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Probabilistic Inference of Viral Quasispecies Subject to Recombination [chapter]

Osvaldo Zagordi, Armin Töpfer, Sandhya Prabhakaran, Volker Roth, Eran Halperin, Niko Beerenwinkel
<span title="">2012</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
We present a jumping hidden Markov model that describes the generation of the viral quasispecies and a method to infer its parameters by analysing next generation sequencing data.  ...  We present an implementation of the EM algorithm to find maximum likelihood estimates of the model parameters and a method to estimate the distribution of viral strains in the quasispecies.  ...  Discussion We have presented a probabilistic model based on a HMM that infers the distribution of haplotypes in a viral quasispecies from NGS data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-29627-7_36">doi:10.1007/978-3-642-29627-7_36</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/e7idaemuy5elzgbxrambbshc5m">fatcat:e7idaemuy5elzgbxrambbshc5m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170829045156/https://grid.cs.gsu.edu/~acaciula1/sites/default/files/Probabilistic_Inference_of_Viral_Quasispecies.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/51/11/5111a8babd87724be785122425c9b5d549af6d65.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-29627-7_36"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Probabilistic Inference of Viral Quasispecies Subject to Recombination

Armin Töpfer, Osvaldo Zagordi, Sandhya Prabhakaran, Volker Roth, Eran Halperin, Niko Beerenwinkel
<span title="">2013</span> <i title="Mary Ann Liebert Inc"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/id6xbd2o6fhy7pts2djgwhtmvy" style="color: black;">Journal of Computational Biology</a> </i> &nbsp;
We present a jumping hidden Markov model that describes the generation of the viral quasispecies and a method to infer its parameters by analysing next generation sequencing data.  ...  We present an implementation of the EM algorithm to find maximum likelihood estimates of the model parameters and a method to estimate the distribution of viral strains in the quasispecies.  ...  Discussion We have presented a probabilistic model based on a HMM that infers the distribution of haplotypes in a viral quasispecies from NGS data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1089/cmb.2012.0232">doi:10.1089/cmb.2012.0232</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23383997">pmid:23383997</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3576916/">pmcid:PMC3576916</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tgyxu2t5nba2nhnc33vhuiueua">fatcat:tgyxu2t5nba2nhnc33vhuiueua</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170829045156/https://grid.cs.gsu.edu/~acaciula1/sites/default/files/Probabilistic_Inference_of_Viral_Quasispecies.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/51/11/5111a8babd87724be785122425c9b5d549af6d65.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1089/cmb.2012.0232"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3576916" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Empirical validation of viral quasispecies assembly algorithms: state-of-the-art and challenges

Mattia C. F. Prosperi, Li Yin, David J. Nolan, Amanda D. Lowe, Maureen M. Goodenow, Marco Salemi
<span title="2013-10-03">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tnqhc2x2aneavcd3gx5h7mswhm" style="color: black;">Scientific Reports</a> </i> &nbsp;
The performance of different assemblers was compared in terms of phylogenetic clustering and recombination with the Sanger clones.  ...  Two intra-host viral population 'quasispecies' samples (type-1 human immunodeficiency and hepatitis C virus) were Sanger-sequenced, and plasmid clone mixtures at controlled proportions were shotgun-sequenced  ...  Quasispecies are composed of different proportions of distinct variants, some at very low frequency, that are often subject to recombination.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/srep02837">doi:10.1038/srep02837</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24089188">pmid:24089188</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3789152/">pmcid:PMC3789152</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/eclswserbzantfg36iybq62l6y">fatcat:eclswserbzantfg36iybq62l6y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200511081759/https://www.nature.com/articles/srep02837.pdf?error=cookies_not_supported&amp;code=4771f5d6-e8a7-4e98-999c-163493ea14d3" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/3f/30/3f30484148817384f8018314cd03ea426b6fb5f8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/srep02837"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3789152" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

HIV-1 Quasispecies Delineation by Tag Linkage Deep Sequencing

Nicholas C. Wu, Justin De La Cruz, Laith Q. Al-Mawsawi, C. Anders Olson, Hangfei Qi, Harding H. Luan, Nguyen Nguyen, Yushen Du, Shuai Le, Ting-Ting Wu, Xinmin Li, Martha J. Lewis (+3 others)
<span title="2014-05-19">2014</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
This approach is demonstrated to deduce ,2000 unique 1.3 kb viral sequences from HIV-1 quasispecies in vivo and after passaging ex vivo with a detection limit of ,0.005% to ,0.001%.  ...  It enables haplotype phasing with high accuracy and sensitivity to interrogate individual viral sequences in a quasispecies.  ...  Acknowledgments We would like to thank J. Zhou and J. Yoshizawa for performing the highthroughput sequencing experiment.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0097505">doi:10.1371/journal.pone.0097505</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24842159">pmid:24842159</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4026136/">pmcid:PMC4026136</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/y2vcecjf6jfjbluhlbs2xgv3xy">fatcat:y2vcecjf6jfjbluhlbs2xgv3xy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171010005010/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0097505&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/19/fc/19fc04d8346626eb299a6c2085ea3a3155495d7e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0097505"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4026136" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data

