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Swineinfluenza A virus(SwIV) infection has considerable economic and animal welfare consequences and, because of the zoonotic potential, can also have public health implications. The 2009 pandemicH1N1‘swine-origin’ infection is now endemic in both pigs and humans. In Europe, avian-like H1avN1, human-like H1huN2, human-like swineH3N2and, since 2009, pandemic H1N1 (pH1N1) lineage viruses andreassortants, constitute the dominant subtypes. In this study, we used a swine pH1N1 challenge virus to investigate the efficacy ofwhole inactivated virus vaccineshomologous or heterologous to the challenge virus as well as a commercial vaccine. We found that vaccine-mediated protection was most effective when vaccine antigen and challenge virus were homologous and correlated with the specific production ofneutralising antibodiesand a cellular response to the challenge virus. We conclude that a conventional whole inactivated SwIV vaccine must be antigenically matched to the challenge strain to be an effective control measure.

This study was designed to determine whether vaccination of pigs with conventional WIV or virus-vectored vaccines reduces pH1N1 swine influenza virus shedding following challenge and can prevent transmission to naive in-contact animals. Even when viral shedding was significantly reduced following challenge, infection was transmissible to susceptible cohoused recipients., Swine influenza A virus (swIAV) infection causes substantial economic loss and disease burden in humans and animals. The 2009 pandemic H1N1 (pH1N1) influenza A virus is now endemic in both populations. In this study, we evaluated the efficacy of different vaccines in reducing nasal shedding in pigs following pH1N1 virus challenge. We also assessed transmission from immunized and challenged pigs to naive, directly in-contact pigs. Pigs were immunized with either adjuvanted, whole inactivated virus (WIV) vaccines or virus-vectored (ChAdOx1 and MVA) vaccines expressing either the homologous or heterologous influenza A virus hemagglutinin (HA) glycoprotein, as well as an influenza virus pseudotype (S-FLU) vaccine expressing heterologous HA. Only two vaccines containing homologous HA, which also induced high hemagglutination inhibitory antibody titers, significantly reduced virus shedding in challenged animals. Nevertheless, virus transmission from challenged to naive, in-contact animals occurred in all groups, although it was delayed in groups of vaccinated animals with reduced virus shedding. IMPORTANCE This study was designed to determine whether vaccination of pigs with conventional WIV or virus-vectored vaccines reduces pH1N1 swine influenza A virus shedding following challenge and can prevent transmission to naive in-contact animals. Even when viral shedding was significantly reduced following challenge, infection was transmissible to susceptible cohoused recipients. This knowledge is important to inform disease surveillance and control strategies and to determine the vaccine coverage required in a population, thereby defining disease moderation or herd protection. WIV or virus-vectored vaccines homologous to the challenge strain significantly reduced virus shedding from directly infected pigs, but vaccination did not completely prevent transmission to cohoused naive pigs.

The prenylation inhibitor lonafarnib (LNF) is a potent antiviral agent providing a breakthrough for the treatment of hepatitis delta virus (HDV). The current study used a maximum likelihood approach to model LNF pharmacokinetic (PK) and pharmacodynamic (PD) parameters and predict the dose needed to achieve 99% efficacy using data from 12 patients chronically infected with HDV and treated with LNF 100 mg twice daily (bid) (group 1) or 200 mg bid (group 2) for 28 days. The LNF-PK model predicted average steady-state LNF concentrations of 860 ng/mL and 1,734 ng/mL in groups 1 and 2, respectively, with an LNF absorption rate ka = 0.43/hour and elimination rate ke = 0.045/hour. The PK/PD model identified an average delay of 0.56 hours and an LNF concentration that decreases HDV production by 50%, EC50 = 227 ng/mL, with a Hill factor h = 1.48. The HDV half-life in blood was 1.87 days, and the average steady-state LNF efficacy in blocking HDV production was ɛ = 87.7% for group 1 and ɛ = 95.2% for group 2. A biphasic HDV decline with an average phase 1 decline (0.9 log10 IU/mL and 1.32 log10 IU/mL) was observed in groups 1 and 2, respectively. Phase 2 was not significantly (P = 0.94) different between the two groups, with an average slope of -0.06 log IU/mL/day. The model suggests an LNF dose of ∼610 mg bid would achieve ɛ = 99%. Conclusion: The first PK/PD modeling study in patients with chronic HDV indicates that a ∼3-fold increase in LNF dose (∼610 mg bid) would achieve 99% antiviral efficacy. A ritonavir-boosted LNF combination may provide a means to increase LNF efficacy with minimal side effects. The modeling findings provide an important advance in understanding HDV dynamics and the basis to optimize LNF therapy for hepatitis D. (Hepatology Communications 2017;1:288-292).

