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Spread of the pandemic Zika virus lineage is associated with NS1 codon usage adaptation in humans

View ORCID ProfileCaio César de Melo Freire, View ORCID ProfileAtila Iamarino, View ORCID ProfileDaniel Ferreira de Lima Neto, View ORCID ProfileAmadou Alpha Sall, View ORCID ProfilePaolo Marinho de Andrade Zanotto
doi: https://doi.org/10.1101/032839
Caio César de Melo Freire
1Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of Sao Paulo, Sao Paulo, Brazil.
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Atila Iamarino
1Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of Sao Paulo, Sao Paulo, Brazil.
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Daniel Ferreira de Lima Neto
1Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of Sao Paulo, Sao Paulo, Brazil.
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Amadou Alpha Sall
2Institut Pasteur de Dakar, Dakar, Senegal.
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Paolo Marinho de Andrade Zanotto
1Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of Sao Paulo, Sao Paulo, Brazil.
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  • For correspondence: pzanotto@usp.br
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ABSTRACT

Zika virus (ZIKV) infections were more common in the zoonotic cycle until the end of the 20th century with few human cases in Africa and Southeastern Asia. Recently, the Asian lineage of ZIKV is spreading along human-to-human chains of transmission in the Pacific Islands and in South America. To better understand its recent urban expansion, we compared genetic differences among the lineages. Herein we show that the recent Asian lineage spread is associated with significant NS1 codon usage adaptation to human housekeeping genes, which could facilitate viral replication and increase viral titers. These findings were supported by a significant correlation with growth in Malthusian fitness. Furthermore, we predicted several epitopes in the NS1 protein that are shared between ZIKV and Dengue. Our results imply in a significant dependence of the recent human ZIKV spread on NS1 translational selection.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted November 25, 2015.
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Spread of the pandemic Zika virus lineage is associated with NS1 codon usage adaptation in humans
Caio César de Melo Freire, Atila Iamarino, Daniel Ferreira de Lima Neto, Amadou Alpha Sall, Paolo Marinho de Andrade Zanotto
bioRxiv 032839; doi: https://doi.org/10.1101/032839
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Spread of the pandemic Zika virus lineage is associated with NS1 codon usage adaptation in humans
Caio César de Melo Freire, Atila Iamarino, Daniel Ferreira de Lima Neto, Amadou Alpha Sall, Paolo Marinho de Andrade Zanotto
bioRxiv 032839; doi: https://doi.org/10.1101/032839

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