Niko Beerenwinkel, Huldrych F. Günthard, Volker Roth, Karin J. Metzner
<span title="2012-09-11">2012</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/67anf6qgandy5adz4rakospiuq" style="color: black;">Frontiers in Microbiology</a> </i> &nbsp;
Here, we review the entire process of inferring viral diversity from sample collection to computing measures of genetic diversity.  ...  , and recombination.  ...  Because of their diversity, intra-host virus populations are often referred to as mutant clouds, swarms, or viral quasispecies.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fmicb.2012.00329">doi:10.3389/fmicb.2012.00329</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22973268">pmid:22973268</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3438994/">pmcid:PMC3438994</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/t3v3gvrkxfc6xdwe35nvmqayqm">fatcat:t3v3gvrkxfc6xdwe35nvmqayqm</a> </span>
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Ultradeep Pyrosequencing of Hepatitis C Virus Hypervariable Region 1 in Quasispecies Analysis

Kamila Caraballo Cortés, Osvaldo Zagordi, Tomasz Laskus, Rafał Płoski, Iwona Bukowska-Ośko, Agnieszka Pawełczyk, Hanna Berak, Marek Radkowski
<span title="">2013</span> <i title="Hindawi Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/icbhosh775h7bgzgot6avm3cua" style="color: black;">BioMed Research International</a> </i> &nbsp;
Genetic variability of hepatitis C virus (HCV) determines pathogenesis of infection, including viral persistence and resistance to treatment.  ...  The aim of the present study was to characterize HCV genetic heterogeneity within a hypervariable region 1 (HVR1) of a chronically infected patient by ultradeep 454 sequencing strategy.  ...  In this analysis, inference of the viral quasispecies is done in probabilistic manner using a Bayesian approach.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2013/626083">doi:10.1155/2013/626083</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23710455">pmid:23710455</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3655449/">pmcid:PMC3655449</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nnvpx6nanvesdoopextkyutrwi">fatcat:nnvpx6nanvesdoopextkyutrwi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190305125634/http://pdfs.semanticscholar.org/c9da/49cf48eb583d33c7dc9388e2934e2043da27.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c9/da/c9da49cf48eb583d33c7dc9388e2934e2043da27.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2013/626083"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> hindawi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3655449" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Models of RNA virus evolution and their roles in vaccine design

Samuel Ojosnegros, Niko Beerenwinkel
<span title="">2010</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/gjnpaecpvjcvfmxmaqxzr4tqum" style="color: black;">Immunome Research</a> </i> &nbsp;
Integration of multiple computational and mathematical approaches with experimental data can help to predict the behavior of viral pathogens and to anticipate their escape dynamics.  ...  Here we review several aspects of viral evolution that can be addressed quantitatively, and we discuss computational methods that have the potential to improve vaccine design.  ...  Acknowledgements This article has been published as part of Immunome Research Volume 6 Supplement 2, 2010: Computational Vaccinology: State-of-the-art Assessments.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1745-7580-6-s2-s5">doi:10.1186/1745-7580-6-s2-s5</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21067547">pmid:21067547</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2981881/">pmcid:PMC2981881</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7wsvjkleg5hdliif56akhdyyji">fatcat:7wsvjkleg5hdliif56akhdyyji</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170814042149/http://authors.library.caltech.edu/42310/1/1745-7580-6-S2-S5.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/47/b4/47b492b0ec0eb812f9c6599184a6a00542013251.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1745-7580-6-s2-s5"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981881" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Read length versus Depth of Coverage for Viral Quasispecies Reconstruction

