Complete genome analysis of a sapovirus in a mixed infected patient of hand foot and mouth disease

Abstract

Objective To understand the potential viral pathogens other than enteroviruses existing in samples of hand foot and mouth disease (HFMD) patient and study their molecular feature and genotype. Methods The deep sequencing analysis of a fecal specimen collected from HFMD patient was conducted by metagenomics and bioinformatics. Results Enterovirus A71 and sapovirus mixed infection was found in this case. The nucleic acid of sapovirus was confirmed positive by RT-PCR and the 7 429 bp complete genome sequence of sapovirus was obtained by assembling sequencing reads which consisted of 3 open reading frames. Phylogenetic analysis revealed that this strain of virus should belong to the genotype 1 of sapovirus having a homology of 99.4% with sapovirus Hu/G1/Zhejiang1/China/2014 strain, which is a currently predominant genotype circulating in China. Conclusions The sapovirus, which is a predominant strain circulating in China, was a mixed infected causative agent existing in HFMD sample identified by deep sequencing. This study will serve as a reference for pathogen detection of HFMD and diarrheal related diseases, as well as provide a sequence reference for molecular feature study of sapovirus in China in the future. Key words: Sapovirus; Deep sequencing; Complete genome sequence; Phylogenetic analysis