Methods of Detecting Influenza

Abstract

Compositions and methods for detecting influenza are provided.

1 - 151 . (canceled) 
     
     
         152 . A kit for detecting the presence of influenza in a sample from a human subject comprising a primer pair and probe for detecting the presence of an influenza B NS gene in the sample, wherein the primer pair comprises a first primer comprising a sequence that is identical to at least 18 contiguous nucleotides of SEQ ID NO: 14 and a second primer comprising a sequence that is complementary to at least 18 contiguous nucleotides of SEQ ID NO: 14; and wherein the probe comprises a sequence that is identical or complementary to at least 18 contiguous nucleotides of SEQ ID NO: 14, and wherein the probe comprises a detectable label. 
     
     
         153 . The kit of  claim 152 , wherein the primer pair comprises a first primer comprising a sequence that is identical to at least 18 contiguous nucleotides of SEQ ID NO: 35 and a second primer comprising a sequence that is identical to at least 18 contiguous nucleotides of SEQ ID NO: 36. 
     
     
         154 . The kit of  claim 153 , wherein the first primer comprises the sequence of SEQ ID NO: 35 and the second primer comprises the sequence of SEQ ID NO: 36. 
     
     
         155 . The kit of  claim 153 , wherein the influenza B NS probe comprises a sequence that is identical or complementary at least 18 contiguous nucleotides of SEQ ID NO: 37. 
     
     
         156 . The kit of  claim 155 , wherein the influenza B NS probe comprises a fluorescent dye and a quencher molecule. 
     
     
         157 . The kit of  claim 153 , further comprising a primer pair and probe for detecting the presence of at least one influenza A gene in the sample selected from an influenza A PA gene, an influenza A PB2 gene, and an influenza A MP gene and/or a primer pair and probe for detecting the presence of an avian influenza gene in the sample selected from an avian influenza MP gene and an avian influenza HA gene. 
     
     
         158 . The kit of  claim 157 , wherein the sequence of the influenza A PA gene is at least 95% identical to SEQ ID NO: 2, the sequence of the influenza A PB2 gene is at least 95% identical to SEQ ID NO: 1, the sequence of the influenza AMP gene is at least 95% identical to SEQ ID NO: 3, the sequence of the avian influenza MP gene is at least 95% identical to SEQ ID NO: 4, and the sequence of the avian influenza HA gene is at least 95% identical to SEQ ID NO: 5. 
     
     
         159 . The kit of  claim 157 , wherein the avian influenza MP probe comprises a sequence that is identical or complementary to at least 18 contiguous nucleotides of SEQ ID NO: 11. 
     
     
         160 . The kit of  claim 153 , further comprising a primer pair and a probe for detecting the presence of respiratory syncytial virus (RSV) A and/or RSV B in the sample. 
     
     
         161 . The kit of  claim 153 , further comprising at least one primer pair and probe for detecting an exogenous control and/or an endogenous control, wherein the exogenous control is a sample processing control, and wherein the endogenous control is a sample adequacy control. 
     
     
         162 . A composition for detecting the presence of influenza in a sample from a human subject comprising a primer pair and probe for detecting the presence of an influenza B NS gene in the sample, wherein the primer pair comprises a first primer comprising a sequence that is identical to at least 18 contiguous nucleotides of SEQ ID NO: 14 and a second primer comprising a sequence that is complementary to at least 18 contiguous nucleotides of SEQ ID NO: 14; and wherein the probe comprises a sequence that is identical or complementary at least 18 contiguous nucleotides of SEQ ID NO: 14, and wherein the probe comprises a detectable label. 
     
     
         163 . The composition of  claim 162 , wherein the primer pair comprises a first primer comprising a sequence that is identical to at least 18 contiguous nucleotides of SEQ ID NO: 35 and a second primer comprising a sequence that is identical to at least 18 contiguous nucleotides of SEQ ID NO: 36. 
     
     
         164 . The composition of  claim 163 , wherein the first primer comprises the sequence of SEQ ID NO: 35 and the second primer comprises the sequence of SEQ ID NO: 36. 
     
