Should a viral genome stay in the host cell or leave? A quantitative dynamics study of how hepatitis C virus deals with this dilemma

Abstract

Virus proliferation involves gene replication inside infected cells and transmission to new target cells. Once positive-strand RNA virus has infected a cell, the viral genome serves as a template for copying ("stay-strategy") or is packaged into a progeny virion that will be released extracellularly ("leave-strategy"). The balance between genome replication and virion release determines virus production and transmission efficacy. The ensuing trade-off has not yet been well characterized. In this study, we use hepatitis C virus (HCV) as a model system to study the balance of the two strategies. Combining viral infection cell culture assays with mathematical modeling, we characterize the dynamics of two different HCV strains (JFH-1, a clinical isolate, and Jc1-n, a laboratory strain), which have different viral release characteristics. We found that 0.63% and 1.70% of JFH-1 and Jc1-n intracellular viral RNAs, respectively, are used for producing and releasing progeny virions. Analysis of the Malthusian parameter of the HCV genome (i.e., initial proliferation rate) and the number of de novo infections (i.e., initial transmissibility) suggests that the leave-strategy provides a higher level of initial transmission for Jc1-n, whereas, in contrast, the stay-strategy provides a higher initial proliferation rate for JFH-1. Thus, theoretical-experimental analysis of viral dynamics enables us to better understand the proliferation strategies of viruses, which contributes to the efficient control of virus transmission. Ours is the first study to analyze the stay-leave trade-off during the viral life cycle and the significance of the replication-release switching mechanism for viral proliferation.

Prediction of elimination of intrahepatic cccDNA in hepatitis B virus-infected patients by a combination of noninvasive viral markers

“…1B, and the estimated parameters and initial values are listed in Table S1. It was estimated that 214 copies of HBV DNA is produced from cccDNA in a cell per day in average; only 0.00126% of the produced HBV DNA is used for recycling back to produce cccDNA (Table S2); and the mean half-life of cccDNA is 51 days in PHH (Table 1), which is consistent with previous results showing the cccDNA half-life and the limited recycling activity in PHH 4,5,7 .…”

“…Here, to precisely quantify both intracellular and extracellular virus dynamics from these biomarkers, we used a multiscale mathematical model of HBV infection combining the intracellular mathematical model (Eqs. (S1-S3)) with the standard virus dynamics model 13,14 , in which an infected cell produces progeny HBVs extracellularly that then are degraded or infect other cells ( Fig. 2A and Eqs.…”

“…S2 and ONLINE METHODS). Note that PHH were maintained at 100% confluent conditions with 2% concentration of dimethyl sulfoxide (DMSO) including medium during the entire infection assay, to supports low cell growth and prevent cell division [3][4][5] . We developed the mathematical model (Fig.…”

“…PHH were seeded into 96-well plate at 7×10 4 cells/well and were inoculated with HBV at 8,000 genome equivalents (GEq)/cell in the presence of 4% polyethylene glycol 8,000 (PEG8000) for 16 h. After washing out free HBV, PHH were continuously treated with ETV at 1 µM, interferon alpha (IFNα) at 1,000 IU/ml, ETV at 1 µM + IFNα at 1000 IU/ml or without treatment (control). Cell division is known to reduce the cccDNA per cell in HBV-infected cells 4 ; therefore, to avoid this, we maintained PHH at 100% confluent conditions during the entire infection assay. Moreover, a high concentration of dimethyl sulfoxide (DMSO) was included in the culture medium as described previously 62 , which does not allow cell growth and prevents cccDNA loss by cell division [3][4][5] .…”

“…Cell division is known to reduce the cccDNA per cell in HBV-infected cells 4 ; therefore, to avoid this, we maintained PHH at 100% confluent conditions during the entire infection assay. Moreover, a high concentration of dimethyl sulfoxide (DMSO) was included in the culture medium as described previously 62 , which does not allow cell growth and prevents cccDNA loss by cell division [3][4][5] . Since the experiments using PHH were conducted under the above conditions, cell growth dynamics were ignored in our analysis.…”