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Mosaic genome structure of simian immunodeficiency virus from west African green monkeys.

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  • 1. Department of Medicine, University of Alabama at Birmingham 35294.
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    • Jin MJ 1
    (1 author)

The EMBO Journal, 01 Jun 1994, 13(12):2935-2947
https://doi.org/10.1002/j.1460-2075.1994.tb06588.x PMID: 8026477 PMCID: PMC395175

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Abstract 

Elucidation of the phylogenetic origins of simian and human immunodeficiency viruses (SIV and HIV) is fundamental to the understanding of HIV pathogenesis and the spread of AIDS worldwide. In this study, we molecularly characterized multiple SIVAGM isolates from four different African green monkey species (vervet, grivet, sabaeus and tantalus monkeys). Phylogenetic analysis of partial (1 kb) env sequences indicated that all SIVAGM strains cluster together, and that they fall into four distinct sequence sub-groups according to their species of origin. However, alignment of long terminal repeat sequences revealed that SIVs from West African sabaeus monkeys contain a structural feature (a duplication of the transactivation response element) thus far only found in otherwise highly divergent lentiviruses infecting sooty mangabeys (SIVSM) and humans (HIV-2). To determine whether there were additional similarities with the SIVSM/HIV-2 group, a full-length replication competent sabaeus provirus was cloned and sequenced. In phylogenetic trees derived from the central and 3' coding regions, the sabaeus virus clustered with SIVAGM isolates from other African green monkey species. However, in trees derived from the 3' half of gag and the adjacent 5' region of pol, the sabaeus virus grouped with the SIVSM/HIV-2 lineage. These results indicated that the sabaeus virus comprised a mosaic genome which must have resulted from recombination of divergent lentiviruses in the distant past. A second, independent sabaeus isolate exhibited similar phylogenetic relationships, suggesting that all West African green monkey viruses share this complex evolutionary history. Taken together, these results indicate that African green monkeys have been infected with SIVAGM for very long periods of time, and that recombination and cross-species transmission in the wild have contributed to the genetic complexity of primate lentiviruses.

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EMBO J. 1994 Jun 15; 13(12): 2935–2947.
PMCID: PMC395175
PMID: 8026477

Mosaic genome structure of simian immunodeficiency virus from west African green monkeys.

M J Jin, H Hui, D L Robertson, M C Müller, F Barré-Sinoussi, V M Hirsch, J S Allan, G M Shaw, P M Sharp, and B H Hahn
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Abstract

Elucidation of the phylogenetic origins of simian and human immunodeficiency viruses (SIV and HIV) is fundamental to the understanding of HIV pathogenesis and the spread of AIDS worldwide. In this study, we molecularly characterized multiple SIVAGM isolates from four different African green monkey species (vervet, grivet, sabaeus and tantalus monkeys). Phylogenetic analysis of partial (1 kb) env sequences indicated that all SIVAGM strains cluster together, and that they fall into four distinct sequence sub-groups according to their species of origin. However, alignment of long terminal repeat sequences revealed that SIVs from West African sabaeus monkeys contain a structural feature (a duplication of the transactivation response element) thus far only found in otherwise highly divergent lentiviruses infecting sooty mangabeys (SIVSM) and humans (HIV-2). To determine whether there were additional similarities with the SIVSM/HIV-2 group, a full-length replication competent sabaeus provirus was cloned and sequenced. In phylogenetic trees derived from the central and 3' coding regions, the sabaeus virus clustered with SIVAGM isolates from other African green monkey species. However, in trees derived from the 3' half of gag and the adjacent 5' region of pol, the sabaeus virus grouped with the SIVSM/HIV-2 lineage. These results indicated that the sabaeus virus comprised a mosaic genome which must have resulted from recombination of divergent lentiviruses in the distant past. A second, independent sabaeus isolate exhibited similar phylogenetic relationships, suggesting that all West African green monkey viruses share this complex evolutionary history. Taken together, these results indicate that African green monkeys have been infected with SIVAGM for very long periods of time, and that recombination and cross-species transmission in the wild have contributed to the genetic complexity of primate lentiviruses.

