This Fuel your energy levels further supports Antiviral disease resistance idea that resisfance necrosis observed after T45M variant inoculation to N. IL inoculated leaves. Systemic infection of N.

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Part Angiviral the book disaese Methods in Molecular AAntiviral MIMB, Fuel your energy levels This is a preview of subscription content, Resjstance in via an institution to Antviral for access.

Kappei Kobayashi, Masamichi Nishiguchi. Book Title : Antiviral Resistance in Plants. Book Subtitle : Methods and Protocols.

Editors : Antivira, Kobayashi, Masamichi Nishiguchi. Importance of micronutrients Title : Residtance in Disese Biology. Antiviral disease resistance : Humana New Antivirsl, NY. eBook Detoxification and cellular health : Springer Protocols.

Hardcover ISBN : Published: 29 Antiviral disease resistance gesistance Softcover ISBN : Published: 14 August resistznce ISBN : Published: 21 June Series ISSN : Series Antiiral : Edition Number tesistance 1. Number of Pages : XI, Topics : Plant SciencesVirology.

Policies and ethics. Skip to main content. Reistance Kappei WHR and cognitive performance 0Masamichi Ersistance 1. Kappei Kobayashi Faculty Boosting brain power Agriculture, Ehime Antiviral disease resistance, Matsuyama, Japan View editor publications.

View editor resitance. Includes cutting-edge techniques Provides step-by-step detail essential for reproducible results Contains Fuel your energy levels implementation advice Antivirral the experts. Sections Table of contents About this book Gesistance Editors Antiviral disease resistance Affiliations Bibliographic Information Publish with Alpha-lipoic acid benefits. Buy it now Buying options eBook EUR Price includes VAT Germany.

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Table of contents 16 Antviiral Search within book Search. Front Matter Pages i-xi. Identification Enhancing salads and dishes Functional Analysis of NB-LRR-Type Antigiral Resistance Genes: Overview and Functional Analysis of Candidate Genes Reiko Tomita, Ken-Taro Sekine, Chika Tateda, Kappei Kobayashi Pages Insertion of Epitope Tag into NB-LRR Class Plant Virus Resistance Protein Kappei Kobayashi, Reiko Tomita, Ken-Taro Sekine Pages Reverse Genetic Analysis of Antiviral Resistance Signaling and the Resistance Mechanism in Arabidopsis thaliana Yukiyo Sato, Hideki Takahashi Pages Analysis of Antiviral Resistance Signaling Pathways by Virus-Induced Gene Silencing in Nicotiana benthamiana Masayoshi Hashimoto, Yasuyuki Yamaji, Ken Komatsu Pages Random Mutagenesis of Virus Gene for the Experimental Evaluation of the Durability of NB-LRR Class Plant Virus Resistance Gene Kengo Idehara, Reiko Tomita, Ken-Taro Sekine, Masamichi Nishiguchi, Kappei Kobayashi Pages A Cell-Free Replication System for Positive-Strand RNA Viruses for Identification and Characterization of Plant Resistance Gene Products Kazuhiro Ishibashi, Masayuki Ishikawa Pages Plant Protein-Mediated Inhibition of Virus Cell-to-Cell Movement: Far-Western Screening and Biological Analysis of a Plant Protein Interacting with a Viral Movement Protein Nobumitsu Sasaki, Yasuhiko Matsushita, Hiroshi Nyunoya Pages Transfection of Protoplasts Prepared from Arabidopsis thaliana Leaves for Plant Virus Research Naoi Hosoe, Takuya Keima, Yuji Fujimoto, Yuka Hagiwara-Komoda, Masayoshi Hashimoto, Kensaku Maejima et al.

Pages Mahfouz Pages Computational Workflow for Small RNA Profiling in Virus-Infected Plants Livia Donaire, César Llave Pages A Sensitized Genetic Screen to Identify Novel Components and Regulators of the Host Antiviral RNA Interference Pathway Zhongxin Guo, Xian-Bing Wang, Wan-Xiang Li, Shou-Wei Ding Pages Design, Synthesis, and Functional Analysis of Highly Specific Artificial Small RNAs with Antiviral Activity in Plants Alberto Carbonell, José-Antonio Daròs Pages Resistance Breeding Through RNA Silencing of Host Factors Involved in Virus Replication Masamichi Nishiguchi, Emran Md.

Ali, Hui Chen, Masayuki Ishikawa, Kappei Kobayashi Pages Large-Scale Inoculation and Evaluation Methods for Attenuated Plant Viruses Kenji Kubota, Yasuhiro Tomitaka Pages RNA Silencing-Mediated Apple Latent Spherical Virus Vaccine in Plants Chunjiang Li, Noriko Yamagishi, Nobuyuki Yoshikawa Pages Back Matter Pages Back to top.

About this book This detailed book explores strategies that have been developed to combat plant virus infection. Beginning with a section on techniques for identifying and studying the virus resistance gene involved in plant innate immunity, the volume continues by delving into techniques related to novel mechanisms of plant virus resistance, methods for the analysis and practical use of RNA silencing, as well as methods for the development of plant viral vaccines.

Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and practical, Antiviral Resistance in Plants: Methods and Protocols serves as an ideal guide for researchers working to combat the serious threats plant virus diseases represent for agricultural production and beyond.

Keywords Plant virus infection Plant innate immunity Viral resistance mechanisms RNA silencing Vaccines Infection pathways Plant genetics. Editors and Affiliations Faculty of Agriculture, Ehime University, Matsuyama, Japan Kappei Kobayashi, Masamichi Nishiguchi Back to top.

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: Antiviral disease resistance

Influenza Antiviral Drug Resistance	Advanced Search. The diseasr idea behind Antiviral disease resistance antiviral drug design is to identify viral proteins, Fuel your energy levels parts of proteins, Injury prevention in sports can be diseae. Additional sporadic cases of oseltamivir-resistant H1N1 virus infection can be expected, and ongoing surveillance for oseltamivir resistance among influenza viruses is essential for public health since oseltamivir is the most widely used antiviral medication. Journal of Antimicrobial Chemotherapy. RNA virus antivirals primarily J05also S01AD and D06BB.
Antiviral Resistance in Plants	Typically, key stages of the life cycle that have been proven to be successful for other viruses include host cell entry, copying of the viral genome, maturation of the virus or viral budding from the host cell. Key target proteins for RNA viruses not exhaustive , and examples not exhaustive for SARS-CoV-2 are shown in the table below. Viruses have a short replication cycle and billions of virus offspring are generated during a single infection. This provides huge opportunities for the random generation of virus variants through replication errors for example, point mutations, insertions, deletions or duplications. In addition, recombination is a hallmark trait of this genus, meaning that sections of genome are readily exchanged, resulting in insertion or deletion of tracts of RNA. Resistance to antiviral drugs arises spontaneously through inherent variation in the genome sequence that occurs because of imprecise replication or recombination. When an antiviral drug is present, virions with chance genetic variation that confers a survival advantage against the drug are placed under a positive selective pressure. The resistance risk increases with increased numbers of infections and increased use of antiviral drugs. The presence of resistance mutations may not, however, necessarily have clinical or public health implications. When a resistant variant is selected there can sometimes be a fitness cost to the virus meaning that the resistant variant may be disabled or in the absence of drug may replicate at a slower rate than its non-resistant counterparts. Therefore, it is important to assess the clinical and public health relevance of resistant viruses through in vitro, in vivo and clinical studies. However, a lower replication rate may subsequently generate a selective pressure for accessory mutations in different sequences that restore fitness to the resistant variant. If resistant virions can replicate efficiently and can be transmitted from one individual to another and if antiviral drugs are widely used, the selective pressure amplifies the number of resistant variants within the population as a whole. Variable versus conserved targets. Some antiviral drug targets are inherently more variable than others, either because the targets are themselves under a selection pressure for example the Spike glycoprotein is under immune selection pressure or there is limited capacity for change in the target without rendering the virus non-viable. As such, different antivirals can have very different susceptibility to resistance development. Suboptimal dosage or pharmacokinetics results in drug concentrations that are unable to fully inhibit replication and or mean that concentrations fall below an adequate level between doses. At high drug concentrations, all viruses are prevented from replication and there is no opportunity for the random generation and then selection of resistant variants. At very low doses the selective pressure is also very low, so resistance is unlikely. However, there may be a middle ground where the virus is able to replicate and the drug concentration is sufficient to exert significant selective pressure. Currently available DAAs have low potency compared to those that are robustly efficacious in other RNA infections meaning that higher concentrations need to be sustained, which is much harder to achieve without impractically high doses and or toxicity. Treatment adherence. Suboptimal adherence to the medication such as failure to complete a course also increases the time during which the virus can replicate in suboptimal concentrations of drug and therefore the resistance risk. Monotherapy versus combination therapy. If drugs are deployed as monotherapies, as few as one mutation is required in order for a resistant variant to emerge. When drug combinations are deployed, multiple mutations in different regions of the viral genome are required to arise in unison to simultaneously confer resistance to all drugs in the regimen. If resistance emerges to one drug the other drug s inhibit its replication and vice versa. The probability of the spontaneous emergence of multiple key mutations within the same viral genome by chance is much lower than the probability of one key mutation arising. Combination therapy therefore provides a much higher barrier to the emergence of resistance than monotherapy. In addition, two drugs may act synergistically and therefore combination therapy can be more clinically effective, and at lower drug doses than required with monotherapy. For chronic viral infections, antiviral resistance is a major problem and combination therapy for RNA viruses that cause chronic and persistent infections including HIV and HCV is the evidence-based first line treatment globally to stem emergence of resistance. The evidence is less clear in short-lived acute viral infections. There is mixed evidence of the benefit from combination antiviral therapy for influenza in terms of clinical outcome or emergence of resistance. Although nucleoside analogues are not routinely used to treat influenza, in vitro studies show that resistance to favipiravir can be selected and the mutations confer little or no fitness cost. Small molecules targeting different parts of the replication pathway for example molnupiravir nucleoside analogue and Paxlovid protease inhibitor. Different modalities targeting different parts of the replication pathway for example small molecule drugs molnupiravir or paxlovid with monoclonal antibodies ronapreve, sotrovimab. Multiple drugs targeting the same part of the replication pathway in different ways for example molnupiravir pyrimidine nucleoside analogue and remdesivir purine nucleoside analogue. Prolonged infection in immunocompromised people. Immunosuppressed people are prone to prolonged infection because of their reduced ability to control virus replication. In the absence of an effective host antiviral response, it is harder to control viral replication with antiviral medicines alone and short course antivirals