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The black-necked crane (Grus nigricollis) is a vulnerable species, breeding exclusively on the high-altitude wetlands of the Qinghai–Tibet Plateau. Bird species harbor diverse communities of microorganisms within their gastrointestinal tracts, which have important roles in the health, nutrition, and physiology of birds. Hitherto, virtually nothing was known about the gut microbial communities associated with wild black-necked cranes. For the first time, this study characterized the gut microbial community compositions, diversity, and functions of black-necked cranes from six wintering areas in China using the Illumina Miseq platform. The taxonomic results revealed that Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes were the four most abundant phyla in the gut of black-necked cranes. At the genus level, 11 genera including Lactobacillus, Pseudomonas, Carnobacterium, Pantoea, Enterococcus, Erwinia, Turicibacter, Bacillus, Phenylobacterium, Sanguibacter, and Psychrobacter were dominant. The differences in the gut microbial community alpha and the beta diversities of black-necked cranes among the six wintering areas were investigated. Furthermore, the representative microbial taxa and their predicted functions in each wintering location were also determined. These data represent the first analysis of the gut microbiome of black-necked cranes, providing a baseline for further microbiological studies and a foundation for the conservation of this bird. [ABSTRACT FROM AUTHOR]

Since 2013, H5N6 highly pathogenic avian influenza viruses (HPAIVs) have been responsible for outbreaks in poultry and wild birds around Asia. H5N6 HPAIV is also a public concern due to sporadic human infections being reported in China. In the current study, we isolated an H5N6 HPAIV strain (A/Muscovy duck/Long An/AI470/2018; AI470) from an outbreak at a Muscovy duck farm in Long An Province in Southern Vietnam in July 2018 and genetically characterized it. Basic Local Alignment Search Tool (BLAST) analysis revealed that the eight genomic segments of AI470 were most closely related (99.6%–99.9%) to A/common gull/Saratov/1676/2018 (H5N6), which was isolated in October 2018 in Russia. Furthermore, AI470 also shared 99.4%–99.9% homology with A/Guangxi/32797/2018, an H5N6 HPAIV strain that infected humans in China in 2018. Phylogenetic analyses of the entire genome showed that AI470 was directly derived from H5N6 HPAIVs that were in South China from 2015 to 2018 and clustered with four H5N6 HPAIV strains of human origin in South China from 2017 to 2018. This indicated that AI470 was introduced into Vietnam from China. In addition, molecular characteristics related to mammalian adaptation among the recent human H5N6 HPAIV viruses, except PB2 E627K, were shared by AI470. These findings are cause for concern since H5N6 HPAIV strains that possess a risk of human infection have crossed the Chinese border. [ABSTRACT FROM AUTHOR]

We isolated Tamdy virus (TAMV; strain XJ01/TAMV/China/2018) from Hyalomma asiaticum ticks infesting Bactrian camels in Xinjiang, China, in 2018. The genome of the strain showed high nucleotide similarity with previously described TAMV strains from Asia. Our study highlights the potential threat of TAMV to public health in China. [ABSTRACT FROM AUTHOR]

Avian orthoavulavirus 13 (AOAV-13), also named avian paramyxovirus 13 (APMV-13), has been found sporadically in wild birds around the world ever since the discovery of AOAV-13 (AOAV-13/wild goose/Shimane/67/2000) in a wild goose from Japan in 2000. However, there are no reports of AOAV-13 in China. In the present study, a novel AOAV-13 virus (AOAV-13/wild goose/China/Hubei/V93-1/2015), isolated from a wild migratory waterfowl in a wetland of Hubei province of China, during active surveillance from 2013 to 2018, was biologically and genetically characterized. Phylogenetic analyses demonstrated a very close genetic relationship among all AOAV-13 strains, as revealed by very few genetic variations. Moreover, pathogenicity tests indicated that the V93-1 strain is a low virulent virus for chickens. However, the genome of the V93-1 virus was found to be 16,158 nucleotides (nt) in length, which is 12 nt or 162 nt longer than the other AOAV-13 strains that have been reported to date. The length difference of 12 nt in strain V93-1 is due to the existence of three repeats of the conserved sequence, "AAAAAT", in the 5′-end trailer of the genome. Moreover, the HN gene of the V93-1 virus is 2070 nt in size, encoding 610 aa, which is the same size as the AOAV-13 strain from Japan, whereas that of two strains from Ukraine and Kazakhstan are 2080 nt in length, encoding 579 aa. We describe a novel AOAV-13 in migratory waterfowl in China, which suggests that diversified trailer region sequences and HN gene lengths exist within serotype AOAV-13, and highlight the need for its constant surveillance in poultry from live animal markets, and especially migratory birds. [ABSTRACT FROM AUTHOR]

