Creation and Support of Operation of a Hospital Net to Treat COVID-19 Patients in Guinea

The paper provides information on the construction, development and functioning of a hospital network for the detection and treatment of patients with dangerous infectious diseases in the Republic of Guinea. With the support of UC RUSAL and with the assistance of the Ministry of Health of Guinea, hospitals have been established to provide medical care to patients suspected of COVID-19. Sick persons are admitted from regional hospitals from all over country. The majority of the hospitalized persons are patients with mild and moderate forms of the disease. Diagnostic studies using RT-PCR to detect SARS-CoV-2 virus RNA are carried out at the premises of stationary (Kindia) and mobile (Fria) laboratories. Testing of the received samples is carried out using diagnostic preparations of domestic and foreign production. This stage of work is performed by employees of the Rospotrebnadzor institutions (the Russian Federation) working on the territory of the Republic of Guinea. In total, since the beginning of the epidemic, more than 630 patients have received treatment in the stated hospitals; more than 20 thousand tests of clinical material samples have been conducted to detect the RNA of the SARS-CoV-2 virus. In addition to residents of Guinea, medical assistance was provided to citizens of Russia, Ukraine, Belarus, Kazakhstan, China, India, Sierra Leone, and the Comoros. The organization of the network of hospitals and their inclusion into the national system for counteracting the spread of new coronavirus infection allowed us to begin active work on the identifcation and treatment of COVID-19 patients in the territory of the Republic of Guinea and make a signifcant contribution to the fght against the epidemic.

Software Solutions for Indication and Identification of Pathogenic Microoranisms Using Time-of-Flight Mass Spectrometry

The effectiveness of differentiation of bacterial pathogens using MALDI-TOF mass spectrometry depends on the quality of sample preparation, compliance with mass spectrometric analysis parameters and statistical approaches used, implemented by various modern software tools. The review provides a brief description of the most known software used in the processing and bioinformation analysis of time-of-flight mass spectrometry data. A list of computer platforms, programs and environments, both commercial and publicly available, is presented. The results of indication and identification of pathogens of particularly dangerous and natural-focal infections by MALDI-TOF mass spectrometry using publicly available software – programming language R, Mass-Up, MicrobeMS, licensed – MatLab, ClinProTools, as well as free web applications, including, Speclust, Ribopeaksare provided. The data on usage of such well-known platforms as MALDI BioTyper, SARAMIS Vitek-MS and Andromas (Andromas SAS, France) for inter- and intra-specific differentiation of closely related species are presented. Results of identification and differentiation of microorganisms applying MALDI-TOF mass spectrometry based on detection of specific proteins for cross-comparison – biomarkers – are given. The analysis shows that the programming language R environment is one of the publicly available universal platforms with an optimal combination of algorithms for processing and interpreting of a large array of mass spectrometric data.

Assessing the Efciency of Detection of Vibrio cholerae Genetic Determinants Through Waterbody Vibrioflora Monitoring System

Objective of the study was to assess the effectiveness of PCR screening of Vibrio cholerae genetic determinants in samples from surface water reservoirs for optimization of the cholera microbiological monitoring system.Materials and methods. The study was carried out as a part of the vibrioflora monitoring in surface water bodies in Irkutsk city. The study design included: 1) PCR screening of V. cholerae genetic determinants in nutrient-enriched (1 % peptone water) samples from surface water reservoirs during the monitoring period (824 samples); 2) studying of the V. cholerae DNA accumulation dynamics applying PCR assay of the samples from surface water reservoirs during cultivation on the enriched media (16 samples in dynamics); 3) experimental study of the detected V. cholerae concentrations in samples from surface water reservoirs. Species-specifc (hlyA, toxR) and serogroup-specifc (wbeT, wbfR) V. cholerae determinants were indicated in PCR with hybridization-fluorescent and electrophoretic detection.Results and discussion. At the frst stage it was found that the proportion of the positive samples through PCR screening (33.9 %) exceeded the percentage of the positive samples in bacteriological examination (19.3 %) (t=6.6; p<0,01). In the assessment of DNA accumulation dynamics, a decrease in the threshold cycle (Ct) by 1.2–5.2 times was recorded, indicating an increase in the V. cholerae concentration and proving the detection of genetic determinants of viable forms during PCR screening. An extended study of PCR-positive but bacteriologically negative samples made it possible to additionally isolate 4 V. cholerae cultures. However, there were no differences in the sensitivity of PCR screening and bacteriological analysis in the experiment with water samples artifcially contaminated with V. cholerae unlike the analysis of the enriched native samples. It can be determined by the metabolism and adaptation peculiarities of the microorganism in different environmental conditions. The results of the integrated study indicate the epidemiological effectiveness of PCR screening which gives grounds to recommend its application in monitoring studies of vibrioflora from environment after preliminary enrichment on liquid nutrient media in the work of federal, territorial, and regional laboratories.

