Genetic Monitoring of Crimean-Congo Hemorrhagic Fever Virus in the South of the European Part of Russia

Presented are the results of gene-typing of CCHF virus detected in clinical samples from CHF patients from the Stavropol, Rostov and Astrakhan Regions in 2011. For 28 samples determined are nucleotide sequences of the fragments 115–652 (S segment) and fragments 984–1469 (M segment). Philogenetic analysis of these nucleotide sequences demonstrated that typical strains circulated in 2011 in the regions under surveillance, importation of the new genetic variants of the virus did not take place. CCHF virus variant affiliated to the subgroup “Astrakhan-2” was detected in the clinical samples for the first time and characterized for its genome S- and M-segment fragments

VNTR loci as indicators of proline-dependent plague microbe strains (Yersinia pestis) in the central caucasian mountain natural plague focus

Y. pestis MLVA typing is used both to seek for similarities and differences between individual isolates upon conducting epidemiological investigations as well as for clonal clustering of intraspecies phylogenetic groups while analyzing microevolution and taxonomy issues. It cannot be ruled out that the most variable loci may be indicators allowing to approximate the unique strain-related properties circulating in certain natural plague foci. The Central Caucasian Highland Natural Plague Focus distinguished by heterogeneity of the circulating strains therein, including proline pro- and auxo-trophy, may represent a convenient model for testing this hypothesis. The purpose of our work was to assess the frequencies of the VNTR alleles associated with proline dependence among the Y. pestis strain VNTR loci, determined during previous MLVA-25 typing in the Central Caucasian Highland Natural Plague Focus. The main task was to identify the most informative sets of VNTR loci suitable for predicting proline pro— and auxotrophy (pro+, pro—). It was found that the loci ms45, ms56, ms46, ms07, ms69, ms62 displayed peak variability by allele frequencies and/or exhibited significant differences of mean allele frequencies in the pro— and pro+ strains. In particular, it was showed that the alleles of the ms45 locus contained 6 tandem repeats suggesting probability for pro+ reaching 0.944, whereas the alleles of the ms45 locus contained 7 tandem repeats with expected probability for pro— reaching 0.783. Moreover, the ms56 and ms46 contained 9 and more than 18 tandem repeats, respectively, thereby pointing at probability for pro+ equal to 0.933 and 0.818, respectively. Diagnostics for pro+/pro— phenotype by using specific statistical methods demonstrated statistical error 13.33% and 26.67% for the pro— and pro+ strains, respectively. All pro+ strains bearing a 6 tandem repeat complex from the ms45 locus, 9 tandem repeats derived from the ms56 locus and ms46 locus-derived 29—30 tandem repeats were accurately diagnosed solely based on these 3 loci. Thus, it is possible to predict some properties of Y. pestis strains based on determining the allele frequencies. While the number of MLVA typed plaque strains isolated in such natural focus has been progressively increased, it may be expected that opportunities for prognosing their properties based on determining locus tandem repeat composition having diagnostic value would be elevated

COVID-19 as a zoonotic infection

Here we discuss the issues for attributing the new coronavirus infection COVID-19 to zoonoses based on the data on probable origin of the SARS-CoV-2 virus, the possible formation of its reservoir in animals (bats) as well as human susceptibility. Today, the dominant point of view is that the outbreak of COVID-19 arose as a result of the SARS-CoV-2 coronavirus overcoming the interspecies barrier, acquiring ability to infect and spread in human population. Comparative phylogenetic analysis at the molecular level showed that SARS-CoV-2 is genetically closest to bat coronaviruses, particularly to the RmYN02 and RaTG13 strains isolated from the horseshoe bat, a species considered to be the main host of SARSCoV and MERS-CoV coronaviruses. The ability of the SARS-CoV-2 coronavirus to infect various wild animal has been revealed. SARS-CoV-2 has been found in minks on farms in the Netherlands with mortality rates ranging from 1.2 to 2.4%. While infecting rhesus monkeys with the SARS-CoV-2, it resulted in productive infection and detected viremia. Cats have been found to be susceptible hosts for the human SARS-CoV-2 virus. A likely explanation for this lies in the high similarity between the human and feline counterpart of the ACE2 receptor. It has been shown that dogs can become infected but transmit no virus to other animals. To date, over the entire period of the pandemic the World Organization for Animal Health provides no information about cases of human infection transmitted from pets. Thus, there is no evidence that animals play a role in the spread of SARS-CoV-2 among people during the current period of the pandemic. Human outbreaks are caused by human-to-human virus transmission, and based on the currently available information, the risk of spreading COVID-19 from animals is considered low. More research is needed to understand how COVID-19 can affect animals of a wide variety of species and how big might be the risks of infection transmission from them to humans

