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Early release - 16 new EBOV genomes from Sierra Leone - Ebolavirus Epidemic 2014-2016 - Virological
<!DOCTYPE html> <html lang="en"> <head> <meta charset="utf-8"> <title>Early release - 16 new EBOV genomes from Sierra Leone - Ebolavirus Epidemic 2014-2016 - Virological</title> <meta name="description" content="Update: Please use BioProject link instead since the sequences have all be finalized: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA257197/ As part of our continued collaboration with the Sierra Leone Ministry of Health&hellip;"> <meta name="generator" content="Discourse 3.3.0.beta1 - https://github.com/discourse/discourse version 9c110ccbd87277af793bc93441348e4e1839de81"> <link rel="icon" type="image/png" href="https://virological.org/uploads/default/optimized/1X/7897c4e655617c4b6fe71a98eaa97a38778f0623_2_32x32.png"> <link rel="apple-touch-icon" type="image/png" href="https://virological.org/uploads/default/optimized/1X/7897c4e655617c4b6fe71a98eaa97a38778f0623_2_180x180.png"> <meta name="theme-color" media="all" content="#ffffff"> <meta name="viewport" content="width=device-width, initial-scale=1.0, minimum-scale=1.0, user-scalable=yes, viewport-fit=cover"> <link rel="canonical" href="https://virological.org/t/early-release-16-new-ebov-genomes-from-sierra-leone/33" /> <link rel="search" type="application/opensearchdescription+xml" href="https://virological.org/opensearch.xml" title="Virological Search"> <link href="/stylesheets/color_definitions_base__2_2ce88ee63cb4b6c91353165224be363ba88fb04f.css?__ws=virological.org" media="all" rel="stylesheet" class="light-scheme"/> <link href="/stylesheets/desktop_33be3dc8682f6a0819c96460049aa59027e7d5f4.css?__ws=virological.org" media="all" rel="stylesheet" data-target="desktop" /> <link href="/stylesheets/chat_33be3dc8682f6a0819c96460049aa59027e7d5f4.css?__ws=virological.org" media="all" rel="stylesheet" data-target="chat" /> <link href="/stylesheets/checklist_33be3dc8682f6a0819c96460049aa59027e7d5f4.css?__ws=virological.org" media="all" rel="stylesheet" data-target="checklist" /> <link href="/stylesheets/discourse-details_33be3dc8682f6a0819c96460049aa59027e7d5f4.css?__ws=virological.org" media="all" rel="stylesheet" data-target="discourse-details" /> <link href="/stylesheets/discourse-lazy-videos_33be3dc8682f6a0819c96460049aa59027e7d5f4.css?__ws=virological.org" media="all" rel="stylesheet" data-target="discourse-lazy-videos" /> <link href="/stylesheets/discourse-local-dates_33be3dc8682f6a0819c96460049aa59027e7d5f4.css?__ws=virological.org" media="all" rel="stylesheet" data-target="discourse-local-dates" /> <link href="/stylesheets/discourse-narrative-bot_33be3dc8682f6a0819c96460049aa59027e7d5f4.css?__ws=virological.org" media="all" rel="stylesheet" data-target="discourse-narrative-bot" /> <link href="/stylesheets/discourse-presence_33be3dc8682f6a0819c96460049aa59027e7d5f4.css?__ws=virological.org" media="all" rel="stylesheet" data-target="discourse-presence" /> <link href="/stylesheets/docker_manager_33be3dc8682f6a0819c96460049aa59027e7d5f4.css?__ws=virological.org" media="all" rel="stylesheet" data-target="docker_manager" /> <link href="/stylesheets/footnote_33be3dc8682f6a0819c96460049aa59027e7d5f4.css?__ws=virological.org" media="all" rel="stylesheet" data-target="footnote" /> <link href="/stylesheets/poll_33be3dc8682f6a0819c96460049aa59027e7d5f4.css?__ws=virological.org" media="all" rel="stylesheet" data-target="poll" /> <link href="/stylesheets/spoiler-alert_33be3dc8682f6a0819c96460049aa59027e7d5f4.css?__ws=virological.org" media="all" rel="stylesheet" data-target="spoiler-alert" /> <link href="/stylesheets/chat_desktop_33be3dc8682f6a0819c96460049aa59027e7d5f4.css?