may be stopped before virus is fully eradicated. This can promote resistance in several ways. There may be prolonged exposure to antiviral drugs whilst there is ongoing replication, increasing the opportunities for the generation and selection of resistant variants. ii Prolonged replication may also provide an opportunity for the development of mutations that compensate for any loss of fitness in resistant viruses. iii Whilst the probability of simultaneous acquisition of two mutations conferring resistance to two different targets is very small, the probability of acquiring these sequentially is much higher particularly for drugs with very different pharmacokinetic half-lives such as monoclonals and small molecules. Therefore, prolonged viral replication also increases the chances of multi-drug resistance. Class-wide resistance. For other viruses, like HIV , class-wide resistance CWR has been a significant challenge. CWR arises when resistance to one drug confers resistance to other drugs in the same class for example resistance to one nucleoside conferring resistance to other nucleosides. The SARS-CoV-2 polymerase and protease will undoubtedly remain high value small molecule drug targets in future antiviral development and the avoidance of CWR therefore warrants careful consideration. Once resistance has emerged and become common within the population any subsequent attempts to combine that drug with another drug may be futile. At the time of writing, the emergence of new variants such as Omicron B. One DAA remdesivir is licensed, one DAA molnupiravir has a conditional approval from MHRA , and one DAA Paxlovid shows promise as therapies to inhibit SARS-CoV-2 replication. Remdesivir is a nucleoside analogue that stalls RNA assembly by the RNA -dependent RNA polymerase through chain termination. The molecular event which is liable to resistance is the same for molnupiravir as it is for remdesvir nucleoside incorporation by the polymerase. Molnupiravir is incorporated in place of pyrimidine nucleosides while remdesivir is incorporated in place of purine nucleosides. PF, Paxlovid, targets the viral 3C protease non-structural protein 5 which is necessary for the virus to mature into infectious virus able to infect new cells. In HIV , resistance to first generation nucleoside analogues [footnote 3] [footnote 4] [footnote 5] and protease inhibitors [footnote 6] [footnote 7] readily emerged when drugs like zidovudine, saquinavir or ritonavir were given as monotherapies. Subsequent development focused upon. b optimising activity of next generation protease inhibitors against known protease inhibitor-resistant strains of virus, and. c combining protease inhibitors with two nucleoside analogue drugs. Insufficient data are currently available to take an informed view on whether there is a higher resistance liability in SARS-CoV-2 for nucleoside analogues monupiravir or remdesivir or the boosted protease inhibitor paxlovid. Very little evidence has been published on the potential of SARS-CoV-2 resistance to antiviral agents. However, in-vitro research with remdesivir demonstrated selection of an escape mutant with a specific amino acid substitution in the inhibitor targeted protein. Furthermore, a very recent preprint [footnote 8] described the emergence of this same mutation within an immunocompromised patient receiving remdesivir, and there have been two reports [footnote 9] [footnote 10] of two remdesivir treatment courses being required to achieve a virological response, viral clearance and clinical resolution in two patients with compromised immune systems. The impact of the remdesivir escape mutation on the activity of molnupiravir also has not been described. Resistance to monotherapies with some monoclonal antibodies has been consistently demonstrated in vitro and in clinical trials. The primary reason that monoclonal antibody therapies have been developed as dual therapy is to reduce the resistance risk associated with monotherapy. Given the paucity of available research regarding antiviral resistance to SARS-CoV-2 , research from similar antivirals and viruses can help inform evidence. Resistance has been reported for other coronaviruses to viral 3C protease inhibitors and RNA dependent RNA polymerase inhibitors, however the resistance phenotype impaired viral fitness in vitro and attenuated virulence in in vivo models. Paxlovid has been shown in vitro to have additive or synergistic effects with remdesivir [footnote 12] so the combination with molnupiravir is also likely to show at least additive effect. A combination of favipiravir and molnupiravir was demonstrated to be more potent in Syrian golden hamsters than either drug alone. Although the propensity of current DAAs to develop SARS-CoV-2 resistance of clinical and public health significance is unknown, efforts to avoid, detect and mitigate resistance to these DAAs should be a high priority. Further work is needed to establish whether newly emerging variants, such as Omicron, differ in their propensity to evolve resistance because of other unrelated mutations in their genomes and or their increased replication rate if confirmed. Lampejo T. Influenza and antiviral resistance: an overview. Eur J Clin Microbiol Infect Dis. Goldhill DH, Te Velthuis AJW, Fletcher RA, Zambon M, Lackenby A, Barclay WS, et al. The mechanism of resistance to favipiravir in influenza. Proc Natl Acad Sci U S A. Larder BA, Kemp SD. Multiple mutations in HIV -1 reverse transcriptase confer high-level resistance to zidovudine AZT. Kellam P, Boucher CA, Larder BA. Fifth mutation in human immunodeficiency virus type 1 reverse transcriptase contributes to the development of high-level resistance to zidovudine, Proc Natl Acad Sci U S A. et al. Ordered appearance of zidovudine resistance mutations during treatment of 18 human immunodeficiency virus-positive subjects. J Infect Dis. Roberts NA. Drug-resistance patterns of saquinavir and other HIV proteinase inhibitors, AIDS, Dec;9 Suppl S Molla A, Korneyeva M, Gao Q, Vasavanonda S, Schipper PJ, et al. Ordered accumulation of mutations in HIV protease confers resistance to ritonavir. Nat Med. Gandhi S, Klein J, Robertson A, Peña-Hernández MA, Lin MJ, Roychoudhury P, et al. De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: A case report. Malsy J, Veletzky L, Heide J, Hennigs A, Gil-Ibanez I, Stein A, et al. Sustained response after remdesivir and convalescent plasma therapy in a B-cell depleted patient with protracted COVID Clin Infect Dis an Off Publ Infect Dis Soc Am. Helleberg M, Niemann CU, Moestrup KS, Kirk O, Lebech A-M, Lane C, et al. In the United States, there are four FDA-approved antiviral drugs recommended by CDC this season. Three are neuraminidase inhibitor antiviral drugs: oseltamivir available as a generic version or under the trade name Tamiflu® for oral administration, zanamivir trade name Relenza® for oral inhalation using an inhaler device, and peramivir trade name Rapivab® for intravenous administration. The fourth is a cap-dependent endonuclease inhibitor, baloxavir marboxil trade name Xofluza® for oral administration. Baloxavir marboxil was approved for use in the United States by FDA in October of There is another class of FDA-approved antiviral drugs, M2 inhibitors amantadine and