{"id":1260,"date":"2021-07-30T19:24:12","date_gmt":"2021-07-30T19:24:12","guid":{"rendered":"http:\/\/wp.cov19longhaulfoundation.org\/?p=1260"},"modified":"2021-07-30T19:24:12","modified_gmt":"2021-07-30T19:24:12","slug":"sars-cov-2-viral-genomics","status":"publish","type":"post","link":"https:\/\/cov19longhaulfoundation.org\/?p=1260","title":{"rendered":"SARS-CoV-2 viral genomics"},"content":{"rendered":"\n<p class=\"wp-block-paragraph\">Authors: This analysis was performed primarily by Matt Olm (<a href=\"mailto:mattolm@stanford.edu\">mattolm@stanford.edu<\/a>) in Justin Sonnenburg&#8217;s lab at Stanford University and Alex Crits-Christoph (<a href=\"mailto:crits-christoph@berkeley.edu\">crits-christoph@berkeley.edu<\/a>) in Jill Banfield&#8217;s lab at University of California, Berkeley<\/p>\n\n\n\n<p class=\"wp-block-paragraph\" style=\"font-size:24px\">As viruses replicate within their hosts during infection, they mutate and accrue genetic diversity in their populations. These populations are usually shared as a single genome representing the consensus genome from a particular patient, and analysis of&nbsp;<strong>inter-patient variation<\/strong>&nbsp;(differences between the consensus genomes from different patients) is useful for understanding how the outbreak spreads, and how the virus evolves globally.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\" style=\"font-size:24px\">We refer to the variation within a single individual as&nbsp;<strong>intra-patient variation<\/strong>, intraspecfic variation, or microdiversity. This genetic variation is less commonly studied, but analysis of this data has the following potential applications:<\/p>\n\n\n\n<ul class=\"wp-block-list\" style=\"font-size:24px\"><li>Identification of the genomic loci least likely to mutate during infection, which could be useful for designing universal primers \/ probes.<\/li><li>Comparison of viral evolution within individuals versus global evolution. This can be useful for understanding how the viral evolutionary pressures and functions.<\/li><li>Estimation of the number of viral particles acquired at the onset of infection and quantifying genetic diversity transferred during transmission.<\/li><\/ul>\n\n\n\n<h2 class=\"wp-block-heading\"><a href=\"https:\/\/github.com\/MrOlm\/covid19_population_genomics#inter-patient-sars-cov-2-genome-variation\"><\/a>Inter-patient SARS-CoV-2 genome variation<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\" style=\"font-size:24px\">To analyze inter-patient variation, we downloaded publicly available SARS-CoV-2 genomes, processed and filtered them, and generated a multiple sequence alignment. Details can be found in the&nbsp;<a href=\"https:\/\/github.com\/MrOlm\/covid19_population_genomics#Methods-1\">Methods<\/a>&nbsp;second, and the genomes and alignment can be downloaded from the&nbsp;<a href=\"https:\/\/github.com\/MrOlm\/covid19_population_genomics#Data-availability-1\">Data availability<\/a>&nbsp;section.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\" style=\"font-size:24px\">After genome alignment, we can visualize genetic diversity across the genome:<\/p>\n\n\n\n<p class=\"has-large-font-size wp-block-paragraph\">For More Information: <a href=\"https:\/\/github.com\/MrOlm\/covid19_population_genomics\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/github.com\/MrOlm\/covid19_population_genomics<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Authors: This analysis was performed primarily by Matt Olm (mattolm@stanford.edu) in Justin Sonnenburg&#8217;s lab at Stanford University and Alex Crits-Christoph (crits-christoph@berkeley.edu) in Jill Banfield&#8217;s lab at University of California, Berkeley [&hellip;]<\/p>\n","protected":false},"author":2,"featured_media":1261,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[149,155,189],"tags":[],"class_list":["post-1260","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-epidemiology","category-etiology","category-genomics"],"_links":{"self":[{"href":"https:\/\/cov19longhaulfoundation.org\/index.php?rest_route=\/wp\/v2\/posts\/1260","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/cov19longhaulfoundation.org\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/cov19longhaulfoundation.org\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/cov19longhaulfoundation.org\/index.php?rest_route=\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/cov19longhaulfoundation.org\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=1260"}],"version-history":[{"count":0,"href":"https:\/\/cov19longhaulfoundation.org\/index.php?rest_route=\/wp\/v2\/posts\/1260\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/cov19longhaulfoundation.org\/index.php?rest_route=\/wp\/v2\/media\/1261"}],"wp:attachment":[{"href":"https:\/\/cov19longhaulfoundation.org\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1260"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/cov19longhaulfoundation.org\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1260"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/cov19longhaulfoundation.org\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1260"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}