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Selected References

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  • Alizon M, Wain-Hobson S, Montagnier L, Sonigo P. Genetic variability of the AIDS virus: nucleotide sequence analysis of two isolates from African patients. Cell. 1986 Jul 4;46(1):63–74. [Abstract] [Google Scholar]
  • Allan JS. Receptor-mediated activation of the viral envelope and viral entry. AIDS. 1993;7 (Suppl 1):S43–S50. [Abstract] [Google Scholar]
  • Allan JS, Kanda P, Kennedy RC, Cobb EK, Anthony M, Eichberg JW. Isolation and characterization of simian immunodeficiency viruses from two subspecies of African green monkeys. AIDS Res Hum Retroviruses. 1990 Mar;6(3):275–285. [Abstract] [Google Scholar]
  • Allan JS, Short M, Taylor ME, Su S, Hirsch VM, Johnson PR, Shaw GM, Hahn BH. Species-specific diversity among simian immunodeficiency viruses from African green monkeys. J Virol. 1991 Jun;65(6):2816–2828. [Europe PMC free article] [Abstract] [Google Scholar]
  • Baier M, Werner A, Cichutek K, Garber C, Müller C, Kraus G, Ferdinand FJ, Hartung S, Papas TS, Kurth R. Molecularly cloned simian immunodeficiency virus SIVagm3 is highly divergent from other SIVagm isolates and is biologically active in vitro and in vivo. J Virol. 1989 Dec;63(12):5119–5123. [Europe PMC free article] [Abstract] [Google Scholar]
  • Baskin GB, Murphey-Corb M, Watson EA, Martin LN. Necropsy findings in rhesus monkeys experimentally infected with cultured simian immunodeficiency virus (SIV)/delta. Vet Pathol. 1988 Nov;25(6):456–467. [Abstract] [Google Scholar]
  • Berkhout B. Structural features in TAR RNA of human and simian immunodeficiency viruses: a phylogenetic analysis. Nucleic Acids Res. 1992 Jan 11;20(1):27–31. [Europe PMC free article] [Abstract] [Google Scholar]
  • Cichutek K, Norley S. Lack of immune suppression in SIV-infected natural hosts. AIDS. 1993;7 (Suppl 1):S25–S35. [Abstract] [Google Scholar]
  • Coffin JM. Structure, replication, and recombination of retrovirus genomes: some unifying hypotheses. J Gen Virol. 1979 Jan;42(1):1–26. [Abstract] [Google Scholar]
  • Coffin JM. Genetic diversity and evolution of retroviruses. Curr Top Microbiol Immunol. 1992;176:143–164. [Abstract] [Google Scholar]
  • Cullen BR. Mechanism of action of regulatory proteins encoded by complex retroviruses. Microbiol Rev. 1992 Sep;56(3):375–394. [Europe PMC free article] [Abstract] [Google Scholar]
  • Daniel MD, Letvin NL, King NW, Kannagi M, Sehgal PK, Hunt RD, Kanki PJ, Essex M, Desrosiers RC. Isolation of T-cell tropic HTLV-III-like retrovirus from macaques. Science. 1985 Jun 7;228(4704):1201–1204. [Abstract] [Google Scholar]
  • Dewhurst S, Embretson JE, Anderson DC, Mullins JI, Fultz PN. Sequence analysis and acute pathogenicity of molecularly cloned SIVSMM-PBj14. Nature. 1990 Jun 14;345(6276):636–640. [Abstract] [Google Scholar]
  • Evans LA, Moreau J, Odehouri K, Seto D, Thomson-Honnebier G, Legg H, Barboza A, Cheng-Mayer C, Levy JA. Simultaneous isolation of HIV-1 and HIV-2 from an AIDS patient. Lancet. 1988 Dec 17;2(8625):1389–1391. [Abstract] [Google Scholar]
  • Faulkner DV, Jurka J. Multiple aligned sequence editor (MASE). Trends Biochem Sci. 1988 Aug;13(8):321–322. [Abstract] [Google Scholar]
  • Fenrick R, Malim MH, Hauber J, Le SY, Maizel J, Cullen BR. Functional analysis of the Tat trans activator of human immunodeficiency virus type 2. J Virol. 1989 Dec;63(12):5006–5012. [Europe PMC free article] [Abstract] [Google Scholar]
  • Fomsgaard A, Hirsch VM, Allan JS, Johnson PR. A highly divergent proviral DNA clone of SIV from a distinct species of African green monkey. Virology. 1991 May;182(1):397–402. [Abstract] [Google Scholar]
