Dynamics of SARS-CoV-2 variants in West Africa: Insights into genomic surveillance in resource-constrained settings

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES Infection Genetics and Evolution Pub Date : 2024-10-20 DOI:10.1016/j.meegid.2024.105681

Josue Togo , Anou Moise Somboro , Oumar Dolo , Fatoumata Tata Traore , Ibrehima Guindo , Djeneba B. Fofana , Eve Todesco , Anne-Geneviève Marcelin , Vincent Calvez , Jane Holl , Robert Leo Murphy , Christophe Rodriguez , Mamoudou Maiga , Almoustapha Issiaka Maiga

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Abstract

SARS-CoV-2 geno-surveillance has been challenging in West Africa. Despite the multiple challenges encountered, particularly in West Africa during the COVID-19 pandemic, efforts were made to circumscribe the spread of the disease and to provide methods and resources for surveillance. We aim to describe the dynamic of SARS-CoV-2 variants and highlight the efforts made in genomic surveillance in West Africa. Therefore, we proceeded to retrieve West African countries' SARS-CoV-2 data from public repository (GISAID) and then ensued to a descriptive statistical analysis. From the start of the pandemic till December 2023, we found less than a million COVID-19 cases notified within the West African region. Overall, the study population was 50.21 % Males with a median age of 37. Regarding genomic data, only 3.02 % of cases were sequenced and deposited in GISAID. Of the available sequence, we noted that most of the variants have circulated in West Africa before the official notification of the variants. Nigeria, Ghana, and Senegal provided together more than half of West Africa's originating sequences when Omicron and Delta variants were the most sequenced in West Africa.

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西非 SARS-CoV-2 变异体的动态：资源有限环境下基因组监测的启示。

在西非，SARS-CoV-2 基因监测工作一直面临挑战。尽管遇到了多重挑战，特别是在 COVID-19 大流行期间的西非，但人们还是努力限制疾病的传播，并为监测提供方法和资源。我们的目的是描述 SARS-CoV-2 变异体的动态，并强调西非在基因组监测方面所做的努力。因此，我们从公共资料库（GISAID）中检索了西非国家的 SARS-CoV-2 数据，然后进行了描述性统计分析。从疫情开始到 2023 年 12 月，我们发现西非地区通报的 COVID-19 病例不到一百万例。总体而言，研究人群中 50.21% 为男性，年龄中位数为 37 岁。在基因组数据方面，只有 3.02% 的病例进行了测序并存入 GISAID。我们注意到，在现有序列中，大多数变异体在正式公布之前就已在西非流行。尼日利亚、加纳和塞内加尔提供了西非一半以上的原始序列，而 Omicron 和 Delta 变体是西非测序最多的变体。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Infection Genetics and Evolution 医学-传染病学

CiteScore

8.40

自引率

0.00%

发文量

215

审稿时长

82 days

期刊介绍： (aka Journal of Molecular Epidemiology and Evolutionary Genetics of Infectious Diseases -- MEEGID) Infectious diseases constitute one of the main challenges to medical science in the coming century. The impressive development of molecular megatechnologies and of bioinformatics have greatly increased our knowledge of the evolution, transmission and pathogenicity of infectious diseases. Research has shown that host susceptibility to many infectious diseases has a genetic basis. Furthermore, much is now known on the molecular epidemiology, evolution and virulence of pathogenic agents, as well as their resistance to drugs, vaccines, and antibiotics. Equally, research on the genetics of disease vectors has greatly improved our understanding of their systematics, has increased our capacity to identify target populations for control or intervention, and has provided detailed information on the mechanisms of insecticide resistance. However, the genetics and evolutionary biology of hosts, pathogens and vectors have tended to develop as three separate fields of research. This artificial compartmentalisation is of concern due to our growing appreciation of the strong co-evolutionary interactions among hosts, pathogens and vectors. Infection, Genetics and Evolution and its companion congress [MEEGID](http://www.meegidconference.com/) (for Molecular Epidemiology and Evolutionary Genetics of Infectious Diseases) are the main forum acting for the cross-fertilization between evolutionary science and biomedical research on infectious diseases. Infection, Genetics and Evolution is the only journal that welcomes articles dealing with the genetics and evolutionary biology of hosts, pathogens and vectors, and coevolution processes among them in relation to infection and disease manifestation. All infectious models enter the scope of the journal, including pathogens of humans, animals and plants, either parasites, fungi, bacteria, viruses or prions. The journal welcomes articles dealing with genetics, population genetics, genomics, postgenomics, gene expression, evolutionary biology, population dynamics, mathematical modeling and bioinformatics. We also provide many author benefits, such as free PDFs, a liberal copyright policy, special discounts on Elsevier publications and much more. Please click here for more information on our author services .