Patent ID: 7435539

Claim:
A method for typing an enterovirus in a clinical sample comprising the steps of: (i) obtaining a clinical sample from a subject, (ii) purifying RNA contained in the sample, (iii) reverse transcribing the RNA with primers effective to reverse transcribe enteroviral RNA to provide a cDNA; (iv) contacting at least a portion of the cDNA with (a) a composition that promotes amplification of a nucleic acid and (b) an oligonucleotide mixture wherein the mixture comprises at least one oligonucleotide that hybridizes to a highly conserved sequence of the sense strand of an enterovirus nucleic acid and at least one oligonucleotide that hybridizes to a highly conserved sequence of the antisense strand of an enterovirus nucleic acid, wherein the highly conserved sequences occur within the VP1 gene or within about 100 nucleotides from a terminus of the VP1 gene, and at least one oligonucleotide comprises, at the 3′ end thereof, a sequence that hybridizes to a sequence encoding a motif chosen from the group consisting of the sequences given by SEQ ID NO:83, SEQ ID NO:84, and SEQ ID NO:85, and at least one oligonucleotide comprises, at the 3′ end thereof, a sequence that hybridizes to a sequence encoding a motif given by SEQ ID NO:86, thereby providing an amplification mixture, such that, upon hybridizing, the oligonucleotides direct amplification of at least a portion of the nucleotide sequence of the VP1 gene of a non-polio enterovirus; (v) carrying out an amplification procedure on the amplification mixture, such that, if an enterovirus is present in the sample, an enterovirus sample amplicon is produced whose sequence comprises a nucleotide sequence of at least a portion of the VP1 region of the enterovirus genome; (vi) determining that the sample amplicon is present; (vii) determining at least a partial nucleotide sequence of the sample amplicon; (viii) providing a database consisting of prototypical nucleotide sequences, wherein each prototypical sequence is the sequence of a standard amplicon obtained from a member of a set of prototypical enterovirus serotypes by carrying out the procedure of steps (ii) through (v) on each prototypical enterovirus serotype, wherein each prototypical sequence comprises at least a portion of the sequence of the VP1 gene, and wherein the sequence of each prototypical VP1 gene is different from the sequence of every other prototypical VP1 gene in the database; (ix) comparing the sequence of the sample amplicon with each prototypical sequence in the database; and (x) identifying the prototypical sequence that has the highest extent of identity to the sequence of the sample amplicon to provide an identified serotype; wherein the type of the sample is the serotype of the identified serotype.