Nguyen, Anh Tran, Thanh Hoang, Van Nghiem, Ngoc Le, Nhu Le, Thanh Phan, Qui Truong, Khanh Le, Nhan Ho, Viet Do, Viet Ha, Tuan Nguyen, Hung Nguyen, Chau Thwaites, Guy van Doorn, H. Le, Tan Additional file 1: Table S1. of Development and evaluation of a non-ribosomal random PCR and next-generation sequencing based assay for detection and sequencing of hand, foot and mouth disease pathogens List of 96 FR26RV-Endoh and FR20RV primer sequences. Table S2. Result summary of consensus sequence variations recorded between 2 replicates of 3 tested swabs. Note: NA: not applicable. Figure S1. Screen snapshots showing the mapping results of EV-A71 MiSeq reads to an EV-A71 reference genome of sample ID15; non-ribosomal rPCR assay (bottom panel), non-ribosomal hexanucleotide primers assay (middle panel) and hexanucleotide assay (top panel); the genome sequencing depth is indicated by the Y axis and covered by red circles. Figure S2. Maximum likelihood phylogenetic tree based on completed VP1 nucleotide sequences (891 nt) of EV-A71 strains obtained from this study (in bold red) and representatives retrieved from GenBank. Scale bars indicated numbers of nucleotide substitution per site. CHN, China; USA, United states; TW, Taiwan; NL, Netherlands; MY, Malaysia; KOR, Korean; VN, Vietnam. Figure S3. Maximum likelihood phylogenetic tree based on completed VP1 nucleotide sequences (891 nt) of CV-A16 strains obtained from this study (in bold red) and representatives retrieved from GenBank. Scale bars indicated numbers of nucleotide substitution per site. CHN, China; US, United states; TL, Thailand; JPN, Japan; AUS, Australia; MY, Malaysia; KOR, Korean; VN, Vietnam. (PDF 783 kb) Hand, foot and mouth disease;Enterovirus A;Random PCR;FR26RV-Endoh primer;Next-generation sequencing 2016-07-07
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