scholarly journals Incomplete influenza A virus genomes are abundant but readily complemented during spatially structured viral spread

2019 ◽  
Author(s):  
Nathan T. Jacobs ◽  
Nina O. Onuoha ◽  
Alice Antia ◽  
Rustom Antia ◽  
John Steel ◽  
...  
Keyword(s):  
Influenza A ◽  
Mutant Virus ◽  
Viral Fitness ◽  
H3n2 Virus ◽  
Multiple Infection ◽  
Mixed System ◽  
Viral Genomes ◽  
Viral Spread ◽  
A Cell

AbstractViral genomes comprising multiple distinct RNA segments can undergo genetic exchange through reassortment, a process that facilitates viral evolution and can have major epidemiological consequences. Segmentation also allows the replication of incomplete viral genomes (IVGs), however, and evidence suggests that IVGs occur frequently for influenza A viruses. Here we quantified the frequency of IVGs using a novel single cell assay and then examined their implications for viral fitness. We found that each segment of influenza A/Panama/2007/99 (H3N2) virus has only a 58% probability of being present in a cell infected with a single virion. These observed frequencies accurately account for the abundant reassortment seen in co-infection, and suggest that an average of 3.7 particles are required for replication of a full viral genome in a cell. This dependence on multiple infection is predicted to decrease infectivity and to slow viral propagation in a well-mixed system. Importantly, however, modeling of spatially structured viral growth predicted that the need for complementation is met more readily when secondary spread occurs locally. This expectation was supported by experimental infections in which the level spatial structure was manipulated. Furthermore, a virus engineered to be entirely dependent on co-infection to replicate in vivo was found to grow robustly in guinea pigs, suggesting that coinfection is sufficiently common in vivo to support propagation of IVGs. The infectivity of this mutant virus was, however, reduced 815-fold relative wild-type and the mutant virus did not transmit to contacts. Thus, while incomplete genomes augment reassortment and contribute to within-host spread, the existence of rare complete IAV genomes may be critical for transmission to new hosts.

scholarly journals Assessing the Viral Fitness of Oseltamivir-Resistant Influenza Viruses in Ferrets, Using a Competitive-Mixtures Model

2010 ◽  
Vol 84 (18) ◽  
pp. 9427-9438 ◽  
Author(s):  
Aeron C. Hurt ◽  
Siti Sarah Nor'e ◽  
James M. McCaw ◽  
Helen R. Fryer ◽  
Jennifer Mosse ◽  
...  
Keyword(s):  
Influenza Viruses ◽  
Mutant Virus ◽  
Viral Fitness ◽  
Relative Fitness ◽  
H3n2 Virus ◽  
Wild Type Virus ◽  
Human Populations ◽  
Type Virus ◽  
Wild Type

ABSTRACT To determine the relative fitness of oseltamivir-resistant strains compared to susceptible wild-type viruses, we combined mathematical modeling and statistical techniques with a novel in vivo “competitive-mixtures” experimental model. Ferrets were coinfected with either pure populations (100% susceptible wild-type or 100% oseltamivir-resistant mutant virus) or mixed populations of wild-type and oseltamivir-resistant influenza viruses (80%:20%, 50%:50%, and 20%:80%) at equivalent infectivity titers, and the changes in the relative proportions of those two viruses were monitored over the course of the infection during within-host and over host-to-host transmission events in a ferret contact model. Coinfection of ferrets with mixtures of an oseltamivir-resistant R292K mutant A(H3N2) virus and a R292 oseltamivir-susceptible wild-type virus demonstrated that the R292K mutant virus was rapidly outgrown by the R292 wild-type virus in artificially infected donor ferrets and did not transmit to any of the recipient ferrets. The competitive-mixtures model was also used to investigate the fitness of the seasonal A(H1N1) oseltamivir-resistant H274Y mutant and showed that within infected ferrets the H274Y mutant virus was marginally outgrown by the wild-type strain but demonstrated equivalent transmissibility between ferrets. This novel in vivo experimental method and accompanying mathematical analysis provide greater insight into the relative fitness, both within the host and between hosts, of two different influenza virus strains compared to more traditional methods that infect ferrets with only pure populations of viruses. Our statistical inferences are essential for the development of the next generation of mathematical models of the emergence and spread of oseltamivir-resistant influenza in human populations.

scholarly journals Multiple Influenza A (H3N2) Mutations Conferring Resistance to Neuraminidase Inhibitors in a Bone Marrow Transplant Recipient