A swine influenza A pandemic 2009 H1N1 (pH1N1) virus was used in a pig challenge model to investigate the efficacy of whole inactivated vaccines homologous or heterologous to the challenge virus as well as a commercial vaccine. Nasal shedding of viral RNA was monitored daily by real-time, quantitative RT-PCR (RRT-qPCR) as detailed (1). Here we report the statistical modelling of the viral RNA shedding kinetics. Keywords: Pandemic 2009 swine influenza a virus, Whole inactivated vaccine, Viral kinetics, Statistical modelling RRT-qPCR

Legalon SIL (SIL) is a chemically hydrophilized version of silibinin, an extract of milk thistle (Silybum marianum) seeds that has exhibited hepatoprotective and antiviral effectiveness against hepatitis C virus (HCV) in patients leading to viral clearance in combination with ribavirin. To elucidate the incompletely understood mode of action of SIL against HCV, mathematical modelling of HCV kinetics and human hepatocyte gene expression studies were performed in uPA-SCID-chimeric mice with humanized livers. Chronically HCV-infected mice (n = 15) were treated for 14 days with daily intravenous SIL at 469, 265 or 61.5 mg/kg. Serum HCV and human albumin (hAlb) were measured frequently, and liver HCV RNA was analysed at days 3 and 14. Microarray analysis of human hepatocyte gene expression was performed at days 0, 3 and 14 of treatment. While hAlb remained constant, a biphasic viral decline in serum was observed consisting of a rapid 1st phase followed by a second slower phase (or plateau with the two lower SIL dosings). SIL effectiveness in blocking viral production was similar among dosing groups (median ε = 77%). However, the rate of HCV-infected hepatocyte decline, δ, was dose-dependent. Intracellular HCV RNA levels correlated (r = 0.66, P = 0.01) with serum HCV RNA. Pathway analysis revealed increased anti-inflammatory and antiproliferative gene expression in human hepatocytes in SIL-treated mice. The results suggest that SIL could lead to a continuous second-phase viral decline, that is potentially viral clearance, in the absence of adaptive immune response along with increased anti-inflammatory and antiproliferative gene expression in human hepatocytes.

Influenza is a major cause of mortality and morbidity worldwide. Despite numerous studies of the pathogenesis of influenza in humans and animal models the dynamics of infection and transmission in individual hosts remain poorly characterized. In this study, we experimentally modelled transmission using the H1N1pdm09 influenza A virus in pigs, which are considered a good model for influenza infection in humans. Using an experimental design that allowed us to observe individual transmission events occurring within an 18-hr period, we quantified the relationships between infectiousness, shed virus titre and antibody titre. Transmission event was observed on 60% of occasions when virus was detected in donor pig nasal swabs and transmission was more likely when donor pigs shed more virus. This led to the true infectious period (mean 3.9 days) being slightly shorter than that predicted by detection of virus (mean 4.5 days). The generation time of infection (which determines the rate of epidemic spread) was estimated for the first time in pigs at a mean of 4.6 days. We also found that the latent period of the contact pig was longer when they had been exposed to smaller amount of shed virus. Our study provides quantitative information on the time lines of infection and the dynamics of transmission that are key parts of the evidence base needed to understand the spread of influenza viruses though animal populations and, potentially, in humans., Author summary Influenza is a major cause of mortality and morbidity worldwide. The relationship between the time course of influenza infection and virus shedding and onward transmission of the virus remains poorly characterized. Pigs are a natural host for influenza infection with shedding patterns similar to humans. Therefore we experimentally infected pigs with the H1N1pdm09 influenza A virus using direct contact challenge and then mixed the infected pigs with a different naïve pig each day to understand when transmission occurred. Using mathematical modeling, we found that transmission events occurred on 60% of occasions when the infected pigs were shedding virus and that the risk of transmission increased with the quantity of virus shed. Also it was clear the incontact pigs started to shed virus later after exposure when the infected pigs were shedding low quantities of virus. Our study therefore provides quantitative information on the time lines of influenza virus infection and the dynamics of transmission. This is important to understand the spread of influenza viruses through animal populations and, potentially, in humans.

