General characteristics of the study population (n = 99 participants).

General characteristics of the study population (n = 99 participants).</p

GISAID accession numbers associated with this study.

GISAID accession numbers associated with this study.</p

SARS-CoV-2 sequence abundance and lineage distributions among African regions in GISAID.

A) Monthly number of sequences by lineage and B) monthly lineage frequency distribution using Pango nomenclature for lineages in Guinea compared to the lineages with a frequency >1% observed in surrounding African regions. All GISAID sequences deposited up to July 31st were used to examine the similarity in lineage distribution between Guinea and close by African regions. The number of sequences used per geographical location is indicated in panel A).</p

Sequences used from GISAID and acknowledgments.

SARS-CoV-2 has claimed several million lives since its emergence in late 2019. The ongoing evolution of the virus has resulted in the periodic emergence of new viral variants with distinct fitness advantages, including enhanced transmission and immune escape. While several SARS-CoV-2 variants of concern trace their origins back to the African continent—including Beta, Eta, and Omicron–most countries in Africa remain under-sampled in global genomic surveillance efforts. In an effort to begin filling these knowledge gaps, we conducted retrospective viral genomic surveillance in Guinea from October 2020 to August 2021. We found that SARS-CoV-2 clades 20A, 20B, and 20C dominated throughout 2020 until the coincident emergence of the Alpha and Eta variants of concern in January 2021. The Alpha variant remained dominant throughout early 2021 until the arrival of the Delta variant in July. Surprisingly, despite the small sample size of our study, we also found the persistence of the early SARS-CoV-2 clade 19B as late as April 2021. Together, these data help fill in our understanding of the SARS-CoV-2 population dynamics in West Africa early in the COVID-19 pandemic.</div

Phylogenetic analysis of SARS-CoV-2 in Guinea.

A) Map of Guinea in the context of Africa indicating the cities where sequenced samples were collected. B) Distribution of the different SARS-CoV-2 clades in our sample set using Nextclade nomenclature. C) Monthly clade frequency in Guinea using all publicly available sequences from Guinea in the GISAID database until July 2021. D) ML phylogenetic temporal reconstruction of full genome sequences from all full genome sequences from this study and temporally subsampled African sequences from GISAID through July 2021. Taxa corresponding to Guinean sequences are highlighted. Branches and tips are colored by country.</p