Spatial And Temporal Transmission Characteristics Of Two HIV Strains CRF07＿BC And CRF55＿01B In China

BackgroundThe transmission routes of HIV has changed dramatically in China over the past ten years.In the early 1990s.At present,the transmission of HIV through blood transfusion,injecting drug users and mother-to-child transmission has been effectively controlled,and sexual transmission has become the main transmission route of HIV.The increasing prevalence of HIV through sexual transmission reflects the changes in China’s social and sexual concepts.At the same time,the rapid development of transportation in China,the increase in the flow of people,the rapid development of Internet and other technologies,and the emergence of a large number of dating software have accelerated and expanded the Inter-provincial transmission of HIV.Therefore,this study intends to analyze HIV gene sequences by molecular biological methods(mainly molecular network and Bayesian methods)to study the correlation of HIV/AIDS in China and the characteristics of its transmission among provinces,and to analyze the relevant influencing factors,so as to provide scientific data for the precise prevention and control of HIV/AIDS transmission in China.Due to its high degree of variability,HIV has reported at least 18 subtypes and 110 Circulating Recombinant forms(CRFs).The results of 5151 HIV genotypes sampled from 31 provinces and cities in 2018 showed that CRF07＿BC subtype had become the most prevalent strain in China(39.7%),and the others were CRF01＿AE(36.9%),CRF08＿BC(9.0%)and subtype B(4.3%).Since the discovery of CRF55＿01B reported in 2013,CRF55＿01B now ranks the fifth in terms of its constituent ratio(the national molecular epidemiological survey in 2015 showed that the constituent ratio of CRF55＿01B was 2.3%,and the national pre-treatment drug resistance results in 2018 showed that the constituent ratio of CRF55＿01B was 3.9%).In the course of transmission,CRF07 BC was divided into two epidemic clusters:CRF07＿BC-MSM(mainly spread in MSMs)and CRF07＿BC-Others(mainly spread in HET and IDU).Early reports of CRF55＿01B were mainly among MSMs.In this study,the Bayesian phylogeography method was used to analyze the spatio-temporal transmission characteristics of CRF07 BC and CRF55＿01B strains,which were found in China and showed a rapid spreading trend,in order to provide relevant data support for understanding the impact of HIV transmission on the AIDS epidemic in China from the molecular surveillance level.Object1.To analyze inter-provincial transmission characteristics of CRF07 BC and CRF55＿01B,two HIV strains in the molecular network,and to provide the basic framework of molecular network for each province to study the inter-provincial transmission of locally reported infected people.2.By delineating the propagation routes of CRF07 BC and CRF55＿01B,two HIV strains in China,it provides data support for the formulation of relevant measures to prevent their rapid spread.MethodsThe first partAll sequences of Chinese HIV pol gene region(HXB2:2253-3312nt,1060bp)were collected from the HIV sequence database of the Los Alamos National Laboratories(LANL)and the National Center for AIDS/STD Control and Prevention of China(NCAIDS),Including the sequences obtained by experiments.Sequences inclusion criteria:sequences length ≥1000bp,mixed base<5%,with information of province and sampling year.Repeated sequences were removed,and epidemiological information such as sex,age,transmission route(risk),sampling year and province were collated.The phylogenetic method(FastTree,etc.)was used to construct the phylogenetic tree for subtypes and subclusters identification.HIV-TRACE(localized HIV-TRACE,built CentOS 7 platform,wrote program offline,improved the original command,made the operation more convenient)was used to determine the optimal genetic distance threshold,and construct the molecular network.The characteristics of the main subtypes and subclusters in the molecular network were analyzed,and parameters such as Clusters proportion,network density and inter-provincial transmission rate were compared.Combined with parameters such as both inter-provincial and intra-provincial transmission rates,and inter-provincial connection ratio,the inter-provincial hot spots were analyzed(both inter-provincial