scholarly journals Mathematical models of Influenza A. virus infections in vitro: Invesigating defective interfering particles and virus release

2021 ◽  
Author(s):  
Laura Liao
Keyword(s):  
Mathematical Models ◽  
Influenza A Virus ◽  
Release Rate ◽  
Influenza A ◽  
Quantitative Methods ◽  
Virus Release ◽  
Virus Infections ◽  
Defective Interfering Particles ◽  
A Cell

In this work, two studies were performed where mathematical models (MM) were used to re-examine and refine quantitative methods based on in vitro assays of influenza A virus infections. In the first study, we investigated the standard experimental method for counting defective interfering particles (DIPs) based on the reduction in standard virus (STV) yield (Bellett & Cooper, 1959). We found the method is valid for counting DIPs provided that: (1) a STV-infected cell’s co-infection window is approximately half its eclipse phase (it blocks infection by other virions before it begins producing progeny virions); (2) a cell co-infected by STV and DIP produces less than 1 STV per 1,000 DIPs; and (3) a high MOI of STV stock (>4 plaque-forming units/cell) is added to perform the assay. Prior work makes no mention of these criteria such that the counting method has been applied incorrectly in several publications discussed herein. We determined influenza A virus meets these criteria, making the method suitable for counting influenza A DIPs. In the second study, we compared a MM with an explicit representation of viral release to a simple MM without explicit release, and investigated whether parameter estimation and the estimation of neuraminidase inhibitor (NAI) efficacy were affected by the use of a simple MM. Since the release rate of influenza A virus is not well-known, a broad range of release rates were considered. If the virus release rate is greater than ∼0.1 h−1, the simple MM provides accurate estimates of infection parameters, but underestimates NAI efficacy, which could lead to underdosing and the emergence of NAI resistance. In contrast, when release is slower than ∼0.1 h−1, the simple MM accurately estimates NAI efficacy, but it can significantly overestimate the infectious lifespan (i.e., the time a cell remains infectious and producing free virus), and it will significantly underestimate the total virus yield and thus the likelihood of resistance emergence. We discuss the properties of, and a possible lower bound for, the influenza A virus release rate. Overall, MMs are a valuable tool in the exploration of the known unknowns (i.e., DIPs, virus release) of influenza A virus infection.

scholarly journals Mathematical models of Influenza A. virus infections in vitro: Invesigating defective interfering particles and virus release

2021 ◽  
Author(s):  
Laura Liao
Keyword(s):  
Mathematical Models ◽  
Influenza A Virus ◽  
Release Rate ◽  
Influenza A ◽  
Quantitative Methods ◽  
Virus Release ◽  
Virus Infections ◽  
Defective Interfering Particles ◽  
A Cell

In this work, two studies were performed where mathematical models (MM) were used to re-examine and refine quantitative methods based on in vitro assays of influenza A virus infections. In the first study, we investigated the standard experimental method for counting defective interfering particles (DIPs) based on the reduction in standard virus (STV) yield (Bellett & Cooper, 1959). We found the method is valid for counting DIPs provided that: (1) a STV-infected cell’s co-infection window is approximately half its eclipse phase (it blocks infection by other virions before it begins producing progeny virions); (2) a cell co-infected by STV and DIP produces less than 1 STV per 1,000 DIPs; and (3) a high MOI of STV stock (>4 plaque-forming units/cell) is added to perform the assay. Prior work makes no mention of these criteria such that the counting method has been applied incorrectly in several publications discussed herein. We determined influenza A virus meets these criteria, making the method suitable for counting influenza A DIPs. In the second study, we compared a MM with an explicit representation of viral release to a simple MM without explicit release, and investigated whether parameter estimation and the estimation of neuraminidase inhibitor (NAI) efficacy were affected by the use of a simple MM. Since the release rate of influenza A virus is not well-known, a broad range of release rates were considered. If the virus release rate is greater than ∼0.1 h−1, the simple MM provides accurate estimates of infection parameters, but underestimates NAI efficacy, which could lead to underdosing and the emergence of NAI resistance. In contrast, when release is slower than ∼0.1 h−1, the simple MM accurately estimates NAI efficacy, but it can significantly overestimate the infectious lifespan (i.e., the time a cell remains infectious and producing free virus), and it will significantly underestimate the total virus yield and thus the likelihood of resistance emergence. We discuss the properties of, and a possible lower bound for, the influenza A virus release rate. Overall, MMs are a valuable tool in the exploration of the known unknowns (i.e., DIPs, virus release) of influenza A virus infection.