France was recognized officially bovine tuberculosis (bTB) free by the European Union in 2001, however an increase of bTB detections has been reported since 2004. Even though the recommended method for bTB control is whole herd depopulation, test-and-cull protocols have been authorized in pilot areas since 2008 and in the rest of France since 2014. BTB impact at the state level and on trade has been thoroughly studied, however the consequences of these control measures at a farm level are poorly understood. We used bovine movement data from the French cattle tracing system and surveillance data from the National reference laboratory to compare time to closure between case farms with a bTB detection and matched control farms between 2004 and 2017 in France. For this purpose, we considered two modes of closure: (i) long-lasting (more than 12 months) depopulation and (ii) change of farm owner. Using a competing risk analysis, we showed that bTB detection significantly increased the odds of long-lasting depopulation (particularly during the first three months after bTB detection) indicating that farmers renounced restocking after the depopulation, whereas it decreased the odds of a change of owner. Larger farms, characterized by an increased average weekly number of cattle, had a lesser risk of long-lasting depopulation. Farms owned by a natural person had an increased risk of closure. We also showed that the possibility to control bTB by test-and-cull protocol decreased the long-lasting depopulation risk. Overall, bTB control measures contribute to reshaping the agricultural landscape by increasing the probability of closure for small vulnerable farms and by favoring large, professionalized and specialized agricultural holdings. Our results also suggest an improvement in control management with the introduction of test-and-cull protocols instead of systematic whole herd depopulation.

BACKGROUND AND AIMS: Detailed hepatitis C virus (HCV) kinetics modeling is scarce in patients with advanced liver disease receiving direct-acting antivirals (DAAs). Due to budget restrictions, patients and health systems would benefit from the shortest possible treatment course. We investigated whether modeling very early HCV kinetics in cirrhotic patients under DAAs therapy could be used to individualize care and reduce treatment duration to achieve cure. METHODS: We included 74 patients with HCV-related liver cirrhosis who received interferon-free treatments for 12–24 weeks. HCV genotype, liver disease stage and treatment regimen were recorded. Viral load was determined prospectively at very frequent intervals until target-not-detected (TND, 7 and a LSM≥21 kPa were significantly (p=0.016) associated with longer CL-EF. CONCLUSIONS: The study provides insights into HCV dynamics during DAAs therapy in patients with compensated and decompensated cirrhosis. Viral kinetics modeling suggests that treatment duration may be optimized in patients with compensated cirrhosis.

