Identification of a Novel Second-Generation Circulating Recombinant Form (CRF48_01B) in Malaysia: A Descendant of the Previously Identified CRF33_01B

Ou, 1993, Independent introduction of two major HIV-1 genotypes into distinct high-risk populations in Thailand., Lancet, 341, 1171, 10.1016/0140-6736(93)91001-3

Kalish, 1995, The evolving molecular epidemiology of HIV-1 envelope subtypes in injecting drug users in Bangkok, Thailand: implications for HIV vaccine trials., AIDS, 9, 851, 10.1097/00002030-199508000-00004

Tovanabutra, 2001, First CRF01_AE/AE/B recombinant of HIV-1 is found in Thailand., AIDS, 15, 1063, 10.1097/00002030-200105250-00018

Kijak, 2004, Lost in translation: implications of HIV-1 codon usage for immune escape and drug resistance., AIDS Rev, 6, 54

Matsuoka-Aizawa, 2003, Isolation and molecular characterization of a nelfinavir (NFV)-resistant human immunodeficiency virus type 1 that exhibits NFV-dependent enhancement of replication., J Virol, 77, 318, 10.1128/JVI.77.1.318-327.2003

Tee, 2006, Identification of a novel circulating recombinant form (CRF33_01B) dissemi01B) disseminating widely among various risk populations in Kuala Lumpur, Malaysia., J Acquir Immune Defic Syndr, 43, 523, 10.1097/01.qai.0000242451.74779.a7

Tovanabutra, 2003, A new circulating recombinant form, CRF15_01B, reinforces the linkage between IDU and heterosexual epidemics in Thailand., AIDS Res Hum Retroviruses, 19, 561, 10.1089/088922203322230923

Tee, 2005, Emergence of HIV-1 CRF01_AE/B unAE/B unique recombinant forms in Kuala Lumpur, Malaysia., AIDS, 19, 119, 10.1097/00002030-200501280-00003

Reid, 2007, Malaysia and harm reduction: the challenges and responses., Int J Drug Policy, 18, 136, 10.1016/j.drugpo.2006.12.015

Wang, 2007, Complex patterns of the HIV-1 epidemic in Kuala Lumpur, Malaysia: evidence for expansion of circulating recombinant form CRF33_01B a01B and detection of multiple other recombinants., Virology, 367, 288, 10.1016/j.virol.2007.05.033

Korber, 2000, Timing the ancestor of the HIV-1 pandemic strains., Science, 288, 1789, 10.1126/science.288.5472.1789

Rambaut, 2004, The causes and consequences of HIV evolution., Nat Rev Genet, 5, 52, 10.1038/nrg1246

Lemey, 2006, HIV evolutionary dynamics within and among hosts., AIDS Rev, 8, 125

Pybus, 2009, Evolutionary analysis of the dynamics of viral infectious disease., Nat Rev Genet, 10, 540, 10.1038/nrg2583

Drummond, 2005, Bayesian coalescent inference of past population dynamics from molecular sequences., Mol Biol Evol, 22, 1185, 10.1093/molbev/msi103

Drummond, 2007, BEAST: Bayesian evolutionary analysis by sampling trees., BMC Evol Biol, 7, 214, 10.1186/1471-2148-7-214

Kato, 1999, Role of naturally occurring basic amino acid substitutions in the human immunodeficiency virus type 1 subtype E envelope V3 loop on viral coreceptor usage and cell tropism., J Virol, 73, 5520, 10.1128/JVI.73.7.5520-5526.1999

Salminen, 1995, Recovery of virtually full-length HIV-1 provirus of diverse subtypes from primary virus cultures using the polymerase chain reaction., Virology, 213, 80, 10.1006/viro.1995.1548

1997, Thompson, JD, Gibson, TJ, Plewniak, F, et al. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools., Nucleic Acids Res, 25, 4876, 10.1093/nar/25.24.4876

Saitou, 1987, The neighbor-joining method: a new method for reconstructing phylogenetic trees., Mol Biol Evol, 4, 406

Kimura, 1980, A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences., J Mol Evol, 16, 111, 10.1007/BF01731581

Felsenstein, 1985, Confidence limits on phylogenies: an approach using the bootstrap., Evolution, 39, 783, 10.1111/j.1558-5646.1985.tb00420.x

Tamura, 2007, MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0., Mol Biol Evol, 24, 1596, 10.1093/molbev/msm092

Lole, 1999, Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination., J Virol, 73, 152, 10.1128/JVI.73.1.152-160.1999

Carr, 1996, Full-length sequence and mosaic structure of a human immunodeficiency virus type 1 isolate from Thailand., J Virol, 70, 5935, 10.1128/JVI.70.9.5935-5943.1996

Pybus, 2003, The epidemiology and iatrogenic transmission of hepatitis C virus in Egypt: a Bayesian coalescent approach., Mol Biol Evol, 20, 381, 10.1093/molbev/msg043

Drummond, 2002, Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data., Genetics, 161, 1307, 10.1093/genetics/161.3.1307

Hasegawa, 1985, Dating of the human-ape splitting by a molecular clock of mitochondrial DNA., J Mol Evol, 22, 160, 10.1007/BF02101694

Rodriguez, 1990, The general stochastic model of nucleotide substitution., J Theor Biol, 142, 485, 10.1016/S0022-5193(05)80104-3

Yang, 1994, Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods., J Mol Evol, 39, 306, 10.1007/BF00160154

Drummond, 2006, Relaxed phylogenetics and dating with confidence., PLoS Biol, 4, e88, 10.1371/journal.pbio.0040088

Robertson, 2000, HIV-1 nomenclature proposal., Science, 288, 55, 10.1126/science.288.5463.55d

Weniger, 1994, The molecular epidemiology of HIV in Asia., AIDS, 8, S13

Abecasis, 2007, Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: subtype G is a circulating recombinant form., J Virol, 81, 8543, 10.1128/JVI.00463-07

Mamadou, 2003, Emergence of complex and diverse CRF02-AG/CRF06-cpx recombinant HIV type 1 strains in Niger, West Africa., AIDS Res Hum Retroviruses, 19, 77, 10.1089/08892220360474005

Adojaan, 2005, Predominance of a rare type of HIV-1 in Estonia., J Acquir Immune Defic Syndr, 39, 598

Lau, 2007, Near full-length sequence analysis of a Unique CRF01_AEAE/B recombinant from Kuala Lumpur, Malaysia., AIDS Res Hum Retroviruses, 23, 1139, 10.1089/aid.2007.0056