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The flyways of many different wild waterfowl pass through the Caspian Sea region. The western coast of the middle Caspian Sea is an area with many wetlands, where wintering grounds with large concentrations of birds are located. It is known that wild waterfowl are a natural reservoir of the influenza A virus. In the mid-2000s, in the north of this region, the mass deaths of swans, gulls, and pelicans from high pathogenicity avian influenza virus (HPAIV) were noted. At present, there is still little known about the presence of avian influenza virus (AIVs) and different avian paramyxoviruses (APMVs) in the region's waterfowl bird populations. Here, we report the results of monitoring these viruses in the wild waterfowl of the western coast of the middle Caspian Sea from 2017 to 2020. Samples from 1438 individuals of 26 bird species of 7 orders were collected, from which 21 strains of AIV were isolated, amounting to a 1.46% isolation rate of the total number of samples analyzed (none of these birds exhibited external signs of disease). The following subtypes were determined and whole-genome nucleotide sequences of the isolated strains were obtained: H1N1 ( n = 2), H3N8 ( n = 8), H4N6 ( n = 2), H7N3 ( n = 2), H8N4 ( n = 1), H10N5 ( n = 1), and H12N5 ( n = 1). No high pathogenicity influenza virus H5 subtype was detected. Phylogenetic analysis of AIV genomes did not reveal any specific pattern for viruses in the Caspian Sea region, showing that all segments belong to the Eurasian clades of classic avian-like influenza viruses. We also did not find the amino acid substitutions in the polymerase complex (PA, PB1, and PB2) that are critical for the increase in virulence or adaptation to mammals. In total, 23 hemagglutinating viruses not related to influenza A virus were also isolated, of which 15 belonged to avian paramyxoviruses. We were able to sequence 12 avian paramyxoviruses of three species, as follows: Newcastle disease virus ( n = 4); Avian paramyxovirus 4 ( n = 5); and Avian paramyxovirus 6 ( n = 3). In the Russian Federation, the Newcastle disease virus of the VII.1.1 sub-genotype was first isolated from a wild bird (common pheasant) in the Caspian Sea region. The five avian paramyxovirus 4 isolates obtained belonged to the common clade in Genotype I, whereas phylogenetic analysis of three isolates of Avian paramyxovirus 6 showed that two isolates, isolated in 2017, belonged to Genotype I and that an isolate identified in 2020 belonged to Genotype II. The continued regular monitoring of AIVs and APMVs, the obtaining of data on the biological properties of isolated strains, and the accumulation of information on virus host species will allow for the adequate planning of epidemiological measures, suggest the most likely routes of spread of the virus, and assist in the prediction of the introduction of the viruses in the western coastal region of the middle Caspian Sea., Competing Interests: The authors declare no conflicts of interest. The funding entities had no role in the design of the study, in the collection of material, analyses or interpretation of data, in the writing of the manuscript, or in the decision to publish the results.

In this study, we characterized for the first time the gut microbiota of Greylag geese (Anser anser) using high-throughput 16S rRNA gene sequencing technology. The results showed that the phyla Firmicutes (78.55%), Fusobacteria (9.38%), Proteobacteria (7.55%), Bacteroidetes (1.82%), Cyanobacteria (1.44%), and Actinobacteria (0.61%) dominated the gut microbial communities in the Greylag geese. Then, the variations of gut microbial community structures and functions among the three geese species, Greylag geese, Bar-headed geese (Anser indicus), and Swan geese (Anser cygnoides), were explored. The greatest gut microbial diversity was found in Bar-headed geese group, while other two groups had the least. The dominant bacterial phyla across all samples were Firmicutes and Proteobacteria, but several characteristic bacterial phyla and genera associated with each group were also detected. At all taxonomic levels, the microbial community structure of Swan geese was different from those of Greylag geese and Bar-headed geese, whereas the latter two groups were less different. Functional KEGG categories and pathways associated with carbohydrate metabolism, energy metabolism, and amino acid metabolism were differentially expressed among different geese species. Taken together, this study could provide valuable information to the vast, and yet little explored, research field of wild birds gut microbiome., (© 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