scholarly journals The mechanism of resistance to favipiravir in influenza

2018 ◽  
Vol 115 (45) ◽  
pp. 11613-11618 ◽  
Author(s):  
Daniel H. Goldhill ◽  
Aartjan J. W. te Velthuis ◽  
Robert A. Fletcher ◽  
Pinky Langat ◽  
Maria Zambon ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Influenza A Virus ◽  
Influenza A ◽  
H1n1 Influenza ◽  
Viral Fitness ◽  
Virus Infections ◽  
Virus Rna ◽  
Evolution Of Resistance ◽  
Emergence Of Resistance

Favipiravir is a broad-spectrum antiviral that has shown promise in treatment of influenza virus infections. While emergence of resistance has been observed for many antiinfluenza drugs, to date, clinical trials and laboratory studies of favipiravir have not yielded resistant viruses. Here we show evolution of resistance to favipiravir in the pandemic H1N1 influenza A virus in a laboratory setting. We found that two mutations were required for robust resistance to favipiravir. We demonstrate that a K229R mutation in motif F of the PB1 subunit of the influenza virus RNA-dependent RNA polymerase (RdRP) confers resistance to favipiravir in vitro and in cell culture. This mutation has a cost to viral fitness, but fitness can be restored by a P653L mutation in the PA subunit of the polymerase. K229R also conferred favipiravir resistance to RNA polymerases of other influenza A virus strains, and its location within a highly conserved structural feature of the RdRP suggests that other RNA viruses might also acquire resistance through mutations in motif F. The mutations identified here could be used to screen influenza virus-infected patients treated with favipiravir for the emergence of resistance.

scholarly journals (In)validating experimentally derived knowledge about influenza A defective interfering particles

2016 ◽  
Vol 13 (124) ◽  
pp. 20160412 ◽  
Author(s):  
Laura E. Liao ◽  
Shingo Iwami ◽  
Catherine A. A. Beauchemin
Keyword(s):  
Mathematical Model ◽  
Experimental Method ◽  
Influenza A Virus ◽  
Influenza A ◽  
Infectious Virus ◽  
Full Length ◽  
Prior Work ◽  
Defective Interfering Particles ◽  
A Cell ◽  
Eclipse Phase

A defective interfering particle (DIP) in the context of influenza A virus is a virion with a significantly shortened RNA segment substituting one of eight full-length parent RNA segments, such that it is preferentially amplified. Hence, a cell co-infected with DIPs will produce mainly DIPs, suppressing infectious virus yields and affecting infection kinetics. Unfortunately, the quantification of DIPs contained in a sample is difficult because they are indistinguishable from standard virus (STV). Using a mathematical model, we investigated the standard experimental method for counting DIPs based on the reduction in STV yield (Bellett & Cooper, 1959, Journal of General Microbiology 21 , 498–509 ( doi:10.1099/00221287-21-3-498 )). We found the method is valid for counting DIPs provided that: (i) an STV-infected cell's co-infection window is approximately half its eclipse phase (it blocks infection by other virions before it begins producing progeny virions), (ii) a cell co-infected by STV and DIP produces less than 1 STV per 1000 DIPs and (iii) a high MOI of STV stock (more than 4 PFU per cell) is added to perform the assay. Prior work makes no mention of these criteria such that the method has been applied incorrectly in several publications discussed herein. We determined influenza A virus meets these criteria, making the method suitable for counting influenza A DIPs.

Serum amyloid P component inhibits influenza A virus infections: in vitro and in vivo studies

2001 ◽  
Vol 52 (1) ◽  
pp. 43-53 ◽  
Author(s):  
A Horváth ◽  
I Andersen ◽  
K Junker ◽  
B Lyck Fogh-Schultz ◽  
E Holm Nielsen ◽  
...  
Keyword(s):  
Influenza A Virus ◽  
Influenza A ◽  
In Vivo Studies ◽  
Virus Infections ◽  
Amyloid P Component ◽  
Serum Amyloid P ◽  
Serum Amyloid P Component ◽  
Amyloid P

scholarly journals Mathematical Model for the Intracellular Kinetics of Influenza a Virus Replication in Vitro

2021 ◽  
Author(s):  
Diana Schwendener Forkel
Keyword(s):  
Influenza A Virus ◽  
Virus Replication ◽  
Influenza A ◽  
Infection Process ◽  
Treatment Modalities ◽  
Viral Production ◽  
A Cell ◽  
Basic Biology ◽  
Kinetics Of