__ws=virological.org" media="all" rel="stylesheet" data-target="chat_desktop" /> <link href="/stylesheets/poll_desktop_33be3dc8682f6a0819c96460049aa59027e7d5f4.css?__ws=virological.org" media="all" rel="stylesheet" data-target="poll_desktop" /> <link href="/stylesheets/desktop_theme_2_ea55fd37c8940e8b1da4dc94924da96f05d2abc8.css?__ws=virological.org" media="all" rel="stylesheet" data-target="desktop_theme" data-theme-id="2" data-theme-name="default"/> <meta id="data-ga-universal-analytics" data-tracking-code="UA-277246-10" data-json="{"cookieDomain":"auto"}" data-auto-link-domains=""> <script async src="https://www.googletagmanager.com/gtag/js?id=UA-277246-10" nonce="yDgYF8TJOG9ke9r809cQhg8fi"></script> <script defer src="/assets/google-universal-analytics-v4-e154af4adb3c483a3aba7f9a7229b8881cdc5cf369290923d965a2ad30163ae8.js" data-discourse-entrypoint="google-universal-analytics-v4" nonce="yDgYF8TJOG9ke9r809cQhg8fi"></script> <link rel="alternate nofollow" type="application/rss+xml" title="RSS feed of 'Early release - 16 new EBOV genomes from Sierra Leone'" href="https://virological.org/t/early-release-16-new-ebov-genomes-from-sierra-leone/33.rss" /> <meta property="og:site_name" content="Virological" /> <meta property="og:type" content="website" /> <meta name="twitter:card" content="summary" /> <meta name="twitter:image" content="https://virological.org/uploads/default/original/1X/7897c4e655617c4b6fe71a98eaa97a38778f0623.png" /> <meta property="og:image" content="https://virological.org/uploads/default/original/1X/7897c4e655617c4b6fe71a98eaa97a38778f0623.png" /> <meta property="og:url" content="https://virological.org/t/early-release-16-new-ebov-genomes-from-sierra-leone/33" /> <meta name="twitter:url" content="https://virological.org/t/early-release-16-new-ebov-genomes-from-sierra-leone/33" /> <meta property="og:title" content="Early release - 16 new EBOV genomes from Sierra Leone" /> <meta name="twitter:title" content="Early release - 16 new EBOV genomes from Sierra Leone" /> <meta property="og:description" content="Update: Please use BioProject link instead since the sequences have all be finalized: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA257197/ As part of our continued collaboration with the Sierra Leone Ministry of Health and Sanitation, Kenema Government Hospital and the VHFC, we recently received a new batch of inactivated EBOV samples from Sierra Leone for sequencing at the Broad Institute. We have now completed another set of 16 EBOV samples and the assembled consensus sequences can be downlo..." /> <meta name="twitter:description" content="Update: Please use BioProject link instead since the sequences have all be finalized: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA257197/ As part of our continued collaboration with the Sierra Leone Ministry of Health and Sanitation, Kenema Government Hospital and the VHFC, we recently received a new batch of inactivated EBOV samples from Sierra Leone for sequencing at the Broad Institute. We have now completed another set of 16 EBOV samples and the assembled consensus sequences can be downlo..." /> <meta property="og:article:section" content="Ebolavirus Epidemic 2014-2016" /> <meta property="og:article:section:color" content="92278F" /> <meta property="article:published_time" content="2014-12-15T18:40:11+00:00" /> <meta property="og:ignore_canonical" content="true" /> </head> <body class="crawler browser-update"> <header> <a href="/"> Virological </a> </header> <div id="main-outlet" class="wrap" role="main"> <div id="topic-title"> <h1> <a href="/t/early-release-16-new-ebov-genomes-from-sierra-leone/33">Early release - 16 new EBOV genomes from Sierra Leone</a> </h1> <div class="topic-category" itemscope itemtype="http://schema.org/BreadcrumbList"> <span itemprop="itemListElement" itemscope