title: Genetic diversity of circulating Saffold viruses in Pakistan and Afghanistan.
abstract: Human cardioviruses or Saffold viruses (SAFVs) of the family Picornaviridae are newly emerging viruses whose genetic and phenotypic diversity are poorly understood. We report here the full genome sequence of 11 SAFV genotypes from Pakistan and Afghanistan, along with a re-evaluation of their genetic diversity and recombination. We detected 88 SAFV from stool samples of 943 acute flaccid paralysis cases using reverse transcriptase-PCR targeting the 5' untranslated region (UTR). Further characterization based on complete VP1 analysis revealed 71 SAFVs belonging to 11 genotypes, including three previously unidentified genotypes. SAFV showed high genetic diversity and recombination based on phylogenetic, pairwise distance distributions and recombination mapping analyses performed herein. Phylogenies based on non-structural and UTRs were highly incongruent indicating frequent recombination events among SAFVs. We improved the SAFV genotyping classification criteria by determining new VP1 thresholds based on the principles used for the classification of enteroviruses. For genotype assignment, we propose a threshold of 23 and 10 % divergence for VP1 nucleotide and amino acid sequences, respectively. Other members of the species Theilovirus, such as Thera virus and Theiler's murine encephalomyelitis virus, are difficult to classify in the same species as SAFV, because they are genetically distinct from SAFV, with 41-56 % aa pairwise distances. The new genetic information obtained in this study will improve our understanding of the evolution and classification of SAFV.
authors.affiliation: Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan.
authors.forename: Asif
authors.initials: A
authors.lastname: Naeem
authors.affiliation: The Meat Inspection Center of Kochi Prefecture, Kochi, Japan.
authors.forename: Takushi
authors.initials: T
authors.lastname: Hosomi
authors.affiliation: Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan.
authors.forename: Yorihiro
authors.initials: Y
authors.lastname: Nishimura
authors.affiliation: Department of Virology, National Institute of Health, Islamabad, Pakistan.
authors.forename: Muhammad Masroor
authors.initials: MM
authors.lastname: Alam
authors.affiliation: Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan.
authors.forename: Tomoichiro
authors.initials: T
authors.lastname: Oka
authors.affiliation: Department of Virology, National Institute of Health, Islamabad, Pakistan.
authors.forename: Syed Sohail Zahoor
authors.initials: SSZ
authors.lastname: Zaidi
authors.affiliation: Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Shimizu
mesh_terms: D020121:5' Untranslated Regions / Q000235:genetics; D000346:Afghanistan; D000595:Amino Acid Sequence; D001483:Base Sequence; D005075:Biological Evolution; D036022:Capsid Proteins / Q000235:genetics; D017943:Cardiovirus / Q000145:classification* / Q000235:genetics*; D018188:Cardiovirus Infections / Q000821:virology; D002874:Chromosome Mapping; D005243:Feces / Q000821:virology; D014644:Genetic Variation; D016679:Genome, Viral / Q000235:genetics*; D005838:Genotype; D006801:Humans; D008969:Molecular Sequence Data; D009123:Muscle Hypotonia / Q000821:virology; D010154:Pakistan; D010641:Phenotype; D017423:Sequence Analysis, RNA; D017945:Theilovirus / Q000235:genetics; D014764:Viral Proteins / Q000235:genetics*
chemical_list: D020121:5' Untranslated Regions; D036022:Capsid Proteins; D014764:Viral Proteins