Table S1 - Characterization of Synthetic Chikungunya Viruses Based on the Consensus Sequence of Recent E1-226V Isolates

Comparison of CHIKV LS3 with the genome sequences of various closely related natural isolates. Only differences between LS3 and each of the other strains are summarized. Dots indicate that the nucleotide at that position is identical to that at the corresponding position in the sequence of LS3. Genomes were aligned with MAFFT and analyzed in Jalview. Numbering is based on the sequence of LR2006_OPY1 (and is equal to LS3 numbering). The nucleotide at position 10670 (indicated in gray) determines whether the strain has the A226V mutation in the E1 protein. Strains with a T at this position have the A226V mutation. Differences not included in the comparison are the 35 nt, 5 nt and 23 nucleotides that are missing from the 3’UTR of the sequences of DRDE-07, D570/06 and ITA07-RA1, respectively. The missing first 19 nt, missing last 13 nt and the insertion of an A after position 11564 in the sequence of IND-06-AP3 were also not included in this comparison. (PDF)基孔肯雅病毒LS3株（CHIKV LS3）与多种密切相关天然分离株的基因组序列比对分析，本比对仅汇总LS3与各其余毒株间的序列差异。比对结果中以点号标注与LS3序列对应位置核苷酸完全一致的位点。所有基因组序列均通过MAFFT完成多序列比对，并使用Jalview进行分析。本次比对采用LR2006_OPY1序列的编号规则，该规则与LS3的编号体系完全一致。第10670位核苷酸（以灰色标注）可决定该毒株是否携带E1蛋白的A226V突变；若该位点的核苷酸为胸腺嘧啶（T），则毒株存在A226V突变。本次比对未纳入的差异包括：DRDE-07、D570/06及ITA07-RA1的3'非翻译区（3' Untranslated Region, 3'UTR）分别缺失的35 nt、5 nt与23 nt；IND-06-AP3序列中缺失的首段19 nt、尾段13 nt，以及其11564位之后插入的1个腺嘌呤（A）。（PDF）