{"id":395,"date":"2020-12-30T17:48:39","date_gmt":"2020-12-30T17:48:39","guid":{"rendered":"https:\/\/research.reading.ac.uk\/cmpe\/?p=395"},"modified":"2021-01-20T17:50:57","modified_gmt":"2021-01-20T17:50:57","slug":"new-paper-an-international-initiative-of-predicting-the-sars-cov-2-pandemic-using-ensemble-data-assimilation","status":"publish","type":"post","link":"https:\/\/research.reading.ac.uk\/cmpe\/new-paper-an-international-initiative-of-predicting-the-sars-cov-2-pandemic-using-ensemble-data-assimilation\/","title":{"rendered":"New paper – An international initiative of predicting the SARS-CoV-2 pandemic using ensemble data assimilation"},"content":{"rendered":"

Evensen, G., Amezcua, J., Bocquet, M., Carrassi, A., Farchi, A., Fowler, A., Houtekamer, P., Jones, C., de Moraes, R., Pulido, M., Sampson, C. and Vossepoel, F. (2020) An international initiative of predicting the Sars-Cov-2 pandemic using ensemble data assimilation. Foundations of Data Science.<\/p>\n

https:\/\/d<\/a>oi.org\/10.3934\/fods.2021001<\/a><\/p>\n

Abstract<\/strong>
\nThis work demonstrates the efficiency of using iterative ensemble smoothers to estimate the parameters of an SEIR model. We have extended a standard SEIR model with age-classes and compartments of sick, hospitalized, and dead. The data conditioned on are the daily numbers of accumulated deaths and the number of hospitalized. Also, it is possible to condition the model on the number of cases obtained from testing. We start from a wide prior distribution for the model parameters; then, the ensemble conditioning leads to a posterior ensemble of estimated parameters yielding model predictions in close agreement with the observations. The updated ensemble of model simulations has predictive capabilities and include uncertainty estimates. In particular, we estimate the effective reproductive number as a function of time, and we can assess the impact of different intervention measures. By starting from the updated set of model parameters, we can make accurate short-term predictions of the epidemic development assuming knowledge of the future effective reproductive number. Also, the model system allows for the computation of long-term scenarios of the epidemic under different assumptions. We have applied the model system on data sets from several countries, i.e., the four European countries Norway, England, The Netherlands, and France; the province of Quebec in Canada; the South American countries Argentina and Brazil; and the four US states Alabama, North Carolina, California, and New York. These countries and states all have vastly different developments of the epidemic, and we could accurately model the SARS-CoV-2 outbreak in all of them. We realize that more complex models, e.g., with regional compartments, may be desirable, and we suggest that the approach used here should be applicable also for these models.<\/strong><\/p>\n","protected":false},"excerpt":{"rendered":"

Evensen, G., Amezcua, J., Bocquet, M., Carrassi, A., Farchi, A., Fowler, A., Houtekamer, P., Jones, C., de Moraes, R., Pulido, M., Sampson, C. and Vossepoel, F. (2020) An international initiative…Read More ><\/a><\/p>\n","protected":false},"author":469,"featured_media":386,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"__cvm_playback_settings":[],"__cvm_video_id":"","footnotes":""},"categories":[1,24],"tags":[],"coauthors":[23],"class_list":["post-395","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-uncategorised","category-publication"],"acf":[],"yoast_head":"\nNew paper - An international initiative of predicting the SARS-CoV-2 pandemic using ensemble data assimilation - Centre for the Mathematics of Planet Earth<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/research.reading.ac.uk\/cmpe\/new-paper-an-international-initiative-of-predicting-the-sars-cov-2-pandemic-using-ensemble-data-assimilation\/\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"New paper - An international initiative of predicting the SARS-CoV-2 pandemic using ensemble data assimilation - Centre for the Mathematics of Planet Earth\" \/>\n<meta property=\"og:description\" content=\"Evensen, G., Amezcua, J., Bocquet, M., Carrassi, A., Farchi, A., Fowler, A., Houtekamer, P., Jones, C., de Moraes, R., Pulido, M., Sampson, C. and Vossepoel, F. (2020) An international initiative...Read More >\" \/>\n<meta property=\"og:url\" content=\"https:\/\/research.reading.ac.uk\/cmpe\/new-paper-an-international-initiative-of-predicting-the-sars-cov-2-pandemic-using-ensemble-data-assimilation\/\" \/>\n<meta property=\"og:site_name\" content=\"Centre for the Mathematics of Planet Earth\" \/>\n<meta