HIV-1 CRF07_BC transmission dynamics in China: two decades of national molecular surveillance

Figures & data

Table 1. Characteristics of study participants.

Attribute	Category	Total	07BC_N	07BC_O
	Total	6213	3597	2616
In/outside the network	In the network	3607	2607	1000
	Outside the network	2606	990	1616
Sampling year	1997–2008	535	90	445
	2009–2010	825	333	492
	2011–2012	977	619	358
	2013–2014	772	620	152
	2015–2017	3104	1935	1169
Risk groups	Heterosexual	2272	833	1439
	PWID	995	24	971
	MSM	2946	2740	206
Gender	Female	964	142	822
	Male	5101	3442	1659
	Unknown	148	13	135
Domicile	Central	386	300	86
	East	999	767	232
	North	1410	1138	272
	Northeast	126	105	21
	Northwest	662	137	525
	South	928	717	211
	Southwest	1702	433	1269
Age at diagnosis	≤20	407	260	147
	21–30	2359	1417	942
	31–40	937	435	502
	41–50	436	236	200
	51–60	225	101	124
	>60	199	52	147
	Unknown	1650	1096	554
Marital status	Married	1261	331	930
	Unmarried	1654	1153	501
	Divorced or widowed	322	133	189
	Unknown	2976	1980	996

Abrreviations: MSM, men who have sex with men; PWID, persons who use injection drugs.

Figure 1. (Left) Maximum-likelihood phylogenetic trees of HIV-1 pol sequences from 6213 individuals (A). Red and blue lines represent study individuals of 07BC_N and 07BC_O respectively. (Middle) Distribution of individuals in two clusters among different populations. The proportion of individuals in 07BC_N among different transmission risk populations (B1), marital status populations (C1), and residential populations (D1). The proportion of individuals in 07BC_O among different transmission risk populations (B2), marital status populations (C2), residential populations (D2). (Right) Cumulative CRF07_BC transmission network from 1997 to 2008 (E1, E2), 2010 (F1, F2), 2014 (G1, G2) and 2017 (H1, H2). One node represents a sequence or an individual. An edge (link) represents the genetic distance (TN93) between connected sequences ≤ 0·007 substitutions/site. Only nodes connected with others within the network are shown. Edge lengths are optimized for visual presentation and do not represent genetic distance. The colour indicates transmission route. Square indicates 07BC_N on the left side of the image (E1, F1, G1, H1) and the circle indicates 07BC_O on the right (E2, F2, G2, H2). MSM: men who have sex with men; PWID, individuals who use injection drugs.

Figure 2. The number of individuals, links, links/individuals and the largest cluster in cumulative transmission networks (CTNs). The number of individuals (A), links (B), links/individuals (C) and the largest cluster (D) in CTNs marks on the y-axis and the sampling year is shown on the x-axis. Blue denotes 07BC_O and orange represents 07BC_N.

Figure 3. Trends of transmission risk parameter (TR) between two clusters. Each network was divided into three population groups according to quartiles degree. Low-level (two quartiles of the population): individuals linked to 0 other individuals. Medium-level (one quartile of the population): individuals linked to 1–5 other individuals. High-level (one quartile of the population): individuals linked to ≥6 other individuals. The sum of the degree of nodes for each cluster was calculated as the parameter of population transmission risk for medium-level and high-level, and the number of individuals as parameter of population transmission risk for low-level. The percentage of TR within two clusters marks on the y-axis and the sampling year is shown on x-axis. Colours correspond to clusters.

Figure 4. Power-law plot fitted from degree distribution between 07BC_N and 07BC_O in CRF07_BC networks. The graphs show the fitted distribution of degree among 07BC_N (blue) and 07BC_O (orange) in each CRF07_BC network. The fitted power-law function of the form y = cx^-r is shown. Besides, the intersection coordinates of two functions from 07BC_N (orange) and 07BC_O (blue) are shown.

Figure 5. Bayesian skyline plot was estimated to reconstruct the demographic history of the two CRF07_BC clusters in China. The x-axis is the time in units of years and the y-axis is equal to the effective population size. The solid line and shaded region represent the median and 95% credibility interval of the effective population size through time. The demographic histories of the 07BC_O (blue) and 07BC_N (red) epidemics, as estimated by the Bayesian skygrid model, are based on subsets of 645 and 993 pol sequences respectively. While it appears that the epidemic among 07BC_O sequences reached its peak in the mid-2000s and is slowing down, all evidence points toward the 07BC_N epidemic still growing.

Figure 6. Transmission category of potential transmission partners. This figure shows, for individuals in the transmission network of a given transmission category for 07BC_O (A) and 07BC_N (B), the transmission category of their potential transmission partners. MSM: men who have sex with men; PWID: persons who inject drugs.