The pandemic spread of African swine fever (ASF) has caused serious effects on the global pig industry. Virus genome sequencing and genomic epidemiology analysis play an important role in tracking the outbreaks of the disease and tracing the transmission of the virus. Here we obtained the full-length genome sequence of African swine fever virus (ASFV) in the first outbreak of ASF in China on August 3^rd, 2018 and compared it with other published genotype II ASFV genomes including 9 genomes collected in China from September 2018 to October 2020. Phylogenetic analysis on genomic sequences revealed that genotype II ASFV has evolved into different genetic clusters with temporal and spatial correlation since being introduced into Europe and then Asia. There was a strong support for the monophyletic grouping of all the ASFV genome sequences from China and other Asian countries, which shared a common ancestor with those from the Central or Eastern Europe. An evolutionary rate of 1.312×10⁻⁵ nucleotide substitutions per site per year was estimated for genotype II ASFV genomes. Eight single nucleotide variations which located in MGF110-1L, MGF110-7L, MGF360-10L, MGF505-5R, MGF505-9R, K145R, NP419L, and I267L were identified as anchor mutations that defined genetic clusters of genotype II ASFV in Europe and Asia. This study expanded our knowledge of the molecular epidemiology of ASFV and provided valuable information for effective control of the disease.

Peste des petits ruminants (PPR) is a highly contagious and lethal disease, primarily affecting sheep, goats, and wild small ruminants. Genomic characterization and evolutionary analysis of the circulating PPR virus (PPRV) strains can provide valuable information for the implementation of efficient control measures. In this study, we generated 28 novel PPRV full-length genome sequences from clinical samples collected during 28 PPR outbreaks in livestock and wildlife hosts across 15 provinces in China from 2014 to 2021. These genome sequences were compared with 135 published PPRV genome sequences, 37 of which were collected from China. The evolutionary rate of the PPRV genome was estimated to be 6.70 × 10 ⁻⁴ nucleotide substitutions per site per year. The predominant PPRV lineage IV can be divided into seven clades, demonstrating the temporal and spatial correlation. PPRV in China from 2007 to 2008 and 2013 to 2024 were grouped into two distinct genetic clades in lineage IV, indicating two independent incursions of the disease in 2007 and 2013. The PPRV in China from 2013 to 2024 shared a common ancestor with a strain from the UAE and evolved into four distinct genetic clusters, which did not exhibit distinct temporal, spatial, and host correlation. We used PPRV/XJYL/2013 as the reference genome, and 997 single-nucleotide variations (SNVs) were identified in PPRV genomes in China from 2013 to 2024. A total of five single-nucleotide variations, located in the 3′ leader, 5′ untranslated region (UTR) of the F gene, H cds, and L cds, were identified as anchor mutations, which defined the genetic clusters of PPRV during this period. One site in the H gene and five sites in the L gene were identified under positive selection. Our study provides significant insights into the molecular epidemiology, evolution, and transmission of PPRV, which will support the development of effective strategies for PPR control and eradication.

African swine fever (ASF) is a lethal contagious viral disease of domestic pigs and wild boars caused by the African swine fever virus (ASFV). The pandemic spread of ASF has had serious effects on the global pig industry. Virus genome sequencing and comparison play an important role in tracking the outbreaks of the disease and tracing the transmission of the virus. Although more than 140 ASFV genome sequences have been deposited in the public databases, the genome-wide diversity of ASFV remains unclear. Here we prepared a curated dataset of ASFV genome sequences by filtering genomes with sequencing errors as well as duplicated genomes. A total of 123 ASFV genome sequences were included in the dataset, representing 10 genotypes collected between 1949 and 2020. Phylogenetic analysis based on whole-genome sequences provided high-resolution topology in differentiating closely related ASFV isolates, and drew new clues in the classification of some ASFV isolates. Genome-wide diversity of ASFV genomes was explored by pairwise sequence similarity comparison and ORF distribution comparison. Tandem repeat sequences were found widely distributed and highly varied in ASFV genomes. Structural variation and highly variable poly G or poly C tracts also contributed to the genome diversity. This study expanded our knowledge on the patterns of genetic diversity and evolution of ASFV, and provided valuable information for diagnosis improvement and vaccine development.

The transmission cycle of Japanese encephalitis virus (JEV), involving pigs and birds as amplifying hosts and mosquitoes as vectors, was elucidated in the 1950s. However, factors contributing to this cycle remain unclear. Here, sheep were infected with a JEV strain isolated from sheep exhibiting neurological symptoms. The results revealed that sheep are susceptible to JEV infection and develop viremia, with levels and duration comparable to those observed in pigs, a known JEV-amplifying host. Mosquitoes fed viremic sheep blood showed an infection rate of 40.6 to 57.1%. These findings indicate that sheep can serve as amplifying hosts for JEV, potentially contributing to JEV transmission and increasing the public health risk of human infections. We propose an alternative, sheep-associated rural domestic JEV transmission cycle, which may be prevalent in specific regions where sheep are bred but pigs are not. This cycle exists along with the well-known pig-associated rural domestic and bird-associated wild cycles.