In the last twenty years, mathematical modelling (MM) has been notably used to capture the infection kinetics of many infectious diseases as it allows insights into the basic biology, infection kinetics, and the mechanisms and efficacy of treatment modalities. MMs of influenza A virus (IAV) infection usually represent the process of virus replication within a cell as a ‘black box’ term for viral production. The simplification is appropriate when we are not interested in the microscopic details of infection. Recently though, MMs have begun to account for the kinetics of intracellular IAV replication. Herein, we examine the MM by Heldt et al., which is able to capture kinetics of IAV infection. It however, does so by adjusting parameters of the MM to various events in the infection process. We developed a robust, yet concise, MM for the intracellular kinetics of influenza A virus infection in vitro with a consistent set of parameters. We use attachment, fusion and RNA data gathered from literature sources to validate our simplified MM and match known infection kinetics consistent throughout infection.

scholarly journals In Vitro System for Modeling Influenza A Virus Resistance under Drug Pressure

2010 ◽  
Vol 54 (8) ◽  
pp. 3442-3450 ◽  
Author(s):  
Ashley N. Brown ◽  
James J. McSharry ◽  
Qingmei Weng ◽  
Elizabeth M. Driebe ◽  
David M. Engelthaler ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Influenza A Virus ◽  
Virus Replication ◽  
Influenza A ◽  
Mdck Cells ◽  
Influenza Virus Infection ◽  
Infection Model ◽  
Virus Infections ◽  
Drug Pressure

ABSTRACT One of the biggest challenges in the effort to treat and contain influenza A virus infections is the emergence of resistance during treatment. It is well documented that resistance to amantadine arises rapidly during the course of treatment due to mutations in the gene coding for the M2 protein. To address this problem, it is critical to develop experimental systems that can accurately model the selection of resistance under drug pressure as seen in humans. We used the hollow-fiber infection model (HFIM) system to examine the effect of amantadine on the replication of influenza virus, A/Albany/1/98 (H3N2), grown in MDCK cells. At 24 and 48 h postinfection, virus replication was inhibited in a dose-dependent fashion. At 72 and 96 h postinfection, virus replication was no longer inhibited, suggesting the emergence of amantadine-resistant virus. Sequencing of the M2 gene revealed that mutations appeared at between 48 and 72 h of drug treatment and that the mutations were identical to those identified in the clinic for amantadine-resistant viruses (e.g., V27A, A30T, and S31N). Interestingly, we found that the type of mutation was strongly affected by the dose of the drug. The data suggest that the HFIM is a good model for influenza virus infection and resistance generation in humans. The HFIM has the advantage of being a highly controlled system where multiplicity parameters can be directly and accurately controlled and measured.

scholarly journals Semi-continuous propagation of influenza A virus and its defective interfering particles: analyzing the dynamic competition to select candidates for antiviral therapy

2021 ◽  
Author(s):  
Lars Pelz ◽  
Daniel Rüdiger ◽  
Tanya Dogra ◽  
Fadi G. Alnaji ◽  
Yvonne Genzel ◽  
...  
Keyword(s):  
Antiviral Therapy ◽  
Influenza A Virus ◽  
Influenza A ◽  
De Novo ◽  
Competitive Inhibition ◽  
Antiviral Treatment ◽  
Small Scale ◽  
Internal Deletion ◽  
Defective Interfering Particles

