A set of reference sequences for the hepatitis C genotypes 4d, 4f, and 4k covering the full open reading frame.
Infection with genotype 4 of the Hepatitis C virus is common in Africa and the Mediterranean area, but has also been found at increasing frequencies in injection drug users in Europe and North America. Full length viral sequences to characterize viral diversity and structure have recently become available mostly for subtype 4a, and studies in Egypt and Saudi Arabia, where high proportions of subtype 4a infected patients exist, have begun to establish optimized treatment regimens. However knowledge about other subtype variants of genotype 4 present in less developed African states is lacking. In this study the full coding region from so far poorly characterized variants of HCV genotype 4 was amplified and sequenced using a long range PCR technique. Sequences were analyzed with respect to phylogenetic relationship, possible recombination and prominent sequence characteristics compared to other known HCV strains. We present for the first time two full-length sequences from the HCV genotype 4k, in addition to five strains from HCV genotypes 4d and 4f. Reference sequences for accurate HCV genotyping are required for optimized treatment, and a better knowledge of the global viral sequence diversity is needed to guide vaccines or new drugs effective in the world wide epidemic.
Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA. t.kuntzen@gmx.de
Thomas
T
Kuntzen
Andrew
A
Berical
Jean
J
Ndjomou
Phil
P
Bennett
Arne
A
Schneidewind
Niall
N
Lennon
Bruce W
BW
Birren
Carla
C
Kuiken
Matthew R
MR
Henn
Peter
P
Simmonds
Todd M
TM
Allen
D000595:Amino Acid Sequence; D001483:Base Sequence; D005838:Genotype; D016174:Hepacivirus / Q000145:classification* / Q000235:genetics*; D006526:Hepatitis C / Q000821:virology; D006801:Humans; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics*; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods; D011995:Recombination, Genetic; D012015:Reference Standards; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA