Fig 1.
Distribution of Y. pestis strains in the DH Rattus tanezumi plague focus between 1953 and 2007.
(A) Spatial and (B) temporal distribution of 175 newly sequenced strains. Geographic abbreviations: Yingjiang (YJ), Lianghe (LH), Longchuan (LC), Ruili (RL), and Mangshi (MS). Smaller letters indicate towns (for example, ZN) Town abbreviations: Zhina (ZN), Xincheng (XC), Jiucheng (JC), Nongzhang (NZ), Pingyuan (PY), Taiping (TP), Husa (HS), Chengzi (CZ), Jinghan (JH), Zhangfeng (ZF), Longba (LB), Wanding (WT), Mengmao (MM), Jiexiang (JX), Nongdao (ND), Zhefang (Z.F), Jiubao (JB), Zhedao (ZD), Mangdong (MD). Circle size represents the number of strains. Different colors represent phylogroups or counties, as shown in the legend. The map was created using the “ggplot2” (v3.4.1) and “sf” (v1.0–13) packages for R software (v4.2.2). The base layer used in the map was obtained from Amap’s open data platform (http://datav.aliyun.com/portal/school/atlas/area_selector).
Fig 2.
Phylogenetic positioning of the Dehong Dai-Jingpo (DH) Y. pestis strains.
A maximum likelihood phylogeny including 175 DH strains and 339 publicly available genomes was generated based on 3,483 SNPs in the core genome. Isolation location for each strain is indicated in the outer circle. For clarity, only phylogroups involving DH strains are marked.
Fig 3.
Population structure of DH Y. pestis strains located in lineage 1.ORI2.
(A) A minimal spanning (MS) tree of 172 DH Y. pestis strains based on 132 SNPs in the core genome, using the Y. pestis CO92 strain as the outgroup. Pink circles indicate sub-phylogroups. The circle size of the MS tree represents the number of strains, while different colors of the circle represent geographical isolation locations, abbreviated as follows: Yingjiang (YJ), Lianghe (LH), Longchuan (LC), Ruili (RL), and Mangshi (MS). (B) A maximum likelihood tree of 172 DH Y. pestis strains based on 132 SNPs in the core genome, using the Y. pestis CO92 strain as the outgroup. Sub-phylogroups are labeled using black lines; SPG2 strains located near the root of the phylogeny are unmarked. Isolation dates and locations are shown in different colors.
Fig 4.
Dynamic changes in Y. pestis subpopulations in the DH Rattus tanezumi plague focus after 1982.
(A) Temporal distribution of DH Y. pestis subpopulations isolated after 1982. (B) Geographical distribution of DH Y. pestis subpopulations isolated between 1982 and 1989. (C) Geographical distribution of DH Y. pestis subpopulations isolated between 1990 and 1999. (D) Geographical distribution of DH Y. pestis subpopulations isolated between 2000 and 2007. The boundaries of urban surfaces are illustrated using black lines. Light grey curves indicate traffic lines. Geographic abbreviations: Yingjiang (YJ), Lianghe (LH), Longchuan (LC), Ruili (RL), and Mangshi (MS). Town abbreviations: Zhina (ZN), Xincheng (XC), Jiucheng (JC), Nongzhang (NZ), Pingyuan (PY), Taiping (TP), Husa (HS), Chengzi (CZ), Jinghan (JH), Zhangfeng (ZF), Longba (LB), Wanding (WT), Mengmao (MM), Jiexiang (JX), Nongdao (ND), Zhefang (Z.F), Jiubao (JB), Zhedao (ZD), Mangdong (MD). The map was created using the “ggplot2” (v3.4.1) and “sf” (v1.0–13) packages for R software (v4.2.2). The base layer used in the map was obtained from Amap’s open data platform (http://datav.aliyun.com/portal/school/atlas/area_selector).
Fig 5.
Southwest to northeast spread routes of Y. pestis isolated after 1982.
Black lines represent the spread routes, and arrows indicate the direction of spread. Numbers indicate the spread events. Counties within the green circle indicate the possible source of DH plague epidemics. Geographic abbreviations: Yingjiang (YJ), Lianghe (LH), Longchuan (LC), Ruili (RL), and Mangshi (MS). The map was created using the “ggplot2” (v3.4.1) and “sf” (v1.0–13) packages for R software (v4.2.2). The base layer used in the map was obtained from Amap’s open data platform (http://datav.aliyun.com/portal/school/atlas/area_selector).