  • Fukasawa M, Miura T, Hasegawa A, Morikawa S, Tsujimoto H, Miki K, Kitamura T, Hayami M. Sequence of simian immunodeficiency virus from African green monkey, a new member of the HIV/SIV group. Nature. 1988 Jun 2;333(6172):457–461. [Abstract] [Google Scholar]
  • Fultz PN, McClure HM, Anderson DC, Switzer WM. Identification and biologic characterization of an acutely lethal variant of simian immunodeficiency virus from sooty mangabeys (SIV/SMM). AIDS Res Hum Retroviruses. 1989 Aug;5(4):397–409. [Abstract] [Google Scholar]
  • Gao F, Yue L, White AT, Pappas PG, Barchue J, Hanson AP, Greene BM, Sharp PM, Shaw GM, Hahn BH. Human infection by genetically diverse SIVSM-related HIV-2 in west Africa. Nature. 1992 Aug 6;358(6386):495–499. [Abstract] [Google Scholar]
  • Gaynor R. Cellular transcription factors involved in the regulation of HIV-1 gene expression. AIDS. 1992 Apr;6(4):347–363. [Abstract] [Google Scholar]
  • George JR, Ou CY, Parekh B, Brattegaard K, Brown V, Boateng E, De Cock KM. Prevalence of HIV-1 and HIV-2 mixed infections in Côte d'Ivoire. Lancet. 1992 Aug 8;340(8815):337–339. [Abstract] [Google Scholar]
  • Grez M, Dietrich U, Balfe P, von Briesen H, Maniar JK, Mahambre G, Delwart EL, Mullins JI, Rübsamen-Waigmann H. 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. 1994 Apr;68(4):2161–2168. [Europe PMC free article] [Abstract] [Google Scholar]
  • Guyader M, Emerman M, Sonigo P, Clavel F, Montagnier L, Alizon M. Genome organization and transactivation of the human immunodeficiency virus type 2. Nature. 1987 Apr 16;326(6114):662–669. [Abstract] [Google Scholar]
  • Higgins DG, Sharp PM. CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene. 1988 Dec 15;73(1):237–244. [Abstract] [Google Scholar]
  • Higgins DG, Sharp PM. Fast and sensitive multiple sequence alignments on a microcomputer. Comput Appl Biosci. 1989 Apr;5(2):151–153. [Abstract] [Google Scholar]
  • Higgins DG, Bleasby AJ, Fuchs R. CLUSTAL V: improved software for multiple sequence alignment. Comput Appl Biosci. 1992 Apr;8(2):189–191. [Abstract] [Google Scholar]
  • Hirsch VM, Olmsted RA, Murphey-Corb M, Purcell RH, Johnson PR. An African primate lentivirus (SIVsm) closely related to HIV-2. Nature. 1989 Jun 1;339(6223):389–392. [Abstract] [Google Scholar]
  • Hirsch VM, Edmondson P, Murphey-Corb M, Arbeille B, Johnson PR, Mullins JI. SIV adaptation to human cells. Nature. 1989 Oct 19;341(6243):573–574. [Abstract] [Google Scholar]
  • Hirsch VM, McGann C, Dapolito G, Goldstein S, Ogen-Odoi A, Biryawaho B, Lakwo T, Johnson PR. Identification of a new subgroup of SIVagm in tantalus monkeys. Virology. 1993 Nov;197(1):426–430. [Abstract] [Google Scholar]
  • Hirsch VM, Dapolito GA, Goldstein S, McClure H, Emau P, Fultz PN, Isahakia M, Lenroot R, Myers G, Johnson PR. A distinct African lentivirus from Sykes' monkeys. J Virol. 1993 Mar;67(3):1517–1528. [Europe PMC free article] [Abstract] [Google Scholar]
  • Hu WS, Temin HM. Retroviral recombination and reverse transcription. Science. 1990 Nov 30;250(4985):1227–1233. [Abstract] [Google Scholar]
  • Hu WS, Temin HM. Effect of gamma radiation on retroviral recombination. J Virol. 1992 Jul;66(7):4457–4463. [Europe PMC free article] [Abstract] [Google Scholar]
  • Huet T, Cheynier R, Meyerhans A, Roelants G, Wain-Hobson S. Genetic organization of a chimpanzee lentivirus related to HIV-1. Nature. 1990 May 24;345(6273):356–359. [Abstract] [Google Scholar]
  • Johnson PR, Goldstein S, London WT, Fomsgaard A, Hirsch VM. Molecular clones of SIVsm and SIVagm: experimental infection of macaques and African green monkeys. J Med Primatol. 1990;19(3-4):279–286. [Abstract] [Google Scholar]
