Kobey Karamendin

• PhD.
• Scientific Production Center of Microbiology and Virology

Paretic and paralyzing syndromes affecting wild birds are widely described in the literature, with outbreaks showing an increase in frequency and intensity worldwide during recent years. In the Iberian Peninsula, a paretic clinical picture without known etiology affecting mostly gulls has been reported during the last few decades. This paretic synd...

In the winter of 2023/2024, the mass death of swans was observed on Lake Karakol on the eastern coast of the Caspian Sea. From 21 December 2023 to 25 January 2024, 1132 swan corpses (Cygnus olor, Cygnus cygnus) were collected and disposed of on the coast by veterinary services and ecologists. Biological samples were collected from 18 birds for anal...

Mass mortality in Caspian terns (Hydroprogne caspia), Pallas’s gulls (Ichthyaetus ichthyaetus), and Caspian gulls (Larus cachinnans) was recorded on the northeastern shores of the Caspian Sea in June 2022. More than 5000 gulls and terns died due to the outbreak. The outbreak was investigated in the field, and representative numbers of samples were...

In recent years, the study of bat viruses has become particularly relevant in light of the coronavirus pandemic and other major outbreaks of viral diseases, such as Ebola fever and the Zika virus. Bats are important reservoirs for many pathogens that can cause diseases in humans and animals. These mam-mals not only serve as primary sources of vario...

Introduction Viral diseases of pinnipeds cause substantial mortality and morbidity and can influence population demography. Viral metagenomic studies can therefore play an important role in pinniped health assessments and disease surveillance relevant to both individual species and in a “One Health” context. Methods This study used a metagenomic a...

The Caspian seal (Pusa caspica), found only in the Caspian Sea, plays a crucial role in its ecosystem as both a primary piscivore and a fundamental environmental indicator. However, Caspian seals face threats from human activities and pathogenic infections. In this study, shotgun metagenomic sequencing was utilized to investigate the bacterial comm...

Viral diseases of pinnipeds cause substantial mortality and morbidity and can influence population demography. Viral metagenomic studies can therefore play an important role in pinniped health assessments and disease surveillance relevant to both individual species and in a 'One Health' context. This study used a metagenomic approach with high thro...

Avian paramyxoviruses (APMV), now classified as, avian avulaviruses according to the new classification, are part of the Avulavirinae subfamily within the Paramyxoviridae family. They are divided into twenty-two species based on a hemagglutination inhibition assay and molecular analyses. Furthermore, they are grouped into three genera Avian metaavu...

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 cons...

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 pr...

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.

Artemia (brine shrimp) holds significant value as a live feed for larval fish and crustaceans, owing to their distinctive dietary requirements. However, it is vital to acknowledge that Artemia also carries potential risk as a vector of infection. We conducted a metagenomic analysis to explore the virome present in Artemia cysts collected from inlan...

Artemia (brine shrimp), holds significant value as a live feed for larval fish and crustaceans, owing to their distinctive dietary requirements. However, it is vital to acknowledge that Artemia also carries potential risk as a vector of infection. We conducted a metagenomic analysis to explore the virome present in Artemia cysts collected from inla...

Avian 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...

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...

The influenza virus strain A/chicken/North Kazakhstan/184/2020 (H5N8) was isolated in North Kazakhstan during a highly pathogenic avian influenza outbreak in 2020. This study aimed to obtain the complete genome sequence of the isolate.

Disease surveillance of marine mammal populations is essential to understand the causes of strandings, identify potential threats to animal health, and to support development of conservation strategies. Here we report the first large multi-pathogen screening of prevalence for viruses, bacteria and parasites in a sample of 177 live, healthy, wild Ca...

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.

An outbreak of a bacterial disease with lethal cases was registered in camels in Kazakhstan in 2018. The disease was characterised by dry, harsh hacking cough and nasal discharge with froathy and bloody liquid. Camels died in a state of hyperexcitement and asphyxia. Investigation of the case has identified the pathogenic form of Paeniclostridium so...

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 furth...

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.

Worldwide studies have shown the importance of controlling the spread of zoonotic infections. In recent years, new pandemic strains of coronaviruses in camels have been identified, which necessitates regular monitoring of the state of viral populations of this animal. The research scope is to identify the spectrum of viral and bacterial populations...