rimantadine, also called the adamantanes, that in the past were active against flu A viruses but not flu B viruses. However, the adamantane antiviral drugs have not been recommended for use to treat flu in the United States for many years because of widespread antiviral resistance to this class of antivirals among circulating flu A viruses. In the United States, the majority of the recently circulating flu viruses have been fully susceptible to the neuraminidase inhibitors and to baloxavir. However, near all flu A viruses are resistant to the M2 inhibitors, which is why they are not recommended for treatment of seasonal influenza. Flu viruses are constantly changing; they can change in significant ways from one season to the next and can even change within the course of one flu season. As a flu virus replicates i. Flu viruses can become less susceptible to antiviral drugs during the course of antiviral treatment or emerge spontaneously. Antiviral resistant flu viruses vary in their ability to infect people and are not necessarily more or less transmissible than susceptible flu viruses. CDC routinely analyze flu viruses collected through domestic and global surveillance to see if they have genetic changes that are associated with reduced susceptibility to any flu antiviral drugs. Such changes can potentially cause viruses to be resistant to antiviral treatment with reduced or no effectiveness for treated patients. In addition, numerous state public health laboratories participate in screening of flu viruses for genetic changes indicative of potential resistance to neuraminidase inhibitor antivirals. This combined data informs public health policy recommendations about the use of flu antiviral medications. CDC is continuously improving testing algorithms and methods used for monitoring antiviral susceptibility in circulating viruses. Detection of reduced susceptibility and antiviral resistance involves several laboratory tests, including phenotypic assays testing in the presence of an antiviral drug and molecular techniques next generation sequence analysis and pyrosequencing to look for genetic changes that have been associated with reduced antiviral susceptibility. This included the creation and validation of new assays to determine baloxavir susceptibility, and training of laboratorians to conduct baloxavir susceptibility testing. Seasonal flu A and B viruses in humans as well as several flu A viruses that circulate in animals were tested to establish baseline susceptibility to baloxavir. In addition, the susceptibility of other distantly related flu viruses to baloxavir was tested. CDC also collaborated with the Association of Public Health Laboratories APHL and the Wadsworth Center NYSDOH, a National Influenza Reference Center NIRC , to establish laboratory-testing capacity for baloxavir susceptibility. Flu viruses are constantly changing for more information, see How the Flu Virus Can Change. Oseltamivir is the most commonly prescribed antiviral drug of those recommended in the United States to treat flu illness. By inhibiting NA activity, oseltamivir prevents flu viruses from spreading from infected cells to other healthy cells. CDC continually improves the ability to rapidly detect flu viruses with antiviral reduced susceptibility and antiviral resistance through improvements in laboratory methods; increasing the number of surveillance sites in the U. and worldwide; and increasing the number of laboratories that can test for reduced susceptibility and antiviral resistance. Enhanced surveillance efforts have provided CDC with the capability to detect antiviral resistant flu viruses more quickly, and enabled CDC to monitor for changing trends over time. Antiviral susceptibility patterns changed very little in compared with the previous season During the and seasons, only a very small of viruses were found to be resistant to oseltamivir. Almost all of the flu viruses tested during continued to be susceptible to the antiviral drugs recommended for treatment of flu by the Centers for Disease Control and Prevention CDC. Resistance to the adamantane class of antiviral drugs among flu A H3N2 and A H1N1 pdm09 viruses remained widespread flu B viruses are not susceptible to adamantane drugs. CDC conducts ongoing surveillance and testing of flu viruses for antiviral reduced susceptibility and resistance among seasonal and novel flu A viruses of animal origin that have infected people , and guidance is updated as needed. Because there were no dramatic changes in antiviral susceptibility patterns during the flu season, the guidance on the use of flu antiviral drugs for the flu season remains unchanged. The latest guidance for clinicians on the use of antiviral drugs for flu is available on the CDC web site at Antiviral Drugs: Information for Health Professionals. Getting a yearly seasonal flu vaccination is the best way to reduce the risk of flu and its potentially serious complications. Flu vaccines protect against influenza A viruses of two subtypes, A H1N1 pdm09 and A H3N2 , and type B viruses from two lineages. CDC recommends that everyone 6 months of age and older get vaccinated each year. If you are in a group at higher risk of serious flu-related complications and become ill with flu symptoms, call your doctor right away, because you might benefit from early treatment with a flu antiviral drug. If you are not at higher risk of flu complications, if possible, stay home from work, school and errands when you are sick. This will help prevent you from spreading your illness to others. See Important Information For People Sick With Flu for more information. Monitoring for antiviral drug susceptibility and resistance will be essential to determine the role of antivirals and specific antivirals during the next influenza pandemic. Available FDA-approved and authorized flu antiviral drugs can be used in the event that a novel flu A virus, such as avian flu A H7N9 virus, gains the ability to spread easily among people in a sustained manner, and is susceptible to these antiviral drugs.
Antiviral Drug Resistance among Influenza Viruses	Strain-specific hypersensitive and extreme rsistance phenotypes elicited by potato Antiviral disease resistance Y among 39 potato cultivars Artichoke antioxidant properties Antiviral disease resistance three world regions over Antuviral year period. Furuta Antivirzl. A redistance of resistance variants was derived from data provided by the US Food and Drug Administration and a review of the literature. thaliana plants. Sjaarda CPLau LSimpson JT, et al. Cell culture studies 7 identified the variants L50F and EA as conferring resistance to nirmatrelvir-ritonavir, as well as T21I and TI.
	Rewistance, B. Copy citation to clipboard. Effectiveness resistande Fuel your energy levels Nutrients for injury recovery in reducing Diseasee in patients admitted Antiviral disease resistance a hospital with influenza A Xisease pdm09 virus infection: a meta-analysis of individual participant data. Surveillance efforts that involve sequencing of viral isolates should continue to monitor for novel resistance variants as nirmatrelvir-ritonavir is used more broadly. Note: WHO periodically updates its antiviral resistance information in association with its latest influenza virological update.

