Collaborative Research on Influenza, Coronavirus Disease 2019 (COVID-19), and Other Respiratory Pathogens in South Africa

PROJECT SUMMARY This project aims to generate a body of data that will assist in formulating appropriate policies for the reduction of morbidity and mortality associated with influenza Coronavirus 2019 (COVID-19) and other respiratory pathogens in South Africa. Specifically we aim to perform influenza virus hemagglutination inhibition (HI) testing of serum samples already collected from PHIRST-C participants in a rural and an urban site and from HUTS participants in 2 key communities before and after the 2021 influenza season to determine rates of recent influenza infection. We also aim to characterize healthcare seeking behavior for respiratory illness during the influenza season in the year following the South African COVID-19 epidemic first and second waves through a survey conducted following the influenza season and compare healthcare seeking behavior for respiratory illness to a survey conducted before the 2021 influenza season and assess the impact of different factors on healthcare seeking behavior. We aim to describe the prevalence of MTB-SARS-CoV-2 coinfection and the impact of coinfection on clinical presentation and outcomes in patients presenting with ILI or suspected COVID-19 at ILI surveillance sites or patients admitted with SRI at pneumonia surveillance sites in South Africa. We aim to pilot the implementation of laboratory-confirmed influenza surveillance among individuals participating to the CoughWatchSA participatory digital surveillance platform, compare influenza virus circulation as detected in facility-based surveillance and through the CoughWatchSA platform and to evaluate concordance between self-reported ARI on the CoughWatchSA platform and laboratory-confirmed infection with influenza. This will be achieved through testing of collected serum samples for the presence of anti-influenza antibodies using HI assay, performing a survey of healthcare utilization and serosurvey at two sites in South Africa and implementation of systematic Mycobacterium tuberculosis testing of all participants enrolled in existing pneumonia and influenza-like illness surveillance programmes. Lastly we will pilot self- swabbing of individuals participating in the Coughwatch app for syndromic influenza surveillance.