Dominance of HIV-1 subtype CRF01_AE in sexually acquired cases leads to a new epidemic in Yunnan province of China

Abstract

Background: Dating back to the first epidemic among injection drug users in 1989, the Yunnan province has had the highest number of human immunodeficiency virus type 1 (HIV-1) infections in China. However, the molecular epidemiology of HIV-1 in Yunnan has not been fully characterized.

Methods and findings: Using immunoassays, we identified 103,015 accumulated cases of HIV-1 infections in Yunnan between 1989 and 2004. We studied 321 patients representing Yunnan's 16 prefectures from four risk groups, 11 ethnic populations, and ten occupations. We identified three major circulating subtypes: C/CRF07_BC/CRF08_BC (53%), CRF01_AE (40.5%), and B (6.5%) by analyzing the sequence of p17, which is part of the gag gene. For patients with known risk factors, 90.9% of injection drug users had C/CRF07_BC/CRF08_BC viruses, whereas 85.4% of CRF01_AE infections were acquired through sexual transmission. No distinct segregation of CRF01_AE viruses was found among the Dai ethnic group. Geographically, C/CRF07_BC/CRF08_BC was found throughout the province, while CRF01_AE was largely confined to the prefectures bordering Myanmar. Furthermore, C/CRF07_BC/CRF08_BC viruses were found to consist of a group of viruses, including C, CRF08_BC, CRF07_BC, and new BC recombinants, based on the characterization of their reverse transcriptase genes.

Conclusions: This is the first report of a province-wide HIV-1 molecular epidemiological study in Yunnan. While C/CRF07_BC/CRF08_BC and CRF01_AE are codominant, the discovery of many sexually transmitted CRF01_AE cases is new and suggests that this subtype may lead to a new epidemic in the general Chinese population. We discuss implications of our results for understanding the evolution of the HIV-1 pandemic and for vaccine development.

Figure 1. Map of the Yunnan Province of the People's Republic of China and Distribution of Reported Cases of HIV-1 Infection in 2004

The color-coded symbols represent the geographic origins of HIV-1 strains as depicted in Figures 2, 3, and 6.

Figure 2. Phylogenetic Neighbor-Joining Tree for HIV-1 p17 Sequences Obtained from All 16 Prefectures of Yunnan

Individual sequences are color coded, with the colors corresponding to those of original geographic sites on the map of Yunnan (Figure 1). The horizontal branch was drawn in accordance with their relative genetic distances. The vertical lines are present purely for clarity of the tree presentation. The bootstrap values of 1,000 replicates are labeled on the major branches. The reference sequences for classifying HIV-1 genotypes were included and were originally obtained from the NIH/NIAID–funded HIV Databases.

Figure 3. Continuation of the Phylogenetic Neighbor-Joining Tree Shown in Figure 2

Two clusters represent the two major circulating HIV-1 subtypes in Yunnan: CRF01_AE (A) and C/CRF07_BC/CRF08_BC (B).

Figure 4. The Distinct Distribution of Two Major HIV-1 Subtypes among Different Risk Groups in Yunnan

The risk factors include sexual contact (Sex), injection drug use (IDU), vertical transmission (VT), and blood transfusion (BT). The p-values are based on analysis using the chi-square test of association or Fisher's exact probability test.

Figure 5. Two Major HIV-1 Subtypes among Different Age and Gender Groups in Yunnan

The upper panel represents subtype CRF01_AE (A), whereas the lower panel is for C/CRF07_BC/CRF08_BC (B). The y-axis indicates the percentage of HIV-1 infection in each age and gender group. There were significantly more females at age 18–25 infected by C/CRF07_BC/CRF08_BC than by CRF01_AE viruses (p < 0.05).

Figure 6. Phylogenetic Neighbor-Joining Tree for HIV-1 RT Fragment Sequences Obtained from 43 Individuals

Individual sequences are color coded, with the colors corresponding to those of original geographic sites on the map of Yunnan (Figure 1). The horizontal branch was drawn in accordance with their relative genetic distances. The vertical lines are present purely for clarity of the tree presentation. The bootstrap values based on 1,000 replicates are labeled on the major branches. The reference sequences for classifying HIV-1 genotypes were included and were originally obtained from the NIH/NIAID–funded HIV Databases.

Figure 7. Bootscanning Analysis of HIV-1 RT Sequences of Six Study Participants

Participants included one CRF01_AE virus 03YN.DH.rlE32 (A), two pure subtype C viruses 03YN.DH.mdC9 (B) and 03YN.DH.lxG9 (C), one new BC recombinant virus 03YN.DH.rlG29 (D and G), one CRF08_BC virus 03YN.HH.gjN165 (E and H), and one CRF07_BC virus 03YN.HH.gjN156 (F and I). The reference sequences obtained from the NIH/NIAID–funded HIV Databases are color-coded and shown on the top. The conditions used for this analysis are shown at the bottom. The boostrap values are based on 100 replicates using the neighbor-joining method.