The Prevalence of Viral Pathogens among Bats in Kazakhstan.

Bats carry thousands of viruses from 28 different families. To determine the presence of various pathogens in bat populations in Kazakhstan, 1149 samples (393 oropharyngeal swabs, 349 brain samples, 407 guano) were collected. The samples were collected from four species of bats (Vespertilio murinus, Nyctalus noctula, Myotis blythii, Eptesicus serotinus) in nine regions. The Coronavirus RNA was found in 38 (4.75%) samples, and the rabies virus in 27 (7.74%) samples from bats. Coronaviruses and the rabies virus were found in bats in six out of nine studied areas. The RNAs of SARS-CoV-2, MERS, TBE, CCHF, WNF, influenza A viruses were not detected in the bat samples. The phylogeny of the RdRp gene of 12 samples made it possible to classify them as alphacoronaviruses and divide them into two groups. The main group (n = 11) was closely related to bat coronaviruses from Ghana, Zimbabwe and Kenya. The second group (n = 1) was closely related to viruses previously isolated in the south of Kazakhstan. The phylogeny of the N gene sequence from a bat from west Kazakhstan revealed its close relationship with isolates from the Cosmopolitan group of rabies viruses (Central Asia). These results highlight the need for a continuous monitoring of volatile populations to improve the surveillance and detection of infectious diseases.

The Prevalence of Pathogens among Ticks Collected from Livestock in Kazakhstan.

Ticks carry and transmit a wide variety of pathogens (bacteria, viruses and protozoa) that pose a threat to humans and animals worldwide. The purpose of this work was to study ticks collected in different regions of Kazakhstan for the carriage of various pathogens. The collected ticks were examined by PCR for the carriage of various pathogens. A total of 3341 tick samples parasitizing three animal species (cattle, sheep and horses) were collected at eight regions of Kazakhstan. Eight tick species were found infesting animals: Dermacentor marginatus (28.08%), Hyalomma asiaticum (21.28%), Hyalomma anatolicum (17.18%), Dermacentor reticulatus (2.01%), Ixodes ricinus (3.35%), Ixodes persulcatus (0.33%), Hyalomma scupense (12.87%) and Hyalomma marginatum (14.90%). Ticks collected from livestock animals were examined for the pathogen spectrum of transmissible infections to determine the degree of their infection. Four pathogen DNAs (lumpy skin disease virus (LSDV), Coxiella burnetti, Teileria annulata, and Babesia caballi) were detected by PCR in Dermacentor marginatus, Hyalomma asiaticum, Hyalomma scupense, Hyalomma anatolicum. The infection of ticks Dermacentor marginatus and Hyalomma asiaticum collected on cattle in the West Kazakhstan region with LSDV was 14.28% and 5.71%, respectively. Coxiella burnetti was found in the ticks Dermacentor marginatus (31.91%) in the Turkestan region and Hyalomma anatolicum (52.63%) in the Zhambyl region. Theileria annulata was found in ticks Hyalomma scupense (7.32%) and Dermacentor marginatus (6.10%) from cattle in the Turkestan region. Babesia caballi was isolated only from the species Hyalomma scupense (17.14%) in the Turkestan region. There were no PCR-positive tick samples collected from sheep. RNA/DNAs of tick-borne encephalitis virus (TBEV), African swine fever virus (ASFV), Hantavirus hemorrhagic fever with renal syndrome (HFRS), and chlamydia pathogens were not found in ticks. The new data give a better understanding of the epidemiology of tick-borne pathogens and the possibility of the emergence of tick-borne animal diseases in Kazakhstan.

The Prevalence and Genetic Variants of the CCHF Virus Circulating among Ticks in the Southern Regions of Kazakhstan.

Crimean-Congo hemorrhagic fever (CCHF) disease cases are registered annually in endemic regions of Kazakhstan. To study the prevalence of various Crimean-Congo hemorrhagic fever virus (CCHFV) genotypes, a total of 694 ticks were collected from southern regions of Kazakhstan in 2021. Hyalomma marginatum (n = 323) (46.5%), Hyalomma anatolicum (n = 138) (19.9%), Hyalomma asiaticum (n = 126) (18.2%), Hyalomma scupense (n = 80) (11.5%) and Ixodes ricinus (n = 27) (3.9%) were collected using the standardized flagging technique from the environment. All the tick samples were analyzed for the presence of CCHFV RNA by RT-PCR. The CCHF-positive samples were found within three Hyalomma asiaticum and one Ixodes ricinus tick sample. For the first time in Kazakhstan, infection of the Ixodes ricinus tick with CCHFV was detected. The results of sequencing and analysis of the S-gene fragment showed that the Asia 1 and Asia 2 CCHF genotypes circulate in the southern regions of Kazakhstan. Viruses isolated in the Zhambyl and Turkestan regions are assigned to the Asia-2 genotype, whereas the virus isolated in the Kyzylorda region to the Asia-1 genotype.

Evidence for flock transmission of individual subtypes and strains of avian influenza viruses: A monitoring study of wild birds in Kazakhstan.

