BACKGROUND: Malawi’s routine national surveillance system has faced challenges including inconsistent testing for SARS-CoV-2 infection, inadequate monitoring of community transmission, and limited capacity to detect new variants. To address these challenges, the Public Health Institute of Malawi established a COVID-19 sentinel surveillance system to monitor SARS-CoV-2 infection trends and variants and inform the nation’s response.
METHODS: The sentinel surveillance was established in July 2022 in 5 health facilities (HF) and 2 busy land points of entry (PoE). At each HF, 10 symptomatic and 5 asymptomatic persons of any age seeking care are systematically sampled per day. We use WHO integrated COVID-19 and Flu case definition of influenza-like illness, acute respiratory infection, and severe acute respiratory infection to identify symptomatic patients. Ten travelers =5 years at the PoEs are similarly sampled. All consented participants provide a nasopharyngeal (NP) swab for RT-PCR test and respond to COVID-19 epidemiological, vaccine and clinical questions. SARS-CoV-2 positive samples are sent to the national reference laboratory for genomic sequencing. We analyzed recruitment data and RT-PCR positivity rates (PR) by site, sex, and age.
RESULTS: Between July 11 and November 4, 2022, 6,038 NP samples were collected and tested. The average number of participants per week was 355 (range 225-508), median age 30 years (interquartile range: 23-41 years). From the HFs, there were 297 symptomatic participants (cumulative PR 8.9%, weekly PR range 1.1-33.6%), 131 asymptomatic (cumulative PR 7.4%, weekly PR range 0-33.3%) and 40 travelers (cumulative PR 3.5%, weekly PR range 1.2-9.1%) with positive SARS-CoV-2 infection at the POEs. The proportion of females infected (8.5%) was higher than males (5.9%) (p<0.001), and PR was higher in those aged =70 years though not statistically significant. PR decreased over time and was generally low among travelers.
CONCLUSIONS: Trends in PR between symptomatic and asymptomatic were similar, highlighting the need to target both groups. The ongoing detection of infections among travelers, despite instituted COVID-19 travel restrictions, indicates the need for continued surveillance in PoEs and provides an opportunity to detect novel variants coming into the country. The COVID-19 sentinel sites ensured that trends in COVID-19 infections were available during low incidence periods.

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