Mbaye Aminata, Diallo Haby, Gnimadi Thibaut Armel Cherif, Kadio Kadio Jean Jacques Olivier, Soumah Abdoul Karim, Koivogui Joel Balle, Monemou Jean Louis, Povogui Moriba Kowa, Kaba Djiba, Hounmenou Castro, Serrano Laetitia, Butel Christelle, Nuñez Nicolas Fernandez, Vidal Nicole, Guichet Emilande, Delaporte Eric, Ayouba Ahidjo, Peeters Martine, Toure Abdoulaye, Keita Alpha Kabinet
Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de Conakry, Conakry, Guinea.
TransVIHMI, University of Montpellier, Institut de Recherche pour le Développement (IRD), INSERM, Montpellier, France.
BMC Infect Dis. 2025 Jan 2;25(1):3. doi: 10.1186/s12879-024-10411-2.
Several variants of SARS-CoV-2 have a demonstrated impact on public health, including high and increased transmissibility, severity of infection, and immune escape. Therefore, this study aimed to determine the SARS-CoV-2 lineages and better characterize the dynamics of the pandemic during the different waves in Guinea.
Whole genome sequencing of 363 samples with PCR cycle threshold (Ct) values under thirty was undertaken between May 2020 and May 2023. The Illumina iSeq 100 technology was used. The sequences were then analyzed using the GeVarli pipeline to generate consensus sequences and variant calling. All sequences isolated in Guinea and available on GISAID were included in the analysis for phylogenetic tree and phylodynamic determination. Nextstain tools were used for these analyses. Statistical analysis was done using GraphPad Prism version 10.
The circulation of SARS-CoV-2 in Guinea can be distributed in three different periods. The first, lasting from May to June 2020, was characterized by lineages B1 and B.1.1. The second period, from January 2021 to July 2021, was characterized by the lineages B.1.1.7 (Alpha), AY.122, B.1.1.318, R1, B.1.525 and B.1.629. The third period, between December 2021 and May 2023, was characterized by the Omicron variant, with nine subvariant majorities found. In addition, detecting variants in the period out of their circulation was documented. The importation and exportation investigation showed the strong movement viral association between Guinea and Senegal on the one hand and Guinea and Nigeria on the other.
In summary, this study contributes to understanding the epidemic dynamics of the disease by describing the significant variants that circulated in Guinee and the distribution of this variant in the population. It also shows the importation and exportation of the virus during the pandemic. Sub-sampling and degradation of samples for sequences were observed. Organization and collaboration between laboratories are needed for a good sample-collecting and storage system for future direction.
严重急性呼吸综合征冠状病毒2（SARS-CoV-2）的几种变体已被证明对公共卫生有影响，包括高传播性和传播性增加、感染严重性以及免疫逃逸。因此，本研究旨在确定SARS-CoV-2谱系，并更好地描述几内亚不同疫情波期间大流行的动态。
在2020年5月至2023年5月期间，对363份聚合酶链反应循环阈值（Ct）值低于30的样本进行了全基因组测序。使用了Illumina iSeq 100技术。然后使用GeVarli管道对序列进行分析，以生成共识序列并进行变异检测。在几内亚分离并可在全球共享流感数据倡议组织（GISAID）上获取的所有序列都被纳入系统发育树和系统发育动力学测定的分析中。使用Nextstain工具进行这些分析。使用GraphPad Prism 10版本进行统计分析。
SARS-CoV-2在几内亚的传播可分为三个不同时期。第一个时期从2020年5月持续到6月，其特征是B1和B.1.1谱系。第二个时期从2021年1月到2021年7月，其特征是B.1.1.7（阿尔法）、AY.122、B.1.1.318、R1、B.1.525和B.1.629谱系。第三个时期在2021年12月至2023年5月之间，其特征是奥密克戎变体，发现了9种主要亚变体。此外，还记录了在变体传播期之外检测到变体。进出口调查显示，一方面几内亚与塞内加尔之间，另一方面几内亚与尼日利亚之间存在强烈的病毒传播关联。
总之，本研究通过描述在几内亚传播的重要变体及其在人群中的分布，有助于了解该疾病的流行动态。它还显示了大流行期间病毒的进出口情况。观察到样本用于测序时的二次抽样和降解情况。为了建立良好的样本采集和储存系统以供未来参考，实验室之间需要进行组织和协作。
