title: Substitution rate and natural selection in parvovirus B19.
abstract: The aim of this study was to estimate substitution rate and imprints of natural selection on parvovirus B19 genotype 1. Studied datasets included 137 near complete coding B19 genomes (positions 665 to 4851) for phylogenetic and substitution rate analysis and 146 and 214 partial genomes for selection analyses in open reading frames ORF1 and ORF2, respectively, collected 1973-2012 and including 9 newly sequenced isolates from Serbia. Phylogenetic clustering assigned majority of studied isolates to G1A. Nucleotide substitution rate for total coding DNA was 1.03 (0.6-1.27) x 10-4substitutions/site/year, with higher values for analyzed genome partitions. In spite of the highest evolutionary rate, VP2 codons were found to be under purifying selection with rare episodic positive selection, whereas codons under diversifying selection were found in the unique part of VP1, known to contain B19 immune epitopes important in persistent infection. Analyses of overlapping gene regions identified nucleotide positions under opposite selective pressure in different ORFs, suggesting complex evolutionary mechanisms of nucleotide changes in B19 viral genomes.
authors: Department of Genetic Research, Institute for biological research "Siniša Stanković", University of Belgrade, 142 Despot Stephan Blvd, 11060 Belgrade, R Serbia.
authors: Gorana G
authors: GG
authors: Stamenković
authors: Institute for Microbiology and Immunology, School of Medicine, University of Belgrade, 1/1 Dr Subotića St, 11000 Belgrade, R Serbia.
authors: Valentina S
authors: VS
authors: Ćirković
authors: Institute for Microbiology and Immunology, School of Medicine, University of Belgrade, 1/1 Dr Subotića St, 11000 Belgrade, R Serbia.
authors: Marina M
authors: MM
authors: Šiljić
authors: Department of Genetic Research, Institute for biological research "Siniša Stanković", University of Belgrade, 142 Despot Stephan Blvd, 11060 Belgrade, R Serbia.
authors: Jelena V
authors: JV
authors: Blagojević
authors: Institute for Microbiology and Immunology, School of Medicine, University of Belgrade, 1/1 Dr Subotića St, 11000 Belgrade, R Serbia.
authors: Aleksandra M
authors: AM
authors: Knežević
authors: Clinic of Obstetrics and Gynecology "Narodni front", 62 Kraljice Natalije St, 11000 Belgrade, R Serbia.
authors: Ivana D
authors: ID
authors: Joksić
authors: Institute for Microbiology and Immunology, School of Medicine, University of Belgrade, 1/1 Dr Subotića St, 11000 Belgrade, R Serbia.
authors: Maja P
authors: MP
authors: Stanojević
mesh_terms: D002213:Capsid / Q000378:metabolism; D036022:Capsid Proteins / Q000235:genetics; D003062:Codon / Q000235:genetics; D004279:DNA, Viral / Q000235:genetics; D000939:Epitopes / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics*; D016679:Genome, Viral / Q000235:genetics; D005838:Genotype; D006801:Humans; D007074:Immunoglobulin G / Q000235:genetics; D007075:Immunoglobulin M / Q000235:genetics; D009711:Nucleotides / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics; D010322:Parvoviridae Infections / Q000821:virology; D016732:Parvovirus B19, Human / Q000235:genetics*; D010802:Phylogeny; D012641:Selection, Genetic / Q000235:genetics*; D055771:Serbia
chemical_list: D036022:Capsid Proteins; D003062:Codon; D004279:DNA, Viral; D000939:Epitopes; D007074:Immunoglobulin G; D007075:Immunoglobulin M; D009711:Nucleotides