Using molecular network analysis to explore the characteristics of HIV-1 transmission in a China-Myanmar border area

Abstract

Background: The China-Myanmar border area is considered a hot spot of active HIV-1 recombination in Southeast Asia. To better understand the characteristics of HIV-1 transmission in this area, a cross-sectional HIV-1 molecular epidemiological survey was conducted in Baoshan Prefecture of Yunnan Province.

Methods: In total, 708 newly reported HIV-1 cases in Baoshan Prefecture from 2019 to 2020 were included in this study. HIV-1 gag, pol and env genes were sequenced, and the spatial and demographic distributions of HIV-1 genotypes were analyzed. The characteristics of HIV-1 transmission were investigated using the HIV-1 molecular network method.

Results: In the 497 samples with genotyping results, 19 HIV-1 genotypes were found, with URFs being the predominant strains (30.2%, 150/497). The main circulating HIV-1 strains were mostly distributed in the northern area of Baoshan. URFs were more likely identified in Burmese individuals, intravenous drug users and those younger than 50 years old. CRF08_BC was more likely detected in farmers and those of Han ethnicity, CRF01_AE in the young and those of Han ethnicity, and CRF07_BC in the subpopulation with junior middle school education and higher. Moreover, CRF118_BC and CRF64_BC were more likely found in the subpopulation aged ≥40 years and ≥50 years, respectively. Among 480 individuals with pol sequence detection, 179 (37.3%) were grouped into 78 clusters, with Baoshan natives being more likely to be in the network. The proportion of the linked individuals showed significant differences when stratified by the regional origin, marital status, age and county of case reporting. In the molecular network, recent infections were more likely to occur among nonfarmers and individuals aged below 30 years.

Conclusions: HIV-1 genetics has become complex in Baoshan. HIV-1 molecular network analysis provided transmission characteristics in the local area, and these findings provided information to prioritize transmission-reduction interventions.

Fig 1. Spatial distribution of HIV-1 genotypes in Baoshan Prefecture.

Dot density maps for CRF01_AE, CRF07_BC, CRF08_BC, CRF64_BC, CRF118_BC, URFs, Subtypes B and C, and CRFs. One dot represents 0.025% of the total cases genotyped. The shapefile of China was downloaded from the GADM database (www.gadm.org), version 3.4, April 2018, from which the shapefile of Baoshan Prefecture of Yunnan Province was extracted using Quantum GIS.

Fig 2. Characteristics of the HIV-1 molecular network in Baoshan Prefecture.

A, Distribution of genetic transmission clusters by cluster size. B, Distribution of sequence pairs by genetic distance. C, Distribution of nodes in clusters by link.

Fig 3. Relationship of the linked individuals in the HIV-1 molecular network in Baoshan Prefecture.

A, Left panel: HIV-1 molecular clusters coded by regional category. Right panel: constitution of linked individuals stratified by regional category. B, Left panel: HIV-1 molecular clusters coded by marital status. Right panel: constitution of linked individuals stratified by marital status. C, Left panel: HIV-1 molecular clusters coded by age. Right panel: constitution of linked individuals stratified by age. D, Left panel: HIV-1 molecular clusters coded by counties where cases were reported. Right panel: constitution of linked individuals stratified by counties where cases were reported.

Fig 4. Distribution of tMRCA in the HIV-1 molecular network.

A, Example inference of recent infection events. In the MCC tree, the tMRCA of the blue clades was post-2019, and these clades were associated with recent infection events. B, Distribution of tMRCA in the HIV-1 molecular network.