A large effective population size for established within-host influenza virus infection
Strains of the influenza virus form coherent global populations, yet exist at the level of single infections in individual hosts. The relationship between these scales is a critical topic for understanding viral evolution. Here we investigate the within-host relationship between selection and the st...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2020-08-01
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| Series: | eLife |
| Subjects: | |
| Online Access: | https://elifesciences.org/articles/56915 |
| _version_ | 1811228062979719168 |
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| author | Casper K Lumby Lei Zhao Judith Breuer Christopher JR Illingworth |
| author_facet | Casper K Lumby Lei Zhao Judith Breuer Christopher JR Illingworth |
| author_sort | Casper K Lumby |
| collection | DOAJ |
| description | Strains of the influenza virus form coherent global populations, yet exist at the level of single infections in individual hosts. The relationship between these scales is a critical topic for understanding viral evolution. Here we investigate the within-host relationship between selection and the stochastic effects of genetic drift, estimating an effective population size of infection Ne for influenza infection. Examining whole-genome sequence data describing a chronic case of influenza B in a severely immunocompromised child we infer an Ne of 2.5 × 107 (95% confidence range 1.0 × 107 to 9.0 × 107) suggesting that genetic drift is of minimal importance during an established influenza infection. Our result, supported by data from influenza A infection, suggests that positive selection during within-host infection is primarily limited by the typically short period of infection. Atypically long infections may have a disproportionate influence upon global patterns of viral evolution. |
| first_indexed | 2024-04-12T09:52:12Z |
| format | Article |
| id | doaj.art-9ed1d3bb14354e0391c9594d3391f019 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-12T09:52:12Z |
| publishDate | 2020-08-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-9ed1d3bb14354e0391c9594d3391f0192022-12-22T03:37:48ZengeLife Sciences Publications LtdeLife2050-084X2020-08-01910.7554/eLife.56915A large effective population size for established within-host influenza virus infectionCasper K Lumby0https://orcid.org/0000-0001-8329-9228Lei Zhao1Judith Breuer2Christopher JR Illingworth3https://orcid.org/0000-0002-0030-2784Department of Genetics, University of Cambridge, Cambridge, United KingdomDepartment of Genetics, University of Cambridge, Cambridge, United KingdomGreat Ormond Street Hospital, London, United Kingdom; Division of Infection and Immunity, University College London, London, United KingdomDepartment of Genetics, University of Cambridge, Cambridge, United Kingdom; Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, United Kingdom; Department of Computer Science, Institute of Biotechnology, University of Helsinki, Helsinki, FinlandStrains of the influenza virus form coherent global populations, yet exist at the level of single infections in individual hosts. The relationship between these scales is a critical topic for understanding viral evolution. Here we investigate the within-host relationship between selection and the stochastic effects of genetic drift, estimating an effective population size of infection Ne for influenza infection. Examining whole-genome sequence data describing a chronic case of influenza B in a severely immunocompromised child we infer an Ne of 2.5 × 107 (95% confidence range 1.0 × 107 to 9.0 × 107) suggesting that genetic drift is of minimal importance during an established influenza infection. Our result, supported by data from influenza A infection, suggests that positive selection during within-host infection is primarily limited by the typically short period of infection. Atypically long infections may have a disproportionate influence upon global patterns of viral evolution.https://elifesciences.org/articles/56915within-host evolutiongenetic drifteffective population sizeselection |
| spellingShingle | Casper K Lumby Lei Zhao Judith Breuer Christopher JR Illingworth A large effective population size for established within-host influenza virus infection eLife within-host evolution genetic drift effective population size selection |
| title | A large effective population size for established within-host influenza virus infection |
| title_full | A large effective population size for established within-host influenza virus infection |
| title_fullStr | A large effective population size for established within-host influenza virus infection |
| title_full_unstemmed | A large effective population size for established within-host influenza virus infection |
| title_short | A large effective population size for established within-host influenza virus infection |
| title_sort | large effective population size for established within host influenza virus infection |
| topic | within-host evolution genetic drift effective population size selection |
| url | https://elifesciences.org/articles/56915 |
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