Login| Sign Up| Help| Contact|

Patent Searching and Data


Title:
METHODS OF DETECTING TRICHOMONAS TENAX
Document Type and Number:
WIPO Patent Application WO/2023/150360
Kind Code:
A4
Abstract:
Provided are methods for detecting T. tenax via LAMP assay. This newly developed LAMP assay has high sensitivity and specificity and provides a quick, cheap, easy and reliable method used for the detection of T. tenax that can be used as a point-of-care test in human and veterinary medicine as well as in epidemiological studies of T. tenax infections in humans, dogs and other mammals.

Inventors:
YAO CHAOQUN (US)
Application Number:
PCT/US2023/012434
Publication Date:
December 07, 2023
Filing Date:
February 06, 2023
Export Citation:
Click for automatic bibliography generation   Help
Assignee:
ADTALEM GLOBAL EDUCATION INC (US)
International Classes:
C12Q1/6893; C12Q1/6876; C12Q1/04; C12Q1/68; C12Q1/6844
Attorney, Agent or Firm:
DICKINSON, Kari (US)
Download PDF:
Claims:
AMENDED CLAIMS received by the International Bureau on 21 October 2023 (21.10.2023)

1. A method for analyzing nucleic acid from a biological sample, comprising: obtaining a biological sample from a subject, or obtaining a biological sample that previously has been obtained from a subject; contacting the biological sample, or nucleic acid obtained from the biological sample, with-at least one polynucleotide primer pair under amplification conditions, thereby generating an amplified nucleic acid mixture comprising one or more amplification products, wherein each primer pair specifically hybridizes to and amplifies a subsequence, a portion thereof or a complement thereof of SEQ ID NO: 1, whereby the subsequence, a portion thereof or a complement thereof that is amplified is non-identical to any subsequence, portion thereof or complement thereof of one or more protozoan parasites or microbes/pathogens selected from among T. vaginalis, S. pyogenes, S. aureus, E. coli, E. faecalis, and C. albicans', and analyzing the amplification products, wherein nucleic acid from T. tenax, if present in the nucleic acid of the biological sample, is amplified under the amplification conditions.

2. The method of claim 1 , wherein analyzing the amplification products comprises determining, in the amplified nucleic acid mixture, the presence or absence of at least one amplicon that is an amplification product of a polynucleotide primer pair, wherein, if the amplicon is present, then T. tenax is determined to be present in the biological sample and if the amplicon is not present, then T. tenax is determined as not being present in the biological sample.

3. The method of claim 1 or claim 2, comprising contacting the biological sample, or nucleic acid obtained from the biological sample, with a set of at least two polynucleotide primer pairs under amplification conditions.

4. The method of any one of claims 1 to 3, wherein at least one polynucleotide primer pair comprises sequences that are identical, or substantially identical, to a subsequence of SEQ ID NO:1, or to a complement of a subsequence of SEQ ID NO:1, wherein the subsequence of SEQ ID NO:1 comprises an ITS region of T. tenax or a portion thereof, the 5.8S rRNA gene of T. tenax or a portion thereof, or any combination of regions or portions thereof comprising an ITS region and/or the 5.8S rRNA gene of T. tenax, whereby an amplified nucleic acid mixture comprising an amplification product of the subsequence of SEQ ID NO: 1 is generated under the amplification conditions.

AMENDED SHEET (ARTICLE 19)

5. The method of any one of claims 1-4, wherein the at least one primer pair comprises a forward primer and a backward primer selected from among the sequences set forth in SEQ ID NOS:2-7.

6. The method of claim 5, wherein the analyzing is by loop-mediated isothermal amplification (LAMP) and the loop-mediated isothermal amplification (LAMP) primers comprise the polynucleotide primer pairs having the sequences set forth in SEQ ID NOS:2-7.

7. The method of claim 5, wherein the analyzing is by polymerase chain reaction (PCR) and the primers comprise a forward primer having the sequence set forth in SEQ ID NO:6 and a reverse primer having the sequence set forth in SEQ ID NO:7.

8. A method of determining the presence or absence of T. tenax in a biological sample, comprising: obtaining a biological sample from a subject, or obtaining a biological sample that previously has been obtained from a subject; contacting the biological sample, or nucleic acid obtained from the biological sample, with a set of loop-mediated isothermal amplification (LAMP) primers under amplification conditions, wherein each forward and backward primer pair of the LAMP primer set specifically hybridizes to and amplifies a subsequence, a portion thereof or a complement thereof of SEQ ID NO:1, whereby the subsequence, a portion thereof or a complement thereof that is amplified is non-identical to any subsequence, portion thereof or complement thereof of one or more protozoan parasites or microbes/pathogens selected from among T. vaginalis, S. pyogenes, S. aureus, E. coli, E. faecalis, and C. albicans', and analyzing the resulting amplification products by loop-mediated isothermal amplification (LAMP) whereby, based on analyzing the amplification products, the presence or absence of T. tenax in the biological sample is determined.

