Quantifying the Diversification of Hepatitis C Virus (HCV) during Primary Infection: Estimates of the In Vivo Mutation Rate

Abstract

Hepatitis C virus (HCV) is present in the host with multiple variants generated by its error prone RNA-dependent RNA polymerase. Little is known about the initial viral diversification and the viral life cycle processes that influence diversity. We studied the diversification of HCV during acute infection in 17 plasma donors, with frequent sampling early in infection. To analyze these data, we developed a new stochastic model of the HCV life cycle. We found that the accumulation of mutations is surprisingly slow: at 30 days, the viral population on average is still 46% identical to its transmitted viral genome. Fitting the model to the sequence data, we estimate the median in vivo viral mutation rate is 2.5×10−5 mutations per nucleotide per genome replication (range 1.6–6.2×10−5), about 5-fold lower than previous estimates. To confirm these results we analyzed the frequency of stop codons (N = 10) among all possible non-sense mutation targets (M = 898,335), and found a mutation rate of 2.8–3.2×10−5, consistent with the estimate from the dynamical model. The slow accumulation of mutations is consistent with slow turnover of infected cells and replication complexes within infected cells. This slow turnover is also inferred from the viral load kinetics. Our estimated mutation rate, which is similar to that of other RNA viruses (e.g., HIV and influenza), is also compatible with the accumulation of substitutions seen in HCV at the population level. Our model identifies the relevant processes (long-lived cells and slow turnover of replication complexes) and parameters involved in determining the rate of HCV diversification.

Interferon-Free Treatment of Hepatitis C Virus in HIV/Hepatitis C Virus-Coinfected Subjects Results in Increased Serum Low-Density Lipoprotein Concentration

“…Interestingly, a recent study examining viral kinetics in serum and liver during treatment with telaprevir/IFN/RBV revealed a slower HCV RNA decline in the liver compared to plasma. 39 Given the estimated 7-day half-life of infected hepatocytes, 40 a persistent burden of intrahepatic HCV is likely still present at day 3 of treatment in this trial, but has likely declined significantly by week 2. Thus, changes in serum LDL-C may be a reflection of intrahepatic HCV burden and direct intracellular viral modulation of cholesterol metabolism.…”

An update on hepatitis C virus

“…It displays enormous genetic diversity, which results from a high mutation rate and a high replication rate. 2,3 Comparison of nucleotide sequences and phylogenetics of global HCV sequences has revealed seven different strains or genotypes differing by 30-35% of nucleotide ABSTRACT sites. Within each genotype, there are further divisions into subtypes (more than 67 subtypes) that differ by 10-15%.…”

Kinetics of hepatitis C virus RNA decay, quasispecies evolution and risk of virological failure during telaprevir-based triple therapy in clinical practice

“…Within an infected individual, the high in vivo HCV mutation rate (2.5-3.2 × 10 −5 per nucleotide per genome replication round) [7], in synergy with a short half-life, and an extremely high daily viral production rate (10 12 particles/day) leads to the generation of a swarm of genetically distinct but closely related viral variants, known as quasispecies [8]. In this heterogeneous viral population, the probability to have at least one viral strain harbouring one or two nucleotide mutations is close to 100% [9].…”