Literature DB >> 29097090

Predictive Modeling of Influenza Shows the Promise of Applied Evolutionary Biology.

Dylan H Morris1, Katelyn M Gostic2, Simone Pompei3, Trevor Bedford4, Marta Łuksza5, Richard A Neher6, Bryan T Grenfell7, Michael Lässig3, John W McCauley8.   

Abstract

Seasonal influenza is controlled through vaccination campaigns. Evolution of influenza virus antigens means that vaccines must be updated to match novel strains, and vaccine effectiveness depends on the ability of scientists to predict nearly a year in advance which influenza variants will dominate in upcoming seasons. In this review, we highlight a promising new surveillance tool: predictive models. Based on data-sharing and close collaboration between the World Health Organization and academic scientists, these models use surveillance data to make quantitative predictions regarding influenza evolution. Predictive models demonstrate the potential of applied evolutionary biology to improve public health and disease control. We review the state of influenza predictive modeling and discuss next steps and recommendations to ensure that these models deliver upon their considerable biomedical promise.
Copyright © 2017 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  Influenza; Predictive evolution; predictive modeling; vaccine strain selection

Mesh:

Substances:

Year:  2017        PMID: 29097090      PMCID: PMC5830126          DOI: 10.1016/j.tim.2017.09.004

Source DB:  PubMed          Journal:  Trends Microbiol        ISSN: 0966-842X            Impact factor:   17.079


  107 in total

Review 1.  Immune history and influenza virus susceptibility.

Authors:  Sarah Cobey; Scott E Hensley
Journal:  Curr Opin Virol       Date:  2017-01-12       Impact factor: 7.090

2.  The influenza virus resource at the National Center for Biotechnology Information.

Authors:  Yiming Bao; Pavel Bolotov; Dmitry Dernovoy; Boris Kiryutin; Leonid Zaslavsky; Tatiana Tatusova; Jim Ostell; David Lipman
Journal:  J Virol       Date:  2007-10-17       Impact factor: 5.103

3.  Natural selection on the influenza virus genome.

Authors:  Yoshiyuki Suzuki
Journal:  Mol Biol Evol       Date:  2006-07-03       Impact factor: 16.240

4.  Permissive secondary mutations enable the evolution of influenza oseltamivir resistance.

Authors:  Jesse D Bloom; Lizhi Ian Gong; David Baltimore
Journal:  Science       Date:  2010-06-04       Impact factor: 47.728

5.  Evolution of Neoantigen Landscape during Immune Checkpoint Blockade in Non-Small Cell Lung Cancer.

Authors:  Valsamo Anagnostou; Kellie N Smith; Patrick M Forde; Noushin Niknafs; Rohit Bhattacharya; James White; Theresa Zhang; Vilmos Adleff; Jillian Phallen; Neha Wali; Carolyn Hruban; Violeta B Guthrie; Kristen Rodgers; Jarushka Naidoo; Hyunseok Kang; William Sharfman; Christos Georgiades; Franco Verde; Peter Illei; Qing Kay Li; Edward Gabrielson; Malcolm V Brock; Cynthia A Zahnow; Stephen B Baylin; Robert B Scharpf; Julie R Brahmer; Rachel Karchin; Drew M Pardoll; Victor E Velculescu
Journal:  Cancer Discov       Date:  2016-12-28       Impact factor: 39.397

Review 6.  The evolution of epidemic influenza.

Authors:  Martha I Nelson; Edward C Holmes
Journal:  Nat Rev Genet       Date:  2007-01-30       Impact factor: 53.242

7.  Antibody landscapes after influenza virus infection or vaccination.

Authors:  J M Fonville; S H Wilks; S L James; A Fox; M Ventresca; M Aban; L Xue; T C Jones; N M H Le; Q T Pham; N D Tran; Y Wong; A Mosterin; L C Katzelnick; D Labonte; T T Le; G van der Net; E Skepner; C A Russell; T D Kaplan; G F Rimmelzwaan; N Masurel; J C de Jong; A Palache; W E P Beyer; Q M Le; T H Nguyen; H F L Wertheim; A C Hurt; A D M E Osterhaus; I G Barr; R A M Fouchier; P W Horby; D J Smith
Journal:  Science       Date:  2014-11-21       Impact factor: 47.728

8.  Stochastic processes are key determinants of short-term evolution in influenza a virus.

Authors:  Martha I Nelson; Lone Simonsen; Cecile Viboud; Mark A Miller; Jill Taylor; Kirsten St George; Sara B Griesemer; Elodie Ghedin; Elodie Ghedi; Naomi A Sengamalay; David J Spiro; Igor Volkov; Bryan T Grenfell; David J Lipman; Jeffery K Taubenberger; Edward C Holmes
Journal:  PLoS Pathog       Date:  2006-12       Impact factor: 6.823