An active surveillance study of avian influenza viruses (AIVs) in wild birds was carried out in Kazakhstan in 2018-2019. In total, 866 samples were collected from wild birds and analyzed for influenza viruses using molecular and virological tests. Genome segments of Asian, European, and Australian lineages were detected in 25 (4.6%) out of 541 waterfowl samples positive for subtype H3N8, and in two (0.6%) out of 325 H3N8 positive samples from terrestrial birds. No highly pathogenic avian influenza virus (AIV) was detected. The results indicated transmission of closely related strains or identical subtypes of AIVs by a flock-unit of migratory birds or annual cyclical pattern of subtype dominance. The simultaneous circulation of genome segments of the Asian, European and Australian genetic lineages of H3N8 AIVs in wild birds in Kazakhstan indicated the important role of Central Asia as a transmission hub of AI viruses linking the East Asian migratory flyways with European flyways and vice versa.

Genome Sequence of Atyrau-5BJN(IL18), a Recombinant Lumpy Skin Disease Virus with Knockout of Virulence Genes.

Here, we present the coding sequence of the genome of the recombinant lumpy skin disease virus (LSDV) Atyrau-5BJN(IL18), obtained by knocking out four genes in the genome of a virulent field LSDV isolate. Genome sequencing confirmed the deletion of genes and the insertion of a foreign sequence in the viral genome.

Serological exposure in Bactrian and dromedary camels in Kazakhstan to a MERS or MERS-like coronavirus.

Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is a camel-borne zoonotic virus endemic across Eastern Africa and the Middle East, with evidence of circulation in Bangladesh and Mongolia. To determine if MERS-CoV was present in Kazakhstan, in 2017-2018, we collected swabs and sera from Bactrian camels (n = 3124) and dromedary (n = 5083). The total seropositivity was 0.54% in Bactrian camels and 0.24% in dromedaries; however, we did not detect MERS-CoV RNA in swab samples. There was no difference in the probability of infection between species or sex, but younger camels had a higher probability of being seropositive, suggesting a recent introduction of the virus to Kazakhstan. The infection of both camel species indicates that they both may play a role as natural reservoirs. These results reinforce the need for continual surveillance, especially at the camel-human interface to understand the risk of zoonotic exposure.

Lumpy skin disease in Kazakhstan.

This study describes the registration of the first cases of lumpy skin disease in July 2016 in the Republic of Kazakhstan. In the rural district of Makash, Kurmangazinsky district of Atyrau region, 459 cattle fell ill and 34 died (morbidity 12.9% and mortality 0.96%). To determine the cause of the disease, samples were taken from sick and dead animals, as well as from insects and ticks. LSDV DNA was detected by PCR in all samples from dead animals and ticks (Dermacentor marginatus and Hyalomma asiaticum), in 14.29% of samples from horseflies (Tabanus bromius), and in one of the samples from two Stomoxys calcitrans flies. The reproductive LSD virus was isolated from organs of dead cattle and insects in the culture of LT and MDBK cells. The virus accumulated in cell cultures of LT and MDBK at the level of the third passage with titers in the range of 5.5-5.75 log 10 TCID50/cm3. Sequencing of the GPCR gene allowed us to identify this virus as a lumpy skin disease virus.

Discovery and Characterization of Novel Bat Coronavirus Lineages from Kazakhstan.

Coronaviruses are positive-stranded RNA viruses that infect a variety of hosts, resulting in a range of symptoms from gastrointestinal illness to respiratory distress. Bats are reservoirs for a high diversity of coronaviruses, and focused surveillance detected several strains genetically similar to MERS-coronavirus, SARS-coronavirus, and the human coronaviruses 229E and NL63. The bat fauna of central Asia, which link China to eastern Europe, are relatively less studied than other regions of the world. Kazakhstan is the world's ninth largest country; however, little is understood about the prevalence and diversity of bat-borne viruses. In this study, bat guano was collected from bat caves in three different sites of southern Kazakhstan that tested positive for coronaviruses. Our phylogenetic reconstruction indicates these are novel bat coronaviruses that belong to the genus Alphacoronavirus. In addition, two distinct lineages of Kazakhstan bat coronaviruses were detected. Both lineages are closely related to bat coronaviruses from China, France, Spain, and South Africa, suggesting that co-circulation of coronaviruses is common in multiple bat species with overlapping geographical distributions. Our study highlights the need for collaborative efforts in understudied countries to increase integrated surveillance capabilities toward better monitoring and detection of infectious diseases.

Genetic diversity of avian avulavirus 1 (Newcastle disease virus genotypes VIg and VIIb) circulating in wild birds in Kazakhstan.

In order to improve current understanding of the molecular epidemiology of avian avulavirus 1 (AAvV-1, formerly avian paramyxovirus 1) in wild birds in Kazakhstan, 860 cloacal swab samples were evaluated. Samples were collected from 37 families of wild birds in nine different regions in the years 2011 and 2014. Overall, 54 positive samples (4.2%) were detected from 17 different families of wild birds, and 16 AAvV-1 isolates were characterized. Three of the isolates contained the fusion protein cleavage site motif RRQKR, and 13 contained KRQKR, which is typical for pathogenic strains of AAvV-1. The AAvV-1 isolates were found to belong to the genotypes VIg and VIIb.

