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

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dc.contributor.authorCheryl Cohen
dc.contributor.authorJackie Kleynhans
dc.contributor.authorAnne von Gottberg
dc.contributor.authorMeredith L McMorrow
dc.contributor.authorNicole Wolter
dc.contributor.authorJinal N Bhiman
dc.contributor.authorJocelyn Moyes
dc.contributor.authorJacques du Toit
dc.contributor.authorMignon du Plessis
dc.contributor.authorFrancesc Xavier Gómez-Olivé
dc.contributor.authorFatimah S Dawood
dc.contributor.authorThulisa Mkhencele
dc.contributor.authorKaiyun Sun
dc.contributor.authorCécile Viboud
dc.contributor.authorMaimuna Carrim
dc.contributor.authorAmelia Buys
dc.contributor.authorNeil A Martinson
dc.contributor.authorKathleen Kahn
dc.contributor.authorStephen Tollman
dc.contributor.authorLimakatso Lebina
dc.contributor.authorFloi Wafawanaka
dc.date.accessioned2024-03-18T09:39:24Z
dc.date.available2024-03-18T09:39:24Z
dc.date.issued2021-12-04
dc.description.abstractBackground: By August 2021, South Africa experienced three SARS-CoV-2 waves; the second and third associated with emergence of Beta and Delta variants respectively. Methods: We conducted a prospective cohort study during July 2020-August 2021 in one rural and one urban community. Mid-turbinate nasal swabs were collected twice-weekly from 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. Results: Among 115,759 nasal specimens from 1,200 members (follow-up rate 93%), 1976 (2%) were SARS-CoV-2-positive. By rRT-PCR and serology combined, 62% (749/1200) of individuals experienced ≥1 SARS-CoV-2 infection episode, and 12% (87/749) experienced reinfection. Of 662 PCR-confirmed episodes with available data, 15% (n=97) were associated with ≥1 symptom. Among 222 households, 200 (90%) had ≥1 SARS-CoV-2-positive individual. Household cumulative infection risk (HCIR) was 25% (213/856). On multivariable analysis, accounting for age and sex, index case lower cycle threshold value (OR 3.9, 95%CI 1.7-8.8), urban community (OR 2.0,95%CI 1.1-3.9), Beta (OR 4.2, 95%CI 1.7-10.1) and Delta (OR 14.6, 95%CI 5.7-37.5) variant infection were associated with increased HCIR. HCIR was similar for symptomatic (21/110, 19%) and asymptomatic (195/775, 25%) index cases (p=0.165). Attack rates were highest in individuals aged 13-18 years and individuals in this age group were more likely to experience repeat infections and to acquire SARS-CoV-2 infection. People living with HIV who were not virally supressed were more likely to develop symptomatic illness, and shed SARS-CoV-2 for longer compared to HIV-uninfected individuals. Conclusions: In this study, 85% 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. Increased household transmission of Beta and Delta variants, likely contributed to successive waves, with >60% of individuals infected by the end of follow-up.
dc.description.librarianPM2023
dc.facultyFaculty of Health Sciences
dc.identifier.urihttps://hdl.handle.net/10539/38084
dc.language.isoen
dc.schoolPublic Health
dc.titleSARS-CoV-2 incidence, transmission and reinfection in a rural and an urban setting: results of the PHIRST-C cohort study, South Africa, 2020-2021
dc.typeArticle
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