To discover sources for novel anti-influenza drugs, we evaluated the antiviral potential of nine extracts from eight medicinal plants and one mushroom ( Avena sativa L., Hordeum vulgare Linn. var. nudum Hook. f., Hippophae rhamnoides Linn., Lycium ruthenicum Murr., Nitraria tangutorum Bobr., Nitraria tangutorum Bobr. by-products, Potentilla anserina L., Cladina rangiferina (L.) Nyl., and Armillaria luteo-virens ) from the Qinghai-Tibetan plateau against the influenza A/H3N2 virus. Concentrations lower than 125 μg/mL of all extracts demonstrated no significant toxicity in MDCK cells. During screening, seven extracts ( A. sativa , H. vulgare , H. rhamnoides , L. ruthenicum , N. tangutorum , C. rangiferina , and A. luteo-virens ) exhibited antiviral activity, especially the water-soluble polysaccharide from the fruit body of the mushroom A. luteo-virens . These extracts significantly reduced the infectivity of the human influenza A/H3N2 virus in vitro when used at concentrations of 15.6-125 μg/mL. Two extracts ( N. tangutorum by-products and P. anserina ) had no A/H3N2 virus inhibitory activity. Notably, the extract obtained from the fruits of N. tangutorum and N. tangutorum by-products exhibited different anti-influenza effects. The results suggest that extracts of A. sativa , H. vulgare , H. rhamnoides , L. ruthenicum , N. tangutorum , C. rangiferina , and A. luteo-virens contain substances with antiviral activity, and may be promising sources of new antiviral drugs.

We have surveyed avian influenza virus (AIV) genomes from live poultry markets within China since 2014. Here we present a total of 16,091 samples that were collected from May 2016 to February 2019 in 23 provinces and municipalities in China. We identify 2048 AIV-positive samples and perform next generation sequencing. AIV-positive rates (12.73%) from samples had decreased substantially since 2016, compared to that during 2014-2016 (26.90%). Additionally, H9N2 has replaced H5N6 and H7N9 as the dominant AIV subtype in both chickens and ducks. Notably, novel reassortants and variants continually emerged and disseminated in avian populations, including H7N3, H9N9, H9N6 and H5N6 variants. Importantly, almost all of the H9 AIVs and many H7N9 and H6N2 strains prefer human-type receptors, posing an increased risk for human infections. In summary, our nation-wide surveillance highlights substantial changes in the circulation of AIVs since 2016, which greatly impacts the prevention and control of AIVs in China and worldwide.

As one of the dominant waterfowl species of wetland areas in the Qinghai-Tibet Plateau, since 2003, artificial rearing of bar-headed geese (Anser indicus) has increased in several provinces of China for the purpose of conservation and economic development. In this study, we systematically characterized the microbial community diversity, compositions and predicted functions of semi-artificially reared bar-headed geese by sampling five different gut locations (the oropharynxs, crops, gizzards, ceca, and cloacae) along the gastrointestinal tracts of three individuals. Alpha diversity analyses showed that the gizzards had the richest species diversity and that the ceca had the least. Beta diversity analyses showed that the cecal samples formed their own cluster, while samples from the oropharynxs, crops, gizzards, and cloacae overlapped with each other. At the phylum level, Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria constituted the top five dominant phyla among all five gastrointestinal sections. At the genus level, a total of 10 genera with proportions above 2.5% were found to be significantly different among the gastrointestinal sections. Furthermore, 53 genera were detected in all gastrointestinal sections of bar-headed geese. PICRUSt data also predicted a group of microbial functions overrepresented in the different segments of the gastrointestinal tracts. Understanding the microbiota along the bar-headed geese gastrointestinal tracts is essential for future microbiological study of this bird and may contribute to the development of geese husbandry.

We isolated Tamdy virus (TAMV; strain XJ01/TAMV/China/2018) from Hyalomma asiaticum ticks infesting Bactrian camels in Xinjiang, China, in 2018. The genome of the strain showed high nucleotide similarity with previously described TAMV strains from Asia. Our study highlights the potential threat of TAMV to public health in China.

Gut microbiome contributes to host health by maintaining homeostasis, increasing digestive efficiency, and facilitating the development of immune system. Wild greylag geese (Anser anser) and ruddy shelducks (Tadorna ferruginea), migrating along the central Asian flyway, appear to be one of the most popular species in the rare birds rearing industries of China. However, the structure and function of the gut microbial communities associated with these two bird species remain poorly understood. Here, for the first time, we compared gut metagenomes from greylag geese to ruddy shelducks and investigated the similarities and differences between these two bird species in detail. Taxonomic classifications revealed the top three bacterial phyla, Firmicutes, Proteobacteria, and Fusobacteria, in both greylag geese and ruddy shelducks. Furthermore, between the two species, 12 bacterial genera were found to be more abundant in ruddy shelducks and 41 genera were significantly higher in greylag geese. A total of 613 genera (approximately 70%) were found to be present in both groups. Metabolic categories related to carbohydrate metabolism, metabolism of cofactors and vitamins, lipid metabolism, amino acid metabolism, and glycan biosynthesis and metabolism were significantly more abundant in ruddy shelducks, while greylag geese were enriched in nucleotide metabolism and energy metabolism. The herbivorous greylag geese gut microbiota harbored more carbohydrate-active enzymes than omnivorous ruddy shelducks. In our study, a range of antibiotic resistance categories were also identified in the gut microbiota of greylag geese and ruddy shelducks. In addition to providing a better understanding of the composition and function of wild birds gut microbiome, this comparative study provides reference values of the artificial domestication of these birds., (© 2018 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.)