2014 ◽  
Vol 58 (12) ◽  
pp. 7188-7197 ◽  
Author(s):  
Alireza Eshaghi ◽  
Sarah Shalhoub ◽  
Paul Rosenfeld ◽  
Aimin Li ◽  
Rachel R. Higgins ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Antiviral Therapy ◽  
Influenza A ◽  
Antiviral Treatment ◽  
Marrow Transplant ◽  
Viral Fitness ◽  
H3n2 Virus ◽  
Resistance Mutations ◽  
Depth Analysis ◽  
Resistant Strains

ABSTRACTImmunocompromised patients are predisposed to infections caused by influenza virus. Influenza virus may produce considerable morbidity, including protracted illness and prolonged viral shedding in these patients, thus prompting higher doses and prolonged courses of antiviral therapy. This approach may promote the emergence of resistant strains. Characterization of neuraminidase (NA) inhibitor (NAI)-resistant strains of influenza A virus is essential for documenting causes of resistance. In this study, using quantitative real-time PCR along with conventional Sanger sequencing, we identified an NAI-resistant strain of influenza A (H3N2) virus in an immunocompromised patient. In-depth analysis by deep gene sequencing revealed that various known markers of antiviral resistance, including transient R292K and Q136K substitutions and a sustained E119K (N2 numbering) substitution in the NA protein emerged during prolonged antiviral therapy. In addition, a combination of a 4-amino-acid deletion at residues 245 to 248 (Δ245-248) accompanied by the E119V substitution occurred, causing resistance to or reduced inhibition by NAIs (oseltamivir, zanamivir, and peramivir). Resistant variants within a pool of viral quasispecies arose during combined antiviral treatment. More research is needed to understand the interplay of drug resistance mutations, viral fitness, and transmission.

scholarly journals A putative antiviral role of plant cytidine deaminases

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 622
Author(s):  
Susana Martín ◽  
José M. Cuevas ◽  
Ana Grande-Pérez ◽  
Santiago F. Elena
Keyword(s):  
Mammalian Cells ◽  
Mutagenic Activity ◽  
Population Diversity ◽  
Viral Fitness ◽  
Cauliflower Mosaic Virus ◽  
Cytidine Deaminases ◽  
Viral Genomes ◽  
Mutational Spectra ◽  
Antiviral Mechanism

Background: A mechanism of innate antiviral immunity operating against viruses infecting mammalian cells has been described during the last decade.  Host cytidine deaminases (e.g., APOBEC3 proteins) edit viral genomes, giving rise to hypermutated nonfunctional viruses; consequently, viral fitness is reduced through lethal mutagenesis.  By contrast, sub-lethal hypermutagenesis may contribute to virus evolvability by increasing population diversity.  To prevent genome editing, some viruses have evolved proteins that mediate APOBEC3 degradation.  The model plant Arabidopsis thaliana genome encodes nine cytidine deaminases (AtCDAs), raising the question of whether deamination is an antiviral mechanism in plants as well. Methods: Here we tested the effects of expression of AtCDAs on the pararetrovirus Cauliflower mosaic virus (CaMV). Two different experiments were carried out. First, we transiently overexpressed each one of the nine A. thaliana AtCDA genes in Nicotiana bigelovii plants infected with CaMV, and characterized the resulting mutational spectra, comparing them with those generated under normal conditions.  Secondly, we created A. thaliana transgenic plants expressing an artificial microRNA designed to knock-out the expression of up to six AtCDA genes.  This and control plants were then infected with CaMV.  Virus accumulation and mutational spectra where characterized in both types of plants. Results:  We have shown that the A. thaliana AtCDA1 gene product exerts a mutagenic activity, significantly increasing the number of G to A mutations in vivo, with a concomitant reduction in the amount of CaMV genomes accumulated.  Furthermore, the magnitude of this mutagenic effect on CaMV accumulation is positively correlated with the level of AtCDA1 mRNA expression in the plant. Conclusions: Our results suggest that deamination of viral genomes may also work as an antiviral mechanism in plants.

scholarly journals Evolution and Biological Evaluation of Matrinic Derivatives with Amantadine Fragments As New Anti-Influenza Virus Agents

Molecules ◽  
2019 ◽  
Vol 24 (5) ◽  
pp. 921 ◽  
Author(s):  
Tianyu Niu ◽  
Xiaoqiang Zhao ◽  
Jing Jiang ◽  
Haiyan Yan ◽  
Yinghong Li ◽  
...  
Keyword(s):  
Influenza A ◽  
Early Stage ◽  
Biological Evaluation ◽  
H3n2 Virus ◽  
New Class ◽  
Ic50 Values ◽  
Virus Replication Cycle ◽  
Sar Analysis ◽  
Better Than