Defective interfering particles (DIPs) of influenza A virus (IAV) are naturally occurring mutants that comprise an internal deletion in one of their eight viral RNA (vRNA) segments, rendering them propagation-incompetent. Upon co-infection with infectious standard virus (STV), DIPs interfere with STV replication through competitive inhibition. Thus, DIPs are proposed as potent antivirals for treatment of the influenza disease. To select corresponding candidates, we studied de novo generation of DIPs and propagation competition between different defective interfering (DI) vRNAs in a STV co-infection scenario in cell culture. A small-scale two-stage cultivation system that allows long-term semi-continuous propagation of IAV and its DIPs was used. Strong periodic oscillations in virus titers were observed due to the dynamic interaction of DIPs and STVs. Using next-generation sequencing, we detected a predominant formation and accumulation of DI vRNAs on the polymerase-encoding segments. Short DI vRNAs accumulated to higher fractions than longer ones, indicating a replication advantage. Yet, an optimum fragment length was observed. Some DI vRNAs showed breaking points in a specific part of their bundling signal (belonging to the packaging signal), suggesting its dispensability for DI vRNA propagation. Over a total cultivation time of 21 days, several individual DI vRNAs accumulated to high fractions, while others decreased. Using reverse genetics for IAV, purely clonal DIPs derived from highly replicating DI vRNAs were generated. We confirm that these DIPs exhibit a superior in vitro interfering efficacy than DIPs derived from lowly accumulated DI vRNAs and suggest promising candidates for efficacious antiviral treatment. Importance Defective interfering particles (DIPs) emerge naturally during viral infection and typically show an internal deletion in the viral genome. Thus, DIPs are propagation-incompetent. Previous research suggests DIPs as potent antiviral compounds for many different virus families due to their ability to interfere with virus replication by competitive inhibition. For instance, the administration of influenza A virus (IAV) DIPs resulted in a rescue of mice from an otherwise lethal IAV dose. Moreover, no apparent toxic effects were observed when only DIPs were administered to mice and ferrets. IAV DIPs show antiviral activity against many different IAV strains, including pandemic and highly pathogenic avian strains, and even against non-homologous viruses, like SARS-CoV-2, by stimulation of innate immunity. Here, we used a cultivation/infection system, which exerted selection pressure toward accumulation of highly competitive IAV DIPs. These DIPs showed a superior interfering efficacy in vitro , and we suggest them for effective antiviral therapy.

scholarly journals Mathematical Model for the Intracellular Kinetics of Influenza a Virus Replication in Vitro

2021 ◽  
Author(s):  
Diana Schwendener Forkel
Keyword(s):  
Influenza A Virus ◽  
Virus Replication ◽  
Influenza A ◽  
Infection Process ◽  
Treatment Modalities ◽  
Viral Production ◽  
A Cell ◽  
Basic Biology ◽  
Kinetics Of

In the last twenty years, mathematical modelling (MM) has been notably used to capture the infection kinetics of many infectious diseases as it allows insights into the basic biology, infection kinetics, and the mechanisms and efficacy of treatment modalities. MMs of influenza A virus (IAV) infection usually represent the process of virus replication within a cell as a ‘black box’ term for viral production. The simplification is appropriate when we are not interested in the microscopic details of infection. Recently though, MMs have begun to account for the kinetics of intracellular IAV replication. Herein, we examine the MM by Heldt et al., which is able to capture kinetics of IAV infection. It however, does so by adjusting parameters of the MM to various events in the infection process. We developed a robust, yet concise, MM for the intracellular kinetics of influenza A virus infection in vitro with a consistent set of parameters. We use attachment, fusion and RNA data gathered from literature sources to validate our simplified MM and match known infection kinetics consistent throughout infection.

scholarly journals Antiviral activity of influenza A virus defective interfering particles against SARS-CoV-2 replication in vitro through stimulation of innate immunity

2021 ◽  
Author(s):  
U. Rand ◽  
S.Y. Kupke ◽  
H. Shkarlet ◽  
M.D. Hein ◽  
T. Hirsch ◽  
...  
Keyword(s):  
Innate Immunity ◽  
Influenza A Virus ◽  
Influenza A ◽  
Immune Escape ◽  
Antiviral Treatment ◽  
Specific Treatment ◽  
Janus Kinase ◽  
Defective Interfering Particles ◽  
Stimulation Of

AbstractSARS-CoV-2 causing COVID-19 emerged in late 2019 and resulted in a devastating pandemic. Although the first approved vaccines were already administered by the end of 2020, vaccine availability is still limited. Moreover, immune escape variants of the virus are emerging against which the current vaccines may confer only limited protection. Further, existing antivirals and treatment options against COVID-19 only show limited efficacy. Influenza A virus (IAV) defective interfering particles (DIPs) were previously proposed not only for antiviral treatment of the influenza disease but also for pan-specific treatment of interferon (IFN)-sensitive respiratory virus infections. To investigate the applicability of IAV DIPs as an antiviral for the treatment of COVID-19, we conducted in vitro co-infection experiments with produced, cell culture-derived DIPs and the IFN-sensitive SARS-CoV-2. We show that treatment with IAV DIPs leads to complete abrogation of SARS-CoV-2 replication. Moreover, this inhibitory effect was dependent on janus kinase/signal transducers and activators of transcription (JAK/STAT) signaling. These results suggest an unspecific stimulation of the innate immunity by IAV DIPs as a major contributor in suppressing SARS-CoV-2 replication. Thus, we propose IAV DIPs as an effective antiviral agent for treatment of COVID-19, and potentially also for suppressing the replication of new variants of SARS-CoV-2.

Sign in / Sign up

Export Citation Format

Share Document