Co-circulation of coronavirus and avian influenza virus in wild birds in Shanghai (2020-2021).

Abstract

Co‐infection of SARS‐CoV‐2 and influenza viruses has been reported worldwide in humans. Wild birds are natural reservoir hosts for coronaviruses (CoVs) and avian influenza viruses (AIVs). It is unknown whether co‐infection with these two types of viruses occurs in wild birds. In this study, the prevalence of co‐infection with CoV and AIV in wild birds in Shanghai, China during 2020–2021 was investigated by detecting these viruses in cloacal, tracheal, and faecal samples. Results showed that the overall rate of samples positive for both CoV and AIV was 3.3% (82/2510; 95% confidence interval [CI]: 2.6%–4.0%), and that was mainly from Anseriformes. In CoV‐positive samples, 38.9% (82/211; 95% CI: 32.5%–45.6%) of them had both CoVs and AIVs, whereas only 26.9% (82/305; 95% CI: 22.2%–32.1%) of AIV‐positive samples had both CoVs and AIVs. These results suggest that CoV infection in wild birds renders them more susceptible to AIV infection. Phylogenetic analysis based on partial RNA‐dependent RNA polymerase (RdRp) gene sequences of CoVs revealed that gamma‐CoVs mainly cluster with duck CoVs and that delta‐CoVs are more diversified and cluster with those of various wild birds. Continual surveillance is necessity to monitor the transmission and evolution of co‐infection of these two types of viruses in their natural hosts.