Want to track pandemic variants faster? Fix the bioinformatics bottleneck.

作者: Christophe Dessimoz , Rob Lanfear , Nick Goldman , Emma B Hodcroft , Duncan R MacCannell

DOI: 10.1038/D41586-021-00525-X

关键词:

摘要: … track influenza and Ebola outbreaks, but often retrospectively or through small updates every week or month — not to track … As experts in bioinformatics and viral evolution, we know that …

参考文章(11)
Nathan L. Yozwiak, Stephen F. Schaffner, Pardis C. Sabeti, Data sharing: Make outbreak research open access Nature. ,vol. 518, pp. 477- 479 ,(2015) , 10.1038/518477A
James Hadfield, Colin Megill, Sidney M Bell, John Huddleston, Barney Potter, Charlton Callender, Pavel Sagulenko, Trevor Bedford, Richard A Neher, Nextstrain: real-time tracking of pathogen evolution Bioinformatics. ,vol. 34, pp. 4121- 4123 ,(2018) , 10.1093/BIOINFORMATICS/BTY407
Tyler N. Starr, Allison J. Greaney, Sarah K. Hilton, Daniel Ellis, Katharine H.D. Crawford, Adam S. Dingens, Mary Jane Navarro, John E. Bowen, M. Alejandra Tortorici, Alexandra C. Walls, Neil P. King, David Veesler, Jesse D. Bloom, Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding. Cell. ,vol. 182, ,(2020) , 10.1016/J.CELL.2020.08.012
Yatish Turakhia, Bryan Thornlow, Angie S. Hinrichs, Nicola De Maio, Landen Gozashti, Robert Lanfear, David Haussler, Russell Corbett-Detig, Ultrafast Sample Placement on Existing Trees (UShER) Empowers Real-Time Phylogenetics for the SARS-CoV-2 Pandemic bioRxiv. ,(2020) , 10.1101/2020.09.26.314971
Yatish Turakhia, Nicola De Maio, Bryan Thornlow, Landen Gozashti, Robert Lanfear, Conor R. Walker, Angie S. Hinrichs, Jason D. Fernandes, Rui Borges, Greg Slodkowicz, Lukas Weilguny, David Haussler, Nick Goldman, Russell Corbett-Detig, Stability of SARS-CoV-2 phylogenies. PLOS Genetics. ,vol. 16, ,(2020) , 10.1371/JOURNAL.PGEN.1009175
Lucy van Dorp, Damien Richard, Cedric C. S. Tan, Liam P. Shaw, Mislav Acman, François Balloux, No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2. Nature Communications. ,vol. 11, pp. 5986- 5986 ,(2020) , 10.1038/S41467-020-19818-2
Jacob E. Lemieux, Katherine J. Siddle, Bennett M. Shaw, Christine Loreth, Stephen F. Schaffner, Adrianne Gladden-Young, Gordon Adams, Timelia Fink, Christopher H. Tomkins-Tinch, Lydia A. Krasilnikova, Katherine C. DeRuff, Melissa Rudy, Matthew R. Bauer, Kim A. Lagerborg, Erica Normandin, Sinéad B. Chapman, Steven K. Reilly, Melis N. Anahtar, Aaron E. Lin, Amber Carter, Cameron Myhrvold, Molly E. Kemball, Sushma Chaluvadi, Caroline Cusick, Katelyn Flowers, Anna Neumann, Felecia Cerrato, Maha Farhat, Damien Slater, Jason B. Harris, John A. Branda, David Hooper, Jessie M. Gaeta, Travis P. Baggett, James O’Connell, Andreas Gnirke, Tami D. Lieberman, Anthony Philippakis, Meagan Burns, Catherine M. Brown, Jeremy Luban, Edward T. Ryan, Sarah E. Turbett, Regina C. LaRocque, William P. Hanage, Glen R. Gallagher, Lawrence C. Madoff, Sandra Smole, Virginia M. Pierce, Eric Rosenberg, Pardis C. Sabeti, Daniel J. Park, Bronwyn L. MacInnis, Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events. Science. ,vol. 371, pp. 05- ,(2021) , 10.1126/SCIENCE.ABE3261
Jemma L. Geoghegan, Xiaoyun Ren, Matthew Storey, James Hadfield, Lauren Jelley, Sarah Jefferies, Jill Sherwood, Shevaun Paine, Sue Huang, Jordan Douglas, Fábio K. Mendes, Andrew Sporle, Michael G. Baker, David R. Murdoch, Nigel French, Colin R. Simpson, David Welch, Alexei J. Drummond, Edward C. Holmes, Sebastián Duchêne, Joep de Ligt, Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand. Nature Communications. ,vol. 11, pp. 6351- 6351 ,(2020) , 10.1038/S41467-020-20235-8
Louis Du Plessis, John T McCrone, Alexander E Zarebski, Verity Hill, Christopher Ruis, Bernardo Gutierrez, Jayna Raghwani, Jordan Ashworth, Rachel Colquhoun, Thomas R Connor, Nuno R Faria, Ben Jackson, Nicholas J Loman, Áine O’toole, Samuel M Nicholls, Kris V Parag, Emily Scher, Tetyana I Vasylyeva, Erik M Volz, Alexander Watts, Isaac I Bogoch, Kamran Khan, COVID-19 Genomics UK (COG-UK) Consortium†, David M Aanensen, Moritz UG Kraemer, Andrew Rambaut, Oliver G Pybus, None, Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK. Science. ,vol. 371, pp. 708- 712 ,(2021) , 10.1126/SCIENCE.ABF2946
Tara Swadi, Jemma L. Geoghegan, Tom Devine, Caroline McElnay, Jillian Sherwood, Phil Shoemack, Xiaoyun Ren, Matt Storey, Sarah Jefferies, Erasmus Smit, James Hadfield, Aoife Kenny, Lauren Jelley, Andrew Sporle, Andrea McNeill, G. Edwin Reynolds, Kip Mouldey, Lindsay Lowe, Gerard Sonder, Alexei J. Drummond, Sue Huang, David Welch, Edward C. Holmes, Nigel French, Colin R. Simpson, Joep de Ligt, Genomic Evidence of In-Flight Transmission of SARS-CoV-2 Despite Predeparture Testing. Emerging Infectious Diseases. ,vol. 27, pp. 687- 693 ,(2021) , 10.3201/EID2703.204714