Algorithm and Results of Short-Term Forecast of Changes in the COVID-19 Spread Coefcient in the Constituent Entities of the Russian Federation

There was a decrease in the number of COVID-19 cases across many entities of the Russian Federation towards the end of summer season-2020. However, the disease remains a relevant threat to the public health and economy and the possibility of a second epidemic wave is not excluded. Rate of infection transmission (Rt) is one of the most important indicators to justify the transition to next stage of removing/introducing restrictive measures on COVID-19.Objective of the work was to describe the algorithm of analysis and short-term forecast of coronavirus spread rate, to assess correspondence between theoretically expected and actual values of this indicator.Materials and methods. Procedure for making a short-term extrapolation forecast of Rt in 10 RF constituent entities, depending on the presence or absence of indicator trends with calculation of a 95 % confdence interval of possible changes in its value is provided.Results and discussion. It is proposed to carry out Rt forecast based on averaged values over a week, combining regression analysis and expert assessment of time series dynamics nature for prompt transition from trend forecasting to extrapolation of stationary observation sequences and vice versa. It has been demonstrated that predicted Rt values are not statistically different from actual values. When making managerial decisions on COVID-19 prevention, special attention should be paid to cases when actual value of Rt exceeds the upper limit of confdence interval. Six (20.0 %) such cases were detected in surveyed entities on calendar weeks 33–35. Three of them were registered in Trans-Baikal Territory, where upward trend was reported during that period of time. The cause of this phenomenon should be analyzed. The put forward algorithm of analysis and forecasting of the Rt value changes, which was tested in 10 entities of Russia, provides a reliable basis for making management decisions on removing/introducing restrictive measures for COVID-19 prevention.

Cases of Orthopoxviral Infections around the World over a Period of 2008–2018

The eradication of smallpox has become one of the greatest successes of modern health science. This great achievement was made possible thanks to the widespread vaccination of the population. The last case of human infection with smallpox virus occurred in 1977. In 1980, at the 33rd session of the World Health Assembly, routine vaccination against that infection was recommended to be discontinued due to severe post-vaccination complications. However, humanity remains vulnerable to other orthopoxvirus infections closely related to smallpox virus. Recently, the cases of human infection with ortopoxviruses such as monkeypox virus, cowpox virus, vaccinia virus have become more frequent. Also, cases of infection of people with previously unknown orthopoxvirus species are recorded. Zoonotic orthopoxviruses pathogenic for humans, circulating in nature, require a detailed study and monitoring of the emergence of new strains. Their occurrence against the background of the cessation of planned vaccination of the population against smallpox virus can lead to the emergence of new highly pathogenic viruses. This review contains information on cases of human infection with orthopoxviruses around the world for the period 2008–2018. It also describes epidemiological anamnesis and the relations between cases of human infection in different countries due to the spread of viruses over a wide area, the movement of people between countries, population contacts with domestic and wild animals. Also, this paper provides information on the infection of people with previously unknown strains of orthopoxviruses.

Assessment of the Use of Gentian Violet and Malachite Green as Selective Agents in the Isolation of Brucella

