Assays for the detection of SARS-CoV-2
The present invention is directed to methods for assaying for the presence of SARS-CoV-2 in a sample, including a clinical sample, and to oligonucleotides, reagents, and kits useful in such assays. In particular, the present invention is directed to such assays that are rapid, accurate and specific for the detection of SARS-CoV-2.
1. A detectably labeled oligonucleotide that is capable of specifically hybridizing to a SARS-CoV-2 polynucleotide, wherein the nucleotide sequence of said detectably labeled oligonucleotide that is capable of specifically hybridizing to said SARS-CoV-2 polynucleotide is able to specifically hybridize to an oligonucleotide having a nucleotide sequence that consists essentially of the nucleotide sequence of SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:7 or SEQ ID NO:8.
2. The detectably labeled oligonucleotide of claim 1 , wherein the nucleotide sequence of said oligonucleotide that is capable of specifically hybridizing to said SARS-CoV-2 polynucleotide is able to specifically hybridize to an oligonucleotide having a nucleotide sequence that consists essentially of the nucleotide sequence of SEQ ID NO:3 or SEQ ID NO:4.
3. The detectably labeled oligonucleotide of claim 1 , wherein the nucleotide sequence of said oligonucleotide that is capable of specifically hybridizing to said SARS-CoV-2 polynucleotide is able to specifically hybridize to an oligonucleotide having a nucleotide sequence that consists essentially of the nucleotide sequence of SEQ ID NO:7 or SEQ ID NO:8.
4. A kit for detecting the presence of SARS-CoV-2 in a clinical sample, wherein said kit comprises
(A) an oligonucleotide primer capable of amplifying a portion of a SARS-CoV-2 polynucleotide; and
(B) a detectably labeled oligonucleotide that is capable of specifically hybridizing to said amplified portion of said SARS-CoV-2 polynucleotide, wherein the nucleotide sequence of said detectably labeled oligonucleotide that is capable of specifically hybridizing to said SARS-CoV-2 polynucleotide is able to specifically hybridize to an oligonucleotide having a nucleotide sequence that consists essentially of the nucleotide sequence of SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:7 or SEQ ID NO:8.
5. The kit of claim 4 , wherein the nucleotide sequence of said detectably labeled oligonucleotide that is capable of specifically hybridizing to said SARS-CoV-2 polynucleotide is able to specifically hybridize to an oligonucleotide having a nucleotide sequence that consists essentially of the nucleotide sequence of SEQ ID NO:3 or SEQ ID NO:4, and wherein said kit permits a determination of the presence or absence of the SARS-CoV-2 ORF1ab in a clinical sample.
6. The kit of claim 4 , wherein the nucleotide sequence of said detectably labeled oligonucleotide that is capable of specifically hybridizing to said SARS-CoV-2 polynucleotide is able to specifically hybridize to an oligonucleotide having a nucleotide sequence that consists essentially of the nucleotide sequence of SEQ ID NO:7 or SEQ ID NO:8, and wherein said kit permits a determination of the presence or absence of the SARS-CoV-2 S gene in a clinical sample.
7. The kit of claim 4 , wherein said kit permits the detection of the D614G polymorphism of the S gene of SARS-CoV-2.
8. The kit of claim 4 , wherein said kit is a multi-chambered, fluidic device.
9. The kit of claim 4 , wherein said detectably labeled oligonucleotide is a TaqMan probe, a molecular beacon probe, a scorpion primer-probe, or a HyBeacon probe.
10. The kit of claim 4 , wherein said detectably labeled oligonucleotide is fluorescently labeled.
11. The kit of claim 4 , wherein said kit comprises two detectably labeled oligonucleotides, wherein the detectable labels of said oligonucleotides are distinguishable, and wherein the nucleotide sequence of one of said two detectably labeled oligonucleotides that is capable of specifically hybridizing to said SARS-CoV-2 polynucleotide is able to specifically hybridize to an oligonucleotide having a nucleotide sequence that consists essentially of the nucleotide sequence of SEQ ID NO:3 or SEQ ID NO:4, and the nucleotide sequence of the second of said two detectably labeled oligonucleotides that is capable of specifically hybridizing to said SARS-CoV-2 polynucleotide is able to specifically hybridize to an oligonucleotide having a nucleotide sequence that consists essentially of the nucleotide sequence of SEQ ID NO:7 or SEQ ID NO:8.
12. The kit of claim 11 , wherein at least one of said detectably labeled oligonucleotides is a TaqMan probe, a molecular beacon probe, a scorpion primer-probe or a HyBeacon™ probe.
