Hepatitis C Virus Phylogenetic Clustering Is Associated with the Social-Injecting Network in a Cohort of People Who Inject Drugs

PLoS ONE

Volumn 7, Issue 10, 2012, Pages

  Sacks Davis, Rachel ^a,b   Daraganova, Galina ^c   Aitken, Campbell ^a,b   Higgs, Peter ^a,b,d   Tracy, Lilly ^e   Bowden, Scott ^e   Jenkinson, Rebecca ^a   Rolls, David ^c   Pattison, Philippa ^c   Robins, Garry ^c   Grebely, Jason ^d   Barry, Alyssa ^c,f   Hellard, Margaret ^a,b  

^a BURNET INSTITUTE   (Australia)

^b MONASH UNIVERSITY   (Australia)

^c UNIVERSITY OF MELBOURNE   (Australia)

^d UNIVERSITY OF NEW SOUTH WALES   (Australia)

^e VICTORIAN INFECTIOUS DISEASES REFERENCE LABORATORY   (Australia)

^f WALTER AND ELIZA HALL INSTITUTE OF MEDICAL RESEARCH   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS DNA; VIRUS RNA;

ADOLESCENT; ADULT; ARTICLE; AUSTRALIA; BLOOD ANALYSIS; BOOTSTRAPPING; COHORT ANALYSIS; DISEASE ASSOCIATION; FEMALE; GENE CLUSTER; GENETIC ASSOCIATION; GENOTYPE; HEALTH SURVEY; HEPATITIS B; HEPATITIS C; HEPATITIS C VIRUS; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; INTRAVENOUS DRUG ABUSE; LONGITUDINAL STUDY; MAJOR CLINICAL STUDY; MALE; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENY; SEQUENCE ANALYSIS; SEROCONVERSION; SOCIAL NETWORK; VIRUS CORE; VIRUS ISOLATION; VIRUS LOAD; VIRUS TRANSMISSION; CLASSIFICATION; DISEASE TRANSMISSION; GENETICS; RISK FACTOR; SUBSTANCE ABUSE; VIROLOGY; YOUNG ADULT;

HEPATITIS C VIRUS;

ADULT; FEMALE; GENOTYPE; HEPACIVIRUS; HEPATITIS C; HUMANS; MALE; PHYLOGENY; RISK FACTORS; SUBSTANCE ABUSE, INTRAVENOUS; YOUNG ADULT;

EID: 84868099766     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0047335     Document Type: Article

References (43)

