Mass Die-Off of Saiga Antelopes, Kazakhstan, 2015.

In 2015, a mass die-off of ≈200,000 saiga antelopes in central Kazakhstan was caused by hemorrhagic septicemia attributable to the bacterium Pasteurella multocida serotype B. Previous analyses have indicated that environmental triggers associated with weather conditions, specifically air moisture and temperature in the region of the saiga antelope calving during the 10-day period running up to the event, were critical to the proliferation of latent bacteria and were comparable to conditions accompanying historically similar die-offs in the same areas. We investigated whether additional viral or bacterial pathogens could be detected in samples from affected animals using 3 different high-throughput sequencing approaches. We did not identify pathogens associated with commensal bacterial opportunisms in blood, kidney, or lung samples and thus concluded that P. multocida serotype B was the primary cause of the disease.

Circulation of avian paramyxoviruses in wild birds of Kazakhstan in 2002-2013.

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.

Continuing evolution of equine influenza virus in Central Asia, 2007-2012.

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.

Isolation and Genetic Characterization of a Novel Adenovirus Associated with Mass Mortality in Great Cormorants (Phalacrocorax carbo).

High mortality in great cormorants (Phalacrocorax carbo) was registered on the Alakol Lake in eastern Kazakhstan in 2021 when about 20% of juveniles died. High-throughput sequencing revealed the presence of a putative novel cormorant adenovirus significantly divergent from known aviadenoviruses. We suggest that this cormorant adenovirus can be considered an emerging threat to the health and conservation of this species.

Aislamiento y caracterización genética de un nuevo adenovirus asociado con la mortalidad masiva en cormoranes grandes (Phalacrocorax carbo). En 2021 se registró una alta mortalidad de cormoranes grandes (Phalacrocorax carbo) en el lago Alakol, en el este de Kazajstán, cuando murieron alrededor del 20% de las aves jóvenes. La secuenciación de alto rendimiento reveló la presencia de un supuesto nuevo adenovirus de cormorán significativamente divergente de los aviadenovirus conocidos. Sugerimos que este adenovirus de cormorán puede considerarse una amenaza emergente para la salud y conservación de esta especie.

Has avian influenza virus H9 originated from a bat source?

Influenza A viruses are important pathogens that can cause diseases with high mortality in humans, animals, and birds; and wild birds are considered the primary reservoir of all subtypes in nature. After discovering the H9 influenza A viruses in bats, questions arose about their potential to serve as an additional natural reservoir and about the priority of the viral origin: Did the virus initially circulate in bats and then transmit to birds or vice versa? Influenza A viruses of the H9 subtype are of particular interest because fatal infections of humans caused by H5, H7, and H10 influenza viruses contained RNA segments from H9 viruses. Recently, a novel subtype of influenza A virus (H19) was reported and it was closely related to the H9 bat influenza A virus by its hemagglutinin structure. The genome of novel H19 has revealed a mixed characteristic genomic signature of both avian and bat influenza viruses. The time to most recent common ancestor (TMRCA) estimates have shown that the divergence time between the bat and avian H9-similar influenza virus occurred approximately at the end of the XVIII century. This article discusses the evolution and possible origin of influenza viruses of the H9 subtype isolated from bats and birds. The obtained data, along with the known data, suggest that the primary reservoir of the H9 influenza virus is wild birds, from which the virus was transmitted to bats. We hypothesize that the novel H19 could be a descendant of an intermediate influenza virus that was in the transition stage of spillover from avian to bat hosts.

Genome Sequence of the Attenuated Equid Alphaherpesvirus 1 Strain AK-2011, Isolated in Kazakhstan.

In 2011, there was an outbreak of a disease with mass abortions among horses in southeastern Kazakhstan. The AK-2011 strain was isolated from an aborted fetus and subsequently identified as equid alphaherpesvirus 1. Here, we describe the nearly complete genome sequence of the AK-2011 strain, attenuated for vaccine development.

