Deciphering contrasting evolutionary phases underlines Zika virus emergence from African ancestry to American pandemic spread

Deciphering contrasting evolutionary phases underlines Zika virus emergence from African ancestry to American pandemic spread | Authorea try { document.documentElement.classList.add('js'); } catch (e) { } var _gaq = _gaq || []; _gaq.push(['_setAccount', 'G-8VDV14Y67G']); _gaq.push(['_trackPageview']); (function() { var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true; ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js'; var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); Skip to main content Preprints Collections Wiley Open Research IET Open Research Ecological Society of Japan All Collections About About Authorea FAQs Contact Us Quick Search anywhere Search for preprint articles, keywords, etc. Search Search ADVANCED SEARCH SCROLL This is a preprint and has not been peer reviewed. Data may be preliminary. 5 February 2026 V1 Latest version Share on Deciphering contrasting evolutionary phases underlines Zika virus emergence from African ancestry to American pandemic spread Authors : Sanjeet Kumar and Kanika Bansal 0000-0003-3740-4917 [email protected] Authors Info & Affiliations https://doi.org/10.22541/au.177030224.45215694/v1 115 views 50 downloads Contents Abstract Supplementary Material Information & Authors Metrics & Citations View Options References Figures Tables Media Share Abstract virus (ZIKV) transitioned from an enzootic African to a globally consequential pathogen during its rapid spread across the Pacific and American continent yet how distinct evolutionary processes shaped lineage establishment and pandemic expansion remain incompletely resolved. Here, we integrate large-scale phylogenomic and comparative mutational analysis of 1,336 ZIKV genomes depicting the genomic signatures associated with successive phases of viral diversification. Using African prototype strain MR766 as reference, Asian lineage evolution was dominated by synonymous mutations (87%), consistent with long-term lineage establishment under strong purifying selection. Despite this, we identified 109 lineage-defining nonsynonymous mutations fixed across Asian strains, enriched in non-structural proteins mapping largely to structurally permissive or surface-exposed regions for functional fine-tuning. In striking contrast, analysis relative to a Pacific Asian strain positioned at the phylogenetic transition point reveals a profound shift towards nonsynonymous substitutions (93.5%), indicative of intensified protein-level diversification during rapid epidemic expansion. Notably, only six amino acid substitutions are fixed across ≥95% of American pandemic strains, demonstrating that extensive mutational turnover accompanied continental spread but with constrained fixation. Collectively, these findings support a phase-dependent model of ZIKV evolution in which gradual lineage formation is shaped by neutral drift and purifying selection, whereas epidemic and pandemic expansion represents a distinct evolutionary regime marked by selective filtering of limited protein-level substitutions. This study provides a unified evolutionary framework for understanding how ZIKV acquired the genomic features that enabled its explosive spread and heightened pathogenic impact. More broadly, our findings underscore how viral genomic signatures can inform epidemic preparedness and constrain expectations of future outbreak evolution. Supplementary Material File (01_manuscript_1.docx) Download 75.68 KB File (01_manuscript_2.docx) Download 75.68 KB File (figure_1.tif) Download 57.16 MB File (table1.docx) Download 135.40 KB Information & Authors Information Version history V1 Version 1 05 February 2026 Copyright This work is licensed under a Non Exclusive No Reuse License. Keywords biostatistics & bioinformatics evolution genetics mutation mutation/mutation rate taxonomy Authors Affiliations Sanjeet Kumar Illumina Solutions Centre View all articles by this author Kanika Bansal 0000-0003-3740-4917 [email protected] CSIR-Institute of Microbial Technology View all articles by this author Metrics & Citations Metrics Article Usage 115 views 50 downloads .FvxKWukQNSOunydq8rnd { width: 100px; } Citations Download citation Sanjeet Kumar, Kanika Bansal. Deciphering contrasting evolutionary phases underlines Zika virus emergence from African ancestry to American pandemic spread. Authorea . 05 February 2026. DOI: https://doi.org/10.22541/au.177030224.45215694/v1 If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. Simply select your manager software from the list below and click Download. For more information or tips please see 'Downloading to a citation manager' in the Help menu . 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