Compositions and methods for detecting zika virus nucleic acid

Abstract

Disclosed are nucleic acid oligomers, including amplification oligomers, capture probes, and detection probes, for detection of Zika virus nucleic acid. Also disclosed are methods of specific nucleic acid amplification and detection using the disclosed oligomers, as well as corresponding reaction mixtures and kits.

What is claimed is: 
     
         1 . A combination of at least two amplification oligomers for amplifying a Zika virus nucleic acid in a sample, the oligomer combination comprising:
 at least two amplification oligomers configured to amplify a target sequence corresponding to a Zika virus target nucleic acid, wherein the first amplification oligomer and the second amplification oligomer are configured to hybridize to opposite ends of the target sequence to generate amplification products;   wherein
 (i) the first amplification oligomer comprises a target-hybridizing sequence selected from the group consisting of SEQ ID NO:29, SEQ ID NO:30, and SEQ ID NO:31, and the second amplification oligomer comprises a target-hybridizing sequence consisting of SEQ ID NO:116; 
 (ii) the first amplification oligomer comprises a target-hybridizing sequence selected from the group consisting of SEQ ID NO:31, SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, and SEQ ID NO:35, and the second amplification oligomer comprises a target-hybridizing sequence consisting of SEQ ID NO:138; or 
 (iii) the first amplification oligomer comprises a target-hybridizing sequence consisting of SEQ ID NO:31, and the second amplification oligomer comprises a target-hybridizing sequence selected from the group consisting of SEQ ID NO:116 and SEQ ID NO:138; 
 wherein the second amplification oligomer target-hybridizing sequence is joined at its end to a T7 promoter sequence. 
   
     
     
         2 . An amplification reaction mixture comprising the at least two amplification oligomers of  claim 1 , wherein (i) the mixture is a buffered aqueous solution; or (ii) the mixture is a dried composition. 
     
     
         3 . A kit comprising the at least two amplification oligomers of  claim 1 . 
     
     
         4 . The combination of  claim 1 , wherein the T7 promoter sequence consists of SEQ ID NO:179. 
     
     
         5 . The combination of  claim 1 , wherein the first amplification oligomer comprises the target-hybridizing sequence selected from the group consisting of SEQ ID NO:29, SEQ ID NO:30, and SEQ ID NO:31, and the second amplification oligomer comprises the target-hybridizing sequence consisting of SEQ ID NO:116. 
     
     
         6 . The combination of  claim 5 , wherein the nucleotide sequence of the second amplification oligomer is SEQ ID NO:94. 
     
     
         7 . The combination of  claim 5 , wherein the first amplification oligomer target-hybridizing sequence is selected from the group consisting of SEQ ID NO:30 and SEQ ID NO:31. 
     
     
         8 . The combination of  claim 1 , wherein the first amplification oligomer comprises the target-hybridizing sequence selected from the group consisting of SEQ ID NO:31, SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, and SEQ ID NO:35, and the second amplification oligomer comprises the target-hybridizing sequence consisting of SEQ ID NO:138. 
     
     
         9 . The combination of  claim 8 , wherein the nucleotide sequence of the second amplification oligomer is SEQ ID NO:97. 
     
     
         10 . The combination of  claim 8 , wherein the first amplification oligomer target-hybridizing sequence is SEQ ID NO:31. 
     
     
         11 . The combination of  claim 1 , wherein the nucleotide sequences of the first amplification and second amplification oligomer are selected from the group consisting of
 (i) SEQ ID NO:30 and SEQ ID NO:94;   (ii) SEQ ID NO:31 and SEQ ID NO:94; and   (iii) SEQ ID NO:31 and SEQ ID NO:97.   
     
     
         12 . A method for determining the presence or absence of a Zika virus nucleic acid in a sample, the method comprising the steps of:
 (A) contacting a sample with a combination of at least two amplification oligomers configured to amplify a target sequence corresponding to a Zika virus target nucleic acid, wherein a first amplification oligomer and a second amplification oligomer are configured to hybridize to opposite ends of the target sequence to generate amplification products;   wherein
 (i) the first amplification oligomer comprises a target-hybridizing sequence selected from the group consisting of SEQ ID NO:29, SEQ ID NO:30, and SEQ ID NO:31, and the second amplification oligomer comprises a target-hybridizing sequence consisting of SEQ ID NO:116; 
 (ii) the first amplification oligomer comprises a target-hybridizing sequence selected from the group consisting of SEQ ID NO:31, SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, and SEQ ID NO:35, and the second amplification oligomer comprises a target-hybridizing sequence consisting of SEQ ID NO:138; or 
 (iii) the first amplification oligomer comprises a target-hybridizing sequence consisting of SEQ ID NO:31, and the second amplification oligomer comprises a target-hybridizing sequence selected from the group consisting of SEQ ID NO:116 and SEQ ID NO:138; 
 wherein the second amplification oligomer target-hybridizing sequence is joined at its end to a T7 promoter sequence; 
   (B) performing an in vitro nucleic acid amplification reaction, wherein any Zika virus target nucleic acid present in the sample is used as a template for generating an amplification product; and   (C) detecting the presence or absence of the amplification product, thereby determining the presence or absence of the Zika virus nucleic acid in the sample.   
     
     
         13 . The method of  claim 12 , wherein the T7 promoter sequence consists of SEQ ID NO:179. 
     
     
         14 . The method of  claim 12 , wherein the first amplification oligomer comprises the target-hybridizing sequence selected from the group consisting of SEQ ID NO:29, SEQ ID NO:30, and SEQ ID NO:31, and the second amplification oligomer comprises the target-hybridizing sequence consisting of SEQ ID NO:116. 
     
     
         15 . The method of  claim 14 , wherein the nucleotide sequence of the second amplification oligomer is SEQ ID NO:94. 
     
     
         16 . The method of  claim 14 , wherein the first amplification oligomer target-hybridizing sequence is selected from the group consisting of SEQ ID NO:30 and SEQ ID NO:31. 
     
     
         17 . The method of  claim 12 , wherein the first amplification oligomer comprises the target-hybridizing sequence selected from the group consisting of SEQ ID NO:31, SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, and SEQ ID NO:35, and the second amplification oligomer comprises the target-hybridizing sequence consisting of SEQ ID NO:138. 
     
     
         18 . The method of  claim 17 , wherein the nucleotide sequence of the second amplification oligomer is SEQ ID NO:97. 
     
     
         19 . The method of  claim 17 , wherein the first amplification oligomer target-hybridizing sequence is SEQ ID NO:31. 
     
     
         20 . The method of  claim 12 , wherein the nucleotide sequences of the first amplification and second amplification oligomer are selected from the group consisting of
 (i) SEQ ID NO:30 and SEQ ID NO:94;   (ii) SEQ ID NO:31 and SEQ ID NO:94; and   (iii) SEQ ID NO:31 and SEQ ID NO:97.