Donor-recipient identification in para- and poly-phyletic trees under alternative HIV-1 transmission hypotheses using approximate bayesian computation

Genetics

Volumn 207, Issue 3, 2017, Pages 1089-1101

  Romero Severson, Ethan O ^a   Bulla, Ingo ^a,b   Hengartner, Nick ^a   Bártolo, Inês ^c   Abecasis, Ana ^d   Azevedo Pereira, José M ^c   Taveira, Nuno ^c,e   Leitner, Thomas ^a  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

^b UNIVERSITY OF GREIFSWALD   (Germany)

^c UNIVERSITY OF LISBON   (Portugal)

^d INSTITUTO DE HIGIENE E MEDICINA TROPICAL   (Portugal)

^e INSTITUTO SUPERIOR DE CIÊNCIAS DA SAÚDE EGAS MONIZ   (Portugal)

Author keywords

Ancestral node state; Approximate bayesian computation; Co infection; Coalescent; Phylogeny; Superinfection

Indexed keywords

APPROXIMATE BAYESIAN COMPUTATION; ARTICLE; BAYES THEOREM; CLINICAL ARTICLE; CONTROLLED STUDY; DISEASE TRANSMISSION; DNA SEQUENCE; FEMALE; GENETIC VARIABILITY; HETEROSEXUALITY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; MALE; MAXIMUM LIKELIHOOD METHOD; MIXED INFECTION; PHYLOGENETIC TREE; PHYLOGENY; POPULATION DYNAMICS; POPULATION SIZE; PRIORITY JOURNAL; SEX RATIO; SEXUAL TRANSMISSION; SUPERINFECTION; CLASSIFICATION; GENETICS; STATISTICAL MODEL; STATISTICS AND NUMERICAL DATA; TRANSMISSION;

VIRUS ENVELOPE PROTEIN;

BAYES THEOREM; DISEASE TRANSMISSION, INFECTIOUS; FEMALE; GENE PRODUCTS, ENV; HIV INFECTIONS; HIV-1; HUMANS; MALE; MODELS, STATISTICAL; PHYLOGENY;

EID: 85032936267     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.117.300284     Document Type: Article

References (39)

