Rare Genotype Characterization


HCV is a highly variable virus. Currently 6 genotypes are distinguished, and each genotype is further subdivided into a varying number of subtypes. These subtypes are often defined only on the basis of short sequence fragments, which are clearly distinct from other sequences in that region. As a consequence, a myriad of poorly defined subtypes now exist, and new ones are added monthly. This is leading to a confusing and inconsistent classification of HCV strains. This project aims to increase the genomic resources available for rare genotypes & subtypes of HCV. 35 rare HCV genomes will be sequenced as part of this project.


Principal External Collaborators

Todd Allen - Ragon Institute of MGH, MIT and Harvard, Massachusetts General Hospital, Harvard Medical School, Boston, MA

Thomas Kuntzen - Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA

Carla Kuiken - Los Alamos National Laboratory, Los Alamos, NM


Funding for this sequencing project was provided by the National Institute of Allergy and Infectious Diseases.

Cohort Description

Samples collected from all over the world and which represent two genomes each for 47 variants for which no complete genomes exist, and one additional genome each for another 8 for which one complete genome is available