Chimeric urokinase type plasminogen activator (uPA)/severely severe combined immunodeficiency (SCID) mice reconstituted with humanized livers are useful for studying hepatitis B virus (HBV) infection in the absence of an adaptive immune response. However, the detailed characterization of HBV infection kinetics necessary to enable in-depth mechanistic studies in this in vivo HBV infection model is lacking. To characterize HBV kinetics post-inoculation (p.i.) to steady state, 42 mice were inoculated with HBV. Serum HBV DNA was frequently measured from 1 minute to 63 days p.i. Total intrahepatic HBV DNA, HBV covalently closed circular DNA (cccDNA), and HBV RNA was measured in a subset of mice at 2, 4, 6, 10, and 13 weeks p.i. HBV half-life (t1/2 ) was estimated using a linear mixed-effects model. During the first 6 hours p.i., serum HBV declined in repopulated uPA/SCID mice with a t1/2 = 62 minutes (95% confidence interval [CI] = 59-67). Thereafter, viral decline slowed followed by a 2-day lower plateau. Subsequent viral amplification was multiphasic with an initial mean doubling time of t2 = 8 ± 3 hours followed by an interim plateau before prolonged amplification (t2 = 2 ± 0.5 days) to a final HBV steady state of 9.3 ± 0.3 log copies (cps)/mL. Serum HBV and intrahepatic HBV DNA were positively correlated (R2 = 0.98). Conclusion HBV infection in uPA/SCID chimeric mice is highly dynamic despite the absence of an adaptive immune response. Serum HBV t1/2 in humanized uPA/SCID mice was estimated to be ∼1 hour regardless of inoculum size. The HBV acute infection kinetics presented here is an important step in characterizing this experimental model system so that it can be effectively used to elucidate the dynamics of the HBV life cycle and thus possibly reveal effective antiviral drug targets. (Hepatology 2018).

Background & aims High cure rates are achieved in HCV genotype-1b patients treated with daclatasvir and asunaprevir, DCV/ASV. Here we analyzed early HCV kinetics in genotype-1b infected Japanese subjects treated with DCV/ASV and retrospectively projected, using mathematical modeling, whether shorter treatment durations might be effective. Methods HCV RNA levels were measured frequently during DCV/ASV therapy in 95 consecutively treated patients at a single center in Japan. Mathematical modeling was used to predict the time to cure, i.e

Background Hepatitis B surface antigen (HBsAg)-seroconversion, or loss of HBsAg and acquisition of anti-hepatitis B surface (HBs) antibodies, defines functional cure of chronic hepatitis B virus (HBV) infection. After HBsAg-loss, little is known regarding the development of anti-HBs antibodies and even less so in individuals co-infected with HIV. Objectives To determine anti-HBs antibody kinetics after HBsAg-loss and explore determinants of HBsAg-seroconversion in HIV-HBV co-infected patients. Study design Patients enrolled in the French HIV-HBV cohort were included if they had >1 study visit after HBsAg-loss. Individual patient kinetics of anti-HBs antibody levels were modeled over time using mixed-effect non-linear regression, whereby maximum specific growth rate and maximal level of antibody production were estimated from a Gompertz growth equation. Results Fourteen (4.6%) of 308 co-infected patients followed in the cohort exhibited HBsAg-loss, all of whom were undergoing antiretroviral therapy. Nine (64.3%) of these patients achieved HBsAg-seroconversion during a median 3.0 years (IQR = 1.1–5.1) after HBsAg-loss. Across individuals with HBsAg-seroconversion, the fastest rates of antibody growth ranged between 0.57–1.93 year−1 (population maximum growth rate = 1.02) and antibody production plateaued between 2.09–3.66 log10 mIU/mL at the end of follow-up (population maximal antibody levels = 2.66). Patients with HBsAg-seroconversion had substantial decreases in HBV DNA viral loads (P = 0.03) and proportion with elevated ALT levels (P = 0.02) and HBeAg-positive serology (P = 0.08). No such differences were observed in those without HBsAg-seroconversion. Conclusions Most co-infected patients with HBsAg-seroconversion produced and maintained stable antibody levels, yet kinetics of anti-HBs production were much slower compared to those observed post-vaccination or after clearance of acute HBV-infection.

