Retrovirus-based pseudotyped virus neutralisation assays overestimate neutralising activity in sera from participants receiving integrase inhibitors

• Published in: Scientific reports Vol. 15; no. 1; pp. 28580 - 13
• Main Authors: McCormack, Mhairi J., Asamaphan, Patawee, Hughes, Ellen C., Banda, Louis, Kasenda, Stephen, Davis, Chris, Szemiel, Agnieszka M., Crampin, Amelia, Amoah, Abena S., Thomson, Emma C., Ho, Antonia, Willett, Brian J.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 05.08.2025; Nature Publishing Group; Nature Portfolio
• Subjects: 631/1647; 631/250; 631/326/596; Adult; Antibodies; Antibodies, Neutralizing - blood; Antibodies, Neutralizing - immunology; Antibodies, Viral - blood; Antibodies, Viral - immunology; Antiretroviral agents; Confidence intervals; Coronaviruses; COVID-19; COVID-19 - blood; COVID-19 - immunology; COVID-19 - virology; Female; Glycoproteins; Hepacivirus - immunology; Hepatitis C; Hepatitis C - immunology; HIV; HIV Infections - blood; HIV Infections - drug therapy; HIV Infections - immunology; HIV Infections - virology; Human immunodeficiency virus; Humanities and Social Sciences; Humans; Immunity; Immunoglobulin G; Inhibitors; Integrase; Integrase inhibitors; Integrase Inhibitors - therapeutic use; Interference; Leukemia; Male; Mann-Whitney U test; Middle Aged; multidisciplinary; Neutralization Tests - methods; Pseudovirus assay; Pyridones; Retroviridae - immunology; SARS-CoV-2 - immunology; Science; Science (multidisciplinary); Serology; Severe acute respiratory syndrome coronavirus 2; Statistical significance; Stomatitis; United Kingdom > UK; Malawi; Pseudovirus assay; HIV; Integrase inhibitors; Interference
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-025-11362-7

Retroviral pseudotype-based virus neutralisation assays are widely used to estimate functional immunity, but may be unsuitable for testing human immunodeficiency virus (HIV)-infected individuals receiving integrase inhibitor treatment. 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  = 1,876), detecting neutralisation across timepoints in 10.5–54.5% of HIV-uninfected vs. 85.5–93.9% of HIV-infected participants ( n  = 96). HIV-infected sera were re-tested using vesicular stomatitis virus (VSV)-based SARS-CoV-2 pseudoviruses, estimating seroprevalence at 5.6–65.2%, 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  = 100, n  = 90 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.