METHODS FOR DETERMINING THE PRESENCE OF SARS CORONAVIRUS IN A SAMPLE

• US 20100279276A1
• Filed: 07/06/2010
• Published: 11/04/2010
• Est. Priority Date: 04/17/2003
• Status: Abandoned Application

• Current Assignee: Gen-Probe Incorporated (Hologic Incorporated)
• Original Assignee: Gen-Probe Incorporated (Hologic Incorporated)
• Inventors: KACIAN, Daniel L.
• Application Number:
  US12/831,205
• Publication Number:
  US 20100279276A1
• Time in Patent Office: Days
• US Class Current: 435/5
• CPC Class Codes: C12Q 1/701 Specific hybridization probes

Abstract

Methods for determining the presence of SARS-CoV in a test sample that include targeting the SARS-CoV 5′ leader sequence or the SARS-CoV 3′ terminal sequence.

Claims

1. A method for determining the presence of SARS-CoV in a test sample, said method comprising the steps of:

a) contacting a test sample a detection probe up to 100 bases in length and comprising a target binding portion which forms a hybrid stable for detection with a target sequence contained within a SARS-CoV 5′

leader sequence or its complement, wherein said probe does not form a hybrid stable for detection with nucleic acid derived from HCoV-OC43 or HCoV-229E under said conditions; and

b) determining whether said hybrid is present in said test sample as an indication of the presence of SARS-CoV in said test sample.

2. The method of claim 1, wherein said target sequence comprises a core sequence of a transcription regulating sequence or its complement.

3. The method of claim 2, wherein said core sequence consists of at least 5 contiguous nucleotides of the sequence of SEQ ID NO:

38 or its complement.

4. The method of claim 3, wherein the core sequence consists of the sequence of SEQ ID NO:

38 or its complement.

5. The method of claim 1 further comprising contacting said test sample with a pair of amplification oligonucleotides under amplification conditions, wherein each member of said pair of amplification oligonucleotides comprises a target binding portion which binds to or extends through at least a portion of said 5′

leader sequence or its complement under said amplification conditions.

6. The method of claim 5, wherein said target binding portion of each member of said pair of amplification oligonucleotides binds to a target region fully contained within said 5′

leader sequence or its complement under said amplification conditions, and wherein said amplification oligonucleotides do not contain any other base sequences which stably hybridize to nucleic acid derived from SARS-CoV under said amplification conditions.

7. The method of claim 1 further comprising contacting said test sample with a pair of amplification oligonucleotides under amplification conditions, wherein a target binding portion of a first member of said pair of amplification oligonucleotides binds to a target region fully contained within said 5′

leader sequence or its complement under said amplification conditions, and wherein a target binding portion of a second member of said pair of amplification oligonucleotides binds to a target region fully contained within a SARS CoV 3′

co-terminal sequence or its complement under said amplification conditions, wherein said amplification oligonucleotides do not contain any other base sequences which stably hybridize to nucleic acid derived from SARS-CoV under said amplification conditions.

8. A method for amplifying a target region of nucleic acid derived from SARS-CoV, said method comprising the steps of:

a) contacting a test sample with one or more amplification oligonucleotides under amplification conditions, wherein a first of said amplification oligonucleotides comprises a target binding portion which binds to a target region fully contained within a SARS-CoV 5′

leader sequence or its complement under said conditions, wherein said first amplification oligonucleotide does not contain any other base sequences which stably hybridize to nucleic acid derived from SARS-CoV under said amplification conditions; and

b) exposing said test sample to said conditions such that said target region, if present in said test sample, is amplified.

9. The method of claim 8, wherein said target region comprises a core sequence of a transcription regulating sequence or its complement.

10. The method of claim 9, wherein said core sequence consists of at least 5 contiguous nucleotides of the sequence of SEQ ID NO:

38 or its complement.

11. The method of claim 10, wherein the core sequence consists of the sequence of SEQ ID NO:

38 or its complement.

12. The method of claim 8, wherein said test sample is contacted with a pair of said amplification oligonucleotides under said conditions, wherein a second of said amplification oligonucleotides comprises a target binding portion which binds to a target region fully contained within said 5′

leader sequence or its complement under said conditions, and wherein said second amplification oligonucleotide does not contain any other base sequences which stably hybridize to nucleic acid derived from SARS-CoV under said conditions.

13. A method for determining the presence of SARS-CoV in a test sample, said method comprising the steps of:

a) contacting a test sample with a detection probe up to 100 bases in length and comprising a target binding portion which forms a hybrid stable for detection with a target sequence contained within a SARS-CoV 3′

co-terminal sequence or its complement, wherein said probe forms a hybrid stable for detection with said target sequence under stringent hybridization conditions, and wherein said probe does not form a hybrid stable for detection with nucleic acid derived from HCoV-OC43 or HCoV-229E under said conditions; and

b) determining whether said hybrid is present in said test sample as an indication of the presence of SARS-CoV in said test sample.

14. The method of claim 13 further comprising contacting said test sample with a pair of amplification oligonucleotides under amplification conditions, wherein each member of said pair of amplification oligonucleotides comprises a target binding portion which binds or extends through at least a portion of said 3′

co-terminal sequence or its complement under said amplification conditions.

15. The method of claim 13, wherein said target binding portion of each member of said pair of amplification oligonucleotides binds to a target region fully contained within said 3′

co-terminal sequence or its complement under said amplification conditions, and wherein said amplification oligonucleotides do not contain any other base sequences which stably hybridize to nucleic acid derived from SARS-CoV under said amplification conditions.

16. A method for amplifying a target region of nucleic acid derived from SARS-CoV, said method comprising the steps of:

a) contacting a test sample with one or more amplification oligonucleotides under amplification conditions, wherein a first of said amplification oligonucleotides comprises a target binding portion which binds to a target region contained within a SARS-CoV 3′

co-terminal sequence or its complement under said conditions; and

b) exposing said test sample to said conditions such that said target region, if present in said test sample, is amplified.

17. The method of claim 16, wherein said test sample is contacted with a pair of said amplification oligonucleotides under said conditions, wherein a second of said amplification oligonucleotides comprises a target binding portion which binds to a target region fully contained within said 3′

co-terminal sequence or its complement under said conditions, and wherein said second amplification oligonucleotide does not contain any other base sequences which stably hybridize to nucleic acid derived from SARS-CoV under said conditions.