The First Case of Foot-and-Mouth Disease Caused by O/ME-SA/IND-2001 Virus in Kazakhstan

In Kazakhstan, foot-and-mouth disease (FMD) outbreaks were recorded in 2011–2013 in the southern and eastern regions where FMD vaccination is in place. In January 2022, in Kiikty village of the Shetsky district, Karaganda Region, Republic of Kazakhstan, cases among cattle clinically similar to foot-and-mouth disease were reported. The aim of the research was to establish the cause of the disease and to perform the typing of the pathogen. Materials and methods. Samples from sick animals were tested using PCR, sequenced and typed in compliance with the protocol developed by the International Office for Epizootic Diseases (OIE). Results and discussion. A cytopathogenic agent has been isolated from the BHK-21 cell culture, identified through real-time RT-PCR and electron microscopically as FMD virus. Molecular genetic studies have revealed that the infection of cattle in the Karaganda Region was caused by the FMD virus circulating in the territory of the countries bordering Kazakhstan (China, Russia, Mongolia) and belonging to type O, topotype ME-SA, genetic line Ind-2001. FMD virus isolated in Kazakhstan is genetically related to the FMD line from Asia and is a new FMDV genotype for Kazakhstan, assigned to the ME-SA topotype of the Ind-2001 genetic line. This study once again proves the need for continuous genetic typing of FMD viruses to improve the effectiveness of preventive measures

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

Comparative Evaluation of Effectiveness of IAVchip DNA Microarray in Influenza A Diagnosis

The paper describes comparative evaluation of IAVchip DNA microarray, reverse transcription PCR (RT-PCR), and real-time RT-PCR versus virus isolation in chicken embryos and shows their diagnostic effectiveness in detection and subtyping of influenza A virus. The tests were evaluated with use of 185 specimens from humans, animals, and birds. IAVchip DNA microarray demonstrates higher diagnostic effectiveness (99.45%) in early influenza A diagnosis as compared to the real-time PCR (98.38%) and RT-PCR (96.22%), thus showing its clear superiority. Diagnostic sensitivity of IAVchip DNA microarray (100%) exceeds the same of RT-PCR (95.95%) and real-time RT-PCR (97.96%) in the range of estimated confidence intervals. IAVchip DNA microarray and real-time RT-PCR displayed equal diagnostic specificity (98.85%), while diagnostic specificity of RT-PCR was 96.40%. IAVchip DNA microarray has an advantage over the other tests for influenza A diagnosis and virus identification as a more rapid method that allows performing simultaneous detection and subtyping of about tens of specimens within one experiment during 8–10 hours. The developed IAVchip DNA microarray is a general test tool that enables identifying simultaneously 16 hemagglutinin (HA) and 9 neuraminidase (NA) subtypes of influenza A virus and also to screen the influenza A viruses from humans, animals, and birds by M and NP genes

New oligonucleotide microarray for rapid diagnosis of avian viral diseases

Abstract 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

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

Opportunistic bacteria and mass mortality in ungulates: lessons from an extreme event

Mass mortality events in wildlife are a growing concern. Under conditions of rapid global change, opportunistic responses in bacterial commensals, triggered by environmental stressors, may be increasingly implicated in die-offs. In 2015, over 200,000 saiga antelope died of hemorrhagic septicemia caused by the pathogen Pasteurella multocida serotype B. We use this case to explore die-offs from commensal bacteria more broadly, looking at factors which might favor such extreme events. We review other recorded disease outbreaks caused by Pasteurellaceae organisms, firstly in saiga and secondly in other wild ungulates, and ask whether the 2015 die-off was unprecedented in terms of mortality rates, numbers dead and spatial scale, and in the nature of the predisposing or environmental factors involved. We also compare these outbreaks with mass mortality events associated with commensal bacteria in wildlife more generally. We identify three additional major die-offs in saiga in which Pasteurellaceae organisms may be implicated, of which one in 1988 closely resembles the 2015 hemorrhagic septicemia event. No other recorded cases in wild ungulates approach the magnitude of these cases for any of the metrics considered, possible exceptions being die-offs in Mongolian gazelles, in which the role of these pathogens is poorly substantiated. Environmental triggers were the most commonly suggested factor leading to pathogenesis, with warm humid conditions most commonly associated with hemorrhagic septicemia. Life history may also be significant – saigas are migratory and the largest pasteurellosis outbreaks outside this species also occur in migratory species of bird or other temperate ungulates aggregating in large numbers. Cases provoked by other commensals tend to be small in magnitude. Exceptions involve interactions between multiple pathogens and climatic conditions or sets of climatic conditions acting on different stages of the host-pathogen life cycle, leading to time lags between infection and subsequent disease. Overall, the scale and rapidity of the saiga die-offs appear unprecedented amongst mortality events caused by bacterial commensals in wild mammals. Experimental research into the genetics and micro-biology of host-pathogen interactions upon changes in the external environment, and monitoring of animals and conditions at calving sites, may eventually reveal the underlying causes of these die-offs