The role of subtyping methodologies in HIV surveillance and vaccine development: a systematic review and meta-analysis

Alexandria Williams; Ferdinard Adungo; Juan Luis Ramirez; Valerie Oriol-Mathieu; Malcolm Macartney; Sonia Menon

doi:10.1097/QAD.0000000000004427

The role of subtyping methodologies in HIV surveillance and vaccine development: a systematic review and meta-analysis

AIDS. 2025 Dec 30. doi: 10.1097/QAD.0000000000004427. Online ahead of print.

Authors

Alexandria Williams¹, Ferdinard Adungo², Juan Luis Ramirez³, Valerie Oriol-Mathieu⁴, Malcolm Macartney⁵, Sonia Menon⁶

Affiliations

¹ Ghent University, Ghent, Belgium; P95 Pharmacovigilance and Epidemiological Services, Leuven, Belgium.
² Kenya Medical Research Institute, Nairobi.
³ P95 Pharmacovigilance and Epidemiological Services, Leuven, Belgium.
⁴ Johnson & Johnson, Leiden, the Netherlands.
⁵ Janssen-Cilag Limited, High Wycombe, United Kingdom.
⁶ Epitech Research, Auderghem, Belgium.

PMID: 41467694
DOI: 10.1097/QAD.0000000000004427

Abstract

Background: HIV genetic diversity has increased over time, with recombinant forms becoming more prevalent and complicating subtype classification and surveillance, particularly in low-and-middle income countries (LMICs). Accurate subtyping is critical for surveillance, vaccine design, and cure strategies, but its reliability depends on methodological choices — the genomic region sequenced, laboratory methods employed, and the subtyping tools used. This study evaluates how these methodologies influence reported recombinant form prevalence across regions.

Methods: This systematic review included over 400 peer-reviewed studies published between January 2010 and June 2021 that reported HIV subtype prevalence across diverse geographic regions. Data on subtyping methodologies were also extracted. To explore associations with recombinant form prevalence, three generalized linear mixed models were developed for meta-analysis.

Results: Our findings show that Sanger sequencing of the pol region, analyzed using tools from the Los Alamos National Laboratory, remains the most widely used subtyping methodology. Over time, there has been a steady increase in studies reporting HIV subtype diversity. In the meta-analysis, specific genome regions and subtyping tools were positively associated with recombinant form prevalence. Despite controlling for region, certain areas remained positively or negatively associated with recombinant form prevalence.

Conclusions: This review highlights the methodological challenges of HIV subtyping and recombinant form detection, which are critical for surveillance, vaccine development, and cure strategies. We highlight the urgent need for accessible, reliable subtyping tools and enhanced capacity-building—particularly in LMICs, where high viral diversity overlaps with the greatest burden of disease.

Keywords: HIV-1/genetics; HIV-1/genotyping; Molecular Epidemiology; Next-Generation Sequencing; Recombination; Surveillance; Vaccine Development; epidemiological; genetic.