This article has been updated


The RV144 trial demonstrated 31% vaccine efficacy at preventing human immunodeficiency virus (HIV)-1 infection1. Antibodies against the HIV-1 envelope variable loops 1 and 2 (Env V1 and V2) correlated inversely with infection risk2. We proposed that vaccine-induced immune responses against V1/V2 would have a selective effect against, or sieve, HIV-1 breakthrough viruses. A total of 936 HIV-1 genome sequences from 44 vaccine and 66 placebo recipients were examined. We show that vaccine-induced immune responses were associated with two signatures in V2 at amino acid positions 169 and 181. Vaccine efficacy against viruses matching the vaccine at position 169 was 48% (confidence interval 18% to 66%; P = 0.0036), whereas vaccine efficacy against viruses mismatching the vaccine at position 181 was 78% (confidence interval 35% to 93%; P = 0.0028). Residue 169 is in a cationic glycosylated region recognized by broadly neutralizing and RV144-derived antibodies. The predicted distance between the two signature sites (21 ± 7 Å) and their match/mismatch dichotomy indicate that multiple factors may be involved in the protection observed in RV144. Genetic signatures of RV144 vaccination in V2 complement the finding of an association between high V1/V2-binding antibodies and reduced risk of HIV-1 acquisition, and provide evidence that vaccine-induced V2 responses plausibly had a role in the partial protection conferred by the RV144 regimen.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Change history

  • 24 September 2012

    The web PDF was replaced to correct a corrupted Ångström symbol in three places


Primary accessions


Data deposits

Sequences are available under GenBank accession numbers JX446645JX448316.


  1. 1.

    et al. Vaccination with ALVAC and AIDSVAX to prevent HIV-1 infection in Thailand. N. Engl. J. Med. 361, 2209–2220 (2009)

  2. 2.

    et al. Immune-correlates analysis of an HIV-1 vaccine efficacy trial. N. Engl. J. Med. 366, 1275–1286 (2012)

  3. 3.

    & Nomenclature for immune correlates of protection after vaccination. Clin. Infect. Dis. 54, 1615–1617 (2012)

  4. 4.

    & Evaluating immune correlates in HIV type 1 vaccine efficacy trials: what RV144 may provide. AIDS Res. Hum. Retroviruses 28, 400–404 (2012)

  5. 5.

    , & Statistical methods for assessing differential vaccine protection against human immunodeficiency virus types. Biometrics 54, 799–814 (1998)

  6. 6.

    , , , & Sieve analysis: methods for assessing from vaccine trial data how vaccine efficacy varies with genotypic and phenotypic pathogen variation. J. Clin. Epidemiol. 54, 68–85 (2001)

  7. 7.

    et al. Genetic impact of vaccination on breakthrough HIV-1 sequences from the STEP trial. Nature Med. 17, 366–371 (2011)

  8. 8.

    et al. Antibody neutralization and escape by HIV-1. Nature 422, 307–312 (2003)

  9. 9.

    et al. Limited neutralizing antibody specificities drive neutralization escape in early HIV-1 subtype C infection. PLoS Pathog. 5, e1000598 (2009)

  10. 10.

    et al. Polyclonal B cell responses to conserved neutralization epitopes in a subset of HIV-1-infected individuals. J. Virol. 85, 11502–11519 (2011)

  11. 11.

    et al. The B cell response is redundant and highly focused on V1V2 during early subtype C infection in a Zambian seroconverter. J. Virol. 85, 905–915 (2011)

  12. 12.

    et al. Risk behaviour and time as covariates for efficacy of the HIV vaccine regimen ALVAC-HIV (vCP1521) and AIDSVAX B/E: a post-hoc analysis of the Thai phase 3 efficacy trial RV 144. Lancet Infect. Dis. 12, 531–537 (2012)

  13. 13.

    , & Genome scanning tests for comparing amino acid sequences between groups. Biometrics 64, 198–207 (2008)

  14. 14.

    Model-based sieve analysis. Preprint at (2012)

  15. 15.

    et al. Statistical interpretation of the RV144 HIV vaccine efficacy trial in Thailand: a case study for statistical issues in efficacy trials. J. Infect. Dis. 203, 969–975 (2011)

  16. 16.

    et al. Phylogenetic dependency networks: inferring patterns of CTL escape and codon covariation in HIV-1 Gag. PLoS Comput. Biol. 4, e1000225 (2008)

  17. 17.

