Four divergent groups of duck astroviruses (DAstVs) have been identified that infect domestic ducks. In March 2021, a fatal disease characterized by visceral urate deposition broke out in 5-day-old Beijing ducks on a commercial farm in Guangdong province, China. The pathogen was confirmed to be a duck astrovirus. The complete genome sequence of this DAstV was obtained by virome sequencing and amplification. Phylogenetic analyses and pairwise comparisons demonstrated that this DAstV represented a novel group of avastrovirus. Thus, we designated this duck astrovirus as DAstV-5 JM strain. DAstV-5 JM shared genome sequence identities of 15–45% with other avastroviruses. Amino acid identities with proteins from other avastroviruses did not exceed 59% for ORF1a, 79% for ORF1b, and 60% for ORF2. The capsid region of JM shared genetic distances of 0.596 to 0.695 with the three official avastrovirus species. In summary, we determined that the DAstV-5 JM strain, causing gout in ducklings, is a novel species of avastrovirus.

Four divergent groups of duck astroviruses (DAstVs) have been identified that infect domestic ducks. In March 2021, a fatal disease characterized by visceral urate deposition broke out in 5-day-old Beijing ducks on a commercial farm in Guangdong province, China. The pathogen was confirmed to be a duck astrovirus. The complete genome sequence of this DAstV was obtained by virome sequencing and amplification. Phylogenetic analyses and pairwise comparisons demonstrated that this DAstV represented a novel group of avastrovirus. Thus, we designated this duck astrovirus as DAstV-5 JM strain. DAstV-5 JM shared genome sequence identities of 15–45% with other avastroviruses. Amino acid identities with proteins from other avastroviruses did not exceed 59% for ORF1a, 79% for ORF1b, and 60% for ORF2. The capsid region of JM shared genetic distances of 0.596 to 0.695 with the three official avastrovirus species. In summary, we determined that the DAstV-5 JM strain, causing gout in ducklings, is a novel species of avastrovirus.

Continuous monitoring and analysis of the evolution, recombination and epidemic of avian influenza virus will help to prevent and control the emergence of new avian influenza virus. The genes of 153 H5N6 avian influenza viruses selected from our long-term surveillance data and the GISAID for the 2016-2019 period were dissected in detail. Our analysis shows that the genes of H5N6 AIVs have been divided into more lineages, and that mutations leading to amino acid replacement of hemagglutinin and neuraminidase occurred mainly between 2017 and 2018. All H5N6 viruses are differentiated into at least 20 distinct genotypes derived from different evolutionary pathways. G1 genotype has replaced other genotypes to become dominant genotype of AIV. The results of animal experiments show that H5N6 of different genotypes has high virulence to mice. which indicates that H5N6 AIVs, especially the reassortment strains, are a potential threat to public health.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), along with Severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East Respiratory Syndrome Coronavirus (MERS-CoV) are three emerging coronaviruses with huge public health in the 21st century. Especially, SARS-CoV-2 causes an unprecedented global pandemic and has spread in over than 200 countries. Clinically, SARS-CoV-2 could co-infected with respiratory pathogens including influenza virus and adenovirus in some present cases. This suggests that the differential diagnosis cannot be ignored. To investigate whether SARS-CoV-2 exists earlier and identify possible co-infection in human with respiratory disease, we performed the detections of SARS-CoV-2 and influenza virus using real-time RT-PCR method and colloidal gold test strip in 534 throat swab samples collected in influenza epidemic season (from January to May of 2019). 336 samples (62.9%) were tested positive for influenza virus, which involved into 230 single influenza A virus (IAV)-positive samples, 4 single influenza B virus (IBV)-positive samples, and 102 IAV and IBV co-infection samples. Unfortunately, we found no positive signal of SARS-CoV-2 in 534 samples. Our finding reveals absence of SARS-CoV-2 infection in human archived samples in before the outbreak of SARS-CoV-2 in China. In addition, this study suggests that IAV was still major respiratory pathogen responsible for respiratory disease in the influenza season.