High resolution evolutionary analysis of within-host hepatitis C virus infection

Abstract

Despite the breakthroughs in the treatment of HCV infection in recent years, we have a limited understanding of how virus diversity generated within individuals impacts the evolution and spread of HCV variants at the population scale. Addressing this gap will be important for building models for molecular epidemiology, which can identify main sources of disease transmission and evaluate the risks of drug-resistance mutations emerging and disseminating in a population. Here, we have undertaken a high-resolution analysis of HCV within-host evolution from four individuals co-infected with HIV. Specifically, we used longread, deep-sequenced data of the full-length HCV envelope glycoprotein, longitudinally sampled from acute to chronic HCV infection to investigate the underlying viral evolutionary dynamics. In three individuals we found strong statistical support for population structure maintaining within-host HCV genetic diversity. Furthermore, we found significant variation in rates of molecular evolution among different regions of the HCV envelope region, both within and between individuals. Lastly, we report the first estimate of the within-host population genetic rate of recombination for HCV (0.28 x 10 -7 recombinations per site per day; interquartile range: 0.13-1.05 x 10 -7 ), which is two orders of magnitude lower than that estimated for HIV-1, and four orders of magnitude lower than the nucleotide substitution rate of the HCV envelope gene. Together, these observations 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.

Opportunistic treatment of hepatitis C virus infection (OPPORTUNI-C): study protocol for a pragmatic stepped wedge cluster randomized trial of immediate versus outpatient treatment initiation among hospitalized people who inject drugs

“…It can be challenging to distinguish closely related variants within a sub-genotype, as HCV is highly diverse, producing thousands of variants within the host that change over time. If we cannot distinguish HCV variants using the protocol outlined above, other techniques using long-reads on MinIon to characterize the virus on a single virus level may be applied to have significant power to distinguish viral variants that have emerged over a long course of infection [27]. In most cases of HCV RNA recurrence, a pragmatic reinfection diagnosis can be made in the absence of whole genome sequencing.…”

Field validation of phylodynamic analytical methods for inference on epidemiological processes in wildlife

“…Applications of coalescent-based analytical techniques to molecular data allow the reconstruction of demographic changes over time of the studied organisms (Drummond et al, 2005). These techniques have been successfully applied to reconstruct the demographic history of pathogens as well as higher order organisms (Raghwani et al, 2019, Pacioni et al, 2015. In parallel, recent efforts have aimed to extend phylogenetic birth-death models to estimate parameters relevant for epidemiological studies.…”

Inconsistent temporal patterns of genetic variation of HCV among high-risk subjects may impact inference of transmission networks

“…A multitude of observational studies suggest that a substantial proportion of PWID carry mixed infections [18]. Furthermore, within-host evolutionary dynamics are complex [19][20][21][22][23][24][25][26]. Multiple co-existing lineages persist over time and are not necessarily detected at every sampling time [19,20,26], even using highthroughput sequencing [20,26], likely resulting from viral population structure [19,20,26,27].…”

“…Furthermore, within-host evolutionary dynamics are complex [19][20][21][22][23][24][25][26]. Multiple co-existing lineages persist over time and are not necessarily detected at every sampling time [19,20,26], even using highthroughput sequencing [20,26], likely resulting from viral population structure [19,20,26,27]. Lineages may exist for many years yet still show a relative lack of evolution [19,20,26,27], and the evolutionary rate is highly variable over time and among lineages [19][20][21][22]26].…”

“…Multiple co-existing lineages persist over time and are not necessarily detected at every sampling time [19,20,26], even using highthroughput sequencing [20,26], likely resulting from viral population structure [19,20,26,27]. Lineages may exist for many years yet still show a relative lack of evolution [19,20,26,27], and the evolutionary rate is highly variable over time and among lineages [19][20][21][22]26]. Furthermore, among-host dynamics are complicated by the possible "reversion" of hostspecific substitutions upon transmission [23,28,29].…”