Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia.
National Public Health Reference Laboratory, Ministry of Health, Banjul, The Gambia.
Lancet Glob Health. 2023 Mar;11(3):e414-e424. doi: 10.1016/S2214-109X(22)00553-8.
COVID-19, caused by SARS-CoV-2, is one of the deadliest pandemics of the past 100 years. Genomic sequencing has an important role in monitoring of the evolution of the virus, including the detection of new viral variants. We aimed to describe the genomic epidemiology of SARS-CoV-2 infections in The Gambia.
Nasopharyngeal or oropharyngeal swabs collected from people with suspected cases of COVID-19 and international travellers were tested for SARS-CoV-2 with standard RT-PCR methods. SARS-CoV-2-positive samples were sequenced according to standard library preparation and sequencing protocols. Bioinformatic analysis was done using ARTIC pipelines and Pangolin was used to assign lineages. To construct phylogenetic trees, sequences were first stratified into different COVID-19 waves (waves 1-4) and aligned. Clustering analysis was done and phylogenetic trees constructed.
Between March, 2020, and January, 2022, 11 911 confirmed cases of COVID-19 were recorded in The Gambia, and 1638 SARS-CoV-2 genomes were sequenced. Cases were broadly distributed into four waves, with more cases during the waves that coincided with the rainy season (July-October). Each wave occurred after the introduction of new viral variants or lineages, or both, generally those already established in Europe or in other African countries. Local transmission was higher during the first and third waves (ie, those that corresponded with the rainy season), in which the B.1.416 lineage and delta (AY.34.1) were dominant, respectively. The second wave was driven by the alpha and eta variants and the B.1.1.420 lineage. The fourth wave was driven by the omicron variant and was predominantly associated with the BA.1.1 lineage.
More cases of SARS-CoV-2 infection were recorded in The Gambia during peaks of the pandemic that coincided with the rainy season, in line with transmission patterns for other respiratory viruses. The introduction of new lineages or variants preceded epidemic waves, highlighting the importance of implementing well structured genomic surveillance at a national level to detect and monitor emerging and circulating variants.
Medical Research Unit The Gambia at London School of Hygiene & Tropical Medicine, UK Research and Innovation, WHO.
由 SARS-CoV-2 引起的 COVID-19 是过去 100 年最致命的大流行之一。基因组测序在监测病毒的进化方面发挥着重要作用，包括检测新的病毒变体。我们旨在描述 SARS-CoV-2 在冈比亚的感染的基因组流行病学。
从疑似 COVID-19 病例和国际旅行者中采集鼻咽或口咽拭子，用标准 RT-PCR 方法检测 SARS-CoV-2。对 SARS-CoV-2 阳性样本进行测序，根据标准文库制备和测序方案进行。使用 ARTIC 管道进行生物信息学分析，使用 Pangolin 分配谱系。为了构建系统发育树，首先将序列分层为不同的 COVID-19 波（波 1-4）并进行对齐。进行聚类分析并构建系统发育树。
2020 年 3 月至 2022 年 1 月，冈比亚记录了 11911 例 COVID-19 确诊病例，共测序了 1638 个 SARS-CoV-2 基因组。病例广泛分布在四个波中，雨季（7-10 月）期间病例更多。每个波的发生都伴随着新的病毒变体或谱系的引入，或者两者都有，通常是那些已经在欧洲或其他非洲国家建立的变体或谱系。第一波和第三波（即与雨季相对应的波）期间本地传播较高，分别以 B.1.416 谱系和 delta（AY.34.1）为主导。第二波由 alpha 和 eta 变体和 B.1.1.420 谱系驱动。第四波由 omicron 变体驱动，主要与 BA.1.1 谱系相关。
冈比亚在与雨季相吻合的大流行高峰期记录了更多的 SARS-CoV-2 感染病例，这与其他呼吸道病毒的传播模式一致。新谱系或变体的引入先于疫情浪潮，这突出了在国家层面实施结构良好的基因组监测以检测和监测新出现和流行的变体的重要性。
英国伦敦卫生与热带医学学院冈比亚医学研究单位，英国研究与创新，世界卫生组织。
