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.

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 analysis at different dates of the epizootic. It was found that the influenza outbreak was associated with a high concentration of migrating birds at Lake Karakol as a result of a sharp cold snap in the northern regions. At different dates of the epizootic, three avian influenza A/H5N1 viruses of clade 2.3.4.4.b were isolated from dead birds and identified as highly pathogenic viruses (HPAIs) based on the amino acid sequence of the hemagglutinin multi-base proteolytic cleavage site (PLREKRRRKR/G). A phylogenetic analysis showed that the viruses isolated from the swans had reassortations in the PB2, PB1, and NP genes between highly pathogenic (HP) and low-pathogenic (LP) avian influenza viruses. Avian influenza viruses A/Cygnus cygnus/Karakol lake/01/2024(H5N1) and A/Mute swan/Karakol lake/02/2024(H5N1) isolated on 10 January 2024 received PB2, PB1, and NP from LPAIV, while A/Mute swan/Mangystau/9809/2023(H5N1) isolated on 26 December 2023 received PB1 and NP from LPAIV, indicating that the H5N1 viruses in this study are new reassortants. All viruses showed amino acid substitutions in the PB2, PB1, NP, and NS1 segments, which are critical for enhanced virulence or adaptation in mammals. An analysis of the genomes of the isolated viruses showed that bird deaths during different periods of the epizootic were caused by different reassortant viruses. Kazakhstan is located at the crossroads of several migratory routes of migratory birds, and the possible participation of wild birds in the introduction of various pathogens into the regions of Kazakhstan requires further study.

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.

Wild migratory birds are a major contributor to the epidemic outbreaks of West Nile Fever (WNF). WNF acquired particular relevance after many large epidemic outbreaks that took place in the late 90s in some countries in Europe, the Middle East, and the United States. These events were characterized by a high proportion of cases with lesions of the central nervous system (in the form of meningitis and encephalitis) and the mortality rate reached 10%. WNF belongs to the Flaviviridae family, the Flavivirus genus, and is part of the antigenic complex of Japanese encephalitis, to which the viruses Alfai, Katsi- pakore, Koutango, Usutu, Japanese encephalitis, St. Louis encephalitis, and the Murray Valley belong. Following the classification of microorganisms pathogenic for humans, WNF belongs to the II group of pathogenicity. In this regard, in the territory of the Republic of Kazakhstan, monitoring of reservoirs of the West Nile virus among wild birds is carried out. We used 230 samples of cloacal washings from wild birds of Sorbulak Lake in Almaty region, small lakes in North Kazakhstan region, ornithological station “Shakpak” in Zhambyl region. West Nile virus was detected in two samples from wild birds of the families Hirun- dinidae and Sylviidae, respectively, from barn swallows (Hirundo rustica) and chiffchaffs (Phylloscopus collybitus), living in the vicinity of the Shakpak ornithological station of Zhambyl region. Biological samples from barn swallows (Hirundo rustica) and chiffchaffs (Phylloscopus collybitus) tested positive for West Nile virus by RT-PCR. Key words: West Nile fever, arbovirus, wild birds, PCR, RNA.

Для тестирования и диагностики обычных и новых вирусов в клинических вирусологических лабораториях требуется экономичный, точный и быстрый анализ. Нами подобраны и сконструированы олигонуклеотиды для выявления вируса гриппа типа А и коронавируса SARS-CoV-2 с применением ОТ-ПЦР-анализа. Создание отечественных тест-систем для диагностики вируса гриппа А и SARS-CoV-2 является острой задачей и обусловлено необходимостью ранней диагностики заболеваний. Целью данного исследования является подбор праймеров и зондов для диагностики гриппа А и SARS-CoV-2 методом ОТ-ПЦР в реальном времени (ОТ-ПЦР РВ). В работе представлены результаты конструирования праймеров и зондов для постановки ОТ-ПЦР РВ для идентификации РНК вирусов гриппа А и SARS-CoV-2. В наших исследованиях по подбору специфических праймеров и зондов в качестве гена мишени для обнаружения вируса гриппа А был выбран М-ген, вируса SARS-CoV-2 — RdRp. Были подобраны и синтезированы пары олигонуклеотидных праймеров для гриппа А: InfM2 F и InfM2 R, а также зонд InfM2 Probe, а для SARS-CoV-2 — RdRp-1 F и RdRp-2 R, зонд RdRp-2 Probe, которые при постановке ОТ-ПЦР РВ с рабочей концентрацией 20 пмоль показали высокую эффективность при выявлении вируса гриппа А и SARS-CoV-2. Подбор праймеров проведен с использованием компьютерных программ PrimerBlast и VectorNTI. Конструированные праймеры и зонды в дальнейшем будут использованы при создании отечественной мультиплексной ОТ-ПЦР РВ тест-системы.

COVID-19 became a true medication target worldwide due to its pandemic scale in 2020. Viral infections are generally hard to cope with, especially, if the viral load and spreading speed seriously surpass the immune reaction, both innate and adaptive. Thus, only relatively few drugs were used clinically to stop either in the early stages of viral reproduction like with the help of Tenvir (Tenofovir) or vaccination to gain collective immunity in a particular population. None of the interferon-based drugs showed clear medical effects in medical trials and during pandemic hospitalization protocols. However, purine-analogs like Tenvir and others showed sustainable survival and recovery rates among SARS-COV-2 virus-infected patients at moderate and severe stages of pneumonia caused by this virus. This article reveals the invitro testing of the Tenvir drug on virus strain, Variant B.1.1, Sampled from Kazakhstan and molecular-genetic characterization of NSP12 (non-structural protein 12) located in ORF1b region of the SARS-COV 2 genome. Tenvir or tenofovir was broadly used against HIV infection and this study shows a sufficient effect on viral spread due to RdRP-inhibiting properties in-vitro.