Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic.
Gavin J. D. Smith,Dhanasekaran Vijaykrishna,Justin Bahl,Samantha Lycett,Michael Worobey,Oliver G. Pybus,Siu Kit Ma,CL Cheung,Jayna Raghwani,Samir Bhatt,J. S. Malik Peiris,Yi Guan,Andrew Rambaut +12 more
Reads0
Chats0
TLDR
It is shown that the new swine-origin influenza A (H1N1) virus emerged in Mexico and the United States was derived from several viruses circulating in swine, and that the initial transmission to humans occurred several months before recognition of the outbreak.Abstract:
In March and early April 2009, a new swine-origin influenza A (H1N1) virus (S-OIV) emerged in Mexico and the United States. During the first few weeks of surveillance, the virus spread worldwide to 30 countries (as of May 11) by human-to-human transmission, causing the World Health Organization to raise its pandemic alert to level 5 of 6. This virus has the potential to develop into the first influenza pandemic of the twenty-first century. Here we use evolutionary analysis to estimate the timescale of the origins and the early development of the S-OIV epidemic. We show that it was derived from several viruses circulating in swine, and that the initial transmission to humans occurred several months before recognition of the outbreak. A phylogenetic estimate of the gaps in genetic surveillance indicates a long period of unsampled ancestry before the S-OIV outbreak, suggesting that the reassortment of swine lineages may have occurred years before emergence in humans, and that the multiple genetic ancestry of S-OIV is not indicative of an artificial origin. Furthermore, the unsampled history of the epidemic means that the nature and location of the genetically closest swine viruses reveal little about the immediate origin of the epidemic, despite the fact that we included a panel of closely related and previously unpublished swine influenza isolates. Our results highlight the need for systematic surveillance of influenza in swine, and provide evidence that the mixing of new genetic elements in swine can result in the emergence of viruses with pandemic potential in humans.read more
Citations
More filters
Journal ArticleDOI
Influenza virus evolution, host adaptation, and pandemic formation.
TL;DR: The evolution of influenza A viruses in their reservoir hosts is reviewed and genetic changes associated with introduction of novel viruses into humans, leading to pandemics and the establishment of seasonal viruses are discussed.
Journal ArticleDOI
Emergence of genomic diversity and recurrent mutations in SARS-CoV-2.
Lucy van Dorp,Mislav Acman,Damien Richard,Liam P. Shaw,Charlotte Ford,Louise Ormond,Christopher J. Owen,Juanita Pang,Cedric C.S. Tan,Florencia A.T. Boshier,Arturo Torres Ortiz,Francois Balloux +11 more
TL;DR: The results are in line with previous estimates and point to all sequences sharing a common ancestor towards the end of 2019, supporting this as the period when SARS-CoV-2 jumped into its human host.
Journal ArticleDOI
Respiratory Viral Infections in Infants: Causes, Clinical Symptoms, Virology, and Immunology
TL;DR: In this review, the complete picture from epidemiology and virology to clinical impact and immunology is explored, finding that both the virus and the immune response contribute to damage to the lungs and subsequent disease, and therefore, any prevention or treatment needs to address both of these factors.
Journal ArticleDOI
Pathways to zoonotic spillover
Raina K. Plowright,Colin R. Parrish,Hamish McCallum,Peter J. Hudson,Albert I. Ko,Andrea L. Graham,James O. Lloyd-Smith +6 more
TL;DR: A synthetic framework for animal-to-human transmission that integrates the relevant mechanisms reveals that all zoonotic pathogens must overcome a hierarchical series of barriers to cause spillover infections in humans.
Journal ArticleDOI
Absolute humidity and the seasonal onset of influenza in the continental United States.
Jeffrey Shaman,Virginia E. Pitzer,Virginia E. Pitzer,Virginia E. Pitzer,Cécile Viboud,Bryan T. Grenfell,Bryan T. Grenfell,Marc Lipsitch +7 more
TL;DR: It is demonstrated that variations of absolute humidity explain both the onset of wintertime influenza transmission and the overarching seasonality of this pathogen in temperate regions.
References
More filters
Journal ArticleDOI
Clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
TL;DR: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved and modifications are incorporated into a new program, CLUSTAL W, which is freely available.
Journal ArticleDOI
MUSCLE: multiple sequence alignment with high accuracy and high throughput
TL;DR: MUSCLE is a new computer program for creating multiple alignments of protein sequences that includes fast distance estimation using kmer counting, progressive alignment using a new profile function the authors call the log-expectation score, and refinement using tree-dependent restricted partitioning.
