Avian influenza A virus adaptation to the equine host and identification of host-specific markers

Avian influenza A viruses (IAVs) are able to overcome the interspecies barrier and adapt to the new non-avian host. The process of adaptation requires the adaptive changes of IAV genome resulting in amino acid substitutions. The aim of this work was the description of amino acid substitutions in avian influenza A viruses (IAVs) occurring during their adaptation to equine host. Today, viruses of the equine influenza H3N8 subtype, first isolated in 1963, represent a single genetic lineage of IAV causing a respiratory disease in horses. We compared the amino acid sequences of the conserved proteins PB2, PB1, PA, NP, M1, M2, NS1 and NEP of equine influenza H3N8 subtype IAV with sequences of avian viruses, both available in the NCBI's Influenza Virus Resource Database. The amino acid substitutions persisting in equine IAV isolates and occurring in avian IAV at <5% frequency were included into the list of equine host-specific markers. We documented amino acid substitutions in the examined IAV proteins of equine IAV isolates in the period 1963-2013 and observed their quasi-linear accumulation. The substitution rate for the virus ribonucleoprotein (RNP) complex (PB2, PB1, PA, and NP) was calculated as R= 0.69 x 10(-3) per position per year. For other examined proteins (M1, M2, NS1, and NEP), calculated R-values ranged from 0.48 x 10(-3) to 1.30 x 10(-3) per position per year. We identified 127 equine host markers distributed among all internal virus proteins, 38 of which were present already in 1963 and other 89 accumulated during the period since 1963 until 2013. Ten equine host marker positions overlap with known human marker positions (Miotto et al., 2010) and five of them are occupied with identical amino acids in IAV of both hosts.