GCID Viral Projects


Humans are constantly exposed to a plethora of viruses that cause disease. Highly infectious pathogens such as influenza virus, rotavirus, enteroviruses, and respiratory syncytial virus are a persistent public health concern. Recent outbreaks caused by West Nile, Zika, and other viruses remind us of the ongoing threat posed by emerging and re-remerging viruses. The viral GCID projects at the JCVI focus on defining the genomes of viruses and characterizing virus-host interactions to better understand viral evolution, elucidate the underlying molecular mechanisms that cause disease, and aid in the development of novel vaccines and therapeutics.

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High-throughput whole-genome next-generation sequencing (NGS) and bioinformatics analyses will be performed for more than 8,000 viral strains representing five viral families, including NIAID priority pathogens. The characterization of their genetic diversity will improve our understanding of critical mechanisms central to viral evolution, pathogenesis, transmission, and antiviral resistance. Specifically, we aim to: 1) compare and contrast the genetic diversity and evolutionary dynamics of viruses circulating within and/or between humans and animal reservoirs, 2) elucidate viral-host-microbiome determinants that influence viral pathogenesis, and 3) perform deep NGS to understand intra-host viral diversity, transmission dynamics, and antiviral resistance. 

The sequencing data will be analyzed using phylogenetics and other bioinformatics algorithms to show the spatial and temporal evolution of these pathogens. These data will help to identify, track, and predict antigenic drift/shift, recombination, escape from natural or vaccine-induced host immune responses, antiviral resistance, inter- and intra-species transmission, and the response of a host's commensal microbiota to viral infection. The information generated from these studies will help us produce superior vaccines and antivirals and are critical for rapid responses to the emergence of novel pathogens (i.e., pandemic preparedness) that arise naturally or as a result of bioterrorism.

Supplemental Projects

  • Chikungunya virus complete-genome sequencing from the Americas to understand its emergence, evolutionary dynamics, and signatures of virulence.
  • A high throughput approach to screen and sequence human samples suspected to be Zika virus positive
  • Definition and characterization of the MHC region and MHC diversity in ferrets used for biomedical research

Project Directors


All Publications that use data generated and/or are supported by the Sequencing Center at JCVI should acknowledge the sponsor as follows: "Research reported in this publication was supported by the National Institute Of Allergy And Infectious Diseases of the National Institutes of Health under Award Number U19AI110819. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health."

Paolo Amedeo, PhD
Staff Scientist
Fortuna Arumemi, MS
Research Associate II
James Christensen
Sr. Software Engineer
Alan Durbin, MS
Research Associate III
Nadia Fedorova, MS
Sr. Data Analyst
Lihui Hu, PhD
Software Engineer
John Miller, PhD
Bioinformatics Analyst
Lauren M. Oldfield, PhD
Assistant Professor
Brett E. Pickett, PhD
Assistant Professor
Harinder Singh, PhD
Staff Scientist
Gene S. Tan, PhD
Assistant Professor
Torrey Williams
Research Associate II