The mutation rates and mutational bias of influenza A virus

Pauly,; Procario, Megan C.; Lauring, Adam S.

doi:10.1101/110197

Cited by 11 publications

(13 citation statements)

References 67 publications

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“…The use of the minigenome assay allowed us to see all mutations generated by polymerase and not just those that would allow viable viruses. Pauly et al have recently shown that the mutation rate for influenza has been significantly underestimated by only counting mutations which occur in plaque forming viruses 47 . Sequencing only viruses which have exited the cell ignores mutations that cause defects in packaging or cellular exit.…”

Section: Discussionmentioning

confidence: 99%

“…Although Primer ID can remove sequencing error, it is still impossible to distinguish between errors due to the flu polymerase and the reverse transcriptase used during the Primer ID reaction. A recent paper has suggested that care must be taken as these two error rates are the same order of magnitude 47 . For this reason, we have not reported an absolute error rate but a relative error rate compared to the drug-free baseline sample.…”

Section: Discussionmentioning

confidence: 99%

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Determining the Mutation Bias of Favipiravir in Influenza Using Next-generation Sequencing

Goldhill

Langat

Xie

et al. 2018

Preprint

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11Favipiravir is a broad spectrum antiviral drug that may be used to treat influenza. Previous 12 research has identified that favipiravir likely acts as a mutagen but the precise mutation bias 13 that favipiravir induces in influenza virus RNAs has not been described. Here, we use next-14 generation sequencing (NGS) with barcoding of individual RNA molecules to accurately and 15 quantitatively detect favipiravir-induced mutations and to sample orders of magnitude 16 more mutations than would be possible through Sanger sequencing. We demonstrate that 17 favipiravir causes mutations and show that favipiravir primarily acts as a guanine analogue 18 and secondarily as an adenine analogue resulting in the accumulation of transition 19 mutations. We also use a standard NGS pipeline to show that the mutagenic effect of 20 favipiravir can be measured by whole genome sequencing of virus. 21 Importance 22New antiviral drugs are needed as a first line of defence in the event of a novel influenza 23 pandemic. Favipiravir is a broad-spectrum antiviral which is effective against influenza. The 24 exact mechanism of how favipiravir works to inhibit influenza is still unclear. We used next-25 generation sequencing (NGS) to demonstrate that favipiravir causes mutations in influenza 26 RNA. The greater depth of NGS sequence information over traditional sequencing methods 27 allowed us to precisely determine the bias of particular mutations caused by favipiravir. NGS 28 can also be used in a standard diagnostic pipeline to show that favipiravir is acting on the 29 virus by revealing the mutation bias pattern typical to the drug. Our work will aid in testing 30 whether viruses are resistant to favipiravir and may help demonstrate the effect of 31 favipiravir on viruses in a clinical setting. This will be important if favipiravir is used during a 32 future influenza pandemic. 33

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Determining the Mutation Bias of Favipiravir in Influenza Using Next-generation Sequencing

Goldhill

Langat

Xie

et al. 2018

Preprint

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“…Further experiments should explore the mutational landscape of PpyrOMLV1 & 2, which appears to be significantly lower than of Influenzaviruses, specifically Influenza A virus, which are characterized by high mutational rate (ca. 1 mutation per genome replication) associated to the absence of RNA proofreading enzymes (271). In addition we evaluated the presence of PpyrOMLV1 & 2 on diverse tissues and organs of P. pyralis.…”

Section: Photinus Pyralis Orthomyxo-like Virusesmentioning

confidence: 99%

Firefly genomes illuminate parallel origins of bioluminescence in beetles

Fallon

Lower

Chang

et al. 2017

Preprint

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SummaryFireflies are among the best-studied of the bioluminescent organisms. Despite longterm interest in the biochemistry, neurobiology, and evolution of firefly flash signals and the widespread biotechnological applications of firefly luciferase, only a limited set of genes related to this complex trait have been described. To investigate the genetic basis of firefly bioluminescence, we generated a high-quality reference genome for the Big Dipper firefly Photinus pyralis, from which the first laboratory luciferase was cloned, using long-read (PacBio), short-read (Illumina), and Hi-C sequencing technologies. To facilitate comparative genomics, we also generated short-read genome assemblies for a Japanese firefly Aquatica lateralis and a bioluminescent click beetle, Ignelater luminosus. Analyses of these genomic datasets supports at least two independent gains of luminescence in beetles, and provides new insights into the evolution of beetle bioluminescence and chemical defenses that likely co-evolved over their 100 million years of evolution.

