Identification of HIV superinfection in seroconcordant couples in Rakai, Uganda, by use of next-generation deep sequencing

Journal of Clinical Microbiology

Volumn 49, Issue 8, 2011, Pages 2859-2867

  Redd, Andrew D ^a   Collinson Streng, Aleisha ^a   Martens, Craig ^b   Ricklefs, Stacy ^b   Mullis, Caroline E ^c   Manucci, Jordyn ^c   Tobian, Aaron A R ^c   Selig, Ethan J ^b   Laeyendecker, Oliver ^a,c   Sewankambo, Nelson ^d,f   Gray, Ronald H ^e   Serwadda, David ^d,f   Wawer, Maria J ^e   Porcella, Stephen F ^b   Quinn, Thomas C ^a,c  

^a NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES   (United States)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

^c DEPARTMENT OF PATHOLOGY   (United States)

^d RAKAI HEALTH SCIENCES PROGRAM   (Uganda)

^e JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

^f MAKERERE UNIVERSITY   (Uganda)

Author keywords

[No Author keywords available]

Indexed keywords

GAG PROTEIN; GLYCOPROTEIN GP 41;

ARTICLE; CLINICAL ARTICLE; CONSENSUS SEQUENCE; DNA SEQUENCE; FEMALE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; MALE; NEXT GENERATION DEEP SEQUENCING; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; STRAIN IDENTIFICATION; SUPERINFECTION; UGANDA; UNINDEXED SEQUENCE; VIRUS CAPSID; VIRUS ENVELOPE; VIRUS GENOME; VIRUS STRAIN;

ADOLESCENT; ADULT; COHORT STUDIES; FAMILY CHARACTERISTICS; FEMALE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HIV; HIV CORE PROTEIN P24; HIV ENVELOPE PROTEIN GP41; HIV INFECTIONS; HUMANS; MALE; MIDDLE AGED; MOLECULAR SEQUENCE DATA; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA; UGANDA; YOUNG ADULT;

EID: 79960940822     PISSN: 00951137     EISSN: 1098660X     Source Type: Journal    
DOI: 10.1128/JCM.00804-11     Document Type: Article

References (31)