EPIDEMIOLOGICAL SITUATION ON CRIMEAN HEMORRHAGIC FEVER IN THE RUSSIAN FEDERATION IN 2016, AND PROGNOSIS FOR 2017

Abstract. This paper presents analysis of epidemiological situation on Crimean hemorrhagic fever (CHF) in Russia in 2016. Summarized are the results of epizootiological survey of the territory of the natural CHF focus in the south of the European part of Russia, discussed are the results of genetic typing of CCHFV RNA isolates. In 2016, the Russian Federation reported 162 cases of CHF. Increase in the incidence of CHF occurred in the Astrakhan, Volgograd Regions, Republic of Kalmykia, and Stavropol Territory. For the first time CHF case was identified in Kabardino-Balkar Republic. In 2016 in stationary points for the long-term observation of the natural CHF focus, high abundance rates of larvae and nymphs of H. marginatum remain. In case of successful Ixodidae ticks wintering and late onset of the hot and dry season in the summer, 2017, there is probability that high numbers of H. marginatum will be retained and the period of the imago activity is prolonged, which may in its turn  contribute to the increase in CHF morbidity rates

Infection Rate in the Population of Ticks <em>Hyalomma marginatum</em> in the Territory of the Crimean Hemorrhagic Fever (CHF) Natural Focus and Assessment of the Link with the CHF Incidence in the Stavropol Region

Objective of the study was to assess the infection rate in the population of the main CCHF virus vector Hyalomma marginatum and its impact on the CHF incidence in the Stavropol Region.Materials and methods. The data on spontaneous infection of H. marginatum ticks in the territory of the CHF natural focus in the Stavropol Region for the period 2012–2018 are presented. In total, more than 22.000 H. marginatum specimens pooled in 1546 samples were tested. The indication of CCHF virus was performed by PCR method using the reagent set for detecting RNA of the CCHF virus “AmplySens® CCHFV-FL” (produced by Central Research Institute of Epidemiology, Russia). To determine the individual infection rate in pools Beklemishev`s method was used. The data on CCHF incidence and amount of tick-bitten persons are taken from official statistics and Annual Epidemiological Report on CHF Incidence provided by the Rospotrebnadzor Administration in the Stavropol Region for the period of 2012–2018.Results and discussion. RNA of CCHF virus was detected in 161 (10.4 %) out of 1546 pooled ticks. The highest infection rate (20 %) was among nymphs. The infection rate for pooled males of H. marginatum was 11 % and for females – 8.5 %. Circulation of Crimean-Congo hemorrhagic fever virus is confirmed in major part of the Stavropol Region. The average infection rate among H. marginatum population was 1.54 % for the period of 2012–2018, ranging from 0.23 % in 2014 to 2.97 % in 2017. It is established that the level of infection rate among H. marginatum population does not affect the CHF incidence in the Stavropol Region. Probably it is not the number of infected ticks in the population that determines the CHF incidence rate but their abundance

Epidemiological Situation on Crimean-Congo Hemorrhagic Fever in the Russian Federation in 2012 and Prognosis for 2013

Represented is epidemiological evaluation of the morbidity rate as regards Crimean-Congo hemorrhagic fever (CCHF) in Russia in 2012. Summarized are the results of epizootiological surveillance over the territory of CHF natural focus in the South of European part of Russia. Forecast of CCHF epidemiological situation development for 2013 is made based on the epizootiological monitoring data

Genetic Profiling of the Causative Agents of Natural-Focal infections, Circulating in the Stavropol Territory

Objective of the study was genetic typing of the strains and nucleic acid isolates of causative agents of natural focal infections, both bacterial and viral etiology, accumulation of data on genetic features of regional strains cir­culating in the Stavropol Territory. Material and methods. To study the genetic spectrum of causative agents of natural- focal infections, analysis of the strains and nucleic acids isolates detected in the samples of field and clinical material was carried out. Indication of causative agents of natural focal infections in the samples was carried out by PCR. For genetic typing of the strains and DNA/RNA isolates of natural focal infections agents, MLVA and sequencing of genome regions with subsequent phylogenetic analysis were used. The analysis of territorial distribution of the causative agent genetic variants and mapping was performed in ArcGIS 10.1. Results and conclusions. MLVA-25 typing of 20 strains of Francisella. tularensis, MLVA-10 typing of 4 Coxiella burnetii isolates, species identification of 20 isolates of Rickettsia sp., sub-species genetic typing of 40 RNA isolates of CCHF virus and 8 RNA isolates of hantaviruses circulating in the Stavropol Territory in 2016-2017 were performed. The studied strains of F. tularensis belong to eight MLVA genotypes. They are mainly confined to specific areas. The isolates of C. burnetii have the same MLVA type. Rickettsia, belonging to 5 species: R. massiliae R. raoultii, R. sibirica, R. aeschlimannii, R. slovaca, RNA-isolates of hantavirus of the «Tula» genotype and variants of the CCHF virus of the Europe-1 and Europe-3 genotypes were identified. The obtained data can be used in the epidemiological investigation of possible cases of infectious diseases to determine the source and pathways of infection

