Genotype data for 60 SNP genetic markers associated with eye, hair, skin color, ABO blood group, sex, core Y-chromosome haplogroups in Kazakh population.

OBJECTIVES: The collection of genotype data was conducted as an essential part of a pivotal research project with the goal of examining the genetic variability of skin, hair, and iris color among the Kazakh population. The data has practical application in the field of forensic DNA phenotyping (FDA). Due to the limited size of forensic databases from Central Asia (Kazakhstan), it is practically impossible to obtain an individual identification result based on forensic profiling of short tandem repeats (STRs). However, the pervasive use of the FDA necessitates validation of the currently employed set of genetic markers in a variety of global populations. No such data existed for the Kazakhs. The Phenotype Expert kit (DNA Research Center, LLC, Russia) was used for the first time in this study to collect data. DATA DESCRIPTION: The present study provides genotype data for a total of 60 SNP genetic markers, which were analyzed in a sample of 515 ethnic Kazakhs. The dataset comprises a total of 41 single nucleotide polymorphisms (SNPs) obtained from the HIrisPlex-S panel. Additionally, there are 4 SNPs specifically related to the AB0 gene, 1 marker associated with the AMELX/Y genes, and 14 SNPs corresponding to the primary haplogroups of the Y chromosome. The aforementioned data could prove valuable to researchers with an interest in investigating genetic variability and making predictions about phenotype based on eye color, hair color, skin color, AB0 blood group, gender, and biogeographic origin within the male lineage.

Lethal pulmonary embolism in a pregnant woman with severe acute respiratory syndrome coronavirus-2 receiving prophylactic anticoagulation: a case report.

BACKGROUND: A limited number of studies have described thrombotic complications in pregnant women with COVID-19. Here we report on fatal pulmonary embolism in a pregnant woman with laboratory confirmed SARS-CoV-2 infection. CASE PRESENTATION: A 28-year-old Kazakh woman was hospitalized with muscle pain, dry cough and a temperature of 37.5 °C at the 29th week of gestation. Upon admission, a blood test demonstrated elevated neutrophil-to-lymphocyte ratio, decreased levels of erythrocytes and hemoglobin, as well as prolonged prothrombin and activated partial thromboplastin time. Within 14 days of admission, she experienced respiratory distress and underwent transfer to the intensive care unit, intubation and a cesarean section. The patient received intravenous antibiotics, antiviral medications, systemic corticosteroids and dual anticoagulation with aspirin and enoxaparin. Death outcome was reported on day 18 of illness despite aggressive supportive care. Histological analysis demonstrated that obstruction of the main pulmonary arthery and disseminated intravascular coagulation were the causes of death. CONCLUSIONS: This case demonstrates that in the management of pregnancy and childbirth in patients with suspected or confirmed COVID-19 infection, special attention should be paid to coagulation system parameters and timely appropriate prophylaxis of thromboembolic complications, which has yet to be determined.

Molecular detection and characterization of bovine viral diarrhea virus type 2 and bluetongue virus 9 in forest flies (Hippobosca equina) collected from livestock in southern Kazakhstan.

Keds are hematophagous ectoparasites of animals belonging to the family Hippoboscidae (Diptera: Hippoboscoidea). Because of their importance as vectors of some pathogens of medical and veterinary importance, they have received special attention. There are numerous studies demonstrating the presence of various parasites and pathogenic bacteria in keds. At the same time, there are very few reports on ked-related viruses. The aim of this study was to perform a molecular survey of viral pathogens in the forest fly (Hippobosca equina) from southern Kazakhstan. In this study, 104H. equina were collected from livestock in Turkistan oblast (southern region of Kazakhstan), which has the largest concentration of livestock in the country. Insect homogenates were screened by PCR for pestiviruses, orbiviruses, flaviviruses, orthobunyaviruses, phleboviruses, orthopoxviruses, capripoxviruses, parapoxviruses, and asfiviruses. The causative agents of two livestock diseases, bovine viral diarrhea virus (BVDV) (3/104; 2.88%; 95% confidence interval (CI): 0.6-8.2%) and bluetongue virus (BTV) (1/104; 0.96%; 95% CI: 0.02-5.24%), were identified and subjected to further analysis. The BTV strain was isolated and all ten genomic RNA segments were sequenced using the Sanger technique. The isolated BTV strain showed >99.6% identity in all genomic segments with the BTV-9 strains belonging to the 'western' topotype. Partial analysis of the 5'-untranslated region demonstrated that both BVDV strains are closely related to Pestivirus B. Flaviviruses, phleboviruses, orthobunyaviruses, poxviruses, and asfiviruses were not detected. This is the first report describing BVDV type 2 in Kazakhstan. The study also confirms the presence of BTV serotype 9 in southern Kazakhstan. The data presented here can help improve preventive measures to control the spread of viral diseases in livestock by using forest flies as an object of epidemiological studies. However, further studies are needed to investigate the vector capacity of H. equina and its suitability for xenodiagnosis of veterinary relevant pathogens.

