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Current HIV Research

Author(s): Yin Yueqi, Zhou Ying, Lu Jing, Guo Hongxiong, Chen Jianshuang, Xuan Yan, Cheng Hao, Yuan Defu, Hu Haiyang, Xu Xiaoqin, Wang Bei* and Fu Gengfeng*

DOI: 10.2174/1570162X18666201026143200

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The Identification of A Novel HIV-1 Second-Generation Recombinant form (CRF01_AE/CRF07_BC) Among Men Who Have Sex with Men in Jiangsu, China

Page: [188 - 194] Pages: 7

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Abstract

Background: CRF01_AE and CRF07_BC are the two major HIV-1 virus strains circulating in China. The proportion of dominant subtypes (CRF01_AE and CRF07_BC) among MSM in Jiangsu province was over 80%. A large number of URFs have been found in China in recent years.

Objective: This study aimed to report on novel HIV-1 recombinants.

Methods: We constructed Phylogenetic trees using the maximum likelihood (ML) method with 1000 bootstrap replicates in IQ-TREE 1.6.8 software and determined recombination breakpoints using SimPlot 3.5.1.

Results: We identified a novel, second-generation HIV-1 recombinant (JS020202) between CRF01_ AE and CRF07_BC. The analysis of near full-length genome (NFLG) showed there were at least 8 breakpoints in the virus, which differed from any previously identified CRF and URF around the world.

Conclusion: Novel diverse CRF01_AE/07_BC suggested the complexity trends of HIV-1 genetics. The emergency situation of diverse recombinant strains should be monitored continuously.

Keywords: HIV-1, recombinant, MSM, near full-length genome, URF, CRF.

