The emergence of novel avian influenza viruses in migratory birds is of concern because of the potential for virus dissemination during fall migration. We report the identification of novel highly pathogenic avian influenza viruses of subtype H5N8, clade 2.3.4.4, and their reassortment with other avian influenza viruses in waterfowl and shorebirds of Siberia.

Acute respiratory infections (ARIs) cause a considerable morbidity and mortality worldwide especially in children. However, there are few studies of the etiological structure of ARIs in Russia. In this work, we analyzed the etiology of ARIs in children (0–15 years old) admitted to Novosibirsk Children’s Municipal Clinical Hospital in 2013–2017. We tested nasal and throat swabs of 1560 children with upper or lower respiratory infection for main respiratory viruses (influenza viruses A and B, parainfluenza virus types 1–4, respiratory syncytial virus, metapneumovirus, four human coronaviruses, rhinovirus, adenovirus and bocavirus) using a RT-PCR Kit. We detected 1128 (72.3%) samples were positive for at least one virus. The most frequently detected pathogens were respiratory syncytial virus (358/1560, 23.0%), influenza virus (344/1560, 22.1%), and rhinovirus (235/1560, 15.1%). Viral co-infections were found in 163 out of the 1128 (14.5%) positive samples. We detected significant decrease of the respiratory syncytial virus-infection incidence in children with increasing age, while the reverse relationship was observed for influenza viruses. We evaluated the distribution of respiratory viruses in children with ARIs and showed the prevalence of respiratory syncytial virus and influenza virus in the etiological structure of infections. This study is important for the improvement and optimization of diagnostic tactics, control and prevention of the respiratory viral infections.

To elucidate the evolutionary pathway, we sequenced the entire genomes of 89 H5N6 highly pathogenic avian influenza viruses (HPAIVs) isolated in Japan during winter 2016-2017 and 117 AIV/HPAIVs isolated in Japan and Russia. Phylogenetic analysis showed that at least 5 distinct genotypes of H5N6 HPAIVs affected poultry and wild birds during that period. Japanese H5N6 isolates shared a common genetic ancestor in 6 of 8 genomic segments, and the PA and NS genes demonstrated 4 and 2 genetic origins, respectively. Six gene segments originated from a putative ancestral clade 2.3.4.4 H5N6 virus that was a possible genetic reassortant among Chinese clade 2.3.4.4 H5N6 HPAIVs. In addition, 2 NS clusters and a PA cluster in Japanese H5N6 HPAIVs originated from Chinese HPAIVs, whereas 3 distinct AIV-derived PA clusters were evident. These results suggest that migratory birds were important in the spread and genetic diversification of clade 2.3.4.4 H5 HPAIVs.

Many high pathogenicity avian influenza (HPAI) cases in wild birds due to H5N1 HPAI virus (HPAIV) infection were reported in northern Japan in the winter of 2021–2022. To investigate the epidemiology of HPAIVs brought to Japan from surrounding areas, a genetic analysis of H5 HPAIVs isolated in northern Japan was performed, and the pathogenicity of the HPAIV in chickens was assessed by experimental infection. Based on the genetic analysis of the hemagglutinin gene, pathogenic viruses detected in northern Japan as well as one in Sakhalin, the eastern part of Russia, were classified into the same subgroup as viruses prevalent in Europe in the same season but distinct from those circulating in Asia in winter 2020–2021. High identities of all eight segment sequences of A/crow/Hokkaido/0103B065/2022 (H5N1) (Crow/Hok), the representative isolates in northern Japan in 2022, to European isolates in the same season could also certify the unlikeliness of causing gene reassortment between H5 HPAIVs and viruses locally circulating in Asia. According to intranasal challenge results in six-week-old chickens, 50% of the chicken-lethal dose of Crow/Hok was calculated as 10^4.5 times of the 50% egg-infectious dose. These results demonstrated that the currently prevalent H5 HPAIVs could spread widely from certain origins throughout the Eurasian continent, including Europe and the Far East, and implied a possibility that contagious viruses are gathered in lakes in the northern territory via bird migration. Active monitoring of wild birds at the global level is essential to estimate the geographical source and spread dynamics of HPAIVs.

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).