US2009176236A1PendingUtilityA1

Compositions and Methods for Detecting Certain Flaviviruses, Including Members of the Japanese Encephalitis Virus Serogroup

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Assignee: ROCHE MOLECULAR SYSTEMS INCPriority: Mar 31, 2003Filed: Dec 19, 2008Published: Jul 9, 2009
Est. expiryMar 31, 2023(expired)· nominal 20-yr term from priority
Inventors:Karen K. Y. Young
C12Q 1/6888C12Q 1/701Y02A50/30C12Q 2600/158
72
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Claims

Abstract

The present invention provides rapid and accurate methods, primers, probes and kits for identifying the presence of a certain flaviviruses in a sample. Flaviviruses that can be detected include members of the Japanese encephalitis virus serogroup, Dengue virus, St. Louis encephalitis virus, Montana myotis leukoencephalitis virus, Modoc virus, and Yellow Fever virus. The primers and probes of the invention can hybridize to regions in the 3′ untranslated region of the viral genomes to be detected.

Claims

exact text as granted — not AI-modified
1 . A kit for detecting and amplifying a flavivirus nucleic acid sequence, the kit comprising a first oligonucleotide that hybridizes to a sequence or complement thereof selected from the group consisting of: SEQ ID NO:29, SEQ ID NO:30, SEQ ID NO:31, SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:39, and SEQ ID NO:40; and
 a detectably-labeled oligonucleotide probe.   
     
     
         2 . The kit of  claim 1 , wherein the kit further comprises a second oligonucleotide that hybridizes to a sequence or complement thereof selected from the group consisting of: SEQ ID NO:29, SEQ ID NO:30, SEQ ID NO:31, SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:39, and SEQ ID NO:40. 
     
     
         3 . The kit of  claim 1 , wherein the kit further comprises a second oligonucleotide that hybridizes to SEQ ID NO:9. 
     
     
         4 . The kit of  claim 1 , wherein the kit further comprises a second oligonucleotide that comprises SEQ ID NO:11. 
     
     
         5 . The kit of  claim 1 , wherein the kit further comprises a second oligonucleotide that comprises SEQ ID NO:15. 
     
     
         6 . The kit of  claim 2 , wherein the first oligonucleotide is selected from the group consisting of SEQ ID NO:64, and SEQ ID NO:65, and wherein the second oligonucleotide is selected from the group consisting of SEQ ID NO:66, and SEQ ID NO:67. 
     
     
         7 . The kit of  claim 2 , wherein the first oligonucleotide hybridizes to SEQ ID NO:68, and the second oligonucleotide hybridizes to a complement of SEQ ID NO:69. 
     
     
         8 . The kit of  claim 1 , wherein the first oligonucleotide comprises at least 20 contiguous nucleic acid residues from a sequence or complement thereof selected from the group consisting of SEQ ID NO:29, SEQ ID NO:30, SEQ ID NO:31, SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:39, and SEQ ID NO:40. 
     
     
         9 . The kit of  claim 8 , wherein the kit further comprises a second oligonucleotide that hybridizes to SEQ ID NO:9. 
     
     
         10 . The kit of  claim 8 , wherein the kit further comprises a second oligonucleotide that comprises SEQ ID NO:11. 
     
     
         11 . The kit of  claim 8 , wherein the kit further comprises a second oligonucleotide that comprises SEQ ID NO:15. 
     
     
         12 . The kit of  claim 1 , wherein the detectably-labeled oligonucleotide probe hybridizes to SEQ ID NO:16, or a complement thereof. 
     
     
         13 . The kit of  claim 1 , wherein the detectably labeled oligonucleotide probe comprises SEQ ID NO:20. 
     
     
         14 . The kit of  claim 1 , wherein the detectably labeled oligonucleotide probe comprises SEQ ID NO:28. 
     
     
         15 . The kit of  claim 1 , wherein the detectably-labeled oligonucleotide probe comprises a fluorescent moiety. 
     
     
         16 . The kit of  claim 5 , wherein at least one nucleotide in SEQ ID NO:15 is non-standard or derivatized. 
     
     
         17 . A method for determining the presence or absence of a flavivirus nucleic acid in a sample, the method comprising:
 contacting the sample with a nucleic acid polymerase and the oligonucleotides set forth in  claim 1 ;   submitting the sample with the oligonucleotides and the polymerase to conditions allowing for amplification of a fragment of the flavivirus nucleic acid by the polymerase, thereby generating an amplified nucleic acid if the flavivirus nucleic acid is present in the sample, and   detecting the amplified nucleic acid, thereby determining the presence or absence of the flavivirus nucleic acid in the sample   
     
     
         18 . A kit for the detection of a nucleic acid of a flavivirus, comprising:
 a) a first oligonucleotide that hybridizes to the complement of SEQ ID NO:1;   b) a second oligonucleotide; and   c) a detectably-labeled oligonucleotide that hybridizes to the complement of SEQ ID NO:16.   
     
     
         19 . The kit of  claim 18 , wherein the second oligonucleotide hybridizes to SEQ ID NO:9. 
     
     
         20 . The kit of  claim 18 , wherein the second oligonucleotide comprises SEQ ID NO:11. 
     
     
         21 . The kit of  claim 18 , wherein the second oligonucleotide comprises SEQ ID NO:15. 
     
     
         22 . The kit of  claim 18 , wherein the first oligonucleotide comprises SEQ ID NO.:4. 
     
     
         23 . The kit of  claim 18 , wherein the first oligonucleotide comprises SEQ ID NO:8. 
     
     
         24 . The kit of  claim 18 , wherein the detectably-labeled oligonucleotide comprises SEQ ID NO:20. 
     
     
         25 . The kit of  claim 18 , wherein the detectably-labeled oligonucleotide comprises SEQ ID NO:28. 
     
     
         26 . The kit of  claim 23 , wherein at least one nucleotide in SEQ ID NO:8 is non-standard or derivatized. 
     
     
         27 . A method for determining the presence or absence of a flavivirus nucleic acid in a sample, the method comprising:
 contacting the sample with a nucleic acid polymerase and the oligonucleotides set forth in  claim 18 ;   submitting the sample with the oligonucleotides and the polymerase to conditions allowing for amplification of a fragment of the flavivirus nucleic acid by the polymerase, thereby generating an amplified nucleic acid if the flavivirus nucleic acid is present in the sample, and   detecting the amplified nucleic acid, thereby determining the presence or absence of the flavivirus nucleic acid in the sample.

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