Analysis of Crimean Hemorrhagic Fever Morbidity Rates in the Russian Federation in 2017 and Prognosis for 2018

This paper presents the analysis of Crimean hemorrhagic fever (CHF) morbidity rates in Russia in 2017; summarized are the results of epidemiological survey of the territory of the natural CHF focus in the south of the European part of Russia, discussed are the results of genetic typing of CCHF virus isolates. In 2017, the Russian Federation reported 78 cases of CHF. Decrease in the incidence of CHF occurred in the Volgograd Region, Stavropol Territory, Astrakhan Region, Republic of Kalmykia, and Rostov Region. For the first time since 1967, CHF case has been identified in Crimea Republic. It is expected that the level of epizootic activity of CHF natural focus in Russia in 2018 will be at least equal to 2017. In case of favorable for Ixodidae ticks weather and climate conditions of the winter 2017–2018, as well as untimely acaricidal treatments, the number of Ixodidae ticks may increase, which along with the high scale of CCHF virus infection in ticks, will contribute to the increase in CHF incidence

Peculiarities of Epidemiological Situation on Crimean Hemorrhagic Fever in the Russian Federation at the Current stage

Objective. The analysis of epidemiological situation on Crimean hemorrhagic fever (CHF) in the Russian Federation at the current stage, identification of ways to improve the epidemiological surveillance and prophylaxis of the disease. Materials and methods. Data from statistical documentation and results of annual epizootiological monitoring of the CHF natural focus provided by the Administrations of the Rospotrebnadzor, Centers of Hygiene and Epidemiology in entities of the Southern and the North-Caucasian Federal Districts, Reference Centre for CHF monitoring, Research Anti-Plague Institutions and Plague Control stations were used for work. Results and conclusions. The CHF epidemio­logical situation remains unstable, the cases of the disease (including fatal) are registered every year. High activity of the CHF natural focus persists. The northward expansion of CHF natural focus boundaries is observed. The main causes of the unfavorable CHF epidemiological situation are associated with increase in the numbers and period of activity of ticks Hyalomma marginatum due to favorable climatic conditions. The list of priority measures to stabilize the CHF epidemiological situation developed by the Rospotrebnadzor has resulted in decrease in CHF cases by 51.9 % in 2017 compared to 2016 across all the territory of the south of the Russian Federation. The CHF morbidity in 2018 was 1.5 times lower than the average multi-year values (72 CHF patients). The number of CHF cases in comparison to 2017 has decreased by 1.3 times in the Stavropol Territory and by 1.4 times in the Rostov Region. The CHF morbidity has increased in the Astrakhan Region (by 3 times) and Volgograd Region (by 2.3 times). Nosocomial CCHF virus infections cases associated with non-compliance to anti-epidemic regime in hospitals while providing treatment of CHF patients were registered in 2011 (in the Rostov Region) and in 2016 (in the Stavropol Territory). This highlights the need to improve the training of health-care staff for admission of patients with this particularly dangerous infection

Analysis of Epidemiological Situation on Crimean Hemorrhagic Fever in the Russian Federation in 2013 and Prognosis for 2014

Crimean hemorrhagic fever remains one of the priority infections in the South of Russia. Within the past five years morbidity rates are retained consistently high in a number of regions; mortality rates are on average 4.4 %. In 2013 registered were 79 cases of CHF in the Southern and North-Caucasian Federal Districts. Therewith performed has been analysis of epidemiological situation on CHF in the Russian Federation for 2013, summarized have been the results of epizootiological surveillance of the natural CHF focus area in the South of European Russia, discussed are the results of genetic CCHF virus typing, identified in 2011-2013 in the South of Russia. Based on epizootiological surveillance data made has been the forecast of epidemiological situation development as regards CHF for 2014