Detection and Phylogenetic Characterization of a Novel Adenovirus Found in Lesser Mouse-Eared Bat (Myotis blythii) in South Kazakhstan.

Bats are an important natural reservoir of various pathogenic microorganisms, and regular monitoring is necessary to track the situation of zoonotic infections. When examining samples from bats in South Kazakhstan, nucleotide sequences of putative novel bat adenovirus (AdV) species were found. Estimates of amino acid identities of the hexon protein have shown that potentially novel Bat mastadenovirus BatAdV-KZ01 shared higher similarity with monkey Rhesus adenovirus 59 (74.29%) than with Bat AdVs E and H (74.00%). Phylogenetically, BatAdV-KZ01 formed a separate clade, distant from Bat AdVs and other mammalian AdVs. Since adenoviruses are essential pathogens for many mammals, including humans and bats, this finding is of interest from both scientific and epidemiological points of view.

Genetic characterization of a new candidate hemagglutinin subtype of influenza A viruses.

ABSTRACTAvian influenza viruses (AIV) have been classified on the basis of 16 subtypes of hemagglutinin (HA) and 9 subtypes of neuraminidase. Here we describe genomic evidence for a new candidate HA subtype, nominally H19, with a large genetic distance to all previously described AIV subtypes, derived from a cloacal swab sample of a Common Pochard (Aythya ferina) in Kazakhstan, in 2008. Avian influenza monitoring in wild birds especially in migratory hotspots such as central Asia is an important approach to gain information about the circulation of known and novel influenza viruses. Genetically, the novel HA coding sequence exhibits only 68.2% nucleotide and 68.5% amino acid identity with its nearest relation in the H9 (N2) subtype. The new HA sequence should be considered in current genomic diagnostic AI assays to facilitate its detection and eventual isolation enabling further study and antigenic classification.

Genome sequence of equine influenza virus isolated from horses in southeast Kazakhstan in 2020.

An influenza virus strain, A/equine/Almaty/268/2020, was isolated from horses in southeast Kazakhstan in 2020. Here, we present the nearly complete genome sequence of this epidemic strain. This study was aimed at obtaining the complete genome sequence of the isolate.

Genome Sequence of Influenza B Epidemic Strain B/Almaty/8/2018.

An influenza virus strain, B/Almaty/8/2018, was isolated in Almaty (in southeastern Kazakhstan) during a human population surveillance study in 2018. Here, we present the nearly complete genome sequence of this epidemic strain, compared to the Yamagata-like and Victoria-like variants of the influenza B virus.

AK-2011 strain for the development of a vaccine against equine rhinopneumonitis.

Equine rhinopneumonitis is an acute, highly contagious disease found virtually worldwide. The purpose of the studies presented in this paper is to develop a technology for the manufacture of a cell-derived equine rhinopneumonitis vaccine, as well as to assess the safety and immunogenicity of the newly developed vaccine in laboratory animals model. The object of the studies was the AK-2011 strain isolated from the horses suffering from rhinopneumonitis during an outbreak of abortions. The viability of the AK-2011 strain was assessed using a continuous line of calf trachea cells, a continuous line of calf kidney cells, a continuous line of sheep kidney cells, a continuous line of bovine kidney cells, a continuous line of green monkey kidney cells, a continuous line of Syrian hamster kidney cells, a primary trypsinized culture of horse kidney cells grown in tubes and flasks and the AK-2011 laboratory strain of equine rhinopneumonitis virus with biological activity of 6.0 lg TCID50/cm 3 . Sequencing and polymerase chain reaction analysis were performed. The virus isolated from the ORF68 gene in Kazakhstan appeared to be the most similar to the T-953 and 2222-03 strains isolated in the USA and Australia, respectively, in terms of phylogenetics. As to primary infections, cytopathic effects (CPEs) induced by the AK-2011 virus stain (dilution 101 ) in calf trachea and horse kidney cell cultures were stable from the first to tenth passages, with biological activity of 5.75-6.00 lg TCID50/cm 3 . CPEs caused by the virus were apparent on days 2-3, further developed intensively and extended to 60-80% of the cell monolayer on days 5-7. The vaccine results can be used to immunize horses on farms against rhinopneumonia, and horses should be immunized twice with an interval of 2-3 months.