1. World Health Organization (1999) Global surveillance and control of hepatitis C. J Viral Hepat 6: 35-47.
2. Seeff LB, (2009) The history of the "natural history" of hepatitis C (1968-2009). Liver Int 29: 89-99.
3. Shepard CW, Finelli L, Alter MJ, (2005) Global epidemiology of hepatitis C virus infection. Lancet Infect Dis 5: 558-567.
4. Nelson PK, Mathers BM, Cowie B, Hagan H, Des Jarlais D, et al. (2011) Global epidemiology of hepatitis B and hepatitis C in people who inject drugs: results of systematic reviews. Lancet 378: 571-583.
5. Aceijas C, Rhodes T, (2007) Global estimates of prevalence of HCV infection among injecting drug users. International Journal of Drug Policy 18: 352-358.
6. Friedman S, Aral S, (2001) Social networks, risk-potential networks, health, and disease. J Urban Health 78: 411-417.
7. De P, Cox J, Boivin J-F, Platt RW, Jolly AM, (2007) The importance of social networks in their association to drug equipment sharing among injection drug users: a review. Addiction 102: 1730-1739.
8. Aitken CK, Lewis JA, Hocking JS, Bowden DS, Hellard ME, (2009) Does Information about IDUs' Injecting Networks Predict Exposure to the Hepatitis C Virus? Hepat Mon 9: 17-32.
9. Latkin C, Yang C, Srikrishnan A, Solomon S, Mehta S, et al. (2011) The relationship between social network factors, HIV, and Hepatitis C among injection drug users in Chennai, India. Drug Alcohol Depend 117: 50-54.
10. Wylie JL, Shah L, Jolly A, (2007) Incorporating geographic settings into a social network analysis of injection drug use and bloodborne pathogen prevalence. Health & Place 13: 617-628.
11. Wylie J, Shah L, Jolly A, (2006) Demographic, risk behaviour and personal network variables associated with prevalent hepatitis C, hepatitis B, and HIV infection in injection drug users in Winnipeg, Canada. BMC Public Health 6: 229.
12. Stumpf MPH, Pybus OG, (2002) Genetic diversity and models of viral evolution for the hepatitis C virus. FEMS Microbiol Lett 214: 143-152.
13. Aitken CK, Lewis J, Tracy SL, Spelman T, Bowden DS, et al. (2008) High incidence of hepatitis C virus reinfection in a cohort of injecting drug users. Hepatology 48: 1746-1752.
14. Miller ER, Hellard ME, Bowden S, Bharadwaj M, Aitken CK, (2009) Markers and risk factors for HCV, HBV and HIV in a network of injecting drug users in Melbourne, Australia. J Infect 58: 375-382.
15. Aitken CK, McCaw RF, Bowden DS, Tracy SL, Kelsall JG, et al. (2004) Molecular epidemiology of hepatitis C virus in a social network of injection drug users. Journal of Infectious Diseases 190: 1586-1595.
16. Brewer DD, Hagan H, Sullivan DG, Muth SQ, Hough ES, et al. (2006) Social structural and behavioral underpinnings of hyperendemic hepatitis C virus transmission in drug injectors. Journal of Infectious Diseases 194: 764-772.
17. Pilon R, Leonard L, Kim J, Vallee D, De Rubeis E, et al. (2011) Transmission Patterns of HIV and Hepatitis C Virus among Networks of People Who Inject Drugs. PLoS One 6: e22245.
18. Romano CM, de Carvalho-Mello IMVG, Jamal LF, de Melo FL, Iamarino A, et al. (2010) Social Networks Shape the Transmission Dynamics of Hepatitis C Virus. PLoS One 5: e11170.
19. McCaw R, Moaven L, Locarnini SA, Bowden DS, (1997) Hepatitis C virus genotypes in Australia. J Viral Hepat 4: 351-357.
20. Kuiken C, Combet C, Bukh J, Shin-I T, Deleage G, et al. (2006) A comprehensive system for consistent numbering of HCV sequences, proteins and epitopes. Hepatology 44: 1355-1361.
21. Dev AT, McCaw R, Sundararajan V, Bowden S, Sievert W, (2002) Southeast Asian patients with chronic hepatitis C: the impact of novel genotypes and race on treatment outcome. Hepatology 36: 1259-1265.
22. Higgins D, Thompson J, Gibson T, Thompson JD, Higgins DG, et al. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
23. Tamura K, Dudley J, Nei M, Kumar S, (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24.
24. Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
25. Morgenstern B, Goel S, Sczyrba A, Dress A, (2003) AltAVisT: A WWW tool for comparison of alternative multiple alignments. Bioinformatics 19: 425-426.
26. Saitou N, Nei M, (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425.
27. Felsenstein J, (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39: 783-791.
28. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol Biol Evol 8: 2731-2739.
29. Nei M, Kumar S (2000) Molecular Evolution and Phylogenetics. New York: Oxford University Press.
30. Rolls DA, Daraganova G, Sacks-Davis R, Hellard M, Jenkinson R, et al. (2012) Modelling Hepatitis C transmission over a social network of injecting drug users. J Theor Biol 297: 73-87.
31. Borgatti SP, Everett MG, Freeman LC (2002) Ucinet for Windows: Software for Social Network Analysis. Harvard, MA: Analytic Technologies.
32. Borgatti SP (2002) NetDraw: Graph Visualization Software. Harvard, MA: Analytic Technologies.
33. Pham ST, Bull RA, Bennett JM, Rawlinson WD, Dore GJ, et al. (2010) Frequent multiple hepatitis C virus infections among injection drug users in a prison setting. Hepatology 52: 1564-1572.
34. Simpson W (2001) The Quadratic Assignment Procedure (QAP). STATA usergroup: 1st North American meeting. Boston, Mass. Available: http://www.stata.com/meeting/1nasug/simpson.pdf. Accessed 2012 Oct 3.
35. Hahn JA, Wylie D, Dill J, Sanchez MS, Lloyd-Smith JO, et al. (2009) Potential impact of vaccination on the hepatitis C virus epidemic in injection drug users. Epidemics 1: 47-57.
36. Volz E, Meyers LA, (2007) Susceptible-infected-recovered epidemics in dynamic contact networks. Proceedings of the Royal Society B: Biological Sciences 274: 2925-2934.
37. Jurgens R, Nowak M, Day M, (2011) HIV and incarceration: prisons and detention. Journal of the International AIDS Society 14: 26.
38. Pollini RA, Alvelais J, Gallardo M, Vera A, Lozada R, et al. (2009) The harm inside: Injection during incarceration among male injection drug users in Tijuana, Mexico. Drug Alcohol Depend 103: 52-58.
39. Wood E, Li K, Small W, Montaner JS, Schechter MT, et al. (2005) Recent Incarceration Independently Associated with Syringe Sharing by Injection Drug Users. Public Health Rep 120: 150-156.
40. Hennekens CH, Buring JE (1987) Epidemiology in Medicine; Mayrent SL, editor. Philadelphia: Lippincott Williams & Wilkins.
41. Bernard EJ, Azad Y, Vandamme AM, Weait M, Geretti AM, (2007) 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.
42. Smith DB, Simmonds P, (1997) Review: Molecular epidemiology of hepatitis C virus. J Gastroenterol Hepatol 12: 522-527.
43. Valente T, Vlahov D, (2001) Selective risk taking among needle exchange participants: implications for supplemental interventions. Am J Public Health 91: 406-411.