Circulation, genomic characteristics, and evolutionary dynamics of class I Newcastle disease virus in China

Newcastle disease caused by Newcastle disease virus (NDV) is one of the most serious threats to chickens and has two clinical forms, typical and atypical, caused by velogenic and lentogenic strains, respectively. To control the epidemic, many vaccines against velogenic class II NDVs have been introduced worldwide, but this has led to accelerated mutation of class II viruses under immune pressure and, on the other hand, to non-vaccine targeting class I NDVs becoming the dominant population in poultry. In this context, this study provided the first large-scale genomic epidemiological and quasispecies dynamic analysis of class I NDVs in China, and found that class I viruses that first appeared in East and South China have spread to central China and become the dominant class with an average evolutionary rate of 1.797 × 10^-3. In addition, single nucleotide polymorphism and intra-host single nucleotide variation analyses show that HN and P genes have high mutation rates and may act as front-runners for NDV to expand their host range and enhance their virulence. This study also found that the class I NDV population has accumulated a number of mutations under positive selection and that six isolates with shortened C-terminal extensions of the HN protein are evolving toward increased virulence. These results not only enrich the research resources but also help us to better understand the dynamic evolution and mutational trends of NDV at the genomic level, which is crucial for monitoring, early warning, and controlling the outbreak of Newcastle disease.