Journal ArticleDOI
BEAST: Bayesian evolutionary analysis by sampling trees
TL;DR: BEAST is a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree that provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions.
Journal ArticleDOI
Emergence of a novel swine-origin influenza A (H1N1) virus in humans.
Seema Jain,Lyn Finelli,Michael W. Shaw,Stephen Lindstrom,Larisa V. Gubareva,Xiyan Xu,Timothy M. Uyeki +6 more
TL;DR: A novel swine-origin influenza A virus was identified as the cause of outbreaks of febrile respiratory infection ranging from self-limited to severe illness and it is likely that the number of confirmed cases underestimates thenumber of cases that have occurred.
Journal ArticleDOI
Antigenic and Genetic Characteristics of Swine-Origin 2009 A(H1N1) Influenza Viruses Circulating in Humans
Rebecca Garten,C. Todd Davis,Colin A. Russell,Colin A. Russell,Bo Shu,Stephen Lindstrom,Amanda Balish,Wendy Sessions,Xiyan Xu,Eugene Skepner,Varough M. Deyde,Margaret Okomo-Adhiambo,Larisa V. Gubareva,John R. Barnes,Catherine B. Smith,Shannon L. Emery,Michael J. Hillman,Pierre Rivailler,James A. Smagala,Miranda de Graaf,Miranda de Graaf,David F. Burke,Ron A. M. Fouchier,Claudia Pappas,Celia Alpuche-Aranda,Hugo López-Gatell,Hiram Olivera,Irma Lopez,Christopher A. Myers,Dennis J. Faix,Patrick J. Blair,Cindy Yu,Kimberly M. Keene,P. David Dotson,David Boxrud,Anthony R. Sambol,Syed H. Abid,Kirsten St. George,Tammy L. Bannerman,Amanda L. Moore,David J. Stringer,Patricia Blevins,Gail J. Demmler-Harrison,Michele Ginsberg,Paula Kriner,Steve Waterman,Sandra Smole,Hugo Guevara,Edward A. Belongia,Patricia A. Clark,Sara T. Beatrice,Ruben O. Donis,Jacqueline M. Katz,Lyn Finelli,Carolyn B. Bridges,Michael W. Shaw,Daniel B. Jernigan,Timothy M. Uyeki,Derek J. Smith,Derek J. Smith,Derek J. Smith,Alexander Klimov,Nancy J. Cox +62 more
TL;DR: The lack of similarity between the 2009 A(H1N1) virus and its nearest relatives indicates that its gene segments have been circulating undetected for an extended period as mentioned in this paper.
Related Papers (5)
Antigenic and Genetic Characteristics of Swine-Origin 2009 A(H1N1) Influenza Viruses Circulating in Humans
Rebecca Garten,C. Todd Davis,Colin A. Russell,Colin A. Russell,Bo Shu,Stephen Lindstrom,Amanda Balish,Wendy Sessions,Xiyan Xu,Eugene Skepner,Varough M. Deyde,Margaret Okomo-Adhiambo,Larisa V. Gubareva,John R. Barnes,Catherine B. Smith,Shannon L. Emery,Michael J. Hillman,Pierre Rivailler,James A. Smagala,Miranda de Graaf,Miranda de Graaf,David F. Burke,Ron A. M. Fouchier,Claudia Pappas,Celia Alpuche-Aranda,Hugo López-Gatell,Hiram Olivera,Irma Lopez,Christopher A. Myers,Dennis J. Faix,Patrick J. Blair,Cindy Yu,Kimberly M. Keene,P. David Dotson,David Boxrud,Anthony R. Sambol,Syed H. Abid,Kirsten St. George,Tammy L. Bannerman,Amanda L. Moore,David J. Stringer,Patricia Blevins,Gail J. Demmler-Harrison,Michele Ginsberg,Paula Kriner,Steve Waterman,Sandra Smole,Hugo Guevara,Edward A. Belongia,Patricia A. Clark,Sara T. Beatrice,Ruben O. Donis,Jacqueline M. Katz,Lyn Finelli,Carolyn B. Bridges,Michael W. Shaw,Daniel B. Jernigan,Timothy M. Uyeki,Derek J. Smith,Derek J. Smith,Derek J. Smith,Alexander Klimov,Nancy J. Cox +62 more