Affiliation: University of Edinburgh
Simmonds P, Tuplin A, Evans D. Detection of genome-scale ordered RNA structure (GORS) in genomes of positive-stranded RNA viruses: Implications for virus evolution and host persistence. RNA. 2004;10:1337-51 pubmed
..These findings potentially reconcile the rapid evolution of RNA viruses over short periods with the documented examples of extreme conservatism evident from their intimate coevolution with their hosts. ..
Gaunt E, Harvala H, Ã–sterback R, Sreenu V, Thomson E, Waris M, et al
. Genetic characterization of human coxsackievirus A6 variants associated with atypical hand, foot and mouth disease: a potential role of recombination in emergence and pathogenicity. J Gen Virol. 2015;96:1067-79 pubmed publisher
..These observations provided evidence that NS gene regions may potentially contribute to clinical phenotypes and outcomes of CVA6 infection. ..
Simmonds P. Methods for virus classification and the challenge of incorporating metagenomic sequence data. J Gen Virol. 2015;96:1193-206 pubmed publisher
..For these, simplified taxonomic proposals and naming conventions represent a practical way to expand the existing virus classification and catalogue our rapidly increasing knowledge of virus diversity. ..
Simmonds P, McIntyre C, Savolainen Kopra C, Tapparel C, Mackay I, Hovi T. Proposals for the classification of human rhinovirus species C into genotypically assigned types. J Gen Virol. 2010;91:2409-19 pubmed publisher
Witteveldt J, Martin Gans M, Simmonds P. Enhancement of the Replication of Hepatitis C Virus Replicons of Genotypes 1 to 4 by Manipulation of CpG and UpA Dinucleotide Frequencies and Use of Cell Lines Expressing SECL14L2 for Antiviral Resistance Testing. Antimicrob Agents Chemother. 2016;60:2981-92 pubmed publisher
..These methods of replication enhancement provide new tools for monitoring the susceptibility and resistance of a wide range of HCV genotypes to DAAs. ..
Simmonds P. SSE: a nucleotide and amino acid sequence analysis platform. BMC Res Notes. 2012;5:50 pubmed publisher
..SSE combines sequence editor functions with analytical tools in a comprehensive and user-friendly package that assists considerably in bioinformatic and evolution research. ..
Simmonds P. Transfusion virology: progress and challenges. Blood Rev. 1998;12:171-7 pubmed
..Establishing a framework for PCR-based screening would also enable the testing for others such as hepatitis A virus, parvovirus B19 and GBV-C/HGV for which serological detection methods cannot be or have not been developed...
Simmonds P, Smith D. Structural constraints on RNA virus evolution. J Virol. 1999;73:5787-94 pubmed
..quot; This places a major restriction on the use of nucleotide or amino acid sequence comparisons to calculate times of divergence of other viruses evolving under the same structural constraints as GB viruses. ..
Simmonds P. The origin of hepatitis C virus. Curr Top Microbiol Immunol. 2013;369:1-15 pubmed publisher
..Further research on a much wider range of mammals is needed to better understand the true genetic diversity of HCV-like viruses and their host ranges in the search for the ultimate origin of HCV in humans. ..