COVID-19 reinfections in The Gambia by phylogenetically distinct SARS-CoV-2 variants—first two confirmed events in west Africa
Authors: Bakary Sanyang, Abdoulie Kanteh, Effua Usuf, Behzad Nadjm, Sheikh Jarju, Alasana Bah, Abdoulie Bojang, Mary Grey-Johnson, Joquina Chiquita Jones, Abdou Gai, Catherine Sarr, Fatoumata Sillah, Oghenebrume Wariri, Francis Oko, Carla Cerami, Karen Forrest, Alhagie Papa Sey, Haruna Jallow, Davis Nwakanma, Abdul Karim Sesay, Umberto D'Alessandro, Anna Roca
Journal: The Lancet Global Health (2021)

At the beginning of the COVID-19 pandemic, in early 2020, the scientific community hypothesised that SARS-CoV-2 transmission would eventually be hindered by herd immunity, conferred by natural infection, vaccination, or both.1Fontanet A Cauchemez S COVID-19 herd immunity: where are we?.Nat Rev Immunol. 2020; 20 (1Fontanet A, Cauchemez S.): 583-584Crossref PubMed Scopus (373) Google Scholar However, essential questions about whether infection with SARS-CoV-2 confers protection against reinfection and the length of time the protection lasts after either infection or vaccination remain open. These answers are crucial for the development of appropriate health control measures worldwide and become more important as new viral variants spread. By March 15, 2021, fewer than 100 reinfections had been reported worldwide, mainly in countries with a high mortality burden. In most cases, reinfections were less severe than the initial infection.2Lee JS Kim SY Kim TS et al.Evidence of severe acute respiratory syndrome coronavirus 2 reinfection after recovery from mild coronavirus disease 2019.Clin Infect Dis. 2020; (published online Nov 21.)https://doi.org/10.1093/cid/ciaa1421Crossref Scopus (53) Google Scholar, 3Hansen CH Michlmayr D Gubbels SM Mølbak K Ethelberg S Assessment of protection against reinfection with SARS-CoV-2 among 4 million PCR-tested individuals in Denmark in 2020: a population-level observational study.Lancet. 2021; 397: 1204-1212Summary Full Text Full Text PDF PubMed Scopus (438) Google Scholar However, recent reports from Brazil, a country that in parts surpassed the threshold of herd immunity after the first wave but had a similarly strong second wave,4Sabino EC Buss LF Carvalho MPS et al.Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence.Lancet. 2021; 397: 452-455Summary Full Text Full Text PDF PubMed Scopus (546) Google Scholar are worrisome. Such resurgence of COVID-19 cases in the second wave can be explained by rapid waning immunity, the expansion of the new SARS-Co-V-2 variants that might evade immunity generated in response to previous infections (ie, B.1.1.7, B.1.351, and P.1), higher transmissibility of new lineages that require a larger herd immunity, or a combination of all these factors.4Sabino EC Buss LF Carvalho MPS et al.Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence.Lancet. 2021; 397: 452-455Summary Full Text Full Text PDF PubMed Scopus (546) Google Scholar Reinfections in west Africa, a region with a lower toll of infections and deaths5WorldometerCOVID-19 coronavirus pandemic.https://www.worldometers.info/coronavirus/Date accessed: April 5, 2021Google Scholar than Europe, North America, or South America, are yet to be described. We aimed to ascertain whether any reinfections had occurred in The Gambia. The Gambia is the smallest country in west Africa, with 4712 cases and 150 deaths reported by March 1, 2021, although the number of cases is probably underestimated.5WorldometerCOVID-19 coronavirus pandemic.https://www.worldometers.info/coronavirus/Date accessed: April 5, 2021Google Scholar At that time, 460 SARS-CoV-2 genomes from confirmed cases had been sequenced in the country, with 430 (93·5%) genomes already submitted on the GISAID database.6GISAIDPhylodynamics of pandemic coronavirus in west Africa.https://www.gisaid.org/phylodynamics/west-africa/Date: 2021Date accessed: April 5, 2021Google Scholar Among these samples, only two main lineages of the virus, lineages A and B, have been