Molecular Epidemiology of HIV-1 Variants in High-Risk Populations
Summary
Understanding the molecular epidemiology of HIV-1 variants among high-risk populations involves tracking viral genetic diversity, recombination events and transmission clusters to guide prevention and treatment. HIV-1 is characterised by extensive subtype variation and frequent inter-subtype recombination, yielding circulating recombinant forms that may alter transmissibility, pathogenicity or resistance profiles. High-risk groups such as men who have sex with men, people who inject drugs and individuals with commercial sexual contacts often exhibit diverse subtype distributions and distinct network structures. Molecular tools including phylogenetic reconstruction, molecular clock analysis and cluster mapping reveal spatial and temporal patterns of variant emergence and spread. These insights inform targeted interventions, from pre-exposure prophylaxis to contact tracing, and underpin global efforts to contain the epidemic. Recent advances have highlighted the role of cross-border transmission, the emergence of second-generation recombinants and the stabilisation of molecular networks under enhanced prevention strategies.
Research from Nature Portfolio
Recent studies have identified a novel recombinant, designated CRF159_01103, derived from two established circulating forms, which emerged in a key high-risk group between 2018 and 2019. Bayesian molecular clock and recombination analyses have elucidated its origin and rising prevalence, illustrating the dynamic complexity of HIV-1 epidemics. Foundational phylogeographic work has traced predominant circulating forms such as CRF07_BC and CRF08_BC to specific geographic sources in the early 1990s, demonstrating how recombinant lineages can arise rapidly in regions with high co-infection rates. Together, these investigations employ deep sequence analysis and robust evolutionary modelling to map the genesis and dissemination of major recombinant strains, offering a template for surveillance frameworks worldwide.
Molecular Epidemiology of HIV-1 Variants in High-Risk Populations publication trend
The graph below shows the total number of articles in molecular epidemiology of hiv-1 variants in high-risk populations across all publications each year (not limited to Nature Index journals).
Technical terms
Molecular epidemiology: The application of genetic and genomic methods to study the distribution and determinants of pathogen variants in populations.
Phylogenetic analysis: The inference of evolutionary relationships among viral sequences to reconstruct transmission histories.
Circulating recombinant form (CRF): An HIV-1 strain formed by recombination between subtypes that has achieved widespread circulation.
Unique recombinant form (URF): A recombinant virus detected in a limited number of individuals without broad dissemination.
Molecular transmission network: A representation of genetically linked cases indicating potential transmission clusters.
Men who have sex with men (MSM): Individuals engaging in sexual activity with other men, representing a population with elevated HIV incidence in many regions.
References
- Characterizing HIV-1 transmission by genetic cluster analysis among newly diagnosed patients in the China-Myanmar border region from 2020 to 2023. Emerging Microbes & Infections (2024).
- Men with a history of commercial heterosexual contact play essential roles in the transmission of HIV-1 CRF55_01B from men who have sex with men to the general population in Guangxi, China. Frontiers in Cellular and Infection Microbiology (2024).
- Evolving molecular HIV clusters revealed genotype-specific dynamics in Guangzhou, China (2008-2020). International Journal of Infectious Diseases (2024).
- Identification of a new HIV-1 circulating recombinant form (CRF159_01103) derived from CRF103_01B and CRF01_AE in Hebei Province, China. Scientific Reports (2024).
- Geographic origin and evolutionary history of China’s two predominant HIV-1 circulating recombinant forms, CRF07_BC and CRF08_BC. Scientific Reports (2016).
- A Comprehensive Mapping of HIV-1 Genotypes in Various Risk Groups and Regions across China Based on a Nationwide Molecular Epidemiologic Survey. PLOS ONE (2012).
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