9. The method of claim 8, wherein, analyzing the amplification products comprises determining the presence or absence of at least one amplicon that is an amplification product obtained by amplification of a subsequence of SEQ ID NO: 1, or a complement of a subsequence of SEQ ID NO: 1, wherein the subsequence of SEQ ID NO: 1 comprises an ITS region of T. tenax or a portion thereof, the 5.8S rRNA gene of T. tenax or a portion thereof, or any combination of regions or portions thereof comprising an ITS region and/or the 5.8S rRNA gene of T. tenax.

AMENDED SHEET (ARTICLE 19)

10. The method of claim 8 or claim 9, wherein the set of loop-mediated isothermal amplification (LAMP) primers comprises the sequences set forth in SEQ ID NOS:2-7.

11. The method of any one of claims 1-10, wherein the biological sample is from a human subject.

12. The method of any one of claims 1-10, wherein the biological sample is from a canine subject.

13. The method of any one of claims 1-12, wherein the amplification conditions comprise TE buffer.

14. The method of any one of claims 6 and 8-13, wherein contacting the biological sample, or nucleic acid obtained from the biological sample, with the set of loop-mediated isothermal amplification (LAMP) primers is performed without one or more of the following treatments prior to contact: cell boiling, extraction of the nucleic acid of the biological sample, purification of the nucleic acid of the biological sample, partial purification of the nucleic acid of the biological sample, and amplification of the nucleic acid of the biological sample.

15. The method of any one of claims 1-14, wherein the biological sample comprises an oral swab, saliva or urine.

16. The method of any one of claims 2-15, wherein one or more of the microbes comprising T. vaginalis, S. pyogenes, S. aureus, E. coli, E. faecalis, and C. albicans, if present in the biological sample, are not detected.

17. The method of any one of claims 2-16, wherein the sensitivity of determining whether T. tenax is present or absent in the biological sample is at least 100-times greater than if the biological sample, or nucleic acid obtained from the biological sample, is contacted with a primer pair for conventional PCR under amplification conditions.

18. A composition comprising a set of loop-mediated isothermal amplification (LAMP) primers comprising more than one polynucleotide primer pair, wherein each polynucleotide primer of at least one polynucleotide primer pair is selected from among a sequence that is identical, or substantially identical, to: a sequence of SEQ ID NO:1, or to a subsequence of SEQ ID NO:1, or to a complement of SEQ ID NO: 1, or to a complement of a subsequence of SEQ ID NO:1, wherein each primer pair specifically hybridizes to and amplifies a subsequence, a portion

AMENDED SHEET (ARTICLE 19) thereof or a complement thereof of SEQ ID NO:1, whereby the subsequence, a portion thereof or a complement thereof that is amplified is non-identical to any subsequence, portion thereof or complement thereof of one or more protozoan parasites or microbes/pathogens selected from among T. vaginalis, S. pyogenes, S. aureus, E. coli, E. faecalis, and C. albicans.

19. The composition of claim 18, wherein at least one polynucleotide primer of the at least one primer pair is identical, or substantially identical, to a subsequence of SEQ ID NO: 1, or to a complement of a subsequence of SEQ ID NO:1, wherein the subsequence of SEQ ID NO: 1 comprises an ITS region of T. tenax or a portion thereof, the 5.8S rRNA gene of T. tenax or a portion thereof, or any combination of regions or portions thereof comprising an ITS region and/or the 5.8S rRNA gene of T. tenax.

20. The composition of claim 18 or claim 19, wherein the set of loop-mediated isothermal amplification (LAMP) comprises the sequences set forth in SEQ ID NOS:2-7.

21. The composition of any one of claims 18-20, further comprising reagents for performing LAMP analysis.

22. The composition of claim 21, wherein the reagents for performing LAMP analysis comprises a buffer and MgSCM.

23. The composition of claim 22, wherein the buffer is TE buffer.

24. A kit, comprising the composition of any one of claims 18-23 and instructions for use in analyzing T. tenax nucleic acid in a biological sample.

AMENDED SHEET (ARTICLE 19)