Identification Of A Novel HIV-1 CRF01_AE/07_BC Recombinant And Full-length Genome Characterization Of An HIV-1 CRF01_AE Strain In Jiangsu Province

Objective:Human immunodeficiency virus(HIV) is the pathogen of acquired immune deficiency syndrome(AIDS).Recently,many countries and regions are facing an increased comlexity of HIV-1 genetic heterogeneity.In China,the main prevailing subtypes,B,CRFs_BC(including CRF07_BC,CRF08_BC,and some URFs_BC) and CRF01_AE,account for about 94.9%of the infections.These subtypes appear to be predominant among distinct high-risk populations.All these subtypes/CRFs predominant in China could be detected in most of high-risk populations,which provides the opportunity for recombination between different subtypes/CRFs.Recently, we found that almost equal proportions(＞28.6%) of subtype B,CRF01_AE and CRFs_BC were circulating among men who have sex with men(MSM) in Jiangsu Province,strongly suggesting there is a very high likelihood of generating new intersubtypes/CRF recombinants.Here we aim to search for the probable new recombinant among high-risk populatons in Jiangsu Province and investigate its origin.Methods:HIV-1 gag-RT,p17 and C2V3 regions or near full-length genomic sequences are obtained by using nested polymerase chain reactions(PCRs).We use several methods such as bootscan analyses and phylogenetic analyses to study the sequences.Results:Fourteen gag-RT regions are sequenced from injection drug users(IDUs) in an epidemiologically linked cohort in Jiangsu,China.The analysis of gag-RT regions shows that one(07JSNJ001) is a novel CRF01_AE/07_BC recombination virus and the others belong to CRF07_BC.The analysis of the near full-length genomic sequence of 07JSNJ001(GenBank accession number FJ238521) shows that 07JSNJ001 is composed of at least 10 interlaced CRF07_BC and CRF01_AE segments,quite distinct from any previously identified circulating recombinant form(CRF) and unique recombinant form(URF) around the world.In addition,a male AIDS patient (JSWX045) who is an IDU infected with CRF01_AE is found in Wuxi City of Jiangsu Province through phylogenetic analyses of p17 and C2V3 sequences.We analyzed 07JSWX045 near full-length genomic sequence(GenBank accession number FJ441290).There are some interesting findings.(1).07JSWX045 is not genetically associated with the CRF01_AE part of the new CRF01_AE/07_BC recombinant identified in Jiangsu.(2).07JSWX045 is phylogenetically close to CRF01_AE strains circulating among Jiangsu MSM.(3).Both 07JSWX045 and the CRF01_AE parent of CRF01/07 recombinant phylogenetically cluster with two different CRF01 AE subgroups circulating in Fujian,respectively.(4).Patient JSWX045 did not receive any antiviral therapy.Two AZT resistance mutations in the RT gene are detected through antiviral drug resistance analysis(ADRA).This provides valuable bioinformatics sites for investigating the epidemic origin and molecular properties of Jiangsu CRF01 AE strains.(5).Patient JSWX045 has two high-risk behaviors including injection drug use and heterosexual contact.He might have been initially infected with CRF01_AE via heterosexual contact,and then introduced this subtype to other people via injection drug use.Conclusion:A novel HIV-1 CRF01_AE/07_BC recombinant is identified for the first time.One IDU infected with CRF01_AE is found when we investigate the origin of CRF01/07.07JSWX045 is not the parental virus of CRF01/07.07JSWX045 is phylogenetically close to CRF01_AE strains circulating among Jiangsu MSM.Both 07JSWX045 and the CRF01_AE parent of CRF01/07 recombinant phylogenetically cluster with two different CRF01_AE subgroups circulating in Fujian,respectively. These results suggest that there is a very high likelihood of generating new intersubtypes/CRF recombinants in Jiangsu Province and at least two genetically independent CRF01 AE descendants are circulating in Jiangsu possibly via two independent introductions from Fujian.It is necessary to strengthen the study of HIV-1 molecular epidemiology in Jiangsu Province.