Recombination in AIDS viruses

Alizon M, Wain-Hobson S, Montagnier L, Sonigo P (1986) Genetic variability of the AIDS virus: nucleotide sequence analysis of two isolates from African patients. Cell 46:63?74

Coffin JM (1979) Structure, replication, and recombination of retrovirus genomes: some unifying hypotheses. J Gen Virol 42:1?26

Coffin JM (1986) Genetic variation in AIDS viruses. Cell 46:1?14

Delassus S, Cheynier R, Wain-Hobson S (1991) Evolution of human immunodeficiency virus type 1 nef and long terminal repeat sequences over 4 years in vivo and in vitro. J Virol 65:225?231

Diaz R, Sabino EC, Mayer A, Mosley JW, Busch MP, The Transfusion Study Group (1994) Evidence of HIV-1 dual infection and recombination in a dually exposed transfusion recipient. J Virol (submitted)

Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783?791

Gao F, Yue L, White AT, Pappas PG, Barchue J, Hanson AP, Greene BM, Sharp PM, Shaw GM, Hahn BH (1992) Human infection by genetically diverse SIVSM-related HIV-2 in West Africa. Nature 358:495?499

Gao F, Yue L, Robertson DL, Hill SC, Hui H, Biggar RJ, Neequaye AE, Whelan TM, Ho DD, Shaw GM, Sharp PM, Hahn BH (1994) Genetic diversity of Human Immunodeficiency Virus type 2: evidence for distinct sequence subtypes with differences in virus biology. J Virol 68:7433?7447

Goodrich DW, Duesberg PH (1990) Retroviral recombination during reverse transcription. Proc Natl Acad Sci USA 87:2052?2056

Grez M, Dietrich U, Balfe P, von Briesen H, Maniar JK, Mahambre G, Delwart EL, Mullins JI, Rubsamen-Waigmann H (1994) Genetic analysis of human immunodeficiency virus type 1 and 2 (HIV-1 and HIV-2) mixed infections in India reveals a recent spread of HIV-1 and HIV-2 from a single ancestor for each of these viruses. J Virol 68:2161?2168

Groenink M, Andeweg AC, Fouchier RAM, Broersen S, van der Jagt RCM, Schuitemaker H, de Goede REY, Bosch ML, Huisman HG, Tersmette M (1992) Phenotype-associated env gene variation among eight related human immunodeficiency virus type 1 clones: evidence for in vivo recombination and determinants of cytotropism outside the V3 domain. J Virol 66:6175?6180

Gurtler LG, Hauser PH, Eberle J, van Brunn A, Knapp S, Zekeng L, Tsague JM, Kaptue L (1994) A new subtype of human immunodeficiency virus type 1 (MVP-5180) from Cameroon. J Virol 68: 1581?1585

Hahn BH (1994) Viral genes and their products. In: Broder S, Merigan T, Botognesi D (eds) Textbook on AIDS medicine. Williams & Williams, New York, pp 21?43

Hahn BH, Shaw GM, Taylor ME, Redfield RR, Markham PD, Salahuddin SZ, Wong-Staal F, Gallo RC, Parks ES, Parks WP (1986) Genetic variation in HTLV-II1/LAV over time in patients with AIDS or at risk for AIDS. Science 232:1548?1553

Hahn CS, Lustig S, Strauss EG, Strauss JH (1988) Western equine encephalitis virus is a recombinant virus. Proc Natl Acad Sci USA 85:5997?6001

Higgins DG, Bleasby AJ, Fuchs R (1992) CLUSTAL V: improved software for multiple sequence alignment. Comput Appl Biosci 8:189?191

Higgins DG, Sharp PM (1988) CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73:237?244

Higgins DG, Sharp PM (1989) Fast and sensitive multiple sequence alignments on a microcomputer. Comput Appl Biosci 5:151?153

Hirsch VM, Olmsted RA, Murphy-Corb M, Purcell RH, Johnson PR (1989) An African primate lentivirus (SIVSM) closely related to HIV-2. Nature 339:389?392

Howell RM, Fitzgibbon JE, Noe M, Ren Z, Gocke DJ, Schwartzer TA, Dubin DT (1991) In vivo sequence variation of the human immunodeficiency virus type 1 env gene: evidence for recombination among variants found in a single individual. AIDS Res Hum Retroviruses 7:869?876

Hu W-S, Temin HM (1990) Retroviral recombination and reverse transcription. Science 250:1227?1233

Hui H, Kim J, Hill SC, Kappes J, Shaw GM, Hahn BH (1994) Sequence analysis of a recombinant HIV-2 provirus. (in preparation)

Javier RT, Sedarati F, Stevens JG (1986) Two avirulent herpes simplex viruses generate lethal recombinants in vivo. Science 234:746?748

