Molecular Characterisation and Phylogeny of Tula Virus in Kazakhstan.

Orthohantaviruses are zoonotic pathogens that play a significant role in public health. These viruses can cause haemorrhagic fever with renal syndrome in Eurasia. In the Republic of Kazakhstan, the first human cases were registered in the year 2000 in the West Kazakhstan region. Small mammals can be reservoirs of orthohantaviruses. Previous studies showed orthohantavirus antigens in wild-living small mammals in four districts of West Kazakhstan. Clinical studies suggested that there might be further regions with human orthohantavirus infections in Kazakhstan, but genetic data of orthohantaviruses in natural foci are limited. The aim of this study was to investigate small mammals for the presence of orthohantaviruses by molecular biological methods and to provide a phylogenetic characterization of the circulating strains in Kazakhstan. Small mammals were trapped at 19 sites in West Kazakhstan, four in Almaty region and at seven sites around Almaty city during all seasons of 2018 and 2019. Lung tissues of small mammals were homogenized and RNA was extracted. Orthohantavirus RT-PCR assays were applied for detection of partial S and L segment sequences. Results were compared to published fragments. In total, 621 small mammals from 11 species were analysed. Among the collected small mammals, 2.4% tested positive for orthohantavirus RNA, one sample from West Kazakhstan and 14 samples from Almaty region. None of the rodents caught in Almaty city were infected. Sequencing parts of the small (S) and large (L) segments specified Tula virus (TULV) in these two regions. Our data show that geographical distribution of TULV is more extended as previously thought. The detected sequences were found to be split in two distinct genetic clusters of TULV in West Kazakhstan and Almaty region. TULV was detected in the common vole (Microtus arvalis) and for the first time in two individuals of the forest dormouse (Dryomys nitedula), interpreted as a spill-over infection in Kazakhstan.

First Indications of Omsk Haemorrhagic Fever Virus beyond Russia.

Omsk haemorrhagic fever virus (OHFV) is the agent leading to Omsk haemorrhagic fever (OHF), a viral disease currently only known in Western Siberia in Russia. The symptoms include fever, headache, nausea, muscle pain, cough and haemorrhages. The transmission cycle of OHFV is complex. Tick bites or contact with infected small mammals are the main source of infection. The Republic of Kazakhstan is adjacent to the endemic areas of OHFV in Russia and febrile diseases with haemorrhages occur throughout the country-often with unclear aetiology. In this study, we examined human cerebrospinal fluid samples of patients with suspected meningitis or meningoencephalitis with unknown origins for the presence of OHFV RNA. Further, reservoir hosts such as rodents and ticks from four Kazakhstan regions were screened for OHFV RNA to clarify if this virus could be the causative agent for many undiagnosed cases of febrile diseases in humans in Kazakhstan. Out of 130 cerebrospinal fluid samples, two patients (1.53%) originating from Almaty city were positive for OHFV RNA. Screening of tick samples revealed positive pools from different areas in the Akmola region. Of the caught rodents, 1.1% out of 621 were positive for OHFV at four trapping areas from the West Kazakhstan region. In this paper, we present a broad investigation of the spread of OHFV in Kazakhstan in human cerebrospinal fluid samples, rodents and ticks. Our study shows for the first time that OHFV can not only be found in the area of Western Siberia in Russia, but can also be detected up to 1.600 km away in the Almaty region in patients and natural foci.

Tick-borne encephalitis virus and West-Nile fever virus as causes of serous meningitis of unknown origin in Kazakhstan.

Flaviviruses are a family of viruses that cause many diseases in humans. Their similarity in the antigenic structure causes a cross-reaction, which complicates the precise diagnostic of disease causing agents. Tick-borne encephalitis virus (TBEV), a member of the flavivirus family, is the cause of tick-borne encephalitis (TBE). Worldwide the awareness of this disease is raising, however, in many countries such as the Republic of Kazakhstan (KZ) there is a lack of serological investigation of flaviviruses in humans. In our study, we focused on two TBE endemic regions of KZ (East Kazakhstan Oblast (EKO) and Almaty (AO)) and a region where TBE cases were registered only since 2010 (Akmola Oblast (AkO)). In KZ, up to 400 cases of serous meningitis of unknown origin were registered annually in the period from 2017 to 2019. Our goals were to calculate the prevalence of antibodies against TBEV in patients with suspected meningitis. We collected 179 sera and 130 cerebrospinal fluid (CSF) samples from patients and included a questionnaire with focus on socio-demographical factors and observed tick bites. The human samples were tested with TBEV and West-Nile fever virus (WNFV) IgM and IgG ELISA, by immunofluorescence assay using a flavivirus biochip, and TBEV-specific real-time RT-PCR. We found TBEV and WNFV antibodies in 31 samples by serological and molecular techniques. Seven serum samples out of 31 showed TBEV-specific antibodies, and three serum pairs had WNFV antibodies. Correlating the serological results with the information gained from the questionnaires it becomes apparent that the number of tick bites is a significant factor for a TBEV infection. This result has an impact on diagnostic in KZ and physicians should be aware that both flaviviruses play a role for serous meningitis of unknown origin in KZ.

Vectors, molecular epidemiology and phylogeny of TBEV in Kazakhstan and central Asia.

