Molecular epidemiological surveillance of Sichuan in 2019
Of the 1291 available sequences in the molecular epidemiological surveillance of Sichuan in 2019, CRF07_BC (676/1291, 52.36%), CRF01_AE (341/1291, 26.41%), CRF08_BC (114/1291, 8.83%), CRF85_BC (68/1291, 5.27%) were the four most epidemic strains (Fig 1A). CRF85_BC was dominating the HIV-1 epidemics in Yibin (58/146), a southeast city in Sichuan province, and also detected in Luzhou (4/174), Leshan (3/120), Chengdu (2/312) and Mianyang (1/70) (Fig 1B). Compare to the data of Sichuan molecular epidemiological surveillance in 2014[22], the proportion of CRF85_BC in Sichuan had increased from 3.66% (14/383) to 5.27%, and it became more widely distributed. To further understand whether CRF85_BC has been involved in ongoing transmission, we looked at sequence diversity by estimating pairwise distances between sequences in 2014(n=14) and sequences in 2019(n=68). We detected a much more diversity in 2019 (mean distance 0.023, SD 0.002) compare to 2014 (mean distance 0.010, SD 0.001), supporting an ongoing evolution of CRF85_BC overtime.
A heterosexual transmission of CRF85_BC in Sichuan provinces.
The epidemiological and clinical features of the patients harboring CRF85_BC did not change significantly between 2014 and 2019 (Table 1). CRF85_BC were only found in heterosexually infected individuals, including commercial sexual transmission (67.6% in 2019 and 42.9% in 2014), Non-marital and non-commercial sexual transmission (27.9% in 2019 and 21.4% in 2014) and spousal transmission (2.9% in 2019 and 35.7% in 2014). Both in 2019 (95.6%) and 2014(78.6%), majority of CRF85_BC were circulating among the persons living with HIV aged 50 years and over (PLHIV50+), significantly higher than other HIV CRFs (P = 0.000, χ2 test). Patients with low education levels took a relatively larger proportion.
Estmated timeline and migration pathway of CRF85_BC
To elucidate the sources and dissemination routes of endemic CRF85_BC geographically, we constructed MCC tree based on 135 Sichuan sequences and 13 most closely related sequences from the Los Alamos HIV Database sequences using Bayesian geographical evolution method. The corresponding median coefficient of rate variation was 0.33(95% highest posterior density (HPD): 0.18-0.49), supporting the selection of a relaxed molecular clock model. Both Bayesian skyline plot and Bayesian skygrid analysis showed that HIV-1 CRF85_BC experienced two fast growth phases during 2011– 2014 and 2017-2019 (Figure 2) with a mean growth rate of 2.5*10-3 per year [95% HPD: 2.1*10-3 - 3.0*10-3]. The tMRCA was inferred to be 2006.6 (95% HPD: 2004.0–2009.1), implying the origin time of the CRF85_BC (table2).
The maximum clade credibility tree showed that CRF85_BC from Yunnan are located at the root of the tree (posterior probability (PP = 1). Sequentially, viral spread form Yunnan to Sichuan (PP = 0.9045), Guangxi (PP = 1), and other regions. The first place where the viral was introduced into Sichuan probably was Yibin in 2008.5 (2007.0-2010.5). Then an explosive epidemic was found in the heterosexual elderly people in this city. Several small clusters further suggested that the virus became epidemic in many cities of Sichuan Province (Luzhou, Guangyuan, et al.) and had rapidly spread to other provinces (such Liaoning, Anhui and Chongqing) (Figure 2B).
Notably, most Sichuan sequences originated form Yibin, except for four sequences. A Guangyuan and Mianyang sequence directly formed a sub cluster with a sequence from Yunnan (PP = 0.9923) while a Luzhou strain grouped significantly (PP = 1) with the sequences from Guangxi (Figure 2B).