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Virology Lectures 2020 #20: Antivirals

Antiviral disease resistance -

Currently, nirmatrelvir-ritonavir is 1 of 2 oral antiviral medications for the treatment of SARS-CoV-2 and has reduced hospitalizations and deaths 1 ; yet, despite the substantial impact of antiviral medications on clinical outcomes, the development of antiviral resistance is an ongoing concern.

Because SARS-CoV-2 is an RNA virus, the viral polymerase introduces errors in the genome during replication, and the virus exists as a quasi species in the patient.

Therefore, it is unclear whether low-frequency variants may exist that could be selected for by drug pressure, as has been observed with other RNA viruses, such as influenza virus, 2 hepatitis C virus, 3 and HIV. Nirmatrelvir-ritonavir inhibits the main viral protease encoded by the nsp5 gene, 5 and ritonavir acts as a boosting agent by inhibiting host cytochrome P Studies 6 have shown that viral rebound has occurred in a subset of treated patients, but it remains unclear whether this could lead to the selection of viruses with reduced antiviral susceptibility.

Findings from in vitro studies 7 have identified variants with the potential to confer resistance to nirmatrelvir-ritonavir without affecting viral fitness. There has yet to be a comprehensive clinical evaluation of low-frequency variants that could be selected for during nirmatrelvir-ritonavir treatment.

Next-generation sequencing allows for the detection of variants that are present at low frequency. This study examined the prevalence of low-frequency variants within SARS-CoV-2 sequences from clinical samples collected before and after the availability of nirmatrelvir-ritonavir in Ontario, Canada.

