Group-specific identification of polioviruses by PCR using primers containing mixed-base or deoxyinosine residue at positions of codon degeneracy

TLDR

The authors designed three serotype‑specific antisense primer sets targeting VP1 codons conserved within each serotype but differing across serotypes, along with sense primers for conserved capsid sequences, incorporating mixed‑base and deoxyinosine residues to accommodate codon degeneracy. The primer sets correctly identified all 48 vaccine‑related and 110 wild poliovirus isolates, failed to amplify 49 non‑polio enterovirus references, and proved useful for rapid screening and determining serotype composition in mixed cultures.

Abstract

We have developed a method for determining the serotypes of poliovirus isolates by PCR. Three sets of serotype-specific antisense PCR-initiating primers (primers seroPV1A, seroPV2A, and seroPV3A) were designed to pair with codons of VP1 amino acid sequences that are conserved within but that differ across serotypes. The sense polarity primers (primers seroPV1S, seroPV2S, and seroPV3S) matched codons of more conserved capsid sequences. The primers contain mixed-base and deoxyinosine residues to compensate for the high rate of degeneracy of the targeted codons. The serotypes of all polioviruses tested (48 vaccine-related isolates and 110 diverse wild isolates) were correctly identified by PCR with the serotype-specific primers. None of the genomic sequences of 49 nonpolio enterovirus reference strains were amplified under equivalent reaction conditions with any of the three primer sets. These primers are useful for the rapid screening of poliovirus isolates and for determining the compositions of cultures containing mixtures of poliovirus serotypes.