Intense and Mild Wave of COVID-19 in The Gambia: a Cohort Analysis
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Abstract
Background
The SARS-CoV-2 pandemic is evolving differently in Africa compared to other regions, with lower transmission and milder clinical presentation. Reasons for this are not fully understood. Recent data from Eastern and Southern Africa suggest that transmission may be higher than measured. Detailed epidemiological data in different African settings is urgently needed.
Methods
We calculated cumulative rates of SAR-CoV-2 infections per 1,000 people at risk in The Gambia (2.42 million individuals) using publicly available data. We evaluated these rates in a cohort of 1,366 employees working at the MRC Unit The Gambia @LSHTM (MRCG) where systematic surveillance of symptomatic cases and contact tracing was implemented. Cumulative rates among the Gambian population were stratified by age groups and, among MRCG staff, by occupational exposure risk. SARS-CoV-2 testing was conducted on oropharyngeal/nasopharyngeal samples with consistent sampling and laboratory procedures across cohorts.
Findings
By September 2020, 3,579 cases of SARS-CoV-2 and 115 deaths had been identified; with 67% of cases detected in August. Among them, 191 cases were MRCG staff; all of them were asymptomatic/mild, with no deaths. The cumulative incidence rate for SARS-CoV-2 infection among MRCG staff (excluding those with occupational exposure risk) was 129 per 1,000, at least 20-fold higher than the estimations based on diagnosed cases in the adult Gambian population.
Interpretation
Our findings are consistent with recent African sero-prevalence studies reporting high community transmission of SAR-CoV-2. Enhanced community surveillance is essential to further understand and predict the future trajectory of the pandemic in Africa.
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SciScore for 10.1101/2020.12.10.20238576: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: G Joint Ethics committee approved the study (Ref L2020.E37). Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources RT-PCR analysis was conducted with 5µL of extracted RNA in 25µL of reaction mix containing, reaction buffer, one-step reverse transcriptase enzyme, either the Takara One Step PrimeScript III RT-PCR Kit (TAKARA Bio) or SuperScript III Platinum™ One-Step qRT-PCR Kit (INVITROGEN, Thermo Fisher Scientific)” and the primer and probe mix. Thermo Fisher Scientific)”suggested: NoneResults from OddPub: We did not detect open data. We …
SciScore for 10.1101/2020.12.10.20238576: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: G Joint Ethics committee approved the study (Ref L2020.E37). Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources RT-PCR analysis was conducted with 5µL of extracted RNA in 25µL of reaction mix containing, reaction buffer, one-step reverse transcriptase enzyme, either the Takara One Step PrimeScript III RT-PCR Kit (TAKARA Bio) or SuperScript III Platinum™ One-Step qRT-PCR Kit (INVITROGEN, Thermo Fisher Scientific)” and the primer and probe mix. Thermo Fisher Scientific)”suggested: NoneResults from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Using MRCG staff as a cohort to estimate infection rates in the Gambian population has important limitations. Although cases in the general population and the MRCG cohort showed similar timelines and the size of the MRCG cohort is relatively large, the MRCG can be considered a cluster. The level of education and the monthly income of the staff is above that of the general population. MRCG staff live mainly in urban areas, where transmission tends to be higher (27) but also lives in less crowded environments, with better access to water and sanitation which would protect them from infection. In addition, MRCG developed policies and undertook significant levels of staff education related to COVID-19, reinforced messages related to social distancing, hand washing and the wearing of face masks at work as well as in the community. Finally, given the nature of the MRCG’s work, the level of background understanding on infectious diseases, even among staff not directly involved in research, is likely to be higher than in the general population. Moreover, the robust surveillance should have further limited transmission due to the rapid identification and isolation of cases. On the other hand, there was no moderate or severe COVID-19 case among the MRCG staff. This mild presentation was not modified by treatment as for instance, not a single member of the MRCG staff met WHO criteria for hospitalization and less so for oxygen supplementation or dexamethasone treatment. The prevalence of...
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
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- No protocol registration statement was detected.
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