and intra-provincial transmission rates were higher than the national average).The second partBased on the analysis of the main HIV subtypes CRF07 BC and CRF55＿01B which are transmitted between provinces in China in the first part,the Bayesian phylogeographic method is further applied.Using a Bayesian Skygrid demographic model and Markov Jumps algorithm,the propagation routes of CRF07＿BC subtype,CRF07 BC-MSM subcluster,CRF07＿BC-Others subcluster and CRF55＿01B subtype in China were analyzed.This method can not only reconstruct the epidemic history,but also dynamically display the propagation trajectory of the virus.In addition,Bayes factor(BF),posterior probability and mean counts were used to evaluate the transmission intensity.Wilcoxon rank sum test and single factor analysis were used to analyze the possible correlative factors of CRF07 BC-MSM cluster and CRF55＿01B subtype spreading in China.ResultsThe first partIn this study,a total of 49685 sequences of HIV/AIDS pol gene region in China from 1991 to 2019 were included and analyzed,among which the male(48.4%),18-29 years old(21.3%)and sexual transmission route(52.3%)accounted for the highest proportion.The main subtypes were CRFO1＿AE(37.9%)and CRF07 BC(33.5%),followed by subtype B(13.7%),CRF08＿BC(5.6%)and CRF55＿01B(2.5%).The results of subcluster were CRFOI AE-Cluster 1(6.7%),CRFO1＿AE-Cluster 2(2.1%),CRF01＿AE-Cluster 4(18.8%)and CRF01＿AE-Cluster 5(6.8%),CRF07＿BC-MSM(17.7%)and CRF07＿BC-Others(15.7%).By identifying the optimum value of the number of molecular clusters and nodes,the optimal genetic distance threshold for the construction of molecular network was determined to be 0.50%.The constructed molecular network is also the basic molecular network framework of HIV epidemic strains of all subtypes in China.The clusters proportion of the above sequences was 40.2%(19976/49685).The clusters proportion of different subtypes and subclusters showed that CRF55＿01B had the highest(60.5%),followed by CRF07＿BC-MSM(59.1%).The clusters proportion of CRF55＿01B and CRF07＿BC-MSM were significantly higher than those of the other seven subtypes(CRFOI AE-Cluster 1,CRFOI AE-Cluster 2,CRF01＿AE-Cluster 4,CRF01＿AE-Cluster 5,CRF07＿BC-Others,CRF08＿BC and subtype B),P<0.05.In addition,the analysis of the influencing factors of the clusters proportion of subtypes and subclusters showed that the ORs of CRF55 01B and CRF07 BC-MSM were higher than those of the other seven subtypes and subclusters.The analysis of the influencing factors of subtypes and subclusters with node edges showed that the ORs of CRF55＿01B and CRF07＿BC-MSM were higher than those of the other seven subtypes and subclusters(P<0.001).The calculation of network density(the ratio of the number of edges in the molecular network to the upper limit of the number of edges,which can be used to describe the density of inter-connections between nodes)of different subtypes and subclusters shows that CRF55＿01B has the highest network density(0.01568),followed by CRF07＿BC-MSM(0.00619).The results showed that the inter-provincial transmission rate of CRF07＿BC-MSM was the highest(44.7%),followed by CRF55＿01B(43.1%),which was significantly higher than that of the other seven subtypes and subclusters(P<0.05).Through molecular network analysis,nine hot spots of CRF07 BC-MSM inter-provincial transmission were found,which were mainly Shenzhen,Shanghai,Chongqing,Beijing,Guizhou,Yunnan,Guangdong(except Shenzhen),Shaanxi and Sichuan.CRF55＿01B has three hot spots of inter-provincial transmission,mainly Shenzhen,Guangdong and Hunan.The second partSection 1:16635 CRF07 BC subtype gene sequences were screened from the total database,7819 of which were classified as CRF07＿BC-Others and 8816 as CRF07 BC-MSM.The tMRCA(the time of most recent common ancestor)of CRF07＿BC in Yunnan in 1995.9(95%confidence interval:1994.5-1997.6),posterior probability=1.In 1997.7(95%confidence interval:1997.0-1997.7),CRF07＿BC-Others(mainly IDU and HET)subcluster was formed along the drug route and spread to Xinjiang,Sichuan,Guizhou and other western provinces,showing an explosive spread in Xinjiang,and then spread to the heterosexuals.Then,the strain spread to MSMs in Sichuan(mainly Chengdu city),showing an explosion of transmission in Chengdu,Sichuan province in 2003.7(95%confidence