publication . Article . 2019

Advances in Visualization Tools for Phylogenomic and Phylodynamic Studies of Viral Diseases

Kristof Theys; Philippe Lemey; Anne-Mieke Vandamme; Guy Baele;
Open Access English
  • Published: 02 Aug 2019 Journal: Frontiers in Public Health, volume 7 (eissn: 2296-2565, Copyright policy)
  • Publisher: Frontiers Media S.A.
  • Country: Belgium
Abstract
Genomic and epidemiological monitoring have become an integral part of our response to emerging and ongoing epidemics of viral infectious diseases. Advances in high-throughput sequencing, including portable genomic sequencing at reduced costs and turnaround time, are paralleled by continuing developments in methodology to infer evolutionary histories (dynamics/patterns) and to identify factors driving viral spread in space and time. The traditionally static nature of visualizing phylogenetic trees that represent these evolutionary relationships/processes has also evolved, albeit perhaps at a slower rate. Advanced visualization tools with increased resolution ass...
Persistent Identifiers
Subjects
free text keywords: Public Health, Review, visualization, phylogenetics, phylogenomics, phylodynamics, infectious disease, epidemiology, evolution, Science & Technology, Life Sciences & Biomedicine, Public, Environmental & Occupational Health, visualization, phylogenetics, phylogenomics, phylodynamics, infectious disease, epidemiology, evolution, EVOLUTIONARY GENETICS, TRANSMISSION TREES, GENOMICS DATA, REAL-TIME, SPREAD, VIRUS, COALESCENT, EMERGENCE, INFERENCE, DYNAMICS, Infectious disease (medical specialty), Phylogenetic tree, Turnaround time, Viral phylodynamics, Data science, Epidemiological Monitoring, Phylogenomics, Phylogenetics, Computer science, Visualization, lcsh:Public aspects of medicine, lcsh:RA1-1270
Related Organizations
Funded by
EC| VIROGENESIS
Project
VIROGENESIS
Virus discovery and epidemic tracing from high throughput metagenomic sequencing
  • Funder: European Commission (EC)
  • Project Code: 634650
  • Funding stream: H2020 | RIA
,
EC| ZIKAlliance
Project
ZIKAlliance
A global alliance for Zika virus control and prevention
  • Funder: European Commission (EC)
  • Project Code: 734548
  • Funding stream: H2020 | RIA
Validated by funder
,
WT| Putting genomic surveillance at the heart of viral epidemic response.
Project
  • Funder: Wellcome Trust (WT)
  • Project Code: 206298
  • Funding stream: Pathogen Biology and Disease Transmission
,
EC| ReservoirDOCs
Project
ReservoirDOCs
The evolutionary dynamics of pathogen emergence and establishment: from Reservoir Detection to Outbreak Control
  • Funder: European Commission (EC)
  • Project Code: 725422
  • Funding stream: H2020 | ERC | ERC-COG
Communities
COVID-19
107 references, page 1 of 8

1.Rife BD Mavian C Chen X Ciccozzi M Salemi M Min J. Phylodynamic applications in 21st century global infectious disease research. Glob Health Res Policy. (2017) 2:13. 10.1186/s41256-017-0034-y 29202081 [OpenAIRE] [PubMed] [DOI]

2.Dellicour S Baele G Dudas G Faria NR Pybus OG Suchard MA. Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak. Nat Comms. (2018) 9:2222. 10.1038/s41467-018-03763-2 29884821 [OpenAIRE] [PubMed] [DOI]

3.Faria NR Rambaut A Suchard MA Baele G Bedford T Ward MJ. HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations. Science. (2014) 346:56–61. 10.1126/science.1256739 25278604 [OpenAIRE] [PubMed] [DOI]

4.Faria NR Kraemer MUG Hill SC Goes de Jesus J Aguiar RS Iani FCM. Genomic and epidemiological monitoring of yellow fever virus transmission potential. Science. (2018) 361:894–9. 10.1126/science.aat7115 30139911 [OpenAIRE] [PubMed] [DOI]

5.Dudas G Carvalho LM Bedford T Tatem AJ Baele G Faria NR. Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nature. (2017) 544:309–15. 10.1038/nature22040 28405027 [OpenAIRE] [PubMed] [DOI]

6.Russell CA Kasson PM Donis RO Riley S Dunbar J Rambaut A Science Forum: improving pandemic influenza risk assessment. eLife. (2014) 3:e03883 10.7554/eLife.03883 25321142 [OpenAIRE] [PubMed] [DOI]

