RT-qPCR investigation of post-mortem tissues during COVID-19.

In 2020, there were numerous cases in Kazakhstan with clinical symptoms of COVID-19 but negative PCR results in nasopharyngeal and oropharyngeal swabs. The diagnosis was confirmed clinically and by CT scans (computed tomography). The problem with such negative PCR results for SARS-CoV-2 infection confirmation still exists and indicates the need to confirm the diagnosis in the bronchoalveolar lavage in such cases. There is also a lack of information about confirmation of SARS-CoV-2 infection in deceased patients. In this study, various tissue materials, including lungs, bronchi, and trachea, were examined from eight patients who died, presumably from SARS-CoV-2 infection, between 2020 and 2022. Naso/oropharyngeal swabs taken from these patients in hospitals tested PCR negative for SARS-CoV-2. This study presents a modified RNA isolation method based on a comparison of the most used methods for RNA isolation in laboratories: QIAamp Viral RNA Mini Kit and TRIzol-based method. This modified nucleic acid extraction protocol can be used to confirm SARS-CoV-2 infection by RT-qPCR in the tissues of deceased patients in disputed cases. RT-qPCR with RNA of SARS-CoV-2 re-extracted with such method from post-mortem tissues that were stored at -80 °C for more than 32 months still demonstrated high-yielding positive results.

Molecular and seroepidemiological investigation of Сoxiella burnetii and spotted fever group rickettsiae in the southern region of Kazakhstan.

Ticks are involved in the circulation of a number of human pathogens, including spotted fever group (SFG) Rickettsia spp. and Coxiella burnetii. Little is known about the occurrence of these microorganisms in the southern region of Kazakhstan. In 2018-2022, a total of 726 ticks were collected from bitten humans, livestock, and vegetation in four oblasts of the southern region of Kazakhstan and subjected to DNA extraction. The overall infection rate of Coxiella spp. and Rickettsia spp. in the ticks was 3.3% (24/726) and 69.9% (300/429), respectively. Phylogenetic analysis of ompA and gltA genes revealed the presence of three pathogenic SFG rickettsiae: Candidatus R. tarasevichiae, R. aeschlimannii and R. raoultii in ticks collected from bitten humans. In addition, Candidatus R. barbariae was detected in six Rhipicephalus turanicus ticks for the first time in Kazakhstan. To determine the seroprevalence of C. burnetii infection, we performed a serological analysis of samples collected from 656 domestic ruminants (cattle, sheep, and goats) in the region. Overall, 23.5% (154/656) of the animals tested were positive for IgG against C. burnetii. Seroprevalence at the herd level was 54% (28/52). Goats (43%; 12/28; odds ratio (OD) = 28.9, p < 0.05) and sheep (31.9%; 137/430; OD = 18.1, p < 0.05) had higher seroprevalence than cattle (2.5%; 5/198). Among the risk factors considered in this study, age (p = 0.003) and the oblast in which the animals were sampled (p = 0.049) were statistically associated with seropostivity for Q fever in sheep, according to the results of multivariate logistic regression analysis. Seroprevalence ranged from 0% to 55.5% in animals in different districts of the southern region of Kazakhstan. Active C. burnetii bacteremia was detected in four of 154 (2.6%) seropositive animals. The data obtained provide strong evidence of the presence of pathogenic rickettsiae and C. burnetii in the southern region of Kazakhstan and emphasize the need to improve epidemiological surveillance in the region.

Genetic Polymorphism of 27 Y-STR Loci in the Western Kazakh Tribes from Kazakhstan and Karakalpakstan, Uzbekistan.

Data on the genetic polymorphism of 27 Y-STR in Kazakhs of the Junior Zhuz has been presented and analyzed in relation to forensic features. A total of 464 representatives of the Western Kazakh tribes of Kazakhstan (Western Kazakhs, n = 405) and Uzbekistan (Karakalpakstan Kazakhs, n = 59) were examined by the Yfiler Plus set. The data are available in the YHRD under accession numbers YA006010 and YA006009. Genetic analysis (AMOVA and MDS) did not show significant differences between the two groups (Kazakhstan and Karakalpakstan Kazakhs) in terms of Y-chromosome diversity. Both groups are characterized by haplogroup C2a1a2 as a founder effect, which dominated two of the three tribes: Alimuly (67%), Baiuly (74.6%), and Zhetiru (25.8%). At the same time, the phylogenetic network for each tribe found its own clusters within C2a1a2. Western Kazakhs and Karakalpakstan Kazakhs present high values of unique haplotypes (84.44% and 96.61%), discrimination capacity (90.37% and 98.30%), and haplotype diversity (0.9991 and 0.9994). A set of 27 Y-STR loci distinguishes closely related individuals within the Western Kazakh tribes quite well. It is suitable for forensic application, and is also optimal for population genetics studies.

Identification and characterization of bluetongue virus in Culicoides spp. and clinically healthy livestock in southeastern Kazakhstan.

OBJECTIVE: Bluetongue is an arthropod-borne disease of ruminants. Here, we investigated the seroprevalence of bluetongue virus (BTV) in livestock and performed the first genetic characterization of BTV isolated from sheep and Culicoides midges in the southeastern region of Kazakhstan. METHODS: Blood samples were collected from 1241 asymptomatic livestock. In addition, 497 Culicoides midges were collected. Samples were analyzed for specific anti-BTV antibodies and BTV RNA by ELISA and conventional RT-PCR, respectively. RESULTS: The overall seroprevalence of BTV antibodies was shown to be 4.3 % (46/1079) in small ruminant and 1 % (1/82) in cattle. Anti-BTV antibodies were not detected in camels (0/80). The minimum infection rate of BTV in Culicoides was shown to be 0.24 %. Seg-2 and Seg-10 sequence analysis demonstrated that all isolates belonged to the 'western' topotype of the BTV-9 strain. CONCLUSION: The present data confirm circulation of BTV in southeastern Kazakhstan.