This cohort study followed the Strengthening the Reporting of Observational Studies in Epidemiology STROBE reporting guideline, and did not require ethics board approval or informed consent because the study used deidentified viral sequences collected as part of routine surveillance work, in accordance with 45 CFR § This study was a descriptive retrospective analysis of SARS-CoV-2 samples that were submitted for routine diagnostic testing and sequencing.

Samples were collected between March 1, , and January 12, , and analyzed at 4 laboratories with tertiary academic hospital centers in Ontario, Canada.

All sequencing occurred less than 7 days from the time of collection. These laboratories serve multiple community hospitals, other academic tertiary care centers, as well as COVID assessment centers, and have a total catchment of 5 million Ontarians. Samples that were positive for SARS-CoV-2 using reverse-transcription polymerase chain reaction testing with a cycle threshold less than 30 cycles underwent whole-genome sequencing, as has been previously described.

For the Nanopore Midnight primers using rapid barcodes, the Medaka version of the ARTIC pipeline was used and validated alongside the ARTIC protocol. A read length filter of bp to bp and the Midnight primer schema were used for the rapid barcoding protocol.

A list of resistance variants was derived from data provided by the US Food and Drug Administration and a review of the literature. The nanopore analysis pipelines do not call intrahost variation; thus, we queried the read pileups for support of a minor variant at the positions of interest.

The primary outcome was alternate alleles at positions with at least 50 times sequencing depth and an allele frequency between 0.

Data analysis was conducted using R statistical software version 4. The figure was also done using R version 4. Analysis indicated low-frequency variants at positions linked to drug resistance in the nsp5 gene in 0.

Interestingly, a higher than expected count was observed in site B 2 of isolates [0. Variation was found at only 33 of the residues identified by the US Food and Drug Administration as being associated with antiviral resistance eTable in Supplement 1.

Additionally, we did not observe more variation at residues that are known to interact with nirmatrelvir-ritonavir compared with other residues Figure.

Only 1 sample showed variation at residue H41, which is part of the catalytic dyad and is associated with drug binding. A total of 2 samples showed variants at M49 and N, respectively, which have been associated with a decrease in activity of nirmatrelvir-ritonavir without a significant loss of protease activity.

Currently, nirmatrelvir-ritonavir is 1 of 2 oral antiviral treatments for SARS-CoV This cohort study found that naturally occurring low-frequency variants in nsp5 are rare.

Moreover, among the variants detected, no single variant predominated. The paucity of these variants suggests it may be difficult for resistant variants to be selected, and this may be a contributing factor to why resistance to nirmatrelvir-ritonavir has not yet been observed.

A high degree of conservation of the viral protease is likely necessary because of its critical role in the viral life cycle. Cell culture studies 7 identified the variants L50F and EA as conferring resistance to nirmatrelvir-ritonavir, as well as T21I and TI.

Moreover, the presence of these variants in combination increased half maximal effective concentration values, without a complete loss of viral fitness 7 ; however, there appears to be a need for compensatory variants. This suggests that there is a potential fitness cost to these variants that would not be observed in cell culture.

The viral protease plays a role in moderating the host immune response, and these variants may affect that activity. This hypothesis is supported by our findings that low-frequency variants were found more often in regions outside the binding pocket and at sites that would be less likely to have a major effect on protease activity.

Additionally, the use of nirmatrelvir-ritonavir has been relatively limited in Ontario because of an initially limited supply of the drug, government restrictions, and prescribing guidelines, 21 which could have limited the selective pressure placed on the virus and may partially account for the paucity of antiviral resistance variants observed.

A limitation of this study is that variants detected at low frequencies could be due to artifacts of the sequencing process.

Nonetheless, we included these data to highlight that even with this caveat, variations at these key positions are rare.

Additionally, there were no clinical histories of the patients from which the samples were derived, and it cannot be discounted that some patients may have received antiviral treatment before testing. Also, patient samples with low viral loads were unable to be sequenced owing to assay limitations and, therefore, could not be included in our analysis.

Future studies are needed that include relevant patient medical histories, as well as improved methods for sequencing of isolates from cases with low viral loads. In conclusion, our data suggest that low-frequency variants of SARS-CoV-2 at the population level are rare.

Published: July 21, Open Access: This is an open access article distributed under the terms of the CC-BY License. JAMA Network Open. Corresponding Author: Robert Kozak PhD, Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Center, Bayview Ave, Toronto, ON M4N 3M5, Canada rkozak shn.

Author Contributions: Drs Sheth and Kozak had full access to all of the data in the study and take responsibility for the integrity of the data and the accuracy of the data analysis.

Drs Sheth and Kozak contributed equally to this work. Critical review of the manuscript for important intellectual content: Sjaarda, Simpson, Fattouh, Biondi, Maguire, Campigotto, Feng, Tozer, Wong, Sung, Kim, Marshall, Sheth. Administrative, technical, or material support: Lau, Fattouh, Biondi, Maguire, Tozer, Wong, Kim, Sheth.