Jin MJ, Hui H, Robertson DL, Muller MC, Barre-Sinoussi F, Hirsch VM, Allan JS, Shaw GM, Sharp PM, Hahn BH (1994) Mosaic genome structure of simian immunodeficiency virus from West African green monkeys. EMBO J 13:2935?2947

Johnson PR, Hirsch VM, Myers G (1991) Genetic diversity and phylogeny of nonhuman primate lentiviruses. In: Koff W (ed) Annual review of AIDS research, vol 1. Marcel Dekker, New York, pp 47?62

Junghans RP, Boone LR, Skalka AM (1982) Retroviral DNA H structures: displacement-assimilation model of recombination. Cell 30: 53?62

Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge

Li W-H, Tanimura M, Sharp PM (1988) Rates and dates of divergence between AIDS virus nucleotide sequences. Mol Biol Evol 5:313?330

Louwagie J, McCutchan F, Peeters M, Brennan TP, Sanders-Buell E, Eddy GA, van der Groen G, Fransen K, Gershey-Damet G-M, Deleys R, Burke DS (1993) Phylogenetic analysis of gag genes from 70 international HIV-1 isolates provides evidence for multiple genotypes. AIDS 7:769?780

Maynard Smith J (1992) Analysing the mosaic structure of genes. J Mol Evol 34:126?129

Myers G, Korber B, Wain-Hobson S, Smith RF, Pavlakis GN (1993) Human retroviruses and AIDS. Theoretical Biology and Biophysics, Los Alamos, NM

Myers G, MacInnes K, Korber B (1992) The emergence of simian/human immunodeficiency viruses. AIDS Res Hum Retroviruses 8:373?386

Peeters M, Fransen K, Delaporte E, Vanden Haesevelde M, GershyDamet G-M, Kestens L, van der Groen G, Piot P (1992) Isolation and characterization of a new chimpanzee lentivirus (simian immunodeficiency virus isolate cpz-ant) from a wild-captured chimpanzee. AIDS 6:447?451

Preston BD, Poiesz BJ, Loeb LA (1988) Fidelity of HIV-1 reverse transcriptase. Science 242:1168?1171

Ranganathan PN, Srinivasan A (1993) Recombination between human immunodeficiency viruses (HIV) type 1 and 2 results in generation of defective hybrid viruses. Biochem Biophys Res Common 193: 311?317

Richetti M, Buc H (1990) Reverse transcriptase and genome variability: the accuracy of DNA replication is enzyme specific and sequence dependent. EMBO J 9:1583?1593

Roberts JD, Bebenek K, Kunkel TA (1988) The accuracy of reverse transcriptase from HIV-1. Science 242:1171?1173

Sabino EC, Shpaer EG, Morgado MG, Korber BTM, Diaz RS, Bongertz V, Cavalcante S, Galvao-Castro B, Mullins JI, Mayer A (1994) Identification of HIV-1 envelope genes recombinant between subtypes B and F in two epidemiologically-linked individuals from Brazil. J Virol 68:6340?6346

Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406?425

Sharp PM, Robertson DL, Gao F, Hahn BH (1994) Origins and diversity of human immunodeficiency viruses. AIDS 8:S27-S42

Strauss JH, Strauss EG (1988) Evolution of RNA viruses. Annu Rev Microbial 42:657?683

Vanden Haesevelde M, Decourt RJ, De Leys RJ, Vanderborght B, van der Groen G, van Heuverswijn H, Saman E (1994) Genomic cloning and complete sequence analysis of a highly divergent African human immunodeficiency virus isolate. J Virol 68:1586?1596

Vartanian J-P, Meyerhans A, Asjo B, Wain-Hobson S (1991) Selection, recombination, and G ? A hypermutation of human immunodeficiency virus type 1 genomes. J Virol 65:1779?1788

Wain-Hobson S (1993) The fastest genome evolution ever described: HIV variation in situ. Curr Opin Genet Dev 3:878?883

Weber J, Grosse F (1989) Fidelity of human immunodeficiency virus type 1 reverse transcriptase in copying natural DNA. Nucleic Acids Res 17:1379?1393

Williams PL, Fitch WM (1990) Phylogeny determinations using dynamically weighted parsimony method. Methods Enzymol 183: 615?626

Wolfs TFW, Zwart G, Bakker M, Goudsmit J (1992) HIV-1 genomic RNA diversification following sexual and parenteral virus transmission. Virology 189:103?110

Zhang, J, Temin HM (1994) Retrovirus recombination depends on the length of sequence identity and is not error prone. J Virol 68:2409?2414

Zhang LQ, MacKenzie P, Cleland A, Holmes EC, Leigh Brown AJ, Simmonds P (1993) Selection for specific sequences in the external envelope protein of human immunodeficiency virus type 1 upon primary infection. J Virol 67:3345?3356

Zhu T, Mo H, Wang N, Nam DS, Can Y, Koup RA, Ho DD (1993) Genotypic and phenotypic characterization of HIV-1 in patients with primary infection. Science 261:1179?1181