9.  Phylogenetic analysis reveals the global migration of seasonal influenza A viruses.

Authors:  Martha I Nelson; Lone Simonsen; Cecile Viboud; Mark A Miller; Edward C Holmes
Journal:  PLoS Pathog       Date:  2007-09-14       Impact factor: 6.823

10.  Coordinated Evolution of Influenza A Surface Proteins.

Authors:  Alexey D Neverov; Sergey Kryazhimskiy; Joshua B Plotkin; Georgii A Bazykin
Journal:  PLoS Genet       Date:  2015-08-06       Impact factor: 5.917

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  30 in total

Review 1.  Evolution and rapid spread of a reassortant A(H3N2) virus that predominated the 2017-2018 influenza season.

Authors:  Barney I Potter; Rebecca Kondor; James Hadfield; John Huddleston; John Barnes; Thomas Rowe; Lizheng Guo; Xiyan Xu; Richard A Neher; Trevor Bedford; David E Wentworth
Journal:  Virus Evol       Date:  2019-12-04

Review 2.  Real-Time Analysis and Visualization of Pathogen Sequence Data.

Authors:  Richard A Neher; Trevor Bedford
Journal:  J Clin Microbiol       Date:  2018-10-25       Impact factor: 5.948

3.  Predictability in the evolution of Orthopteran cardenolide insensitivity.

Authors:  Lu Yang; Nitin Ravikanthachari; Ricardo Mariño-Pérez; Riddhi Deshmukh; Mariana Wu; Adam Rosenstein; Krushnamegh Kunte; Hojun Song; Peter Andolfatto
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2019-06-03       Impact factor: 6.237

4.  Predicting the short-term success of human influenza virus variants with machine learning.

Authors:  Maryam Hayati; Priscila Biller; Caroline Colijn
Journal:  Proc Biol Sci       Date:  2020-04-08       Impact factor: 5.349

5.  Experimental Evolution of Extreme Resistance to Ionizing Radiation in Escherichia coli after 50 Cycles of Selection.

Authors:  Steven T Bruckbauer; Joseph D Trimarco; Joel Martin; Brian Bushnell; Katherine A Senn; Wendy Schackwitz; Anna Lipzen; Matthew Blow; Elizabeth A Wood; Wesley S Culberson; Christa Pennacchio; Michael M Cox
Journal:  J Bacteriol       Date:  2019-03-26       Impact factor: 3.490

6.  Structures and functions linked to genome-wide adaptation of human influenza A viruses.

Authors:  Thorsten R Klingen; Jens Loers; Stephanie Stanelle-Bertram; Gülsah Gabriel; Alice C McHardy
Journal:  Sci Rep       Date:  2019-04-18       Impact factor: 4.379

7.  Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution.

Authors:  John Huddleston; John R Barnes; Thomas Rowe; Xiyan Xu; Rebecca Kondor; David E Wentworth; Lynne Whittaker; Burcu Ermetal; Rodney Stuart Daniels; John W McCauley; Seiichiro Fujisaki; Kazuya Nakamura; Noriko Kishida; Shinji Watanabe; Hideki Hasegawa; Ian Barr; Kanta Subbarao; Pierre Barrat-Charlaix; Richard A Neher; Trevor Bedford
Journal:  Elife       Date:  2020-09-02       Impact factor: 8.140

Review 8.  Challenges of Making Effective Influenza Vaccines.

Authors:  Sigrid Gouma; Elizabeth M Anderson; Scott E Hensley
Journal:  Annu Rev Virol       Date:  2020-05-11       Impact factor: 10.431

9.  Antigenic waves of virus-immune coevolution.

Authors:  Jacopo Marchi; Michael Lässig; Aleksandra M Walczak; Thierry Mora
Journal:  Proc Natl Acad Sci U S A       Date:  2021-07-06       Impact factor: 11.205

Review 10.  SARS-CoV-2 variants, spike mutations and immune escape.

Authors:  William T Harvey; Alessandro M Carabelli; Ben Jackson; Ravindra K Gupta; Emma C Thomson; Ewan M Harrison; Catherine Ludden; Richard Reeve; Andrew Rambaut; Sharon J Peacock; David L Robertson
Journal:  Nat Rev Microbiol       Date:  2021-06-01       Impact factor: 78.297

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