    Phylogenies and the comparative method. Am. Nat. 125, 1–15 (1985)

  18. 18.

    & Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics 21, 2531–2533 (2005)

  19. 19.

    et al. Envelope-constrained neutralization-sensitive HIV-1 after heterosexual transmission. Science 303, 2019–2022 (2004)

  20. 20.

    et al. Potent and broad neutralization of HIV-1 subtype C by plasma antibodies targeting a quaternary epitope including residues in the V2 loop. J. Virol. 85, 3128–3141 (2011)

  21. 21.

    et al. A short segment of the HIV-1 gp120 V1/V2 region is a major determinant of resistance to V1/V2 neutralizing antibodies. J. Virol. 86, 8319–8323 (2012)

  22. 22.

    et al. Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9. Nature 480, 336–343 (2011)

  23. 23.

    et al. Computational characterization of B-cell epitopes. Mol. Immunol. 45, 3477–3489 (2008)

  24. 24.

    , & Covariability of selected amino acid positions for HIV type 1 subtypes C and B. AIDS Res. Hum. Retroviruses 21, 1016–1030 (2005)

  25. 25.

    , , & An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope. PLoS Comput. Biol. 3, e231 (2007)

  26. 26.

    et al. The analysis of failure times in the presence of competing risks. Biometrics 34, 541–554 (1978)

  27. 27.

    & Applying Cox regression to competing risks. Biometrics 51, 524–532 (1995)

  28. 28.

    & Proportional hazards tests and diagnostics based on weighted residuals. Biometrika 81, 515–526 (1994)

  29. 29.

    Comparison of competing risks failure time methods and time-independent methods for assessing strain variations in vaccine protection. Stat. Med. 19, 3065–3086 (2000)

  30. 30.

    The positive false discovery rate: a Bayesian interpretation and the q-value. Ann. Stat. 31, 2013–2035 (2003)

Download references


We thank B. F. Haynes and F. A. Matsen for advice and comments, and I. A. Wilson and R. L. Stanfield for assistance. This study was supported in part by an Interagency Agreement Y1-AI-2642-12 between US Army Medical Research and Material Command (USAMRMC) and the National Institutes of Allergy and Infectious Diseases. This work was also supported by a cooperative agreement (W81XWH-07-2-0067) between the Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., and the US Department of Defense (DOD). Additional support was provided to P.B.G. through the NIH grant 2R37AI05465-10. The opinions herein are those of the authors and should not be construed as official or representing the views of the US Department of Defense or the Department of the Army.

Author information

Author notes

    • Morgane Rolland
    • , Paul T. Edlefsen
    • , Peter B. Gilbert
    • , James I. Mullins
    •  & Jerome H. Kim

    These authors contributed equally to this work.


  1. US Military HIV Research Program, Silver Spring, Maryland 20910, USA

    • Morgane Rolland
    • , Sodsai Tovanabutra
    • , Eric Sanders-Buell
    • , Meera Bose
    • , Shana Howell
    • , Adam Bates
    • , Michelle Lazzaro
    • , Annemarie O’Sullivan
    • , Esther Lei
    • , Andrea Bradfield
    • , Grace Ibitamuno
    • , Robert J. O’Connell
    • , Merlin L. Robb
    • , Nelson L. Michael
    •  & Jerome H. Kim
  2. Statistical Center for HIV/AIDS Research and Prevention, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA

    • Paul T. Edlefsen
    • , Tomer Hertz
    • , Allan C. deCamp
    • , Craig A. Magaret
    • , Hasan Ahmed
    • , Michal Juraska
    •  & Peter B. Gilbert
  3. Department of Microbiology, University of Washington, Seattle, Washington 98195, USA

    • Brendan B. Larsen
    • , Lennie Chen
    • , Philip Konopa
    • , Snehal Nariya
    • , Julia N. Stoddard
    • , Kim Wong
    • , Hong Zhao
    • , Wenjie Deng
    • , Brandon S. Maust
    •  & James I. Mullins
  4. Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA

