Full-length genome analyses of two new simian immunodeficiency virus (SIV) strains from mustached monkeys (C. Cephus) in gabon illustrate a complex evolutionary history among the SIVmus/mon/gsn lineage

Viruses

Volumn 6, Issue 7, 2014, Pages 2880-2898

  Liégeois, Florian ^a,b   Schmidt, Fabian ^c   Boué, Vanina ^a,b   Butel, Christelle ^a   Mouacha, Fatima ^a   Ngari, Paul ^b   Ondo, Bertrand Mve ^b   Leroy, Eric ^b   Heeney, Jonathan L ^c   Delaporte, Eric ^a   Peeters, Martine ^a   Rouet, François ^b,d  

^a INSTITUT DE RECHERCHE POUR LE DÉVELOPPEMENT   (France)

^b CENTRE INTERNATIONAL DE RECHERCHES MÉDICALES DE FRANCEVILLE   (Gabon)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^d INSTITUT PASTEUR DU CAMBODGE   (Cambodia)

Author keywords

Bushmeat; Cross species transmission; Evolution; Gabon; Lentivirus; Non human primate; molecular phylogeny; SIV

Indexed keywords

CYSTEINE; DNA FRAGMENT; GAG PROTEIN; GLYCOPROTEIN GP 120; MITOCHONDRIAL RNA; POL PROTEIN; RNA 12S; VIRUS ENVELOPE PROTEIN; VIRUS PROTEIN;

ARTICLE; CERCOPITHECUS; CERCOPITHECUS CEPHUS CEPHUS; CLADISTICS; DNA EXTRACTION; DNA SEQUENCE; ENVELOPE GENE; ENZYME LINKED IMMUNOSORBENT ASSAY; GABON; GENETIC SIMILARITY; GENETIC VARIABILITY; GENOME ANALYSIS; LONG TERMINAL REPEAT; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA GENE; RNA STRUCTURE; SEROLOGY; SIMIAN IMMUNODEFICIENCY VIRUS; STRUCTURAL GENE; VIRUS CHARACTERIZATION; VIRUS GENE; VIRUS GENOME; VIRUS STRAIN; AMINO ACID SEQUENCE; ANIMAL; CLASSIFICATION; EVOLUTION; GENETIC REASSORTMENT; GENETICS; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; ISOLATION AND PURIFICATION; MOLECULAR GENETICS; OPEN READING FRAME; PHYLOGEOGRAPHY; PROTEIN TERTIARY STRUCTURE; SEQUENCE HOMOLOGY; SIMIAN ACQUIRED IMMUNODEFICIENCY SYNDROME; TRANSMISSION; VIROLOGY;

AMINO ACID SEQUENCE; ANIMALS; BIOLOGICAL EVOLUTION; CERCOPITHECUS; GABON; GENOME, VIRAL; HIV-1; HUMANS; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PHYLOGENY; PHYLOGEOGRAPHY; PROTEIN STRUCTURE, TERTIARY; REASSORTANT VIRUSES; SEQUENCE HOMOLOGY, AMINO ACID; SIMIAN ACQUIRED IMMUNODEFICIENCY SYNDROME; SIMIAN IMMUNODEFICIENCY VIRUS; VIRAL PROTEINS;

EID: 84904667594     PISSN: 19994915     EISSN: None     Source Type: Journal    
DOI: 10.3390/v6072880     Document Type: Article

References (40)

