PMID- 35298900 OWN - NLM STAT- MEDLINE DCOM- 20220603 LR - 20230110 IS - 1474-4457 (Electronic) IS - 1473-3099 (Print) IS - 1473-3099 (Linking) VI - 22 IP - 6 DP - 2022 Jun TI - SARS-CoV-2 incidence, transmission, and reinfection in a rural and an urban setting: results of the PHIRST-C cohort study, South Africa, 2020-21. PG - 821-834 LID - S1473-3099(22)00069-X [pii] LID - 10.1016/S1473-3099(22)00069-X [doi] AB - BACKGROUND: By August, 2021, South Africa had been affected by three waves of SARS-CoV-2; the second associated with the beta variant and the third with the delta variant. Data on SARS-CoV-2 burden, transmission, and asymptomatic infections from Africa are scarce. We aimed to evaluate SARS-CoV-2 burden and transmission in one rural and one urban community in South Africa. METHODS: We conducted a prospective cohort study of households in Agincourt, Mpumalanga province (rural site) and Klerksdorp, North West province (urban site) from July, 2020 to August, 2021. We randomly selected households for the rural site from a health and sociodemographic surveillance system and for the urban site using GPS coordinates. Households with more than two members and where at least 75% of members consented to participate were eligible. Midturbinate nasal swabs were collected twice a week from household members irrespective of symptoms and tested for SARS-CoV-2 using real-time RT-PCR (RT-rtPCR). Serum was collected every 2 months and tested for anti-SARS-CoV-2 antibodies. Main outcomes were the cumulative incidence of SARS-CoV-2 infection, frequency of reinfection, symptomatic fraction (percent of infected individuals with >/=1 symptom), the duration of viral RNA shedding (number of days of SARS-CoV-2 RT-rtPCR positivity), and the household cumulative infection risk (HCIR; number of infected household contacts divided by the number of susceptible household members). FINDINGS: 222 households (114 at the rural site and 108 at the urban site), and 1200 household members (643 at the rural site and 557 at the urban site) were included in the analysis. For 115 759 nasal specimens from 1200 household members (follow-up 92.5%), 1976 (1.7%) were SARS-CoV-2-positive on RT-rtPCR. By RT-rtPCR and serology combined, 749 of 1200 individuals (62.4% [95% CI 58.1-66.4]) had at least one SARS-CoV-2 infection episode, and 87 of 749 (11.6% [9.4-14.2]) were reinfected. The mean infection episode duration was 11.6 days (SD 9.0; range 4-137). Of 662 RT-rtPCR-confirmed episodes (>14 days after the start of follow-up) with available data, 97 (14.7% [11.9-17.9]) were symptomatic with at least one symptom (in individuals aged <19 years, 28 [7.5%] of 373 episodes symptomatic; in individuals aged >/=19 years, 69 [23.9%] of 289 episodes symptomatic). Among 222 households, 200 (90.1% [85.3-93.7]) had at least one SARS-CoV-2-positive individual on RT-rtPCR or serology. HCIR overall was 23.9% (195 of 817 susceptible household members infected [95% CI 19.8-28.4]). HCIR was 23.3% (20 of 86) for symptomatic index cases and 23.9% (175 of 731) for asymptomatic index cases (univariate odds ratio [OR] 1.0 [95% CI 0.5-2.0]). On multivariable analysis, accounting for age and sex, low minimum cycle threshold value (30) of the index case (OR 5.3 [2.3-12.4]) and beta and delta variant infection (vs Wuhan-Hu-1, OR 3.3 [1.4-8.2] and 10.4 [4.1-26.7], respectively) were associated with increased HCIR. People living with HIV who were not virally supressed (>/=400 viral load copies per mL) were more likely to develop symptomatic illness when infected with SAR-CoV-2 (OR 3.3 [1.3-8.4]), and shed SARS-CoV-2 for longer (hazard ratio 0.4 [95% CI 0.3-0.6]) compared with HIV-uninfected individuals. INTERPRETATION: In this study, 565 (85.3%) 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 was likely to have contributed to successive waves of SARS-CoV-2 infection, with more than 60% of individuals infected by the end of follow-up. FUNDING: US CDC, South Africa National Institute for Communicable Diseases, and Wellcome Trust. CI - Copyright (c) 2022 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license. Published by Elsevier Ltd.. All rights reserved. FAU - Cohen, Cheryl AU - Cohen C AD - Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. Electronic address: cherylc@nicd.ac.za. FAU - Kleynhans, Jackie AU - Kleynhans J AD - Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. FAU - von Gottberg, Anne AU - von Gottberg A AD - Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. FAU - McMorrow, Meredith L AU - McMorrow ML AD - Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA. FAU - Wolter, Nicole AU - Wolter N AD - Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. FAU - Bhiman, Jinal N AU - Bhiman JN AD - Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. FAU - Moyes, Jocelyn AU - Moyes J AD - Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. FAU - du Plessis, Mignon AU - du Plessis M AD - Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. FAU - Carrim, Maimuna AU - Carrim M AD - Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. FAU - Buys, Amelia AU - Buys A AD - Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa. FAU - Martinson, Neil A AU - Martinson NA AD - Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa; Johns Hopkins University Center for TB Research, Baltimore, MD, USA. FAU - Kahn, Kathleen AU - Kahn K AD - MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. FAU - Tollman, Stephen AU - Tollman S AD - MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. FAU - Lebina, Limakatso AU - Lebina L AD - Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa; Africa Health Research Institute, KwaZulu-Natal, South Africa. FAU - Wafawanaka, Floidy AU - Wafawanaka F AD - MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. FAU - du Toit, Jacques D AU - du Toit JD AD - MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. FAU - Gomez-Olive, Francesc Xavier AU - Gomez-Olive FX AD - MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. FAU - Dawood, Fatimah S AU - Dawood FS AD - Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA. FAU - Mkhencele, Thulisa AU - Mkhencele T AD - Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa. FAU - Sun, Kaiyuan AU - Sun K AD - Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA. FAU - Viboud, Cecile AU - Viboud C AD - Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA. FAU - Tempia, Stefano AU - Tempia S AD - Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA. CN - PHIRST-C Group LA - eng GR - 069683/Z/02/Z/WT_/Wellcome Trust/United Kingdom GR - 085477/Z/08/Z/WT_/Wellcome Trust/United Kingdom GR - 058893/Z/99/A/WT_/Wellcome Trust/United Kingdom GR - Wellcome Trust/United Kingdom GR - 085477/B/08/Z/WT_/Wellcome Trust/United Kingdom GR - 221003/Z/20/Z/WT_/Wellcome Trust/United Kingdom GR - U01IP001048/ACL HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. DEP - 20220314 PL - United States TA - Lancet Infect Dis JT - The Lancet. Infectious diseases JID - 101130150 RN - SARS-CoV-2 variants SB - IM UOF - medRxiv. 2021 Dec 04;:. PMID: 34909794 CIN - Lancet Infect Dis. 2022 Jun;22(6):748-750. PMID: 35298902 MH - *COVID-19/epidemiology MH - Cohort Studies MH - Disease Susceptibility MH - *HIV Infections MH - Humans MH - Incidence MH - Prospective Studies MH - Reinfection MH - SARS-CoV-2 MH - South Africa/epidemiology PMC - PMC8920516 COIS- Declaration of interests CC has received grant support from Sanofi Pasteur, the US Centers for Disease Control and Prevention (CDC), Wellcome Trust, the Programme for Applied Technologies in Health (PATH), Bill & Melinda Gates Foundation, and the South African Medical Research Council (SA-MRC). AvG has received grant support from the US CDC, the African Society for Laboratory Medicine and Africa Centres for Disease Control and Prevention, the SA-MRC, WHO Regional Office for Africa, the Fleming Fund, WHO, and Wellcome Trust. NW reports grants from Sanofi Pasteur and the Bill & Melinda Gates Foundation. NAM has received a grant to his institution from Pfizer to conduct research in patients with pneumonia. JM has received grant support from Sanofi Pasteur and PATH. JB has received grant funds from the European and Developing Countries Clinical Trials Partnership, the Fleming Fund, and the SA-MRC. All other authors declare no competing interests. FIR - Bhiman, Jinal N IR - Bhiman JN FIR - Buys, Amelia IR - Buys A FIR - Carrim, Maimuna IR - Carrim M FIR - Cohen, Cheryl IR - Cohen C FIR - de Gouveia, Linda IR - de Gouveia L FIR - du Plessis, Mignon IR - du Plessis M FIR - du Toit, Jacques IR - du Toit J FIR - Gomez-Olive, Francesc X IR - Gomez-Olive FX FIR - Kahn, Kathleen IR - Kahn K FIR - Kgasago, Kgaugelo P IR - Kgasago KP FIR - Kleynhans, Jackie IR - Kleynhans J FIR - Kotane, Retshidisitswe IR - Kotane R FIR - Lebina, Limakatso IR - Lebina L FIR - Martinson, Neil A IR - Martinson NA FIR - McMorrow, Meredith L IR - McMorrow ML FIR - Moloantoa, Tumelo IR - Moloantoa T FIR - Moyes, Jocelyn IR - Moyes J FIR - Tempia, Stefano IR - Tempia S FIR - Tollman, Stephen IR - Tollman S FIR - von Gottberg, Anne IR - von Gottberg A FIR - Wafawanaka, Floidy IR - Wafawanaka F FIR - Wolter, Nicole IR - Wolter N EDAT- 2022/03/18 06:00 MHDA- 2022/06/07 06:00 PMCR- 2022/06/01 CRDT- 2022/03/17 20:12 PHST- 2021/12/07 00:00 [received] PHST- 2022/01/25 00:00 [revised] PHST- 2022/02/01 00:00 [accepted] PHST- 2022/03/18 06:00 [pubmed] PHST- 2022/06/07 06:00 [medline] PHST- 2022/03/17 20:12 [entrez] PHST- 2022/06/01 00:00 [pmc-release] AID - S1473-3099(22)00069-X [pii] AID - 10.1016/S1473-3099(22)00069-X [doi] PST - ppublish SO - Lancet Infect Dis. 2022 Jun;22(6):821-834. doi: 10.1016/S1473-3099(22)00069-X. Epub 2022 Mar 14.