Graphical Abstract

[1]
Zhuang J, Jetzt AE, Sun G, et al. Human immunodeficiency virus type 1 recombination: rate, fidelity, and putative hot spots. J Virol 2002; 76(22): 11273-82.
[http://dx.doi.org/10.1128/JVI.76.22.11273-11282.2002] [PMID: 12388687]
[2]
Jetzt AE, Yu H, Klarmann GJ, Ron Y, Preston BD, Dougherty JP. High rate of recombination throughout the human immunodeficiency virus type 1 genome. J Virol 2000; 74(3): 1234-40.
[http://dx.doi.org/10.1128/JVI.74.3.1234-1240.2000] [PMID: 10627533]
[3]
Yu H, Jetzt AE, Ron Y, Preston BD, Dougherty JP. The nature of human immunodeficiency virus type 1 strand transfers. J Biol Chem 1998; 273(43): 28384-91.
[http://dx.doi.org/10.1074/jbc.273.43.28384] [PMID: 9774465]
[4]
Onafuwa-Nuga A, Telesnitsky A. The remarkable frequency of human immunodeficiency virus type 1 genetic recombination. Microbiol Mol Biol Rev 2009; 73(3): 451-80.
[http://dx.doi.org/10.1128/MMBR.00012-09] [PMID: 19721086]
[5]
Delviks-Frankenberry K, Galli A, Nikolaitchik O, Mens H, Pathak VK, Hu WS. Mechanisms and factors that influence high frequency retroviral recombination. Viruses 2011; 3(9): 1650-80.
[http://dx.doi.org/10.3390/v3091650] [PMID: 21994801]
[6]
Hemelaar J. Implications of HIV diversity for the HIV-1 pandemic. J Infect 2013; 66(5): 391-400.
[http://dx.doi.org/10.1016/j.jinf.2012.10.026] [PMID: 23103289]
[7]
Tongo M, Dorfman JR, Martin DP. High degree of HIV-1 group m (HIV-1M) genetic diversity within circulating recombinant forms: insight into the early events of HIV-1M evolution. J Virol 2015; 90(5): 2221-9.
[http://dx.doi.org/10.1128/JVI.02302-15] [PMID: 26656688]
[8]
Hemelaar J. The origin and diversity of the HIV-1 pandemic. Trends Mol Med 2012; 18(3): 182-92.
[http://dx.doi.org/10.1016/j.molmed.2011.12.001] [PMID: 22240486]
[9]
Thomson MM, Nájera R. Molecular epidemiology of HIV-1 variants in the global AIDS pandemic: an update. AIDS Rev 2005; 7(4): 210-24.
[PMID: 16425961]
[10]
Faria NR, Rambaut A, Suchard MA, et al. HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations. Science 2014; 346(6205): 56-61.
[http://dx.doi.org/10.1126/science.1256739] [PMID: 25278604]
[11]
Chen M, Zhu Q, Xing H, et al. The characteristics of pretreatment HIV-1 drug resistance in western Yunnan, China. Epidemiol Infect 2020; 148: e102.
[http://dx.doi.org/10.1017/S095026882000093X] [PMID: 32381145]
[12]
Chen M, Ma Y, Chen H, et al. Spatial clusters of HIV-1 genotypes in a recently infected population in Yunnan, China. BMC Infect Dis 2019; 19(1): 669.
[http://dx.doi.org/10.1186/s12879-019-4276-9] [PMID: 31357947]
[13]
Sun L, Jia L, Liu Y, et al. Multiple HIV-1 subtypes were found circulating in shijingshan district of beijing, china. AIDS Res Hum Retroviruses 2019; 35(5): 494-9.
[http://dx.doi.org/10.1089/aid.2018.0263] [PMID: 30681000]
[14]
Deng X, Liu J, Li J, et al. Prevalence of HIV-1 drug-resistance genotypes among unique recombinant forms from yunnan province, china in 2016-2017. AIDS Res Hum Retroviruses 2020; 36(5): 389-98.
[http://dx.doi.org/10.1089/aid.2019.0041] [PMID: 31914782]
[15]
NCAIDS. NCSTD; CDC C. Update the AIDS/STD epidemic in China the third quarter of 2018. Chinese Journal of AIDS and STD 2018; 24(11): 11075.
[16]
Xiao P, Zhou Y, Lu J, et al. HIV-1 genotype diversity and distribution characteristics among heterosexually transmitted population in Jiangsu province, China. Virol J 2019; 16(1): 51.
[http://dx.doi.org/10.1186/s12985-019-1162-4] [PMID: 31023323]
[17]
Yuan R, Cheng H, Chen LS, Zhang X, Wang B. Prevalence of different HIV-1 subtypes in sexual transmission in China: a systematic review and meta-analysis. Epidemiol Infect 2016; 144(10): 2144-53.
[http://dx.doi.org/10.1017/S0950268816000212] [PMID: 26892485]
[18]
Zhang L, Wang YJ, Wang BX, Yan JW, Wan YN, Wang J. Prevalence of HIV-1 subtypes among men who have sex with men in China: a systematic review. Int J STD AIDS 2015; 26(5): 291-305.