13. The kit of claim 11 , wherein the distinguishable detectable labels of said oligonucleotides are fluorescent labels.
14. The kit of claim 11 , wherein said kit permits the detection of the D614G polymorphism of the S gene of SARS-CoV-2.
15. The kit of claim 11 , wherein said kit is a multi-chambered, fluidic device.
16. The kit of claim 11 , wherein said detectably labeled oligonucleotide is fluorescently labeled.
17. A method for detecting the presence of SARS-CoV-2 in a clinical sample, wherein said method comprises incubating said clinical sample in vitro in the presence of a detectably labeled oligonucleotide that is capable of specifically hybridizing to a SARS-CoV-2 ORF1ab or SARS-CoV-2 S gene polynucleotide, wherein the nucleotide sequence of said detectably labeled oligonucleotide that is capable of specifically hybridizing to said SARS-CoV-2 polynucleotide is able to specifically hybridize to an oligonucleotide having a nucleotide sequence that consists essentially of the nucleotide sequence of SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:7 or SEQ ID NO:8; wherein said method detects the presence of SARS-CoV-2 in said clinical sample by detecting the presence of SARS-CoV-2 ORF1ab and/or SARS-CoV-2 S gene.
18. The method of claim 17 , wherein the nucleotide sequence of said detectably labeled oligonucleotide that is capable of specifically hybridizing to said SARS-CoV-2 polynucleotide is able to specifically hybridize to an oligonucleotide having a nucleotide sequence that consists essentially of the nucleotide sequence of SEQ ID NO:3 or SEQ ID NO:4, and wherein said method detects the presence of SARS-CoV-2 in said clinical sample by detecting the presence of SARS-CoV-2 ORF1ab.
19. The method of claim 17 , wherein the nucleotide sequence of said detectably labeled oligonucleotide that is capable of specifically hybridizing to said SARS-CoV-2 polynucleotide is able to specifically hybridize to an oligonucleotide having a nucleotide sequence that consists essentially of the nucleotide sequence of SEQ ID NO:7 or SEQ ID NO:8, and wherein said method detects the presence of SARS-CoV-2 in said clinical sample by detecting the presence of SARS-CoV-2 S gene.
20. The method of claim 19 , wherein said method detects the presence or absence of the D614G polymorphism of the S gene of SARS-CoV-2.
21. The method of claim 17 , wherein said method comprises a PCR amplification of said SARS-CoV-2 polynucleotide.
22. The method of claim 17 , wherein said detectably labeled oligonucleotide is a TaqMan probe, a molecular beacon probe, a scorpion primer-probe, or a HyBeacon probe.
23. The method of claim 17 , wherein said method comprises a LAMP amplification of said SARS-CoV-2 polynucleotide.
24. The method of claim 17 , wherein said detectably labeled oligonucleotide is fluorescently labeled.
25. The method of claim 17 , wherein said method comprises incubating said clinical sample in the presence of two detectably labeled oligonucleotides, wherein the detectable labels of said oligonucleotides are distinguishable, and wherein the nucleotide sequence of one of said two detectably labeled oligonucleotides that is capable of specifically hybridizing to said SARS-CoV-2 polynucleotide is able to specifically hybridize to an oligonucleotide having a nucleotide sequence that consists essentially of the nucleotide sequence of SEQ ID NO:3 or SEQ ID NO:4, and the nucleotide sequence of the second of said two detectably labeled oligonucleotides that is capable of specifically hybridizing to said SARS-CoV-2 polynucleotide is able to specifically hybridize to an oligonucleotide having a nucleotide sequence that consists essentially of the nucleotide sequence of SEQ ID NO:7 or SEQ ID NO:8; wherein said method detects the presence of SARS-CoV-2 in said clinical sample by detecting the presence of both SARS-CoV-2 ORF1ab and SARS-CoV-2 S gene.
26. The method of claim 25 , wherein said method detects the presence or absence of the D614G polymorphism of the S gene of SARS-CoV-2.
27. The method of claim 25 , wherein said method comprises a PCR amplification of said SARS-CoV-2 polynucleotide.
28. The method of claim 25 , wherein said detectably labeled oligonucleotide is a TaqMan probe, a molecular beacon probe, a scorpion primer-probe, or a HyBeacon probe.
29. The method of claim 25 , wherein said method comprises a LAMP amplification of said SARS-CoV-2 polynucleotide.
30. The method of claim 25 , wherein said detectably labeled oligonucleotide is fluorescently labeled.