Skip to main content

Advertisement

SpringerLink
Log in

Transmission network characteristics based on env and gag sequences from MSM during acute HIV-1 infection in Beijing, China

  • Original Article
  • Published:
Archives of Virology Aims and scope Submit manuscript

Abstract

Molecular epidemiology can be used to identify human immunodeficiency virus (HIV) transmission clusters, usually using pol sequence for analysis. In the present study, we explored appropriate parameters to construct a simple network using HIV env and gag sequences instead of pol sequences for constructing a phylogenetic tree and a genetic transmission subnetwork, which were used to identify individuals with many potential transmission links and to explore the evolutionary dynamics of the virus among men who have sex with men (MSM) in Beijing. We investigated 70 acute HIV-1 infections, which consisted of HIV-1 subtype B (15.71%), the circulating recombinant forms CRF01_AE (47.14%), CRF07_BC (21.43%), CRF55_01B (1.43%), and CRF65_cpx (4.29%), and an unknown subtype (10.00%). By exploring the similarities and differences among HIV env, gag and pol sequences in describing the dynamics of the HIV-1 CRF01_AE transmission subnetwork among Beijing MSM, we found that four key points of the env sequences (strains E-2011_BJ.CY_16014, E-2011_BJ.FT_16017, E-2011_BJ.TZ_16064, and E-2011_BJ.XW_16035) contained more transmission information than gag sequences (three key points: strains G-2011_BJ.CY_16014, G-2011_BJ.FT_16017, and G-2011_BJ.XW_16035) and pol sequences (two key points: strains P-2011_BJ.CY_16014 and P-2011_BJ.XW_16035). Although the env and gag sequence results were similar to pol sequences in describing the dynamics of the HIV-1 CRF01_AE transmission subnetwork, we were able to obtain more precise information, allowing identification of key points of subnetwork expansion, based on HIV env and gag sequences instead of pol sequences. Taken together, the key points we found will improve our current understanding of how HIV spreads between MSM populations in Beijing and help to better target preventative interventions for promoting public health.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  1. Zhao J, Chen L, Chaillon A, Zheng C, Cai W, Yang Z et al (2016) The dynamics of the HIV epidemic among men who have sex with men (MSM) from 2005 to 2012 in Shenzhen, China. Sci Rep 6:28703

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Shang H, Zhang L (2015) MSM and HIV-1 infection in China. Natl Sci Rev 2:388–391

    Article  Google Scholar 

  3. Ye S, Xiao Y, Jin C, Cassell H, Blevins M, Sun J et al (2012) Effectiveness of integrated HIV prevention interventions among Chinese men who have sex with men: evaluation of a 16-city public health program. PLoS One 7:e50873

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Mao H, Ma W, Lu H, Wang L, Zheng H, Zhu Y et al (2014) High incidence of HIV and syphilis among migrant men who have sex with men in Beijing, China: a prospective cohort study. BMJ Open 4:e005351

    Article  PubMed  PubMed Central  Google Scholar 

  5. Little SJ, Kosakovsky Pond SL, Anderson CM, Young JA, Wertheim JO, Mehta SR et al (2014) Using HIV networks to inform real time prevention interventions. PLoS One 9:e98443

    Article  PubMed  PubMed Central  Google Scholar 

  6. Wang X, Wu Y, Mao L, Xia W, Zhang W, Dai L et al (2015) Targeting HIV prevention based on molecular epidemiology among deeply sampled subnetworks of men who have sex with men. Clin Infect Dis 61:1462–1468

    Article  PubMed  PubMed Central  Google Scholar 

  7. Wertheim JO, Leigh Brown AJ, Hepler NL, Mehta SR, Richman DD, Smith DM et al (2014) The global transmission network of HIV-1. J Infect Dis 209:304–313

    Article  PubMed  Google Scholar 

  8. Brenner BG, Wainberg MA (2013) Future of phylogeny in HIV prevention. J Acquir Immune Defic Syndr 63(Suppl 2):S248–S254

    Article  PubMed  PubMed Central  Google Scholar 

  9. Li X, Xue Y, Lin Y, Gai J, Zhang L, Cheng H et al (2016) Evolutionary dynamics and complicated genetic transmission network patterns of HIV-1 CRF01_AE among MSM in Shanghai, China. Sci Rep 6:34729

