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Existing seroprevalence studies in Malawi have primarily used convenience samples and enzyme-linked immunosorbent assays (ELISAs). We assessed SARS-CoV-2 neutralisation in a longitudinal Malawian population-based cohort, assessing protective immunity post-infection and vaccination. Sera were obtained from rural (Karonga,\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u2009958) and urban (Lilongwe,\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u2009918) based participants at three-monthly intervals (February 2021-April 2022). Neutralising antibodies against SARS-CoV-2 were measured using human immunodeficiency (HIV)-based pseudotype assays in HIV-uninfected participants, and vesicular stomatitis virus-based assays in HIV-infected participants and an HIV-uninfected subset. Nucleocapsid ELISAs identified vaccinated participants also infected. SARS-CoV-2 neutralisation profiles increased in complexity over time from rising vaccination coverage and emerging variants. Neutralising antibody prevalence was higher in Lilongwe than Karonga (68.1% (CI 63.5\u201372.4) vs. 45.4% (CI 41.6\u201349.3), Survey 4). Hybrid immune and solely vaccinated participants exhibited higher titres than those solely infected. Children\u2009&lt;\u200915 years had the lowest neutralising antibody titres among infected (not vaccinated) participants. People living with HIV had lower neutralising responses than those HIV-uninfected, particularly post vaccination. We therefore recommend surveillance of children and people living with HIV as low neutralisation responses increase reinfection risk. COVID-19 vaccination should be prioritised for HIV-infected individuals.\n                  <\/jats:p>","DOI":"10.1038\/s41598-025-22599-7","type":"journal-article","created":{"date-parts":[[2025,10,29]],"date-time":"2025-10-29T16:29:32Z","timestamp":1761755372000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Characterising protective immune responses to SARS-CoV-2 in urban and rural Malawi between February 2021 and April 2022"],"prefix":"10.1038","volume":"15","author":[{"given":"Mhairi J.","family":"McCormack","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Louis","family":"Banda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen","family":"Kasenda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ellen C.","family":"Hughes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lina","family":"Leonhard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Annie","family":"Mwale","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Estelle","family":"McLean","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alison","family":"Price","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amelia","family":"Crampin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Chaima","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abena S.","family":"Amoah","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tonney S.","family":"Nyirenda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antonia","family":"Ho","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brian J.","family":"Willett","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,10,29]]},"reference":[{"key":"22599_CR1","doi-asserted-by":"publisher","unstructured":"Burki, T. 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BJW received funding through UKRI. The other coauthors declare no competing interests.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"Ethical approval was granted by the Malawi College of Medicine Research Ethics Committee (P11\/20\/3177\u201311th December 2020) and the University of Glasgow College of Medicine, Veterinary and Life Sciences Research and Ethics Committee (200200056\u20138th February 2021). All procedures were performed in compliance with the relevant laws and institutional guidelines. The study adhered to the Declaration of Helsinki principles.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethical approval"}}],"article-number":"37914"}}