  • Johnson PR, Fomsgaard A, Allan J, Gravell M, London WT, Olmsted RA, Hirsch VM. Simian immunodeficiency viruses from African green monkeys display unusual genetic diversity. J Virol. 1990 Mar;64(3):1086–1092. [Europe PMC free article] [Abstract] [Google Scholar]
  • Junghans RP, Boone LR, Skalka AM. Retroviral DNA H structures: displacement-assimilation model of recombination. Cell. 1982 Aug;30(1):53–62. [Abstract] [Google Scholar]
  • Khan AS, Galvin TA, Lowenstine LJ, Jennings MB, Gardner MB, Buckler CE. A highly divergent simian immunodeficiency virus (SIVstm) recovered from stored stump-tailed macaque tissues. J Virol. 1991 Dec;65(12):7061–7065. [Europe PMC free article] [Abstract] [Google Scholar]
  • Kodama T, Silva DP, Daniel MD, Phillips-Conroy JE, Jolly CJ, Rogers J, Desrosiers RC. Prevalence of antibodies to SIV in baboons in their native habitat. AIDS Res Hum Retroviruses. 1989 Jun;5(3):337–343. [Abstract] [Google Scholar]
  • Kodama T, Wooley DP, Naidu YM, Kestler HW, 3rd, Daniel MD, Li Y, Desrosiers RC. Significance of premature stop codons in env of simian immunodeficiency virus. J Virol. 1989 Nov;63(11):4709–4714. [Europe PMC free article] [Abstract] [Google Scholar]
  • Li WH, Tanimura M, Sharp PM. Rates and dates of divergence between AIDS virus nucleotide sequences. Mol Biol Evol. 1988 Jul;5(4):313–330. [Abstract] [Google Scholar]
  • Li Y, Naidu YM, Daniel MD, Desrosiers RC. Extensive genetic variability of simian immunodeficiency virus from African green monkeys. J Virol. 1989 Apr;63(4):1800–1802. [Europe PMC free article] [Abstract] [Google Scholar]
  • Li Y, Kappes JC, Conway JA, Price RW, Shaw GM, Hahn BH. Molecular characterization of human immunodeficiency virus type 1 cloned directly from uncultured human brain tissue: identification of replication-competent and -defective viral genomes. J Virol. 1991 Aug;65(8):3973–3985. [Europe PMC free article] [Abstract] [Google Scholar]
  • Lowenstine LJ, Pedersen NC, Higgins J, Pallis KC, Uyeda A, Marx P, Lerche NW, Munn RJ, Gardner MB. Seroepidemiologic survey of captive Old-World primates for antibodies to human and simian retroviruses, and isolation of a lentivirus from sooty mangabeys (Cercocebus atys). Int J Cancer. 1986 Oct 15;38(4):563–574. [Abstract] [Google Scholar]
  • Marx PA, Li Y, Lerche NW, Sutjipto S, Gettie A, Yee JA, Brotman BH, Prince AM, Hanson A, Webster RG, et al. Isolation of a simian immunodeficiency virus related to human immunodeficiency virus type 2 from a west African pet sooty mangabey. J Virol. 1991 Aug;65(8):4480–4485. [Europe PMC free article] [Abstract] [Google Scholar]
  • McClure HM, Anderson DC, Fultz PN, Ansari AA, Lockwood E, Brodie A. Spectrum of disease in macaque monkeys chronically infected with SIV/SMM. Vet Immunol Immunopathol. 1989 May;21(1):13–24. [Abstract] [Google Scholar]
  • McKeating JA, Willey RL. Structure and function of the HIV envelope. AIDS. 1989;3 (Suppl 1):S35–S41. [Abstract] [Google Scholar]
  • Müller MC, Saksena NK, Nerrienet E, Chappey C, Hervé VM, Durand JP, Legal-Campodonico P, Lang MC, Digoutte JP, Georges AJ, et al. Simian immunodeficiency viruses from central and western Africa: evidence for a new species-specific lentivirus in tantalus monkeys. J Virol. 1993 Mar;67(3):1227–1235. [Europe PMC free article] [Abstract] [Google Scholar]
  • Murphey-Corb M, Martin LN, Rangan SR, Baskin GB, Gormus BJ, Wolf RH, Andes WA, West M, Montelaro RC. Isolation of an HTLV-III-related retrovirus from macaques with simian AIDS and its possible origin in asymptomatic mangabeys. Nature. 1986 May 22;321(6068):435–437. [Abstract] [Google Scholar]
