Detectable signals of episodic risk effects on acute HIV transmission: Strategies for analyzing transmission systems using genetic data

Epidemics

Volumn 5, Issue 1, 2013, Pages 44-55

  Alam, Shah Jamal ^a   Zhang, Xinyu ^a   Romero Severson, Ethan Obie ^a   Henry, Christopher ^a   Zhong, Lin ^a   Volz, Erik M ^a   Brenner, Bluma G ^b   Koopman, James S ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

^b MCGILL UNIVERSITY   (Canada)

Author keywords

Acute infection clusters; Episodic risk; Identifiability; Individual based model

Indexed keywords

ARTICLE; EPIDEMIC; GENE CLUSTER; GENETIC DATABASE; HIGH RISK BEHAVIOR; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; MALE HOMOSEXUAL; PHYLOGENY; PRIORITY JOURNAL; RISK FACTOR; SEXUAL BEHAVIOR; VIRUS TRANSMISSION;

ACUTE DISEASE; ADULT; CANADA; CLUSTER ANALYSIS; COMPUTER SIMULATION; GENETIC VARIATION; HIV INFECTIONS; HOMOSEXUALITY, MALE; HUMANS; MALE; MODELS, GENETIC; POPULATION SURVEILLANCE; PREVALENCE; RISK; SEXUAL BEHAVIOR; SEXUAL PARTNERS; STOCHASTIC PROCESSES; UNITED STATES;

EID: 84873447619     PISSN: 17554365     EISSN: 18780067     Source Type: Journal    
DOI: 10.1016/j.epidem.2012.11.003     Document Type: Article

References (43)