A series of novel tricyclic matrinic derivatives with 11-adamantyl substitution were designed, synthesized, and evaluated for their activities against Influenza A H3N2 virus, based on the privileged structure strategy. Structure-activity relationship (SAR) analysis indicated that the introduction of an 11-adamantyl might be helpful for the potency. Among them, compounds 9f and 9j exhibited the promising anti-H3N2 activities with IC50 values of 7.2 μM and 10.2 μM, respectively, better than that of lead 1. Their activities were further confirmed at the protein level. Moreover, compound 9f displayed a high pharmacokinetic (PK) stability profile in whole blood and a safety profile in vivo. In primary mechanism, compound 9f could inhibit the virus replication cycle at early stage by targeting M2 protein, consistent with that of the parent amantadine. This study provided powerful information for further strategic optimization to develop these compounds into a new class of anti-influenza agents.

scholarly journals Why viruses sometimes disperse in groups†

2019 ◽  
Vol 5 (1) ◽  
Author(s):  
Rafael Sanjuán ◽  
María-Isabel Thoulouze
Keyword(s):  
Genetic Relatedness ◽  
Lipid Vesicles ◽  
Viral Fitness ◽  
Target Cells ◽  
Spatial And Temporal Scales ◽  
Viral Genomes ◽  
Antiviral Responses ◽  
Viral Spread ◽  
Protein Matrices ◽  
Viral Components

AbstractMany organisms disperse in groups, yet this process is understudied in viruses. Recent work, however, has uncovered different types of collective infectious units, all of which lead to the joint delivery of multiple viral genome copies to target cells, favoring co-infections. Collective spread of viruses can occur through widely different mechanisms, including virion aggregation driven by specific extracellular components, cloaking inside lipid vesicles, encasement in protein matrices, or binding to cell surfaces. Cell-to-cell viral spread, which allows the transmission of individual virions in a confined environment, is yet another mode of clustered virus dissemination. Nevertheless, the selective advantages of dispersing in groups remain poorly understood in most cases. Collective dispersal might have emerged as a means of sharing efficacious viral transmission vehicles. Alternatively, increasing the cellular multiplicity of infection may confer certain short-term benefits to viruses, such as overwhelming antiviral responses, avoiding early stochastic loss of viral components required for initiating infection, or complementing genetic defects present in different viral genomes. However, increasing infection multiplicity may also entail long-term costs, such as mutation accumulation and the evolution of defective particles or other types of cheater viruses. These costs and benefits, in turn, should depend on the genetic relatedness among collective infectious unit members. Establishing the genetic basis of collective viral dispersal and performing controlled experiments to pinpoint fitness effects at different spatial and temporal scales should help us clarify the implications of these spread modes for viral fitness, pathogenicity, and evolution.

scholarly journals Influenza Hemagglutinin and Neuraminidase: Yin–Yang Proteins Coevolving to Thwart Immunity

Viruses ◽  
2019 ◽  
Vol 11 (4) ◽  
pp. 346 ◽  
Author(s):  
Ivan Kosik ◽  
Jonathan W. Yewdell
Keyword(s):  
Influenza A ◽  
Antigenic Variation ◽  
Innate Immune ◽  
Viral Fitness ◽  
Adaptive Immune ◽  
Influenza Hemagglutinin ◽  
Immune Pressure ◽  
Virion Release ◽  
Infectious Cycle

Influenza A virions possess two surface glycoproteins—the hemagglutinin (HA) and neuraminidase (NA)—which exert opposite functions. HA attaches virions to cells by binding to terminal sialic acid residues on glycoproteins/glycolipids to initiate the infectious cycle, while NA cleaves terminal sialic acids, releasing virions to complete the infectious cycle. Antibodies specific for HA or NA can protect experimental animals from IAV pathogenesis and drive antigenic variation in their target epitopes that impairs vaccine effectiveness in humans. Here, we review progress in understanding HA/NA co-evolution as each acquires epistatic mutations to restore viral fitness to mutants selected in the other protein by host innate or adaptive immune pressure. We also discuss recent exciting findings that antibodies to HA can function in vivo by blocking NA enzyme activity to prevent nascent virion release and enhance Fc receptor-based activation of innate immune cells.