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.

Molecular and serological survey of bovine viral diarrhea virus infection in cattle in Kazakhstan.

The aim of this study was to estimate the occurrence of bovine viral diarrhea virus (BVDV) infection and to assess the population immunity in cattle vaccinated against BVDV in different regions of Kazakhstan. Cattle samples were collected in 12 oblasts (43 districts) of Kazakhstan. A total of 2477 cattle from 114 herds and 21 Bukhara deer (Cervus elaphus bactrianus) were examined by ELISA and conventional RT-PCR. Univariate and multivariate logistic regression analysis was performed to identify risk factors associated with BVDV infection in the country. In total, antibodies against BVDV were found in 79.3% (1965/2477) of all the animals and 92.1% (105/114) of all the herds examined. Seroprevalence in unvaccinated and vaccinated animals was 48.6% (447/920) and 98.7% (1391/1410), respectively. Seroprevalence in deer was 19.1% (4/21). The BVDV RNA was detected in six unvaccinated cattle (0.2%). Sequence analysis of the 5'-untranslated region demonstrated that four of the detected strains belonged to BVDV-1 and two strains to BVDV-2. Regression analysis revealed that age, production type, housing method, farm size, and geographic location were risk factors for BVDV infection in cattle in Kazakhstan. The present data confirm circulation of BVDV-1 and BVDV-2 in Kazakhstan and highlight the need to improve strategies for prevention and control of BVDV infection in the country.

Prevalence and genetic diversity of coronaviruses, astroviruses and paramyxoviruses in wild birds in southeastern Kazakhstan.

Wild birds are natural reservoirs of many emerging viruses, including some zoonoses. Considering that the territory of Kazakhstan is crossed by several bird migration routes, it is important to know pathogenic viruses circulating in migratory birds in this region. Therefore, the aim of this study was to identify the host range, diversity and spatial distribution of avian paramyxoviruses, coronaviruses, and astroviruses in free-ranging wild birds in the southeastern region of Kazakhstan. For this purpose, we collected tracheal and cloacal swabs from 242 wild birds belonging to 51 species and screened them using conventional PCR assays. Overall, 4.1% (10/242) and 2.9% (7/242) of all examined birds tested positive for coronaviruses and astroviruses, respectively. Coronaviruses were found in the orders Pelecaniformes (30%; 3/10), Charadriiformes (30%; 3/10), Columbiformes (20%; 2/10), Anseriformes (10%; 1/10), and Passeriformes (10%; 1/10). All detected strains belonged to the genus Gammacoronavirus. Astroviruses were detected in birds representing the orders Passeriformes (57%; 4/7), Coraciiformes (14%; 1/7), Charadriiformes (14%; 1/7), and Columbiformes (14%; 1/7). Paramyxoviruses were observed in only two birds (0.8%; 2/242). Both strains were closely related to the species APMV-22, which had not been previously detected in Kazakhstan. Phylogenetic analysis of the partial RdRp gene sequences of the virus strains revealed three different clades of astroviruses, two clades of coronaviruses, and one clade of paramyxoviruses. The results of this study provide valuable information on the diversity and spatial distribution of paramyxoviruses, coronaviruses, and astroviruses in wild birds in southeastern Kazakhstan and highlight the importance of further thorough monitoring of wild birds in this region.

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.

Building Scientific Capability and Reducing Biological Threats: The Effect of Three Cooperative Bio-Research Programs in Kazakhstan.

