About this project

The Prospective Household observational cohort study of Influenza, Respiratory Syncytial virus and other respiratory pathogens community burden and Transmission dynamics in South Africa (The PHIRST Study) was a prospective cohort study in a rural and urban site from 2017-2018, with approximately 100 new households enrolled each year and followed up for 10 months. Nasopharyngeal swabs were collected twice-weekly from consenting household members irrespective of symptoms and tested for influenza virus, respiratory syncytial virus (RSV), B. pertussis and S. pneumoniae using a real-time reverse transcription polymerase chain reaction. We collected and tested over 100,000 nasopharyngeal swabs and over 7,000 serum samples. Although the follow-up of the cohort has stopped, we are currently doing serology testing and analysis.


To estimate the community burden of influenza and RSV, including:

  • the incidence of influenza and RSV infection in the community;
  • the symptomatic fraction associated with influenza and RSV infection;
  • the severity associated with symptomatic infections;
  • the fraction of individuals with symptomatic infection seeking medical care.

To assess the transmission dynamics of influenza and RSV infections in the community, including:

  • the estimation of the household secondary infection risk (SIR), serial interval and length of shedding;
  • the estimation of transmission of infection between age groups within the household and possibly the community;
  • the estimation of the effective reproductive number (Rt) and its variation over time in the community.

The PHIRST study will improve our understanding of the community burden of influenza, RSV, pertussis, tuberculosis and pneumococcal infection in South Africa. It will also provide data on the carriage prevalence of meningococcus, diphtheria and group A streptococcus. The data generated from this study will also provide important information on the transmission dynamics of influenza, RSV, pertussis and pneumococcus in the community allowing to better strategize interventions (including targeted vaccination strategies) and evaluate their potential impact.


The study was approved by the University of the Witwatersrand Human Research Ethics Committee (Reference 150808).