detected. Lineage B constitutes almost 98% of the total genomes sequenced, with the sub-lineage B.1 being the most prevalent, found in 20% of the sequences. Naso-oropharyngeal 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. Screening of asymptomatic health-care workers and those proposing to travel across international borders also takes place. The standard test for COVID-19 diagnosis in The Gambia, as of March 15, 2021, is real-time PCR of SARS-CoV-2 specific viral gene sequences. Confirmation of reinfections were done by genomic analysis. Library preparation and sequencing were done using the ARTIC (version 3) protocol for SARS-CoV-2 that targeted whole genome sequencing.7Quick J nCoV-2019 sequencing protocol v3 (LoCost) V.3.https://www.protocols.io/view/ncov-2019-sequencing-protocol-v3-locost-bh42j8yeDate: 2020Date accessed: March 1, 2021Google Scholar Libraries were pooled in multiplexes of 24 per flow cell and sequenced on a GridION platform (Oxford Nanopore Technologies, UK). Bioinformatics analysis was done using the ARTIC (version 3) bioinformatics pipeline for SARS-CoV-2 genome analysis.8Loman N Rowe W Rambaut A nCoV-2019 novel coronavirus bioinformatics protocol.https://artic.network/ncov-2019/ncov2019-bioinformatics-sop.htmlDate: 2020Date accessed: March 1, 2021Google Scholar Genome alignments against the reference were visualised on the Interactive Genomics Viewer.9Thorvaldsdóttir H Robinson JT Mesirov JP Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.Brief Bioinform. 2013; 14: 178-192Crossref PubMed Scopus (5713) Google Scholar Mutations were confirmed using the GISAID CoVsurver.10GISAIDCoVsurver: mutation analysis of hCoV-19.https://www.gisaid.org/epiflu-applications/covsurver-mutations-app/Date accessed: February 17, 2021Google Scholar Lineage assignment was done using Pangolin (version 2.3.0).11GitHubPangolin.https://github.com/cov-lineages/pangolinDate: 2020Date accessed: March 1, 2021Google Scholar The Gambian Government and MRCG joint ethics committee approved the study presented here (Ref L2021.E04). We have phylogenetically confirmed two reinfections among healthy Gambian individuals aged 31 years and 36 years, with a time lag of 5 months and 6 months, respectively. Both individuals had mild symptoms during the second infection that lasted less than 1 week. For the initial infection, one individual had mild symptoms, whereas the other was asymptomatic (tested as a contact of a positive case). Epidemiological, clinical, and molecular details of both infections are shown in the table.TableClinical, epidemiological, and molecular characteristics of the two individuals with SARS-CoV-2 reinfectionsPatient APatient BSexFemaleFemaleAge, years3136ComorbiditiesNoneNoneFirst infectionDate of infectionAug 30, 2020July 31, 2020Clinical presentationWHO criteria for mild infection*Symptomatic patient meeting the case definition for COVID-19 without evidence of viral pneumonia or hypoxia.AsymptomaticCt value ORF-1/N gene36·7/34·1Negative/38·0LineageB.1 (discovered in March, 2020, in the UK, Mexico, and USA)B.1.235 (discovered January, 2020, in the UK, USA, and Spain)Second infectionDate of infectionJan 21, 2021Feb 1, 2021Clinical presentationWHO criteria for mild infection*Symptomatic patient meeting the case definition for COVID-19 without evidence of viral pneumonia or hypoxia.WHO criteria for mild infection*Symptomatic patient meeting the case definition for COVID-19 without evidence of viral pneumonia or hypoxia.Ct value E gene/N gene34·0/33·120·9/19·1LineageB.1.1.74 (discovered in March, 2020, in the UK, Ireland, and Belgium)B.1 (discovered in March, 2020, in the UK, Mexico, and USA)Ct=cycle threshold. ORF-1=open reading frame 1.