Genomic epidemiological analysis of county-scale spread pattern of Yersinia pestis over 50 years in a prefecture of the Southwestern China

Plague, one of the most devastating infectious diseases in human history, is caused by the bacterium Yersinia pestis. Since 1950s, twice plague epidemics that lead to 1153 human cases and 379 death were recorded in DeHong Dai - JingPo Autonomous Prefecture (DH), Yunnan Province, China. The genetic diversity and transmission details of Y. pestis strains in this region kept unknown. Here, we performed high-resolution genomic epidemiological analysis on 175 Y. pestis strains isolated from five counties and 19 towns in DH from 1953 to 2007, which were involved in two epidemic periods. Phylogenetic analysis revealed that the majority of DH strains were located in 1.ORI2, which could be further subdivided into seven sub-phylogroups (SPG1-SPG7). Epidemic1 strains were mainly distributed in SPG1, while Ep idemic2 strains all located in SPG2-SPG7. The dominant sub-phylogroups of Y. pestis in DH varied during different periods, present a phenomenon of population shift. Genomic evidence showed that Epidemic2 strains might originated from the southwest of DH (e.g. LongChuan or RuiLi County) or its bordering countries, and then spread to the northeast. Interestingly, our result also revealed that N01, the first observed strain of Epidemic2 and the MRCA of all seven sub-phylogroups, was isolated in LongChuan County, suggesting that LongChuan are likely the origin source of the two epidemics. Our study infers a fine-scale phylogeny and spread pattern of DH Y. pestis population, which extend our knowledge on genetic diversity of Y. pestis and provides clues for future prevention and control of plague in this region.