1. Hahn, B.H.; Shaw, G.M.; de Cock, K.M.; Sharp, P.M. AIDS as a zoonosis: Scientific and public health implications. Science 2000, 287, 607-614.
2. Locatelli, S.; Peeters, M. Cross-species transmission of simian retroviruses: How and why they could lead to the emergence of new diseases in the human population. AIDS 2012, 26, 659-673.
3. Allan, J.S.; Short, M.; Taylor, M.E.; Su, S.; Hirsch, V.M.; Johnson, P.R.; Shaw, G.M.; Hahn, B.H. Species-specific diversity among simian immunodeficiency viruses from african green monkeys. J. Virol. 1991, 65, 2816-2828.
4. Beer, B.E.; Bailes, E.; Goeken, R.; Dapolito, G.; Coulibaly, C.; Norley, S.G.; Kurth, R.; Gautier, J.P.; Gautier-Hion, A.; Vallet, D.;et al. Simian immunodeficiency virus (SIV) from sun-tailed monkeys (Cercopithecus solatus): Evidence for host-dependent evolution of SIV within the C. Lhoesti superspecies. J. Virol. 1999, 73, 7734-7744.
5. Bibollet-Ruche, F.; Bailes, E.; Gao, F.; Pourrut, X.; Barlow, K.L.; Clewley, J.P.; Mwenda, J.M.; Langat, D.K.; Chege, G.K.; McClure, H.M.; et al. New simian immunodeficiency virus infecting de brazza's monkeys (Cercopithecus neglectus): Evidence for a Cercopithecusmonkey virus clade. J. Virol. 2004, 78, 7748-7762.
6. Souquiere, S.; Bibollet-Ruche, F.; Robertson, D.L.; Makuwa, M.; Apetrei, C.; Onanga, R.; Kornfeld, C.; Plantier, J.C.; Gao, F.; Abernethy, K.;et al. Wild Mandrillus sphinx are carriers of two types of lentivirus. J. Virol. 2001, 75, 7086-7096.
7. Aghokeng, A.F.; Bailes, E.; Loul, S.; Courgnaud, V.; Mpoudi-Ngolle, E.; Sharp, P.M.; Delaporte, E.; Peeters, M. Full-length sequence analysis of SIVmus in wild populations of mustached monkeys (Cercopithecus cephus) from Cameroon provides evidencefor two co-circulating SIVmus lineages. Virology 2007, 360, 407-418.
8. Liegeois, F.; Boue, V.; Mouacha, F.; Butel, C.; Ondo, B.M.; Pourrut, X.; Leroy, E.; Peeters, M.; Rouet, F. New STLV-3 strains and a divergent SIVmus strain identified in non-human primate bushmeat in Gabon. Retrovirology 2012, 9, 28.
9. Bibollet-Ruche, F.; Galat-Luong, A.; Cuny, G.; Sarni-Manchado, P.; Galat, G.; Durand, J.P.; Pourrut, X.; Veas, F. Simian immunodeficiency virus infection in a patas monkey (Erythrocebus patas): Evidence for cross-species transmission from african green monkeys (Cercopithecus aethiops sabaeus) in the wild. J. Gen. Virol. 1996, 77, 773-781.
10. Jin, M.J.; Rogers, J.; Phillips-Conroy, J.E.; Allan, J.S.; Desrosiers, R.C.; Shaw, G.M.; Sharp, P.M.; Hahn, B.H. Infection of a yellow baboon with simian immunodeficiency virus from african green monkeys: Evidence for cross-species transmission in the wild. J. Virol. 1994, 68, 8454-8460.
11. Van Rensburg, E.J.; Engelbrecht, S.; Mwenda, J.; Laten, J.D.; Robson, B.A.; Stander, T.; Chege, G.K. Simian immunodeficiency viruses (SIVs) from eastern and southern Africa: Detection of a SIVagm variant from a chacma baboon. J. Gen. Virol. 1998, 79, 1809-1814.
12. Courgnaud, V.; Abela, B.; Pourrut, X.; Mpoudi-Ngole, E.; Loul, S.; Delaporte, E.; Peeters, M. Identification of a new simianimmunodeficiency virus lineage with a vpu gene present among different Cercopithecusmonkeys (C. mona, C. cephus, and C. nictitans) from Cameroon. J. Virol. 2003, 77, 12523-12534.
