Near full-length genome analysis of HCV genotype 5 strains from South Africa.
Hepatitis C virus (HCV) genotype 5 is the predominant genotype in South Africa. However, to date, only 2 full-length genotype 5 genomes have been sequenced and only one is from South Africa. This study characterized HCV genotype 5 sequences from South Africa, including six near full-length genomes, as well as the E1 region from an additional 12 genotype 5 samples. Phylogenetic analysis of these near full-length genome sequences revealed that all genotype 5 sequences formed a close cluster with high bootstrap support. Bayesian analysis of the E1 region was used to estimate the time of the most recent common ancestor (tMRCA). The tMRCA for HCV genotype 5a was estimated at 114-134 years before the last sampling date. In conclusion, this study provides six near full-length genotype 5 nucleotide sequences for use as references to design efficient vaccines and for the development of new antiviral agents, and provides further insight into the diversity of HCV genotypes circulating in South Africa.
HIV and Hepatitis Research Unit, Department of Virology, University of Limpopo, Medunsa Campus/National Health Laboratory Service, Pretoria, South Africa. Electronic address: maemup@yahoo.com.
Maemu P
MP
Gededzha
HIV and Hepatitis Research Unit, Department of Virology, University of Limpopo, Medunsa Campus/National Health Laboratory Service, Pretoria, South Africa. Electronic address: selokela.selabe@ul.ac.za.
Selokela G
SG
Selabe
Division of Digestive Diseases, University of Cincinnati College of Medicine, Cincinnati, OH, USA. Electronic address: blackajt@ucmail.uc.edu.
Jason T
JT
Blackard
HIV and Hepatitis Research Unit, Department of Virology, University of Limpopo, Medunsa Campus/National Health Laboratory Service, Pretoria, South Africa. Electronic address: thanda.k@gmail.com.
Thanda
T
Kyaw
HIV and Hepatitis Research Unit, Department of Virology, University of Limpopo, Medunsa Campus/National Health Laboratory Service, Pretoria, South Africa. Electronic address: jeffrey.mphahlele@ul.ac.za.
M Jeffrey
MJ
Mphahlele
D001499:Bayes Theorem; D019143:Evolution, Molecular; D014644:Genetic Variation; D016679:Genome, Viral; D005838:Genotype; D016174:Hepacivirus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D006526:Hepatitis C / Q000821:virology*; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D017423:Sequence Analysis, RNA; D013019:South Africa
Bayesian coalescent; HCV genotype 5a; Near full-length