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Discovery of a persistent Zika virus lineage in Bahia, Brazil

Samia N. Naccache, Julien Thézé, Silvia I. Sardi, Sneha Somasekar, Alexander L. Greninger, Antonio C. Bandeira, Gubio S. Campos, Laura B. Tauro, Nuno R. Faria, Oliver G. Pybus, View ORCID ProfileCharles Y. Chiu
doi: https://doi.org/10.1101/049916
Samia N. Naccache
1Department of Laboratory Medicine, University of California, San Francisco, CA 94107, USA.
2UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 91407, USA.
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Julien Thézé
3Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
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Silvia I. Sardi
4Laboratory of Virology, Health Institute of Science, Federal University of Bahia, Salvador, Bahia, Brazil
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Sneha Somasekar
1Department of Laboratory Medicine, University of California, San Francisco, CA 94107, USA.
2UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 91407, USA.
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Alexander L. Greninger
5Department of Laboratory Medicine, University of Washington, Seattle, CA 98195, USA.
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Antonio C. Bandeira
6Alianca Hospital, Salvador, Bahia, Brazil
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Gubio S. Campos
4Laboratory of Virology, Health Institute of Science, Federal University of Bahia, Salvador, Bahia, Brazil
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Laura B. Tauro
7Center of Research Gonzalo Moniz, Foundation Fiocruz, Salvador, Bahia, Brazil
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Nuno R. Faria
3Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
8Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA 67030-000.
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Oliver G. Pybus
3Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
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Charles Y. Chiu
1Department of Laboratory Medicine, University of California, San Francisco, CA 94107, USA.
2UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 91407, USA.
9Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, CA 94107
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  • ORCID record for Charles Y. Chiu
  • For correspondence: charles.chiu@ucsf.edu
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Abstract

Metagenomic next-generation sequencing coupled with capture probe enrichment was used to recover 11 whole and partial Zika virus (ZIKV) genomes from patients in Bahia, Brazil from April 2015 to January 2016, where the majority of suspected Brazilian ZIKV cases have been reported. Phylogenetic reconstructions and molecular clock analyses using the newly generated data uncovered the existence of a Bahia-specific ZIKV lineage sharing a common ancestor in mid-2014, indicating sustained circulation of this strain in Bahia since that date.

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Posted April 24, 2016.
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Discovery of a persistent Zika virus lineage in Bahia, Brazil
Samia N. Naccache, Julien Thézé, Silvia I. Sardi, Sneha Somasekar, Alexander L. Greninger, Antonio C. Bandeira, Gubio S. Campos, Laura B. Tauro, Nuno R. Faria, Oliver G. Pybus, Charles Y. Chiu
bioRxiv 049916; doi: https://doi.org/10.1101/049916
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Discovery of a persistent Zika virus lineage in Bahia, Brazil
Samia N. Naccache, Julien Thézé, Silvia I. Sardi, Sneha Somasekar, Alexander L. Greninger, Antonio C. Bandeira, Gubio S. Campos, Laura B. Tauro, Nuno R. Faria, Oliver G. Pybus, Charles Y. Chiu
bioRxiv 049916; doi: https://doi.org/10.1101/049916

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