A one-year genomic surveillance of SARS-CoV-2 in patients from two sites in Burkina Faso

Background: Despite the availability of vaccines against SARS‑CoV‑2, mortality due to COVID-19 continues to increase, with nearly 7 million deaths reported globally. Continued analysis of the evolution and genomic diversity can provide necessary information to timely inform public health responses. We report the dynamics of SARS‑CoV‑2 lineages in Burkina Faso between August 2021 and September 2022.Methodology: A total of 188 patients, whose nasopharyngeal and/or oropharyngeal swabs tested positive for SARS-CoV-2 by RT-PCR at the National Influenza Reference Laboratory (NIRL) of the Institut de Recherche en Sciences de la Santé (IRSS) in Burkina Faso, were sequenced, and the whole genomes of the virus annotated and screened for mutations using the ARTIC protocol and Oxford Nanopore Technology. Subsequently, different SARS-CoV-2 lineages were assigned using NextClade. The socio-demographic characteristics of the study participants were collected. Descriptive statistics on the data were conducted using R software version 4.3.2. Comparisons were made using the Chi-square test for qualitative variables, and statistical significance was set at p<0.05.Results: Majority of the 188 COVID-19 positive cases lived in urban areas (85.1%), travelling from high-risk transmission zones. Of 134 SARS-CoV-2 genomes successfully sequenced and submitted to the NextClade database, the Delta (50.7%, n=68) and Omicron (42.5%, n=57) variants were predominant. The most frequent lineages detected were B.1.617.2 (20.1%, n=27), BA.1.13 (17.2%, n=23), and AY.133 (14.2%, n=19). Temporal trend showed that the pandemic was driven by the Delta variant which was progressively replaced by the Omicron variant of SARS-CoV-2.Conclusion: Although heterogeneity was seemingly not important during the study period, the Delta variant which was the most predominant variant in the country, was progressively replaced by the Omicron variant. Continuous genomic surveillance might be necessary to timely detect the virulent variants.