Influenza virus infection in pigs is a major farming problem, causing considerable economic loss and posing a zoonotic threat. In addition the pig is an excellent model for understanding immunity to influenza viruses as this is a natural host pathogen system. Experimentally, influenza virus is delivered to pigs intra-nasally, by intra-tracheal instillation or by aerosol, but there is little data comparing the outcome of different methods. We evaluated the shedding pattern, cytokine responses in nasal swabs and immune responses following delivery of low or high dose swine influenza pdmH1N1 virus to the respiratory tract of pigs intra-nasally or by aerosol and compared them to those induced in naturally infected contact pigs. Our data shows that natural infection by contact induces remarkably high innate and adaptive immune response, although the animals were exposed to a very low virus dose. In contacts, the kinetics of virus shedding were slow and prolonged and more similar to the low dose directly infected animals. In contrast the cytokine profile in nasal swabs, antibody and cellular immune responses of contacts more closely resemble immune responses in high dose directly inoculated animals. Consideration of these differences is important for studies of disease pathogenesis and assessment of vaccine protective efficacy. Electronic supplementary material The online version of this article (doi:10.1186/s13567-016-0390-5) contains supplementary material, which is available to authorized users.

Heterogeneity of infectiousness is an important feature of the spread of many infections, with implications for disease dynamics and control, but its relevance to human influenza virus is still unclear. For a transmission event to occur, an infected individual needs to release infectious particles via respiratory symptoms. Key factors to take into account are virus dynamics, particle release in relation to respiratory symptoms, the amount of virus shed and, importantly, how these vary between infected individuals. A quantitative understanding of the process of influenza transmission is relevant to designing effective mitigation measures. Here we develop an influenza infection dynamics model fitted to virological, systemic and respiratory symptoms to investigate how within-host dynamics relates to infectiousness. We show that influenza virus shedding is highly heterogeneous between subjects. From analysis of data on experimental infections, we find that a small proportion (

Influenza virus kinetics (VK) is used as a surrogate of infectiousness, while the natural history of influenza is described by symptom dynamics (SD). We used an original virus kinetics/symptom dynamics (VKSD) model to characterize human influenza virus infection and illness, based on a population approach. We combined structural equations and a statistical model to describe intra- and interindividual variability. The structural equations described influenza based on the target epithelial cells, the virus, the innate host response, and systemic symptoms. The model was fitted to individual VK and SD data obtained from 44 volunteers experimentally challenged with influenza A/H1N1 virus. Infection and illness parameters were calculated from best-fitted model estimates. We predicted that the cytokine level and NK cell activity would peak at days 2.2 and 4.2 after inoculation, respectively. Infectiousness, measured as the area under the VK curve above a viral titer threshold, lasted between 7.0 and 1.3 days and was 15 times lower in participants without systemic symptoms than in those with systemic symptoms ( P < 0.001). The latent period, defined as the time between inoculation and infectiousness, varied from 0.7 to 1.9 days. The incubation period, defined as the time from inoculation to first symptoms, varied from 1.0 to 2.4 days. Our approach extends previous work by including the innate response and providing realistic estimates of infection and illness parameters, taking into account the strong interindividual variability. This approach could help to optimize studies of influenza VK and SD and to predict the effect of antivirals on infectiousness and symptoms.

BackgroundModelling HCV RNA decline kinetics under therapy has proven useful for characterizing treatment effectiveness.MethodsHere we model HCV viral kinetics (VK) in 72 patients given a combination of danoprevir, a protease inhibitor, and mericitabine, a nucleoside polymerase inhibitor, for 14 days in the INFORM-1 trial. A biphasic VK model with time-varying danoprevir and mericitabine effectiveness and Bliss independence for characterizing the interaction between both drugs provided the best fit to the VK data.ResultsThe average final antiviral effectiveness of the drug combination varied between 0.998 for 100 mg three times daily of danoprevir and 500 mg twice daily of mericitabine and 0.9998 for 600 mg twice daily of danoprevir and 1,000 mg twice daily of mericitabine. Using the individual parameters estimated from the VK data collected over 2 weeks, we were not able to reproduce the low sustained virological response rates obtained in a more recent study where patients were treated with a combination of mericitabine and ritonavir-boosted danoprevir for 24 weeks.ConclusionsThis suggests that drug-resistant viruses emerge after 2 weeks of treatment and that longer studies are necessary to provide accurate predictions of longer treatment outcomes.

