Cohort profile: A Prospective Household cohort study of Influenza, Respiratory syncytial virus and other respiratory pathogens community burden and Transmission dynamics in South Africa, 2016-2018

Cheryl Cohen; Meredith L McMorrow; Neil A Martinson; Kathleen Kahn; Florette K Treurnicht; Jocelyn Moyes; Thulisa Mkhencele; Orienka Hellferscee; Limakatso Lebina; Matebejane Moroe; Katlego Motlhaoleng; Francesc Xavier Gómez-Olivé; Ryan Wagner; Stephen Tollman; Floidy Wafawanaka; Sizzy Ngobeni; Jackie Kleynhans; Azwifari Mathunjwa; Amelia Buys; Lorens Maake; Nicole Wolter; Maimuna Carrim; Stuart Piketh; Brigitte Language; Angela Mathee; Anne von Gottberg; Stefano Tempia; PHIRST group

doi:10.1111/irv.12881

Cohort profile: A Prospective Household cohort study of Influenza, Respiratory syncytial virus and other respiratory pathogens community burden and Transmission dynamics in South Africa, 2016-2018

Influenza Other Respir Viruses. 2021 Nov;15(6):789-803. doi: 10.1111/irv.12881. Epub 2021 Jul 23.

Authors

Cheryl Cohen^{1

2}, Meredith L McMorrow^{3

4

5}, Neil A Martinson^{6

7

8}, Kathleen Kahn⁹, Florette K Treurnicht¹⁰, Jocelyn Moyes^{1

2}, Thulisa Mkhencele¹, Orienka Hellferscee^{1

11}, Limakatso Lebina⁸, Matebejane Moroe⁸, Katlego Motlhaoleng⁸, Francesc Xavier Gómez-Olivé⁹, Ryan Wagner⁹, Stephen Tollman⁹, Floidy Wafawanaka⁹, Sizzy Ngobeni⁹, Jackie Kleynhans^{1

2}, Azwifari Mathunjwa¹, Amelia Buys¹, Lorens Maake¹, Nicole Wolter^{1

11}, Maimuna Carrim^{1

11}, Stuart Piketh¹², Brigitte Language¹², Angela Mathee^{13

14}, Anne von Gottberg^{1

11}, Stefano Tempia^{3

4

15}; PHIRST group

Affiliations

¹ Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
² School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
³ Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
⁴ Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa.
⁵ United States Public Health Service, Rockville, Maryland, USA.
⁶ Perinatal HIV Research Unit, Medical Research Council (MRC) Soweto Matlosana Collaborating Centre for HIV/AIDS and Tuberculosis, Tygerberg, South Africa.
⁷ Center for Tuberculosis Research, Division of Infectious Diseases, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA.
⁸ Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, University of the Witwatersrand, Johannesburg, South Africa.
⁹ MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
¹⁰ Division of Medical Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa.
¹¹ School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
¹² Climatology Research Group, Unit for Environmental Science and Management, School of Geo and Spatial Science, North-West University, Potchefstroom, South Africa.
¹³ Environment and Health Research Unit, South African Medical Research Council, Johannesburg, South Africa.
¹⁴ Environmental Health Department, Faculty of Health Sciences, University of Johannesburg, Johannesburg, South Africa.
¹⁵ MassGenics, Duluth, Georgia, USA.

Abstract

Purpose: The PHIRST study (Prospective Household cohort study of Influenza, Respiratory Syncytial virus, and other respiratory pathogens community burden and Transmission dynamics in South Africa) aimed to estimate the community burden of influenza and respiratory syncytial virus (RSV) including the incidence of infection, symptomatic fraction, and to assess household transmission.

Participants: We enrolled 1684 individuals in 327 randomly selected households in a rural and an urban site over three consecutive influenza and two RSV seasons. A new cohort of households was enrolled each year. Participants were sampled with nasopharyngeal swabs twice-weekly during the RSV and influenza seasons of the year of enrolment. Serology samples were collected at enrolment and before and after the influenza season annually.

Findings to date: There were 122 113 potential individual follow-up visits over the 3 years, and participants were interviewed for 105 783 (87%) of these. Out of 105 683 nasopharyngeal swabs, 1258 (1%) and 1026 (1%) tested positive on polymerase chain reaction (PCR) for influenza viruses and RSV, respectively. Over one third of individuals had PCR-confirmed influenza each year. Overall, there was influenza transmission to 10% of household contacts of an index case.

Future plans: Future planned analyses include analysis of influenza serology results and RSV burden and transmission. Households enrolled in the PHIRST study during 2016-2018 were eligible for inclusion in a study of SARS-CoV-2 transmission initiated in July 2020. This study uses similar testing frequency to assess the community burden of SARS-CoV-2 infection and the role of asymptomatic infection in virus transmission.

Keywords: South Africa; burden; cohort profile; influenza; respiratory syncytial virus; transmission.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, P.H.S.

MeSH terms

COVID-19*
Cohort Studies
Humans
Influenza, Human* / epidemiology
Prospective Studies
Respiratory Syncytial Virus Infections* / epidemiology
Respiratory Syncytial Virus, Human*
SARS-CoV-2
South Africa / epidemiology

Abstract

Publication types

MeSH terms

Grants and funding