This report summarizes the results of influenza surveillance in South Africa for the period of week 1 through week 32, 2022, and was compiled by the World Health Organization (WHO) National Influenza Centre (NIC) housed at the Centre for Respiratory Diseases and Meningitis (CRDM) of the National Institute for Communicable Diseases (NICD). During 2022, influenza activity was observed from week 1 through 32, with an increased period of activity in the normal winter influenza season.

Influenza circulation was dominated by A(H1N1)pdm09, followed by A(H3N2) and B/Victoria. While some antigenic drift was observed, strains fell within the same phylogenetic clades as 2022 Southern Hemisphere vaccine strains. This report includes data from individuals meeting syndromic case definitions within three respiratory illness surveillance programmes: Viral Watch influenza-like illness (VW) surveillance in outpatients (n=732) at private general practitioners, influenza-like illness (ILI) surveillance in outpatients (n=1028) at public health clinics and pneumonia surveillance in hospitalized patients (n=4340). Together, the three surveillance programmes contributed data from all nine provinces in South Africa.

Influenza activity was observed from weeks 1 through 32, with an overall detection rate for 2022 from 3 January through 14 August of 11% (648/6100). Using the Moving Epidemic Method (MEM), the levels of activity reached moderate and low levels in the ILI and pneumonia surveillance programmes, respectively. Influenza single infections were dominated by influenza A(H1N1)pdm09 (62%, 387/621), followed by A(H3N2) (30%, 186/621) and B/Victoria (8%, 48/621). Dual infections were detected in three individuals [A(H1N1)pdm09 and B lineage inconclusive, A(H1N1)pdm09 and A(H3N2), A(H1N1)pdm09 and B/Victoria]. Influenza B/Yamagata was not detected. Subtype/lineage could not be determined for 4% (24/648) of infections, due to low viral load. Despite a low vaccine coverage (12%, 61/521) in the Viral Watch programme, vaccine effectiveness for any influenza, influenza A(H1N1)pdm09 and influenza A(H3N2) adjusted for age and season was 65% (95%CI: 30%, 82%), 46% (95% CI: -20%, 76%) and 91% (95%CI: 31%, 99%), respectively. Vaccine effectiveness for influenza B/Victoria could not be determined due to small numbers. Cell culture-derived influenza virus isolates were obtained with an 85% (155/183) success rate. Haemagglutinin inhibition (HAI) assays performed at the NICD demonstrated that 46% (29/63) of tested A(H1N1)pdm09, 100% (22/22) of A(H3N2) and 100% (9/9) of B/Victoria viruses were recognized by antisera raised against current vaccine and vaccine-like strains.

All samples tested for (12/12 A(H1N1) pdm09 and 3/3 A(H3N2)) were susceptible to zanamivir, oseltamivir, peramivir and laninamivir. No known resistance mutations were detected among the 91 sequenced viruses. Genetic analysis of the haemagglutinin gene of South African 2022 influenza viruses was available for 80 A(H1N1)pdm09, 9 A(H3N2) and 2 B/Victoria viruses. Influenza A(H1N1)pdm09 viruses clustered into two major genetic subgroups namely 6B.1A.5a.1 and 6B.1A.5a.2, with the majority (59/80, 74%) belonging to the 6B.1A.5a.2 clade together with the 2022 A(H1N1)pdm09 vaccine strain for the Southern Hemisphere (A/Victoria/2570/2019). All A(H3N2) strains clustered within the 3C.2a1b.2a.2 clade along with the current Southern Hemisphere A(H3N2) vaccine strain (A/Darwin/9/2021). Both B/Victoria viruses clustered in the V1A.3a.2 subclade together with the current Southern Hemisphere influenza vaccine strain (B/Austria/1359417/2021). Following easing of COVID-19 restrictions, South Africa experienced the first typical influenza season since the start of the pandemic. The influenza season was ongoing as of week 43 of 2022, with a biphasic pattern in which infections later in the season were dominated by B/Victoria and A(H3N2) viruses. Individuals, especially those in high risk categories, are encouraged to receive the annual influenza vaccine.