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.


Journal of virology. 2019-07-15; 93.14:
Human Monoclonal Antibodies Potently Neutralize Zika Virus and Select for Escape Mutations on the Lateral Ridge of the Envelope Protein
Bailey MJ, Broecker F, Freyn AW, Freyn A, Choi A, Brown JA, Fedorova N, Simon V, Lim JK, Evans MJ, García-Sastre A, Palese P, Tan GS
PMID: 31043537
mBio. 2019-04-02; 10.2:
Antibodies Elicited by an NS1-Based Vaccine Protect Mice against Zika Virus
Bailey MJ, Broecker F, Duehr J, Arumemi F, Krammer F, Palese P, Tan GS
PMID: 30940710
Virus research. 2019-04-02; 263.173-178.
Optimization of qRT-PCR assay for zika virus detection in human serum and urine
Del Pilar Martinez Viedma M, Puri V, Oldfield LM, Shabman RS, Tan GS, Pickett BE
PMID: 30742853
Scientific reports. 2018-10-26; 8.1: 15843.
Whole genome sequencing, variant analysis, phylogenetics, and deep sequencing of Zika virus strains
Shrivastava S, Puri V, Dilley KA, Ngouajio E, Shifflett J, Oldfield LM, Fedorova NB, Hu L, Williams T, Durbin A, Amedeo P, Rashid S, Shabman RS, Pickett BE
PMID: 30367096
Genome announcements. 2018-06-14; 6.24:
Sequences of Zika Virus Genomes from a Pediatric Cohort in Nicaragua
Oldfield LM, Fedorova N, Puri V, Shrivastava S, Amedeo P, Durbin A, Rocchi I, Williams T, Shabman RS, Tan GS, Balmaseda A, Kuan G, Saborio S, Gordon A, Harris E, Pickett BE
PMID: 29903816
Genome announcements. 2018-01-25; 6.4:
Whole-Genome Sequences of Zika Virus FLR Strains after Passage in Vero or C6/36 Cells
Moser LA, Oldfield LM, Fedorova N, Puri V, Shrivastava S, Amedeo P, Isom R, Hu L, Durbin A, Rocchi I, Williams T, Tan GS, Shabman RS, Bernard KA, Pickett BE
PMID: 29371358
PloS one. 2017-05-31; 12.5: e0178199.
Identification of diagnostic peptide regions that distinguish Zika virus from related mosquito-borne Flaviviruses
Lee AJ, Bhattacharya R, Scheuermann RH, Pickett BE
PMID: 28562637
PLoS pathogens. 2017-02-01; 13.2: e1006164.
Zika Virus Antagonizes Type I Interferon Responses during Infection of Human Dendritic Cells
Bowen JR, Quicke KM, Maddur MS, O'Neal JT, McDonald CE, Fedorova NB, Puri V, Shabman RS, Pulendran B, Suthar MS
PMID: 28152048


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

Co-Principal Investigator

Key Staff

  • Mark Novotny
  • Torrey Williams

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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