Genomic diversity and selection pressure analyses of low-virulence Yersinia pestis lineages.

Yersinia pestis, the causative agent of plague, is a highly virulent pathogen that has caused three historical pandemics and currently persists in multiple active natural foci worldwide, posing a serious threat to human health and public safety. Distinct phylogenetic lineages of Y. pestis exhibit differences in virulence, among which the Microtus biovar within the 0.PE4 lineage is nearly avirulent to large mammals. Comparative genomics between low-virulence and highly virulent populations is therefore key to elucidating the evolutionary basis of virulence. However, comprehensive population-genomic analysis of the low-virulence lineage remains limited, particularly those integrating multiple types of genomic variations. In this study, we analyzed 169 low-virulence strains and 215 representative high-virulence strains collected from long-term national surveillance data in China and public databases. Phylogenetic and spatiotemporal analyses revealed geographic clustering within the low-virulence 0.PE4 lineage. The 0.PE4.3 subclade circulating in China and Mongolia was further subdivided into three regionally associated tertiary lineages, with two more finely resolved quaternary lineages identified specifically in Inner Mongolia. Comparative genomic analyses with representative high-virulence genomes identified mutations fixed in the most recent common ancestor (MRCA) of the low-virulence population and its subclades. Among these, 81 single nucleotide polymorphisms (SNPs), 19 insertion and deletions (Indels), and 5 large fragment losses are shared by all low-virulence strains, defining the genomic features of their MRCA. Together with selection pressure analysis, we identified five genes (ail, rovA, tssH, cdiA, and alr) under strong positive selection, which are involved in virulence, metabolism, and adaptation. Collectively, this study reconstructs the phylogenetic topology of the global low-virulence Y. pestis population and identifies key genomic variations that occurred during its evolutionary process, providing valuable insights for fine-scale tracing and identifying potential molecular targets for elucidating virulence mechanisms.