     
         165 . The composition of  claim 163 , wherein the influenza B NS probe comprises a sequence that is identical or complementary at least 18 contiguous nucleotides of SEQ ID NO: 37. 
     
     
         166 . The composition of  claim 165 , wherein the influenza B NS probe comprises a fluorescent dye and a quencher molecule. 
     
     
         167 . A method of detecting the presence of influenza in a sample from a subject comprising: (A) obtaining a sample from the subject; and (B) amplifying nucleic acids from the sample with a primer pair for detecting the presence of an influenza B NS gene in the sample, wherein the primer pair comprises a first primer comprising a sequence that is identical to at least 18 contiguous nucleotides of SEQ ID NO: 14 and a second primer comprising a sequence that is complementary to at least 18 contiguous nucleotides of SEQ ID NO: 14. 
     
     
         168 . The method of  claim 167 , wherein amplification of the influenza B NS gene with the primer pair produces an amplicon comprising a sequence that is at least 95% identical to SEQ ID NO: 14. 
     
     
         169 . The method of  claim 167 , wherein the primer pair comprises a first primer comprising a sequence that is identical to at least 18 contiguous nucleotides of SEQ ID NO: 35 and a second primer comprising a sequence that is identical to at least 18 contiguous nucleotides of SEQ ID NO: 36. 
     
     
         170 . The method of  claim 169 , wherein amplification of the influenza B NS gene with the primer pair produces an amplicon, and wherein the method comprises contacting the amplicon with an influenza B NS probe. 
     
     
         171 . The method of  claim 170 , wherein the influenza B NS probe comprises a sequence that is identical or complementary to at least 18 contiguous nucleotides of SEQ ID NO: 37. 
     
     
         172 . The method of  claim 171 , wherein influenza B NS probe comprises a fluorescent dye and a quencher molecule. 
     
     
         173 . The method of  claim 169 , wherein the method further comprises detecting the presence of at least one influenza A gene selected from an influenza A PA gene, an influenza A PB2 gene, an influenza A MP gene and/or detecting the presence of an avian influenza gene selected from an avian influenza MP gene and an avian influenza HA gene. 
     
     
         174 . The method of  claim 173 , wherein the method comprises amplifying nucleic acids from the sample with a primer pair for detecting the presence of influenza A MP gene in the sample and/or a primer pair for detecting the presence of the avian influenza MP gene in the sample. 
     
     
         175 . The method of  claim 174 , wherein
 amplification of the influenza A MP gene produces an influenza A MP amplicon, and wherein the method comprises contacting the influenza A MP amplicon with an influenza A MP probe, and/or   amplification of the avian influenza MP gene produces an avian influenza MP amplicon, and wherein the method comprises contacting the avian influenza MP amplicon with an avian influenza MP probe.   
     
     
         176 . The method of  claim 175 , wherein the avian influenza MP probe comprises a sequence that is identical or complementary to at least 18 contiguous nucleotides of SEQ ID NO: 11. 
     
     
         177 . The method of  claim 169 , wherein the sample from the subject is selected from a nasopharyngeal swab sample, a nasal aspirate sample, a nasal wash sample, a nasal swab sample, an oropharyngeal swab sample, a throat swab sample, a bronchoalveolar lavage sample, a bronchial aspirate sample, a bronchial wash sample, an endotracheal aspirate sample, an endotracheal wash sample, a tracheal aspirate sample, a nasal secretion sample, a mucus sample, and a sputum sample. 
     
     
         178 . A method of treating a subject with influenza comprising:
 (A) detecting the presence of influenza in a sample from the subject according to  claim 167 , and   (B) treating the subject by administering an antiviral therapy to the subject.   
     
     
         179 . A cartridge, comprising:
 a plurality of processing chambers in fluidic communication, and   a DNA-binding substrate for binding nucleic acid in fluidic communication with the processing chambers,   wherein the processing chambers comprise reagents for lysing cells from a sample, amplification and detection of nucleic acid from the sample, and a composition according to  claim 162 .