interval:2002.4-2004.8),and then spread to Chongqing,Guangdong,Shaanxi and other provinces,forming a CRF07 BC-MSM subcluster(mainly MSMs).The CRF07＿BC-MSM subcluster was spread from Sichuan to 16 major provinces,including Guangdong,Chongqing,Henan,Guizhou,Hunan,Beijing,Jiangsu,Zhejiang,Shaanxi,Shanghai,Shenzhen,Shandong,Yunnan,Hubei,Xinjiang and Liaoning(BF≥100,posterior probability≥0.8).The CRF07 BC-MSM subcluster was widely spread in 25 provinces nationwide,including Sichuan,Guangdong,Chongqing,Henan,Guizhou,Hunan,Beijing,Jiangsu,Zhejiang,Shaanxi,Shanghai,Shenzhen,Shandong,Yunnan,Hubei,Xinjiang,Liaoning,Gansu,Shanxi,Heilongjiang,Anhui,Guangxi,Qinghai,Ningxia,Inner Mongolia(BF≥100,posterior probability≥0.8).The difference between CRF07＿BC-MSM subcluster belonging to the molecular cluster and those not belonging to the molecular cluster showed that the infected people carrying CRF07 BC-MSM were more likely to gather in five regions(Beijing-Tianjin-Hebei Urban Agglomeration,Yangtze River Delta,Pearl River Delta,Chengdu-Chongqing City Group and the Central of China),OR=1.46(1.32-1.61),P<0.0001.The mean counts(obtained by Bayesian calculation)of CRF07 BC-MSM import provinces were compared between located in five regions and non-five regions,the results demonstrated that the provinces with more CRF07 BC-MSM inputs were also mainly distributed in the five regions(P=0.03 76).Section 2:A total of 1237 gene sequences of CRF55＿01B subtype were screened from the database.The results showed that CRF55＿01B was mainly transmitted in MSMs,but gradually spread to HET(P<0.001).The tMRCA of CRF55＿01B in Shenzhen,Guangdong Province in 2003.0(95%confidence interval:2001.2-2004.6),posterior probability=1.Before 2007,it was only spread in Guangdong province.After 2010,CRF55＿01B spread rapidly to the whole country.The CRF55＿01B was spread from Guangdong and Shenzhen to 11 provinces,which were Hunan,Beijing,Guangxi,Jiangxi,Henan,Guizhou,Hebei,Anhui,Shandong,Hubei and Yunnan(BF≥50,posterior probability≥0.8).The CRF55 01B was widely spread in 14 provinces nationwide,including Guangdong,Shenzhen,Hunan,Beijing,Guangxi,Hubei,Jiangxi,Guizhou,Hebei,Anhui,Shanghai,Shandong,Henan,and Yunnan(BF≥50,posterior probability≥0.8).The difference between CRF55＿01B belonging to the molecular cluster and those not belonging to the molecular cluster showed that the infected people carrying CRF55＿01B were more likely to gather in the provinces along the Beijing-Guangzhou and Beijing-Kowloon Railways,OR=2.06(1.55-2.73),P<0.0001.The mean counts(obtained by Bayesian calculation)of CRF55＿01B import provinces were compared between located on the Beijing-Guangzhou and Beijing-Kowloon railways and located on others,the results demonstrated that the provinces with more CRF55＿01B inputs were also mainly located along the Beijing-Guangzhou and Beijing-Kowloon railways(P<0.0001).Conclusion1.In this study,the molecular network framework of each subtype and subcluster of HIV/AIDS in China was constructed by sorting out the sequences library of a large sample covering the whole country.Compared with other subtypes and subclusters,CRF07＿BC-MSM subcluster and CRF55＿01B subtype in China are the main HIV strains transmitted between provinces in China,with high clusters proportion and inter-provincial transmission rate and high transmission density.2.There were two subclusters of CRF07 BC.The CRF07＿BC-Others subcluster first exploded in Xinjiang in 1997,and the CRF07＿BC-MSM subcluster first exploded in Chengdu,Sichuan in 2003.In addition,the infected people carrying CRF07 BC-MSM were more likely to gather in Beijing-Tianjin-Hebei Urban Agglomeration,Yangtze River Delta,Pearl River Delta,Chengdu-Chongqing City Group and the Central of China.3.CRF55＿01B subtype originated from MSM in Shenzhen,Guangdong Province around 2003.After 2010,CRF55＿01B spread rapidly throughout the country,and the infected people carrying CRF55＿01B were more likely to gather in the provinces along the Beijing-Guangzhou and Beijing-Kowloon Railways.4.The prevalence of CRF07 BC and CRF55＿01B in China is closely related to the high-speed flow of people caused by the rapid development of transportation,which suggests that the prevention and control of infectious diseases should be strengthened while developing the economy and transportation.