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. 2022 Dec 14;14(12):2788.
doi: 10.3390/v14122788.

Genomic Epidemiology of SARS-CoV-2 in Western Burkina Faso, West Africa

Yacouba Sawadogo  1   2 , Lokman Galal  3   4 , Essia Belarbi  5 , Arsène Zongo  6 , Grit Schubert  5 , Fabian Leendertz  7 , Abdoulie Kanteh  8 , Abdul Karim Sesay  8 , Annette Erhart  9 , Anne-Laure Bañuls  4   10 , Zékiba Tarnagda  11 , Sylvain Godreuil  3   4   10 , Halidou Tinto  12 , Abdoul-Salam Ouedraogo  1   2   6   10
Affiliations

Genomic Epidemiology of SARS-CoV-2 in Western Burkina Faso, West Africa

Yacouba Sawadogo et al. Viruses. .

Abstract

Background: After its initial detection in Wuhan, China, in December 2019, SARS-CoV-2 has spread rapidly, causing successive epidemic waves worldwide. This study aims to provide a genomic epidemiology of SARS-CoV-2 in Burkina Faso.

Methods: Three hundred and seventy-seven SARS-CoV-2 genomes obtained from PCR-positive nasopharyngeal samples (PCR cycle threshold score < 35) collected between 5 May 2020, and 31 January 2022 were analyzed. Genomic sequences were assigned to phylogenetic clades using NextClade and to Pango lineages using pangolin. Phylogenetic and phylogeographic analyses were performed to determine the geographical sources and time of virus introduction in Burkina Faso.

Results: The analyzed SARS-CoV-2 genomes can be assigned to 10 phylogenetic clades and 27 Pango lineages already described worldwide. Our analyses revealed the important role of cross-border human mobility in the successive SARS-CoV-2 introductions in Burkina Faso from neighboring countries.

Conclusions: This study provides additional insights into the genomic epidemiology of SARS-CoV-2 in West Africa. It highlights the importance of land travel in the spread of the virus and the need to rapidly implement preventive policies. Regional cross-border collaborations and the adherence of the general population to government policies are key to prevent new epidemic waves.

Keywords: Burkina Faso; COVID-19; SARS-CoV-2; West Africa; genomic epidemiology; whole genome sequencing.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
COVID-19 confirmed cases and SARS-CoV-2 genetic diversity in western Burkina Faso. Timeline showing the collection dates of the confirmed COVID-19 cases in western Burkina Faso from 9 March 2020 to 20 March 2022 and the during this period (blue line). The colors of bars represent the clades (NextClade nomenclature) that were identified and the heights of bars correspond to the number of sequenced samples each week and passing the global initiative on sharing avian influenza data (GISAID) quality control.
Figure 2
Figure 2
Dated phylogenetic tree showing the 18 transmission clusters identified in western Burkina Faso. The tree branches are color-coded according to each geographic region. The estimated time to the most recent common ancestor (TMRCA) values of Burkina Faso transmission clusters are highlighted by black arrows and circles with consecutive numbering according to the detection date (sample with the earliest collection date within that cluster; see Table 1).
See this image and copyright information in PMC

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