itemtype="http://schema.org/ListItem"> <a href="/c/ebolavirus-epidemic-2014/6" class="badge-wrapper bullet" itemprop="item"> <span class='badge-category-bg' style='background-color: #92278F'></span> <span class='badge-category clear-badge'> <span class='category-name' itemprop='name'>Ebolavirus Epidemic 2014-2016</span> </span> </a> <meta itemprop="position" content="1" /> </span> </div> </div> <div itemscope itemtype='http://schema.org/DiscussionForumPosting'> <meta itemprop='headline' content='Early release - 16 new EBOV genomes from Sierra Leone'> <link itemprop='url' href='https://virological.org/t/early-release-16-new-ebov-genomes-from-sierra-leone/33'> <meta itemprop='datePublished' content='2014-12-15T18:40:11Z'> <meta itemprop='articleSection' content='Ebolavirus Epidemic 2014-2016'> <meta itemprop='keywords' content=''> <div itemprop='publisher' itemscope itemtype="http://schema.org/Organization"> <meta itemprop='name' content='Virological'> <div itemprop='logo' itemscope itemtype="http://schema.org/ImageObject"> <meta itemprop='url' content='https://virological.org/uploads/default/original/1X/7897c4e655617c4b6fe71a98eaa97a38778f0623.png'> </div> </div> <div id='post_1' class='topic-body crawler-post'> <div class='crawler-post-meta'> <span class="creator" itemprop="author" itemscope itemtype="http://schema.org/Person"> <a itemprop="url" href='https://virological.org/u/Kristian_Andersen'><span itemprop='name'>Kristian_Andersen</span></a> </span> <link itemprop="mainEntityOfPage" href="https://virological.org/t/early-release-16-new-ebov-genomes-from-sierra-leone/33"> <span class="crawler-post-infos"> <time datetime='2014-12-15T18:40:11Z' class='post-time'> December 15, 2014, 6:40pm </time> <meta itemprop='dateModified' content='2014-12-15T18:40:11Z'> <span itemprop='position'>1</span> </span> </div> <div class='post' itemprop='text'> <p><strong>Update:</strong><br> Please use BioProject link instead since the sequences have all be finalized:<br> <a href="http://www.ncbi.nlm.nih.gov/bioproject/PRJNA257197/" class="onebox" target="_blank">http://www.ncbi.nlm.nih.gov/bioproject/PRJNA257197/</a></p> <p>As part of our continued collaboration with the Sierra Leone Ministry of Health and Sanitation, Kenema Government Hospital and <a href="http://vhfc.org/">the VHFC</a>, we recently received a new batch of inactivated EBOV samples from Sierra Leone for sequencing at the Broad Institute. We have now completed another set of 16 EBOV samples and the assembled consensus sequences can be downloaded here:</p> <p>New link (45 sequences):<br> <a href="http://cl.ly/281I071K3c1V" class="onebox" target="_blank">http://cl.ly/281I071K3c1V</a></p> <p>The sequences were generated by 101bp PE Illumina sequencing using the protocols described in the Gire <em>et al.</em> and Matranga <em>et al.</em> papers. The genomes were assembled using Trinity, followed by an alignment refinement step with NovoAlign. The average bp coverage for this dataset was 362x [17x - 827x].</p> <p>We are in the process of gathering metadata, but at this moment we don’t have any exact dates or other metadate for the individual samples.</p> <p>We are currently in the process of preparing the data for GenBank and SRA submissions. Please note that this is an early release, so accuracy can’t be guaranteed at this stage.</p> <p><strong>Disclaimer:</strong><br> Please feel free to download, share, use, and analyze this data. We are currently in the process of preparing a publication and will post progress on this forum. If you intend to use these sequences for publication prior to the release of our paper, please contact us directly.