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Meta-Analysis
. 2025 Jan 31;17(2):204.
doi: 10.3390/v17020204.

Genetic Diversity and Spatiotemporal Distribution of SARS-CoV-2 Variants in Guinea: A Meta-Analysis of Sequence Data (2020-2023)

Thibaut Armel Chérif Gnimadi  1   2   3 , Kadio Jean-Jacques Olivier Kadio  1 , Mano Joseph Mathew  2   3 , Haby Diallo  1 , Abdoul Karim Soumah  1 , Alpha Kabiné Keita  1 , Castro Gbêmêmali Hounmenou  1 , Nicolas Fernandez-Nuñez  4 , Nicole Vidal  4 , Emilande Guichet  4 , Ahidjo Ayouba  4 , Eric Delaporte  4 , Martine Peeters  4 , Abdoulaye Touré  1 , Alpha Kabinet Keita  1   4
Affiliations
Meta-Analysis

Genetic Diversity and Spatiotemporal Distribution of SARS-CoV-2 Variants in Guinea: A Meta-Analysis of Sequence Data (2020-2023)

Thibaut Armel Chérif Gnimadi et al. Viruses. .

Abstract

In Guinea, genomic surveillance has been established to generate sequences of and to identify locally circulating SARS-CoV-2 variants. This study aims to describe the distributions, genetic diversity, and origins of SARS-CoV-2 lineages circulating in Guinea during the COVID-19 pandemic. A migration analysis was performed by selecting all sequences generated in Guinea for variants of concern and interest. From March 2020 to December 2023, 1038 sequences were generated in Guinea and submitted to the Global Initiative on Sharing All Influenza Data (GISAID) database. Of these, 73.1% corresponded to SARS-CoV-2 variants of concern, which were further grouped into Omicron (69.4%), Delta (21.9%), Alpha (6.6%), and Eta (2.1%). Other variants accounted for 26.9% of the total. Among the total variants analyzed, 75 importations into Guinea from various countries worldwide were identified. Most of the importations (40%) originated from African countries, followed in significance by those from European countries (25.3%) and Asia (18.6%). A significant migratory flow was observed within Guinea. The genomic surveillance reported in this study revealed the diversity of SARS-CoV-2 variants circulating in Guinea, emphasizing the importance of large-scale sequencing analyses in understanding the dynamics of the pandemic.

Keywords: SARS-CoV-2; genetic diversity; guinea; phylodynamic.

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Conflict of interest statement

The authors declare no conflicts of interest. The funders had no role in the design of the study, in the collection, analyses, or interpretation of data, in the writing of the manuscript, or in the decision to publish the results.

Figures

Figure 1
Figure 1
Trends in the prevalence of major variants circulating in Guinea from March 2020 to December 2024. The Y-axis shows the distribution (n = 1038) of various variants across the various months (X-axis), while different colors represent the lineages.
Figure 2
Figure 2
Map showing the sampled regions (n = 1038) and the color scheme showing the number of sequences generated from samples collected in each region.
Figure 3
Figure 3
Frequencies of amino-acid substitutions across all the SARS-CoV-2 proteins in all high-quality genomes submitted to GISAID for Guinea (n = 644/1038). The mutations are sorted and colored by gene.
Figure 4
Figure 4
(A) Number of importation events by world region of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages (Alpha, Eta, Delta, Omicron {BA.1, BA.2, BA.5, BQ.1, XBB.1}, and sublineages) into Guinea from March 2020 to December 2023. (B) Geographical distribution of the importations.
Figure 5
Figure 5
Number and origin of importation events of the different SARS-CoV-2 lineages (Alpha, Eta, Delta, Omicron {BA.1, BA.2, BA.5, BQ.1 and XBB.1.5}, and sublineages) into Guinea between March 2020 and December 2023.
Figure 6
Figure 6
Timescale phylogeny of SARS-CoV-2 lineages (Alpha, Eta, Delta, Omicron {BA.1, BA.2, BA.5, BQ.1 and XBB.1.5} and sublineages). Five hundred sequences were subsampled from a global dataset to maximize genetic distances while retaining all genomes from Guinea. The branches are scaled in decimal time, and sampling dates are capped on each lineage’s last sampling date, the latest sampling month in Guinea in this study.
Figure 7
Figure 7
Number of SARS-CoV-2 imports and exports into and out of various regions in Guinea.
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