13. Bailes, E.; Gao, F.; Bibollet-Ruche, F.; Courgnaud, V.; Peeters, M.; Marx, P.A.; Hahn, B.H.; Sharp, P.M. Hybrid origin of SIV in chimpanzees. Science 2003, 300, 1713.
14. Beer, B.E.; Foley, B.T.; Kuiken, C.L.; Tooze, Z.; Goeken, R.M.; Brown, C.R.; Hu, J.; St Claire, M.; Korber, B.T.; Hirsch, V.M. Characterization of novel simian immunodeficiency viruses from red-capped mangabeys from Nigeria (SIVrcmng409 and-ng411). J. Virol. 2001, 75, 12014-12027.
15. Schindler, M.; Munch, J.; Kutsch, O.; Li, H.; Santiago, M.L.; Bibollet-Ruche, F.; Muller-Trutwin, M.C.; Novembre, F.J.; Peeters, M.; Courgnaud, V.;et al. Nef-mediatedsuppression of T cell activation was lost in a lentiviral lineage that gave rise to HIV-1. Cell 2006, 125, 1055-1067.
16. Hsu, K.; Seharaseyon, J.; Dong, P.; Bour, S.; Marban, E. Mutual functional destruction of HIV-1 vpu and host task-1 channel. Mol. Cell. 2004, 14, 259-267
17. Kingdon, J. The Kingdon Field Guide to African Mammals; Princeton University Press: Princeton, NJ, USA, 1997.
18. Groves, C. Primate taxonomy. Smithsonian Series in Comparative Evolutionary Biology; Smithsonian Institution Press: Washington, DC, USA, 2001.
19. Van der Kuyl, A.C.; Dekker, J.T.; Goudsmit, J. Primate genus Miopithecus: Evidence for the existence of species and subspecies of dwarf guenons based on cellular and endogenous viral sequences. Mol. Phylogenet Evol. 2000, 14, 403-413.
20. Basic Local Alignment Search Tool: Blast. Available online: http://blast.ncbi.nlm.nih.gov/ Blast.cgi (accessed on 12 November 2012).
21. Simon, F.; Souquiere, S.; Damond, F.; Kfutwah, A.; Makuwa, M.; Leroy, E.; Rouquet, P.; Berthier, J.L.; Rigoulet, J.; Lecu, A.;et al. Synthetic peptide strategyfor the detection of and discrimination among highly divergent primate lentiviruses. AIDS Res. Hum. Retrovir. 2001, 17, 937-952.
22. Peeters, M.; Courgnaud, V.; Abela, B.; Auzel, P.; Pourrut, X.; Bibollet-Ruche, F.; Loul, S.; Liegeois, F.; Butel, C.; Koulagna, D.;et al. Risk to human health from a plethora of simian immunodeficiency viruses in primate bushmeat. Emerg. Infect. Dis. 2002, 8, 451-457.
23. Liegeois, F.; Courgnaud, V.; Switzer, W.M.; Murphy, H.W.; Loul, S.; Aghokeng, A.; Pourrut, X.; Mpoudi-Ngole, E.; Delaporte, E.; Peeters, M. Molecular characterization of a novel simian immunodeficiency virus lineage (SIVtal) from northern talapoins (Miopithecus ogouensis). Virology 2006, 349, 55-65.
24. Liegeois, F.; Lafay, B.; Formenty, P.; Locatelli, S.; Courgnaud, V.; Delaporte, E.; Peeters, M. Full-length genome characterization of a novel simian immunodeficiency virus lineage (SIVolc) from olive colobus (Procolobus verus) and new SIVwrcPbbstrains from western red colobus (Piliocolobus badius badius) from the tai forest in Ivory Coast. J. Virol. 2009, 83, 428-439.
25. Liegeois, F.; Butel, C.; Mouinga-Ondeme, A.; Verrier, D.; Motsch, P.; Gonzalez, J.P.; Peeters, M.; Rouet, F.; Onanga, R. Full-length genome sequence of a simian immunodeficiency virus from a wild-captured sun-tailed monkey in Gabon provides evidence for a species-specific monophyletic SIVsun lineage. AIDS Res. Hum. Retrovir. 2011, 27, 1237-1241.