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
Cohen, C, McMorrow, ML, Martinson, NA, Kahn, K, Treurnicht, FK, Moyes, J, Mkhencele, T, Hellferscee, O, Lebina, L, Moroe, M, Motlhaoleng, K, Gómez-Olivé, FX, Wagner, R, Tollman, S, Wafawanaka, F, Ngobeni, S, Kleynhans, J, Mathunjwa, A, Buys, A, Maake, L, Wolter, N, Carrim, M, Piketh, S, Language, B, Mathee, A, von Gottberg, A, Tempia, S and for the PHIRST group (2021). Influenza and Other Respiratory Viruses 15(6): 789-803. DOI: 10.1111/irv.12881
Asymptomatic transmission and high community burden of seasonal influenza in an urban and a rural community in South Africa, 2017-18 (PHIRST): a population cohort study.
Cohen, C, Kleynhans, J, Moyes, J, McMorrow, ML, Treurnicht, FK, Hellferscee, O, Mathunjwa, A, von Gottberg, A, Wolter, N, Martinson, NA, Kahn, K, Lebina, L, Mothlaoleng, K, Wafawanaka, F, Gómez-Olivé, FX, Mkhencele, T, Mathee, A, Piketh, S, Language, B, Tempia, S, Buys, A, Mathee, A, von Gottberg, A, Language, B, Cohen, C, Maake, L, Wafawanaka, F, Treurnicht, F, Kleynhans, J, Moyes, J, Kahn, K, Mothlaoleng, K, Lebina, L, Carrim, M, McMorrow, ML, Martinson, NA, Wolter, N, Hellferscee, O, Wagner, RG, Tempia, S, Piketh, S, Mkhencele, T and Gómes-Olivé, FX (2021). The Lancet Global Health 9(6): e863-e874. DOI: 10.1016/S2214-109X(21)00141-8.
A cross-sectional study measuring contact patterns using diaries in an urban and a rural community in South Africa, 2018.
Kleynhans, J, Tempia, S, McMorrow, ML, von Gottberg, A, Martinson, NA, Kahn, K, Moyes, J, Mkhencele, T, Lebina, L, Gómez-Olivé, FX, Wafawanaka, F, Mathunjwa, A, Cohen, C, Buys, A, Mathee, A, Language, B, Maake, L, Treurnicht, F, Mothlaoleng, K, Carrim, M, Wolter, N, Hellferscee, O, Wagner, RG, Piketh, S and the, Pg (2021). BMC Public Health 21(1): 1055. DOI: 10.1186/s12889-021-11136-6
Housing Quality in a Rural and an Urban Settlement in South Africa.
Mathee, A, Moyes, J, Mkhencele, T, Kleynhans, J, Language, B, Piketh, S, Moroe, E, Wafawanaka, F, Martinson, N, McMorrow, M, Tempia, S, Kahn, K and Cohen, C (2021). International Journal of Environmental Research and Public Health 18(5): 2240. DOI: 10.3390/ijerph18052240.
Estimating the contribution of HIV-infected adults to household pneumococcal transmission in South Africa, 2016-2018: A hidden Markov modelling study.
Thindwa, D, Wolter, N, Pinsent, A, Carrim, M, Ojal, J, Tempia, S, Moyes, J, McMorrow, M, Kleynhans, J, Gottberg, Av, French, N, PHIRST group, Cohen, C and Flasche, S (2021). PLOS Computational Biology 17(12): e1009680. DOI: 10.1371/journal.pcbi.1009680
Unmasking Pneumococcal Carriage in a High Human Immunodeficiency Virus (HIV) Prevalence Population in two Community Cohorts in South Africa, 2016-2018: The PHIRST Study
Carrim M, Tempia S, Thindwa D, Martinson NA, Kahn K, Flasche S, Hellferscee O, Treurnicht FK, McMorrow ML, Moyes J, Mkhencele T, Mathunjwa A, Kleynhans J, Lebina L, Mothlaoleng K, Wafawanaka F, Gómez-Olivé FX, Cohen C, von Gottberg A, Wolter N; PHIRST group. (2023). Clin Infect Dis DOI: 10.1093/cid/ciac499
Incidence and transmission dynamics of Bordetella pertussis infection in rural and urban communities, South Africa, 2016‒2018
Moosa F, Tempia S, Kleynhans J, McMorrow M, Moyes J, du Plessis M, et al. 2023. Emerging Infectious Disease journal. 29(2):294. DOI: 10.3201/eid2902.221125.
Transient increased risk of influenza infection following RSV infection in South Africa: findings from the PHIRST study, South Africa, 2016–2018
Waterlow, NR, Kleynhans, J, Wolter, N, Tempia, S, Eggo, RM, Hellferscee, O, Lebina, L, Martinson, N, Wagner, RG, Moyes, J, von Gottberg, A, Cohen, C and Flasche, S (2023). BMC Medicine 21(1): 441. DOI: 10.1186/s12916-023-03100-5


Project Protocol

Funders and Collaborators

National Institute for Communicable Diseases
United States Centers for Disease Control and Prevention
Perinatal HIV Research Unit
4 Agincourt
MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt)
4 Wits
University of the Witwatersrand
Department of Science and Innovation
South African Population Research Infrastructure Network
South African Medical Research Council
9 Fogarty
Fogarty International Center
The ISI Foundation
11 NWU
North West University Unit for Environmental Sciences and Management


Agincourt, Mpumalanga Province
The study is conducted within the Agincourt health and socio-demographic surveillance system site (HDSS) at the MRC/Wits Rural Public Health and Health Transitions Research Unit. The population is approximately 120,000 people living in 20,000 households and 31 villages covering 450km2 and is set in the rural Bushbuckridge sub-district of Mpumalanga Province. While HIV prevalence is high, life expectancy is improving with marked epidemiological transition leading to rising prevalence of non-communicable disease including cardio-metabolic conditions and stroke.
Klerksdorp, North West Province
Klerksdorp is located in the local municipality of Matlosana in North West Province and has a population of over 385,000 people and is 115 km2. The city of Klerksdorp is surrounded by the townships of Jouberton, Alabama, Kanana, Khuma, and Tigane. The townships are organized into extensions that include mostly single-family houses and shacks. Prevalence of HIV in Klerksdorp is approximately 12%. Annual incidence of tuberculosis is extremely high approaching 1200/100,000 with an HIV coinfection rate of over 80%.