[http://dx.doi.org/10.1177/0956462414543841] [PMID: 25033880]
[19]
Yin Y, Liu Y, Zhu J, et al. The prevalence, temporal trends, and geographical distribution of HIV-1 subtypes among men who have sex with men in China: A systematic review and meta-analysis. Epidemiol Infect 2019; 147: e83.
[http://dx.doi.org/10.1017/S0950268818003400] [PMID: 30869019]
[20]
Su Q, Liang H, Cen P, Bi Z, Zhou P. HIV type 1 subtypes based on the pol gene and drug resistance mutations among antiretroviral-naive patients from Guangxi, Southern China. AIDS Res Hum Retroviruses 2012; 28(7): 725-8.
[http://dx.doi.org/10.1089/aid.2011.0246] [PMID: 21916807]
[21]
Chen M, Ma Y, Duan S, et al. Genetic diversity and drug resistance among newly diagnosed and antiretroviral treatment-naive HIV-infected individuals in western Yunnan: a hot area of viral recombination in China. BMC Infect Dis 2012; 12: 382.
[http://dx.doi.org/10.1186/1471-2334-12-382] [PMID: 23270497]
[22]
Zhang J, Guo Z, Pan X, et al. Highlighting the crucial role of Hangzhou in HIV-1 transmission among men who have sex with men in Zhejiang, China. Sci Rep 2017; 7(1): 13892.
[http://dx.doi.org/10.1038/s41598-017-14108-2] [PMID: 29066776]
[23]
Zhang W, Chen J, Pan X, et al. Trends of HIV-1 Subtypes Among Young People in Hangzhou, China. AIDS Res Hum Retroviruses 2017; 33(3): 219-27.
[http://dx.doi.org/10.1089/aid.2016.0117] [PMID: 27762600]
[24]
Barouch DH, Korber B. HIV-1 vaccine development after STEP. Annu Rev Med 2010; 61: 153-67.
[http://dx.doi.org/10.1146/annurev.med.042508.093728] [PMID: 20059334]
[25]
Gaschen B, Taylor J, Yusim K, et al. Diversity considerations in HIV-1 vaccine selection. Science 2002; 296(5577): 2354-60.
[http://dx.doi.org/10.1126/science.1070441] [PMID: 12089434]
[26]
Taylor BS, Sobieszczyk ME, McCutchan FE, Hammer SM. The challenge of HIV-1 subtype diversity. N Engl J Med 2008; 358(15): 1590-602.
[http://dx.doi.org/10.1056/NEJMra0706737] [PMID: 18403767]
[27]
Stone M, Bainbridge J, Sanchez AM, et al. Comparison of detection limits of fourth- and fifth-generation combination hiv antigen-antibody, p24 antigen, and viral load assays on diverse hiv isolates. J Clin Microbiol 2018; 56(8): e02045-17.
[http://dx.doi.org/10.1128/JCM.02045-17] [PMID: 29793968]
[28]
TenoRes Study Group. Global epidemiology of drug resistance after failure of WHO recommended first-line regimens for adult HIV-1 infection: a multicentre retrospective cohort study. Lancet Infect Dis 2016; 16(5): 565-75.
[http://dx.doi.org/10.1016/S1473-3099(15)00536-8] [PMID: 26831472]
[29]
Hemelaar J, Elangovan R, Yun J, et al. WHO–UNAIDS Network for HIV Isolation Characterisation. Global and regional molecular epidemiology of HIV-1, 1990-2015: a systematic review, global survey, and trend analysis. Lancet Infect Dis 2019; 19(2): 143-55.
[http://dx.doi.org/10.1016/S1473-3099(18)30647-9] [PMID: 30509777]
[30]
Lyu H, Dong Z, Roobavannan M, Kandasamy J, Pande S. Prospects of interventions to alleviate rural-urban migration in Jiangsu Province, China based on sensitivity and scenario analysis Hydrolog Sci J 2020.
[http://dx.doi.org/10.1080/02626667.2020.1802030]
[31]
Yang HT, Xing H, Jia CM, et al. [A molecular epidemiological study on the human immunodeficiency virus infection in Jiangsu province]. Chinese Journal of Epidemiology 2003; 24(11): 976-9.
[PMID: 14687495]
[32]
Shi P, Li L, Ding P. H; Y. Characteristics of AIDS prevalence in Jiangsu province and relevant strategy for its prevention and control. Chinese Journal of AIDS and STD 2007; 13(3): 224-6.
[33]
Guo H, Wei JF, Yang H, Huan X, Tsui SK, Zhang C. Rapidly increasing prevalence of HIV and syphilis and HIV-1 subtype characterization among men who have sex with men in Jiangsu, China. Sex Transm Dis 2009; 36(2): 120-5.
[http://dx.doi.org/10.1097/OLQ.0b013e31818d3fa0] [PMID: 19125142]
[34]
