ArticleJournal of molecular evolution2009
Using non-homogeneous models of nucleotide substitution to identify host shift events: application to the origin of the 1918 'Spanish' influenza pandemic virus.
Article in Journal of molecular evolution, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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22 citing papers in PubMed.
- A Mutation-Selection Model of Protein Evolution under Persistent Positive Selection.Molecular biology and evolution · 2022Article
- Inference of population genetic parameters from an irregular time series of seasonal influenza virus sequences.Genetics · 2021Article
- Comprehensive profiling of translation initiation in influenza virus infected cells.PLoS pathogens · 2019Article
- Deep mutational scanning identifies sites in influenza nucleoprotein that affect viral inhibition by MxA.PLoS pathogens · 2017Article
- Bayesian molecular clock dating of species divergences in the genomics era.Nature reviews. Genetics · 2016Review
- Positive Selection in CD8+ T-Cell Epitopes of Influenza Virus Nucleoprotein Revealed by a Comparative Analysis of Human and Swine Viral Lineages.Journal of virology · 2015Article
- How to calculate the non-synonymous to synonymous rate ratio of protein-coding genes under the Fisher-Wright mutation-selection framework.Biology letters · 2015Article
- Improving pandemic influenza risk assessment.eLife · 2014Article
- Epistatically interacting substitutions are enriched during adaptive protein evolution.PLoS genetics · 2014Article
- Intrasubtype reassortments cause adaptive amino acid replacements in H3N2 influenza genes.PLoS genetics · 2014Article
- Phylodynamics of the emergence of influenza viruses after cross-species transmission.PloS one · 2013Article
- Estimating reassortment rates in co-circulating Eurasian swine influenza viruses.The Journal of general virology · 2012Article
- Surprising results on phylogenetic tree building methods based on molecular sequences.BMC bioinformatics · 2012Article
- Estimating the distribution of selection coefficients from phylogenetic data using sitewise mutation-selection models.Genetics · 2012Article
- Pathogenic responses among young adults during the 1918 influenza pandemic.Emerging infectious diseases · 2012Review
- Insights on influenza pathogenesis from the grave.Virus research · 2011Review
- Phylogenetic and epidemic modeling of rapidly evolving infectious diseases.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2011Review
- Charting the host adaptation of influenza viruses.Molecular biology and evolution · 2011Article
- Oligonucleotide motifs that disappear during the evolution of influenza virus in humans increase alpha interferon secretion by plasmacytoid dendritic cells.Journal of virology · 2011Article
- The modes of evolutionary emergence of primal and late pandemic influenza virus strains from viral reservoir in animals: an interdisciplinary analysis.Influenza research and treatment · 2011Article
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Abstract
Nonhomogeneous Markov models of nucleotide substitution have received scant attention. Here we explore the possibility of using nonhomogeneous models to identify host shift nodes along phylogenetic trees of pathogens evolving in different hosts. It has been noticed that influenza viruses show marked differences in nucleotide composition in human and avian hosts. We take advantage of this fact to identify the host shift event that led to the 1918 'Spanish' influenza. This disease killed over 50 million people worldwide, ranking it as the deadliest pandemic in recorded history. Our model suggests that the eight RNA segments which eventually became the 1918 viral genome were introduced into a mammalian host around 1882-1913. The viruses later diverged into the classical swine and human H1N1 influenza lineages around 1913-1915. The last common ancestor of human strains dates from February 1917 to April 1918. Because pigs are more readily infected with avian influenza viruses than humans, it would seem that they were the original recipient of the virus. This would suggest that the virus was introduced into humans sometime between 1913 and 1918.
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