Osvaldo Zagordi, Martin Däumer, Christian Beisel, Niko Beerenwinkel, Art F. Y. Poon
<span title="2012-10-03">2012</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
Virus samples can now be sequenced efficiently with very deep coverage to infer the genetic diversity of the underlying virus populations.  ...  Here, we investigate how the differences between two common platforms provided by 454/Roche and Illumina affect viral diversity estimation and the reconstruction of viral haplotypes.  ...  Computational methods for viral quasispecies assembly include combinatorial optimization techniques [17, 20, 21, 22, 23] and generative probabilistic models [24, 25, 26] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0047046">doi:10.1371/journal.pone.0047046</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23056573">pmid:23056573</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3463535/">pmcid:PMC3463535</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lhy3e3pyxzaw7gszdjqdign53m">fatcat:lhy3e3pyxzaw7gszdjqdign53m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171005021232/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0047046&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b2/30/b230fe039037d3f7c61feafd7ed3534b29801fdd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0047046"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3463535" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Classification of small ruminant lentivirus subtype A2, subgroups 1 and 2 based on whole genome comparisons and complex recombination patterns

Aaron M. Dickey, Timothy P. L. Smith, Michael L. Clawson, Michael P. Heaton, Aspen M. Workman
<span title="2020-12-11">2020</span> <i title="F1000 Research Ltd"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lz7xw3k77zcg5f66jhfurufu64" style="color: black;">F1000Research</a> </i> &nbsp;
Conclusions: The viral subgroup framework developed to classify SRLV consensus genomes along a continuum of recombination suggests that animals with the TMEM154 E35/K35 genotype may represent a reservoir  ...  Methods: The goals of this study were to analyze sequence variation within and among SRLV subtype A2 subgroups 1 and 2 and to identify genome-scale recombination patterns.  ...  Homogenates were then subjected to two freeze/thaw cycles to further ensure cell lysis.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.12688/f1000research.27898.1">doi:10.12688/f1000research.27898.1</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/35035904">pmid:35035904</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8749911/">pmcid:PMC8749911</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tmjt5gkcprexxguvmzwr4wbr5a">fatcat:tmjt5gkcprexxguvmzwr4wbr5a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210428000820/https://digitalcommons.unl.edu/cgi/viewcontent.cgi?article=1477&amp;context=hruskareports" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/20/23/2023ea10822aebc0c7f1c214017d0e4439a9dc77.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.12688/f1000research.27898.1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8749911" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations

Francesca Di Giallonardo, Armin Töpfer, Melanie Rey, Sandhya Prabhakaran, Yannick Duport, Christine Leemann, Stefan Schmutz, Nottania K. Campbell, Beda Joos, Maria Rita Lecca, Andrea Patrignani, Martin Däumer (+7 others)
<span title="2014-06-27">2014</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations. Nucleic Acids Research, 42(14):e115.  ...  To study complex heterogeneous virus populations comprehensively, novel methods are required that allow for complete reconstruction of the individual viral haplotypes.  ...  ACKNOWLEDGEMENTS We are grateful to our patients for their commitment and participation in the ZPHI study. We thank Ch. Grube, B.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gku537">doi:10.1093/nar/gku537</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24972832">pmid:24972832</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4132706/">pmcid:PMC4132706</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/iccbcmdayzghhedrlzoxadwvve">fatcat:iccbcmdayzghhedrlzoxadwvve</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190430202327/https://www.zora.uzh.ch/id/eprint/102379/1/Nucl.%20Acids%20Res.-2014-Giallonardo-e115.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/95/d5/95d58b7033945e53d496b8a638a6bb588d2f5476.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gku537"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4132706" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A Framework for Inferring Fitness Landscapes of Patient-Derived Viruses Using Quasispecies Theory

D. Seifert, F. Di Giallonardo, K. J. Metzner, H. F. Gunthard, N. Beerenwinkel
<span title="2014-11-17">2014</span> <i title="Genetics Society of America"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/j4jbzoikwjh4nhplkbx7xsr32y" style="color: black;">Genetics</a> </i> &nbsp;
Using the equilibrium distribution of the quasispecies model, an established model of intrahost viral evolution, we linked fitness parameters to the composition of the virus population, which can be estimated  ...  For inference, we developed a Bayesian Markov chain Monte Carlo method to sample from the posterior distribution of fitness values.  ...  Acknowledgments This work was supported by ETH research grant ETH-33 13-1 (to N. Literature Cited  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1534/genetics.114.172312">doi:10.1534/genetics.114.172312</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25406469">pmid:25406469</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4286684/">pmcid:PMC4286684</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3c2oglblhfesxjfpveznjivvgi">fatcat:3c2oglblhfesxjfpveznjivvgi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170820152242/http://www.genetics.org/content/genetics/199/1/191.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f4/34/f434e6177f6d9884c2898e684aac5b6caeab4bc6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1534/genetics.114.172312"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286684" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Recent advances in inferring viral diversity from high-throughput sequencing data

