Phylogeography, phylodynamics and the recent outbreak of lineage 3 porcine reproductive and respiratory syndrome viruses in China

Abstract

Novel highly pathogenic porcine reproductive and respiratory syndrome viruses (PRRSVs) have attracted increasing attention owing to their continual high emergence and recent re‐emergence. Recently, lineage 3 PRRSVs, belonging to the type 2 viruses, with novel characteristics and increased virulence have been continuously re‐emerging in China, thereby posing a great threat to pig farming. However, available information about lineage 3 is limited. Here, we carried out molecular epidemiological investigations for PRRSV surveillance in most regions of China from 2007 to 2017. More than 3,000 samples were obtained, amounting to 73 sequences of lineage 3 viruses. The origin, demographic history and spread pattern of lineage 3 PRRSVs were investigated combining with the database globally. Phylogeography and phylodynamic analyses within a Bayesian statistical framework revealed that lineage 3 viruses originated in Taiwan. Followed by subsequent propagation to different areas and geography, it dichotomized into two endemic clusters. South China has become an epicentre for these viruses, which diffused into China's interiors in recent years. Furthermore, viral dispersal route analysis revealed the risk of viral diffusion. Overall, the origin, epidemic history and geographical evolution of lineage 3 PRRSVs were comprehensively analysed in this study. In particular, the epicentre of southern China and the diffusion routines of the viruses are highlighted in this study, and the possible continuous transmission of the novel lineages poses the biggest threat to pig farmers.

Major swine viral diseases: an Asian perspective after the African swine fever introduction

“…After the two HP-PRRSV outbreaks, molecular epidemiology of PRRSV2 in China was complicated by the emergence of various novel PRRSV2 strains, possibly due to multiple introductions, including 1) the emergence of the NAD30-like viruses (lineage 1) in 2012 [27], 2) the emergence of the NADC34-like viruses (lineage 1) in 2018 [14,28] and 3) the diversified genetics of the lineage 3 viruses [29]. The presence of these novel PRRSVs in Asian countries requires further studies.…”

Unraveling the Global Phylodynamic and Phylogeographic Expansion of Mycoplasma gallisepticum: Understanding the Origin and Expansion of This Pathogen in Ecuador

“…A recent algorithm implemented in the TempEst software enables the exploration of the degree and pattern of the temporal signal in the datasets [ 41 ]. This approach has been successfully applied to guarantee a closer relationship between genetic information and the temporal pattern [ 42 , 43 ]. In the current study, the data obtained from the mgc2 marker showed a linear correlation between genetic distance and temporal structure, with an R 2 = 0.95 ( Figure 1 A).…”

Genetic characterization of a novel recombinant PRRSV2 from lineage 8, 1 and 3 in China with significant variation in replication efficiency and cytopathic effects

“…In 2013, a novel NADC30‐like PRRSV named JL580 emerged in northeast of China and lineage 1 rapidly spread throughout China (Bian et al, ; Li, Zhuang, et al, ; Wang et al, ; Zhao et al, ). Reemergence of lineage 3 was reported in 2010 in mainland China and became epidemic since then (Dong et al, ; Han, Xu, Wang, & He, ; Lu et al, ; Shi et al, ; Sun, Han, et al, ; Sun, Li, et al, ; Zhang et al, ). Lineage 8 is further categorized into sublineages 8.3–8.7 (HP‐PRRSV related), sublineage 8.1 (CH‐1a related) and sublineage 8.2 (Gao et al, ).…”