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....

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...

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 a...

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...

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 obt...

Introduction: Previously unknown paramyxovirus strains were isolated from wild birds in 2013-2014 in Kazakhstan and subsequently identified as representatives of the novel Avian avulavirus 20 species. The aims and tasks were molecular genetic characterization of novel avulaviruses and investigation of their phylogenetic relationships. Material an...

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.

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...

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.

The levels of thyroid hormones (total thyroxine, free thyroxine, and total triiodothyronine) in the blood serum of the Caspian seal Pusa caspica are reported for the first time. The serum levels of thyroid hormones in Caspian seal were comparable to those in the harbor seal Phoca vitulina. An increased plasma level of total thyroxine was found in s...

Five avian paramyxoviruses of serotype 8 (APMV-8) were isolated during a study monitoring wild birds in Kazakhstan in 2013 and each was further characterized. The viruses were isolated from three White-fronted geese (Anser albifrons), one Whooper swan (Cygnus cygnus), and one Little stint (Calidris minuta). Before our study, only two complete APMV-...

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...

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 ag...

A retrospective phylogenetic characterization of the hemagglutinin, neuraminidase and nucleoprotein genes of equine influenza virus A/equine/Kirgizia/26/1974 (H7N7) which caused an outbreak in Kirgizia (a former Soviet Union republic, now Kyrgyzstan) in 1977 was conducted. It was defined that it was closely related to the strain London/1973 isolate...

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 relationship...

P-­‐016 MONITORING FOR THE MAIN FISH VIRUSES IN KAZAKHSTAN A. KYDYRMANOV*, A. SEIDALINA, S. SULEIMENOVA, K. KARAMENDIN, YE. KASSYMBEKOV Institute of Microbiology and Virology, Almaty, Kazakstan Up to date in Kazakhstan, the research on infectious diseases of fish has not yet been conducted. Therefore, virological monitoring of fishing ponds and...

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.

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.

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/2...

GenBank Accession Numbers KF712451-KF712458 represent sequences from the 8 segments of Influenza A virus (A/equine/South Kazakhstan/236/2012(H3N8)). ##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

GenBank Accession Numbers KF712451-KF712458 represent sequences from the 8 segments of Influenza A virus (A/equine/South Kazakhstan/236/2012(H3N8)). ##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

GenBank Accession Numbers KF712451-KF712458 represent sequences from the 8 segments of Influenza A virus (A/equine/South Kazakhstan/236/2012(H3N8)). ##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

GenBank Accession Numbers KF712451-KF712458 represent sequences from the 8 segments of Influenza A virus (A/equine/South Kazakhstan/236/2012(H3N8)). ##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

GenBank Accession Numbers KF712451-KF712458 represent sequences from the 8 segments of Influenza A virus (A/equine/South Kazakhstan/236/2012(H3N8)). ##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

GenBank Accession Numbers KF712451-KF712458 represent sequences from the 8 segments of Influenza A virus (A/equine/South Kazakhstan/236/2012(H3N8)). ##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

GenBank Accession Numbers KF712451-KF712458 represent sequences from the 8 segments of Influenza A virus (A/equine/South Kazakhstan/236/2012(H3N8)). ##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

GenBank Accession Numbers KF712451-KF712458 represent sequences from the 8 segments of Influenza A virus (A/equine/South Kazakhstan/236/2012(H3N8)). ##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

Dmitrieva, L., Kondakov, A. A., Oleynikov, E., Kydyrmanov, A., Karamendin, K., Kasimbekov, Y., . . . Goodman, S. J. (2013). Assessment of Caspian Seal By-Catch in an Illegal Fishery Using an Interview-Based Approach. PLoS One, 8(6), e67074. doi:10.1371/journal.pone.0067074

The Caspian seal (Pusa caspica) has declined by more than 90% since 1900 and is listed as endangered by IUCN. We made the first quantitative assessment of Caspian seal by-catch mortality in fisheries in the north Caspian Sea by conducting semi-structured interviews in fishing communities along the coasts of Russia (Kalmykia, Dagestan), Kazakhstan a...

