.J., Muench, H., 1938. A simple method of estimating fifty percent endpoints. Am. J. Hyg. 27, 493-497.

Rima, B.K., 1983. The proteins of morbilliviruses. J Gen Virol 64 (Pt 6), 1205-1219.

Schneider, H., Kaelin, K., Billeter, M.A., 1997. Recombinant measles viruses defective for RNA editing and V protein synthesis are viable in cultured cells. Virology 227, 314-322. Wolf, A.I., Mozdzanowska, K., Williams, K.L., Singer, D., Richter, M., Hoffmann, R., Caton, A.J., Otvos, L, Erikson, J., 2011. Vaccination with M2e-based multiple antigenic peptides: characterization of the B cell response and protection efficacy in inbred and outbred mice. PloS one 6, e28445.

Zhang, S., Chen, L, Zhang, G., Yan, Q., Yang, X., Ding, B., Tang, Q., Sun, S., Hu, Z., Chen, M., 2013. An amino acid of human parainfluenza virus type 3 nucleoprotein is critical for template function and cytoplasmic inclusion body formation. J Virol 87, 12457-12470.

Print Out (Original in Electronic Form)

(This sheet is not part of and does not count as a sheet of the international application)

Indications are Made All designations

FOR RECEIVING OFFICE USE ONLY -4 This form was received with the

international application: yes

(yes or no)

-4-1 Authorized officer

Kuiper-Cristina, Nathalie

FOR INTERNATIONAL BUREAU USE ONLY -5 This form was received by the

international Bureau on:

-5-1 Authorized officer