Tracing the Spatial Circulation of Yersinia pestis of Medieval Biovar in the Eastern Caspian Sea Region in the 20th Century Based on Genome-Wide SNP Analysis

A comprehensive analysis of the accumulated epidemiological and epizootiological data in combination with results from phylogenetic analysis of Yersinia pestis strains creates the basis for establishing patterns of spatialtemporal distribution of the plague pathogen and opens up the prospect of long-term forecasting of natural plague foci activation. Previously, we traced the distribution pathways of Y. pestis, medieval biovar, in the plague foci of the Northern and Northwestern Caspian Sea regions in the 20th and early 21st centuries.The purpose of this work was to identify the regularities of circulation of Y. pestis, medieval biovar, in four natural plague foci located in the Eastern Caspian Sea region.Materials and methods. A complex study of the phenotypic and genetic properties of 16 Y. pestis strains isolated in the Ustyurt, Mangyshlak, Karakum and Kopetdag autonomous desert plague foci in 1926–1985 was carried out. They were compared with strains from other natural plague foci in Eastern Europe and Central Asia obtained in 1917–2003. Whole-genome sequencing of 12 of those strains was performed. Phylogenetic analysis included the genomes of other 19 Y. pestis strains that we had sequenced earlier. Based on the 1717 polymorphic nucleotides (SNPs) identified in the core genome, a dendrogram of the relations of the studied strains was constructed.Results and discussion. All 16 Y. pestis strains from the Ustyurt, Mangyshlak, Kopetdag, and Karakum desert foci belong to the 2.MED1 branch of the medieval biovar. All investigated strains from the first three foci and most of the strains from the Karakum focus are in the Caspian 2.MED1 branch, and three strains from the Karakum desert focus are included in the Central Asian one. We have revealed several waves of dissemination of the strains under the 2.MED1 phylogenetic branch of Y. pestis of the medieval biovar in the Eastern Caspian Sea region in the 20th century

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

TUBERCULOSIS CONCURRENT WITH HIV INFECTION IN THE SIBERIAN FEDERAL DISTRICT IN 2010-2012

The authors analyze the epidemic situation associated with tuberculosis concurrent with HIV infection in the subjects of the Siberian Federal District (SFD) in 2010-2012. There was a further overall (1.4-fold) increase in the detection of coinfection in the district; at the same time the rate of its increase decreased as compared to the previous years. In spite of the lower incidence of tuberculosis in SFD in the years under study, the proportion of patients of HIV-associated tuberculosis increased in the structure of new cases. No stabilization of the epidemics of HIV infection makes unfavorable the prognosis of further spread of tuberculosis concurrent with HIV infection. The timely detection of patients with HIV infection, as well as antiretroviral therapy and adequate tuberculosis chemoprophylactic coverage of patients with already detected HIV infection will be able to reduce the tense epidemic situation

Sociodemographic characteristics of patients with pulmonary and extrapulmonary tuberculosis

The investigators retrospectively analyzed the demographic, social, and clinical structure of 197 patients with pulmonary tuberculosis treated at the Novosibirsk Research Institute of Tuberculosis, Ministry of Health, and 50 patients with prostatic tuberculosis and compared the indicators in question. The cohort was established to be considerably heterogeneous; gender differences were found in the pattern of pulmonary tuberculosis. Pulmonary tuberculosis was detected in nearly half (45.7%) of the patients during preventive examinations; bacterial excretion was found in 78.2% of the patients (82.6% of men and 71.1% of women). The patients with prostatic tuberculosis were ascertained to have a higher social well-being than those with pulmonary tuberculosis: the former had higher educational level and they were less prone to practice bad habits

Peripheral lymph node tuberculosis: its paradoxical course in a HIV-infected patient

Периферическая лимфатическая система инфицируется микобактерией туберкулеза (МБТ) во время лимфогенной диссеминации, но не у всех пациентов развивается клинически документированное поражение лимфоузлов