TreeKnit: Inferring ancestral reassortment graphs of influenza viruses
When two influenza viruses co-infect the same cell, they can exchange genome segments in a process known as reassortment. Reassortment is an important source of genetic diversity and is known to have been involved in the emergence of most pandemic influenza strains. However, because of the difficult...
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| Vydané v: | PLoS computational biology Ročník 18; číslo 8; s. e1010394 |
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| Hlavní autori: | , , |
| Médium: | Journal Article |
| Jazyk: | English |
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19.08.2022
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| Abstract | When two influenza viruses co-infect the same cell, they can exchange genome segments in a process known as reassortment. Reassortment is an important source of genetic diversity and is known to have been involved in the emergence of most pandemic influenza strains. However, because of the difficulty in identifying reassortment events from viral sequence data, little is known about their role in the evolution of the seasonal influenza viruses. Here we introduce TreeKnit, a method that infers ancestral reassortment graphs (ARG) from two segment trees. It is based on topological differences between trees, and proceeds in a greedy fashion by finding regions that are compatible in the two trees. Using simulated genealogies with reassortments, we show that TreeKnit performs well in a wide range of settings and that it is as accurate as a more principled bayesian method, while being orders of magnitude faster. Finally, we show that it is possible to use the inferred ARG to better resolve segment trees and to construct more informative visualizations of reassortments. |
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| AbstractList | When two influenza viruses co-infect the same cell, they can exchange genome segments in a process known as reassortment. Reassortment is an important source of genetic diversity and is known to have been involved in the emergence of most pandemic influenza strains. However, because of the difficulty in identifying reassortment events from viral sequence data, little is known about their role in the evolution of the seasonal influenza viruses. Here we introduce TreeKnit, a method that infers ancestral reassortment graphs (ARG) from two segment trees. It is based on topological differences between trees, and proceeds in a greedy fashion by finding regions that are compatible in the two trees. Using simulated genealogies with reassortments, we show that TreeKnit performs well in a wide range of settings and that it is as accurate as a more principled bayesian method, while being orders of magnitude faster. Finally, we show that it is possible to use the inferred ARG to better resolve segment trees and to construct more informative visualizations of reassortments. When two influenza viruses co-infect the same cell, they can exchange genome segments in a process known as reassortment. Reassortment is an important source of genetic diversity and is known to have been involved in the emergence of most pandemic influenza strains. However, because of the difficulty in identifying reassortment events from viral sequence data, little is known about their role in the evolution of the seasonal influenza viruses. Here we introduce TreeKnit, a method that infers ancestral reassortment graphs (ARG) from two segment trees. It is based on topological differences between trees, and proceeds in a greedy fashion by finding regions that are compatible in the two trees. Using simulated genealogies with reassortments, we show that TreeKnit performs well in a wide range of settings and that it is as accurate as a more principled bayesian method, while being orders of magnitude faster. Finally, we show that it is possible to use the inferred ARG to better resolve segment trees and to construct more informative visualizations of reassortments. Influenza viruses evolve quickly and escape immune defenses which requires frequent update of vaccines. Understanding this evolution is key to an effective public health response. The genome of influenza viruses is made up of 8 pieces called segments, each coding for different viral proteins. Within each segment, evolution is an asexual process in which genetic diversity is generated by mutations. But influenza also diversifies through reassortment which can occur when two different viruses infect the same cell: offsprings can then contain a combination of segments from both viruses. Reassortment is