The first human infections with avian influenza virus (AIV) H9N2 were reported in 1998 (Guo et al. 1999). As of October 18th, 2019, 59 cases of human infection with H9N2 have been reported globally, including 50 cases in China, three in Bangladesh, four in Egypt, one in Pakistan and one in Oman (World Health Organization. https://www.who.int/wer/en/; Peacock et al. 2019). Among the 59 patients, three (5.1%) presented with severe pneumonia and 56 had mild influenza-like symptoms (World Health Organization. https://www.who.int/influenza/human_animal_interface/HAI_Risk_Assessment/en/). In general, human infections with H9N2 are sporadic and the majority of cases are mild and non-fatal, and there is no evidence of human-to-human transmission to date (Peacock et al. 2019).

During the 2018–2019 flu season, the number of patients with influenza-like illness that presented at Wuhan JinYinTan Hospital (Hubei, China) increased and more patients showing severe illness compared to previous years. To characterize the epidemic influenza virus, 54 oropharyngeal swabs collected from patients with influenza-like illness between January and February 2019, with influenza A-positive, were subjected to next-generation sequencing (NGS). Among of 54 swabs, full-length genomes of H9N2 viruses were obtained from 16 swab samples, and the H9N2 isolates were confirmed by Haemagglutination inhibition (HI) assay and RT-PCR (see supplementary materials for details). Furthermore, these 16 orophyaryngeal swabs were negative for seasonal influenza (H1, H3, and influenza B virus) and other subtypes AIV tested by RT-PCR and the next generation sequencing. Namely, sixteen patients were confirmed to have H9N2 virus infection. 16 inpatients infected with H9N2 virus were included in this study. The history of hospitalization and physical examination, hematological, biochemical, radiological, and microbiological test results were collected. Among 16 patients, 11 (68.8%) had severe illness (including four deaths), whereas symptoms of H9N2 infection are usually mild. We further explored the epidemiological and clinical characteristics of these cases to provide a much-needed theoretical basis for the prevention and treatment of human H9N2 infection.

The median age of the 16 patients was 61.5 years old (range 13 months to 88 years old) (Supplementary Table S1). Five patients (31.3%) were 65 years of age or older, two patients (12.5%) were infants. There were more male (n?=?10) than female patients (Supplementary Table S1). The 16 confirmed cases were distributed over five districts of Hubei Province, and 56.3% (9/16) were in Wuhan, the capital city of Hubei Province (Supplementary Figure S1).

To identify the sources and transmission routes of the human H9N2 AIVs, an epidemiological retrospective study was conducted in seven patients between June and July 2019 (other nine patients were failed to be contacted) (Table 1). Five (71.4%) patients had antibodies against H9N2 in their convalescent sera as indicated by HI assay (Table 1, Supplementary Table S2). Among the seven patients (median age, 61 years old), five (71.4%) were male. Most patients (5/7, 71.4%) had underlying health conditions. Three patients (patients 7, 8, and 10) had been exposed to live poultry. None of the patients had ever traveled (Table 1). Thirteen serum samples were collected from six patients (patient 4 died) and seven family members. Six out of seven tested family members carried anti-H9N2 antibodies (Table 1, Supplementary Table S2), none of them had a history of poultry exposure. Three family members of two patients had also developed flu-like symptoms, and two of them carried H9N2 antiboby (wife of patient 1, patient 1-W; husband of patient 16, patient 16-H; the sera of father of patient 16 was not collected). These findings indicate that, there is a possibility of human-to-human transmission of H9N2.