26. Tamura, K.; Peterson, D.; Peterson, N.; Stecher, G.; Nei, M.; Kumar, S. Mega5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 2011, 28, 2731-2739.
27. Lole, K.S.; Bollinger, R.C.; Paranjape, R.S.; Gadkari, D.; Kulkarni, S.S.; Novak, N.G.; Ingersoll, R.; Sheppard, H.W.; Ray, S.C. Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J. Virol. 1999, 73:152-160.
28. Thompson, J.D.; Gibson, T.J.; Plewniak, F.; Jeanmougin, F.; Higgins, D.G. The clustal_x windows interface: Flexible strategies for multiplesequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997, 25, 4876-4882.
29. Huelsenbeck, J.P.; Ronquist, F. Mrbayes: Bayesian inference of phylogenetic trees. Bioinformatics 2001, 17, 754-755
30. Guindon, S.; Dufayard, J.F.; Lefort, V.; Anisimova, M.; Hordijk, W.; Gascuel, O. New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of phyml 3.0. Syst. Biol. 2010, 59, 307-321.
31. Tracer, v1.4. Available online: http://beast.bio.ed.ac.uk/Tracer (accessed on 15 January 2013).
32. Milne, I.; Lindner, D.; Bayer, M.; Husmeier, D.; McGuire, G.; Marshall, D.F.; Wright, F. Topali v2: A rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops. Bioinformatics 2009, 25, 126-127.
33. Xia, X. Dambe5: A comprehensive software package for data analysis in molecular biology and evolution. Mol. Biol. Evolut. 2013, 30, 1720-1728.
34. Petersen, B.; Petersen, T.N.; Andersen, P.; Nielsen, M.; Lundegaard, C. A generic method for assignment of reliability scores applied to solvent accessibility predictions. BMC Struct. Biol. 2009, 9, 51.
35. Locatelli, S.; Lafay, B.; Liegeois, F.; Ting, N.; Delaporte, E.; Peeters, M. Full molecular characterization of a simian immunodeficiency virus, SIVwrcPbtfrom temminck's red colobus (Piliocolobus badius temminckii) from Abuko nature reserve, the Gambia. Virology 2008, 376, 90-100.
36. Worobey, M.; Telfer, P.; Souquiere, S.; Hunter, M.; Coleman, C.A.; Metzger, M.J.; Reed, P.; Makuwa, M.; Hearn, G.; Honarvar, S.;et al. Island biogeography reveals the deep history of SIV. Science 2010, 329, 1487.
37. Suzuki, Y.; Glazko, G.V.; Nei, M. Overcredibility of molecular phylogenies obtained by bayesian phylogenetics. Proc. Natl. Acad. Sci. USA 2002, 99, 16138-16143.
38. Aghokeng, A.F.; Ayouba, A.; Mpoudi-Ngole, E.; Loul, S.; Liegeois, F.; Delaporte, E.; Peeters, M. Extensive survey on the prevalence and genetic diversity of SIVs in primate bushmeat provides insights into risks for potential new cross-species transmissions. Infect. Genet. Evolut. 2010, 10, 386-396.
39. Gautier-Hion, A.; Colyn, M.; Gauthier, J.P. Histoire Naturelle Des Primates d'Afrique Centrale; Libreville Ecofac; Backhuys Publishers: Netherlands, UK, 1999.
40. Lauck, M.; Switzer, M.W.; Sibley, D.S.; Hyeroba, D.; Tumukunde, A.; Geoffrey Weny, G.; Taylor, B.; Shankar, A.; Ting, N.;et al. Discovery and full genome characterization of two highly divergent simian immunodeficiency viruses infecting black-and-white colobus monkeys (Colobus. guereza) in Kibale National Park, Uganda. Retrovirology 2013, 10, 107