Genomic epidemiology of SARS-CoV-2 infections in The Gambia: an analysis of routinely collected surveillance data between March, 2020, and January, 2022

Abstract

Background: COVID-19, caused by SARS-CoV-2, is one of the deadliest pandemics of the past 100 years. Genomic sequencing has an important role in monitoring of the evolution of the virus, including the detection of new viral variants. We aimed to describe the genomic epidemiology of SARS-CoV-2 infections in The Gambia.

Methods: Nasopharyngeal or oropharyngeal swabs collected from people with suspected cases of COVID-19 and international travellers were tested for SARS-CoV-2 with standard RT-PCR methods. SARS-CoV-2-positive samples were sequenced according to standard library preparation and sequencing protocols. Bioinformatic analysis was done using ARTIC pipelines and Pangolin was used to assign lineages. To construct phylogenetic trees, sequences were first stratified into different COVID-19 waves (waves 1-4) and aligned. Clustering analysis was done and phylogenetic trees constructed.

Findings: Between March, 2020, and January, 2022, 11 911 confirmed cases of COVID-19 were recorded in The Gambia, and 1638 SARS-CoV-2 genomes were sequenced. Cases were broadly distributed into four waves, with more cases during the waves that coincided with the rainy season (July-October). Each wave occurred after the introduction of new viral variants or lineages, or both, generally those already established in Europe or in other African countries. Local transmission was higher during the first and third waves (ie, those that corresponded with the rainy season), in which the B.1.416 lineage and delta (AY.34.1) were dominant, respectively. The second wave was driven by the alpha and eta variants and the B.1.1.420 lineage. The fourth wave was driven by the omicron variant and was predominantly associated with the BA.1.1 lineage.

Interpretation: More cases of SARS-CoV-2 infection were recorded in The Gambia during peaks of the pandemic that coincided with the rainy season, in line with transmission patterns for other respiratory viruses. The introduction of new lineages or variants preceded epidemic waves, highlighting the importance of implementing well structured genomic surveillance at a national level to detect and monitor emerging and circulating variants.

Funding: Medical Research Unit The Gambia at London School of Hygiene & Tropical Medicine, UK Research and Innovation, WHO.

Figure 1

Distribution of samples received for sequencing from March, 2020 to January, 2022 *This threshold was introduced in July, 2020.

Figure 2

Proportion of samples collected and successfully sequenced and COVID-19 case numbers in The Gambia

Figure 3

COVID-19-associated cases and deaths relative to pandemic containment measures implemented (A) and trajectory of major SARS-CoV-2 lineages and variants (B) in The Gambia from March, 2020, to January, 2022 RDT=rapid diagnostic (antigen) test.

Figure 4

SARS-CoV-2 lineages in the first (A), second (B), third (C), and fourth (D) waves of the COVID-19 pandemic in The Gambia “Others” includes lineages present in ten or fewer samples (appendix p 83). The y-axis is on a logarithmic scale.

Figure 5

Maximum likelihood tree of 1313 SARS-CoV-2 genomes sampled in The Gambia from March, 2020, to January, 2022 Sequences in which less than 10% of bases were ambiguous were used to construct the phylogenetic tree.

Figure 6

Maximum likelihood tree of the closest SARS-CoV-2 genomes to those sampled in The Gambia in the first (A), second (B), third (C), and fourth (D) waves of the COVID-19 pandemic Data are from March, 2020, to January, 2022. Branch tips represent the continent where closest global sequences were sampled from. All trees were rooted on the SARS-CoV-2 reference genome (GenBank accession number MN908947.3).