akin to sexual reproduction and can generate viruses that combine segments from diverged viral lineages. Reassortment is a crucial component of viral evolution, but it is challenging to reconstruct where reassortments happened and which segments share history. Here, we develop a method called TreeKnit to detect reassortment events. TreeKnit is based on genealogical trees of single segments that can be reconstructed using standard bioinformatics tools. Inconsistencies between these trees are then used as signs of reassortment. We show that TreeKnit is as accurate as other recent methods, but runs much faster. Our method will facilitate the study of reassortment and its consequences for influenza evolution. When two influenza viruses co-infect the same cell, they can exchange genome segments in a process known as reassortment. Reassortment is an important source of genetic diversity and is known to have been involved in the emergence of most pandemic influenza strains. However, because of the difficulty in identifying reassortment events from viral sequence data, little is known about their role in the evolution of the seasonal influenza viruses. Here we introduce TreeKnit, a method that infers ancestral reassortment graphs (ARG) from two segment trees. It is based on topological differences between trees, and proceeds in a greedy fashion by finding regions that are compatible in the two trees. Using simulated genealogies with reassortments, we show that TreeKnit performs well in a wide range of settings and that it is as accurate as a more principled bayesian method, while being orders of magnitude faster. Finally, we show that it is possible to use the inferred ARG to better resolve segment trees and to construct more informative visualizations of reassortments.When two influenza viruses co-infect the same cell, they can exchange genome segments in a process known as reassortment. Reassortment is an important source of genetic diversity and is known to have been involved in the emergence of most pandemic influenza strains. However, because of the difficulty in identifying reassortment events from viral sequence data, little is known about their role in the evolution of the seasonal influenza viruses. Here we introduce TreeKnit, a method that infers ancestral reassortment graphs (ARG) from two segment trees. It is based on topological differences between trees, and proceeds in a greedy fashion by finding regions that are compatible in the two trees. Using simulated genealogies with reassortments, we show that TreeKnit performs well in a wide range of settings and that it is as accurate as a more principled bayesian method, while being orders of magnitude faster. Finally, we show that it is possible to use the inferred ARG to better resolve segment trees and to construct more informative visualizations of reassortments. When two influenza viruses co-infect the same cell, they can exchange genome segments in a process known as reassortment. Reassortment is an important source of genetic diversity and is known to have been involved in the emergence of most pandemic influenza strains. However, because of the difficulty in identifying reassortments events from viral sequence data, little is known about its role in the evolution of the seasonal influenza viruses. Here we introduce TreeKnit, a method that infers ancestral reassortment graphs (ARG) from two segment trees. It is based on topological differences between trees, and proceeds in a greedy fashion by finding regions that are compatible in the two trees. Using simulated genealogies with reassortments, we show that TreeKnit performs well in a wide range of settings and that it is as accurate as a more principled bayesian method, while being orders of magnitude faster. Finally, we show that it is possible to use the inferred ARG to better resolve segment trees and to construct more informative visualizations of reassortments. |
| Audience | Academic |
| Author | Neher, Richard A. Vaughan, Timothy G. Barrat-Charlaix, Pierre |
| AuthorAffiliation | 1 Biozentrum, Universität Basel, Basel, Switzerland International Center for Theoretical Physics - South American Institute for Fundamental Research, BRAZIL 3 ETH Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland 2 Swiss Institute of Bioinformatics, Basel, Switzerland |
| AuthorAffiliation_xml | – name: International Center for Theoretical Physics - South American Institute for Fundamental Research, BRAZIL – name: 3 ETH Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland – name: 2 Swiss Institute of Bioinformatics, Basel, Switzerland – name: 1 Biozentrum, Universität Basel, Basel, Switzerland |