</p> </div> <div itemprop="interactionStatistic" itemscope itemtype="http://schema.org/InteractionCounter"> <meta itemprop="interactionType" content="http://schema.org/LikeAction"/> <meta itemprop="userInteractionCount" content="0" /> <span class='post-likes'></span> </div> <div itemprop="interactionStatistic" itemscope itemtype="http://schema.org/InteractionCounter"> <meta itemprop="interactionType" content="http://schema.org/CommentAction"/> <meta itemprop="userInteractionCount" content="0" /> </div> </div> <div id='post_2' itemprop='comment' itemscope itemtype='http://schema.org/Comment' class='topic-body crawler-post'> <div class='crawler-post-meta'> <span class="creator" itemprop="author" itemscope itemtype="http://schema.org/Person"> <a itemprop="url" href='https://virological.org/u/Kristian_Andersen'><span itemprop='name'>Kristian_Andersen</span></a> </span> <span class="crawler-post-infos"> <time itemprop='datePublished' datetime='2014-12-15T22:25:19Z' class='post-time'> December 15, 2014, 10:25pm </time> <meta itemprop='dateModified' content='2014-12-15T22:25:19Z'> <span itemprop='position'>2</span> </span> </div> <div class='post' itemprop='text'> <p>Sorry, just to clarify - these 16 sequences are entirely new samples - so together with the previous 21 sequences, we now have 37 additional sequences.</p> </div> <div itemprop="interactionStatistic" itemscope itemtype="http://schema.org/InteractionCounter"> <meta itemprop="interactionType" content="http://schema.org/LikeAction"/> <meta itemprop="userInteractionCount" content="0" /> <span class='post-likes'></span> </div> <div itemprop="interactionStatistic" itemscope itemtype="http://schema.org/InteractionCounter"> <meta itemprop="interactionType" content="http://schema.org/CommentAction"/> <meta itemprop="userInteractionCount" content="0" /> </div> </div> <div id='post_3' itemprop='comment' itemscope itemtype='http://schema.org/Comment' class='topic-body crawler-post'> <div class='crawler-post-meta'> <span class="creator" itemprop="author" itemscope itemtype="http://schema.org/Person"> <a itemprop="url" href='https://virological.org/u/arambaut'><span itemprop='name'>arambaut</span></a> </span> <span class="crawler-post-infos"> <time itemprop='datePublished' datetime='2014-12-15T22:49:55Z' class='post-time'> December 15, 2014, 10:49pm </time> <meta itemprop='dateModified' content='2014-12-15T22:49:55Z'> <span itemprop='position'>3</span> </span> </div> <div class='post' itemprop='text'> <p>A group of them from both the previous set and this new one have some stuff going on at the end:<br> <div class="lightbox-wrapper"><a class="lightbox" href="//virological.org/uploads/default/39/e60de9934e4d79cf.png" title="e60de9934e4d79cf.png"><img src="//virological.org/uploads/default/39/e60de9934e4d79cf.png" width="690" height="224"><div class="meta"><svg class="fa d-icon d-icon-far-image svg-icon" aria-hidden="true"><use xlink:href="#far-image"></use></svg><span class="filename">e60de9934e4d79cf.png</span><span class="informations">826×269</span><svg class="fa d-icon d-icon-discourse-expand svg-icon" aria-hidden="true"><use xlink:href="#discourse-expand"></use></svg></div></a></div></p> </div> <div itemprop="interactionStatistic" itemscope itemtype="http://schema.org/InteractionCounter"> <meta itemprop="interactionType" content="http://schema.org/LikeAction"/> <meta itemprop="userInteractionCount" content="0" /> <span class='post-likes'></span> </div> <div itemprop="interactionStatistic" itemscope itemtype="http://schema.org/InteractionCounter"> <meta itemprop="interactionType" content="http://schema.org/CommentAction"/> <meta itemprop="userInteractionCount" content="1" /> </div> </div> <div id='post_4' itemprop='comment' itemscope itemtype='http://schema.org/Comment' class='topic-body crawler-post'> <div class='crawler-post-meta'> <span class="creator" itemprop="author" itemscope itemtype="http://schema.org/Person"> <a itemprop="url" href='https://virological.org/u/arambaut'><span itemprop='name'>arambaut</span></a> </span> <span class="crawler-post-infos"> <time itemprop='datePublished' datetime='2014-12-15T23:04:09Z' class='post-time'> December 15, 2014, 11:04pm </time> <meta itemprop='dateModified' content='2014-12-15T23:04:09Z'> <span itemprop='position'>4</span> </span> </div> <div class='post' itemprop='text'> <p>One of this new set (G3724) was in the original set from the summer (accession KM233053).