Background In the South of Kazakhstan, Almaty Oblastʼ (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 Oblastʼ and Kyzylorda Oblastʼ. 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 Oblastʼ and not in Kyzylorda Oblastʼ. The positive TBEV pools were found within Ixodes persulcatus, Haemaphysalis punctata and Dermacentor marginatus. These tick species prevailed only in Almaty Oblastʼ whereas in Kyzylorda Oblastʼ 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 Oblastʼ clusters in the Siberian subtype within two different clades. Conclusions We provided new data about the TBEV MIR in ticks in Almaty Oblastʼ 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.

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.

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.

and polyomavirus KI was most prevalent in adults 25-64 that died, which is the group most affected by HIV. No fatal cases due to the coronaviruses were detected in single infections in any age group. Influenza A and RSV was most detected in fatal cases in the elderly.Conclusion: Influenza, RSV, hMPV and rhinovirus infection is associated with severe respiratory disease in South Africa if compared to healthy controls. In fatal disease, rhinovirus and RSV may be true pathogens in children however in HIV positive adults the role of viruses such as KI polyomaviruses and Adenovirus needs further investigation.

To better understand the contribution of Rickettsia spp. to prevalent flea-borne diseases in Kazakhstan, we evaluated fleas collected in the Almaty Oblast of southeastern Kazakhstan for the presence of rickettsiae by quantitative real-time PCR (qPCR). We found that fleas captured from Kazakhstan’s common Great Gerbil (Rhombomys opimus) and corresponding burrows were infected with rickettsiae. The most commonly found rickettsia-infected flea species was Xenopsylla gerbilli, and the most commonly found rickettsia was Candidatus R. asemboensis. Further studies may include testing these and other fleas samples for the presence of additional disease agents, including Bartonella spp. and Yersinia pestis.