property=\"article:published_time\" content=\"2020-12-30T17:48:39+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2021-01-20T17:50:57+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/research.reading.ac.uk\/cmpe\/wp-content\/uploads\/sites\/163\/2021\/01\/magazines-1108801_640.jpg\" \/>\n\t<meta property=\"og:image:width\" content=\"640\" \/>\n\t<meta property=\"og:image:height\" content=\"494\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/jpeg\" \/>\n<meta name=\"author\" content=\"Donna Walton\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Donna Walton\" \/>\n\t<meta name=\"twitter:label2\" content=\"Estimated reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"2 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\/\/research.reading.ac.uk\/cmpe\/new-paper-an-international-initiative-of-predicting-the-sars-cov-2-pandemic-using-ensemble-data-assimilation\/\",\"url\":\"https:\/\/research.reading.ac.uk\/cmpe\/new-paper-an-international-initiative-of-predicting-the-sars-cov-2-pandemic-using-ensemble-data-assimilation\/\",\"name\":\"New paper - An international initiative of predicting the SARS-CoV-2 pandemic using ensemble data assimilation - Centre for the Mathematics of Planet Earth\",\"isPartOf\":{\"@id\":\"https:\/\/research.reading.ac.uk\/cmpe\/#website\"},\"datePublished\":\"2020-12-30T17:48:39+00:00\",\"dateModified\":\"2021-01-20T17:50:57+00:00\",\"author\":{\"@id\":\"https:\/\/research.reading.ac.uk\/cmpe\/#\/schema\/person\/ed94c3d9e2aa2dce8ea35fee5b9664bf\"},\"breadcrumb\":{\"@id\":\"https:\/\/research.reading.ac.uk\/cmpe\/new-paper-an-international-initiative-of-predicting-the-sars-cov-2-pandemic-using-ensemble-data-assimilation\/#breadcrumb\"},\"inLanguage\":\"en-GB\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\/\/research.reading.ac.uk\/cmpe\/new-paper-an-international-initiative-of-predicting-the-sars-cov-2-pandemic-using-ensemble-data-assimilation\/\"]}]},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\/\/research.reading.ac.uk\/cmpe\/new-paper-an-international-initiative-of-predicting-the-sars-cov-2-pandemic-using-ensemble-data-assimilation\/#breadcrumb\",\"itemListElement\":[{\"@type\":\"ListItem\",\"position\":1,\"name\":\"Home\",\"item\":\"https:\/\/research.reading.ac.uk\/cmpe\/\"},{\"@type\":\"ListItem\",\"position\":2,\"name\":\"New paper – An international initiative of predicting the SARS-CoV-2 pandemic using ensemble data assimilation\"}]},{\"@type\":\"WebSite\",\"@id\":\"https:\/\/research.reading.ac.uk\/cmpe\/#website\",\"url\":\"https:\/\/research.reading.ac.uk\/cmpe\/\",\"name\":\"Centre for the Mathematics of Planet Earth\",\"description\":\"at the University of Reading\",\"potentialAction\":[{\"@type\":\"SearchAction\",\"target\":{\"@type\":\"EntryPoint\",\"urlTemplate\":\"https:\/\/research.reading.ac.uk\/cmpe\/?s={search_term_string}\"},\"query-input\":\"required name=search_term_string\"}],\"inLanguage\":\"en-GB\"},{\"@type\":\"Person\",\"@id\":\"https:\/\/research.reading.ac.uk\/cmpe\/#\/schema\/person\/ed94c3d9e2aa2dce8ea35fee5b9664bf\",\"name\":\"Donna Walton\",\"image\":{\"@type\":\"ImageObject\",\"inLanguage\":\"en-GB\",\"@id\":\"https:\/\/research.reading.ac.uk\/cmpe\/#\/schema\/person\/image\/5a16b776489b86a745e714b503102424\",\"url\":\"https:\/\/secure.gravatar.com\/avatar\/96cdf5ace3b619fa34625ee0dc43cc24a03354aaf4e0f4c43cc1b11ddfe7929b?s=96&d=mm&r=g\",\"contentUrl\":\"https:\/\/secure.gravatar.com\/avatar\/96cdf5ace3b619fa34625ee0dc43cc24a03354aaf4e0f4c43cc1b11ddfe7929b?s=96&d=mm&r=g\",\"caption\":\"Donna Walton\"},\"url\":\"https:\/\/research.reading.ac.uk\/cmpe\/author\/xd923591reading-ac-uk\/\"}]}<\/script>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"New paper - An international initiative of predicting the SARS-CoV-2 pandemic using ensemble data assimilation - Centre for the Mathematics of Planet Earth","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/research.reading.ac.uk\/cmpe\/new-paper-an-international-initiative-of-predicting-the-sars-cov-2-pandemic-using-ensemble-data-assimilation\/","og_locale":"en_GB","og_type":"article","og_title":"New paper - An international initiative of predicting the SARS-CoV-2 pandemic using ensemble data assimilation - Centre for the Mathematics of Planet Earth","og_description":"Evensen, G., Amezcua, J., Bocquet, M., Carrassi, A., Farchi, A., Fowler, A., Houtekamer, P., Jones, C., de Moraes, R., Pulido, M., Sampson, C. and Vossepoel, F. (2020) An international initiative...Read More >","og_url":"https:\/\/research.reading.ac.uk\/cmpe\/new-paper-an-international-initiative-of-predicting-the-sars-cov-2-pandemic-using-ensemble-data-assimilation\/","og_site_name":"Centre