Combining molecular network analysis and field epidemiology to quantify local HIV transmission and highlight ongoing epidemics

Abstract

ABSTRACT: Objectives: This study aimed to establish a collaborative approach to quantify local HIV transmission, which is an issue of great concern to public health. Methods: We linked HIV-1 pol gene sequences to demographic information and epidemiological investigations in Hangzhou (a central city in East China). We estimated local acquisition rates from a collaboration of molecular network analysis (with a distance-based approach) and epidemiological investigations. Results: Among 1064 newly diagnosed patients with HIV, 857 pol sequences were acquired and subsequently analyzed. Multiple subtypes were identified, with circulating recombinant form (CRF)07_BC (42.5%) and CRF01_AE (39.2%) predominating, followed by 13 other subtypes and 26 unique recombinant forms. By integrating the molecular network analysis and epidemiological investigations, we estimated that the proportion of local infection was 63.2%. The multivariable analyses revealed that individuals in clusters were more likely to be local residents, be aged 50 years or older, work as farmers, and have a higher first cluster of differentiation 4 count level (P <0.05). The proportions of local acquisitions over 70% were observed in local residents (79.9%, 242/303), individuals aged 50 years or older (73.6%, 181/246), and farmers (75.6%, 99/131). Conclusion: The molecular network analysis can augment traditional HIV epidemic surveillance. This study establishes a paradigm for quantifying local HIV transmission for generalization in other areas.

Keywords

• HIV-1
• Molecular network
• Molecular epidemiology
• Local acquisition
• Phylogenetic