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

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.

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

“…The prospective household cohort study of SARS-CoV-2, influenza, and respiratory syncytial virus community burden, transmission dynamics, and viral interaction in South Africa (PHIRST-C) was based on a previously conducted study (PHIRST) at the same sites in 2016–18. 8 , 9 The rural site, Agincourt study area in Bushbuckridge subdistrict (Mpumalanga province), is within a health and sociodemographic surveillance system (HDSS) run by the Medical Research Council and University of the Witwatersrand Rural Public Health and Health Transitions Research Unit, Agincourt. 10 , 11 The urban site, Jouberton township in Klerksdorp, is located in the North West province ( appendix pp 1–2, 25 ).…”

SARS-CoV-2 Seroprevalence in a Rural and Urban Household Cohort during First and Second Waves of Infections, South Africa, July 2020–March 2021

“…Recruitment to this study began in July 2020, and follow-up will continue through August 2021. Households that previously participated in the PHIRST study during 2016–2018 ( 11 , 12 ) and additional randomly selected households were eligible. Households with > 3 household members of any age were enrolled if > 80% of members consented.…”

Estimating the contribution of HIV-infected adults to household pneumococcal transmission in South Africa, 2016–2018: A hidden Markov modelling study

“…Households were randomly selected, and were eligible for the study if they had ≥3 household members and the household members resided in the household for ≥1 year prior to study commencement, had no plan to relocate during study duration, and consented to participate in the study. Also, enrolment ensured that more than half of the households included at least one child aged <5 years, and a new cohort was enrolled every study year [ 30 , 31 ].…”

“…In all HIV infected individuals, specimens were collected for CD4+ T cell and quantitative HIV viral load testing. Newly HIV diagnosed patients were referred to the local HIV/ART clinic [ 30 ].…”