Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil.
MRC Centre for Global Infectious Disease Analysis, Jameel Institute, Imperial College London, London, United Kingdom.
PLoS Negl Trop Dis. 2023 Sep 28;17(9):e0011536. doi: 10.1371/journal.pntd.0011536. eCollection 2023 Sep.
Since 2014, Brazil has experienced an unprecedented epidemic caused by chikungunya virus (CHIKV), with several waves of East-Central-South-African (ECSA) lineage transmission reported across the country. In 2018, Rio de Janeiro state, the third most populous state in Brazil, reported 41% of all chikungunya cases in the country. Here we use evolutionary and epidemiological analysis to estimate the timescale of CHIKV-ECSA-American lineage and its epidemiological patterns in Rio de Janeiro. We show that the CHIKV-ECSA outbreak in Rio de Janeiro derived from two distinct clades introduced from the Northeast region in mid-2015 (clade RJ1, n = 63/67 genomes from Rio de Janeiro) and mid-2017 (clade RJ2, n = 4/67). We detected evidence for positive selection in non-structural proteins linked with viral replication in the RJ1 clade (clade-defining: nsP4-A481D) and the RJ2 clade (nsP1-D531G). Finally, we estimate the CHIKV-ECSA's basic reproduction number (R0) to be between 1.2 to 1.6 and show that its instantaneous reproduction number (Rt) displays a strong seasonal pattern with peaks in transmission coinciding with periods of high Aedes aegypti transmission potential. Our results highlight the need for continued genomic and epidemiological surveillance of CHIKV in Brazil, particularly during periods of high ecological suitability, and show that selective pressures underline the emergence and evolution of the large urban CHIKV-ECSA outbreak in Rio de Janeiro.
自 2014 年以来，巴西经历了一场由基孔肯雅病毒（CHIKV）引起的前所未有的疫情，该国报告了几波中东南非（ECSA）谱系传播。2018 年，巴西人口第三多的里约热内卢州报告了该国所有基孔肯雅热病例的 41%。在这里，我们使用进化和流行病学分析来估计 CHIKV-ECSA-美国谱系的时间尺度及其在里约热内卢的流行模式。我们表明，里约热内卢的 CHIKV-ECSA 爆发源自 2015 年中期（克隆 RJ1，来自里约热内卢的 63/67 个基因组）和 2017 年中期（克隆 RJ2，来自里约热内卢的 4/67 个基因组）从东北部地区引入的两个不同分支。我们在与 RJ1 分支（克隆定义：nsP4-A481D）和 RJ2 分支（nsP1-D531G）中与病毒复制相关的非结构蛋白中检测到与正选择相关的证据。最后，我们估计 CHIKV-ECSA 的基本繁殖数（R0）在 1.2 到 1.6 之间，并表明其瞬时繁殖数（Rt）显示出强烈的季节性模式，传播峰值与埃及伊蚊传播潜力高的时期一致。我们的研究结果强调了巴西需要继续对 CHIKV 进行基因组和流行病学监测，特别是在生态适宜性高的时期，并表明选择压力强调了里约热内卢大型城市 CHIKV-ECSA 爆发的出现和演变。
