title: Consensus-degenerate hybrid oligonucleotide primers (CODEHOPs) for the detection of novel viruses in non-human primates.
abstract: Consensus-degenerate hybrid oligonucleotide primers (CODEHOPs) have proven to be a powerful tool for the identification of novel genes. CODEHOPs are designed from highly-conserved regions of multiply-aligned protein sequences from members of a gene family and are used in PCR amplification to identify distantly-related genes. The CODEHOP approach has been used to identify novel pathogens by targeting amino acid motifs conserved in specific pathogen families. We initiated a program utilizing the CODEHOP approach to develop PCR-based assays targeting a variety of viral families that are pathogens in non-human primates. We have also developed and further improved a computer program and website to facilitate the design of CODEHOP PCR primers. Here, we detail the method for the development of pathogen-specific CODEHOP PCR assays using the papillomavirus family as a target. Papillomaviruses constitute a diverse virus family infecting a wide variety of mammalian species, including humans and non-human primates. We demonstrate that our pan-papillomavirus CODEHOP assay is broadly reactive with all major branches of the virus family and show its utility in identifying a novel non-human primate papillomavirus in cynomolgus macaques.
authors.affiliation: Center for Childhood Infections and Prematurity Research, Seattle Children's Research Institute, 1900 Ninth Ave., 8th Floor, Seattle, WA 98101-1304, USA.
authors.forename: Jeannette P
authors.initials: JP
authors.lastname: Staheli
authors.forename: Jonathan T
authors.initials: JT
authors.lastname: Ryan
authors.forename: A Gregory
authors.initials: AG
authors.lastname: Bruce
authors.forename: Richard
authors.initials: R
authors.lastname: Boyce
authors.forename: Timothy M
authors.initials: TM
authors.lastname: Rose
mesh_terms: D000818:Animals; D017124:Conserved Sequence; D017931:DNA Primers / Q000235:genetics; D004279:DNA, Viral / Q000235:genetics; D006801:Humans; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D018419:Primate Diseases / Q000821:virology*; D011323:Primates / Q000235:genetics* / Q000821:virology*; D014777:Virus Diseases / Q000821:virology*; D014780:Viruses / Q000235:genetics*
chemical_list: D017931:DNA Primers; D004279:DNA, Viral