</p> </div> <div itemprop="interactionStatistic" itemscope itemtype="http://schema.org/InteractionCounter"> <meta itemprop="interactionType" content="http://schema.org/LikeAction"/> <meta itemprop="userInteractionCount" content="0" /> <span class='post-likes'></span> </div> <div itemprop="interactionStatistic" itemscope itemtype="http://schema.org/InteractionCounter"> <meta itemprop="interactionType" content="http://schema.org/CommentAction"/> <meta itemprop="userInteractionCount" content="1" /> </div> </div> <div id='post_5' itemprop='comment' itemscope itemtype='http://schema.org/Comment' class='topic-body crawler-post'> <div class='crawler-post-meta'> <span class="creator" itemprop="author" itemscope itemtype="http://schema.org/Person"> <a itemprop="url" href='https://virological.org/u/dpark'><span itemprop='name'>dpark</span></a> </span> <span class="crawler-post-infos"> <time itemprop='datePublished' datetime='2014-12-16T00:43:04Z' class='post-time'> December 16, 2014, 12:43am </time> <meta itemprop='dateModified' content='2014-12-16T00:43:04Z'> <span itemprop='position'>5</span> </span> </div> <div class='post' itemprop='text'> <p><a class="mention" href="/u/arambaut">@arambaut</a> - Oh yeah sorry about that. With each batch, we’ve been running an old sample from this summer as a control. Last week when I passed the assemblies to Kristian it was clearly labeled, but this week I forgot to. That’s the exact same sample from this summer, ignore it.</p> </div> <div itemprop="interactionStatistic" itemscope itemtype="http://schema.org/InteractionCounter"> <meta itemprop="interactionType" content="http://schema.org/LikeAction"/> <meta itemprop="userInteractionCount" content="0" /> <span class='post-likes'></span> </div> <div itemprop="interactionStatistic" itemscope itemtype="http://schema.org/InteractionCounter"> <meta itemprop="interactionType" content="http://schema.org/CommentAction"/> <meta itemprop="userInteractionCount" content="0" /> </div> </div> <div id='post_6' itemprop='comment' itemscope itemtype='http://schema.org/Comment' class='topic-body crawler-post'> <div class='crawler-post-meta'> <span class="creator" itemprop="author" itemscope itemtype="http://schema.org/Person"> <a itemprop="url" href='https://virological.org/u/Kristian_Andersen'><span itemprop='name'>Kristian_Andersen</span></a> </span> <span class="crawler-post-infos"> <time itemprop='datePublished' datetime='2014-12-16T03:04:51Z' class='post-time'> December 16, 2014, 3:04am </time> <meta itemprop='dateModified' content='2014-12-16T03:04:51Z'> <span itemprop='position'>6</span> </span> </div> <div class='post' itemprop='text'> <p><a class="mention" href="/u/dpark">@dpark</a>. Any thoughts on the ends? Must be artifacts - I have actually seen this happen before (adapters?), so the reads should probably just be trimmed back. It might be good to check the bams.