    • Chris Carrico
    • , Sergey Menis
    •  & William R. Schief
  5. IAVI Neutralizing Antibody Center and Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, California 92037, USA

    • Chris Carrico
    • , Sergey Menis
    •  & William R. Schief
  6. Royal Thai Army Component, AFRIMS, Bangkok 10400, Thailand

    • Vatcharain Assawadarachai
    • , Mark S. deSouza
    •  & Sorachai Nitayaphan
  7. Thai Ministry of Public Health, Nonthaburi 11000, Thailand

    • Supachai Rerks-Ngarm
  8. Vaccine Research Center, NIAID, NIH, Bethesda, Maryland 20892, USA

    • Jason S. McLellan
    • , Ivelin Georgiev
    •  & Peter D. Kwong
  9. Microsoft Research, Redmond, Washington 98052, USA

    • Jonathan M. Carlson


  1. Search for Morgane Rolland in:

  2. Search for Paul T. Edlefsen in:

  3. Search for Brendan B. Larsen in:

  4. Search for Sodsai Tovanabutra in:

  5. Search for Eric Sanders-Buell in:

  6. Search for Tomer Hertz in:

  7. Search for Allan C. deCamp in:

  8. Search for Chris Carrico in:

  9. Search for Sergey Menis in:

  10. Search for Craig A. Magaret in:

  11. Search for Hasan Ahmed in:

  12. Search for Michal Juraska in:

  13. Search for Lennie Chen in:

  14. Search for Philip Konopa in:

  15. Search for Snehal Nariya in:

  16. Search for Julia N. Stoddard in:

  17. Search for Kim Wong in:

  18. Search for Hong Zhao in:

  19. Search for Wenjie Deng in:

  20. Search for Brandon S. Maust in:

  21. Search for Meera Bose in:

  22. Search for Shana Howell in:

  23. Search for Adam Bates in:

  24. Search for Michelle Lazzaro in:

  25. Search for Annemarie O’Sullivan in:

  26. Search for Esther Lei in:

  27. Search for Andrea Bradfield in:

  28. Search for Grace Ibitamuno in:

  29. Search for Vatcharain Assawadarachai in:

  30. Search for Robert J. O’Connell in:

  31. Search for Mark S. deSouza in:

  32. Search for Sorachai Nitayaphan in:

  33. Search for Supachai Rerks-Ngarm in:

  34. Search for Merlin L. Robb in:

  35. Search for Jason S. McLellan in:

  36. Search for Ivelin Georgiev in:

  37. Search for Peter D. Kwong in:

  38. Search for Jonathan M. Carlson in:

  39. Search for Nelson L. Michael in:

  40. Search for William R. Schief in:

  41. Search for Peter B. Gilbert in:

  42. Search for James I. Mullins in:

  43. Search for Jerome H. Kim in:


M.R. conducted the sequence analysis with contributions from B.B.L., W.D. and B.S.M.; P.T.E. and P.B.G. conducted the site-scanning sieve analyses. M.R., S.T., E.S.-B. and J.I.M. designed the sequencing experiments. B.B.L., L.C., P.K., S.N., J.N.S., K.W., H.Z., M.B., S.H., A. Bates, M.L., A.O’S., E.L., A. Bradfield, G.I. and V.A. performed viral sequencing. T.H., A.C.deC., C.A.M., H.A. and M.J. contributed statistical analyses. C.C., S.M. and W.R.S. developed the EPIMAP approach. J.S.M., I.G. and P.D.K. identified antibody contact residues and performed V2 structural analyses. J.M.C. performed phylogenetic dependency network analyses. R.J.O’C., M.S.deS., S.N., S.R.-N., M.L.R., N.L.M. and J.H.K. conducted the RV144 trial. M.R., P.T.E., P.B.G., J.I.M. and J.H.K. designed the studies, analysed data, prepared the manuscript (with contributions from J.M.C., P.D.K. and W.R.S.) and supervised the project.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Morgane Rolland.

Supplementary information

PDF files

  1. 1.

    Supplementary Information 1

    This file contains Supplementary Figures 1–5, Supplementary Methods, Supplementary Tables 1–11 and Supplementary Note 1.

  2. 2.

    Supplementary Information 2

    This Supplementary Information file contains the Code for differential VE and for the site-scanning methods.

About this article

Publication history





Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.