Natural selection dominates the codon preference and host adaptability of the novel goose astrovirus related to gout symptons, with non-structural protein playing a key role.

Abstract

Since 2017, the primary cause of fatal gout in Chinese goslings has been identified as new goose astrovirus (N-GoAstV). Its infection can progress to severe liver and kidney damage, cause a mortality rate reaching up to 50 %, significantly impacting China's poultry industry. In this study, we conducted an assessment of codon usage bias (CUB) and host adaptation on the coding sequences of 179 N-GoAstVs derived from different hosts, including chickens, ducks, geese, and muscovy ducks. The results indicated that the complete coding sequences (CCDs) and open reading frames (ORFs) of N-GoAstV preferentially utilize codons ending in A or U not G or C, and that the effective number of codons (ENC) value for N-GoAstV exceeded 50, suggesting a relatively low CUB. Meanwhile, the primary factor influencing the CUB of N-GoAstV was recognized as natural selection, in addition to other influences like mutation pressure. The similarity index (SiD) value analysis indicated that among the three ORFs, ORF1a exhibited the smallest SiD value and the highest adaptability to the host. In contrast, ORF1b demonstrated the highest SiD value, likely due to its greater conservation. Furthermore, ORF1a and 1b had experienced less mutational pressure and total variance compared to ORF2. The results indicated that the CUPs of non-structural proteins could be important for viral adaptation and evasion of the immune system. Correlation analysis (COA) revealed significant differences in CUPs among the two major genotypes of N-GoAstV, while no differences were observed in CUPs across N-GoAstV derived from various host sources. Host adaptation analysis indicated that both geese and ducks may serve as suitable hosts for N-GoAstV. In this study, CUB and host-adaptation analysis were shown to provide valuable insights into the pathogenic mechanisms and facilitate targeted vaccine research for N-GoAstV.