Phylogenetic patterns recover known HIV epidemiological relationships and reveal common transmission of multiple variants

Nature Microbiology

Volumn 3, Issue 9, 2018, Pages 983-988

  Leitner, Thomas ^a   Romero Severson, Ethan ^a  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONTACT EXAMINATION; EPIDEMIOLOGICAL LINKAGE; GENE SEQUENCE; GENETIC LINKAGE; GENETIC VARIABILITY; GEOGRAPHIC DISTRIBUTION; HUMAN IMMUNODEFICIENCY VIRUS; INFECTION RISK; LETTER; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENY; PLACENTAL TRANSFER; PRIORITY JOURNAL; VIRUS TRANSMISSION; GENETICS; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; NUCLEOTIDE SEQUENCE; SEQUENCE ANALYSIS; TRANSMISSION; VIROLOGY;

VIRUS RNA;

BASE SEQUENCE; HIV INFECTIONS; HIV-1; HUMANS; PHYLOGENY; RNA, VIRAL; SEQUENCE ANALYSIS, RNA;

EID: 85051101609     PISSN: None     EISSN: 20585276     Source Type: Journal    
DOI: 10.1038/s41564-018-0204-9     Document Type: Letter

References (42)

1. Wertheim, J. O. et al. Social and genetic networks of HIV-1 transmission in New York City. PLoS Pathog. 13, e1006000 (2017)
2. Pillay, D. et al. PANGEA-HIV: phylogenetics for generalised epidemics in Africa. Lancet Infect. Dis. 15, 259–261 (2015)
3. Lewis, F., Hughes, G. J., Rambaut, A., Pozniak, A. & Leigh Brown, A. J. Episodic sexual transmission of HIV revealed by molecular phylodynamics. PLoS Med. 5, e50 (2008)
4. Poon, A. F. et al. Near real-time monitoring of HIV transmission hotspots from routine HIV genotyping: an implementation case study. Lancet HIV 3, e231–e238 (2016)
5. Romero-Severson, E. O., Bulla, I. & Leitner, T. Phylogenetically resolving epidemiologic linkage. Proc. Natl Acad. Sci. USA 113, 2690–2695 (2016)
6. Wymant, C. et al. PHYLOSCANNER: analysing within- and between-host pathogen genetic diversity to identify transmission, multipleInfection, recombination and contamination. Preprint at bioRxiv 10.1101/157768 (2017)
7. Leitner, T. & Albert, J. Reconstruction of HIV-1 transmission chains for forensic purposes. AIDS Rev. 2, 241–251 (2000)
8. Abecasis, A. B. et al. Science in court: the myth of HIV fingerprinting. Lancet Infect. Dis. 11, 78–79 (2011)
9. Bernard, E. J., Azad, Y., Vandamme, A. M., Weait, M. & Geretti, A. M. HIV forensics: pitfalls and acceptable standards in the use of phylogenetic analysis as evidence in criminal investigations of HIV transmission. HIV Med. 8, 382–387 (2007)
10. Romero-Severson, E., Skar, H., Bulla, I., Albert, J. & Leitner, T. Timing and order of transmission events is not directly reflected in a pathogen phylogeny. Mol. Biol. Evol. 31, 2472–2482 (2014)
11. Volz, E. M., Romero-Severson, E. & Leitner, T. Phylodynamic inference across epidemic scales. Mol. Biol. Evol. 34, 1276–1288 (2017)
12. Gottlieb, G. S. et al. Dual HIV-1 infection associated with rapid disease progression. Lancet 363, 619–622 (2004)
13. Grobler, J. et al. 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 (2004)
14. Yang, O. O. et al. Human immunodeficiency virus type 1 clade B superinfection: evidence for differential immune containment of distinct clade B strains. J. Virol. 79, 860–868 (2005)
15. Smith, D. M. et al. Lack of neutralizing antibody response to HIV-1 predisposes to superinfection. Virology 355, 1–5 (2006)
16. Smith, D. M. et al. Incidence of HIV superinfection following primary infection. JAMA 292, 1177–1178 (2004)
17. Korber, B., Hraber, P., Wagh, K. & Hahn, B. H. Polyvalent vaccine approaches to combat HIV-1 diversity. Immunol. Rev. 275, 230–244 (2017)
18. Ypma, R. J., van Ballegooijen, W. M. & Wallinga, J. Relating phylogenetic trees to transmission trees of infectious disease outbreaks. Genetics 195, 1055–1062 (2013)
