Phylogeny and Historical-Geographical Analysis of <i>Yersinia pestis</i> Strains from Vietnam

Abstract

Objective of the work was to identify molecular-genetic peculiarities, to conduct whole genome sequencing and phylogenetic analysis of Yersinia pestis strains isolated inVietnam between 1962 and 1989.Materials and methods. We have studied the properties of 50 Y. pestis strains, carried out whole genome sequencing of 18 and fragment sequencing of 32 strains from Vietnam. Phylogenetic analysis was performed on the basis of whole genome SNPanalysis by 1391 identified SNPs. Whole genome SNP-analysis and search for marker SNPs were conducted applying Wombac 2.0 software package. Phylogenetic diagram construction was done using Maximum Likelihood algorithm.Results and discussion. Several phylogenetic branches and Y. pestis populations coinciding with geographical and historical dissemination of the strains have been distinguished. The major part of the strains from Vietnam falls under the branch designated by us as 1.ORI2v. Two strains form a separate branch together with the strain from India belonging to 1.ORI2 line, one more strain, 55-801 Saigon, is set among the strains of 1.ORI1 line. Based on the data obtained and evidence from the literature sources it can be assumed that introduction of plague into Vietnam occurred through several waves: Nha Trang city in 1898, by sea; north provinces of the country – 1908. The second wave of Y. pestis dissemination across the territory of Vietnam began in 1960s with the emergence of the strains from the natural plague focus in Yunnan province, China.

Genomic diversity of Yersinia pestis from Yunnan Province, China, implies a potential common ancestor as the source of two plague epidemics

“…1a and 2 ). A high-resolution phylogenetic tree, containing only 1.ORI2 strains showed that the five Vietnam strains 19 , 20 , isolated in 1962 (Saigon-Nhatraung-62-3), 1967 (140-Dalat), 1986 (P-13273, P-13272), and 1988 (P-14709) were grouped together and formed a distinct clade (Supplementary Figs. 1b and 2 , Supplementary Data 2 ).…”

<i>Yersinia pestis</i> Strains of the 1.ORI Line as Etiological Agent of the Plague Pandemic III

“…кроме того, в литературе имеются данные, что штаммы ветви 1.ORI1 занесены с территории китая (гонконг) во вьетнам [8,11]. это подтверждают данные полногеномного секвенирования штаммов восточного биовара из вьетнама [12]. в работе G. Morelli et al с помощью филогенетического анализа показано существование девяти волн радиации ветви 1.ORI2: 1.ORI2а -берет свое начало в китае, откуда в 1896 г. на корабле из гонконга занесена в бомбей; 1.ORI2ii -распространилась по территории Юго-восточной азии; 1.ORI2iiiохватила северную африку (марокко, сенегал); 1.ORI2iv -распространилась в центральную и Южную африку; 1.ORI2v -характерна для Южной америки; 1.ORI2vi -была распространена в европе; 1.ORI2vii -еще одна линия эволюции в центральной и Южной африке; 1.ORI2viii -эта линия попала из индии в европу и оттуда в Южную америку; 1.ORI2ix -линия берет начало в китае, откуда привнесена во вьетнам и мьянму, после чего состоялся обратный занос из мьянмы в китайскую провинцию Юньнань [8,11].…”