The newly emerged lineage 1 porcine reproductive and respiratory syndrome viruses (PRRSVs) (especially the NADC30‐like and NADC34‐like viruses) have posed a direct threat to the Chinese pig industry since 2013. The phylogenetic, epidemic, and recombinant properties of these viruses have not yet systematically analyzed in China. This report presents regular surveillance and field epidemiological studies for PRRSV across China from 2007 to 2019. From over 4000 detected clinical samples, 70 open reading frame 5 sequences and 4 complete genomes of lineage 1 viruses were successfully obtained. Combined with global data, we conducted an extensive and systematic molecular phylogeny analysis using a maximum likelihood tree. The Chinese lineage 1 viruses were clustered and their temporal and spatial distribution was further explored. Multiple viral introductions of lineage 1 virus from the United States to China were detected, and some became endemic in China. There are three sub‐lineage 1 clusters: lineage 1.5 (NADC34‐like), lineage 1.6, and New Intro cluster (NADC30‐like). These viruses show high genetic diversity and a wide distribution in China, with Henan province showing the highest diversity. Moreover, Chinese lineage 1 viruses have developed an endemic NADC30‐like cluster. The demographic feature of this cluster showed a more or less constant population expansion history with a recent decreasing trend. Moreover, the genome recombination of Chinese lineage 1 with two dominant clusters (Chinese HP‐PRRSVs: lineage 8.7 and VR2332‐like: lineage 5.1) was frequently detected, both of which have commercial vaccine strains available. Furthermore, recombination hotspots were discovered near NSP9 and ORF2‐4 regions of the genome. Overall, these findings provide important insights into the evolution and geographical diversity of Chinese lineage 1 PRRSV. These results will facilitate the development of programs for the control and prevention of the emerging lineage 1 viruses in China.

Lineage 3 of porcine reproductive and respiratory syndrome viruses, which belong to North America type 2, has a long epidemic history in China. The novel lineage 3 viruses constantly emerging in recent years are characterized by a high detection rate and significant pathogenicity. In this study, we investigated the prevalence of lineage 3 in southern China and selected two isolated strains for genome and virulence analyses. A cross‐sectional epidemiology investigation indicated that the prevalence of lineage 3 antigens was 35.68% (95% CI: 27.6–44.3%) among 227 samples collected from over 100 infected farms from January 2016 to July 2017 in southern China. Two novel isolates of lineage 3 were selected. After 20 passages, Marc‐145 cells were not susceptible to those viruses. Full‐length genome analysis indicated that the two strains share 95.2% homology with each other and 95.7%–96.2% with highly pathogenic porcine reproductive and respiratory syndrome viruses (HP‐PRRSVs; JXA1‐like strain, lineage 8.7). Phylogenetic and molecular evolutionary results showed that for the two isolates, HP‐PRRSV provides most of the ORF1 gene. Animal experiment revealed discrepancies in virulence between the strains. Although challenge resulted in 100% morbidity, the isolate carrying most of the HP‐PRRSV ORF1 caused severe clinical symptoms and 40% mortality, whereas the other isolate containing part of the ORF1 gene caused no mortality. Overall, these findings suggest that lineage 3 viruses might be commonly circulating in most of southern China. Frequent recombination events within HP‐PRRSVs of this lineage with changing virulence could represent potential threats to the pig industry.

Since 2018, the outbreaks of genotype II African swine fever virus (ASFV) in China and several eastern Asian countries have caused a huge impact on the local swine industry, resulting in huge economic losses. However, little is known about the origin, genomic diversity, evolutionary features, and epidemiological history of the genotype II ASFV. Here, 14 high-quality complete genomes of ASFVs were generated via sequencing of samples collected from China over the course of 3 years, followed by phylogenetic and phylodynamic analyses. The strains identified were relatively homogeneous, with a total of 52 SNPs and 11 indels compared with the prototype strain HLJ/2018, among which there were four exceptionally large deletions (620–18,023 nt). Evolutionary analyses revealed that ASFV strains distributed in eastern Asia formed a monophyly and a ‘star-like’ structure centered around the prototype strain, suggesting a single origin. Additionally, phylogenetic network analysis and ancestral reconstruction of geographic state indicated that genotype II ASFV strains in eastern Asia likely originated from Western Europe. Overall, these results contribute to the understanding of the history and current status of genotype II ASFV strains in eastern Asian, which could be of considerable importance in disease control and prevention.