Susana Posada-Cespedes, David Seifert, Niko Beerenwinkel
<span title="">2017</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5j5tygnu2zbtfadqasaz4ytl3a" style="color: black;">Virus Research</a> </i> &nbsp;
Rapidly evolving RNA viruses prevail within a host as a collection of closely related variants, referred to as viral quasispecies.  ...  In addition, we address some of the experimental approaches designed to improve the biological signal-to-noise ratio.  ...  This ensemble of variants has been referred to as a viral quasispecies (Domingo et al., 2005; Lauring and Andino, 2010) .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.virusres.2016.09.016">doi:10.1016/j.virusres.2016.09.016</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27693290">pmid:27693290</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mgjzhmio5fhhzpedajjfsskmnu">fatcat:mgjzhmio5fhhzpedajjfsskmnu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190325083630/https://core.ac.uk/download/pdf/82205984.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/7a/a7/7aa78fa22e1525e8f97524e5341a877405551d0e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.virusres.2016.09.016"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> elsevier.com </button> </a>

A beginner's guide for FMDV quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencing

<span title="2019-11-04">2019</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/op7ztx4fhvairowgqifu7dnvsi" style="color: black;">Briefings in Bioinformatics</a> </i> &nbsp;
Deep sequencing of viral genomes is a powerful tool to study RNA virus complexity.  ...  In this work we present a suitable and affordable guide to explore the sub-consensus variability and to reconstruct viral quasispecies from Illumina sequencing data.  ...  QuRe assesses the complexity of viral quasispecies by using a built-in Poisson error correction method and a postreconstruction probabilistic clustering.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbz086">doi:10.1093/bib/bbz086</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31697321">pmid:31697321</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7110011/">pmcid:PMC7110011</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wonniil7u5acvlnwg5v3k2t23e">fatcat:wonniil7u5acvlnwg5v3k2t23e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200513124046/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC7110011&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/00/9f/009fb84eff4b71d93fdc6af3c1fdb9553a5491eb.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbz086"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7110011" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Ecological connectivity shapes quasispecies structure of RNA viruses in an Antarctic lake

A. López-Bueno, A. Rastrojo, R. Peiró, M. Arenas, A. Alcamí
<span title="2015-08-11">2015</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nbyiz76nd5hj5pb4uyhtgl3cxe" style="color: black;">Molecular Ecology</a> </i> &nbsp;
This is the first example of viral quasispecies from natural aquatic ecosystems and points to ecological connectivity as a modulating factor of quasispecies complexity.  ...  viral quasispecies from the catchment area or replication in a more diverse host community.  ...  We thank Roche for their support to the Antarctic expedition.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/mec.13321">doi:10.1111/mec.13321</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26198078">pmid:26198078</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kwjjx5xpmbgmjel7ke3irmyf7e">fatcat:kwjjx5xpmbgmjel7ke3irmyf7e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170921213029/http://digital.csic.es/bitstream/10261/133635/1/Alcami%20A%20Ecological%20connectivity.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c8/d9/c8d997838461f570098dc1ffc10aa88fc9421683.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/mec.13321"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Deconvoluting the Composition of Low-Frequency Hepatitis C Viral Quasispecies: Comparison of Genotypes and NS3 Resistance-Associated Variants between HCV/HIV Coinfected Hemophiliacs and HCV Monoinfected Patients in Japan

Masato Ogishi, Hiroshi Yotsuyanagi, Takeya Tsutsumi, Hiroyuki Gatanaga, Hirotaka Ode, Wataru Sugiura, Kyoji Moriya, Shinichi Oka, Satoshi Kimura, Kazuhiko Koike, Ferruccio Bonino
<span title="2015-03-06">2015</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
Herein, we characterize a methodological framework based on Illumina MiSeq next-generation sequencing (NGS) coupled with bioinformatics of quasispecies reconstruction (QSR) to realize highly accurate variant  ...  The core-to-NS3 protease coding sequences in 10 HCV monoinfected patients, 5 of whom had a history of blood transfusion, and 11 HCV/HIV coinfected patients with hemophilia, were studied.  ...  Ltd) for use of the MiSeq sequencing facility and technical assistance. Author Contributions  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0119145">doi:10.1371/journal.pone.0119145</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25748426">pmid:25748426</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4351984/">pmcid:PMC4351984</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/g6ky236lunh3xlp3x3ieyldl3u">fatcat:g6ky236lunh3xlp3x3ieyldl3u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171010153942/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0119145&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/62/e1/62e119aa3e220ff87b1fed9cbacd0e3247ebac77.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0119145"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4351984" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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