Recent clinical trials of direct-acting-antiviral agents (DAAs) against hepatitis C virus (HCV) achieved90% sustained virological response (SVR) rates, suggesting that cure often took place before the end of treatment (EOT). We sought to evaluate retrospectively whether early response kinetics can provide the basis to individualize therapy to achieve optimal results while reducing duration and cost.58 chronic HCV patients were treated with 12-week sofosbuvir+simeprevir (n=19), sofosbuvir+daclatasvir (n=19), or sofosbuvir+ledipasvir in three French referral centers. HCV was measured at baseline, day 2, every other week, EOT and 12weeks post EOT. Mathematical modeling was used to predict the time to cure, i.e.,1 virus copy in the entire extracellular body fluid.All but one patient who relapsed achieved SVR. Mean age was 60±11years, 53% were male, 86% HCV genotype-1, 9% HIV coinfected, 43% advanced fibrosis (F3), and 57% had cirrhosis. At weeks 2, 4 and 6, 48%, 88% and 100% of patients had HCV15IU/ml, with 27%, 74% and 91% of observations having target not detected, respectively. Modeling results predicted that 23 (43%), 16 (30%), 7 (13%), 5 (9%) and 3 (5%) subjects were predicted to reach cure within 6, 8, 10, 12 and 13weeks of therapy, respectively. The modeling suggested that the patient who relapsed would have benefitted from an additional week of sofosbuvir+ledipasvir. Adjusting duration of treatment according to the modeling predicts reduced medication costs of 43-45% and 17-30% in subjects who had HCV15IU/ml at weeks 2 and 4, respectively.The use of early viral kinetic analysis has the potential to individualize duration of DAA therapy with a projected average cost saving of 16-20% per 100-treated persons.

Several studies have proven oseltamivir to be efficient in reducing influenza viral titer and symptom intensity. However, the usefulness of oseltamivir can be compromised by the emergence and spread of drug-resistant virus. The selective pressure exerted by different oseltamivir therapy regimens have received little attention. Combining models of drug pharmacokinetics, pharmacodynamics, viral kinetics and symptom dynamics, we explored the efficacy of oseltamivir in reducing both symptoms (symptom efficacy) and viral load (virological efficacy). We simulated samples of 1000 subjects using previously estimated between-subject variability in viral and symptom dynamic parameters to describe the observed heterogeneity in a patient population. We simulated random mutations conferring resistance to oseltamivir. We explored the effect of therapy initiation time, dose, intake frequency and therapy duration on influenza infection, illness dynamics, and emergence of viral resistance. Symptom and virological efficacies were strongly associated with therapy initiation time. The proportion of subjects shedding resistant virus was 27-fold higher when prophylaxis was initiated during the incubation period compared with no treatment. It fell to below 1% when treatment was initiated after symptom onset for twice-a-day intakes. Lower doses and prophylaxis regimens led to lower efficacies and increased risk of resistance emergence. We conclude that prophylaxis initiated during the incubation period is the main factor leading to resistance emergence., Author Summary Oseltamivir is currently the most commonly used drug against influenza but the emergence and spread of oseltamivir-resistant virus is threatening its usefulness. A previously published study quantified the risk of drug-resistance emergence and spread. In this work we investigate under what conditions drug-resistance is likely to occur and how we can mitigate it. For this purpose, we simulated populations of influenza-infected subjects under different treatment conditions varying drug dose, intake frequency and duration of therapy. We used an approach that mimics the randomness of drug-resistance emergence and allowed for between-subject variability. We measured the effect of treatment on reducing infection and symptoms and on drug-resistance emergence. We found that for subjects starting oseltamivir during the influenza incubation period, the risk of resistance emergence is dramatically increased. Thus, our findings suggest that standard prophylaxis should only be used after exclusion of an influenza infection in the incubation period by use of a rapid test. If existing infection cannot be excluded, then prophylaxis should be done with increased dose, intake frequency and duration in order to avoid emergence of drug-resistant strains and to preserve oseltamivir efficacy.