TY - JOUR
T1 - High-resolution evolutionary analysis of within-host hepatitis C virus infection
AU - Raghwani, Jayna
AU - Wu, Chieh-Hsi
AU - Ho, Cynthia K. Y.
AU - de Jong, Menno
AU - Molenkamp, Richard
AU - Schinkel, Janke
AU - Pybus, Oliver G.
AU - Lythgoe, Katrina A.
PY - 2019/6/1
Y1 - 2019/6/1
N2 - Background. Despite recent breakthroughs in treatment of hepatitis C virus (HCV) infection, we have limited understanding of how virus diversity generated within individuals impacts the evolution and spread of HCV variants at the population scale. Addressing this gap is important for identifying the main sources of disease transmission and evaluating the risk of drug-resistance mutations emerging and disseminating in a population. Methods. We have undertaken a high-resolution analysis of HCV within-host evolution from 4 individuals coinfected with human immunodeficiency virus 1 (HIV-1). We used long-read, deep-sequenced data of full-length HCV envelope glycoprotein, longitudinally sampled from acute to chronic HCV infection to investigate the underlying viral population and evolutionary dynamics. Results. We found statistical support for population structure maintaining the within-host HCV genetic diversity in 3 out of 4 individuals. We also report the first population genetic estimate of the within-host recombination rate for HCV (0.28 × 10?7 recombination/site/year), which is considerably lower than that estimated for HIV-1 and the overall nucleotide substitution rate estimated during HCV infection. Conclusions. Our findings indicate that population structure and strong genetic linkage shapes within-host HCV evolutionary dynamics. These results will guide the future investigation of potential HCV drug resistance adaptation during infection, and at the population scale.
AB - Background. Despite recent breakthroughs in treatment of hepatitis C virus (HCV) infection, we have limited understanding of how virus diversity generated within individuals impacts the evolution and spread of HCV variants at the population scale. Addressing this gap is important for identifying the main sources of disease transmission and evaluating the risk of drug-resistance mutations emerging and disseminating in a population. Methods. We have undertaken a high-resolution analysis of HCV within-host evolution from 4 individuals coinfected with human immunodeficiency virus 1 (HIV-1). We used long-read, deep-sequenced data of full-length HCV envelope glycoprotein, longitudinally sampled from acute to chronic HCV infection to investigate the underlying viral population and evolutionary dynamics. Results. We found statistical support for population structure maintaining the within-host HCV genetic diversity in 3 out of 4 individuals. We also report the first population genetic estimate of the within-host recombination rate for HCV (0.28 × 10?7 recombination/site/year), which is considerably lower than that estimated for HIV-1 and the overall nucleotide substitution rate estimated during HCV infection. Conclusions. Our findings indicate that population structure and strong genetic linkage shapes within-host HCV evolutionary dynamics. These results will guide the future investigation of potential HCV drug resistance adaptation during infection, and at the population scale.
UR - https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85062690334&origin=inward
UR - https://www.ncbi.nlm.nih.gov/pubmed/30602023
U2 - https://doi.org/10.1093/infdis/jiy747
DO - https://doi.org/10.1093/infdis/jiy747
M3 - Article
C2 - 30602023
SN - 0022-1899
VL - 219
SP - 1722
EP - 1729
JO - Journal of infectious diseases
JF - Journal of infectious diseases
IS - 11
ER -