The aim of the work is to evaluate ability of gentian violet and malachite green to inhibit 2 Brucella test strains and 8 strains of unwanted organisms and the influence of autoclaving on their activity. The study also aims to evaluate variability of inhibition in different batches of colorants and necessity in adjustment of their concentration.Materials and methods. The study included 3 imported lots of gentian violet and malachite green. Inhibitors were put into nutrient medium containing pancreatic hydrolysates of gelatin and fsh meal, yeast extract, sodium chloride, glucose, sodium pyrosulfate, and agar. The same medium without colorants was used as a control medium. Effect of the colorants was studied with the help of test strains of Brucella abortus 19 ВА, B. melitensis Rev I, Enterococcus faecium VKM B-602, Escherichia coli ATCC 25922, Proteus vulgaris HX 19 222, Pseudomonas aeruginosa 22/99, Serracia plymuthica 1, Shigella flexneri 1a 8516, Staphylococcus aureus ATCC 25923, Yersinia enterocolitica C-187.Results and discussion. We have determined biological parameters of nutrient media containing gentian violet (5,0; 2,5 1,25 mg/L) and malachite green (2.0; 1.0; 0.5 mg/L) when cultivating brucella. Gentian violet is able to inhibit Brucella greatly at concentration of 5 mg/L. S. aureus ATCC 25923 did not show any growth on the media containing malachite green or gential violet (5.0 and 2.5 mg/L). Malachite green inhibited the growth of enterococcus more actively than gentian violet. However, it inhibited swarming growth of Proteus less successfully than gentian violet. Other unwanted organisms were not sensitive to such concentrations of colorants at all. We have demonstrated the necessity to combine colorants with other selective agents, as well as advisability to put gentian violet into sterile media, while malachite green – into the media before its autoclaving. Adjustments to the concentration of gentian violet should be made when producing nutrient medium, as variations in inhibiting activity in different batches of this colorant were revealed.

Efciency of Anti-Epidemic Measures that Ensure Access to Work in Rotational Shifts under Conditions of Covid-19 Pandemic

Objective – integral analysis of effectiveness of anti-epidemic measures applied towards employees of the Amur gas processing plant assigned for rotational work under conditions of COVID-19 pandemic.Materials and methods. Sero-epidemiological study included a questionnaire survey of 1461 workers who arrived through the “clean corridor” in the Amur Region, followed by sampling of biological material (blood and respiratory smears). Testing of blood sera for the presence of antibodies to SARS-CoV-2 of two classes (IgM and IgG) was carried out applying enzyme immunoassay. Using PCR, respiratory smears were examined for the presence of the agent RNA in them. Statistical processing of the results obtained was carried out using conventional methodsResults and discussion. The presence of antibodies of the IgG class was revealed in (4.7±0.55) % of cases. In a small cohort (1.7±0.34 %) of practically healthy individuals, asymptomatic infection was detected, confrmed either by a positive PCR result (0.76±0.23 %), or by the detection of IgM antibodies (1.0±0.08 %). On the basis of the study carried out by the Federal Service for Surveillance in the Sphere of Consumer Rights Protection and Human Welfare on August 01, 2020, “Temporary recommendations on the procedure for admitting to work on a rotational basis under the risk of COVID-19 spread in the Amur Region” were approved. These recommendations set out the algorithm for observation of incoming workers and the order for triage of shift workers after testing by ELISA and PCR. The results of the study demonstrate the effectiveness of anti-epidemic measures related to ensuring the procedure for admission to work on a rotational basis under the risks of the spread of COVID-19.

Analysis of Q Fever Incidence in the Russian Federation Between 1957 and 2019

Objective of the study was to analyze the long-term incidence of Q fever in the Russian Federation, to recommend approaches to improve epizootiological and epidemiological surveillance of this infection, taking into account the current state of laboratory diagnostics and monitoring of foci.Materials and methods. A retrospective epidemiological analysis of the Q fever incidence using the data contained in Form No 2 of the state statistical report «Information on infectious and parasitic diseases» was conducted in the Russian Federation for the period of 1957– 2019, by the Federal Districts (FD) and administrative territories, and based on the results of the research of the Reference Center for Rickettsioses of the Omsk Research Institute of Natural Focal Infections.Results and discussion. Between 1957 and 2019, 13 836 cases of Q fever were officially registered in the Russian Federation. The maximum value of the morbidity rate per 100 thousand of the population was registered in 1957 (1.0 0/0000), the minimum one – in 2008 (0.01 0/0000). From 1997 to 2019, out of 2672 registered in 24 entities of the Russian Federation cases of Q fever, 2224 (83.20 %) occurred in the Southern FD with 2106 (78.8 %) cases in the Astrakhan Region. In the Stavropol Territory of the North Caucasus FD, 173 (6.47 %) cases of the disease were detected. 112 (4.19 %) cases were registered in the Central FD, with the maximum number in the Voronezh Region (82). In the Volga FD, 81 (3.03 %) cases were identified, 54 of which in the Ulyanovsk Region. 42 (1.61 %) cases of the disease were registered in the North-Western FD, 33 – in the Leningrad Region and St. Petersburg. In the Siberian FD, 39 (1.46 %) cases of Q fever were reported, 24 were diagnosed in the Novosibirsk Region. In the Ural FD, 1 (0.04 %) case of infection was detected. In the Far Eastern FD, there is no registration of Q fever. Presented are medical products for Q fever diagnostics authorized in Russia. Sanitation of the foci among farm animals should be carried out in accordance with the current sanitary-epidemiological and veterinary-sanitary rules.

