title: 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.
abstract: BACKGROUND
  African non-human primates (NHPs) are natural hosts for simian immunodeficiency viruses (SIV), the zoonotic transmission of which led to the emergence of HIV-1 and HIV-2. However, our understanding of SIV diversity and evolution is limited by incomplete taxonomic and geographic sampling of NHPs, particularly in East Africa. In this study, we screened blood specimens from nine black-and-white colobus monkeys (Colobus guereza occidentalis) from Kibale National Park, Uganda, for novel SIVs using a combination of serology and "unbiased" deep-sequencing, a method that does not rely on genetic similarity to previously characterized viruses.
  
  
  RESULTS
  We identified two novel and divergent SIVs, tentatively named SIVkcol-1 and SIVkcol-2, and assembled genomes covering the entire coding region for each virus. SIVkcol-1 and SIVkcol-2 were detected in three and four animals, respectively, but with no animals co-infected. Phylogenetic analyses showed that SIVkcol-1 and SIVkcol-2 form a lineage with SIVcol, previously discovered in black-and-white colobus from Cameroon. Although SIVkcol-1 and SIVkcol-2 were isolated from the same host population in Uganda, SIVkcol-1 is more closely related to SIVcol than to SIVkcol-2. Analysis of functional motifs in the extracellular envelope glycoprotein (gp120) revealed that SIVkcol-2 is unique among primate lentiviruses in containing only 16 conserved cysteine residues instead of the usual 18 or more.
  
  
  CONCLUSIONS
  Our results demonstrate that the genetic diversity of SIVs infecting black-and-white colobus across equatorial Africa is greater than previously appreciated and that divergent SIVs can co-circulate in the same colobine population. We also show that the use of "unbiased" deep sequencing for the detection of SIV has great advantages over traditional serological approaches, especially for studies of unknown or poorly characterized viruses. Finally, the detection of the first SIV containing only 16 conserved cysteines in the extracellular envelope protein gp120 further expands the range of functional motifs observed among SIVs and highlights the complex evolutionary history of simian retroviruses.
authors.forename: Michael
authors.initials: M
authors.lastname: Lauck
authors.forename: William M
authors.initials: WM
authors.lastname: Switzer
authors.forename: Samuel D
authors.initials: SD
authors.lastname: Sibley
authors.forename: David
authors.initials: D
authors.lastname: Hyeroba
authors.forename: Alex
authors.initials: A
authors.lastname: Tumukunde
authors.forename: Geoffrey
authors.initials: G
authors.lastname: Weny
authors.forename: Bill
authors.initials: B
authors.lastname: Taylor
authors.forename: Anupama
authors.initials: A
authors.lastname: Shankar
authors.forename: Nelson
authors.initials: N
authors.lastname: Ting
authors.forename: Colin A
authors.initials: CA
authors.lastname: Chapman
authors.forename: Thomas C
authors.initials: TC
authors.lastname: Friedrich
authors.forename: Tony L
authors.initials: TL
authors.lastname: Goldberg
authors.affiliation: Wisconsin National Primate Research Center, Madison, WI, USA. doconnor@primate.wisc.edu.
authors.forename: David H
authors.initials: DH
authors.lastname: O'Connor
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D003104:Colobus; D014644:Genetic Variation; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing; D008969:Molecular Sequence Data; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics*; D017385:Sequence Homology; D016097:Simian Acquired Immunodeficiency Syndrome / Q000821:virology*; D015302:Simian Immunodeficiency Virus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D014454:Uganda
chemical_list: D012367:RNA, Viral