Validation of two multiplex real-time PCR assays based on single nucleotide polymorphisms of the HA1 gene of equine influenza A virus in order to differentiate between clade 1 and clade 2 Florida sublineage isolates

Journal of Veterinary Diagnostic Investigation : Official Publication of the American Association of Veterinary Laboratory Diagnosticians, Inc
Hanna BristerNicola Pusterla

Abstract

We validated 2 multiplex real-time PCR (rtPCR) assays based on single nucleotide polymorphisms (SNPs) of the hemagglutinin-1 ( HA1) gene of H3N8 equine influenza A virus (EIV) to determine clade affiliation of prototype and field isolates. Initial validation of the 2 multiplex rtPCR assays (SNP1 and SNP2) was performed using nucleic acid from 14 EIV Florida sublineage clade 1 and 2 prototype strains. We included in our study previously banked EIV rtPCR-positive nasal secretions from 341 horses collected across the United States in 2012-2017 to determine their clade affiliation. All 14 EIV prototype strains were identified correctly as either Florida sublineage clade 1 or clade 2 using the 2 SNP target positions. Of 341 EIV rtPCR-positive samples, 337 (98.8%) and 4 (1.2%) isolates were classified as belonging to clade 1 and 2 Florida sublineage EIV, respectively. All clade 1 Florida sublineage EIV strains were detected in domestic horses, three clade 2 Florida sublineage EIV strains originated from horses recently imported into the United States, and one clade 2 Florida sublineage EIV strain originated from a healthy horse recently vaccinated with a modified-live intranasal EIV vaccine containing the American lineage strain A/eq...Continue Reading

References

Apr 6, 1999·Revue Scientifique Et Technique·A J GuthrieP P Bosman
Mar 17, 2009·Journal of Veterinary Diagnostic Investigation : Official Publication of the American Association of Veterinary Laboratory Diagnosticians, Inc·William C WilsonLuis L Rodriguez
Mar 13, 2015·Equine Veterinary Journal·L J LegrandS L Pronost
Mar 11, 2016·Journal of Veterinary Diagnostic Investigation : Official Publication of the American Association of Veterinary Laboratory Diagnosticians, Inc·Pedro N BernardinoNicola Pusterla

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Citations

Jun 3, 2021·Animal Health Research Reviews·Luís DionísioAna I Faustino-Rocha
Aug 29, 2021·Viruses·Fatai S OladunniThomas M Chambers
Sep 7, 2021·The Veterinary Journal·Nicola PusterlaEmir Hodzic
Mar 11, 2020·Cold Spring Harbor Perspectives in Medicine·Thomas M Chambers

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Methods Mentioned

BETA
nucleic acid sequencing
PCR
nucleic acid purification

Software Mentioned

primer express
BLAST

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