title: Evolutionary Dynamics and Complicated Genetic Transmission Network Patterns of HIV-1 CRF01_AE among MSM in Shanghai, China.
abstract: To explore the evolutionary dynamics and molecular transmission patterns of HIV-1 CRF01_AE in depth among men who have sex with men (MSM) in Shanghai, we constructed phylogenetic tree and genetic transmission networks based on 1, 152 pol sequences from MSM, 282 from other risk groups and 795 references. Phylogenetic analyses identified two distinct major CRF01_AE lineages and a Shanghai-based sub-lineage. The estimated tMRCAs for lineage 1 and 2 were 1996.0 (1992.9-1999.2) and 1997.8 (1994.3-2001.4), respectively. Of the 1, 152 MSM, 681 (59.1%) were identified as belonging to 241 separate networks. Of these 681 individuals in networks, 74.2% were linked to cases diagnosed in different years, 4.3% were linked to heterosexual women, and 0.7% were linked to persons who inject drugs. A total of 71 networks including 180 individuals diagnosed in Shanghai with the same domicile were found. Recent infection (P = 0.022) and sampling year after 2011 (P < 0.001) were significantly associated with potential transmission links among the networks. Besides, a significant transmission of viruses with drug resistant mutations at V179D/E were found in the networks. Given these findings, we propose that genetic transmission analysis is a useful tool in HIV intervention strategies to curb the spread of virus and promoting public health.
authors.affiliation: Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention; Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China.|School of Public Health, Southeast University, Nanjing, China.
authors.forename: Xiaoshan
authors.initials: X
authors.lastname: Li
authors.affiliation: Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention; Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China.
authors.forename: Yile
authors.initials: Y
authors.lastname: Xue
authors.affiliation: Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention; Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Lin
authors.affiliation: Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention; Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Gai
authors.affiliation: Research Center for Public Health, School of Medicine, Tsinghua University, Beijing, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention; Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China.
authors.forename: Hua
authors.initials: H
authors.lastname: Cheng
authors.affiliation: Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention; Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Ning
authors.affiliation: Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention; Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China.
authors.forename: Leiming
authors.initials: L
authors.lastname: Zhou
authors.affiliation: School of Public Health, Nantong University, Nantong, China.
authors.forename: Kexin
authors.initials: K
authors.lastname: Zhu
authors.affiliation: Biomedical Sciences Department, Institute of Tropical Medicine of Antwerp, Belgium.
authors.forename: Guido
authors.initials: G
authors.lastname: Vanham
authors.affiliation: Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention; Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China.
authors.forename: Laiyi
authors.initials: L
authors.lastname: Kang
authors.affiliation: Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention; Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention; Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China.
authors.forename: Minghua
authors.initials: M
authors.lastname: Zhuang
authors.affiliation: Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention; Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China.
authors.forename: Qichao
authors.initials: Q
authors.lastname: Pan
authors.affiliation: Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention; Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China.
authors.forename: Ping
authors.initials: P
authors.lastname: Zhong
mesh_terms: D000328:Adult; D019380:Anti-HIV Agents / Q000627:therapeutic use; D002681:China / Q000453:epidemiology; D024882:Drug Resistance, Viral / Q000235:genetics; D019143:Evolution, Molecular; D005260:Female; D005838:Genotype; D015658:HIV Infections / Q000188:drug therapy / Q000453:epidemiology / Q000635:transmission* / Q000821:virology; D015497:HIV-1 / Q000145:classification / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D018451:Homosexuality, Male / Q000523:psychology; D006801:Humans; D008297:Male; D009154:Mutation; D010802:Phylogeny; D012309:Risk-Taking; D060756:Social Networking; D015819:Substance Abuse, Intravenous / Q000453:epidemiology / Q000523:psychology / Q000821:virology*; D013997:Time Factors
chemical_list: D019380:Anti-HIV Agents