Identification of a Small Benzamide Inhibitor of Influenza Virus Using a Cell-Based Screening

Chemotherapy ◽  
2016 ◽  
Vol 61 (3) ◽  
pp. 159-166 ◽  
Author(s):  
Woo-Jin Shin ◽  
Ky-Youb Nam ◽  
Nam-Doo Kim ◽  
Sei-Hwan Kim ◽  
Kyoung-Tai No ◽  
...  
Keyword(s):  
Avian Influenza ◽  
Influenza A ◽  
H1n1 Influenza ◽  
Influenza Viruses ◽  
Global Pandemic ◽  
Lethal Infection ◽  
Avian Influenza A Virus ◽  
A Cell ◽  
Antiviral Activities

Background: The zoonotic transmission of highly pathogenic avian influenza viruses and the global pandemic of H1N1 influenza in 2009 signified the need for a wider coverage of therapeutic options for the control of influenza. Methods: An in-house compound library was screened using a cytopathic effect inhibition assay. Selected hits were then tested in vivo and used as a core skeleton for derivative synthesis. Results: The hit compound (BMD-2601505) was effective [50% effective concentration (EC50) of 60-70 μM] in reducing the death rate of cells infected with human influenza A and B viruses as well as avian influenza A virus. Furthermore, BMD-2601505 reduced the weight loss and increased the survival after lethal infection. The compound was further modified to enhance its antiviral potency. Results show that one derivative with bromobenzene moiety was most effective (EC50 of 22-37 μM) against the influenza viruses tested. Conclusion: We identified a small benzamide compound exhibiting antiviral activity against influenza viruses. The results warrant further evaluation of antiviral activities against drug-resistant influenza isolates.

Replication and transmission of an influenza A(H3N2) virus harboring the polymerase acidic I38T substitution, in guinea pigs.

2021 ◽  
Vol 102 (10) ◽  
Author(s):  
Zeineb Mhamdi ◽  
Julie Carbonneau ◽  
Marie-Christine Venable ◽  
Mariana Baz ◽  
Yacine Abed ◽  
...  
Keyword(s):  
Guinea Pigs ◽  
Influenza A ◽  
Reverse Genetics ◽  
Mdck Cells ◽  
A549 Cells ◽  
Viral Fitness ◽  
Viral Population ◽  
H3n2 Virus ◽  
The Impact

The polymerase acidic (PA) I38T substitution is a dominant marker of resistance to baloxavir. We evaluated the impact of I38T on the fitness of a contemporary influenza A(H3N2) virus. Influenza A/Switzerland/9715293/2013 (H3N2) wild-type (WT) virus and its I38T mutant were rescued by reverse genetics. Replication kinetics were compared using ST6GalI-MDCK and A549 cells and infectivity/contact transmissibility were evaluated in guinea pigs. Nasal wash (NW) viral titres were determined by TCID50 ml−1 in ST6GalI-MDCK cells. Competition experiments were performed and the evolution of viral population was assessed by droplet digital RT-PCR. I38T did not alter in vitro replication. I38T induced comparable titres vs the WT in guinea pigs NWs and the two viruses transmitted equally by direct contact. However, a 50 %:50 % mixture inoculum evolved to mean WT/I38T ratios of 71 %:29 % and 66.4 %:33.6 % on days 4 and 6 p.i., respectively. Contemporary influenza A(H3N2)-I38T PA variants may conserve a significant level of viral fitness.

scholarly journals Differential Viral-Host Immune Interactions Associated with Oseltamivir-Resistant H275Y and Wild-Type H1N1 A(pdm09) Influenza Virus Pathogenicity

Viruses ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 794
Author(s):  
Beatriz Vidaña ◽  
Pamela Martínez-Orellana ◽  
Jaime Martorell ◽  
Massimiliano Baratelli ◽  
Jorge Martínez ◽  
...  
Keyword(s):  
Influenza A ◽  
Clinical Signs ◽  
Viral Fitness ◽  
Type I ◽  
Lung Pathology ◽  
Wild Type ◽  
Viral Kinetics ◽  
Influenza A H1n1

Oseltamivir is a common therapy against influenza A virus (IAV) infections. The acquisition of oseltamivir resistance (OR) mutations, such as H275Y, hampers viral fitness. However, OR H1N1 viruses have demonstrated the ability to spread throughout different populations. The objective of this work was to compare the fitness of two strains of OR (R6 and R7) containing the H275Y mutation, and a wild-type (F) pandemic influenza A (H1N1) 2009 (pdm09) virus both in vitro and in vivo in mice and to select one OR strain for a comparison with F in ferrets. R6 showed faster replication and pathogenicity than R7 in vitro and in mice. Subsequently, R6 was selected for the fitness comparison with the F strain in ferrets. Ferrets infected with the F virus showed more severe clinical signs, histopathological lung lesions, and viral quantification when compared to OR R6-infected animals. More importantly, differential viral kinetics correlated with differential pro-inflammatory host immune responses in the lungs of infected ferrets, where OR-infected animals developed a protective higher expression of type I IFN and Retinoid acid Inducible Gene I (RIG-I) genes early after infection, resulting in the development of milder disease. These results suggest the presence of early specific viral-host immune interactions relevant in the development of influenza-associated lung pathology.

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