Genomics of Zika Virus

We are investigating the genomics, phylodynamics, and genotype-phenotype correlations of Zika virus (ZIKV). Our interest is to not only generate next-generation sequence data, but to mine this sequence data to better understand the evolution, pathogenesis, and transmission of ZIKV following the outbreak in Brazil in 2015. To meet these goals, we established collaborations across the globe to obtain clinical samples of infected patients or virus isolates, along with the associated metadata. By integrating the sequence data and the associated metadata, we have established laboratory and bioinformatics-based methods that enable us to investigate scientific questions including: the tropism of ZIKV for dendritic cells and the antiviral response of the cells during infection (Bowen et al. 2017); investigating the phylogenetic diversity of strains obtained by Biodefense and Emerging Infections (BEI) Resources and distributed to virologists (manuscript in preparation); the genetic determinants of ZIKV host adaptation in C6/36 mosquito vs. Vero cells; and the diversity of ZIKV circulating in limited geographic regions, including Barbados, Colombia, and the state of Chiapas, Mexico.


Human Monoclonal Antibodies Potently Neutralize Zika Virus and Select for Escape Mutations on the Lateral Ridge of the Envelope Protein.
Journal of virology. 2019-07-15; 93.14:
PMID: 31043537
Optimization of qRT-PCR assay for zika virus detection in human serum and urine.
Virus research. 2019-04-02; 263.173-178.
PMID: 30742853
Antibodies Elicited by an NS1-Based Vaccine Protect Mice against Zika Virus.
mBio. 2019-04-02; 10.2:
PMID: 30940710
Whole genome sequencing, variant analysis, phylogenetics, and deep sequencing of Zika virus strains.
Scientific reports. 2018-10-26; 8.1: 15843.
PMID: 30367096
Sequences of Zika Virus Genomes from a Pediatric Cohort in Nicaragua.
Genome announcements. 2018-06-14; 6.24:
PMID: 29903816
Whole-Genome Sequences of Zika Virus FLR Strains after Passage in Vero or C6/36 Cells.
Genome announcements. 2018-01-25; 6.4:
PMID: 29371358
Zika Virus Antagonizes Type I Interferon Responses during Infection of Human Dendritic Cells.
PLoS pathogens. 2017-02-01; 13.2: e1006164.
PMID: 28152048
Identification of diagnostic peptide regions that distinguish Zika virus from related mosquito-borne Flaviviruses.
PloS one. 2017-01-01; 12.5: e0178199.
PMID: 28562637


Funding provided by the National Institute of Allergy and Infectious Diseases U19AI110819 and Administrative Supplement.

Co-Principal Investigator

Key Staff

  • Mark Novotny
  • Torrey Williams

Related Research


Mehul Suthar
Emory University

Gustavo Aroca
Clinica de la Costa

Sujatha Rashid
BEI Resources

Marquita Gittens-St.Hilaire
University of the West Indies

Eva Harris
UC Berkley

Kristen Bernard
University of Wisconsin

Ivette Lorenzana
Universidad Nacional Autónoma de Honduras

John Biegel