| Author_xml | – sequence: 1 givenname: Pierre surname: Barrat-Charlaix fullname: Barrat-Charlaix, Pierre – sequence: 2 givenname: Timothy G. orcidid: 0000-0001-6220-2239 surname: Vaughan fullname: Vaughan, Timothy G. – sequence: 3 givenname: Richard A. orcidid: 0000-0003-2525-1407 surname: Neher fullname: Neher, Richard A. |
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| CitedBy_id | crossref_primary_10_1016_j_aam_2023_102595 crossref_primary_10_1146_annurev_micro_032521_022006 crossref_primary_10_1128_spectrum_01762_23 crossref_primary_10_1093_molbev_msae078 crossref_primary_10_1016_j_medj_2025_100639 crossref_primary_10_1093_molbev_msaf133 crossref_primary_10_1371_journal_pcbi_1013301 crossref_primary_10_3390_v15112208 |
| Cites_doi | 10.1111/j.1750-2659.2007.00030.x 10.1242/bio.2012281 10.1093/bioinformatics/btu033 10.1371/journal.pgen.1004037 10.1109/BIBM.2008.78 10.1101/2021.05.15.442587 10.1534/genetics.111.128876 10.1126/science.220.4598.671 10.1093/nar/gkq1232 10.1093/molbev/msp077 10.1371/journal.pbio.0030300 10.1007/s13238-010-0008-z 10.1371/journal.ppat.1000012 10.1038/nrmicro2614 10.1093/genetics/141.4.1605 10.1073/pnas.1918304117 10.1016/j.jmva.2006.11.013 10.1371/journal.ppat.1006685 10.1186/1471-2105-9-532 10.1186/1471-2164-12-S2-S3 10.1017/S0016672300010156 10.1093/bioinformatics/bty407 10.1093/bioinformatics/17.8.754 10.1186/1471-2148-13-1 10.1093/molbev/msu300 10.1073/pnas.0904991106 10.1093/molbev/msu287 |
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| References | A Stamatakis (pcbi.1010394.ref006) 2014; 30 AD Neverov (pcbi.1010394.ref007) 2014; 10 UC de Silva (pcbi.1010394.ref013) 2012; 1 N Nagarajan (pcbi.1010394.ref014) 2011; 39 NF Müller (pcbi.1010394.ref009) 2020; 117 J Hadfield (pcbi.1010394.ref028) 2018; 34 GJD Smith (pcbi.1010394.ref002) 2009; 106 pcbi.1010394.ref017 LT Nguyen (pcbi.1010394.ref023) 2014; 32 G Cardona (pcbi.1010394.ref019) 2008; 9 EC Holmes (pcbi.1010394.ref010) 2005; 3 BQ Minh (pcbi.1010394.ref005) 2020 RA Neher (pcbi.1010394.ref026) 2011; 188 M Meilă (pcbi.1010394.ref020) 2007; 98 G Dudas (pcbi.1010394.ref027) 2015; 32 WG Hill (pcbi.1010394.ref025) 1966; 8 M Villa (pcbi.1010394.ref008) 2017; 13 R Rabadan (pcbi.1010394.ref012) 2008; 2 JP Huelsenbeck (pcbi.1010394.ref022) 2001; 17 RR Hudson (pcbi.1010394.ref024) 1995; 141 A Yurovsky (pcbi.1010394.ref015) 2011; 12 V Svinti (pcbi.1010394.ref016) 2013; 13 pcbi.1010394.ref021 MI Nelson (pcbi.1010394.ref011) 2008; 4 MN Price (pcbi.1010394.ref004) 2009; 26 S Kirkpatrick (pcbi.1010394.ref018) 1983; 220 Y Guan (pcbi.1010394.ref003) 2010; 1 E Simon-Loriere (pcbi.1010394.ref001) 2011; 9 |
| References_xml | – volume: 2 start-page: 9 issue: 1 year: 2008 ident: pcbi.1010394.ref012 article-title: Non-random reassortment in human influenza A viruses publication-title: Influenza and Other Respiratory Viruses doi: 10.1111/j.1750-2659.2007.00030.x – volume: 1 start-page: 385 issue: 4 year: 2012 ident: pcbi.1010394.ref013 article-title: A comprehensive analysis of reassortment in influenza A virus publication-title: Biology Open doi: 10.1242/bio.2012281 – volume: 30 start-page: 1312 issue: 9 year: 2014 ident: pcbi.1010394.ref006 article-title: RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies publication-title: Bioinformatics (Oxford, England) doi: 10.1093/bioinformatics/btu033 – volume: 10 start-page: e1004037 issue: 1 year: 2014 ident: pcbi.1010394.ref007 article-title: Intrasubtype Reassortments Cause Adaptive Amino Acid Replacements in H3N2 Influenza Genes publication-title: PLOS Genetics doi: 10.1371/journal.pgen.1004037 – ident: pcbi.1010394.ref021 doi: 10.1109/BIBM.2008.78 – year: 2020 ident: pcbi.1010394.ref005 article-title: IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era publication-title: Molecular Biology and Evolution – ident: pcbi.1010394.ref017 doi: 10.1101/2021.05.15.442587 – volume: 188 start-page: 975 issue: 4 year: 2011 ident: pcbi.1010394.ref026 article-title: Genetic draft and quasi-neutrality in large facultatively sexual populations publication-title: Genetics doi: 10.1534/genetics.111.128876 – volume: 220 start-page: 671 issue: 4598 year: 1983 ident: pcbi.1010394.ref018 article-title: Optimization by Simulated Annealing publication-title: Science doi: 10.1126/science.220.4598.671 – volume: 39 start-page: e34 issue: 6 year: 2011 ident: pcbi.1010394.ref014 article-title: GiRaF: robust, computational identification of influenza reassortments via graph mining publication-title: Nucleic Acids Research doi: 10.1093/nar/gkq1232 – volume: 26 start-page: 1641 issue: 7 year: 2009 ident: pcbi.1010394.ref004 article-title: FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix publication-title: Molecular Biology and Evolution doi: 10.1093/molbev/msp077 – volume: 3 start-page: e300 issue: 9 year: 2005 ident: pcbi.1010394.ref010 article-title: Whole-Genome Analysis of Human Influenza A Virus Reveals Multiple Persistent Lineages and Reassortment among Recent H3N2 Viruses publication-title: PLOS Biology doi: 10.1371/journal.pbio.0030300 – volume: 1 start-page: 9 issue: 1 year: 2010 ident: pcbi.1010394.ref003 article-title: The emergence of pandemic influenza viruses publication-title: Protein & Cell doi: 10.1007/s13238-010-0008-z – volume: 4 start-page: e1000012 issue: 2 year: 2008 ident: pcbi.1010394.ref011 article-title: Multiple Reassortment Events in the Evolutionary History of H1N1 Influenza A Virus Since 1918 publication-title: PLOS Pathogens doi: 10.1371/journal.ppat.1000012 – volume: 9 start-page: 617 issue: 8 year: 2011 ident: pcbi.1010394.ref001 article-title: Why do RNA viruses recombine? publication-title: Nature Reviews Microbiology doi: 10.1038/nrmicro2614 – volume: 141 start-page: 1605 issue: 4 year: 1995 ident: pcbi.1010394.ref024 article-title: Deleterious Background Selection with Recombination publication-title: Genetics doi: 10.1093/genetics/141.4.1605 – volume: 117 start-page: 17104 issue: 29 year: 2020 ident: pcbi.1010394.ref009 article-title: Bayesian inference of reassortment networks reveals fitness benefits of reassortment in human influenza viruses publication-title: Proceedings of the National Academy of Sciences doi: 10.1073/pnas.1918304117 – volume: 98 start-page: 873 issue: 5 year: 2007 ident: pcbi.1010394.ref020 article-title: Comparing clusterings—an information based distance publication-title: Journal of Multivariate Analysis doi: 10.1016/j.jmva.2006.11.013 – volume: 13 start-page: e1006685 issue: 11 year: 2017 ident: pcbi.1010394.ref008 article-title: Fitness cost of reassortment in human influenza publication-title: PLOS Pathogens doi: 10.1371/journal.ppat.1006685 – volume: 9 start-page: 532 issue: 1 year: 2008 ident: pcbi.1010394.ref019 article-title: Extended Newick: it is time for a standard representation of phylogenetic networks publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-9-532 – volume: 12 start-page: S3 issue: 2 year: 2011 ident: pcbi.1010394.ref015 article-title: FluReF, an automated flu virus reassortment finder based on phylogenetic trees publication-title: BMC Genomics doi: 10.1186/1471-2164-12-S2-S3 – volume: 8 start-page: 269 issue: 3 year: 1966 ident: pcbi.1010394.ref025 article-title: The effect of linkage on limits to artificial selection publication-title: Genetics Research doi: 10.1017/S0016672300010156 – volume: 34 start-page: 4121 issue: 23 year: 2018 ident: pcbi.1010394.ref028 article-title: Nextstrain: real-time tracking of pathogen evolution publication-title: Bioinformatics doi: 10.1093/bioinformatics/bty407 – volume: 17 start-page: 754 issue: 8 year: 2001 ident: pcbi.1010394.ref022 article-title: MRBAYES: Bayesian inference of phylogenetic trees publication-title: Bioinformatics doi: 10.1093/bioinformatics/17.8.754 – volume: 13 start-page: 1 issue: 1 year: 2013 ident: pcbi.1010394.ref016 article-title: New approaches for unravelling reassortment pathways publication-title: BMC Evolutionary Biology doi: 10.1186/1471-2148-13-1 – volume: 32 start-page: 268 issue: 1 year: 2014 ident: pcbi.1010394.ref023 article-title: IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies publication-title: Molecular Biology and Evolution doi: 10.1093/molbev/msu300 – volume: 106 start-page: 11709 issue: 28 year: 2009 ident: pcbi.1010394.ref002 article-title: Dating the emergence of pandemic influenza viruses publication-title: Proceedings of the National Academy of Sciences doi: 10.1073/pnas.0904991106 – volume: 32 start-page: 162 issue: 1 year: 2015 ident: pcbi.1010394.ref027 article-title: Reassortment between Influenza B Lineages and the Emergence of a Coadapted PB1–PB2–HA Gene Complex publication-title: Molecular Biology and Evolution doi: 10.1093/molbev/msu287 |
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| SubjectTerms | Analysis Bayesian analysis Bioinformatics Biology and Life Sciences Chemical processes Computer and Information Sciences Computer Science Evolution Genealogy Genetic diversity Genomes Genomics Graphs Influenza Influenza viruses Medicine and Health Sciences Methods Mutation Orthomyxoviridae Pandemics Physical Sciences Proteins RNA Segments Trees Trees (mathematics) Viruses |
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| Title | TreeKnit: Inferring ancestral reassortment graphs of influenza viruses |
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