Antrax in Primorsky Territory (1919–2020). Communication 1. Historical Records and Characteristics of Stationary Potentially Hazardous as Regards Antrax Areas

The aim of the study was to analyze the state of stationary potentially hazardous areas as regards anthrax in the Primorsky Territory and update the Cadastre of stationary potentially hazardous as regards anthrax areas (SPHA) of the Russian Federation (2005).Materials and methods. The collection and survey of accounting and reporting documents, archival and informational materials, records on anthrax from veterinary institutions, Rospotrebnadzor, municipalities by the 72 registered anthrax SPHA of the Primorsky Territory have been carried out. The reference book of the Russian Soviet Federative Socialist Republic’s settlements endemic for anthrax (1976), the Cadastre of the stationary potentially hazardous as regards anthrax areas in the Russian Federation (2005) were used.Results and discussion. The description of anthrax cases in the Primorsky Territory goes back to 1894, the official registration of the disease – since 1919. The last cases of the disease in farm animals and population were noted in Kavalerovsky and Oktyabrsky districts in 1979. When updating the SPHA (2005), information on 82 dormant sites of the Territory in 22 municipal and six urban districts was clarified. In six districts of the Territory, anthrax was not officially registered. Most of the SPHAs are centered on the Khanka plain, where the network of transport routes, the largest number of livestock and population are concentrated. The data on the number of sick animals and people over a period of 1919–1929 have not survived, and in the period between 1980 and 2020 anthrax was not reported in the region. 173 animals and 34 humans were diagnosed with anthrax in 1929–1979 in Primorye. High epizootic activity was noted in the period of 1919–1941. In the Asian part of the Russian Federation, Primorsky Territory belongs to the regions under a mild epizootic and epidemiological disadvantage as regards anthrax. Monitoring of anthrax has shown that the persistence of the pathogen in the soils of ten districts of the Territory could be facilitated by the absence of soil toxicity (86,8 %) and an average nutritional value (23,5 %) in relation to the anthrax microbe.

Biological Properties and Genetic Characteristics of Francisella tularensis Strains Isolated in the Territory of the Rostov Region in 2020

Objective of the study was to investigate biological properties and genetic characteristics of tularemia agent strains isolated from natural foci of the Rostov Region in 2020.Materials and methods. Field material from natural foci of the Rostov Region was examined by serological, bacteriological, biological, and molecular-genetic methods. Cultural-morphological, biochemical, antigenic and pathogenic properties of isolated cultures were studied. Protein profles were obtained through MALDI-TOF MS using mass spectrometer Autoflex speed III Bruker Daltonics and Flex Control of Biotyper software. The genetic characteristics of the strains were determined by VNTR and INDEL typing and SNP analysis.Results and discussion. Six strains of tularemia pathogen were isolated from mouse-like rodents using biological method. The investigation of their biological features and data of PCR analysis and INDEL typing with canonical markers showed that all strains are typical representatives of the Francisella tularensis subsp. holarctica biovar EryR. VNTR typing by six genetic loci revealed that all strains belong to four individual genotypes. The strain isolated in 2020 in the Salsky district was identical to the strain which was isolated in the same area in 1989. Based on the whole genome sequencing of two strains, we established that they are closest to the cultures isolated in Turkey (2009, 2012) and Khanty-Mansiysk (2013) by the studied set of SNP markers. Thus, we found that both identical (or closely related) clones of the tularemia agent and new strains with unique genotypes which previously were not described for the Rostov Region can circulate in natural foci of this region for a long period of time.