Cooperative research programs aimed at reducing biological threats have increased scientific capabilities and capacities in Kazakhstan. The German Federal Foreign Office's German Biosecurity Programme, the United Kingdom's International Biological Security Programme and the United States Defense Threat Reduction Agency's Biological Threat Reduction Program provide funding for partner countries, like Kazakhstan. The mutual goals of the programs are to reduce biological threats and enhance global health security. Our investigation examined these cooperative research programs, summarizing major impacts they have made, as well as common successes and challenges. By mapping various projects across the three programs, research networks are highlighted which demonstrate best communication practices to share results and reinforce conclusions. Our team performed a survey to collect results from Kazakhstani partner scientists on their experiences that help gain insights into enhancing day-to-day approaches to conducting cooperative scientific research. This analysis will serve as a basis for a capability maturity model as used in industry, and in addition builds synergy for future collaborations that will be essential for quality and sustainment.

Monitoring of pathogenic Borrelia burgdorferi sensu lato in the Almaty oblast, Kazakhstan.

Lyme borreliosis (LB) is one of the most common vector-borne diseases transmitted by ticks. It is caused by the Borrelia burgdorferi sensu lato (s.l.) genospecies. The Almaty oblast of Kazakhstan is considered endemic for LB. Nevertheless, there are significant gaps in the tick surveillance for LB agents in the region. We evaluated B. burgdorferi s.l. prevalence in 413 ixodid ticks collected from bitten people and the seroprevalence of antibodies to B. burgdorferi s.l. in 589 residents of the Almaty oblast, Kazakhstan. All samples were collected between 2018 and 2020. Borrelia burgdorferi s.l. DNA was detected in 24 % (9/38) of I. persulcatus ticks that attacked humans in the city of Almaty and the Talgar and Karasay districts. Multilocus sequence typing identified two novel B. afzelii sequence types in I. persulcatus. The seroprevalence of IgG antibodies against B. burgdorferi s.l. in the analyzed population was detected to be 5.8 %. The obtained results confirm active circulation of B. burgdorferi s.l. in the Almaty oblast of Kazakhstan and raise concern regarding LB preventive measures in the region.

The prevalence of Borrelia in Ixodes persulcatus in southeastern Kazakhstan.

Borreliosis is one of the most common vector-borne zoonotic diseases in the world. Limited data are available regarding Borrelia spp. and their genotypes in Kazakhstan. The goal of this study was to investigate the prevalence of Borrelia spp. in ixodid ticks collected in the southeastern region of Kazakhstan. A total of 1907 ixodid ticks were collected by flagging vegetation at three collection areas in the Almaty oblast between 2015 and 2018. They were grouped into 407 pools and examined by qPCR for Borrelia burgdorferi sensu lato (s.l.). A conventional PCR with specific primers targeting 16S rRNA gene was used to differentiate B. burgdorferi s.l. genospecies. Sequence analysis of the PCR products was performed for sixteen samples. Lyme borreliosis agents were only detected in adult questing Ixodes persulcatus. The overall B. burgdorferi s.l. prevalence in I. persulcatus estimated as the minimum infection rate reached 10.7 %. Borrelia burgdorferi sensu stricto was not detected in any of the tick pools. Partial 16S rRNA gene sequencing revealed the presence of B. miyamotoi, B. afzelii, and B. garinii. Borrelia afzelii was the dominant genospecies in Almaty oblast. A significantly lower proportion of B. garinii positive tick pools was detected in the Zailiyskiy Alatau as compared to the Dzungarian Alatau (χ2 = 16.243; p = 0.0001) and Yenbekshikazakh district (χ2 = 7.4156; p = 0.0065). The obtained results indicate the epidemiological significance of B. afzelii and B. garinii in southeastern Kazakhstan. These new data aim to improve the diagnostics of Lyme borreliosis and monitoring of tick-borne infections in Kazakhstan.

Tick-borne pathogens and their vectors in Kazakhstan - A review.