1. Altfeld, M., T. M. Allen, X. G. Yu, M. N. Johnston, D. Agrawal et al., 2002 HIV-1 superinfection despite broad CD8+ T-cell responses containing replication of the primary virus. Nature 420: 434–439.
2. Anisimova, M., and O. Gascuel, 2006 Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative. Syst. Biol. 55: 539–552.
3. Bartolo, I., C. Rocha, J. Bartolomeu, A. Gama, R. Marcelino et al., 2009 Highly divergent subtypes and new recombinant forms prevail in the HIV/AIDS epidemic in Angola: new insights into the origins of the AIDS pandemic. Infect. Genet. Evol. 9: 672– 682.
4. Boily, M. C., R. F. Baggaley, L. Wang, B. Masse, R. G. White et al., 2009 Heterosexual risk of HIV-1 infection per sexual act: systematic review and meta-analysis of observational studies. Lancet Infect. Dis. 9: 118–129.
5. Carrillo, F. Y., R. Sanjuan, A. Moya, and J. M. Cuevas, 2007 The effect of co- and superinfection on the adaptive dynamics of vesicular stomatitis virus. Infect. Genet. Evol. 7: 69–73.
6. Cohen, M. S., G. M. Shaw, A. J. McMichael, and B. F. Haynes, 2011 Acute HIV-1 infection. N. Engl. J. Med. 364: 1943–1954.
7. Dollo, L., 1893 Les lois de l’évolution. Bull. Soc. Belge Géol. Pal. Hydr. 7: 164–166.
8. Genz, A., F. Bretz, T. Miwa, X. Mi, F. Leisch et al., 2017 mvtnorm: multivariate normal and t distributions, R package version 1.0–6.
9. Gottlieb, G. S., D. C. Nickle, M. A. Jensen, K. G. Wong, J. Grobler et al., 2004 Dual HIV-1 infection associated with rapid disease progression. Lancet 363: 619–622.
10. Grobler, J., C. M. Gray, C. Rademeyer, C. Seoighe, G. Ramjee et al., 2004 Incidence of HIV-1 dual infection and its association with increased viral load set point in a cohort of HIV-1 subtype C-infected female sex workers. J. Infect. Dis. 190: 1355–1359.
11. Guindon, S., F. Lethiec, P. Duroux, and O. Gascuel, 2005 PHYML Online–a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res. 33: W557–W559.
12. Katoh, K., and H. Toh, 2008 Recent developments in the MAFFT multiple sequence alignment program. Brief. Bioinform. 9: 286–298.
13. Keele, B. F., E. E. Giorgi, J. F. Salazar-Gonzalez, J. M. Decker, K. T. Pham et al., 2008 Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. Proc. Natl. Acad. Sci. USA 105: 7552–7557.
14. Leigh Brown, A. J., 1997 Analysis of HIV-1 env gene sequences reveals evidence for a low effective number in the viral population. Proc. Natl. Acad. Sci. USA 94: 1862–1865.
15. Leitner, T., and J. Albert, 1999 The molecular clock of HIV-1 unveiled through analysis of a known transmission history. Proc. Natl. Acad. Sci. USA 96: 10752–10757.
16. Leitner, T., and W. M. Fitch, 1999 The phylogenetics of known transmission histories, in The Evolution of HIV, edited by K. A. Crandall. Johns Hopkins University Press, Baltimore.
17. Li, H., K. J. Bar, S. Wang, J. M. Decker, Y. Chen et al., 2010 High multiplicity infection by HIV-1 in men who have sex with men. PLoS Pathog. 6: e1000890.
18. Nijhuis, M., C. A. Boucher, P. Schipper, T. Leitner, R. Schuurman et al., 1998 Stochastic processes strongly influence HIV-1 evolution during suboptimal protease-inhibitor therapy. Proc. Natl. Acad. Sci. USA 95: 14441–14446.
19. Nordborg, M., 2001 Coalescent Theory. Wiley Online Library, Hoboken, NJ.
20. Parekh, B. S., M. S. Kennedy, T. Dobbs, C. P. Pau, R. Byers et al., 2002 Quantitative detection of increasing HIV type 1 antibodies after seroconversion: a simple assay for detecting recent HIV infection and estimating incidence. AIDS Res. Hum. Retro-viruses 18: 295–307.
21. Pennings, P. S., S. Kryazhimskiy, and J. Wakeley, 2014 Loss and recovery of genetic diversity in adapting populations of HIV. PLoS Genet. 10: e1004000.
22. Rieder, P., B. Joos, A. U. Scherrer, H. Kuster, D. Braun et al., 2011 Characterization of human immunodeficiency virus type 1 (HIV-1) diversity and tropism in 145 patients with primary HIV-1 infection. Clin. Infect. Dis. 53: 1271–1279.
23. Romero-Severson, E., H. Skar, I. Bulla, J. Albert, and T. Leitner, 2014 Timing and order of transmission events is not directly reflected in a pathogen phylogeny. Mol. Biol. Evol. 31: 2472– 2482.
24. Romero-Severson, E. O., I. Bulla, and T. Leitner, 2016 Phylogenetically resolving epidemiologic linkage. Proc. Natl. Acad. Sci. USA 113: 2690–2695.
25. Ronen, K., C. O. McCoy, F. A. Matsen, D. F. Boyd, S. Emery et al., 2013 HIV-1 superinfection occurs less frequently than initial infection in a cohort of high-risk Kenyan women. PLoS Pathog. 9: e1003593.
26. Ronquist, F., and J. P. Huelsenbeck, 2003 MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572–1574.
27. Salazar-Gonzalez, J. F., M. G. Salazar, B. F. Keele, G. H. Learn, E. E. Giorgi et al., 2009 Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection. J. Exp. Med. 206: 1273–1289.
28. Sanborn, K. B., M. Somasundaran, K. Luzuriaga, and T. Leitner, 2015 Recombination elevates the effective evolutionary rate and facilitates the establishment of HIV-1 infection in infants after mother-to-child transmission. Retrovirology 12: 96.
29. Shankarappa, R., J. B. Margolick, S. J. Gange, A. G. Rodrigo, D. Upchurch et al., 1999 Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. J. Virol. 73: 10489–10502.
30. Shattock, R. J., and J. P. Moore, 2003 Inhibiting sexual transmission of HIV-1 infection. Nat. Rev. Microbiol. 1: 25–34.
31. Skar, H., R. N. Gutenkunst, K. Wilbe Ramsay, A. Alaeus, J. Albert et al., 2011 Daily sampling of an HIV-1 patient with slowly progressing disease displays persistence of multiple env subpop-ulations consistent with neutrality. PLoS One 6: e21747.
32. Skar, H., J. Albert, and T. Leitner, 2013 Towards estimation of HIV-1 date of infection: a time-continuous IgG-model shows that seroconversion does not occur at the midpoint between negative and positive tests. PLoS One 8: e60906.
33. Smith, D. M., J. K. Wong, G. K. Hightower, C. C. Ignacio, K. K. Koelsch et al., 2004 Incidence of HIV superinfection following primary infection. JAMA 292: 1177–1178.
34. Smith, D. M., J. K. Wong, G. K. Hightower, C. C. Ignacio, K. K. Koelsch et al., 2005 HIV drug resistance acquired through superinfection. AIDS 19: 1251–1256.
35. Smith, D. M., M. C. Strain, S. D. Frost, S. K. Pillai, J. K. Wong et al., 2006 Lack of neutralizing antibody response to HIV-1 predisposes to superinfection. Virology 355: 1–5.
36. van der Kuyl, A. C., and M. Cornelissen, 2007 Identifying HIV-1 dual infections. Retrovirology 4: 67.
37. Wakeley, J., 2009 Coalescent Theory: An Introduction. Roberts and Company Publishers, Greenwood Village, CO.
38. Yang, O. O., E. S. Daar, B. D. Jamieson, A. Balamurugan, D. M. Smith et al., 2005 Human immunodeficiency virus type 1 clade B superinfection: evidence for differential immune containment of distinct clade B strains. J. Virol. 79: 860– 868.
39. Zanini, F., J. Brodin, L. Thebo, C. Lanz, G. Bratt et al., 2015 Population genomics of intrapatient HIV-1 evolution. Elife 4: e11282.