Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution
- University of Washington, United States
- Centers for Disease Control and Prevention (CDC), United States
- The Francis Crick Institute, United Kingdom
- The Francis Crick Insitute, United Kingdom
- National Institute of Infectious Diseases, Japan
- National Instituite of Infectious Diseases, Japan
- Peter Doherty Institute for Infection and Immunity, United States
- Peter Doherty Institute for Infection and Immunity, Australia
- University of Basel, Switzerland
- Fred Hutchinson Cancer Research Center, United States
Abstract
Seasonal influenza virus A/H3N2 is a major cause of death globally. Vaccination remains the most effective preventative. Rapid mutation of hemagglutinin allows viruses to escape adaptive immunity. This antigenic drift necessitates regular vaccine updates. Effective vaccine strains need to represent H3N2 populations circulating one year after strain selection. Experts select strains based on experimental measurements of antigenic drift and predictions made by models from hemagglutinin sequences. We developed a novel influenza forecasting framework that integrates phenotypic measures of antigenic drift and functional constraint with previously published sequence-only fitness estimates. Forecasts informed by phenotypic measures of antigenic drift consistently outperformed previous sequence- only estimates, while sequence-only estimates of functional constraint surpassed more comprehensive experimentally-informed estimates. Importantly, the best models integrated estimates of both functional constraint and either antigenic drift phenotypes or recent population growth.
Data availability
Sequence data are available from GISAID using accession ids provided in Supplemental File S1.Source code, derived data from serological measurements, fitness metric annotations, and resulting fitness model performance data are available in the project's GitHub repository (https://github.com/blab/flu-forecasting).Raw serological measurements are restricted from public distribution by previous data sharing agreements.
Article and author information
Author details
Pierre Barrat-Charlaix
Funding
Cancer Research UK (FC001030)
- Lynne Whittaker
- Burcu Ermetal
- Rodney Stuart Daniels
- John W McCauley
National Institute of Allergy and Infectious Diseases (U19AI117891-01)
- Trevor Bedford
National Institute of Allergy and Infectious Diseases (R01AI127893-01)
- Pierre Barrat-Charlaix
- Richard A Neher
- Trevor Bedford
Medical Research Council (FC001030)
- Lynne Whittaker
- Burcu Ermetal
- Rodney Stuart Daniels
- John W McCauley
Wellcome (FC001030)
- Lynne Whittaker
- Burcu Ermetal
- Rodney Stuart Daniels
- John W McCauley
Ministry of Health, Labour and Welfare (10110400)
- Seiichiro Fujisaki
- Kazuya Nakamura
- Noriko Kishida
- Shinji Watanabe
- Hideki Hasegawa
Japan Agency for Medical Research and Development (JPfk0108118)
- Shinji Watanabe
Australian Government Department of Health
- Ian Barr
- Kanta Subbarao
National Institute of Allergy and Infectious Diseases (F31AI140714)
- John Huddleston
National Institute of General Medical Sciences (R35GM119774-01)
- Trevor Bedford
Pew Charitable Trusts
- Trevor Bedford
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.
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Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution
eLife 9:e60067.
https://doi.org/10.7554/eLife.60067
Further reading
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- Evolutionary Biology
- Epidemiology and Global Health
- Microbiology and Infectious Disease
- Genetics and Genomics
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The insect brain and the timing of its development underwent evolutionary adaptations. However, little is known about the underlying developmental processes. The central complex of the brain is an excellent model to understand neural development and divergence. It is produced in large parts by type II neuroblasts, which produce intermediate progenitors, another type of cycling precursor, to increase their neural progeny. Type II neuroblasts lineages are believed to be conserved among insects, but little is known on their molecular characteristics in insects other than flies. Tribolium castaneum has emerged as a model for brain development and evolution. However, type II neuroblasts have so far not been studied in this beetle. We created a fluorescent enhancer trap marking expression of Tc-fez/earmuff, a key marker for intermediate progenitors. Using combinatorial labeling of further markers, including Tc-pointed, we characterized embryonic type II neuroblast lineages. Intriguingly, we found nine lineages per hemisphere in the Tribolium embryo while Drosophila produces only eight per brain hemisphere. These embryonic lineages are significantly larger in Tribolium than they are in Drosophila and contain more intermediate progenitors. Finally, we mapped these lineages to the domains of head patterning genes. Notably, Tc-otd is absent from all type II neuroblasts and intermediate progenitors, whereas Tc-six3 marks an anterior subset of the type II lineages. Tc-six4 specifically marks the territory where anterior-medial type II neuroblasts differentiate. In conclusion, we identified a conserved pattern of gene expression in holometabolan central complex forming type II neuroblast lineages, and conserved head patterning genes emerged as new candidates for conferring spatial identity to individual lineages. The higher number and greater lineage size of the embryonic type II neuroblasts in the beetle correlate with a previously described embryonic phase of central complex formation. These findings stipulate further research on the link between stem cell activity and temporal and structural differences in central complex development.
