title: Phylogenetic analysis of the full-length SARS-CoV sequences: evidence for phylogenetic discordance in three genomic regions.
abstract: The origin of the severe acute respiratory syndrome-coronavirus (SARS-CoV) remains unclear. Evidence based on Bayesian scanning plots and phylogenetic analysis using maximum likelihood (ML) and Bayesian methods indicates that SARS-CoV, for the largest part of the genome ( approximately 80%), is more closely related to Group II coronaviruses sequences, whereas in three regions in the ORF1ab gene it shows no apparent similarity to any of the previously characterized groups of coronaviruses. There is discordant phylogenetic clustering of SARS-CoV and coronaviruses sequences, throughout the genome, compatible with either ancient recombination events or altered evolutionary rates in different lineages, or a combination of both.
authors.affiliation: National Retrovirus Reference Center, Department of Hygiene and Epidemiology, Athens University Medical School, Athens, Greece.
authors.forename: G
authors.initials: G
authors.lastname: Magiorkinis
authors.forename: E
authors.initials: E
authors.lastname: Magiorkinis
authors.forename: D
authors.initials: D
authors.lastname: Paraskevis
authors.forename: A M
authors.initials: AM
authors.lastname: Vandamme
authors.forename: M
authors.initials: M
authors.lastname: Van Ranst
authors.forename: V
authors.initials: V
authors.lastname: Moulton
authors.forename: A
authors.initials: A
authors.lastname: Hatzakis
mesh_terms: D019143:Evolution, Molecular; D016679:Genome, Viral; D006801:Humans; D010802:Phylogeny; D011995:Recombination, Genetic; D045473:Severe acute respiratory syndrome-related coronavirus / Q000145:classification* / Q000235:genetics*; D016415:Sequence Alignment; D014764:Viral Proteins / Q000235:genetics
chemical_list: D014764:Viral Proteins