19. McNearney, T. et al. Relationship of human immunodeficiency virus type 1 sequence heterogeneity to stage of disease. Proc. Natl Acad. Sci. USA 89, 10247–10251 (1992)
20. Wolfs, T. F. W., Zwart, G., Bakker, M. & Goudsmit, J. HIV-1 genomic RNA diversification following sexual parenteral virus transmission. Virology 189, 103–110 (1992)
21. Zhang, L. Q. et al. Selection for specific sequences in the external envelope protein of human immunodeficiency virus type 1 upon primary infection. J. Virol. 67, 3345–3356 (1993)
22. Salazar-Gonzalez, J. F. et al. Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection. J. Exp. Med. 206, 1273–1289 (2009)
23. Fischer, W. et al. Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing. PLoS ONE 5, e12303 (2010)
24. Shankarappa, R. et al. Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. J. Virol. 73, 10489–10502 (1999)
25. Keele, B. F. et al. Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. Proc. Natl Acad. Sci. USA 105, 7552–7557 (2008)
26. Rieder, P. et al. 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 (2011)
27. Leitner, T., Escanilla, D., Franzén, C., Uhlén, M. & Albert, J. Accurate reconstruction of a known HIV-1 transmission history by phylogenetic tree analysis. Proc. Natl Acad. Sci. USA 93, 10864–10869 (1996)
28. Lemey, P. et al. Molecular footprint of drug-selective pressure in a human immunodeficiency virus transmission chain. J. Virol. 79, 11981–11989 (2005)
29. Didelot, X., Fraser, C., Gardy, J. & Colijn, C. Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks. Mol. Biol. Evol. 34, 997–1007 (2017)
30. Jombart, T. et al. Bayesian reconstruction of disease outbreaks by combining epidemiologic and genomic data. PLoS Comput. Biol. 10, e1003457 (2014)
31. Kenah, E., Britton, T., Halloran, M. E. & Longini, I. M. Jr. Molecular infectious disease epidemiology: survival analysis and algorithms linking phylogenies to transmission trees. PLoS Comput. Biol. 12, e1004869 (2016)
32. Kumar, A. et al. Infant transmitted/founder HIV-1 viruses from peripartum transmission are neutralization resistantto paired maternal plasma. PLoS Pathog. 14, e1006944 (2018)
33. Patel, P. et al. Estimating per-act HIV transmission risk: a systematic review. AIDS 28, 1509–1519 (2014)
34. Li, H. et al. High multiplicity infection by HIV-1 in men who have sex with men. PLoS Pathog. 6, e1000890 (2010)
35. Romero-Severson, E. O. et al. Donor–recipient identification in para- and poly-phyletic trees under alternative HIV-1 transmission hypotheses using approximate Bayesian computation. Genetics 207, 1089–1101 (2017)
36. Aldovini, A. & Young, R. A. Mutations of RNA and protein sequences involved in human immunodeficiency virus type 1 packaging result in production of noninfectious virus. J. Virol. 64, 1920–1926 (1990)
37. Rusert, P. et al. Quantification of infectious HIV-1 plasma viral load using a boosted in vitro infection protocol. Virology 326, 113–129 (2004)
38. Ronquist, F. & Huelsenbeck, J. P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572–1574 (2003)
39. Foley, B. et al. HIV Sequence Compendium 2015 (Los Alamos National Laboratory, 2015)
40. Leitner, T., Kumar, S., & Albert, J. Tempo and mode of nucleotide substitutions in gag and env gene fragments in human immunodeficiency virus type 1 populations with a known transmission history. J. Virol. 71, 4761–4770 (1997); erratum 72, 2565 (1998)
41. Leitner, T., Korber, B. T., Daniels, M., Calef, C. & Foley, B. in HIV Sequence Compendium 2005 (eds Leitner, T. et al.) 41–48 (Theoretical Biology and Biophysics, Los Alamos National Laboratory, 2005)
42. Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013)