Tick-borne diseases (TBDs), in particular Crimean-Congo hemorrhagic fever (CCHF) and tick-borne encephalitis (TBE), have been found to be expanding beyond their traditional geographic locations in Kazakhstan, which led to increased awareness and concern against TBDs in recent years. The tick fauna of Kazakhstan includes more than 30 species of human-biting ixodid ticks, recognized as carriers of a number of dangerous infectious pathogens that cause CCHF, TBE, tularemia, tick-borne rickettsioses and Lyme borreliosis. This paper presents the current knowledge of the main vectors of tick-borne pathogens (TBP) occurring in Kazakhstan, as well as a review of recent studies of ticks performed with the use of molecular methods being currently developed and widely utilized by Kazakh epidemiologists.

Mycobacterium tuberculosis RD-Rio Strain in Kazakhstan.

Mycobacterium tuberculosis RD-Rio strains are still rare in the former Soviet Union countries and Asia. We describe a strain in Kazakhstan that belongs to the RD-Rio secondary branch, which is endemic to northwest Russia and eastern Europe. Although RD-Rio strains are frequently multidrug resistant, this heterogeneous branch included only drug-susceptible isolates.

A biolistic method for high-throughput production of transgenic wheat plants with single gene insertions.

BACKGROUND: The relatively low efficiency of biolistic transformation and subsequent integration of multiple copies of the introduced gene/s significantly complicate the genetic modification of wheat (Triticum aestivum) and other plant species. One of the key factors contributing to the reproducibility of this method is the uniformity of the DNA/gold suspension, which is dependent on the coating procedure employed. It was also shown recently that the relative frequency of single copy transgene inserts could be increased through the use of nanogram quantities of the DNA during coating. RESULTS: A simplified DNA/gold coating method was developed to produce fertile transgenic plants, via microprojectile bombardment of callus cultures induced from immature embryos. In this method, polyethyleneglycol (PEG) and magnesium salt solutions were utilized in place of the spermidine and calcium chloride of the standard coating method, to precipitate the DNA onto gold microparticles. The prepared microparticles were used to generate transgenics from callus cultures of commercial bread wheat cv. Gladius resulting in an average transformation frequency of 9.9%. To increase the occurrence of low transgene copy number events, nanogram amounts of the minimal expression cassettes containing the gene of interest and the hpt gene were used for co-transformation. A total of 1538 transgenic wheat events were generated from 15,496 embryos across 19 independent experiments. The variation of single copy insert frequencies ranged from 16.1 to 73.5% in the transgenic wheat plants, which compares favourably to published results. CONCLUSIONS: The DNA/gold coating procedure presented here allows efficient, large scale transformation of wheat. The use of nanogram amounts of vector DNA improves the frequency of single copy transgene inserts in transgenic wheat plants.

Molecular snapshot of Mycobacterium tuberculosis population in Kazakhstan: a country-wide study.

Republic of Kazakhstan is among the 27 high multidrug-resistant tuberculosis (MDR-TB) burden countries in the world. Here, we analyzed the population structure and phylogeography of Mycobacterium tuberculosis in Kazakhstan and impact of the identified genotypes on spread of drug resistant strains. A total of 159 M. tuberculosis isolates from different regions of Kazakhstan were typed using 24-MIRU-VNTR and spoligotyping, and the profiles were compared to the MIRU-VNTRplus and SITVIT_WEB databases. Eight isolates with double VNTR alleles were excluded from further analysis that was performed on 151 isolates. They were assigned to 10 families, Beijing (n = 109) being the largest and dominated by a single clonal cluster 94-32 and derived profiles (n = 101). The other families were represented mainly by LAM (n = 17), Ural (n = 8), NEW-1 (n = 3) and a new cluster named KAZ-1 (n = 8). Beijing, LAM and Ural isolates were detected in all parts of the country while Iran-specific family NEW-1 was found only in southern Kazakhstan (P = 0.001). A reduced scheme of 10 most polymorphic VNTR loci provided a discrimination similar to that achieved by 15-MIRU scheme and may be recommended for rapid preliminary screening of the clinical isolates in Kazakhstan. Multi-drug resistance was significantly more prevalent among Beijing (64/109) and LAM (7/17) strains compared to strains of other families (1/25; P = 0.0006 and 0.01, respectively). High prevalence of the genetically closely related MDR strains of the Beijing genotype found in different regions of Kazakhstan highlights their crucial impact on the current TB epidemic in this country.