Following its emergence at the end of 2021, the Omicron SARS-CoV-2 variant rapidly spread around the world and became a dominant variant of concern (VOC). The appearance of the new strain provoked a new pandemic wave with record incidence rates. Here, we analyze the dissemination dynamics of Omicron strains in Saint Petersburg, Russia’s second largest city. The first case of Omicron lineage BA.1 was registered in St. Petersburg on 10 December 2021. Rapid expansion of the variant and increased incidence followed. The peak incidence was reached in February 2022, followed by an observed decline coinciding with the beginning of spread of the BA.2 variant. SARS-CoV-2 lineage change dynamics were shown in three categories: airport arrivals; clinical outpatients; and clinical inpatients. It is shown that the distribution of lineage BA.1 occurred as a result of multiple imports. Variability within the BA.1 and BA.2 lineages in St. Petersburg was also revealed. On the basis of phylogenetic analysis, an attempt was made to trace the origin of the first imported strain, and an assessment was made of the quarantine measures used to prevent the spread of this kind of infection.

In this report, we document and analyze a case in which the Irkut virus (IRKV) (Mononegavirales: Rhabdoviridae) caused a fatal human case following a bat bite in June 2021. Unfortunately, the available data did not permit a detailed taxonomic classification of the carrier bat (Chiroptera). The event occurred in the southwestern part of the Sikhote-Alin mountain region (Russian Far East) covered by the Ussuri taiga forest. The symptoms of the illness began with the following: fever; pronounced psychomotor and motor agitation; tremor of the lower jaw and tongue; aphasia; dyslexia; and dysphagia. These rapidly developed, leading to a severe and fatal encephalitis. The patient was not vaccinated for rabies and did not receive rabies immunoglobulin. Using brain sections prepared from the deceased, molecular diagnostics were performed: immunofluorescence (polyclonal anti-rabies immunoglobulin) indicating the presence of the lyssavirus antigen; and RT-PCR indicating traces of viral RNA. Sectional material (brain) was used for whole-genome sequencing, resulting in a near-complete sequence of the lyssavirus genome. The obtained genomic sequence was identified as the Irkut virus. A comparative analysis of the new sequence and other currently available IRKV sequences (NCBI) revealed differences. Specifically, amino acid differences between antigenic sites in the isolate and those of the rabies vaccine strain used regionally were noted. The patient history and subsequent analysis confirm human IRKV infection following bat contact. Like other fatal cases of IRKV infection described earlier, this case occurred in the southern part of the Russian Far East. Two have occurred in the southwestern part of the Sikhote-Alin mountain region. This indicates the possible existence of an active, natural viral focus.

Arboviruses, including but not limited to dengue virus (DENV), Zika virus (ZIKV), and chikungunya virus (CHIKV), pose a significant global threat to human health. The transmission of DENV, ZIKV, and CHIKV is facilitated by mosquitoes belonging to the genus Aedes, which are prevalent in both urban and rural regions of Vietnam. In 2023 an investigation into the population of mosquitoes was conducted in a number of provinces located within the central region of Vietnam. A total of 12,546 mosquitoes were collected during the study. The mosquitoes collected comprised the genera Culex spp., Aedes spp., Anopheles spp., and Armigeres spp. The Aedes spp. mosquitoes were predominant, being collected in 908 pools. These were then examined by RT-qPCR for the detection of DENV, ZIKV, and CHIKV. DENV viral RNA was detected in 92 mosquito pools, ZIKV was detected in 1 mosquito pool, and CHIKV was not detected. The typing of samples containing DENV RNA was carried out. It is evident from the results of the typing process that three distinct types of DENV have been identified. The three main dengue virus types are DENV-1, DENV-2, and DENV-4.

Since its beginnings in 2019, the COVID-19 pandemic is still a problem of global medical concern. Southern Vietnam is one of the country's vast regions, including 20 provinces and the densely populated metropolis Ho Chi Minh City. A randomized retrospective study was performed to investigate the epidemiology and genetic diversity of COVID-19. Whole-genome sequencing of 126 SARS-CoV-2 samples collected from Southern Vietnam between January 2020 and December 2021 revealed the main circulating variants and their distribution. Epidemiological data were obtained from the Department of Preventive Medicine of the Vietnamese Ministry of Health. To identify circulating variants, RNA, extracted from 126 nasopharyngeal swabs of patients with suspected COVID-19 were sequenced on Illunina MiSeq to obtain near complete genomes SARS-CoV-2. Due to the effectiveness of restrictive measures in Vietnam, it was possible to keep incidence at a low level. The partial relaxation of restrictive measures, and the spread of Delta lineages, contributed to the beginning of a logarithmic increase in incidence. Lineages 20A-H circulated in Southern Vietnam during 2020. Spread of the Delta lineage in Southern Vietnam began in March 2021, causing a logarithmic rise in the number of COVID-19 cases. Pandemic dynamics in Southern Vietnam feature specific variations in incidence, and these reflect the success of the restrictive measures put in place during the early stages of the pandemic.

BACKGROUND: Bats are a reservoir of a large number of viruses, including coronaviruses. Monitoring viruses in bats is an important task. AIM: To detect viruses belonging to Coronaviridae family in bats which habitat in European part of Russia. MATERIALS AND METHODS: We used PCR amplification of viral genome fragments, followed by high-throughput sequencing. RESULTS: RdRp gene fragments of at least two different alphacoronaviruses (Bat coronavirus, Coronaviridae) were revealed in four bats of three species. CONCLUSIONS: Our results demonstrate the presence of viruses of the Alphacoronavirus genus in 4 of 17 bats. Coronavirus-positive animals were captured in 2021 in Moscow, Moscow Region and Rostov-on-Don, these four animals have been found to be carriers of different isolates of the same alphacoronavirus, which allows us to suggest the possibility of transmission of this virus between animals between different species. One animal was found as carrier of genome fragments of two different alphacoronaviruses.