title: Evolution of type 2 vaccine derived poliovirus lineages. Evidence for codon-specific positive selection at three distinct locations on capsid wall.
abstract: Partial sequences of 110 type 2 poliovirus strains isolated from sewage in Slovakia in 2003-2005, and most probably originating from a single dose of oral poliovirus vaccine, were subjected to a detailed genetic analysis. Evolutionary patterns of these vaccine derived poliovirus strains (SVK-aVDPV2) were compared to those of type 1 and type 3 wild poliovirus (WPV) lineages considered to have a single seed strain origin, respectively. The 102 unique SVK-aVDPV VP1 sequences were monophyletic differing from that of the most likely parental poliovirus type 2/Sabin (PV2 Sabin) by 12.5-15.6%. Judging from this difference and from the rate of accumulation of synonymous transversions during the 22 month observation period, the relevant oral poliovirus vaccine dose had been administered to an unknown recipient more than 12 years earlier. The patterns of nucleotide substitution during the observation period differed from those found in the studied lineages of WPV1 or 3, including a lower transition/transversion (Ts/Tv) bias and strikingly lower Ts/Tv rate ratios at the 2(nd) codon position for both purines and pyrimidines. A relatively low preference of transitions at the 2(nd) codon position was also found in the large set of VP1 sequences of Nigerian circulating (c)VDPV2, as well as in the smaller sets from the Hispaniola cVDPV1 and Egypt cVDPV2 outbreaks, and among aVDPV1and aVDPV2 strains recently isolated from sewage in Finland. Codon-wise analysis of synonymous versus non-synonymous substitution rates in the VP1 sequences suggested that in five codons, those coding for amino acids at sites 24, 144, 147, 221 and 222, there may have been positive selection during the observation period. We conclude that pattern of poliovirus VP1 evolution in prolonged infection may differ from that found in WPV epidemics. Further studies on sufficiently large independent datasets are needed to confirm this suggestion and to reveal its potential significance.
authors.affiliation: Virology Unit, Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare (THL), Helsinki, Finland. tapani.hovi@thl.fi
authors.forename: Tapani
authors.initials: T
authors.lastname: Hovi
authors.forename: Carita
authors.initials: C
authors.lastname: Savolainen-Kopra
authors.forename: Teemu
authors.initials: T
authors.lastname: Smura
authors.forename: Soile
authors.initials: S
authors.lastname: Blomqvist
authors.forename: Haider
authors.initials: H
authors.lastname: Al-Hello
authors.forename: Merja
authors.initials: M
authors.lastname: Roivainen
mesh_terms: D019943:Amino Acid Substitution; D001483:Base Sequence; D001499:Bayes Theorem; D036022:Capsid Proteins / Q000737:chemistry / Q000235:genetics*; D003062:Codon; D017124:Conserved Sequence; D019143:Evolution, Molecular; D005814:Genes, Viral; D049810:Genetic Speciation; D005838:Genotype; D006801:Humans; D008957:Models, Genetic; D008958:Models, Molecular; D009010:Monte Carlo Method; D010802:Phylogeny; D017354:Point Mutation; D017955:Poliovirus / Q000235:genetics* / Q000276:immunology; D011055:Poliovirus Vaccine, Oral; D020836:Protein Structure, Quaternary; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D012722:Sewage / Q000821:virology
chemical_list: D036022:Capsid Proteins; D003062:Codon; D011055:Poliovirus Vaccine, Oral; D012722:Sewage; C442540:VP1 protein, Poliovirus