New oligonucleotide microarray for rapid diagnosis of avian viral diseases.

BACKGROUND: We developed a new oligonucleotide microarray comprising 16 identical subarrays for simultaneous rapid detection of avian viruses: avian influenza virus (AIV), Newcastle disease virus (NDV), infection bronchitis virus (IBV), and infectious bursal disease virus (IBDV) in single- and mixed-virus infections. The objective of the study was to develop an oligonucleotide microarray for rapid diagnosis of avian diseases that would be used in the course of mass analysis for routine epidemiological surveillance owing to its ability to test one specimen for several infections. METHODS AND RESULTS: The paper describes the technique for rapid and simultaneous diagnosis of avian diseases such as avian influenza, Newcastle disease, infectious bronchitis and infectious bursal disease with use of oligonucleotide microarray, conditions for hybridization of fluorescent-labelled viral cDNA on the microarray and its specificity tested with use of AIV, NDV, IBV, IBDV strains as well as biomaterials from poultry. Sensitivity and specificity of the developed microarray was evaluated with use of 122 specimens of biological material: 44 cloacal swabs from sick birds and 78 tissue specimens from dead wild and domestic birds, as well as with use of 15 AIV, NDV, IBV and IBDV strains, different in their origin, epidemiological and biological characteristics (RIBSP Microbial Collection). This microarray demonstrates high diagnostic sensitivity (99.16% within 95% CI limits 97.36-100%) and specificity (100%). Specificity of the developed technique was confirmed by direct sequencing of NP and M (AIV), VP2 (IBDV), S1 (IBV), NP (NDV) gene fragments. CONCLUSION: Diagnostic effectiveness of the developed DNA microarray is 99.18% and therefore it can be used in mass survey for specific detection of AIV, NDV, IBV and IBDV circulating in the region in the course of epidemiological surveillance. Rather simple method for rapid diagnosis of avian viral diseases that several times shortens duration of assay versus classical diagnostic methods is proposed.

Recombinant Sheep Pox Virus Proteins Elicit Neutralizing Antibodies.

The aim of this work was to evaluate the immunogenicity and neutralizing activity of sheep pox virus (SPPV; genus Capripoxvirus, family Poxviridae) structural proteins as candidate subunit vaccines to control sheep pox disease. SPPV structural proteins were identified by sequence homology with proteins of vaccinia virus (VACV) strain Copenhagen. Four SPPV proteins (SPPV-ORF 060, SPPV-ORF 095, SPPV-ORF 117, and SPPV-ORF 122), orthologs of immunodominant L1, A4, A27, and A33 VACV proteins, respectively, were produced in Escherichia coli. Western blot analysis revealed the antigenic and immunogenic properties of SPPV-060, SPPV-095, SPPV-117 and SPPV-122 proteins when injected with adjuvant into experimental rabbits. Virus-neutralizing activity against SPPV in lamb kidney cell culture was detected for polyclonal antisera raised to SPPV-060, SPPV-117, and SPPV-122 proteins. To our knowledge, this is the first report demonstrating the virus-neutralizing activities of antisera raised to SPPV-060, SPPV-117, and SPPV-122 proteins.

Seroprevalence of infectious diseases in saiga antelope (Saiga tatarica tatarica) in Kazakhstan 2012-2014.

286 serum samples were collected from three sub-populations of saiga in Kazakhstan (Betpakdala, Ustyurt and Volga-Ural) between 2012 and 2014, and were tested for the presence of antibodies to Brucella spp., bluetongue virus, peste des petits ruminants (PPR) virus, Akabane virus, Schmallenberg virus, Chlamydophila, Toxoplasma, Mycobacterium avium subspecies paratuberculosis and Coxiella burnetii (Q Fever). Seropositives to Coxiella burnetii of saiga were detected and the adjusted seroprevalence of Q Fever antibodies was 0.07 (95% confidence interval (CI): 0.03-0.10). Seropositives to Akabane virus were detected in all three populations and the adjusted seroprevalence values for this virus were very high (all were>0.13). Lower adjusted seroprevalence values were estimated for PPR Virus and Mycobacterium avium subsp. paratuberculosis (0.005 and 0.006). No seropositives for bluetongue, Toxoplasma, Brucella or Schmallenberg were detected.

Molecular and genetic analysis of NS gene from high pathogenic strains of the avian influenza (H5N1) virus isolated in Kazakhstan.

The high pathogenic strains of the avian influenza H5N1 virus isolated in Kazakhstan have NS of different genotypes. The influenza virus strains isolated in 2005 is of NS1E Qinghai genotype. A/swan/Mangystau/3/2006 strain is of NS2A genotype that is typical for Gs/Gd-like strains. The results of the analysis allow assuming that A/swan/Mangystau/3/2006 strain has been brought onto the territory of Kazakhstan from the European part of the continent along the Black Sea-Mediterranean flyway.