</p> </div> <div itemprop="interactionStatistic" itemscope itemtype="http://schema.org/InteractionCounter"> <meta itemprop="interactionType" content="http://schema.org/LikeAction"/> <meta itemprop="userInteractionCount" content="0" /> <span class='post-likes'></span> </div> <div itemprop="interactionStatistic" itemscope itemtype="http://schema.org/InteractionCounter"> <meta itemprop="interactionType" content="http://schema.org/CommentAction"/> <meta itemprop="userInteractionCount" content="0" /> </div> </div> <div id='post_7' itemprop='comment' itemscope itemtype='http://schema.org/Comment' class='topic-body crawler-post'> <div class='crawler-post-meta'> <span class="creator" itemprop="author" itemscope itemtype="http://schema.org/Person"> <a itemprop="url" href='https://virological.org/u/arambaut'><span itemprop='name'>arambaut</span></a> </span> <span class="crawler-post-infos"> <time itemprop='datePublished' datetime='2014-12-16T14:54:39Z' class='post-time'> December 16, 2014, 2:54pm </time> <meta itemprop='dateModified' content='2014-12-16T14:54:39Z'> <span itemprop='position'>7</span> </span> </div> <div class='post' itemprop='text'> <p>Here is a tree (with all available genomes) and a root-to-tip divergence plot for those with known dates. The new Sierra Leone genomes are in dark blue. The end bits mentioned above were trimmed out of the alignment.<br> <div class="lightbox-wrapper"><a class="lightbox" href="//virological.org/uploads/default/41/38d2f54686f50e4e.png" title="38d2f54686f50e4e.png"><img src="//virological.org/uploads/default/41/38d2f54686f50e4e.png" width="483" height="500"><div class="meta"><svg class="fa d-icon d-icon-far-image svg-icon" aria-hidden="true"><use xlink:href="#far-image"></use></svg><span class="filename">38d2f54686f50e4e.png</span><span class="informations">1280×1325</span><svg class="fa d-icon d-icon-discourse-expand svg-icon" aria-hidden="true"><use xlink:href="#discourse-expand"></use></svg></div></a></div><br> $$slope=1.24{\times 10^{-3}}$$</p> <p>As an estimate of evolutionary rate, this is slower than the estimate in the <a href="http://www.sciencemag.org/content/345/6202/1369.full">Gire et al paper</a> but still within the credible intervals of that estimate. This may be because the elevating effect of transient deleterious mutations is being diluted out as the data spans a greater time interval. This is now much closer to the long term rate of evolution estimated over 38 years of EBOV outbreaks in <a href="http://currents.plos.org/outbreaks/article/phylogenetic-analysis-of-guinea-2014-ebov-ebolavirus-outbreak-2/">Dudas and Rambaut, 2014</a> & <a href="http://jvi.asm.org/content/87/5/2608.long">Carroll et al 2012</a>.</p> </div> <div itemprop="interactionStatistic" itemscope itemtype="http://schema.org/InteractionCounter"> <meta itemprop="interactionType" content="http://schema.org/LikeAction"/> <meta itemprop="userInteractionCount" content="0" /> <span class='post-likes'></span> </div> <div itemprop="interactionStatistic" itemscope itemtype="http://schema.org/InteractionCounter"> <meta itemprop="interactionType" content="http://schema.org/CommentAction"/> <meta itemprop="userInteractionCount" content="1" /> </div> </div> <div id='post_8' itemprop='comment' itemscope itemtype='http://schema.org/Comment' class='topic-body crawler-post'> <div class='crawler-post-meta'> <span class="creator" itemprop="author" itemscope itemtype="http://schema.org/Person"> <a itemprop="url" href='https://virological.org/u/dpark'><span itemprop='name'>dpark</span></a> </span> <span class="crawler-post-infos"> <time itemprop='datePublished' datetime='2014-12-16T17:42:24Z' class='post-time'> December 16, 2014, 5:42pm </time> <meta itemprop='dateModified' content='2014-12-16T17:42:24Z'> <span itemprop='position'>8</span> </span> </div> <div class='post' itemprop='text'> <p><a class="mention" href="/u/arambaut">@arambaut</a> - so there are two explanations for a slower substitution rate: one is that we’re seeing more purifying selection bringing the rate further down from the baseline mutation rate. The other is that we’re just getting better estimates now because our denominator (the time spanned by our data) is larger. Thoughts? Maybe both?