* Symptomatic patient meeting the case definition for COVID-19 without evidence of viral pneumonia or hypoxia. Open table in a new tab Ct=cycle threshold. ORF-1=open reading frame 1. Genome-wide sequence comparisons for the two viruses of each patient to the reference shows mutations on the S gene, which encodes for the virus spike protein (appendix p 3). The spike protein mediates receptor recognition and binding during infection, playing an important part in viral transmission.12Huang Y Yang C Xu XF Xu W Liu SW Structural and functional properties of SARS-CoV-2 spike protein: potential antivirus drug development for COVID-19.Acta Pharmacol Sin. 2020; 41: 1141-1149Crossref PubMed Scopus (1401) Google Scholar Although it is still unclear as to what extent immune responses against a previous variant will protect against reinfection by a different variant, mutations of the viral spike protein are predicted to enhance infectivity.13Zhang L Jackson CB Mou H et al.SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity.Nat Commun. 2020; 116013Crossref Scopus (613) Google Scholar In both patients, we have seen more mutations in the S gene in the variants from the second infection episodes than in those from the first episode (two amino-acid changing mutations in the first infection and four in the second infection). One of these mutations associated with enhanced infectivity (D614G)14Ozono S Zhang Y Ode H et al.SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity.Nat Commun. 2021; 12: 848Crossref PubMed Scopus (316) Google Scholar was present in all four infections. Certain mutations on the receptor-binding domain of the spike protein confer resistance to commonly elicited antibodies during SARS-CoV-2 infection in vitro.15Weisblum Y Schmidt F Zhang F et al.Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants.eLife. 2020; 9: 9Crossref Scopus (888) Google Scholar One such mutation is N440K, detected in patient A's reinfection. Other mutations identified include A1020S, which is involved in viral oligomerisation interfaces; and G946V, detected in the last quarter of 2020 among different variants, including B.1.1.7. Overall, these reinfections are potentially a consequence of divergent mutations enhancing transmission of the virus, but this will need to be assessed in a larger pool of reinfected individuals. Two (B.1·235 and B.1.1.74) of the three lineages involved in these two reinfections are uncommon in the country, representing 3% and less than 1% of the Gambian isolates, respectively.6GISAIDPhylodynamics of pandemic coronavirus in west Africa.https://www.gisaid.org/phylodynamics/west-africa/Date: 2021Date accessed: April 5, 2021Google Scholar In summary, our data conclude that at least two reinfections have occurred in The Gambia. These events have occurred in healthy young individuals infected with similar viral variants in the first and second episode. If reinfections with similar strains are possible, herd immunity in west Africa could take longer than expected as a large majority of cases are asymptomatic or with mild disease and these probably develop weaker immune responses.16Long QX Tang XJ Shi QL et al.Clinical and immunological assessment of asymptomatic SARS-CoV-2 infections.Nat Med. 2020; 26: 1200-1204Crossref PubMed Scopus (2031) Google Scholar In the absence of widespread vaccination, reinfections could become more common when the new variants become predominant in the region. Community-based immunological studies are urgently needed. We declare no competing interests. We thank the Prevention and Treatment of COVID-19 Associated Severe Pneumonia (PaTS) field team (led by Mr Bakary Dibba) and the PaTS support teams: the research support (led by Asheme Mahmoud), clinical trials support, transport, and operations teams. We are also grateful to the entire staff of the COVID-19 Risk Coordinating team. We acknowledge the excellent technical support by the diagnostic teams from PaTS, the unit COVID-19 diagnostics, and The Gambia National Public Health Laboratory. This study was funded by the UK Research and Innovation as part of the COVID-19 strategic priorities supplementary funding for the Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine (grant reference MC_PC_19084). Download .pdf (.21 MB) Help with pdf files Supplementary appendix