Metaviromic Profiling of Genetic Diversity and Prevalence of Suid Herpesviruses Circulating in China

Three species of suid herpesviruses (SuHVs) have been reported in pigs, specifically pseudorabies virus (PRV), porcine cytomegalovirus (PoCMV), and porcine lymphotropic herpesvirus (PLHV). However, their genetic diversity and epidemic circulating status in China remain largely unclear. In this study, 7200 nasal swabs and 2571 serum samples were collected from pigs across 17 provincial regions in China in 2017. All samples were pooled into 22 libraries based on sample type and geographic origin for high-throughput next-generation sequencing. Metaviromic analysis identified all three SuHV species, revealing marked variations in their detection rates and viral abundance. Notably, PoCMV and PRV were detected in all 17 sampled provinces, accompanied by high viral genome sequence abundance (RPM > 1 × 102), while PLHV was only found in nasal swabs from 10 provinces, with extremely low sequence abundance (RPM < 2). Further phylogenetic and genetic diversity analyses revealed notable molecular characteristics of the three circulating SuHVs: PoCMV exhibited substantial genetic diversity with at least two major evolutionary clades identified in Chinese pig populations; variant genotype II PRV strains were confirmed as the predominant circulating lineage; and potential PLHV variants with partial sequence divergence from the reference strain were also found to circulate in China. These findings enrich the molecular epidemiological data of SuHVs in Chinese pig populations and highlight the previously overlooked, highly widespread circulation of PoCMV, warranting attention to its potential impacts on swine health and production performance.