D.I. Ivanovsky Institute of Virology Russian Academy of Medical Sciences

Nairoviridae is a family for negative-sense RNA viruses with genomes of about 17.2-21.1 kb. These viruses are maintained in and/or transmitted by arthropods among birds, reptiles and mammals. Norwaviruses and orthonairoviruses can cause febrile illness in humans. Several orthonairoviruses can infect mammals, causing mild, severe and sometimes, fatal diseases. Nairovirids produce enveloped virions containing two or three single-stranded RNA segments with open reading frames that encode a nucleoprotein (N), sometimes a glycoprotein precursor (GPC), and a large (L) protein containing an RNA-directed RNA polymerase (RdRP) domain. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) report on the family Nairoviridae, which is available at www.ictv.global/report/nairoviridae.

Limosilactobacillus fermentum strain 3872 (LF3872) was originally isolated from the breast milk of a healthy woman during lactation and the breastfeeding of a child. Ligilactobacillus salivarius strain 7247 (LS7247) was isolated at the same time from the intestines and reproductive system of a healthy woman. The genomes of these strains contain genes responsible for the production of peptidoglycan-degrading enzymes and factors that increase the permeability of the outer membrane of Gram-negative pathogens. In this work, the anti-Salmonella and intestinal homeostatic features of the LF3872 and LS7247 consortium were studied. A multi-drug resistant (MDR) strain of Salmonella enteritidis (SE) was used in the experiments. The consortium effectively inhibited the adhesion of SE to intact and activated human, porcine, and chicken enterocytes and reduced invasion. The consortium had a bactericidal effect on SE in 6 h of co-culturing. A gene expression analysis of SE showed that the cell-free supernatant (CFS) of the consortium inhibited the expression of virulence genes critical for the colonization of human and animal enterocytes. The CFS stimulated the production of an intestinal homeostatic factor-intestinal alkaline phosphatase (IAP)-in Caco-2 and HT-29 enterocytes. The consortium decreased the production of pro-inflammatory cytokines IL-8, TNF-α, and IL-1β, and TLR4 mRNA expression in human and animal enterocytes. It stimulated the expression of TLR9 in human and porcine enterocytes and stimulated the expression of TLR21 in chicken enterocytes. The consortium also protected the intestinal barrier functions through the increase of transepithelial electrical resistance (TEER) and the inhibition of paracellular permeability in the monolayers of human and animal enterocytes. The results obtained suggest that a LF3872 and LS7247 consortium can be used as an innovative feed additive to reduce the spread of MDR SE among the population and farm animals.

Abstract Background: Since 2011, the Global Influenza Hospital Surveillance Network (GIHSN) has used active surveillance to prospectively collect epidemiological and virological data on patients hospitalized with influenza virus infection. Here, we describe influenza virus strain circulation in the GIHSN participant countries during 2017–2018 season and examine factors associated with complicated hospitalization among patients admitted with laboratory-confirmed influenza illness.Methods: The study enrolled patients hospitalized in a GIHSN hospital in the previous 48 h with acute respiratory symptoms and who had symptoms consistent with influenza within the 7 days before admission. Enrolled patients were tested by reverse transcription-polymerase chain reaction to confirm influenza virus infection. “Complicated hospitalization” was defined as a need for mechanical ventilation, admission to an intensive care unit, or in-hospital death. In each of four age strata (<15, 15–<50, 50–<65, and ≥65 years), factors associated with complicated hospitalization in influenza-positive patients were identified by mixed effects logistic regression and those associated with length of hospital stay using a linear mixed-effects regression model.Results: The study included 12,803 hospitalized patients at 14 coordinating sites in 13 countries, of which 4,306 (34%) tested positive for influenza. Influenza viruses B/Yamagata, A/H3N2, and A/H1N1pdm09 strains dominated and cocirculated, although the dominant strains varied between sites. Complicated hospitalization occurred in 10.6% of influenza-positive patients. Factors associated with complicated hospitalization in influenza-positive patients included chronic obstructive pulmonary disease (15–<50 years and ≥65 years), diabetes (15–<50 years), male sex (50–<65 years), hospitalization during the last 12 months (50–<65 years), and current smoking (≥65 years). Chronic obstructive pulmonary disease (50–<65 years), other chronic conditions (15–<50 years), influenza A (50–<65 years), and hospitalization during the last 12 months (<15 years) were associated with a longer hospital stay. The proportion of patients with complicated influenza did not differ between influenza A and B.Conclusions: Complicated hospitalizations occurred in over 10% of patients hospitalized with influenza virus infection. Factors commonly associated with complicated or longer hospitalization differed by age group but commonly included chronic obstructive pulmonary disease, diabetes, and hospitalization during the last 12 months.

Peribunyaviruses are enveloped and possess three distinct, single-stranded, negative-sense RNA segments comprising 11.2–12.5 kb in total. The family includes globally distributed viruses in the genera Orthobunyavirus, Herbevirus, Pacuvirus and Shangavirus. Most viruses are maintained in geographically-restricted vertebrate–arthropod transmission cycles that can include transovarial transmission from arthropod dam to offspring. Others are arthropod-specific. Arthropods can be persistently infected. Human infection occurs through blood feeding by an infected vector arthropod. Infections can result in a diversity of human and veterinary clinical outcomes in a strain-specific manner. Segment reassortment is evident between some peribunyaviruses. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the family Peribunyaviridae, which is available at ictv.global/report/peribunyaviridae.

