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We evaluated these assays for measuring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and hepatitis C virus (HCV) neutralisation in people living with HIV. SARS-CoV-2 neutralisation was assessed using HIV-based SARS-CoV-2 pseudoviruses in sera from a longitudinal Malawian cohort (\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u20091,876), detecting neutralisation across timepoints in 10.5\u201354.5% of HIV-uninfected vs. 85.5\u201393.9% of HIV-infected participants (\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u200996). HIV-infected sera were re-tested using vesicular stomatitis virus (VSV)-based SARS-CoV-2 pseudoviruses, estimating seroprevalence at 5.6\u201365.2%, suggesting HIV-based assays overestimate neutralisation. HIV-based VSV-glycoprotein(G) pseudoviruses confirmed non-specific inhibition in 75.0-87.9% of HIV-infected participants. HCV neutralisation was assessed in UK-based HCV patients (\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u2009100,\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u200990 HIV-infected) using murine leukaemia virus (MLV)-based HCV pseudoviruses. Non-HCV-specific inhibition was detected in integrase inhibitor recipients. Median neutralisation of MLV(HCV) pseudoviruses was higher in integrase inhibitor recipients (71.8% vs. 21.3%). Testing HIV(SARS-CoV-2) and MLV(HCV) pseudoviruses against antiretroviral drugs showed interference by integrase inhibitors (specifically, dolutegravir). Isolating IgG from serum removed the interference by residual drugs. Retrovirus-based assays are therefore unsuitable for testing individuals receiving integrase inhibitors. Protective immunity to viruses has likely been over-reported in HIV prevalent populations.\n                  <\/jats:p>","DOI":"10.1038\/s41598-025-11362-7","type":"journal-article","created":{"date-parts":[[2025,8,5]],"date-time":"2025-08-05T14:24:41Z","timestamp":1754403881000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Retrovirus-based pseudotyped virus neutralisation assays overestimate neutralising activity in sera from participants receiving integrase inhibitors"],"prefix":"10.1038","volume":"15","author":[{"given":"Mhairi J.","family":"McCormack","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patawee","family":"Asamaphan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ellen C.","family":"Hughes","sequence":"additional","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":"Chris","family":"Davis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Agnieszka M.","family":"Szemiel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amelia","family":"Crampin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abena S.","family":"Amoah","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emma C.","family":"Thomson","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":[[2025,8,5]]},"reference":[{"key":"11362_CR1","doi-asserted-by":"publisher","first-page":"1205","DOI":"10.1038\/s41591-021-01377-8","volume":"27","author":"DS Khoury","year":"2021","unstructured":"Khoury, D. 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