Background. Surveillance programmes for influenza and other respiratory pathogens are important to generate vaccine effectiveness (VE) estimates and to inform vaccine composition. We aimed to explore the feasibility and acceptability of home-based testing. Methods In 3/9 provinces in South Africa, we established a self-referral system for individuals aged ≥18 years with respiratory symptoms of ≤10 days duration. Following electronic consent, swab collection material was delivered to participants who also completed a questionnaire including self-reported vaccination status. Swabs were tested by PCR for influenza, respiratory syncytial virus (RSV) and SARS-CoV-2. A test negative methodology was used to estimate influenza VE. Results Of 1456 samples collected between 1 December 2021 and 31 August 2022, 73 (5%) tested positive for influenza, 38 (3%) tested positive for RSV and 394 (27%) for SARS-CoV-2. We subtyped 55% (40/73) of the influenza positive specimens; 16/40 (40%) were influenza A (A(H1N1)pdm09; 10/40 (25%)A (H3N2)) and all 14/40(35%) influenza B were B/Victoria. Only 20% (279/1451) of participants reported influenza-like illness case definition symptoms of fever and cough. Influenza vaccine coverage was 11% (157/1454). The overall influenza VE was 26% (95% confidence interval, -73%;69%). Of the completed acceptability questionnaires, 123/127 (97%) participants would make use of the service again. 36% (46/127) of enrolled participants were recruited through the testing centre’s webpage and 13% (17/127) through social media. Conclusions Home-based swabbing was feasible and acceptable. We were able to calculate an influenza VE, although a large sample size and verification of vaccine status may improve the VE estimate in the future.

Background Estimates of the disease burden associated with different respiratory viruses are severely limited in low- and middle-income countries, especially in Africa. Methods We estimated age-specific numbers and rates of medically and non-medically attended influenza-like illness (ILI) and severe respiratory illness (SRI) that were associated with influenza, respiratory syncytial virus (RSV), rhinovirus, human metapneumovirus, adenovirus, enterovirus and parainfluenza virus types 1-3 after adjusting for the attributable fraction (AF) of virus detection to illness in South Africa during 2013-2015. Rates were reported per 100,000 population. Results The mean annual rates were 51,383 and 4,196 for ILI and SRI, respectively. Of these, 26% (for ILI) and 46% (for SRI) were medically attended. Among outpatients with ILI, rhinovirus had the highest AF-adjusted rate (7,221), followed by influenza (6,443) and adenovirus (1,364); whereas, among inpatients with SRI, rhinovirus had the highest AF-adjusted rate (400), followed by RSV (247) and influenza (130). Rhinovirus (9,424) and RSV (2,026) had the highest AF-adjusted rates among children aged <5 years with ILI or SRI, respectively; whereas rhinovirus (757) and influenza (306) had the highest AF-adjusted rates among individuals aged ≥65 years with ILI or SRI, respectively Conclusions There was a substantial burden of ILI and SRI in South Africa during 2013-2015. Rhinovirus and influenza had a prominent disease burden among patients with ILI. Rhinovirus had the highest burden of illness among patients of any age with SRI, followed by RSV. RSV and influenza were the most prominent causes of SRI in children and the elderly, respectively.

Introduction: We describe epidemiology and outcomes of confirmed SARS-CoV-2 infection and admissions among children <18 years in South Africa, an upper-middle income setting with high inequality. Methods: Laboratory and hospital COVID-19 surveillance data, 28 January - 19 September 2020 was used. Testing rates were calculated as number of tested for SARS-CoV-2 divided by population at risk; test positivity rates were calculated as positive tests divided by total number of tests. In-hospital case fatality ratio (CFR) was calculated based on hospitalized positive admissions with outcome data who died in-hospital and death was judged SARS-CoV-2 related by attending physician. Findings: 315,570 children aged <18 years were tested for SARS-CoV-2; representing 8.9% of all 3,548,738 tests and 1.6% of all children in the country. Of children tested, 46,137 (14.6%) were positive. Children made up 2.9% (n=2,007) of all SARS-CoV-2 positive admissions to sentinel hospitals. Among children, 47 died (2.6% case-fatality). In-hospital deaths were associated with male sex [adjusted odds ratio (aOR) 2.18 (95% confidence intervals (CI) 1.08 - 4.40)] vs female; age <1 year [aOR 4.11 (95% CI 1.08-15.54)], age 10-14 years [aOR 4.20 (95% CI1.07-16.44)], age 15-17 years [aOR 4.86 (95% 1.28 -18.51)] vs age 1-4 years; admission to a public hospital [aOR 5.07(95% 2.01 -12.76)] vs private hospital and ≥1 underlying conditions [aOR 12.09 (95% CI 4.19-34.89)] vs none Conclusions: Children with underlying conditions were at greater risk of severe SARS-CoV-2 outcomes. Children > 10 years and those with underlying conditions should be considered for increased testing and vaccination.