Русский перевод оригинальной статьи (Russian translation of the original article): Dmitrieva, L., Kondakov, A. A., Oleynikov, E., Kydyrmanov, A., Karamendin, K., Kasimbekov, Y., . . . Goodman, S. J. (2013). Assessment of Caspian Seal By-Catch in an Illegal Fishery Using an Interview-Based Approach. PLoS One, 8(6), e67074. doi:10.1371/journal.pone...

Supporting file containing Section S1 and Figure S1. Section S1. Extended methods and questionnaire for fishermen interviews. Figure S1. Evidence of mass entanglement of Caspian seal groups. More than 20 Caspian seal carcasses entangled in a single sturgeon net (Photo © Brian Deacon, KBR-I&M, Leatherhead, UK, used with permission under a Creative C...

Although the important role of the non-structural (NS1 and NEP) gene of influenza A in virulence of the virus is well established, our knowledge about the extent of variation in the NS gene pool of influenza A viruses in their natural reservoirs in Kazakhstan is incomplete. 17 influenza A viruses of different subtypes were studied in this paper. Se...

Studing of influenza virus ecology and evolution in Kazakhstan is of particular interest since Re-pulic occupies unique geographical position in the middle of Eurasia and transpalearctic flyways of migratory birds across its great territory. A total of 95 influenza A virus isolates were obtained from 15 duck, eight gull, two grebe species, and by o...

Morbillivirus infections in Caspian seals (Phoca caspica) have been reported since 1997 and implicated in mass mortality of this species in 2000. In this study, we conducted virological survey on circulation of morbilliviruses in Caspian seals in interepizootic period. Seals were live sampled during tagging with satellite transmitters in late fall...

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...

GenBank Accession Numbers HQ541739-HQ541746 represent sequences from the 8 segments of Influenza A virus (A/herring gull/Atyrau/2186/2007(H11N2)).

GenBank Accession Numbers GU953271-GU953274 and HQ541747-HQ541750 represent sequences from the 8 segments of Influenza A virus (A/turkey/Almaty/535/2004(H11N9)).

GenBank Accession Numbers HQ541739-HQ541746 represent sequences from the 8 segments of Influenza A virus (A/herring gull/Atyrau/2186/2007(H11N2)).

GenBank Accession Numbers GU953271-GU953274 and HQ541747-HQ541750 represent sequences from the 8 segments of Influenza A virus (A/turkey/Almaty/535/2004(H11N9)).

GenBank Accession Numbers HQ541739-HQ541746 represent sequences from the 8 segments of Influenza A virus (A/herring gull/Atyrau/2186/2007(H11N2)).

GenBank Accession Numbers HQ541739-HQ541746 represent sequences from the 8 segments of Influenza A virus (A/herring gull/Atyrau/2186/2007(H11N2)).

GenBank Accession Numbers GU953271-GU953274 and HQ541747-HQ541750 represent sequences from the 8 segments of Influenza A virus (A/turkey/Almaty/535/2004(H11N9)).

GenBank Accession Numbers HQ541739-HQ541746 represent sequences from the 8 segments of Influenza A virus (A/herring gull/Atyrau/2186/2007(H11N2)).

GenBank Accession Numbers HQ541739-HQ541746 represent sequences from the 8 segments of Influenza A virus (A/herring gull/Atyrau/2186/2007(H11N2)).

GenBank Accession Numbers HQ541739-HQ541746 represent sequences from the 8 segments of Influenza A virus (A/herring gull/Atyrau/2186/2007(H11N2)).

GenBank Accession Numbers HQ541739-HQ541746 represent sequences from the 8 segments of Influenza A virus (A/herring gull/Atyrau/2186/2007(H11N2)).

GenBank Accession Numbers GU953271-GU953274 and HQ541747-HQ541750 represent sequences from the 8 segments of Influenza A virus (A/turkey/Almaty/535/2004(H11N9)).

On Jul 11, 2012 this sequence version replaced gi:292384371.

In recent years there has been a substantial increase in cystic echinococcosis in Kazakhstan. There are several factors that have contributed to this change in the epidemiology of the disease. The primary reason was the degradation of traditional nomadic system of livestock breeding and closing of large collective farms. Small private farms have st...