1. Anderson R.M., May R.M. Infectious Diseases of Humans: Dynamics and Control 1991, Oxford University Press, USA.
2. Alam S.J., Romero-Severson E., Kim J.-H., Emond G., Koopman J.S. Dynamic sex roles among men who have sex with men and transmissions from primary HIV infection. Epidemiology 2010, 21:669-675.
3. Baek S.K., Bernhardsson S., Minnhagen P. Zipf's law unzipped. Journal of Physics 2007, 13. 10.1088/1367-2630/13/4/043004.
4. Blount J.H. A new approach for gonorrhea epidemiology. American Journal of Public Health 1972, 62:710-712.
5. Brenner B.G., Moodie E.M. HIV sexual networks: the Montreal experience. Statistical Communications in Infectious Diseases 2012, 4. 10.1515/1948-4690.1039.
6. Brenner B.G., Roger M., Routy J.P., et al. High rates of forward transmission events after acute/early HIV-1 infection. Journal of Infectious Diseases 2007, 195.
7. Brenner B.G., Roger M., Stephens D., Moisi D., Hardy I., Weinberg J., Turgel R., Charest H., Koopman J.S., Wainberg M.A. Transmission clustering drives the onward spread of the male-sex-male (MSM) epidemic in Quebec. Journal of Infectious Diseases 2011, 83:751-759.
8. Danon L., Ford A.P., House T., Jewell C.P., Keeling M.J., Roberts G.O., Ross J.V., Vernon M.C. Networks and the epidemiology of infectious disease. Interdisciplinary Perspectives on Infectious Diseases 2011, 10.1155/2011/284909.
9. Grassly N.C., Fraser C. Mathematical models of infectious disease transmission. Nature Reviews Microbiology 2008, 6:477-487.
10. Graw F., Leitner T., Ribeiro R.M. Agent-based and phylogenetic analyses reveal how HIV-1 moves between risk groups: injecting drug users sustain the heterosexual epidemic in Latvia. Epidemics 2012, 4:104-116.
11. Goodreau S.M., Golden M.R. Biological and demographic causes of high HIV and sexually transmitted disease prevalence in men who have sex with men. Sexually Transmitted Infections 2007, 83:458-462.
12. Hall H.I., Song R., Rhodes P., Prejean J., An Q., Lee L.M., Karon J., Brookmeyer R., Kaplan E.H., McKenna M.T., Janssen R.S., et al. Estimation of HIV incidence in the United States. JAMA: The Journal of the American Medical Association 2008, 300.
13. Hughes G.J., Fearnhill E., Dunn D., Lycett S., Rambaut A., Leigh Brown A.J. Molecular phylodynamics of the heterosexual HIV epidemic in the United Kingdom. PLoS Pathogens 2009, 5. 10.1371/journal.ppat.1000590.
14. Jacquez J.A., Koopman J.S., Simon C.P., Longini I.M. Role of the primary infection in epidemics of HIV infection in gay cohorts. Journal of Acquired Immune Deficiency Syndromes 1994, 7:1169-1184.
15. Jacquez J.A. Numerical parameter identifiability and estimability: integrating identifiability. Estimability and optimal sampling design. Mathematical Biosciences 1985, 77:201-227.
16. Kim J.-H., Riolo R.L., Koopman J.S. HIV transmission by stage of infection and pattern of sexual partnerships. Epidemiology 2010, 21:676-684.
17. Koopman J.S. Infection transmission science and models. Japanese Journal of Infectious Diseases 2005, 58:S3-S8.
18. Koopman J.S., Jacquez J.A., Welch G.W., Simon C.P., Foxman B., Pollock S.M., Barth-Jones D., dams A.L., Lange K. The role of early HIV infection in the spread of HIV through populations. Journal of Acquired Immune Deficiency Syndromes and Human Retrovirology 1997, 14:249-258.
19. Koopman J.S., Simon C.P., Riolo C.P. When to control endemic infections by focusing on high-risk groups. Epidemiology 2005, 16:621-627.
20. Leigh Brown A.J., Lycett S., Weinert L., Hughes G.L., Fearnill E., Dunn D.T. Transmission network parameters estimated from HIV sequences for a nationwide epidemic. Journal of Infectious Diseases 2011, 204:1463-1469.
21. Leventhal G.E., Kouyos R., Stadler T., von Wyl V., Yerly S., et al. Inferring epidemic contact structure from phylogenetic trees. PLoS Computational Biology 2012, 8:e1002413. 10.1371/journal.pcbi.1002413.
22. Lewis F., Hughes G.J., Rambaut A., Pozniak A., Leigh Brown A.J. Episodic sexual transmission of HIV revealed by molecular phylodynamics. PLoS Medicine 2008, 5. 10.1371/journal.pmed.0050050.
23. Murray M. Determinants of cluster distribution in the molecular epidemiology of tuberculosis. Proceedings of National Academy of Science 2002, 99:1538-1543.
24. O'Dea E.B., Wilke C.O. Contact heterogeneity and phylodynamics: how contact networks shape parasite evolutionary trees. Interdisciplinary Perspectives on Infectious Diseases 2011, 10.1155/2011/238743.
25. Pilcher C.D., Joaki G., Hoffman I.F., Martinson F.E., Mapanje C., Stewart P.W., Powers K.A., Galvin S., Chilongozi D., Gama S., Price M.A., Fiscus S.A., Cohen M.S. Amplified transmission of HIV-1: comparison of HIV-1 concentrations in semen and blood during acute and chronic infection. AIDS 2007, 21:1723-1730.
26. Potterat J.J., Rothenberg R. The case-finding effectiveness of self-referral system for gonorrhea: a preliminary report. American Journal of Public Health 1977, 67:174-176.
27. Powers K.A., Ghani A.C., Miller W.C., Hoffman I.F., Pettifor A.E., Kamanga G., Martinson F., Cohen M.S. The role of acute and early HIV infection in the spread of HIV and implications for transmission prevention strategies in Lilongwe, Malawi: a modelling study. The Lancet 2011, 378:256-268.
28. Prejean J., Song R., Hernandez A., Ziebell R., Green T., Walker F., Lin L.S., An Q., Mermin J., Lansky A., Hall H.I., et al. Estimated HIV incidence in the United States, 2006-2009. PLoS One 2011, 6. 10.1371/journal.pone.0017502.
29. Prosperi M.C.F., Ciccozzi M., Fanti L., et al. A novel methodology for large-scale phylogeny partition. Nature Communications 2011, 2. 10.1038/ncomms1325.
30. Rocha L.E.C., Liljeros F., Holme P. Simulated epidemics in an empirical spatiotemporal network of 50,185 sexual contacts. PLoS Computational Biology 2011, 7(3).
31. Romero-Severson E.O., Alam S.J., Volz E., Koopman J.S. Heterogeneity in number and type of sexual contacts in a gay urban cohort. Statistical Communications in Infectious Diseases 2012, 4. 10.1515/1948-4690.1042.
32. Simon H.A. On a class of skew distribution functions. Biometrika 1955, 42:425-440.
33. Vittinghoff E., Douglas J., Judson F., McKirnan D., Macqueen K., Buchbinder S.R. Per-contact risk of human immunodeficiency virus transmission between male sexual partners. American Journal of Epidemiology 1999, 150:306-311.
34. Volz E.M. Complex population dynamics and the coalescent under neutrality. Genetics 2012, 190:187-201.
35. Volz E.M., Kosakovsky Pond S.L., Ward M.J., Leigh Brown A.J., Frost S.D.W. Phylodynamics of infectious disease epidemics. Genetics 2009, 183:1421-1430.
36. Volz E.M., Frost S.D.W., Rothenberg R., Meyers L.A. Epidemiological bridging by injection drug use drives an early HIV epidemic. Epidemics 2010, 2:155-164.
37. Volz E.M., Koopman J.S., Ward M.J., Leigh Brown A., Frost S.D.W. Simple epidemiological dynamics explain phylogenetic clustering of HIV from patients with recent infection. PLoS Computational Biology 2012, 8. 10.1371/journal.pcbi.1002552.
38. Wagner B.G., Garcia-Lerma J.G., Blower S. Factors limiting the transmissions of HIV mutations conferring drug resistance: fitness cost and genetic bottlenecks. Scientific Reports 2012, 10.1038/srep00320.
39. Wainberg M. Drugs that prevent HIV infection. Nature 2011, 469.
40. Wawer M.J., Gray R.H., Sewankambo N.K., Serwadda D., Li X., Laeyendecker O., Kiwanuka N., Kigozi G., Kiddugavu M., Lutalo T., Nalugoda F., Wabwire-Mangen F., Meehan M.P., Quinn T.C. Rates of HIV-1 transmission per coital act, by stage of HIV-1 infection, in Uganda. Journal of Infectious Diseases 2005, 191:1403-1409.
41. Welch D. Is network clustering detectable in transmission trees?. Viruses 2011, 3:659-676.
42. Welch D., Bansal S., Hunter D.R. Statistical inference to advance network models in epidemiology. Epidemics 2011, 3:38-45.
43. Zhang X., Zhong L., Romero-Severson E., Alam S.J., Henry C.J., Volz E.M., Koopman J.S. Episodic HIV risk behavior can greatly amplify HIV prevalence and the fraction of transmissions from acute HIV infection. Statistical Communications in Infectious Diseases 2012, 4. 10.1515/1948-4690.1041.