for the Mathematics of Planet Earth","article_published_time":"2020-12-30T17:48:39+00:00","article_modified_time":"2021-01-20T17:50:57+00:00","og_image":[{"width":640,"height":494,"url":"https:\/\/research.reading.ac.uk\/cmpe\/wp-content\/uploads\/sites\/163\/2021\/01\/magazines-1108801_640.jpg","type":"image\/jpeg"}],"author":"Donna Walton","twitter_card":"summary_large_image","twitter_misc":{"Written by":"Donna Walton","Estimated reading time":"2 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"WebPage","@id":"https:\/\/research.reading.ac.uk\/cmpe\/new-paper-an-international-initiative-of-predicting-the-sars-cov-2-pandemic-using-ensemble-data-assimilation\/","url":"https:\/\/research.reading.ac.uk\/cmpe\/new-paper-an-international-initiative-of-predicting-the-sars-cov-2-pandemic-using-ensemble-data-assimilation\/","name":"New paper - An international initiative of predicting the SARS-CoV-2 pandemic using ensemble data assimilation - Centre for the Mathematics of Planet Earth","isPartOf":{"@id":"https:\/\/research.reading.ac.uk\/cmpe\/#website"},"datePublished":"2020-12-30T17:48:39+00:00","dateModified":"2021-01-20T17:50:57+00:00","author":{"@id":"https:\/\/research.reading.ac.uk\/cmpe\/#\/schema\/person\/ed94c3d9e2aa2dce8ea35fee5b9664bf"},"breadcrumb":{"@id":"https:\/\/research.reading.ac.uk\/cmpe\/new-paper-an-international-initiative-of-predicting-the-sars-cov-2-pandemic-using-ensemble-data-assimilation\/#breadcrumb"},"inLanguage":"en-GB","potentialAction":[{"@type":"ReadAction","target":["https:\/\/research.reading.ac.uk\/cmpe\/new-paper-an-international-initiative-of-predicting-the-sars-cov-2-pandemic-using-ensemble-data-assimilation\/"]}]},{"@type":"BreadcrumbList","@id":"https:\/\/research.reading.ac.uk\/cmpe\/new-paper-an-international-initiative-of-predicting-the-sars-cov-2-pandemic-using-ensemble-data-assimilation\/#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/research.reading.ac.uk\/cmpe\/"},{"@type":"ListItem","position":2,"name":"New paper – An international initiative of predicting the SARS-CoV-2 pandemic using ensemble data assimilation"}]},{"@type":"WebSite","@id":"https:\/\/research.reading.ac.uk\/cmpe\/#website","url":"https:\/\/research.reading.ac.uk\/cmpe\/","name":"Centre for the Mathematics of Planet Earth","description":"at the University of Reading","potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/research.reading.ac.uk\/cmpe\/?s={search_term_string}"},"query-input":"required name=search_term_string"}],"inLanguage":"en-GB"},{"@type":"Person","@id":"https:\/\/research.reading.ac.uk\/cmpe\/#\/schema\/person\/ed94c3d9e2aa2dce8ea35fee5b9664bf","name":"Donna Walton","image":{"@type":"ImageObject","inLanguage":"en-GB","@id":"https:\/\/research.reading.ac.uk\/cmpe\/#\/schema\/person\/image\/5a16b776489b86a745e714b503102424","url":"https:\/\/secure.gravatar.com\/avatar\/96cdf5ace3b619fa34625ee0dc43cc24a03354aaf4e0f4c43cc1b11ddfe7929b?s=96&d=mm&r=g","contentUrl":"https:\/\/secure.gravatar.com\/avatar\/96cdf5ace3b619fa34625ee0dc43cc24a03354aaf4e0f4c43cc1b11ddfe7929b?s=96&d=mm&r=g","caption":"Donna Walton"},"url":"https:\/\/research.reading.ac.uk\/cmpe\/author\/xd923591reading-ac-uk\/"}]}},"cc_featured_image_caption":{"caption_text":false,"source_text":false,"source_url":false},"_links":{"self":[{"href":"https:\/\/research.reading.ac.uk\/cmpe\/wp-json\/wp\/v2\/posts\/395","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/research.reading.ac.uk\/cmpe\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/research.reading.ac.uk\/cmpe\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/research.reading.ac.uk\/cmpe\/wp-json\/wp\/v2\/users\/469"}],"replies":[{"embeddable":true,"href":"https:\/\/research.reading.ac.uk\/cmpe\/wp-json\/wp\/v2\/comments?post=395"}],"version-history":[{"count":1,"href":"https:\/\/research.reading.ac.uk\/cmpe\/wp-json\/wp\/v2\/posts\/395\/revisions"}],"predecessor-version":[{"id":397,"href":"https:\/\/research.reading.ac.uk\/cmpe\/wp-json\/wp\/v2\/posts\/395\/revisions\/397"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/research.reading.ac.uk\/cmpe\/wp-json\/wp\/v2\/media\/386"}],"wp:attachment":[{"href":"https:\/\/research.reading.ac.uk\/cmpe\/wp-json\/wp\/v2\/media?parent=395"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/research.reading.ac.uk\/cmpe\/wp-json\/wp\/v2\/categories?post=395"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/research.reading.ac.uk\/cmpe\/wp-json\/wp\/v2\/tags?post=395"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/research.reading.ac.uk\/cmpe\/wp-json\/wp\/v2\/coauthors?post=395"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}