SARS-CoV-2 incidence, transmission and reinfection in a rural and an urban setting: results of the PHIRST-C cohort study, South Africa, 2020-2021

Cohen, C.; Kleynhans, J.; von Gottberg, A.; McMorrow, M.; Wolter, N.; Bhiman, J.; Moyes, J.; du Plessis, M.; Carrim, M.; Buys, A.; Martinson, N. A.; Kahn, K.; Tollman, S.; Lebina, L.; Wafawanaka, F.; du Toit, J.; Gomez-Olive, F. X.; Dawood, F.; Mkhencele, T.; Sun, K.; Viboud, C.; Tempia, S.

Background By March 2021, South Africa experienced two waves of SARS-CoV-2 infections; the second associated with emergence of Beta variant. We estimated the burden and transmission of SARS-CoV-2 over the two waves. Methods We conducted a prospective cohort study during July 2020-March 2021 in one rural and one urban community. Mid-turbinate nasal swabs were collected twice-weekly from consenting household members irrespective of symptoms and tested for SARS-CoV-2 using real-time reverse transcription polymerase chain reaction (rRT-PCR). Serum was collected every two months and tested for anti-SARS-CoV-2 antibodies. Household cumulative infection risk (HCIR) was defined as the proportion of household members with infection following SARS-CoV-2 introduction. Findings Among 71,759 nasal specimens from 1,189 members (follow-up rate 93%), 834 (1%) were SARS-CoV-2-positive. By PCR detection and serology combined, 34% (406/1189) of individuals experienced [≥]1 SARS-CoV-2 infection episode, and 3% (12/406) experienced reinfection. Infection by PCR and/or serology before the second wave was 84% (95% confidence interval (CI) 65%-93%) protective against re-infection. Of 254 PCR-confirmed episodes with available data, 17% (n=43) were associated with [≥]1 symptom, of which 21% (9/43) were medically attended. Among 222 included households, 161 (73%) had [≥]1 SARS-CoV-2-positive individual. HCIR was 16% (66/411). On multivariable analysis, index case lower cycle threshold value (OR 5.8, 95% CI 1.8-19.1), urban community (OR 3.1, 95% CI 1.5-6.2) and infection with Beta variant (OR 3.7, 95% CI 1.6-8.4) were associated with increased HCIR. HCIR was similar for symptomatic (8/67,12%) and asymptomatic (61/373, 16%) index cases (p-0.302). Interpretation In this study, 83% of SARS-CoV-2 infections were asymptomatic and index case symptom status did not affect HCIR, suggesting a limited role for control measures targeting symptomatic individuals. Previous infection was protective against SARS-CoV-2 infection in the second wave although household transmission increased following the emergence of Beta variant. Funding US Centers for Disease Control and Prevention