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The human adenovirus (HAdV) is a common pathogen in children that can cause acute respiratory virus infection (ARVI). However, the molecular epidemiological and clinical information relating to HAdV among hospitalized children with ARVI is rarely reported in Russia. A 4-year longitudinal (2019–2022) study among hospitalized children (0–17 years old) with ARVI in Novosibirsk, Russia, was conducted to evaluate the epidemiological and molecular characteristics of HAdV. Statistically significant differences in the detection rates of epidemiological and virological data of all positive viral detections of HAdV were analyzed using a two-tailed Chi-square test. The incidence of HAdV and other respiratory viruses such as human influenza A and B viruses, respiratory syncytial virus, coronavirus, parainfluenza virus, metapneumovirus, rhinovirus, bocavirus, and SARS-CoV-2 was investigated among 3190 hospitalized children using real-time polymerase chain reaction. At least one of these respiratory viruses was detected in 74.4% of hospitalized cases, among which HAdV accounted for 4%. A total of 1.3% co-infections with HAdV were also registered. We obtained full-genome sequences of 12 HAdVs, which were isolated in cell cultures. Genetic analysis revealed the circulation of adenovirus of genotypes C1, C2, C5, C89, and 108 among hospitalized children in the period from 2019–2022. [ABSTRACT FROM AUTHOR]

Avian coronaviruses (ACoV) have been shown to be highly prevalent in wild bird populations. More work on avian coronavirus detection and diversity estimation is needed for the breeding territories of migrating birds, where the high diversity and high prevalence of Orthomyxoviridae and Paramyxoviridae have already been shown in wild birds. In order to detect ACoV RNA, we conducted PCR diagnostics of cloacal swab samples from birds, which we monitored during avian influenza A virus surveillance activities. Samples from two distant Asian regions of Russia (Sakhalin region and Novosibirsk region) were tested. Amplified fragments of the RNA-dependent RNA-polymerase (RdRp) of positive samples were partially sequenced to determine the species of Coronaviridae represented. The study revealed a high presence of ACoV among wild birds in Russia. Moreover, there was a high presence of birds co-infected with avian coronavirus, avian influenza virus, and avian paramyxovirus. We found one case of triple co-infection in a Northern Pintail (Anas acuta). Phylogenetic analysis revealed the circulation of a Gammacoronavirus species. A Deltacoronavirus species was not detected, which supports the data regarding the low prevalence of deltacoronaviruses among surveyed bird species. [ABSTRACT FROM AUTHOR]

A wide range of human respiratory viruses are known that may cause acute respiratory infections (ARIs), such as influenza A and B viruses (HIFV), respiratory syncytial virus (HRSV), coronavirus (HCoV), parainfluenza virus (HPIV), metapneumovirus (HMPV), rhinovirus (HRV), adenovirus (HAdV), bocavirus (HBoV), and others. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the COronaVIrus Disease (COVID) that lead to pandemic in 2019 and significantly impacted on the circulation of ARIs. The aim of this study was to analyze the changes in the epidemic patterns of common respiratory viruses among children and adolescents hospitalized with ARIs in hospitals in Novosibirsk, Russia, from November 2019 to April 2022. During 2019 and 2022, nasal and throat swabs were taken from a total of 3190 hospitalized patients 0–17 years old for testing for HIFV, HRSV, HCoV, HPIV, HMPV, HRV, HAdV, HBoV, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by real-time PCR. The SARS-CoV-2 virus dramatically influenced the etiology of acute respiratory infections among children and adolescents between 2019 and 2022. We observed dramatic changes in the prevalence of major respiratory viruses over three epidemic research seasons: HIFV, HRSV, and HPIV mainly circulated in 2019–2020; HMPV, HRV, and HCoV dominated in 2020–2021; and HRSV, SARS-CoV-2, HIFV, and HRV were the most numerous agents in 2021–2022. Interesting to note was the absence of HIFV and a significant reduction in HRSV during the 2020–2021 period, while HMPV was absent and there was a significant reduction of HCoV during the following epidemic period in 2021–2022. Viral co-infection was significantly more frequently detected in the 2020–2021 period compared with the other two epidemic seasons. Certain respiratory viruses, HCoV, HPIV, HBoV, HRV, and HAdV, were registered most often in co-infections. This cohort study has revealed that during the pre-pandemic and pandemic periods, there were dramatic fluctuations in common respiratory viruses registered among hospitalized patients 0–17 years old. The most dominant virus in each research period differed: HIFV in 2019–2020, HMPV in 2020–2021, and HRSV in 2021–2022. Virus–virus interaction was found to be possible between SARS-CoV-2 and HRV, HRSV, HAdV, HMPV, and HPIV. An increase in the incidence of COVID-19 was noted only during the third epidemic season (January to March 2022). [ABSTRACT FROM AUTHOR]

In this retrospective, single-center study, we conducted an analysis of 13,699 samples from different individuals obtained from the Federal Research Center of Fundamental and Translational Medicine, from 1 April to 30 May 2020 in Novosibirsk region (population 2.8 million people). We identified 6.49% positive for SARS-CoV-2 cases out of the total number of diagnostic tests, and 42% of them were from asymptomatic people. We also detected two asymptomatic people, who had no confirmed contact with patients with COVID-19. The highest percentage of positive samples was observed in the 80+ group (16.3%), while among the children and adults it did not exceed 8%. Among all the people tested, 2423 came from a total of 80 different destinations and only 27 of them were positive for SARS-CoV-2. Out of all the positive samples, 15 were taken for SARS-CoV-2 sequencing. According to the analysis of the genome sequences, the SARS-CoV-2 variants isolated in the Novosibirsk region at the beginning of the pandemic belonged to three phylogenetic lineages according to the Pangolin classification: B.1, B.1.1, and B.1.1.129. All Novosibirsk isolates contained the D614G substitution in the Spike protein, two isolates werecharacterized by an additional M153T mutation, and one isolate wascharacterized by the L5F mutation. [ABSTRACT FROM AUTHOR]

During 2006, H5N1 HPAI caused an epizootic in wild birds, resulting in a die-off of Laridae in the Novosibirsk region at Chany Lake. In the present study, we infected common gulls (Larus canus) with a high dose of the H5N1 HPAI virus isolated from a common gull to determine if severe disease could be induced over the 28 day experimental period. Moderate clinical signs including diarrhea, conjunctivitis, respiratory distress and neurological signs were observed in virus-inoculated birds, and 50% died. The most common microscopic lesions observed were necrosis of the pancreas, mild encephalitis, mild myocarditis, liver parenchymal hemorrhages, lymphocytic hepatitis, parabronchi lumen hemorrhages and interstitial pneumonia. High viral titers were shed from the oropharyngeal route and virus was still detected in one bird at 25 days after infection. In the cloaca, the virus was detected sporadically in lower titers. The virus was transmitted to direct contact gulls. Thus, infected gulls can pose a significant risk of H5N1 HPAIV transmission to other wild migratory waterfowl and pose a risk to more susceptible poultry species. These findings have important implications regarding the mode of transmission and potential risks of H5N1 HPAI spread by gulls. [ABSTRACT FROM AUTHOR]