1. Altfeld, M., et al. 2002. HIV-1 superinfection despite broad CD8+ T-cell responses containing replication of the primary virus. Nature 420:434-439. (Pubitemid 35415656)
2. Braibant, M., et al. 2010. Disease progression due to dual infection in an HLA-B57-positive asymptomatic long-term nonprogressor infected with a nef-defective HIV-1 strain. Virology 405:81-92.
3. Chohan, B., L. Lavreys, S. M. Rainwater, and J. Overbaugh. 2005. Evidence for frequent reinfection with human immunodeficiency virus type 1 of a different subtype. J. Virol. 79:10701-10708. (Pubitemid 41098609)
4. Collinson-Streng, A. N., et al. 2009. Geographic HIV type 1 subtype distribution in Rakai District, Uganda. AIDS Res. Hum. Retroviruses 25:1045-1048.
5. Conroy, S. A., et al. 2010. Changes in the distribution of HIV-1 subtypes D and A in Rakai District, Uganda between 1994 and 2002. AIDS Res. Hum. Retroviruses 26:1087-1091.
6. Gonzales, M. J., et al. 2003. Lack of detectable human immunodeficiency virus type 1 superinfection during 1072 person-years of observation. J. Infect. Dis. 188:397-405.
7. Gunthard, H. F., et al. 2009. HIV-1 superinfection in an HIV-2-infected woman with subsequent control of HIV-1 plasma viremia. Clin. Infect. Dis. 48:e117-e120.
8. Herbinger, K. H., et al. 2006. Frequency of HIV type 1 dual infection and HIV diversity: analysis of low- and high-risk populations in Mbeya Region, Tanzania. AIDS Res. Hum. Retroviruses 22:599-606.
9. Jost, S., et al. 2002. A patient with HIV-1 superinfection. N. Engl. J. Med. 347:731-736.
10. Kiwanuka, N., et al. 2009. HIV-1 subtypes and differences in heterosexual transmission of HIV among HIV-1 discordant couples in Rakai, Uganda. AIDS 23:2479-2484.
11. McCutchan, F. E., et al. 2005. In-depth analysis of a heterosexually acquired human immunodeficiency virus type 1 superinfection: evolution, temporal fluctuation, and intercompartment dynamics from the seronegative window period through 30 months postinfection. J. Virol. 79:11693-11704. (Pubitemid 41279288)
12. Pacold, M., et al. 2010. Comparison of methods to detect HIV dual infection. AIDS Res. Hum. Retroviruses 26:1291-1296.
13. Piantadosi, A., B. Chohan, V. Chohan, R. S. McClelland, and J. Overbaugh. 2007. Chronic HIV-1 infection frequently fails to protect against superinfection. PLoS Pathog. 3:e177.
14. Piantadosi, A., M. O. Ngayo, B. Chohan, and J. Overbaugh. 2008. Examination of a second region of the HIV type 1 genome reveals additional cases of superinfection. AIDS Res. Hum. Retroviruses 24:1221.
15. Rachinger, A., et al. 2010. Absence of HIV-1 superinfection 1 year after infection between 1985 and 1997 coincides with a reduction in sexual risk behavior in the seroincident Amsterdam cohort of homosexual men. Clin. Infect. Dis. 50:1309-1315.
16. Rachinger, A., T. D. van de Ven, J. A. Burger, H. Schuitemaker, and A. B. van't Wout. 2010. Evaluation of pre-screening methods for the identification of HIV-1 superinfection. J. Virol. Methods 165:311-317.
17. Ramos, A., et al. 2002. Intersubtype human immunodeficiency virus type 1 superinfection following seroconversion to primary infection in two injection drug users. J. Virol. 76:7444-7452. (Pubitemid 34760966)
18. Roche. 2009. emPCR method manual - Lib-L-MV. Roche, Branford, CT.
19. Rozera, G., et al. 2009. Massively parallel pyrosequencing highlights minority variants in the HIV-1 env quasispecies deriving from lymphomonocyte subpopulations. Retrovirology 6:15.
20. Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
21. Smith, D. M., et al. 2006. Lack of neutralizing antibody response to HIV-1 predisposes to superinfection. Virology 355:1-5. (Pubitemid 44585057)
22. Smith, D. M., et al. 2004. Incidence of HIV superinfection following primary infection. JAMA 292:1177-1178. (Pubitemid 39167405)
23. Smith, D. M., et al. 2005. HIV drug resistance acquired through superinfection. AIDS 19:1251-1256. (Pubitemid 41224893)
24. Streeck, H., et al. 2008. Immune-driven recombination and loss of control after HIV superinfection. J. Exp. Med. 205:1789-1796.
25. Taylor, J. E., and B. T. Korber. 2005. HIV-1 intra-subtype superinfection rates: estimates using a structured coalescent with recombination. Infect. Genet. Evol. 5:85-95.
26. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 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.
27. van der Kuyl, A. C., et al. 2010. Analysis of infectious virus clones from two HIV-1 superinfection cases suggests that the primary strains have lower fitness. Retrovirology 7:60.
28. Wawer, M. J., et al. 1998. A randomized, community trial of intensive sexually transmitted disease control for AIDS prevention, Rakai, Uganda. AIDS. 12:1211-1225. (Pubitemid 28302424)
29. Willerth, S. M., et al. 2010. Development of a low bias method for characterizing viral populations using next generation sequencing technology. PLoS One 5:e13564.
30. Yang, O. O., 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. (Pubitemid 40053869)
31. Zagordi, O., R. Klein, M. Daumer, and N. Beerenwinkel. 2010. Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies. Nucleic Acids Res. 38:7400-7409.