COVID-19 reinfections in The Gambia by phylogenetically distinct SARS-CoV-2 variants – first two confirmed events in West Africa

21 June 2021
At the beginning of the COVID-19 pandemic, the scientific community hypothesised that SARS-CoV-2 transmission would eventually be hindered by herd immunity, conferred by natural infection, vaccination, or both. However, it remains unclear whether initial infection with SARS-CoV-2 confers protection against reinfection and how long this protection would last.

A study on SARS-CoV-2 led by the Medical Research Council Unit The Gambia at  LSHTM published in the  Lancet Global Health Journal, reported two cases of SARS-CoV-2 reinfection in the Gambia , both within 5 to 6 months after first infection. Both patients were young and had mild or no symptoms in either episode of infection.

At the time, two main lineages of the virus, lineages A and B, have been detected in The Gambia. Lineage B constitutes almost 98% of the total genomes sequenced, with the sub-lineage B.1 being the most common (20%). Samples are collected as part of the national surveillance and by the Medical Research Council Unit The Gambia (MRCG) at the London School of Hygiene and Tropical Medicine through clinical, occupational health, and research activities, including the PaTS trial (NCT04703608), from symptomatic individuals or contacts of known COVID-19 cases. Asymptomatic health-care workers and international travellers also screened. Diagnosis is done by real-time PCR of SARS-CoV-2 specific viral gene sequences.

Bakary Sanyang, a PhD student and first author of the publication said “Results from this analysis highlights the possibility of SARS-CoV-2 reinfections in unvaccinated or under vaccinated populations and the potential implications on efforts to bring the COVID-19 pandemic to halt. Genomic data of circulating strains of the virus are useful in vaccine development. Unfortunately, genomic surveillance of the circulating variants of SARS-CoV-2 in West Africa is largely limited, leaving huge gaps in information on the evolution of the virus in the region. This, coupled with limited vaccine rollout and uptake in the region, poses a major question of how such rapid evolution of the virus would affect effectiveness of current vaccines in this population.”​

Anna Roca Professor of Epidemiology and senior author of the publication commented “This analysis is another example of the Gambian reaction to the COVID epidemic, in terms of public health and research response, both key elements in this health crisis. On the one hand, it underlines the strong partnership between the MRCG/LSHTM Unit and the Gambian Government through the National Public Health labs. On the other hand, it shows the strong collaboration within the Unit between the research teams (the PaTS trial), the Clinical Services Department and the Genomics platform”.

According to Dr Abdul Karim Sesay Head Genomics Laboratory “The MRC Unit The Gambia at LSHTM have moved, from a position of no ownership previously, and research scientist acted as a post-box for most of their genomics output, to the establishment of, a highly equipped facility, with capacity for wide range of genomics application including human whole genome sequencing, to controlling our own destiny. The investment in a Genomics platform in the unit the past 4 years has paid off spectacularly as demonstrated by our effort and success with sequencing Covid-19 positives isolates in The Gambia. And working with Ministry of Health, National Public Health Laboratory and in collaboration with research teams in the unit (as the PaTS trial), and the platform having a direct impact in the country’s pandemic .”

Mutations in the S-gene of variants from the two infection episodes for each patient (a = patient 1 and b = patient 2) compared to the Wuhan reference (NC_045512.2). In each figure, on the first track is the reference. The middle track shows variant from the first episode and bottom track shows variant from reinfection. The grey colour along the tracks indicates similarity between the query sequence and the reference, whereas the coloured points indicate nucleotide differences between the query and the reference. Different nucleotides are shown with different colours. The box in the bottom left corner shows, for each infection episode, nucleotide mutations on the S gene and their corresponding amino acid changes.