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In 2015, in the Kazakh part of the northern Caspian Sea region, during the monitoring of wild birds for avian influenza viruses, a highly pathogenic A/flamingo/Mangistau/6570/2015(H5N1) influenza virus was isolated from a dead flamingo. This study aimed to obtain the complete genome sequence of the isolate.

In 2014, a novel Avian orthoavulavirus 16 species was described among wild birds in Korea. In 2018, after massive parallel sequencing of archival strains of Avian orthoavulaviruses, isolated in 2006 in Central Kazakhstan, isolates belonging to this serotype were detected. The obtained data allowed to trace the evolution of this serotype in Asia and to reveal its evolutionary relationships with other Avulavirinae subfamily species. It was determined that Avian orthoavulavirus 16 is phylogenetically very close to Avian orthoavulavirus 1 (Newcastle disease virus) in its genomic characteristics. It is known that Avian orthoavulavirus 1 is divided into two phylogenetically distant Classes I and II. Avian orthoavulavirus 16 turned out to be very close to lentogenic Class I, which circulates mainly among wild birds. It was suggested that Avian orthoavulaviruses 1 and 16 may have common evolutionary origin and in ecological terms, both serotypes are circulating among wild birds of the order Anseriformes (ducks and geese), but Avian orthoavulavirus 1 has gradually replaced Avian orthoavulavirus 16 from active circulation., Microbiology; Virology, Avian paramyxovirus, Avian orthoavulavirus, AOAV-16, Next-generation sequencing, Evolution, Kazakhstan

An influenza virus strain, A/Almaty/6327/2014 (H1N1), was isolated in Almaty (in southeastern Kazakhstan) during a human population surveillance study in 2014. Here, we present the nearly complete genome sequence of this epidemic strain that was compared to the postpandemic variants of A(H1N1)pdm09.

An avian influenza virus strain, A/mallard/Balkhash/6304/2014 (H1N1), was isolated during a wild bird monitoring study in Kazakhstan in 2014. The virus was isolated from a wild mallard duck (Anas platyrhynchos) in eastern Kazakhstan., An avian influenza virus strain, A/mallard/Balkhash/6304/2014 (H1N1), was isolated during a wild bird monitoring study in Kazakhstan in 2014. The virus was isolated from a wild mallard duck (Anas platyrhynchos) in eastern Kazakhstan. Here, we present the near-complete genome sequence of the virus.

Equine influenza (EI) continues to be an important respiratory pathogen of horses worldwide. Since 2007 several outbreaks of EI have occurred in Central Asian countries, including Kazakhstan, western Mongolia, India and western China. Phylogenetic analysis showed that two H3N8 equine influenza virus (EIV) isolates from Kazakhstan, A/equine/Almaty/26/2007 and A/equine/South Kazakhstan/236/12, were related to Florida sublineage 2, with high similarity to EIVs circulating in the same period in neighbouring countries. New outbreaks of EI during 2011 and 2012 in Kazakhstan and other Central Asian countries were caused by viruses of the same lineage. Genetic characterization of the viruses showed formation of a small EIV cluster with specific genetic signatures and continued evolution of this lineage in Central Asia between 2007 and 2012. The main genetic changes were observed in hemagglutinin gene without any antigenic drift. Although no vaccination policy was carried out in Kazakhstan, application of Florida clade 2-based vaccines is recommended.

Virulent strains of avian orthoavulavirus 1, historically known as Newcastle disease virus (NDV), are widespread and cause high levels of mortality in poultry worldwide. Wild birds may play an important role in the maintenance ofCormoranes como posibles víctimas y reservorios del virus velogénicos de la enfermedad de Newcastle (

A comprehensive influenza virus monitoring study of wild birds was carried out at important flyway resting places and wintering sites in Kazakhstan over eight years. More than 3200 birds belonging to 155 species were sampled. Nearly three-fourths of the birds belonged to the orders Anseriformes and Charadriiformes. In total, 118 hemagglutinating agents were isolated, and 95 of them were identified as influenza A viruses. The influenza viruses comprised eight different subtypes with a high prevalence of H13 and H3 viruses and also included low-pathogenic H5 viruses. The vast majority of the H13 viruses were isolated from members of the family Laridae, whereas the H3 viruses mostly originated from members of the family Anatidae, both in concordance with other monitoring studies. All virus isolates were recovered from cloacal swabs or fecal samples only. The influenza viruses were identified mainly in wetlands north of the Caspian Sea. These findings should be integrated in the design of further wild-bird-monitoring activities.

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.

Background Screening wild birds for avian paramyxoviruses is of increasing importance. 6913 samples of tracheal and cloacal swabs were collected during 2002–2013 and tested to study the prevalence of APMVs in wild avifauna of Kazakhstan. As a result, 45 isolates were obtained during this period and their ecological niches and genetic relationships were defined. Methods Tracheal and cloacal samples from wild birds were collected using sterile swabs placed in viral transport medium and kept in liquid nitrogen until delivery to the laboratory. Samples were inoculated into 10-day-old embryonated chicken eggs and reverse transcription PCR (RT-PCR) assays were performed via a one-step protocol. The PCR products were sequenced and phylogenetic trees were constructed using the ‘Neighbour Joining’ method. Results Six thousand nine hundred thirteen samples from 183 bird species were investigated and 45 isolates belonging to four different serotypes APMV-1, APMV-4, APMV-6 and APMV-8 were identified. All APMVs were isolated predominantly from birds belonging to Anatidae family (ducks and geese) and only one APMV-4 isolate was obtained from shorebird (Curlew) on the Caspian seashore. Genetic studies showed that the recovered APMV-1 strains had highest homology with European isolates. APMV-4 strains isolated in 2003, and APMV-6 and APMV-8 isolated in 2013 were 99 % identical to isolates from Far East. Conclusion This is the first reported characterization of avian paramyxoviruses from wild birds isolated in Kazakhstan. These data confirm the wide distribution of APMV-1, APMV-4 and APMV-6 in the Asian subcontinent. The obtained data contribute to the accumulation of knowledge on the genetic diversity and prevalence of APMVs in wild bird populations. Electronic supplementary material The online version of this article (doi:10.1186/s12985-016-0476-8) contains supplementary material, which is available to authorized users.

An avian paramyxovirus 6 strain was isolated during a wild bird monitoring study in Kazakhstan in 2013. The virus was isolated from a wild duck red-crested pochard ( Netta rufina ) in southeastern Kazakhstan. Here, we present the complete genome sequence of the virus.

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.