TY - JOUR
T1 - Near full-length genome analysis of HCV genotype 5 strains from South Africa
AU - Gededzha, Maemu P.
AU - Selabe, Selokela G.
AU - Blackard, Jason T.
AU - Kyaw, Thanda
AU - Mphahlele, M. Jeffrey
N1 - Funding Information:
This work was supported by grants from Medical Research Council , National Research Foundation , National Health Laboratory Service Research Trust , and The Stella & Paul Loewestein Charitable & Educational Trust in South Africa.
PY - 2014/1
Y1 - 2014/1
N2 - 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.
AB - 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.
KW - Bayesian coalescent
KW - HCV genotype 5a
KW - Near full-length
UR - http://www.scopus.com/inward/record.url?scp=84896938266&partnerID=8YFLogxK
U2 - 10.1016/j.meegid.2013.10.022
DO - 10.1016/j.meegid.2013.10.022
M3 - Article
C2 - 24220189
AN - SCOPUS:84896938266
SN - 1567-1348
VL - 21
SP - 118
EP - 123
JO - Infection, Genetics and Evolution
JF - Infection, Genetics and Evolution
ER -