  • Myers G, MacInnes K, Korber B. The emergence of simian/human immunodeficiency viruses. AIDS Res Hum Retroviruses. 1992 Mar;8(3):373–386. [Abstract] [Google Scholar]
  • Novembre FJ, Hirsch VM, McClure HM, Fultz PN, Johnson PR. SIV from stump-tailed macaques: molecular characterization of a highly transmissible primate lentivirus. Virology. 1992 Feb;186(2):783–787. [Abstract] [Google Scholar]
  • Ohta Y, Masuda T, Tsujimoto H, Ishikawa K, Kodama T, Morikawa S, Nakai M, Honjo S, Hayami M. Isolation of simian immunodeficiency virus from African green monkeys and seroepidemiologic survey of the virus in various non-human primates. Int J Cancer. 1988 Jan 15;41(1):115–122. [Abstract] [Google Scholar]
  • Peeters M, Fransen K, Delaporte E, Van den Haesevelde M, Gershy-Damet GM, Kestens L, van der Groen G, Piot P. Isolation and characterization of a new chimpanzee lentivirus (simian immunodeficiency virus isolate cpz-ant) from a wild-captured chimpanzee. AIDS. 1992 May;6(5):447–451. [Abstract] [Google Scholar]
  • Peeters M, Gershy-Damet GM, Fransen K, Koffi K, Coulibaly M, Delaporte E, Piot P, van der Groen G. Virological and polymerase chain reaction studies of HIV-1/HIV-2 dual infection in Côte d'Ivoire. Lancet. 1992 Aug 8;340(8815):339–340. [Abstract] [Google Scholar]
  • Pieniazek D, Peralta JM, Ferreira JA, Krebs JW, Owen SM, Sion FS, Filho CF, Sereno AB, de Sa CA, Weniger BG, et al. Identification of mixed HIV-1/HIV-2 infections in Brazil by polymerase chain reaction. AIDS. 1991 Nov;5(11):1293–1299. [Abstract] [Google Scholar]
  • Rayfield M, De Cock K, Heyward W, Goldstein L, Krebs J, Kwok S, Lee S, McCormick J, Moreau JM, Odehouri K, et al. Mixed human immunodeficiency virus (HIV) infection in an individual: demonstration of both HIV type 1 and type 2 proviral sequences by using polymerase chain reaction. J Infect Dis. 1988 Dec;158(6):1170–1176. [Abstract] [Google Scholar]
  • Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987 Jul;4(4):406–425. [Abstract] [Google Scholar]
  • Sakai H, Sakuragi J, Sakuragi S, Kawamura M, Adachi A. Compatibility of Tat and Rev transactivators in the primate lentiviruses. Arch Virol. 1993;129(1-4):1–10. [Abstract] [Google Scholar]
  • Sakuragi J, Fukasawa M, Shibata R, Sakai H, Kawamura M, Akari H, Kiyomasu T, Ishimoto A, Hayami M, Adachi A. Functional analysis of long terminal repeats derived from four strains of simian immunodeficiency virus SIVAGM in relation to other primate lentiviruses. Virology. 1991 Nov;185(1):455–459. [Abstract] [Google Scholar]
  • Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. [Europe PMC free article] [Abstract] [Google Scholar]
  • Shibata R, Adachi A. SIV/HIV recombinants and their use in studying biological properties. AIDS Res Hum Retroviruses. 1992 Mar;8(3):403–409. [Abstract] [Google Scholar]
  • Shibata R, Miura T, Hayami M, Sakai H, Ogawa K, Kiyomasu T, Ishimoto A, Adachi A. Construction and characterization of an infectious DNA clone and of mutants of simian immunodeficiency virus isolated from the African green monkey. J Virol. 1990 Jan;64(1):307–312. [Europe PMC free article] [Abstract] [Google Scholar]
  • Tao J, Frankel AD. Electrostatic interactions modulate the RNA-binding and transactivation specificities of the human immunodeficiency virus and simian immunodeficiency virus Tat proteins. Proc Natl Acad Sci U S A. 1993 Feb 15;90(4):1571–1575. [Europe PMC free article] [Abstract] [Google Scholar]
  • Tsujimoto H, Hasegawa A, Maki N, Fukasawa M, Miura T, Speidel S, Cooper RW, Moriyama EN, Gojobori T, Hayami M. Sequence of a novel simian immunodeficiency virus from a wild-caught African mandrill. Nature. 1989 Oct 12;341(6242):539–541. [Abstract] [Google Scholar]
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