Minimum InDel pattern analysis of the Zika virus

BMC Genomics
Hyeji LeeYong-Hak Kim

Abstract

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.

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Software Mentioned

Clustal W
Clustal
InDel
minInDel
BLOSUM
Findel
TranslatorX
Geneious

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