Yang Y, Zhao XP, Zou HC, et al. Phylogenetic and temporal dynamics of human immunodeficiency virus type 1 CRF01_AE and CRF07_BC among recently infected antiretroviral therapy-naïve men who have sex with men in Jiangsu province, China, 2012 to 2015: A molecular epidemiology-based study. Medicine (Baltimore) 2018; 97(6): e9826.
[http://dx.doi.org/10.1097/MD.0000000000009826] [PMID: 29419684]
[35]
Hu H, Liu X, Zhang Z, Xu J, Fu G, Huan X. [Recent infected and newly reported HIV cases in Jiangsu province, 2011-2013]. Chinese Journal of Epidemiology 2014; 35(10): 1115-8.
[PMID: 25567015]
[36]
Li W, Chu J, Wei F, et al. Molecular characteristic of HIV-1 CRF01_AE in Nanjing from 2015 to 2017. Infect Genet Evol 2019; 75: 104038.
[http://dx.doi.org/10.1016/j.meegid.2019.104038] [PMID: 31520786]
[37]
Burki T. HIV in China: a changing epidemic. Lancet Infect Dis 2018; 18(12): 1311-2.
[http://dx.doi.org/10.1016/S1473-3099(18)30680-7] [PMID: 30507454]
[38]
Liu YY, Tao HD, Liu J, et al. Prevalence and associated factors of HIV infection among men who have sex with men in Hefei, China, 2013-2014: a cross-sectional study. Int J STD AIDS 2016; 27(4): 305-12.
[http://dx.doi.org/10.1177/0956462415580886] [PMID: 25887062]
[39]
Yue Z, Fang C, Fan D, Xiaojie L, Xiaodong W, Naipeng L, et al. Status of multiple sexual partners and its correlates among HIV- positive men who have sex with men Chinese Journal of AIDS and STD 2017; 8: 734-.
[40]
Nadai Y, Eyzaguirre LM, Constantine NT, et al. Protocol for nearly full-length sequencing of HIV-1 RNA from plasma. PLoS One 2008; 3(1): e1420.
[http://dx.doi.org/10.1371/journal.pone.0001420] [PMID: 18183300]
[41]
Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol 2016; 33(7): 1870-4.
[http://dx.doi.org/10.1093/molbev/msw054] [PMID: 27004904]
[42]
Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4(4): 406-25.
[PMID: 3447015]
[43]
Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10(3): 512-26.
[PMID: 8336541]
[44]
Efron B, Halloran E, Holmes S. Bootstrap confidence levels for phylogenetic trees. Proc Natl Acad Sci USA 1996; 93(14): 7085-90.
[http://dx.doi.org/10.1073/pnas.93.14.7085] [PMID: 8692949]
[45]
Felsenstein J. Confidence Limits on Phylogenies: An Approach Using the Bootstrap. Evolution 1985; 39(4): 783-91.
[http://dx.doi.org/10.1111/j.1558-5646.1985.tb00420.x] [PMID: 28561359]
[46]
Siepel AC, Halpern AL, Macken C, Korber BT. A computer program designed to screen rapidly for HIV type 1 intersubtype recombinant sequences. AIDS Res Hum Retroviruses 1995; 11(11): 1413-6.
[http://dx.doi.org/10.1089/aid.1995.11.1413] [PMID: 8573400]
[47]
Lole KS, Bollinger RC, Paranjape RS, et al. Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol 1999; 73(1): 152-60.
[http://dx.doi.org/10.1128/JVI.73.1.152-160.1999] [PMID: 9847317]
[48]
Schultz AK, Bulla I, Abdou-Chekaraou M, Gordien E, Morgenstern B, Zoaulim F, et al. jpHMM: recombination analysis in viruses with circular genomes such as the hepatitis B virus Nucleic Acids Res 2012; 40(Web Server issue): 193-8.
[49]
Guo H, Guo D, Wei JF, et al. First detection of a novel HIV Type 1 CRF01_AE/07_BC recombinant among an epidemiologically linked cohort of IDUs in Jiangsu, China. AIDS Res Hum Retroviruses 2009; 25(4): 463-7.
[http://dx.doi.org/10.1089/aid.2008.0250] [PMID: 19320602]
[50]
Feng Y, Li X, Zang X, et al. Identification of a novel HIV-1 second-generation recombinant form (CRF01_AE/CRF07_BC) in Jilin, China. AIDS Res Hum Retroviruses 2014; 30(8): 819-22.
[http://dx.doi.org/10.1089/aid.2014.0071] [PMID: 24892359]
[51]
Jiao Y, Wang Y, Kong D, et al. Characterization of a new HIV-1 CRF01_AE/CRF07_BC recombinant virus form among men who have sex with men in beijing, china. AIDS Res Hum Retroviruses 2018; 34(6): 550-4.
[http://dx.doi.org/10.1089/aid.2018.0049] [PMID: 29589485]
[52]
Zhang M, Xin R, Li H, Dong L, Chang W. Identification of two novel hiv-1 second-generation recombinant forms (crf01_ae/07_bc) in shaanxi, china. AIDS Res Hum Retroviruses 2019; 35(2): 191-5.
[http://dx.doi.org/10.1089/aid.2018.0137] [PMID: 30117337]