7.German D Grabowski MK Beyrer C. Enhanced use of phylogenetic data to inform public health approaches to HIV among men who have sex with men. Sex Health. (2016) 14:89–96. 10.1071/SH16056 27584826 [OpenAIRE] [PubMed] [DOI]

8.Grenfell BT Pybus OG Gog JR Wood JLN Daly JM Mumford JA. Unifying the epidemiological and evolutionary dynamics of pathogens. Science. (2004) 303:327–32. 10.1126/science.1090727 14726583 [OpenAIRE] [PubMed] [DOI]

9.Baele G Suchard MA Rambaut A Lemey P. Emerging concepts of data integration in pathogen phylodynamics. Syst Biol. (2016) 66:e47–e65. 10.1093/sysbio/syw054 28173504 [OpenAIRE] [PubMed] [DOI]

10.Baele G Dellicour S Suchard MA Lemey P Vrancken B. Recent advances in computational phylodynamics. Curr Opin Virol. (2018) 31:24–32. 10.1016/j.coviro.2018.08.009 30248578 [OpenAIRE] [PubMed] [DOI]

11.Quick J Loman NJ Durrafour S Simpson JT Severi E Cowley L. Real-time, portable genome sequencing for Ebola surveillance. Nature. (2016) 530:228–32. 10.1038/nature16996 26840485 [OpenAIRE] [PubMed] [DOI]

12.Baele G Lemey P Rambaut A Suchard MA. Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST. Bioinformatics. (2017) 33:1798–805. 10.1093/bioinformatics/btx088 28200071 [OpenAIRE] [PubMed] [DOI]

13.Ayres DL Cummings MP Baele G Darling AE Lewis PO Swofford DL. BEAGLE 3: improved performance, scaling and usability for a high-performance computing library for statistical phylogenetics. Syst Biol. (2019). 10.1093/sysbio/syz020 31034053 [OpenAIRE] [PubMed] [DOI]

14.Darwin C On the Origin of Species by Means of Natural Selection. London: Murray (1859).

15.Minin VM Suchard MA. Fast, accurate and simulation-free stochastic mapping. Philos Trans R Soc Lond B Biol Sci. (2008) 363:3985–95. 10.1098/rstb.2008.0176 18852111 [OpenAIRE] [PubMed] [DOI]

107 references, page 1 of 8
Abstract
Genomic and epidemiological monitoring have become an integral part of our response to emerging and ongoing epidemics of viral infectious diseases. Advances in high-throughput sequencing, including portable genomic sequencing at reduced costs and turnaround time, are paralleled by continuing developments in methodology to infer evolutionary histories (dynamics/patterns) and to identify factors driving viral spread in space and time. The traditionally static nature of visualizing phylogenetic trees that represent these evolutionary relationships/processes has also evolved, albeit perhaps at a slower rate. Advanced visualization tools with increased resolution ass...
Persistent Identifiers
Subjects
free text keywords: Public Health, Review, visualization, phylogenetics, phylogenomics, phylodynamics, infectious disease, epidemiology, evolution, Science & Technology, Life Sciences & Biomedicine, Public, Environmental & Occupational Health, visualization, phylogenetics, phylogenomics, phylodynamics, infectious disease, epidemiology, evolution, EVOLUTIONARY GENETICS, TRANSMISSION TREES, GENOMICS DATA, REAL-TIME, SPREAD, VIRUS, COALESCENT, EMERGENCE, INFERENCE, DYNAMICS, Infectious disease (medical specialty), Phylogenetic tree, Turnaround time, Viral phylodynamics, Data science, Epidemiological Monitoring, Phylogenomics, Phylogenetics, Computer science, Visualization, lcsh:Public aspects of medicine, lcsh:RA1-1270
Related Organizations
Funded by
EC| VIROGENESIS
Project
VIROGENESIS
Virus discovery and epidemic tracing from high throughput metagenomic sequencing
  • Funder: European Commission (EC)
  • Project Code: 634650
  • Funding stream: H2020 | RIA
,
EC| ZIKAlliance
Project
ZIKAlliance
A global alliance for Zika virus control and prevention
  • Funder: European Commission (EC)
  • Project Code: 734548
  • Funding stream: H2020 | RIA
Validated by funder
,
WT| Putting genomic surveillance at the heart of viral epidemic response.
Project
  • Funder: Wellcome Trust (WT)
  • Project Code: 206298
  • Funding stream: Pathogen Biology and Disease Transmission
,
EC| ReservoirDOCs
Project
ReservoirDOCs
The evolutionary dynamics of pathogen emergence and establishment: from Reservoir Detection to Outbreak Control
  • Funder: European Commission (EC)
  • Project Code: 725422
  • Funding stream: H2020 | ERC | ERC-COG
Communities
COVID-19
107 references, page 1 of 8

