RecDraw: A software package for the representation of HIV-1 recombinant structures

AIDS Research and Human Retroviruses

Volumn 26, Issue 12, 2010, Pages 1317-1321

  Kijak, Gustavo H ^a,b   Tovanabutra, Sodsai ^a,b   Beyrer, Chris ^c   Sanders Buell, Eric E ^a,b   Arroyo, Miguel A ^a,d   Robb, Merlin L ^a,b   Michael, Nelson L ^a,d   McCutchan, Francine E ^a,b   Kim, Jerome H ^a,d  

^a US Military HIV Research Program   (United States)

^b HENRY M JACKSON FOUNDATION FOR THE ADVANCEMENT OF MILITARY MEDICINE   (United States)

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

^d WALTER REED ARMY INSTITUTE OF RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHINA; COMPUTER PROGRAM; HUMAN IMMUNODEFICIENCY VIRUS 1; INDIA; INTERNET; NONHUMAN; PRIORITY JOURNAL; RNA RECOMBINATION; SOUTHEAST ASIA; VIRUS GENOME; VIRUS RECOMBINANT; VIRUS STRAIN;

CHINA; EVOLUTION, MOLECULAR; HIV INFECTIONS; HIV-1; HUMANS; MOLECULAR EPIDEMIOLOGY; RECOMBINATION, GENETIC; SOFTWARE; VIROLOGY;

EID: 78650272143     PISSN: 08892229     EISSN: None     Source Type: Journal    
DOI: 10.1089/aid.2010.0127     Document Type: Article

References (20)

1. Kijak GH and McCutchan FE: HIV diversity, molecular ep-idemiology, and the role of recombination. Curr Infect Dis Rep 2005;7:480-488.
2. Mansky LM and Temin HM: Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase. J Virol 1995;69:5087-5094.
3. Felsenstein J and Yokoyama S: The evolutionary advantage of recombination. II. Individual selection for recombination. Genetics 1976;83:845-859.
4. Jung A, Maier R, Vartanian JP, et al.: Recombination: Mul-tiply infected spleen cells in HIV patients. Nature 2002; 418:144.
5. Hu WS and Temin HM. Retroviral recombination and re-verse transcription. Science 1990;250:1227-1233.
6. McCutchan FE, Hoelscher M, Tovanabutra S, et al.: In-depth analysis of a heterosexually acquired human immunodefi-ciency virus type 1 superinfection: Evolution, temporal fluctuation, and intercompartment dynamics from the seronegative window period through 30 months postinfec-tion. J Virol 2005;79:11693-11704.
7. Fan J, Negroni M, and Robertson DL: The distribution of HIV-1 recombination breakpoints. Infect Genet Evol 2007;7:717-723.
8. Keele BF, Giorgi EE, Salazar-Gonzalez JF, et al.: Identifica-tion and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. Proc Natl Acad Sci USA 2008;105:7552-7557.
9. McCutchan FE, Carr JK, Murphy D, et al.: Precise mapping of recombination breakpoints suggests a common parent of two BC recombinant HIV type 1 strains circulating in China. AIDS Res Hum Retroviruses 2002;18:1135-1140.
10. Lole KS, Bollinger RC, Paranjape RS, et al.: Full-length human immunodeficiency virus type 1 genomes from sub-type C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol 1999;73:152-160.
11. Schultz AK, Zhang M, Bulla I, et al.: jpHMM: Improving the reliability of recombination prediction in HIV-1. Nucleic Acids Res 2009;37(Web Server issue):W647-651.
12. Salminen MO, Carr JK, Burke DS, and McCutchan FE: Identification of breakpoints in intergenotypic recombinants of HIV type 1 by bootscanning. AIDS Res Hum Retroviruses 1995;11:1423-1425.
13. De Oliveira T, Deforche K, Cassol S, et al.: An automated genotyping system for analysis of HIV-1 and other microbial sequences. Bioinformatics 2005;21:3797-3800.
14. DeNooy W, Mrvar A, and Batagelj V: Exploratory Social Net-work Analysis with Pajek. Cambridge, United Kingdom, 2005.
15. Tovanabutra S, Sanders EJ, Graham SM, et al.: Evaluation of HIV type 1 strains in men having sex with men and in fe-male sex workers in Mombasa, Kenya. AIDS Res Hum Retroviruses 2010;26:123-131.
16. Tovanabutra S, Polonis V, De Souza M, et al.: First CRF01-AE/B recombinant of HIV-1 is found in Thailand. AIDS 2001;15:1063-1065.
17. Tovanabutra S, Kijak GH, Beyrer C, et al.: Identification of CRF34-01B, a second circulating recombinant form unre-lated to and more complex than CRF15-01B, among inject-ing drug users in northern Thailand. AIDS Res Hum Retroviruses 2007;23:829-833.
18. Kijak GH, Tovanabutra S, Sanders-Buell E, et al.: Distin-guishing molecular forms of HIV-1 in Asia with a high-throughput, fluorescent genotyping assay, MHAbce v.2. Virology 2007;358:178-191.
19. Tee KK, Li XJ, Nohtomi K, Ng KP, Kamarulzaman A, and Takebe Y: Identification of a novel circulating recombinant form (CRF33-01B) disseminating widely among various risk populations in Kuala Lumpur, Malaysia. J Acquir Immune Defic Syndr 2006;43:523-529.
20. Takebe Y, Motomura K, Tatsumi M, Lwin HH, Zaw M, and Kusagawa S: High prevalence of diverse forms of HIV-1 intersubtype recombinants in Central Myanmar: Geo-graphical hot spot of extensive recombination. AIDS 2003;17:2077-2087.