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Research Project Description

Next Generation Sequencing Fellowship
Division of Viral Diseases
National Center for Immunization and Respiratory Diseases
Centers for Disease Control and Prevention
Atlanta, GA


Project Description:

A fellowship opportunity is currently available in the Division of Viral Diseases (DVD) of the National Center for Immunization and Respiratory Diseases (NCIRD) at the Centers for Disease Control and Prevention (CDC).

DVD is responsible for disease surveillance for many RNA viruses associated with vaccine preventable and non-vaccine preventable viral diseases. The availability of next-generation sequencing technology now makes it possible to routinely obtain full genomic sequence information from viral samples. As part of the new Advanced Molecular Detection Initiative, DVD has a goal of developing a standardized pipeline for high efficiency genomic sequencing of RNA viruses.

To help accomplish this goal, the selected participant will join the DVD Sequencing Core Team. Under the guidance of a mentor, opportunities may include:

  • Evaluating existing laboratory protocols for whole-genome sequencing of RNA viruses, comparing quality, limit of detection, efficiency, cost and throughput
  • Optimizing and standardizing protocols and workflows for each of the RNA virus studies in DVD (i.e., polioviruses, measles virus, rotaviruses, etc.)
  • Evaluating existing NGS platforms to determine which is most suitable for efficient sequencing of RNA viruses

The results of this fellowship will provide DVD with an optimized standardized workflow that will be used to generate sequence data for the RNA viruses for input into the bioinformatics analysis pipeline development. The selected participant will collaborate with subject matter experts and team members who are working on various RNA viruses throughout DVD, and will provide technical and experimental support for constructing libraries and using several NGS platforms (e.g., Illumina, Ion Torrent) to obtain genomic sequence data.

This program, administered by ORAU through its contract with the U.S. Department of Energy to manage the Oak Ridge Institute for Science and Education, was established through an interagency agreement between DOE and CDC. The initial appointment is for one year, but may be renewed upon recommendation of CDC contingent on the availability of funds. The participant will received a monthly stipend commensurate with education level and experience. Proof of health insurance is required for participation in this program. The appointment is full-time at CDC in the Atlanta, Georgia, area. Participants do not become employees of CDC or the program administrator, and there are no fringe benefits paid.


  • A Bachelor’s or Master’s degree in virology, microbiology, molecular biology, genetics or a related discipline received within the last five years.
  • Experience in molecular biology, sequencing and sequence analysis is desired.

How to Apply:

To be considered, please send a current CV/resume to the attention of Please reference CDC-NCIRD-2014-0064 in all communications.