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

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  1   2 , Meredith L McMorrow  3   4   5 , Neil A Martinson  6   7   8 , Kathleen Kahn  9 , Florette K Treurnicht  10 , Jocelyn Moyes  1   2 , Thulisa Mkhencele  1 , Orienka Hellferscee  1   11 , Limakatso Lebina  8 , Matebejane Moroe  8 , Katlego Motlhaoleng  8 , Francesc Xavier Gómez-Olivé  9 , Ryan Wagner  9 , Stephen Tollman  9 , Floidy Wafawanaka  9 , Sizzy Ngobeni  9 , Jackie Kleynhans  1   2 , Azwifari Mathunjwa  1 , Amelia Buys  1 , Lorens Maake  1 , Nicole Wolter  1   11 , Maimuna Carrim  1   11 , Stuart Piketh  12 , Brigitte Language  12 , Angela Mathee  13   14 , Anne von Gottberg  1   11 , Stefano Tempia  3   4   15 ; PHIRST group
Affiliations

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 et al. Influenza Other Respir Viruses. 2021 Nov.

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.

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Conflict of interest statement

Cheryl Cohen has received research grants awarded to her institution from Sanofi Pasteur, US Centers for Disease Control and Prevention. Cheryl Cohen has had costs for travel to a meeting supported by Parexel. Maimuna Carrim was awarded the Robert Austrian Research Award in Pneumococcal Vaccinology sponsored by Pfizer. Neil Martinson has a research grant awarded to his institution by Pfizer South Africa. Anne von Gottberg has received research grants awarded to her institution from Sanofi Pasteur, Pfizer and US Centers for Disease Control and Prevention.

Figures

FIGURE 1
FIGURE 1
Location of rural (Agincourt) and urban (Jouberton) study sites in South Africa
FIGURE 2
FIGURE 2
Weekly numbers of nasopharyngeal samples tested and influenza and respiratory syncytial virus (RSV) detections and timing of serology blood draws, a rural and an urban site, South Africa, 2016–2018
FIGURE 3
FIGURE 3
Flow chart of participant enrolment at the rural and urban sites, South Africa, 2016–2018. (A) Rural (Agincourt) and (B) urban (Jouberton). Individuals or households were not included if they withdrew or moved away before completing >10 visits with collection of a nasopharyngeal swab. Bars indicate timing of serology blood draws. Grey bars indicate number of nasopharyngeal swabs tested each visit. Blood draw dates in year 2016 were Draw 1 (16 March to 15 April) and Draw 2 (17 October to 24 November). Blood draw dates in year 2017 were 2016 cohort Draw 1 (6 February to 4 March), Draw 2 (3–26 May), Draw 3 (2–18 October); 2017 cohort Draw 1 (24 November 2016 to 24 February 2017), Draw 2 (2–26 May) and Draw 3 (12–27 October). Blood draw dates in year 2018 were 2016 cohort Draw 1 (29 January to 9 February), Draw 2 (4 May to 6 June), Draw 3 (1 October to 5 November); 2017 cohort Draw 1 (12 February to 9 March), Draw 2 (4 May to 4 June), Draw 3 (17–31 October); 2018 cohort Draw 1 (28 November 2017 to 24 January 2018), Draw 2 (21 April to 1 June 2018) and Draw 3 (1–31 October)
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