Minimum InDel pattern analysis of the Zika virus

Hyeji Lee,Yunhee Choi,Mai Phuong Nguyen,Yong-Hak Kim

doi:10.1186/s12864-018-4935-z

Abstract

BackgroundThe 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.ResultsWe 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.ConclusionsThe minInDel pattern analysis showed that the minInDel in the E protein is targetable for the rapid detection and determination of the virus types.

Highlights

The Zika virus (ZIKV) can cause microcephaly and congenital abnormalities in the foetus
This study aims at analysing the minimum insertions and deletions (InDels) patterns of closely related ZIKV and Dengue virus (DENV) on the basis of a consensus polyprotein sequence to reduce the burdens of ambiguous InDels and unreliable substitutions in aligned sequences for a divergent population
The minInDel patterns based on the length of the consensus sequences of the ZIKV and DENV strains divided the ZIKV strains into two types (ZIKV-I and -II), according to the variation in the length of the E protein (Fig. 1)

Summary

Introduction

The Zika virus (ZIKV) can cause microcephaly and congenital abnormalities in the foetus. Recent genomic studies have provided insights into the evolutionary patterns of ZIKV strains from the current and ZIKV genomes differentiated into African and Asian lineages, as determined by phylogenetic studies [7, 8, 11]. Recent phylogenetic trees of ZIKV showed a strong evolutionary bias towards a greater number of Asian strains than African strains. InDels occur to a lesser degree than substitutions in viruses as well as in cells [17, 18] Their occurrence represents a loss of function, independent of the evolutionary time for all of the sequences and is likely to increase an active subspace (length), where their orthologues are separated prior to the high-frequency substitutions under selective constraints. We must reduce the distribution of the composition bias between the true InDels and the alignment of finite sequences

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Conclusion