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]

Simple Summary: Modern evolutionary biology offers a wide variety of methods to explore the evolution of species and to describe their relationships. The methods of DNA/RNA sequence analysis have been developing for decades and have become increasingly popular and reasonably reliable. Nevertheless, final phylogenetic trees for many taxa are still under debate because both classical and genomics-based approaches have their own limitations for phylogenetic tree reconstruction. Here, we propose the use of younger 'omics' methods, namely quantitative metabolomics, to aid the phylogeny reconstruction of vertebrates. We show that metabolomics-based hierarchical clustering analysis trees match, although not perfectly, to the genomics-based trees. In the current pilot study, we propose the use of quantitative metabolomics to reconstruct the phylogeny of vertebrates, namely birds. We determined the concentrations of the 67 most abundant metabolites in the eye lenses of the following 14 species from 6 orders of the class Aves (Birds): the Black kite (Milvus migrans), Eurasian magpie (Pica pica), Northern raven (Corvus corax), Eurasian coot (Fulica atra), Godlewski's bunting (Emberiza godlewskii), Great crested grebe (Podiceps cristatus), Great tit (Parus major), Hawfinch (Coccothraustes coccothraustes), Hooded crow (Corvus cornix), House sparrow (Passer domesticus), Rock dove (Columba livia), Rook (Corvus frugilegus), Short-eared owl (Asio flammeus) and Ural owl (Strix uralensis). Further analysis shows that the statistical approaches generally used in metabolomics can be applied for differentiation between species, and the most fruitful results were obtained with hierarchical clustering analysis (HCA). We observed the grouping of conspecific samples independently of the sampling place and date. The HCA tree structure supports the key role of genomics in the formation of the lens metabolome, but it also indicates the influence of the species lifestyle. A combination of genomics-based and metabolomics-based phylogeny could potentially resolve arising issues and yield a more reliable tree of life. [ABSTRACT FROM AUTHOR]

An H5N6 highly pathogenic avian influenza virus (HPAIV) outbreak occurred in poultry in Japan during January 2018, and H5N6 HPAIVs killed several wild birds in 3 prefectures during Winter 2017–2018. Time-measured phylogenetic analyses demonstrated that the Hemagglutinin (HA) and internal genes of these isolates were genetically similar to clade 2.3.4.4.B H5N8 HPAIVs in Europe during Winter 2016–2017, and Neuraminidase (NA) genes of the poultry and wild bird isolates were gained through distinct reassortments with AIVs that were estimated to have circulated possibly in Siberia during Summer 2017 and Summer 2016, respectively. Lethal infectious dose to chickens was similar between the poultry and wild-bird isolates. H5N6 HPAIVs during Winter 2017–2018 in Japan had higher 50% chicken lethal doses and lower transmission efficiency than the H5Nx HPAIVs that caused previous outbreaks in Japan, thus explaining in part why cases during the 2017–2018 outbreak were sporadic. • ・The N6 genes of H5N6 HPAIVs differed in origin between poultry and wild birds. • ・Reassortment of H5N6 HPAIVs likely occurred during Summer in 2016 and 2017. • ・Infectivity and transmissibility of H5N6 HPAIVs in Japan were low in chickens. [ABSTRACT FROM AUTHOR]

The rarely identified influenza A viruses of the H15 hemagglutinin subtype have been isolated exclusively in Australia. Here we report the isolation of an H15N4 influenza A virus (A/teal/Chany/7119/2008) in Western Siberia, Russia. Phylogenetic analysis demonstrated that the internal genes of the A/teal/Chany/7119/2008 strain belong to the Eurasian clade and that the H15 and N4 genes were introduced into the gene pool of circulating endemic avian influenza viruses through reassortment events. [ABSTRACT FROM AUTHOR]