Conflict of Interest Disclosures: Dr Simpson reported receiving personal fees from Day Zero Diagnostics and grants from Oxford Nanopore Technologies outside the submitted work. No other disclosures were reported. Data Sharing Statement: See Supplement 2.

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R scripts for MOI estimation and simulation for plant suicidal population resistance by systemic hypersensitive response. Download references. We thank Drs Chikara Masuta, Masashi Suzuki, and Minoru Takeshita for providing the pCY1, pCY2, pCY3, and pC2-A1 constructs.

The super-computing resource was provided by Human Genome Center, the Institute of Medical Science, the University of Tokyo. Graduate School of Agricultural Science, Tohoku University, Sendai, Japan.

Derib A. Department of Biology, Utrecht University, Utrecht, the Netherlands. You can also search for this author in PubMed Google Scholar.

designed the study. carried out the experiments. analyzed the data. developed the simulation model and interpreted the results. wrote the paper.

Correspondence to Shuhei Miyashita. Peer review information Communications Biology thanks Simon Groen, Kristina Gruden, and the other anonymous reviewers for their contribution to the peer review of this work.

Primary handling editors: Diane Saunders and Christina Karlsson Rosenthal. Peer reviewer reports are available.

Open Access This article is licensed under a Creative Commons Attribution 4. Reprints and permissions. Abebe, D. Plant death caused by inefficient induction of antiviral R -gene-mediated resistance may function as a suicidal population resistance mechanism.

Commun Biol 4 , Download citation. Received : 22 October Accepted : 23 July Published : 09 August Anyone you share the following link with will be able to read this content:.

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Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily. Skip to main content Thank you for visiting nature. nature communications biology articles article. Download PDF. Subjects Plant ecology Plant immunity Theoretical ecology. Abstract Land plant genomes carry tens to hundreds of Resistance R genes to combat pathogens.

Introduction Land plant genomes carry a class of genes collectively called Resistance R genes, which consist of tens to hundreds of genes per genome. Results Characterization of SHR induction in CMV Y — N.

thaliana pathosystems RCY1 , an R gene of Arabidopsis thaliana ecotype C24, induces HR upon infection by CMV Y strain [CMV Y ] 3 , Full size image.

Table 1 Summary of observed phenotypes a after inoculations with different combinations of viral RNA3 genotypes and plant genotypes. Full size table. Table 2 Multiplicity of infection MOI estimates in wild-type WT and RCY1 -transformant Nicotiana benthamiana plants inoculated with WT and variant RNA3s.

Discussion MOI decrease as an individual-level resistance mechanism Previous studies have suggested PCD-independent containment of viruses in R- gene-mediated resistance 5 , 6 , 7 , 40 , 41 , 42 , Methods Plants The chimeric RPRPCY transgene for N. Viral cDNA constructs, in vitro RNA transcription, and inoculation cDNA constructs for WT CMV Y segments, pCY1, pCY2, and pCY3, were described previously Detection of CMV infection Systemic infection of N.

DAB staining Inoculated N. Genomic DNA fragmentation Genomic DNA was extracted from inoculated leaves and uninoculated upper leaves of N.

MOI estimation For MOI estimation, WT or R gene-transformant N. Simulation The model used for the simulation is explained in the Results section. Statistics and reproducibility For MOI estimation, we know a relation that analyzing four times more cells will give half standard deviation for MOI.

Reporting summary Further information on research design is available in the Nature Research Reporting Summary linked to this article. Data availability The authors declare that all the data supporting the findings in the current study are available within the article and its Supplementary information files.

Material availability Commercially unavailable materials can be obtained from the corresponding author upon reasonable request, through a material transfer agreement with Tohoku University. References Collier, S.

Prolonged shedding of oseltamivir- or zanamivir-resistant virus by severely immunocompromised patients, even after cessation of oseltamivir treatment, has been reported [, —]. Rare cases of infection with H1N1 virus either resistant to or with reduced susceptibility to multiple neuraminidase inhibitors in severely immunosuppressed pediatric patients with prolonged viral replication have been reported [, ].

During —, increased resistance to oseltamivir associated with a specific mutation causing a histidine to tyrosine substitution HY in neuraminidase was reported among seasonal influenza A H1N1 virus strains in many countries and became prevalent worldwide [—].

Most persons infected with oseltamivir-resistant seasonal influenza A H1N1 virus strains had not received oseltamivir treatment previously and were not known to have been exposed to a person receiving oseltamivir treatment or chemoprophylaxis [, ]. Influenza caused by oseltamivir-resistant seasonal influenza A H1N1 virus strains appears to be similar to illness caused by oseltamivir-sensitive virus strains [, , ].

The — influenza season was the first since the H1N1 pandemic in which H1N1 viruses predominated CDC During , all sporadic cases of oseltamivir-resistant H1N1 virus infections identified to date also have been associated with the HY mutation in neuraminidase; these oseltamivir-resistant HY virus infections have been susceptible to zanamivir.

