Department of Microbiology, Daegu Catholic University School of Medicine, Daegu, 42472, Republic of Korea.
BMC Genomics. 2018 Jul 13;19(1):535. doi: 10.1186/s12864-018-4935-z.
The Zika virus (ZIKV) can cause microcephaly and congenital abnormalities in the foetus. Recent studies have provided insights into the evolution of ZIKV from the current and previous outbreaks, but the types have not been determined.
We analysed the insertions and deletions (InDels) in 212 ZIKV polyproteins and 5 Dengue virus (DENV) reference sequences. Spearman correlation tests for the minimum InDel (minInDel) patterns were used to assess the type of polyprotein. Using the minInDel frequencies calculated from polyproteins with 11 elements, likelihood estimation was conducted to correct the evolutionary distance. The minInDel-corrected tree topology clearly distinguished between the ZIKV types (I and II) with a unique minInDel character in the E protein. From the 10-year average genetic distance, the African and Asian lineages of ZIKV-II were estimated to have occurred ~ 270 years ago, which is unlikely for ZIKV-I.
The minInDel pattern analysis showed that the minInDel in the E protein is targetable for the rapid detection and determination of the virus types.
寨卡病毒（ZIKV）可导致胎儿小头畸形和先天性异常。最近的研究提供了对 ZIKV 从当前和以前爆发的演变的深入了解，但尚未确定其类型。
我们分析了 212 种 ZIKV 多蛋白和 5 种登革热病毒（DENV）参考序列中的插入和缺失（InDels）。使用最小插入缺失（minInDel）模式的斯皮尔曼相关检验来评估多蛋白的类型。使用具有 11 个元件的多蛋白计算的 minInDel 频率进行似然估计以校正进化距离。minInDel 校正的树拓扑结构清楚地区分了 ZIKV 类型（I 和 II），在 E 蛋白中具有独特的 minInDel 特征。从 10 年平均遗传距离估计，ZIKV-II 的非洲和亚洲谱系发生在约 270 年前，这对于 ZIKV-I 来说不太可能。
minInDel 模式分析表明，E 蛋白中的 minInDel 可用于快速检测和确定病毒类型。
