Naeem Asif, Hosomi Takushi, Nishimura Yorihiro, Alam Muhammad Masroor, Oka Tomoichiro, Zaidi Syed Sohail Zahoor, Shimizu Hiroyuki
Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan.
The Meat Inspection Center of Kochi Prefecture, Kochi, Japan.
J Gen Virol. 2014 Sep;95(Pt 9):1945-1957. doi: 10.1099/vir.0.066498-0. Epub 2014 Jun 4.
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.
人心病毒或微小核糖核酸病毒科的萨福尔德病毒（SAFVs）是新出现的病毒，人们对其遗传和表型多样性了解甚少。我们在此报告来自巴基斯坦和阿富汗的11种SAFV基因型的全基因组序列，以及对其遗传多样性和重组的重新评估。我们使用针对5'非翻译区（UTR）的逆转录聚合酶链反应，从943例急性弛缓性麻痹病例的粪便样本中检测到88种SAFV。基于完整的VP1分析的进一步表征显示，71种SAFV属于11种基因型，包括三种以前未鉴定的基因型。基于本文进行的系统发育、成对距离分布和重组图谱分析，SAFV显示出高度的遗传多样性和重组。基于非结构区和UTR的系统发育高度不一致，表明SAFV之间频繁发生重组事件。我们根据用于肠道病毒分类的原则确定了新的VP1阈值，从而改进了SAFV基因分型分类标准。对于基因型分配，我们分别提出VP1核苷酸和氨基酸序列差异的阈值为23%和10%。蒂洛病毒属的其他成员，如特拉病毒和泰勒氏小鼠脑脊髓炎病毒，很难与SAFV归为同一物种，因为它们在遗传上与SAFV不同，成对氨基酸距离为41%-56%。本研究获得的新遗传信息将增进我们对SAFV进化和分类的理解。
