Co-Infection and Phylogenetic Evolution of Chicken Infectious Anemia Virus in Marek’s Disease Tumour-Bearing Flocks in Central China During 2020-2023

The avian immunosuppressive and neoplastic diseases are great threats to the poultry industry causing huge economic losses worldwide. Most recently, the emerging hypervirulent variants of Marek’s disease virus (HV-MDV), partially co-infected with avian leukosis virus (ALV) and/or reticuloendotheliosis virus (REV), have been identified as the key driver of tumour outbreaks in vaccinated chicken flocks, but the role of chicken infectious anaemia virus (CIAV) remains unclear. Herein, we have investigated the prevalence and co-infection of CIAV in 72 clinical tumour-bearing flocks collected from central China during 2020-2023, which has shown a CIAV positivity rate of 59.7% (43/72). Notably, the incidence of CIAV mono-infection increased significantly from 0% (0/30) in 2020-2021 to 26.2% (11/42) in 2022-2023, whereas CIAV+MDV co-infection decreased from 66.7% (20/30) to 28.6% (12/42). A total of 20 viral genomes of epidemic CIAV isolates from diverse sources were obtained, and the phylogenetic analysis including 91 reference isolates were clustered into four major lineages (A–D), with a clade C further subdivided into subclades C1 and C2. Clade C1 consisted predominantly of Asian isolates, with 88.5% (46/52) of the isolates originated from mainland China. Among the 20 new isolates, 17 were clustered in subclade C1, two in C2, and one in B. The VP1 gene phylogeny showed a topology largely consistent with that of the whole-genome analysis. Moreover, all newly characterized isolates contained glutamine (Q) at VP1 residue 394, a molecular marker associated with high pathogenicity. Collectively, our data suggest that prevalent HV-MDV variants together with CIAV co-infections are the primary drivers of the ongoing tumour outbreaks in Chinese poultry flocks. Furthermore, the increased pathogenicity observed in CIAV mono-infections, likely resulting from an independently evolving lineage among circulating Chinese strains, will pose a significant challenge for future control of disease.