%0 Journal Article
%T Hepatitis C virus whole genome position weight matrix and robust primer design
%A Ping Qiu
%A Xiao-Yan Cai
%A Luquan Wang
%A Jonathan R Greene
%A Bruce Malcolm
%J BMC Microbiology
%D 2002
%I BioMed Central
%R 10.1186/1471-2180-2-29
%X A position weight matrix (PWM) and a consensus sequence were built for each region of HCV and subsequently assembled into a whole genome consensus sequence and PWM. For each of the 10 regions, the number of occurrences of each base at a given position was compiled. These counts were converted to frequencies that were used to calculate log odds scores. Using over 100 complete and 14,000 partial HCV genomes from GenBank, a consensus HCV genome sequence was generated along with a PWM reflecting heterogeneity at each position. The PWM was used to identify the most conserved regions for primer design.This approach allows rapid identification of conserved regions for robust primer design and is broadly applicable to sets of genomes with all levels of genetic heterogeneity.Genetic heterogeneity is a hallmark of RNA viruses in general, and the hepatitis C virus (HCV) in particular, due to the lack of fidelity of viral RNA-dependent RNA polymerases [1,2]. In HCV, this genetic diversity has been organized into six major genotypes and numerous subtypes (over 80). Isolates of the same genotype have an average DNA sequence identity of 95%, but different genotypes have DNA sequence identity close to 65% on average [2-5].Nucleic acid-based assays, such as the polymerase chain reaction (PCR), the ligase chain reaction (LCR), nucleic acid sequence-based amplification (NASBA), branched chain DNA (bDNA) and sequence analysis itself, rely on the efficient hybridization of oligonucleotides to the targeted sequence. Mismatches between the oligonucleotides and the targeted nucleic acid can affect duplex stability and may compromise the ability of a system to amplify and detect the targeted sequences. Numerous factors determine the effect of mismatches, including: the length of the oligonucleotide, the nature and position of the mismatches, the temperature of hybridization, the presence of co-solvents and the concentrations of oligonucleotides, as well as monovalent and divalent cations [6
%U http://www.biomedcentral.com/1471-2180/2/29