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

Abstract

The crucial role of recombination in HIV-1 biology is being increasingly recognized. In vitro studies have shown that up to 30 strand-transfer events may occur per viral replication cycle. Thus, recombination may surpass mutation as a major mechanism driving HIV-1 evolution. Currently, recombinant strains comprise 37% of the full-genome HIV-1 sequence database, including sequences representing 47 Circulating Recombinant Forms (CRFs) and more than 250 different Unique Recombinant Forms (URFs). Mapping of recombination breakpoints helps establish relationships among strains that are related by descent, such as CRF07_BC and CRF08_BC in China, and sheds light on their origin and epidemic spread. Additionally, unrelated recombinants sharing common breakpoints may reflect recombination hotspots within the viral genome. Here we present a software tool, RecDraw, for the graphical representation and efficient comparison of recombinant HIV-1 structures and breakpoints. RecDraw is a platform-flexible, Java stand-alone application available through http://www.hivresearch.org/research.php?ServiceID = 5&SubServiceID = 6 .

FIG. 1.

Genomic structure of 70 HIV-1 inter-subtype recombinants sampled in Southeast Asia, China, and India, represented using RecDraw. Full-genome sequences were retrieved from the Los Alamos HIV database and recombination breakpoints were mapped using jpHMM. The vertical line highlights HXB2 position 6332, and strains sharing a common CRF01_AE ->subtype B recombination breakpoint are indicated by black arrows. See text for details.

FIG. 2.

Extended network of inter-subtype recombinant HIV strains in Southeast Asia, China, and India. 01B, BC, 01C, and 01BC inter-subtype recombinants are represented as red, blue, gray, and green nodes, respectively. Lines connecting the nodes link strains that share common recombination breakpoints, allowing for 27 bp of mapping imprecision (i.e., the average distance between the jpHMM-predicted and previously published breakpoints, as determined by Schultz et al.). The network diagram was built using UCINET version 6.275/ NetDraw version 2.091 (Analytic Technologies, Lexington, KY). Strains are grouped by country of sampling. Depicted strains include: 1: ID.AB547463, 2: ID.AB547464, 3: 01B.MM.1999.mCSW104, 4: 01B.MY.2003.03MYKL018_1, 5: 01B.MY.2004.04MYKL016_1, 6: 01B.MY.2004.04MYKL019_1, 7: 01B.MY.2005.05MYKL043_1, 8: 01B.MY.2006.06MMYKLD46, 9: 01B.MY.2007.07MYKLD47, 10: 01B.MY.2007.07MYKLD48, 11: 01B.MY.2007.07MYKLD49, 12: 01B.TH.1269 12_69 AF490973, 13: 01B.TH.CM237, 14: 01B.TH.MU2003, 15: 01B.TH.NP1623, 16: 01B.TH.TH1326 AY082968, 17: 01B.TH.TH283, 18: 01B.TH.TH9_95 AF490974, 19: 01B.TH.1996.M005, 20: 01B.TH.1996.M043, 21: 01B.TH.1996.M171, 22: 01B.TH.1999.OUR2574, 23: 01B.TH.2000.00TH_C2254_BE, 24: 01B.TH.2000.00TH_R1741, 25: 01B.TH.2001.OUR033I, 26: 01B.TH.2002.OUR740I, 27: 01B.TH.2002.OUR840I, 28: 01B.TH.2002.OUR846I, 29: 01B.TH.2002.OUR847I, 30: 15_01B.TH.1996.M169, 31: 15_01B.TH.1999.99TH_MU2079, 32: 15_01B.TH.1999.99TH_R2399, 33: 15_01B.TH.2002.02TH_OUR1331, 34: 15_01B.TH.2002.02TH_OUR1332, 35: 33_01B.MY.2005.05MYKL007_1, 36: 33_01B.MY.2005.05MYKL015_2, 37: 33_01B.MY.2005.05MYKL031_1, 38: 33_01B.MY.2005.05MYKL045_1, 39: 34_01B.TH.1999.OUR1969P, 40: 34_01B.TH.1999.OUR2275P, 41: 34_01B.TH.1999.OUR2478P, 42: 07_BC.CN.CNGL179, 43: 07_BC.CN.1997.97CN001 C54, 44: 07_BC.CN.1998.98CN009, 45: 07_BC.CN.2005.pXJDC6441-2, 46: 07_BC.CN.2005.XJDC6431_2, 47: 07_BC.CN.2005.XJDC6441, 48: 07_BC.CN.2005.XJN0084, 49: 07_BC.TW.2004.TW_D3, 50: 0708.CN.2000.HH069, 51: 0708.CN.2000.HH086, 52: 07B.TW.2004.TW_D60, 53: 08_BC.CN.patent seq, 54: 08_BC.CN.1997.97CNGX_6F, 55: 08_BC.CN.1997.97CNGX_7F, 56: 08_BC.CN.1997.97CNGX_9F, 57: 08_BC.CN.1998.98CN006, 58: BC.CN.1996.YNRL9607, 59: BC.CN.1996.YNRL9613, 60: BC.CN.1996.YNRL9618, 61: BC.IN.1999.NARI10-1, 62: BC.IN.2002.INDNARI_0218440, 63: BC.IN.2002.NARI7-1, 64: BC.IN.2002.NARI9-1, 65: BC.MM.1999.mIDU103, 66: BC.MM.1999.mIDU106, 67: 01C.TH.NP1809, 68: 01B.MM.2000.mIDU502, 69: 01BC.MM.1999.mIDU107, 70: 01BC.MM.2000.mCSW503. See text for details.