Complete Genome Sequence of a Novel Avian Paramyxovirus (APMV-13) Isolated from a Wild Bird in Kazakhstan.

A novel avian paramyxovirus was identified during annual viral surveillance of wild bird populations in Kazakhstan in 2013. The virus was isolated from a white fronted goose (Anser albifrons) in northern Kazakhstan. Here, we report the complete genome sequence of the isolate, which we suggest should constitute a novel serotype

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

Detection of influenza virus and pathogens of acute respiratory viral infections in population of Kazakhstan during 2018-2019 epidemic season

Influenza and other acute respiratory viral infections are the most common infectious diseases of our time, causing a significant harm to human health as well as great economic damage. At least five groups of viruses, including more than 300 subtypes, are currently related to ARVI pathogens. Such infectious agents are characterized by a high degree of variability resulting in replaced virus antigenic characteristics augmenting their contagiousness, immunoevasion, and resistance to chemotherapeutic drugs. Of relevance, influenza and other ARVIs also pose a threat due to subsequent rapid formation of bacterially-associated respiratory diseases as well as their continuous variability and emergence of new pathogenic species. In recent years, subtype A (H1N1) and A (H3N2) with predominance of pandemic strain, as well as type B influenza viruses have been simultaneously found in circulation. Most common among the causative agents of noninfluenza ARVIs, are respiratory syncytial virus, rhino- and adenoviruses, as well as I/III parainfluenza viruses. Here we present the results of virological and serological studies of clinical samples collected during the 2018—2019 epidemic season in the territory of the Republic of Kazakhstan after analyzing 2794 clinical samples (2530 nasopharyngeal swabs and 264 blood serum samples) of patients diagnosed with ARVI, ARI, bronchitis, and pneumonia. Examining nasopharyngeal swabs by using RT-PCR showed that the mixed etiology influenza viruses with predominant A/H1N1pdm virus circulated in Kazakhstan. In particular, influenza virus genetic material was found in 511 swabs (20.20% of total examined samples), so that influenza A virus RNA was detected in 508 biological samples such as A/H1N1 — in 289, A/H3N2 — 209, unverified virus subtype — 10 samples. Type B influenza virus was detected in 3 samples. Analyzing 264 blood serum samples by the HAI assay and ELISA showed the presence of antibodies specific to influenza A/H1N1, A/H3N2, and B viruses in the population of various regions of Kazakhstan, thereby indirectly confirming their co-circulation. 42 influenza virus strains were isolated in chicken embryos, of which 28 were assigned to A/H1N1pdm virus, 13 — A/H3N2 virus, and one isolate was identified as influenza B virus. The laboratory diagnostics of clinical samples for ARVIs revealed that respiratory syncytial virus prevailed among identified non-influenza agents, whereas rhino- and adenoviruses were less common. Metapneumoviruses, bocaviruses, coronaviruses, and type I parainfluenza viruses were detected in few cases. Comparison of our study data with the data on 2017—2018 circulation of influenza pathogens showed that in Kazakhstan influenza A and B viruses continued to circulate, with the dominance of A/H1N1pdm virus as it was in the previous epidemic season. Identification of non-influenza viruses, the causative agents of 2018—2019 respiratory infections, showed the predominance of respiratory syncytial virus that correlated with the aforementioned results

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

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

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

Schematic diagram showing the genomic organization of novel APMV.

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