Genetic and antigenic characterization of H1 influenza viruses from United States swine from 2008.

A Lorusso,N S Lewis,S L Swenson,C A Russell,K M Lager,M L Harland,D Alt,A L Vincent,D J Smith,D O Bayles,M R Gramer

doi:10.1099/vir.0.027557-0

Abstract

Prior to the introduction of the 2009 pandemic H1N1 virus from humans into pigs, four phylogenetic clusters (α-, β-, γ- and δ) of the haemagglutinin (HA) gene from H1 influenza viruses could be found in US swine. Information regarding the antigenic relatedness of the H1 viruses was lacking due to the dynamic and variable nature of swine lineage H1. We characterized 12 H1 isolates from 2008 by using 454 genome-sequencing technology and phylogenetic analysis of all eight gene segments and by serological cross-reactivity in the haemagglutination inhibition (HI) assay. Genetic diversity was demonstrated in all gene segments, but most notably in the HA gene. The gene segments from the 2009 pandemic H1N1 formed clusters separate from North American swine lineage viruses, suggesting progenitors of the pandemic virus were not present in US pigs immediately prior to 2009. Serological cross-reactivity paired with antigenic cartography demonstrated that the viruses in the different phylogenetic clusters are also antigenically divergent.

Highlights

Influenza in swine is an acute respiratory disease caused by influenza A virus
This study offers the first antigenic mapping of H1 viruses currently circulating in the swine population
No large contigs were produced for gene segment 8 of A/swine/Ohio/02026/2008, which was subsequently amplified by standard RT-PCR procedures for sequencing

Summary

Introduction

Influenza A virus contains a negativesense ssRNA genome organized into eight individual segments, allowing for reassortment and production of novel viruses (Lamb & Krug, 2007). HA and NA proteins are encoded by segments 4 and 6 of the viral genome, located on the virion surface, and are the primary target for the host immune response (Skehel & Wiley, 2000). The HA protein is the most important determinant of virulence and host specificity as its binding site and binding pocket recognize sialic acid-containing cell surface receptors on host epithelial cells (Ayora-Talavera et al, 2009; de Wit et al, 2010; Nicholls et al, 2008; Shinya et al, 2006). The remaining six segments encode the following structural and accessory proteins: PB2 (segment 1), PB1 (segment 2), PA (segment 3), NP (segment 5), M1

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