Genomic epidemiology and the role of international and regional travel in the SARS-CoV-2 epidemic in Zimbabwe: a retrospective study of routinely collected surveillance data.
Genomic epidemiology and the role of international and regional travel in the SARS-CoV-2 epidemic in Zimbabwe: a retrospective study of routinely collected surveillance data.
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DOI：
10.1016/s2214-109x(21)00434-4
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发表时间：
2021-12
期刊：
影响因子：
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通讯作者：
SARS-CoV-2 Research Group
中科院分区：
文献类型：
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作者：
Mashe T;Takawira FT;de Oliveira Martins L;Gudza-Mugabe M;Chirenda J;Munyanyi M;Chaibva BV;Tarupiwa A;Gumbo H;Juru A;Nyagupe C;Ruhanya V;Phiri I;Manangazira P;Goredema A;Danda S;Chabata I;Jonga J;Munharira R;Masunda K;Mukeredzi I;Mangwanya D;Trotter A;Le Viet T;Rudder S;Kay G;Baker D;Thilliez G;Gutierrez AV;O'Grady J;Hove M;Mutapuri-Zinyowera S;Page AJ;Kingsley RA;Mhlanga G;COVID-19 Genomics UK Consortium;SARS-CoV-2 Research Group
在SARS-CoV-2测序方面取得的进展使我们能够识别新的变体，跟踪其进化并监测其传播。我们的目标是使用全基因组测序来描述SARS-CoV-2爆发的分子流行病学，并为津巴布韦实施有效的公共卫生干预措施提供信息。我们对2020年3月20日至10月16日期间从津巴布韦9个实验室收集的鼻咽样本进行了回顾性研究。根据对国际入境人员的检疫程序或对有症状者或阳性病例的密切接触者进行感染检测，采集了样本。在诊断性PCR检测中循环阈值小于30的样本进行测序处理。我们于2020年7月（自第一例病例起120天）开始分析，并于2020年10月（自第一例病例起210天）进行了随访。利用最大似然和贝叶斯方法建立了津巴布韦和全球样本基因组序列的系统发育关系。在研究期间收集的92 299份鼻咽标本中，pcr阳性8099份，测序328份，序列质量控制合格156份。156名参与者中有83名（53%）是女性。在最初的210天里，至少有26次SARS-CoV-2独立传入津巴布韦，与12个全球谱系有关。156例中有151例（97%）的刺突蛋白发生了Asp614Gly突变。大多数病例（93例（60%））是从津巴布韦境外输入的。在疫情发生6天后报告了社区传播。在国际和区域移民将SARS-CoV-2引入津巴布韦后，最初的公共卫生干预措施推迟了该病毒在社区传播的发生。全球全基因组序列数据对于揭示主要传播途径和指导干预策略至关重要。卫生组织、非洲疾控中心、生物技术和生物科学研究理事会、医学研究理事会、国家卫生研究所和基因组研究有限公司。
Advances in SARS-CoV-2 sequencing have enabled identification of new variants, tracking of its evolution, and monitoring of its spread. We aimed to use whole genome sequencing to describe the molecular epidemiology of the SARS-CoV-2 outbreak and to inform the implementation of effective public health interventions for control in Zimbabwe. We performed a retrospective study of nasopharyngeal samples collected from nine laboratories in Zimbabwe between March 20 and Oct 16, 2020. Samples were taken as a result of quarantine procedures for international arrivals or to test for infection in people who were symptomatic or close contacts of positive cases. Samples that had a cycle threshold of less than 30 in the diagnostic PCR test were processed for sequencing. We began our analysis in July, 2020 (120 days since the first case), with a follow-up in October, 2020 (at 210 days since the first case). The phylogenetic relationship of the genome sequences within Zimbabwe and global samples was established using maximum likelihood and Bayesian methods. Of 92 299 nasopharyngeal samples collected during the study period, 8099 were PCR-positive and 328 were available for sequencing, with 156 passing sequence quality control. 83 (53%) of 156 were from female participants. At least 26 independent introductions of SARS-CoV-2 into Zimbabwe in the first 210 days were associated with 12 global lineages. 151 (97%) of 156 had the Asp614Gly mutation in the spike protein. Most cases, 93 (60%), were imported from outside Zimbabwe. Community transmission was reported 6 days after the onset of the outbreak. Initial public health interventions delayed onset of SARS-CoV-2 community transmission after the introduction of the virus from international and regional migration in Zimbabwe. Global whole genome sequence data are essential to reveal major routes of spread and guide intervention strategies. WHO, Africa CDC, Biotechnology and Biological Sciences Research Council, Medical Research Council, National Institute for Health Research, and Genome Research Limited.