High SARS-CoV-2 incidence and asymptomatic fraction during Delta and Omicron BA.1 waves in The Gambia

Abstract

Little is known about SARS-CoV-2 infection risk in African countries with high levels of infection-driven immunity and low vaccine coverage. We conducted a prospective cohort study of 349 participants from 52 households in The Gambia between March 2021 and June 2022, with routine weekly SARS-CoV-2 RT-PCR and 6-monthly SARS-CoV-2 serology. Attack rates of 45% and 57% were seen during Delta and Omicron BA.1 waves respectively. Eighty-four percent of RT-PCR-positive infections were asymptomatic. Children under 5-years had a lower incidence of infection than 18-49-year-olds. One prior SARS-CoV-2 infection reduced infection risk during the Delta wave only, with immunity from ≥2 prior infections required to reduce the risk of infection with early Omicron lineage viruses. In an African population with high levels of infection-driven immunity and low vaccine coverage, we find high attack rates during SARS-CoV-2 waves, with a high proportion of asymptomatic infections and young children remaining relatively protected from infection.

Fig. 1. SARS-CoV-2 epidemic curves in The Gambia in relation to study follow-up and sampling.

Top panel shows case numbers reported in The Gambia (WHO COVID-19 Dashboard. Geneva: World Health Organization, 2020. Available online: https://covid19.who.int/). Middle panel shows RT-PCR-positive events in the study cohort. Cases are coloured by SARS-CoV-2 variant period (pre-Delta, Delta, Omicron), based on dates derived from wider sequence data from The Gambia, corresponding to weeks when >50% of sequenced isolates were first Delta (7 July 2021) or Omicron-lineage (4 December 2021) viruses. Bottom panel shows a number of individuals providing samples for serological analysis during V1 (bleed 1; baseline), V2 (bleed 2; 6-month visit) and V3 (bleed 3; 12-month visit) timepoints. RT-PCR reverse-transcriptase polymerase chain reaction.

Fig. 2. Results of SARS-CoV-2 anti-spike serology and SARSCoV-2 RT-PCR in participants during study follow-up.

Each row represents a participant numbered consecutively, grouped together in households. Columns represent follow-up visits. A participant’s follow-up time was divided into weekly breaks. Given the asynchronicity of recruitment, visits are not necessarily aligned with the same weekly breaks for all participants. As a result, a small number of weekly breaks for some participants may contain two visits. In such a situation, the result of the visit is determined hierarchically (seropositive, seronegative, RT-PCR-positive, RT-PCR-negative, missing). Seropositive and seronegative relate to positive and negative results in a serum anti-spike antibody assay. RT-PCR reverse-transcriptase polymerase chain reaction.

Fig. 3. The cumulative incidence of SARS-CoV-2 infection by prior infection status.

The cumulative incidence over follow-up time is expressed as a risk (number infected/number at-risk) and displayed for A the whole study period or B stratified by Delta- and Omicron-variant periods. P-value calculated by log-rank test for association between prior infection status and infection incidence (A) and for interaction between Delta and Omicron periods (B). The test for interaction assesses whether the association between prior infection status and infection incidence is modified by the circulating variant (i.e., is the effect of one prior infection on infection incidence different between Delta and Omicron). All p-values are two-sided. Shaded area represents the 95% confidence interval.