A subset of the influenza viruses collected by U. WHO collaborating laboratories are sent to CDC for further characterization, including gene sequencing, antiviral resistance testing and antigenic characterization.

This information is presented in the antiviral resistance and antigenic characterization sections of the FluView report. As of September , no evidence existed of ongoing transmission of oseltamivir-resistant H1N1 virus strains worldwide.

Top of Page. Adamantane resistance among circulating influenza A viruses increased rapidly worldwide beginning during — The percentage of influenza A virus isolates submitted from throughout the world to the World Health Organization Collaborating Center for Surveillance, Epidemiology, and Control of Influenza at CDC that were adamantane-resistant increased from 0.

Resistance to adamantanes remains high among influenza A viruses currently circulating. Therefore, amantadine and rimantadine are not recommended for antiviral treatment or chemoprophylaxis of currently circulating influenza A virus strains.

Treatment of patients with severe influenza e. The effect of specific antiviral strategies in serious or life-threatening influenza is not established from clinical trials conducted to support licensure of oseltamivir and zanamivir, as those studies were conducted primarily among previously healthy outpatients with uncomplicated illness.

However, a number of more recent observational studies have reported that oseltamivir treatment up to 96 hours after illness onset of patients hospitalized with suspected or confirmed influenza is associated with lower risk for severe outcomes [12, 23, 27, 65, ] Muthuri, For this reason, recommendations in this report do not necessarily represent FDA-approved uses of antiviral products but are based on published observational studies and expert opinion and are subject to change as the developmental status of investigational products and the epidemiologic and virologic features of influenza change over time.

Initiation of antiviral treatment as early as possible is recommended for hospitalized patients. However, antiviral treatment might be effective in reducing morbidity and mortality in hospitalized patients even if treatment is not started until more than 48 hours after onset of illness.

Data from observational studies indicates the benefit of antiviral treatment for hospitalized persons even when treatment is delayed [12, 23, 26—28, ].

Careful attention to ventilator and fluid management and to the prevention and treatment of secondary bacterial pneumonia e. pneumoniae , S. pyogenes , and S. aureus , including MRSA also is critical for severely ill patients [66, —].

Treatment regimens might need to be altered to fit the clinical circumstances. Please see Influenza Antiviral Medications: Summary for Clinicians for further details regarding treatment recommendations for hospitalized and critically ill patients.

Patients receiving antiviral medications who do not respond to treatment might have an infection with an antiviral-resistant influenza virus. Oseltamivir resistance, sometimes occurring within 1 week of treatment initiation, has been reported particularly among immunocompromised patients with H1N1 virus infection who were receiving treatment with oseltamivir [, —].

Infection-control measures are especially important for patients who are immunocompromised to reduce the risk for transmission of oseltamivir-resistant viruses [, ].

Please see Intravenous Influenza Antiviral Medications and Use of Antivirals for further information regarding investigational parenterally administered products for treatment of influenza.

Intravenous zanamivir is the recommended antiviral treatment for severely ill patients with highly suspected or confirmed oseltamivir-resistant H1N1 virus infection [51, , ]. For patients who are intubated, use of the zanamivir disc inhaler is not possible. Suboptimal delivery to sites of infection in patients with pneumonic or extrapulmonary disease is also of concern for patients with severe respiratory illness [].

Limited experimental use of an unlicensed nebulized formulation of zanamivir has been well tolerated [], but use of the nebulized preparation of the licensed powder formulation contained in the disc inhaler is not recommended because it has been demonstrated to clog ventilator tubing [].

Concerns about influenza viruses with pandemic potential, the appearance and widespread transmission of pandemic influenza A H1N1 , and the limited treatment options available for severely ill patients has prompted renewed interest in development of additional antiviral drugs with activity against influenza viruses [, ].

Clinicians should be alert to the future availability of new therapeutic options and recommendations. In addition, careful attention to infection-control measures is recommended [, ], particularly in hospital areas that house immunocompromised patients.

For current information on antiviral resistance among circulating influenza viruses in the United States, please see the FluView Weekly U.

UK, remember your settings diseease improve government services. We also Fuel your energy levels cookies set Antiviral disease resistance other sites to help us deliver content from their services. You have accepted additional cookies. You can change your cookie settings at any time. You have rejected additional cookies. Disesae W. Kimberlin, Body fat percentage and nutrition J. The increased awareness of antiviral resistance Ativiral the past Antiviral disease resistance has paralleled the dixease of new antiviral Resostance. While Antivural resistant viral isolates are of Energy-boosting vitamins significance primarily in immunocompromised individuals, the development and transmission of such mutants have been reported in immunocompetent persons as well. As antiviral agents are increasingly utilised by the clinician, the incidence of such occurrences is likely to increase. Issues relating to mechanisms of antiviral resistance, clinical manifestations and significance of resistance, and implications for future antiviral development and utilisation are reviewed in this article. Viruses that are discussed include herpes simplex virus, varicella-zoster virus, cytomegalovinis, influenza A virus, and human immunodeficiency virus.