1.Rife BD Mavian C Chen X Ciccozzi M Salemi M Min J. Phylodynamic applications in 21st century global infectious disease research. Glob Health Res Policy. (2017) 2:13. 10.1186/s41256-017-0034-y 29202081 [OpenAIRE] [PubMed] [DOI]

2.Dellicour S Baele G Dudas G Faria NR Pybus OG Suchard MA. Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak. Nat Comms. (2018) 9:2222. 10.1038/s41467-018-03763-2 29884821 [OpenAIRE] [PubMed] [DOI]

3.Faria NR Rambaut A Suchard MA Baele G Bedford T Ward MJ. HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations. Science. (2014) 346:56–61. 10.1126/science.1256739 25278604 [OpenAIRE] [PubMed] [DOI]

4.Faria NR Kraemer MUG Hill SC Goes de Jesus J Aguiar RS Iani FCM. Genomic and epidemiological monitoring of yellow fever virus transmission potential. Science. (2018) 361:894–9. 10.1126/science.aat7115 30139911 [OpenAIRE] [PubMed] [DOI]

5.Dudas G Carvalho LM Bedford T Tatem AJ Baele G Faria NR. Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nature. (2017) 544:309–15. 10.1038/nature22040 28405027 [OpenAIRE] [PubMed] [DOI]

6.Russell CA Kasson PM Donis RO Riley S Dunbar J Rambaut A Science Forum: improving pandemic influenza risk assessment. eLife. (2014) 3:e03883 10.7554/eLife.03883 25321142 [OpenAIRE] [PubMed] [DOI]

7.German D Grabowski MK Beyrer C. Enhanced use of phylogenetic data to inform public health approaches to HIV among men who have sex with men. Sex Health. (2016) 14:89–96. 10.1071/SH16056 27584826 [OpenAIRE] [PubMed] [DOI]

8.Grenfell BT Pybus OG Gog JR Wood JLN Daly JM Mumford JA. Unifying the epidemiological and evolutionary dynamics of pathogens. Science. (2004) 303:327–32. 10.1126/science.1090727 14726583 [OpenAIRE] [PubMed] [DOI]

9.Baele G Suchard MA Rambaut A Lemey P. Emerging concepts of data integration in pathogen phylodynamics. Syst Biol. (2016) 66:e47–e65. 10.1093/sysbio/syw054 28173504 [OpenAIRE] [PubMed] [DOI]

10.Baele G Dellicour S Suchard MA Lemey P Vrancken B. Recent advances in computational phylodynamics. Curr Opin Virol. (2018) 31:24–32. 10.1016/j.coviro.2018.08.009 30248578 [OpenAIRE] [PubMed] [DOI]

11.Quick J Loman NJ Durrafour S Simpson JT Severi E Cowley L. Real-time, portable genome sequencing for Ebola surveillance. Nature. (2016) 530:228–32. 10.1038/nature16996 26840485 [OpenAIRE] [PubMed] [DOI]

12.Baele G Lemey P Rambaut A Suchard MA. Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST. Bioinformatics. (2017) 33:1798–805. 10.1093/bioinformatics/btx088 28200071 [OpenAIRE] [PubMed] [DOI]

13.Ayres DL Cummings MP Baele G Darling AE Lewis PO Swofford DL. BEAGLE 3: improved performance, scaling and usability for a high-performance computing library for statistical phylogenetics. Syst Biol. (2019). 10.1093/sysbio/syz020 31034053 [OpenAIRE] [PubMed] [DOI]

14.Darwin C On the Origin of Species by Means of Natural Selection. London: Murray (1859).

15.Minin VM Suchard MA. Fast, accurate and simulation-free stochastic mapping. Philos Trans R Soc Lond B Biol Sci. (2008) 363:3985–95. 10.1098/rstb.2008.0176 18852111 [OpenAIRE] [PubMed] [DOI]

107 references, page 1 of 8
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