Serological Screening for Middle East Respiratory Syndrome Coronavirus and Hepatitis E Virus in Camels in Kazakhstan.

After the recent Middle East Respiratory Syndrome coronavirus (MERS-CoV) pandemic in 2013, more attention has been paid to the camel as an important source of zoonotic viral infections. Almost simultaneously, in 2013, new genotypes 7 and 8 of the hepatitis E virus (HEV) were discovered in dromedary and Bactrian camels, respectively. HEV 7 was further shown to be associated with chronic viral hepatitis in a transplant recipient. In this study, serological screening for antibodies to MERS-CoV and hepatitis E virus was carried out on large camel farms in the south and west of Kazakhstan. 6.42% of the tested camels were found to be positive for antibodies to the hepatitis E virus, which indicates its circulation in local camel population. For the first time, antibodies to the hepatitis E virus were found in Bactrians, which have been little studied to date. Antibodies to MERS-CoV were not found in the camel sera.

Phylogenetic analysis of avian influenza viruses of H11 subtype isolated in Kazakhstan.

Avian influenza viruses A/turkey/Almaty/535/04 (H11N9) and A/herring gull/Atyrau/2186/07 (H11N2) isolated in Kazakhstan were characterized as low pathogenic in biological and genetic studies. Putative glycosylation sites were identical to the putative sites in published H11, N2, and N9 isolates sequences. Compared with published data no additional basic amino acid residues were found in the hemagglutinin (HA) cleavage site of these Kazakhstan strains. Phylogenetic analysis revealed a rare case of Eurasian-American reassortment in the HA gene of A/herring gull/Atyrau/2186/07 (H11N2) virus and significant sequence difference of the HA and the neuraminidase genes of the virus A/turkey/Almaty/535/04 (H11N9) from the previously published GenBank viruses.

Cormorants as a Potentially Important Reservoir and Carrier of Newcastle Disease Virus on the Asian Continent.

Despite numerous disease prevention measures and control programs, Newcastle disease (ND) remains one of the most significant infections in poultry worldwide, especially in developing countries. It is known that wild birds, mainly of the Anseriformes order, are the main carrier of lentogenic (non-pathogenic) variants of Newcastle disease virus (NDV) in nature. But the question of the reservoir of velogenic (highly pathogenic) NDV in nature still remains open. In the 1970s, 1990s, and 2000s in North America during epizootics among cormorants, velogenic NDV strains were isolated. It was later concluded that cormorants play an important role in the maintenance and circulation of NDV in North America. New data have been obtained on the circulation of velogenic NDV strains in wild birds in Central Asia: VIIb and XIII genotype strains were isolated from cormorants for the first time in Kazakhstan. Interestingly, outbreaks of NDV registered in poultry in Central and Southern Asia were phylogenetically close to the viruses from cormorants that support the idea that cormorants can serve as the potential reservoir of velogenic NDV in developing countries of Asia. The seasonal migrations of cormorants may contribute to the distribution of the virus throughout Asia but more evidence must be obtained to confirm this hypothesis. There is increasing evidence of the introduction of NDV into the poultry farms from wild nature worldwide. This article continues the discussion on the likelihood of cormorants to serve as a reservoir and carrier of NDV on the Asian continent.

High Mortality in Terns and Gulls Associated with Infection with the Novel Gull Adenovirus.

High mortality in Caspian Terns (Hydroprogne caspia) and Great Black-headed Gulls (Larus ichthyaetus), was recorded on the northeastern shores of the Caspian Sea in June 2013. Retrospective high throughput sequencing of archived tissue samples conducted in 2018 revealed the presence of the recently identified novel gull adenovirus similar to that associated with mortality in gulls in the Netherlands in 2001. We suggest that that this gull adenovirus specifically can be considered as an emerging threat to the health and conservation of gulls and terns.