The post-integrational gap repair is a critical and poorly studied stage of the lentiviral life cycle. It might be performed by various cellular DNA repair pathways but the exact mechanism of the repair process has not yet been described. One of the reasons for that is the lack of a functional quantitative assay that could precisely measure the amount of integrated viral DNA that has completed the post-integrational gap repair stage. Here, we present an approach that is based on a widely used Alu-specific PCR for the estimation of integrated viral DNA but includes several steps that allow discrimination between integrated-repaired and integrated-unrepaired viral DNA forms. We used the approach for the estimation of the kinetics of gap repair in a viral vector system and showed that the gap repair process starts at 17 h post infection and lasts 10 more hours. We also showed that the addition of Nu7441 – a small molecule inhibitor of DNA-breaks sensor kinase in the non-homologous end joining DNA repair pathway – specifically inhibits the gap repair process while having no influence on the integration itself.

Rabies epidemic situation in the Tver Region has been studied. Animals of different species that had confirmed clinical rabies were statistically analyzed. It was established that the features of the course of epizootics in the Tver region correspond to the regularities characteristic of rabies of the natural-focal type. As a result of sequencing of the rabies virus N gene and phylogenetic analysis, the isolates studied were assigned to the central phylogenetic group. With the help of the geoinformatic system, nosological maps of the Tver region were obtained and the spatial- temporal features of the course of the epizootic process of rabies infection were studied.

Sera of 3951 inhabitants of Central, Privolzhsky and Northwest federal districts of Russia were examined with the use of ELISA-IgG and neutralization test. Antibodies to West Nile virus (WN) were detected in the sera of residents of Voronezh (1,6% of cases), Tula (1,5%), Tambov (0,7%) and Lipetsk(0,6%) regions. Two positive samples have been detected in residents of Moscow and Moscow region, which were possibly infected, during theirs travel to endemic for WN fever regions. All sera obtained from Kaluga, Ryazan, Tver, Vologda, Ulyanovsk regions and The Republic of Tatarstan were negative. Our data, in combination with the morbidity rate of WN fever indicate on epidemiological activity of foci of this infection in the South, the North Caucasus, Privolzhsky (Saratovskaya region) and Central (the forest-steppe zone and Tula region) districts. The northern border of circulation of WN virus probably dispose of the latitude of the Tula region.

To simultaneously analyze HIV-1 samples from all Russian regions to characterize the epidemiology of HIV infection in the country as a whole. The most extensive study was conducted to examine nucleotide sequences of the pol gene of HIV-1 samples isolated from HIV-positive persons in different regions of Russia, with the diagnosis date being fixed during 1987-2015. The nucleotide sequences of the HIV-1 genome were analyzed using computer programs and on-line applications to identify a virus subtype and new recombinant forms. The nucleotide sequences of the pol gene were analyzed in 1697 HIV-1 samples and the findings were that the genetic variant subtype A1 (IDU-A) was dominant throughout the entire territory of Russia (in more than 80% of all infection cases). Other virus variants circulating in Russia were analyzed; the phenomenon of the higher distribution of the recombinant form CRF63/02A in Siberia, which had been previously described in the literature, was also confirmed. Four new recombinant forms generated by the virus subtype A1 (IDU-A) and B and two AG recombinant forms were found. There was a larger genetic distance between the viruses of IDU-A variant circulating among the injecting drug users and those infected through heterosexual contact, as well as a change in the viruses of subtype G that caused the outbreak in the south of the country over time in 1988-1989. The findings demonstrate continuous HIV-1 genetic variability and recombination over time in Russia, as well as increased genetic diversity with higher HIV infection rates in the population.

In diverse global regions with significant human immunodeficiency virus (HIV) burden, programmatic, cultural, and provider-, patient-, and virus-related factors may result in HIV drug resistance, with global implications. This article reviews such common and unique challenges in Russia, Latin America and the Caribbean, China, and India, to suggest potential solutions.

The immune-modulating activity of "Ferrovir" medication in system in vitro was analyzed using neoplastic cellular line MT-4 as a model. Ferrovir decreased number of cells containing such markers of activation as CD28+, CD38+, CD62L+, CD69+ and HLA-DR+.Under 24 hours incubation period of cells in presence of 500 mkg per ml of medication, indices of decreasing of number of cells expressing these proteins (IRE), for proteins CD28, CD38, CD62L and HLA-DR made up to 1,9 ± 0,4, 1,3 ± 0,4, 1,2 ± 0,4, 1,1 ± 0,06 correspondingly. At prolonged incubation of cells in presence of Ferovir, the maximal effect was observed after 7 days of incubation and IRE for proteins mentioned above made up to 3,2, 3,4, 6,2, 1,4 и 3,1 correspondingly. Only for protein CD62L was marked a significant decreasing of number of cells bringing this marker and at 11th day of cells cultivation in presence of Ferrovir (IRE 3.89). It is possible that such an action of Ferrovir can decrease the process of spreading of cells containing integrated pathogenic material through organs and tissues of organism and slow down generalization of infectious process. The obtained results indicate that Ferrovir has an immune-modulating activity in vitro since it can decrease activating potential of neoplastic line of cells MT-4. These features can be useful in treatment of various type of cancer, HIV-infection and other human diseases. The decreasing of level of activation of cells of immune system also decreases risk of development of opportunistic infections.