Molecular Characteristics of Chicken Infectious Anemia Virus in Central and Eastern China from 2020 to 2022

SIMPLE SUMMARY: An immune-suppressive disease known as chicken infectious anemia (CIA) develops after infection with chicken infectious anemia virus (CIAV). This study involved a systematic analysis of the epidemiology and genomics of CIAV in the provinces of Henan, Anhui, Jiangsu, and Hubei in China. The positive rates of the samples from each province flock ranged from 50% to 80%. Meanwhile, coinfections of CIAV with Marek’s disease virus, avian leukosis virus, infectious bursal disease virus, and fowl adenovirus were also identified. This study revealed the diversity of CIAV genomes as well as key mutation sites and intricate recombinants. The study findings underscore the importance of CIAV surveillance and provide a basis for further investigation into the evolution and molecular characteristics of CIAV strains. ABSTRACT: To evaluate the recent evolution of CIAV in China, 43 flocks of chickens from the provinces of Henan, Jiangsu, Hubei, and Anhui were screened via polymerase chain reaction during 2020–2022. Of these, 27 flocks tested positive for CIAV nucleic acids, including 12 which were positive for other immunosuppression viruses. Additionally, 27 CIAV strains were isolated, and their whole genomes were sequenced. The AH2001 and JS2002 strains shared the highest identity at 99.56%, and the HB2102 and HB2101 strains shared the lowest identity at 95.34%. Based on the genome sequences of these strains and reference strains, a phylogenetic tree was constructed and divided into eight main branches. Most of the strains were grouped with the East Asian strains, whereas the HB2101 strain belonged to the Brazil and Argentina cluster. A recombination event was detected in multiple strains, in which AH2002 recombined from KJ728827/China/2014 (from Taiwan Province) and HN2203, and AH2202 recombined from KX811526/China/2017 (from Shandong Province) and HN2203. All the obtained strains had a highly pathogenic Gln amino acid site at position 394 of the VP1. Overall, our findings demonstrate the importance of CIAV monitoring and provide data that aid in understanding the evolution of CIAV.