Comparative genomic analysis of pre-epidemic and epidemic Zika virus strains for virological factors potentially associated with the rapidly expanding epidemic

Zhu, Zheng; Chan, Jasper Fuk-Woo; Tee, Kah-Meng; Choi, Garnet Kwan-Yue; Lau, Susanna Kar-Pui; Woo, Patrick Chiu-Yat; Tse, Herman; Yuen, Kwok-Yung

The E protein is the major surface protein of flaviviruses and is involved in viral attachment, fusion, penetration, hemagglutination, host range and cell tropism. 45 Structurally, three domains could be found in the E protein of flaviviruses based on X-ray crystallographic structural studies. Domain I is located in the middle of the E protein and contains the N terminus with glycosylation sites. Domain II contains the fusion peptide at the distal side and flanks one side of domain I. Domain III flanks the other side of domain I and is the major antigenic region in the E protein. It also contains the receptorbinding site and is, therefore, an important therapeutic and vaccine target of flaviviruses. E345K substitution at the E protein of DENV-4 is associated with reduced viral virulence. 46 Importantly, we found a number of amino acid substitutions in the E protein of the epidemic ZIKV strain (Figure 2A Comparative genomic analysis of Zika virus Z Zhu et al NS1 of flaviviruses is a glycoprotein that may contain multiple N-glycosylation sites and disulfide bonds that may affect virus viability and virulence. 47 Significant NS1 codon usage adaptation to human housekeeping genes by the recent Asian lineage of ZIKV has been suggested to be a facilitator of viral replication and increased viral titers. 48 NS1 may exist in different forms, depending on the variable formation of N-glycosylation sites and disulfide bonds. The monomers of NS1 are soluble and hydrophilic, whereas the NS1 homodimers may associate with the endoplasmic reticular membranes. 49, 50 The NS1 protein also exists in a soluble hexamer form that is secreted by mammalian cells. 19 Mutations at the NS1 N-glycosylation sites may significantly affect viral replication and virulence in YFV. 51 Deletion studies suggest that NS1 is required for initiation of RNA synthesis and especially during early negative strand RNA genome synthesis. 19 Using the available genomic data in this study, we were not able to find any putative N-glycosylation sites in NS1 of the ZIKV genomes, but we found four different amino acid substitutions between the African and the Asian lineages (E842D, K859R, A984V and V1026I). The importance of these substitutions will await further verifications.