High-accuracy identification of incident HIV-1 infections using a sequence clustering based diversity measure

PLoS ONE

Volumn 9, Issue 6, 2014, Pages

  Xia, Xia Yu ^a   Ge, Meng ^a,c   Hsi, Jenny H ^b   He, Xiang ^b   Ruan, Yu Hua ^b   Wang, Zhi Xin ^a   Shao, Yi Ming ^b   Pan, Xian Ming ^a  

^a TSINGHUA UNIVERSITY   (China)

^b CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION   (China)

^c Chinese Academy of Sciences   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ASSAY; CLIENT SERVER APPLICATION; CLUSTER ANALYSIS; CONTROLLED STUDY; CORRELATION COEFFICIENT; DIAGNOSTIC ACCURACY; DOT MATRIX PAIRWISE ALIGNMENT; GENE SEQUENCE; GENETIC RECOMBINATION; GENETIC VARIABILITY; HUMAN; HUMAN CELL; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; INCIDENCE; INDEL MUTATION; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE CLUSTERING BASED DIVERSITY; VIRUS STRAIN; VIRUS TRANSMISSION; GENETICS; HIV INFECTIONS; SERODIAGNOSIS; SEROTYPE; STATISTICAL MODEL; TRANSMISSION;

AIDS SERODIAGNOSIS; HIV INFECTIONS; HIV-1; HUMANS; INCIDENCE; MODELS, STATISTICAL; SEQUENCE ALIGNMENT; SEROGROUP;

EID: 84903398991     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0100081     Document Type: Article

References (27)

1. Hall HI, Song R, Rhodes P, Prejean J, An Q, et al. (2008) Estimation of HIV incidence in the United States. JAMA 300: 520-529.
2. Guy R, Gold J, Calleja JM, Kim AA, Parekh B, et al. (2009) Accuracy of serological assays for detection of recent infection with HIV and estimation of population incidence: a systematic review. Lancet Infect Dis 9: 747-759.
3. Justman J, El-Sadr WM (2010) AIDS response at a crossroads. Science, 329, 120.
4. Brookmeyer R (2009) Should biomarker estimates of HIV incidence be adjusted? AIDS 23: 485-491.
5. Janssen RS, Satten GA, Stramer SL, Rawal BD, O'Brien TR, et al. (1998) New testing strategy to detect early HIV-1 infection for use in incidence estimates and for clinical and prevention purposes. JAMA 280: 42-48. (Pubitemid 28414995)
6. Parekh BS, Kennedy MS, Dobbs T, Pau CP, Byers R, 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 Retroviruses 18: 295-307. (Pubitemid 34253148)
7. Chawla A, Murphy G, Donnelly C, Booth CL, Johnson M, et al. (2007) Human immunodeficiency virus (HIV) antibody avidity testing to identify recent infection in newly diagnosed HIV type 1 (HIV-1)-seropositive persons infected with diverse HIV-1 subtypes. J Clin Microbiol 45: 415-420.
8. Murphy G, Parry JV (2008) Assays for the detection of recent infections with human immunodeficiency virus type 1. Euro Surveill 13.
9. Karita E, Price M, Hunter E, Chomba E, Allen S, et al. (2007) Investigating the utility of the HIV-1 BED capture enzyme immunoassay using cross-sectional and longitudinal seroconverter specimens from Africa. AIDS 21: 403-408.
10. Hayashida T, Gatanaga H, Tanuma J, Oka S (2008) Effects of low HIV type 1 load and antiretroviral treatment on IgG-capture BED-enzyme immunoassay. AIDS Res Hum Retroviruses 24: 495-498. (Pubitemid 351457743)
11. UNAIDS (2006) UNAIDS Reference Group on estimates, modelling and projections-statement on the use of the BED assay for the estimation of HIV-1 incidence for surveillance or epidemic monitoring. Wkly Epidemiol Rec 81: 40.
12. Incidence Assay Critical Path Working Group (2011) More and better information to tackle HIV epidemics: towards improved HIV incidence assays. PLoS Med 8: e1001045.
13. Shankarappa R, Margolick JB, Gange SJ, Rodrigo AG, Upchurch D, et al. (1999) Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. J Virol 73: 10489-10502.
14. Lee HY, Perelson AS, Park SC, Leitner T (2008) Dynamic correlation between intrahost HIV-1 quasispecies evolution and disease progression. PLoS Comput Biol 4: e1000240.
15. Kouyos RD, von Wyl V, Yerly S, Boni J, Rieder P, et al. (2011) Ambiguous nucleotide calls from population-based sequencing of HIV-1 are a marker for viral diversity and the age of infection. Clin Infect Dis 52: 532-539.
16. Park SY, Love TM, Nelson J, Thurston SW, Perelson AS, et al. (2011) Designing a genome-based HIV incidence assay with high sensitivity and specificity. AIDS 25: F13-19.
17. Yang J, Xia X, He X, Yang S, Ruan Y, et al. (2012) A new pattern-based method for identifying recent HIV-1 infections from the viral env sequence. Sci China Life Sci 55: 328-335.
18. Allam O, Samarani S, Ahmad A (2011) Hammering out HIV-1 incidence with Hamming distance. AIDS, 25, 2047-2048.
19. Li H, Bar KJ, Wang S, Decker JM, Chen Y, et al. (2010) High Multiplicity Infection by HIV-1 in Men Who Have Sex with Men. PLoS Pathog 6: e1000890.
20. Keele BF, Giorgi EE, Salazar-Gonzalez JF, Decker JM, Pham KT, 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. (Pubitemid 351830056)
21. Mansky LM, Temin HM (1995) Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase. J Virol 69: 5087-5094.
22. Fiebig EW, Wright DJ, Rawal BD, Garrett PE, Schumacher RT, et al. (2003) Dynamics of HIV viremia and antibody seroconversion in plasma donors: implications for diagnosis and staging of primary HIV infection. AIDS 17: 1871-1879. (Pubitemid 37070272)
23. Loytynoja A, Goldman N (2008) Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science 320: 1632-1635. (Pubitemid 351931252)
24. Baldi P, Brunak S, Chauvin Y, Andersen CA, Nielsen H (2000) Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics 16: 412-424. (Pubitemid 30487963)
25. Ragonnet-Cronin M, Aris-Brosou S, Joanisse I, Merks H, Vallee D, et al. (2012) Genetic diversity as a marker for timing infection in HIV-infected patients: evaluation of a 6-month window and comparison with BED. J Infect Dis 206: 756-764.
26. Tey J, Ang LW, Tay J, Cutter JL, James L, et al. Determinants of Late-Stage HIV Disease at Diagnosis in Singapore, 1996 to 2009. Ann Acad Med Singapore 41: 194-199.
27. China MOH, UNAIDS WHO (2011) Estimates for the HIV/AIDS epidemic in China. Available: http://www.chinaids.org.cn/n1971/n2151/n777994.files/n777993. pdf.