You are here
Consensus-degenerate hybrid oligonucleotide primers (CODEHOPs) for the detection of novel viruses in non-human primates.
Title | Consensus-degenerate hybrid oligonucleotide primers (CODEHOPs) for the detection of novel viruses in non-human primates. |
Publication Type | Journal Article |
Year of Publication | 2009 |
Authors | Staheli, JP, Ryan, JT, A Bruce, G, Boyce, R, Rose, TM |
Journal | Methods |
Volume | 49 |
Issue | 1 |
Pagination | 32-41 |
Date Published | 2009 Sep |
ISSN | 1095-9130 |
Keywords | Animals, Conserved Sequence, DNA Primers, DNA, Viral, Humans, Phylogeny, Polymerase Chain Reaction, Primate Diseases, Primates, Virus Diseases, Viruses |
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. |
DOI | 10.1016/j.ymeth.2009.05.011 |
Alternate Journal | Methods |
PubMed ID | 19477279 |
PubMed Central ID | PMC2751581 |
Grant List | P51 RR000166-48 / RR / NCRR NIH HHS / United States P51-RR00166 / RR / NCRR NIH HHS / United States R24 RR021346-04 / RR / NCRR NIH HHS / United States R24-RR021346 / RR / NCRR NIH HHS / United States |