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“…The most commonly identified mechanism of mutagen resistance in RNA viruses is altered baseline polymerase fidelity. We determined the baseline mutation rate of our three 5FU resistant variants using a Luria-Delbrück fluctuation test that can measure the rates of all 12 mutational classes ((11) and Figure 3). We also evaluated PB1 V43I, which has been reported to be a fidelity variant (20, 43).…”

Section: Resultsmentioning

confidence: 99%

“…As in many RNA viruses, influenza virus’ low fidelity is due to the absence of proofreading and repair mechanisms during genome replication (8-10). We have previously estimated influenza’s mutation rate to be greater than 1 × 10 −4 mutations per nucleotide per RNA strand replicated, which suggests that approximately 2 new mutations are introduced into every newly synthesized genome (11). As a result, influenza viruses exist as swarms of distinct genetic variants, which provide a rich substrate for natural selection of adaptive mutations.…”

Section: Introductionmentioning

confidence: 99%

Epistatic interactions within the influenza virus polymerase complex mediate mutagen resistance and replication fidelity

Pauly

Lyons

Lauring

2017

Preprint

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Lethal mutagenesis is a broad-spectrum antiviral strategy that employs mutagenic nucleoside analogs to exploit the high mutation rate and low mutational tolerance of many RNA viruses. Studies of mutagen-resistant viruses have identified determinants of replicative fidelity and the importance of mutation rate to viral population dynamics. We have previously demonstrated the effective lethal mutagenesis of influenza A virus using three nucleoside analogs as well as the virus's high genetic barrier to mutagen resistance. Here, we investigate the mutagen-resistant phenotypes of mutations that were enriched in drug-treated populations. We find that PB1 T123A has higher replicative fitness than the wild type, PR8, and maintains its level of genome production during 5-fluorouracil (2,4-dihydroxy-5-fluoropyrimidine) treatment. Surprisingly, this mutagen-resistant variant also has an increased baseline rate of C-to-U and G-to-A mutations. A second drug-selected mutation, PA T97I, interacts epistatically with PB1 T123A to mediate high-level mutagen resistance, predominantly by limiting the inhibitory effect of nucleosides on polymerase activity. Consistent with the importance of epistatic interactions in the influenza virus polymerase, our data suggest that nucleoside analog resistance and replication fidelity are strain dependent. Two previously identified ribavirin {1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1H-1,2,4-triazole-3-carboxamide} resistance mutations, PB1 V43I and PB1 D27N, do not confer drug resistance in the PR8 background, and the PR8-PB1 V43I polymerase exhibits a normal baseline mutation rate. Our results highlight the genetic complexity of the influenza A virus polymerase and demonstrate that increased replicative capacity is a mechanism by which an RNA virus can counter the negative effects of elevated mutation rates.IMPORTANCE RNA viruses exist as genetically diverse populations. This standing genetic diversity gives them the potential to adapt rapidly, evolve resistance to antiviral therapeutics, and evade immune responses. Viral mutants with altered mutation rates or mutational tolerance have provided insights into how genetic diversity arises and how it affects the behavior of RNA viruses. To this end, we identified variants within the polymerase complex of influenza virus that are able to tolerate drugmediated increases in viral mutation rates. We find that drug resistance is highly dependent on interactions among mutations in the polymerase complex. In contrast to other viruses, influenza virus counters the effect of higher mutation rates primarily by maintaining high levels of genome replication. These findings suggest the importance of maintaining large population sizes for viruses with high mutation rates and show that multiple proteins can affect both mutation rate and genome synthesis. KEYWORDS evolution, influenza, mutagenesis, polymerase, virus

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The mutation rates and mutational bias of influenza A virus

Cited by 11 publications

References 67 publications

Determining the Mutation Bias of Favipiravir in Influenza Using Next-generation Sequencing

Determining the Mutation Bias of Favipiravir in Influenza Using Next-generation Sequencing

Firefly genomes illuminate parallel origins of bioluminescence in beetles

Epistatic interactions within the influenza virus polymerase complex mediate mutagen resistance and replication fidelity

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