A Highly Pathogenic H5N1 Influenza A Virus Isolated from a Flamingo on the Caspian Sea Shore.

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.

Evolution of Avian orthoavulavirus 16 in wild avifauna of Central Asia.

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.

Near-Complete Genome Sequence of Avian Influenza Virus Strain A/mallard/Balkhash/6304/2014 (H1N1) from 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.

Cormorants as Potential Victims and Reservoirs of Velogenic Newcastle Disease Virus (Orthoavulavirus-1) in Central Asia.

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 of Avian orthoavulavirus 1 in nature. Prior to 2014, most of the lentogenic NDV strains isolated from Central Asia were obtained from the avian order Anseriformes (ducks and geese). Wild birds were monitored from 2014-2016 to detect the circulation of NDV. A total of 1522 samples belonging to 73 avian species were examined, and 26 positive samples were identified. The isolates of Avian orthoavulavirus 1 belonged to three genotypes: viruses from doves (Columbiformes) and cormorants (Suliformes) were attributed to the velogenic genotypes VI and XIII, respectively, while the isolate from poultry belonged to lentogenic genotype I. The isolation of Avian orthoavulavirus 1 from doves may confirm their role as a reservoir of pigeon paramyxoviruses (antigenic variant of the genotype VI NDV) in nature and indicates the potential threat of introduction of velogenic strains into the poultry population. Our study describes an epizootic scenario in Kazakhstan among cormorants with mortality among juveniles of up to 3 wk of age and isolation of the NDV from apparently healthy birds. These observations may support the idea that cormorants are one of the potential reservoirs and victims of velogenic Avian orthoavulavirus 1 in Central Asia. The seasonal migrations of cormorants may partially contribute to viral dissemination throughout the continent; however, this hypothesis needs more evidence.

Cormoranes como posibles víctimas y reservorios del virus velogénicos de la enfermedad de Newcastle (Orthoavulavirus-1) en Asia Central. Las cepas virulentas del Orthoavulavirus aviar 1, históricamente conocido como virus de la enfermedad de Newcastle (NDV), están muy extendidas y causan altos niveles de mortalidad en avicultura en todo el mundo. Las aves silvestres pueden desempeñar un papel importante en el mantenimiento del Orthoavulavirus aviar 1 en la naturaleza. Antes del año 2014, la mayoría de las cepas de Newcastle lentogénicas aisladas de Asia Central se obtenían del orden aviar Anseriformes (patos y gansos). Las aves silvestres fueron monitoreadas entre los años 2014 y 2016 para detectar la circulación de virus de Newcastle. Se examinaron un total de 1522 muestras pertenecientes a 73 especies de aves, y se identificaron 26 muestras positivas. Los aislamientos de Orthoavulavirus aviar 1pertenecían a tres genotipos: los virus de palomas (Columbiformes) y de cormoranes (Suliformes) se atribuyeron a los genotipos velogénicos VI y XIII, respectivamente, mientras que los aislamientos de aves comerciales pertenecieron al genotipo lentogénico I. El aislamiento del Orthoavulavirus aviar 1 lentogénico de las palomas puede confirmar su papel como reservorio de los paramixovirus de paloma (variantes antigénicas del genotipo VI del virus de Newcastle) en la naturaleza e indica la amenaza potencial de la introducción de cepas velogénicas en la población avícola. Este estudio describe un escenario epizoótico en Kazajstán entre cormoranes con mortalidad de aves jóvenes de hasta tres semanas de edad y aislamiento del virus de Newcastle de aves aparentemente sanas. Estas observaciones pueden apoyar la idea de que los cormoranes son uno de los reservorios potenciales y también víctimas del Orthoavulavirus aviar 1 velogénico en Asia Central. Las migraciones estacionales de cormoranes pueden contribuir parcialmente a la diseminación viral en todo el continente; Sin embargo, esta hipótesis requiere de más evidencia.

Nearly Complete Genome Sequence of Human Influenza Virus Strain A/Almaty/6327/2014 (H1N1) from Central Asia.

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.