BACKGROUND: In the South of Kazakhstan, Almaty Oblast' (region) is endemic for tick-borne encephalitis, with 0.16-0.32 cases/100,000 population between 2016-2018. The purpose of this study was to determine the prevalence and circulating subtypes of tick-borne encephalitis virus (TBEV) in Almaty Oblast' and Kyzylorda Oblast'. METHODS: In 2015 we investigated 2341 ticks from 7 sampling sites for the presence of TBEV. Ticks were pooled in 501 pools and isolated RNA was tested for the presence of TBEV by RT-qPCR. For the positive samples, the E gene was amplified, sequenced and a phylogenetic analysis was carried out. RESULTS: A total of 48 pools were TBEV-positive by the RT-qPCR. TBEV-positive ticks were only detected in three districts of Almaty Oblast' and not in Kyzylorda Oblast'. The positive TBEV pools were found within Ixodes persulcatus, Haemaphysalis punctata and Dermacentor marginatus. These tick species prevailed only in Almaty Oblast' whereas in Kyzylorda Oblast' Hyalomma asiaticum and D. marginatus are endemic. The minimum infection rates (MIR) in the sampling sites were 4.4% in Talgar, 2.8% in Tekeli and 1.1% in Yenbekshikazakh, respectively. The phylogenetic analysis of the generated sequences indicates that TBEV strains found in Almaty Oblast' clusters in the Siberian subtype within two different clades. CONCLUSIONS: We provided new data about the TBEV MIR in ticks in Almaty Oblast' and showed that TBEV clusters in the Siberian Subtype in two different clusters at the nucleotide level. These results indicate that there are different influences on the circulating TBEV strains in south-eastern Kazakhstan. These influences might be caused by different routes of the virus spread in ticks which might bring different genetic TBEV lineages to Kazakhstan. The new data about the virus distribution and vectors provided here will contribute to an improvement of monitoring of tick-borne infections and timely anti-epidemic measures in Kazakhstan.

Phylogenetic Characteristics of West Nile Virus Isolated From Culex modestus Mosquitoes in West Kazakhstan.

West Nile virus is widespread in southern Russia, where the fever appears annually. Since Western Kazakhstan borders on southern Russia, we examined mosquitoes in this region for the presence of West Nile virus. Virus was detected in a small proportion of Culex modestus mosquitoes (3/239 pools) and isolates are related to strains from Volgograd, Russia. A screen for West Nile virus IgG was conducted and ~5% of the local human population tested positive.

Survey for Rickettsiae Within Fleas of Great Gerbils, Almaty Oblast, Kazakhstan.

Little is known of the endemicity of flea-borne rickettsiae in Kazakhstan. Thus, a survey for rickettsiae within great gerbil fleas was conducted in Almaty oblast. High prevalence of Rickettsia asembonensis was detected among Xenopsylla gerbilli, demonstrating that flea-borne rickettsiae are endemic to southeastern Kazakhstan. Interestingly, no Rickettsia typhi were detected in these same fleas.

Biosurveillance in Central Asia: Successes and Challenges of Tick-Borne Disease Research in Kazakhstan and Kyrgyzstan.

Central Asia is a vast geographic region that includes five former Soviet Union republics: Kazakhstan, Kyrgyzstan, Tajikistan, Turkmenistan, and Uzbekistan. The region has a unique infectious disease burden, and a history that includes Silk Road trade routes and networks that were part of the anti-plague and biowarfare programs in the former Soviet Union. Post-Soviet Union biosurveillance research in this unique area of the world has met with several challenges, including lack of funding and resources to independently conduct hypothesis driven, peer-review quality research. Strides have been made, however, to increase scientific engagement and capability. Kazakhstan and Kyrgyzstan are examples of countries where biosurveillance research has been successfully conducted, particularly with respect to especially dangerous pathogens. In this review, we describe in detail the successes, challenges, and opportunities of conducting biosurveillance in Central Asia as exemplified by our recent research activities on ticks and tick-borne diseases in Kazakhstan and Kyrgyzstan.

Crimean-Congo haemorrhagic fever virus in Kazakhstan (1948-2013).

Crimean-Congo haemorrhagic fever (CCHF) is a pathogenic and often fatal arboviral disease with a distribution spanning large areas of Africa, Europe and Asia. The causative agent is a negative-sense single-stranded RNA virus classified within the Nairovirus genus of the Bunyaviridae family. Cases of CCHF have been officially recorded in Kazakhstan since the disease was first officially reported in modern medicine. Serological surveillance of human and animal populations provide evidence that the virus was perpetually circulating in a local enzoonotic cycle involving mammals, ticks and humans in the southern regions of the country. Most cases of human disease were associated with agricultural professions such as farming, shepherding and fruit-picking; the typical route of infection was via tick-bite although several cases of contact transmission associated with caring for sick patients have been documented. In total, 704 confirmed human cases of CCHF have been registered in Kazakhstan from 1948-2013 with an overall case fatality rate of 14.8% for cases with a documented outcome. The southern regions of Kazakhstan should be considered endemic for CCHF with cases reported from these territories on an annual basis. Modern diagnostic technologies allow for rapid clinical diagnosis and for surveillance studies to monitor for potential expansion in known risk areas.