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Huang X, Lodi S, Fox Z, Li W, Phillips A, Porter K et al (2013) Rate of CD4 decline and HIV-RNA change following HIV seroconversion in men who have sex with men: a comparison between the Beijing PRIMO and CASCADE cohorts. J Acquir Immune Defic Syndr 62:441–446

    Article  CAS  PubMed  Google Scholar 

  11. Fiebig EW, Wright DJ, Rawal BD, Garrett PE, Schumacher RT, Peddada L et al (2003) Dynamics of HIV viremia and antibody seroconversion in plasma donors: implications for diagnosis and staging of primary HIV infection. AIDS 17:1871–1879

    Article  PubMed  Google Scholar 

  12. Zhao Q, Shi L, Jiang Y, Wen Y, Pan P, Zhang G et al (2014) Contact tracing of a possible case of HIV sexual transmission by using Miseq platform. Zhonghua Yu Fang Yi Xue Za Zhi 48:471–475

    CAS  PubMed  Google Scholar 

  13. Kaye M, Chibo D, Birch C (2008) Phylogenetic investigation of transmission pathways of drug-resistant HIV-1 utilizing pol sequences derived from resistance genotyping. J Acquir Immune Defic Syndr 49:9–16

    Article  CAS  PubMed  Google Scholar 

  14. Zhou Z, Wagar N, DeVos JR, Rottinghaus E, Diallo K, Nguyen DB et al (2011) Optimization of a low cost and broadly sensitive genotyping assay for HIV-1 drug resistance surveillance and monitoring in resource-limited settings. PLoS One 6:e28184

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Xin RL, Feng Y, Cheng CL, Hu YY, Meng ZF, Xing H et al (2009) Primers of gag gene for HIV-1 subtyping in China and application thereof in practice. Zhonghua Yi Xue Za Zhi 89:876–880

    CAS  PubMed  Google Scholar 

  16. Leitner T, Escanilla D, Franzen C, Uhlen M, Albert J (1996) Accurate reconstruction of a known HIV-1 transmission history by phylogenetic tree analysis. Proc Natl Acad Sci USA 93:10864–10869

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Leigh Brown AJ, Lycett SJ, Weinert L, Hughes GJ, Fearnhill E, Dunn DT (2011) Transmission network parameters estimated from HIV sequences for a nationwide epidemic. J Infect Dis 204:1463–1469

    Article  PubMed  PubMed Central  Google Scholar 

  18. Lin Y, Xue Y, Wang X, Zhou L, Wang Y, Shen F et al (2016) HIV-1 transmission clusters among men who have sex with men in Shanghai. Chin J AIDS STD 22:165–169

    Google Scholar 

  19. Liu K, Linder CR, Warnow T (2011) RAxML and FastTree: comparing two methods for large-scale maximum likelihood phylogeny estimation. PLoS One 6:e27731

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Ragonnet-Cronin M, Hodcroft E, Hue S, Fearnhill E, Delpech V, Brown AJ et al (2013) Automated analysis of phylogenetic clusters. BMC Bioinform 14:317

    Article  Google Scholar 

  21. Brenner BG, Roger M, Stephens D, Moisi D, Hardy I, Weinberg J et al (2011) Transmission clustering drives the onward spread of the HIV epidemic among men who have sex with men in Quebec. J Infect Dis 204:1115–1119

    Article  PubMed  PubMed Central  Google Scholar 

  22. Aldous JL, Pond SK, Poon A, Jain S, Qin H, Kahn JS et al (2012) Characterizing HIV transmission networks across the United States. Clin Infect Dis 55:1135–1143

    Article  PubMed  PubMed Central  Google Scholar 

  23. Su G, Morris JH, Demchak B, Bader GD (2014) Biological network exploration with Cytoscape 3. Curr Protoc Bioinform 47:8–13

    Google Scholar 

  24. Kohl M, Wiese S, Warscheid B (2011) Cytoscape: software for visualization and analysis of biological networks. Methods Mol Biol 696:291–303

    Article  CAS  PubMed  Google Scholar 

  25. Ye J, Zang W, Su X, Lu H, Hao M, Xin R et al (2014) Molecular epidemiological characteristics of HIV-1 strains isolated from newly diagnosed MSM subjects (2006–2010) in Beijing, China. Chin J Virol 30:138–142

