Modern-day SIV Viral Diversity Generated by Extensive Recombination and Cross-species Transmission

Overview

Journal PLoS Pathog

Specialty Microbiology

Date 2017 Jul 4

PMID 28672035

Citations 33

Authors

Sidney M Bell

Trevor Bedford

Affiliations

Soon will be listed here.

Abstract

Cross-species transmission (CST) has led to many devastating epidemics, but is still a poorly understood phenomenon. HIV-1 and HIV-2 (human immunodeficiency virus 1 and 2), which have collectively caused over 35 million deaths, are the result of multiple CSTs from chimpanzees, gorillas, and sooty mangabeys. While the immediate history of HIV is known, there are over 45 lentiviruses that infect specific species of primates, and patterns of host switching are not well characterized. We thus took a phylogenetic approach to better understand the natural history of SIV recombination and CST. We modeled host species as a discrete character trait on the viral phylogeny and inferred historical host switches and the pairwise transmission rates between each pair of 24 primate hosts. We identify 14 novel, well-supported, ancient cross-species transmission events. We also find that lentiviral lineages vary widely in their ability to infect new host species: SIVcol (from colobus monkeys) is evolutionarily isolated, while SIVagms (from African green monkeys) frequently move between host subspecies. We also examine the origins of SIVcpz (the predecessor of HIV-1) in greater detail than previous studies, and find that there are still large portions of the genome with unknown origins. Observed patterns of CST are likely driven by a combination of ecological circumstance and innate immune factors.

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References

Van Heuverswyn F, Li Y, Neel C, Bailes E, Keele B, Liu W . Human immunodeficiency viruses: SIV infection in wild gorillas. Nature. 2006; 444(7116):164. DOI: 10.1038/444164a. View

Aiewsakun P, Katzourakis A . Time-Dependent Rate Phenomenon in Viruses. J Virol. 2016; 90(16):7184-95. PMC: 4984659. DOI: 10.1128/JVI.00593-16. View

Faria N, Suchard M, Rambaut A, Streicker D, Lemey P . Simultaneously reconstructing viral cross-species transmission history and identifying the underlying constraints. Philos Trans R Soc Lond B Biol Sci. 2013; 368(1614):20120196. PMC: 3678322. DOI: 10.1098/rstb.2012.0196. View

Chen Z, Telfier P, Gettie A, Reed P, Zhang L, Ho D . Genetic characterization of new West African simian immunodeficiency virus SIVsm: geographic clustering of household-derived SIV strains with human immunodeficiency virus type 2 subtypes and genetically diverse viruses from a single feral sooty.... J Virol. 1996; 70(6):3617-27. PMC: 190237. DOI: 10.1128/JVI.70.6.3617-3627.1996. View

Darc M, Ayouba A, Esteban A, Learn G, Boue V, Liegeois F . Origin of the HIV-1 group O epidemic in western lowland gorillas. Proc Natl Acad Sci U S A. 2015; 112(11):E1343-52. PMC: 4371950. DOI: 10.1073/pnas.1502022112. View

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(6):659-73. DOI: 10.1097/QAD.0b013e328350fb68. View

Aghokeng A, Bailes E, Loul S, Courgnaud V, Mpoudi-Ngolle E, Sharp P . Full-length sequence analysis of SIVmus in wild populations of mustached monkeys (Cercopithecus cephus) from Cameroon provides evidence for two co-circulating SIVmus lineages. Virology. 2006; 360(2):407-18. PMC: 1900428. DOI: 10.1016/j.virol.2006.10.048. View

Harris R, Hultquist J, Evans D . The restriction factors of human immunodeficiency virus. J Biol Chem. 2012; 287(49):40875-83. PMC: 3510791. DOI: 10.1074/jbc.R112.416925. View

Katoh K, Standley D . MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013; 30(4):772-80. PMC: 3603318. DOI: 10.1093/molbev/mst010. View

10.

Courgnaud V, Abela B, Pourrut X, Mpoudi-Ngole E, Loul S, Delaporte E . Identification of a new simian immunodeficiency virus lineage with a vpu gene present among different cercopithecus monkeys (C. mona, C. cephus, and C. nictitans) from Cameroon. J Virol. 2003; 77(23):12523-34. PMC: 262559. DOI: 10.1128/jvi.77.23.12523-12534.2003. View

11.

Bailes E, Gao F, Bibollet-Ruche F, Courgnaud V, Peeters M, Marx P . Hybrid origin of SIV in chimpanzees. Science. 2003; 300(5626):1713. DOI: 10.1126/science.1080657. View

12.

Parrish C, Holmes E, Morens D, Park E, Burke D, Calisher C . Cross-species virus transmission and the emergence of new epidemic diseases. Microbiol Mol Biol Rev. 2008; 72(3):457-70. PMC: 2546865. DOI: 10.1128/MMBR.00004-08. View

13.

Kosakovsky Pond S, Posada D, Gravenor M, Woelk C, Frost S . GARD: a genetic algorithm for recombination detection. Bioinformatics. 2006; 22(24):3096-8. DOI: 10.1093/bioinformatics/btl474. View

14.

Damond F, Descamps D, Farfara I, Telles J, Puyeo S, Campa P . Quantification of proviral load of human immunodeficiency virus type 2 subtypes A and B using real-time PCR. J Clin Microbiol. 2001; 39(12):4264-8. PMC: 88534. DOI: 10.1128/JCM.39.12.4264-4268.2001. View

15.

Pandrea I, Apetrei C, Gordon S, Barbercheck J, Dufour J, Bohm R . Paucity of CD4+CCR5+ T cells is a typical feature of natural SIV hosts. Blood. 2006; 109(3):1069-76. PMC: 1785133. DOI: 10.1182/blood-2006-05-024364. View

16.

Riddick N, Hermann E, Loftin L, Elliott S, Wey W, Cervasi B . A novel CCR5 mutation common in sooty mangabeys reveals SIVsmm infection of CCR5-null natural hosts and efficient alternative coreceptor use in vivo. PLoS Pathog. 2010; 6(8):e1001064. PMC: 2928783. DOI: 10.1371/journal.ppat.1001064. View

17.

Apetrei C, Robertson D, Marx P . The history of SIVS and AIDS: epidemiology, phylogeny and biology of isolates from naturally SIV infected non-human primates (NHP) in Africa. Front Biosci. 2004; 9:225-54. DOI: 10.2741/1154. View

18.

Souquiere S, Bibollet-Ruche F, Robertson D, Makuwa M, Apetrei C, Onanga R . Wild Mandrillus sphinx are carriers of two types of lentivirus. J Virol. 2001; 75(15):7086-96. PMC: 114437. DOI: 10.1128/JVI.75.15.7086-7096.2001. View

19.

Ishikawa K, Janssens W, Banor J, Shinno T, Piedade J, Sata T . Genetic analysis of HIV type 2 from Ghana and Guinea-Bissau, West Africa. AIDS Res Hum Retroviruses. 2002; 17(17):1661-3. DOI: 10.1089/088922201753342077. View

20.

Jin M, Rogers J, Phillips-Conroy J, Allan J, Desrosiers R, Shaw G . 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(12):8454-60. PMC: 237322. DOI: 10.1128/JVI.68.12.8454-8460.1994. View