Novel avian paramyxovirus isolated from gulls in Caspian seashore in Kazakhstan.

Three isolates APMV/gull/Kazakhstan/5976/2014, APMV/gull/Kazakhstan/ 5977/2014 and APMV/gull/Kazakhstan/5979/2014, were obtained from independent samples during annual surveillance for avian influenza and paramyxoviruses in wild birds from the Caspian Sea coast in Western Kazakhstan, and were initially identified as putative paramyxoviruses on the basis of electron microscopy. Hemagglutination Inhibition Assays with antisera to nine known APMV serotypes (APMV1-9) indicated no relation to any of them. Next generation sequencing of whole genome sequences indicated the three isolates were genetically identical, and had a nucleotide structure typical for all APMVs, consisting of six genes 3'-NP-P-M-F-HN-L-5'. Phylogenetic analyses, and assessment of amino acid identities, suggested the most closely related lineages to be APMV-2, 8, 10 and 15, but the novel isolate had less than 64% identity to them and all other known avian paramyxoviruses. This value was above levels considered to generally define other APMV serotypes. Estimates of the evolutionary divergence of the nucleotide sequences of the genomes of APMVs have shown that novel Kazakhstan APMV strain was closest to APMV-2, APMV-8, APMV-10 and APMV-15, with calculated distance values of 2.057, 2.058, 2.026 and 2.286 respectively, which is above values considered to differentiate other serotypes (observed minimum was 1.108 between APMV-1 and recently isolated APMV/UPO216/Korea). Together, the data suggest that isolate APMV/gull/Kazakhstan/5976/2014 and other two should be considered as the first representative of a novel APMV-20 group, and is the first time that avian paramyxoviruses have been found infecting members of the gull family, extending the known taxonomic host range

Additional file 1: Table S1. of Circulation of avian paramyxoviruses in wild birds of Kazakhstan in 2002–2013

Avian species tested for APMVs in Kazakhstan, 2002–2013. (DOCX 48 kb

Estimates of evolutionary divergence at the nucleotide level between all APMV serotypes sequences.

<p>Estimates of evolutionary divergence at the nucleotide level between all APMV serotypes sequences.</p

Hemagglutination Inhibition assay with antisera to reference APMVs and homologous rabbit antiserum.

<p>Hemagglutination Inhibition assay with antisera to reference APMVs and homologous rabbit antiserum.</p

Percent amino acid sequence identities in F and HN genes of avian paramyxoviruses representing all known APMV groups.

<p>Percent amino acid sequence identities in F and HN genes of avian paramyxoviruses representing all known APMV groups.</p

Electron microscopy morphology of negatively stained isolate APMV/gull/Kazakhstan/5976/2014.

<p>Magnification x 50000.</p

Phylogenetic relationships on nucleotide level between novel APMV serotype and others.

<p>Phylogenetic relationships on nucleotide level between novel APMV serotype and others.</p

Schematic diagram showing the genomic organization of novel APMV.

<p>Schematic diagram showing the genomic organization of novel APMV.</p