Identifying changes in selective constraints: host shifts in influenza.
The natural reservoir of Influenza A is waterfowl. Normally, waterfowl viruses are not adapted to infect and spread in the human population. Sometimes, through reassortment or through whole host shift events, genetic material from waterfowl viruses is introduced into the human population causing wor...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2009-11-01
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| Series: | PLoS Computational Biology |
| Online Access: | http://europepmc.org/articles/PMC2770840?pdf=render |
| _version_ | 1819051460246110208 |
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| author | Asif U Tamuri Mario Dos Reis Alan J Hay Richard A Goldstein |
| author_facet | Asif U Tamuri Mario Dos Reis Alan J Hay Richard A Goldstein |
| author_sort | Asif U Tamuri |
| collection | DOAJ |
| description | The natural reservoir of Influenza A is waterfowl. Normally, waterfowl viruses are not adapted to infect and spread in the human population. Sometimes, through reassortment or through whole host shift events, genetic material from waterfowl viruses is introduced into the human population causing worldwide pandemics. Identifying which mutations allow viruses from avian origin to spread successfully in the human population is of great importance in predicting and controlling influenza pandemics. Here we describe a novel approach to identify such mutations. We use a sitewise non-homogeneous phylogenetic model that explicitly takes into account differences in the equilibrium frequencies of amino acids in different hosts and locations. We identify 172 amino acid sites with strong support and 518 sites with moderate support of different selection constraints in human and avian viruses. The sites that we identify provide an invaluable resource to experimental virologists studying adaptation of avian flu viruses to the human host. Identification of the sequence changes necessary for host shifts would help us predict the pandemic potential of various strains. The method is of broad applicability to investigating changes in selective constraints when the timing of the changes is known. |
| first_indexed | 2024-12-21T12:04:17Z |
| format | Article |
| id | doaj.art-f36c75a4f9d2405096c9b0daf7ee63e8 |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-12-21T12:04:17Z |
| publishDate | 2009-11-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-f36c75a4f9d2405096c9b0daf7ee63e82022-12-21T19:04:44ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582009-11-01511e100056410.1371/journal.pcbi.1000564Identifying changes in selective constraints: host shifts in influenza.Asif U TamuriMario Dos ReisAlan J HayRichard A GoldsteinThe natural reservoir of Influenza A is waterfowl. Normally, waterfowl viruses are not adapted to infect and spread in the human population. Sometimes, through reassortment or through whole host shift events, genetic material from waterfowl viruses is introduced into the human population causing worldwide pandemics. Identifying which mutations allow viruses from avian origin to spread successfully in the human population is of great importance in predicting and controlling influenza pandemics. Here we describe a novel approach to identify such mutations. We use a sitewise non-homogeneous phylogenetic model that explicitly takes into account differences in the equilibrium frequencies of amino acids in different hosts and locations. We identify 172 amino acid sites with strong support and 518 sites with moderate support of different selection constraints in human and avian viruses. The sites that we identify provide an invaluable resource to experimental virologists studying adaptation of avian flu viruses to the human host. Identification of the sequence changes necessary for host shifts would help us predict the pandemic potential of various strains. The method is of broad applicability to investigating changes in selective constraints when the timing of the changes is known.http://europepmc.org/articles/PMC2770840?pdf=render |
| spellingShingle | Asif U Tamuri Mario Dos Reis Alan J Hay Richard A Goldstein Identifying changes in selective constraints: host shifts in influenza. PLoS Computational Biology |
| title | Identifying changes in selective constraints: host shifts in influenza. |
| title_full | Identifying changes in selective constraints: host shifts in influenza. |
| title_fullStr | Identifying changes in selective constraints: host shifts in influenza. |
| title_full_unstemmed | Identifying changes in selective constraints: host shifts in influenza. |
| title_short | Identifying changes in selective constraints: host shifts in influenza. |
| title_sort | identifying changes in selective constraints host shifts in influenza |
| url | http://europepmc.org/articles/PMC2770840?pdf=render |
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