Nonstructural Proteins Are Preferential Positive Selection Targets in Zika Virus and Related Flaviviruses

Abstract

The Flavivirus genus comprises several human pathogens such as dengue virus (DENV), Japanese encephalitis virus (JEV), and Zika virus (ZIKV). Although ZIKV usually causes mild symptoms, growing evidence is linking it to congenital birth defects and to increased risk of Guillain-Barré syndrome. ZIKV encodes a polyprotein that is processed to produce three structural and seven nonstructural (NS) proteins. We investigated the evolution of the viral polyprotein in ZIKV and in related flaviviruses (DENV, Spondweni virus, and Kedougou virus). After accounting for saturation issues, alignment uncertainties, and recombination, we found evidence of episodic positive selection on the branch that separates DENV from the other flaviviruses. NS1 emerged as the major selection target, and selected sites were located in immune epitopes or in functionally important protein regions. Three of these sites are located in an NS1 region that interacts with structural proteins and is essential for virion biogenesis. Analysis of the more recent evolutionary history of ZIKV lineages indicated that positive selection acted on NS5 and NS4B, this latter representing the preferential target. All selected sites were located in the N-terminal portion of NS4B, which inhibits interferon response. One of the positively selected sites (26M/I/T/V) in ZIKV also represents a selection target in sylvatic DENV2 isolates, and a nearby residue evolves adaptively in JEV. Two additional positively selected sites are within a protein region that interacts with host (e.g. STING) and viral (i.e. NS1, NS4A) proteins. Notably, mutations in the NS4B region of other flaviviruses modulate neurovirulence and/or neuroinvasiveness. These results suggest that the positively selected sites we identified modulate viral replication and contribute to immune evasion. These sites should be prioritized in future experimental studies. However, analyses herein detected no selective events associated to the spread of the Asian/American ZIKV lineage.

RNA editing by the host ADAR system affects the molecular evolution of the Zika virus

“…The PHYML protein comparison with the Spondweni virus as the outgroup, the available flavivirus phylogenies (e.g., Grard et al., ; Sironi et al., ), and our own midpoint rooting analysis all agree that the root for the ZIKV ML phylogeny lies somewhere along the internal branch that bipartitions the ten African genomes from the 46 Asian, Oceanian, and New World sequences (Figure ). Within the Asian, Oceanian, and New World group, the two Malaysian genomes diverge first, followed by the split of the Micronesian sequence from the French Polynesian, Chinese, and American subtree (Faria et al., ; Wang et al., ).…”

Phylodynamics of Yellow Fever Virus in the Americas: new insights into the origin of the 2017 Brazilian outbreak

“…We also detected a large number of amino acid mutations ( n = 35) that arose during recent dispersion of modern-lineage (subclade 1E) in Brazil and Venezuela, which could reflect more frequent viral replication cycles in large susceptible populations of primates from non-endemic regions and/or selective pressures for new viral variants with specific phenotypic characteristics. Of note, most (91%) amino acid substitutions detected in YFV modern-lineage accumulated within non-structural proteins that have been pointed as relevant selection targets in evolution of Flaviviruses 27 , 28 .…”

Characterization of the Zika virus two-component NS2B-NS3 protease and structure-assisted identification of allosteric small-molecule antagonists

“…1A). The structural C, prM, and E proteins assemble to build the mature viral particles, while the non-structural proteins are responsible for viral replication and propagation (Sironi et al, 2016). …”