    CAS  Google Scholar 

  26. Hu W, Zhang X, Li W, Wei F, Liu Z, Yan H (2013) Analysis of HIV-1 subtypes among acute HIV-1 infectors from men who have sex with men. Chin J AIDS STD 19:236–238

    CAS  Google Scholar 

  27. Mehta SR, Murrell B, Anderson CM, Kosakovsky Pond SL, Wertheim JO, Young JA et al (2016) Using HIV sequence and epidemiologic data to assess the effect of self-referral testing for acute HIV infection on incident diagnoses in San Diego, California. Clin Infect Dis 63:101–107

    Article  PubMed  PubMed Central  Google Scholar 

  28. Hightower GK, May SJ, Perez-Santiago J, Pacold ME, Wagner GA, Little SJ et al (2013) HIV-1 clade B pol evolution following primary infection. PLoS One 8:e68188

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Perrin L, Kaiser L, Yerly S (2003) Travel and the spread of HIV-1 genetic variants. Lancet Infect Dis 3:22–27

    Article  PubMed  Google Scholar 

  30. Ramakrishnan R, Mehta R, Sundaravaradan V, Davis T, Ahmad N (2006) Characterization of HIV-1 envelope gp41 genetic diversity and functional domains following perinatal transmission. Retrovirology 3:42

    Article  PubMed  PubMed Central  Google Scholar 

  31. Korber B, Gaschen B, Yusim K, Thakallapally R, Kesmir C, Detours V (2001) Evolutionary and immunological implications of contemporary HIV-1 variation. Br Med Bull 58:19–42

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This work was supported by the National Science and Technology Major Project of the 12th Five-Year Plan (No. 2012ZX10001001-001), China-US Cooperation Global AIDS Program (2016 to 2017, 4.2), the Funding for Chinese overseas talents returning to China in 2016 (B.S.), the Capital Health Research and Development of Special Found (2016-1-2182), the Beijing Municipal of Science and Technology Major Project (D141100000314002, D141100000314005, D161100000416002), the National Natural Science Foundation of China (81571973, 81601795), the Beijing Municipal Administration of Hospitals’ Youth Program (QML20161702), the Basic-Clinical Research Cooperation Fund of Capital Medical University (16JL18, 17JL20), and the Beijing Key Laboratory for HIV/AIDS Research (BZ0089).

Author information

Author notes

  1. Zhimin Zhang and Lili Dai contributed equally to this work.

Authors and Affiliations

  1. National AIDS Reference Laboratory, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China

    Zhimin Zhang, Yan Jiang, Kaidi Feng, Fengjiao Yu, Jun Yao, Wenge Xing & Maofeng Qiu

  2. Center for Infectious Diseases, Beijing You’an Hospital, Capital Medical University, Beijing, 100069, China

    Lili Dai, Lifeng Liu, Wei Xia, Lijun Sun, Tong Zhang, Hao Wu & Bin Su

Authors
  1. Zhimin Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Lili Dai
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yan Jiang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Kaidi Feng
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Lifeng Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Wei Xia
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Fengjiao Yu
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Jun Yao
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Wenge Xing
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Lijun Sun
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Tong Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Hao Wu
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Bin Su
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Maofeng Qiu
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

JY, WX, BS, and MQ conceived the study, designed the experiments, and analyzed the data. ZZ, LD, KF, and FY performed the experiments; YJ, LL, WX, JY, WX, LS, TZ, and HW contributed reagents and materials; and ZZ, BS, and MQ wrote the article. All authors read and approved the final manuscript.

Corresponding authors

Correspondence to Bin Su or Maofeng Qiu.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

All procedures performed in studies involving human participants were in accordance with the ethical standards of the Beijing You’an Hospital research ethics committee and the National Center for AIDS/STD Control and Prevention, China CDC, and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards.

Informed consent

Informed consent was obtained from all individual participants included in the study.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Zhang, Z., Dai, L., Jiang, Y. et al. Transmission network characteristics based on env and gag sequences from MSM during acute HIV-1 infection in Beijing, China. Arch Virol 162, 3329–3338 (2017). https://doi.org/10.1007/s00705-017-3485-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00705-017-3485-z

Search

Navigation