Human infection of avian influenza A H3N8 virus and the viral origins: a descriptive study.

BACKGROUND: The H3N8 avian influenza virus (AIV) has been circulating in wild birds, with occasional interspecies transmission to mammals. The first human infection of H3N8 subtype occurred in Henan Province, China, in April, 2022. We aimed to investigate clinical, epidemiological, and virological data related to a second case identified soon afterwards in Hunan Province, China. METHODS: We analysed clinical, epidemiological, and virological data for a 5-year-old boy diagnosed with H3N8 AIV infection in May, 2022, during influenza-like illness surveillance in Changsha City, Hunan Province, China. H3N8 virus strains from chicken flocks from January, 2021, to April, 2022, were retrospectively investigated in China. The genomes of the viruses were sequenced for phylogenetic analysis of all the eight gene segments. We evaluated the receptor-binding properties of the H3N8 viruses by using a solid-phase binding assay. We used sequence alignment and homology-modelling methods to study the effect of specific mutations on the human receptor-binding properties. We also conducted serological surveillance to detect the H3N8 infections among poultry workers in the two provinces with H3N8 cases. FINDINGS: The clinical symptoms of the patient were mild, including fever, sore throat, chills, and a runny nose. The patient's fever subsided on the same day of hospitalisation, and these symptoms disappeared 7 days later, presenting mild influenza symptoms, with no pneumonia. An H3N8 virus was isolated from the patient's throat swab specimen. The novel H3N8 virus causing human infection was first detected in a chicken farm in Guangdong Province in December, 2021, and subsequently emerged in several provinces. Sequence analyses revealed the novel H3N8 AIVs originated from multiple reassortment events. The haemagglutinin gene could have originated from H3Ny AIVs of duck origin. The neuraminidase gene belongs to North American lineage, and might have originated in Alaska (USA) and been transferred by migratory birds along the east Asian flyway. The six internal genes had originated from G57 genotype H9N2 AIVs that were endemic in chicken flocks. Reassortment events might have occurred in domestic ducks or chickens in the Pearl River Delta area in southern China. The novel H3N8 viruses possess the ability to bind to both avian-type and human-type sialic acid receptors, which pose a threat to human health. No poultry worker in our study was positive for antibodies against the H3N8 virus. INTERPRETATION: The novel H3N8 virus that caused human infection had originated from chickens, a typical spillover. The virus is a triple reassortment strain with the Eurasian avian H3 gene, North American avian N8 gene, and dynamic internal genes of the H9N2 viruses. The virus already possesses binding ability to human-type receptors, though the risk of the H3N8 virus infection in humans was low, and the cases are rare and sporadic at present. Considering the pandemic potential, comprehensive surveillance of the H3N8 virus in poultry flocks and the environment is imperative, and poultry-to-human transmission should be closely monitored. FUNDING: National Natural Science Foundation of China, National Key Research and Development Program of China, Strategic Priority Research Program of the Chinese Academy of Sciences, Hunan Provincial Innovative Construction Special Fund: Emergency response to COVID-19 outbreak, Scientific Research Fund of Hunan Provincial Health Department, and the Hunan Provincial Health Commission Foundation.

Genetic characteristics and nucleic acid detection results of SARS-CoV-2 in 2297 clinical samples

Objective To analyze the genomics characteristics and nucleic acid detection results of the severe Acute respiratory syndrome coronavirus 2（SARS-CoV-2） in 2 297 clinical samples collected in January and February, 2020 in Laboratory of Microbiology of Changsha Municipal Center for Disease Control and Prevention. Methods Viral RNA of throat swabs or respiratory tract specimens of coronavirus disease 2019（COVID-19） suspected cases from January 19, 2020 to February 29, 2020 was extracted and SARS-CoV-2 nucleic acid was detected by real-time reverse transcription polymerase chain reaction.The full length genome of SARS-CoV-2 in positive samples was enriched by using viral genome capture kit and sequenced on Illumina MiSeq platform.The raw reads were mapped and aligned with SPAdes software v 3.13.0.Reference SARS-CoV-2 sequences were obtained from GISAID（https://www.gisaid.org） andviral genetic evolution and antigen variation were analyzed. Results A total of 215 SARS-Co V2-nucleic acid positive samples were identified from 2 297 clinical samples.Among the SARS-Co V2-positive samples, 110 were males and 105 were from females.The male to female ratio was 1.05∶1.The highest positive rate was among 40-<60 years old people（11.35%） and the lowest positive rate was in children under 6 years old（5.49%）.The peak of newly confirmed cases was in the 5 th week（January 26 to February 1, 2020） and then decreased.There was no newly positive case after February 25, 2020.Five SARS-Co V2-whole genome sequences were obtained and there were 4 to 6 nucleotide mutations compared to the Wuhan reference strain, and the homology was more than 99.90%.Most mutations occurred only once except C8782 T and T28144 C, indicating random mutations.Phylogenetic analysis revealed that the 5 sequences belonged to the L/B or S/A lineages and were highly homologous with strains prevalent in other provinces of China at the same time. Conclusions With the quick nucleic acid tests and quarantine measures, the SARS-Co V2-positive cases in Changsha began to decline after a 2-week increasing period, and there was no new confirmed cases 6 weeks later.The genomes of SARS-Co V-2 prevalent in Changsha are highly homology with the Wuhan strains in the early 2020 and no obvious mutation is found in the local pandemic period. Reset