Does Avian Coronavirus Co-Circulate with Avian Paramyxovirus and Avian Influenza Virus in Wild Ducks in Siberia?

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.

Changes in the Etiology of Acute Respiratory Infections among Children in Novosibirsk, Russia, between 2019 and 2022: The Impact of the SARS-CoV-2 Virus.

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).

Detection of coronaviruses in insectivorous bats of Fore-Caucasus, 2021.

Coronaviruses (CoVs) pose a huge threat to public health as emerging viruses. Bat-borne CoVs are especially unpredictable in their evolution due to some unique features of bat physiology boosting the rate of mutations in CoVs, which is already high by itself compared to other viruses. Among bats, a meta-analysis of overall CoVs epizootiology identified a nucleic acid observed prevalence of 9.8% (95% CI 8.7-10.9%). The main objectives of our study were to conduct a qPCR screening of CoVs' prevalence in the insectivorous bat population of Fore-Caucasus and perform their characterization based on the metagenomic NGS of samples with detected CoV RNA. According to the qPCR screening, CoV RNA was detected in 5 samples, resulting in a 3.33% (95% CI 1.1-7.6%) prevalence of CoVs in bats from these studied locations. BetaCoVs reads were identified in raw metagenomic NGS data, however, detailed characterization was not possible due to relatively low RNA concentration in samples. Our results correspond to other studies, although a lower prevalence in qPCR studies was observed compared to other regions and countries. Further studies should require deeper metagenomic NGS investigation, as a supplementary method, which will allow detailed CoV characterization.

Genomic and Epidemiological Features of COVID-19 in the Novosibirsk Region during the Beginning of the Pandemic.

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.