</p> <p>Also, regarding the funny SNPs on the end, they’re definitely technical artifacts and I’m tuning the knobs a bit on our assembly refinement parameters to clean that up before submitting to Genbank. This is what we mean by preliminary! Turns out that those assemblies happen to end in the middle of a semi-palindromic section of sequence, and the “SNPs” are actually coming from the other side of the palindrome (so they end up having great read support, but they’re still not real).</p> </div> <div itemprop="interactionStatistic" itemscope itemtype="http://schema.org/InteractionCounter"> <meta itemprop="interactionType" content="http://schema.org/LikeAction"/> <meta itemprop="userInteractionCount" content="0" /> <span class='post-likes'></span> </div> <div itemprop="interactionStatistic" itemscope itemtype="http://schema.org/InteractionCounter"> <meta itemprop="interactionType" content="http://schema.org/CommentAction"/> <meta itemprop="userInteractionCount" content="1" /> </div> </div> <div id='post_9' itemprop='comment' itemscope itemtype='http://schema.org/Comment' class='topic-body crawler-post'> <div class='crawler-post-meta'> <span class="creator" itemprop="author" itemscope itemtype="http://schema.org/Person"> <a itemprop="url" href='https://virological.org/u/arambaut'><span itemprop='name'>arambaut</span></a> </span> <span class="crawler-post-infos"> <time itemprop='datePublished' datetime='2014-12-17T16:43:01Z' class='post-time'> December 17, 2014, 4:43pm </time> <meta itemprop='dateModified' content='2014-12-17T16:43:01Z'> <span itemprop='position'>9</span> </span> </div> <div class='post' itemprop='text'> <p>I suspect a bit of both. We did see elevated dN/dS rates in the June data and if it were the former then we would predict this would be dropping as the rate drops. Here is a BEAST density for the new rate compared with the long-term and the June data:<br> <div class="lightbox-wrapper"><a class="lightbox" href="//virological.org/uploads/default/42/cef6d174eb1bed32.png" title="cef6d174eb1bed32.png"><img src="//virological.org/uploads/default/42/cef6d174eb1bed32.png" width="500" height="500"><div class="meta"><svg class="fa d-icon d-icon-far-image svg-icon" aria-hidden="true"><use xlink:href="#far-image"></use></svg><span class="filename">cef6d174eb1bed32.png</span><span class="informations">1500×1500</span><svg class="fa d-icon d-icon-discourse-expand svg-icon" aria-hidden="true"><use xlink:href="#discourse-expand"></use></svg></div></a></div><br> The ZEBOV and the October analyses are done with a relaxed clock, the June 2014 with a strict clock.</p> </div> <div itemprop="interactionStatistic" itemscope itemtype="http://schema.org/InteractionCounter"> <meta itemprop="interactionType" content="http://schema.org/LikeAction"/> <meta itemprop="userInteractionCount" content="0" /> <span class='post-likes'></span> </div> <div itemprop="interactionStatistic" itemscope itemtype="http://schema.org/InteractionCounter"> <meta itemprop="interactionType" content="http://schema.org/CommentAction"/> <meta itemprop="userInteractionCount" content="0" /> </div> </div> </div> </div> <footer class="container wrap"> <nav class='crawler-nav'> <ul> <li itemscope itemtype='http://schema.org/SiteNavigationElement'> <span itemprop='name'> <a href='/' itemprop="url">Home </a> </span> </li> <li itemscope itemtype='http://schema.org/SiteNavigationElement'> <span itemprop='name'> <a href='/categories' itemprop="url">Categories </a> </span> </li> <li itemscope itemtype='http://schema.org/SiteNavigationElement'> <span itemprop='name'> <a href='/guidelines' itemprop="url">FAQ/Guidelines </a> </span> </li> <li itemscope itemtype='http://schema.org/SiteNavigationElement'> <span itemprop='name'> <a href='/tos' itemprop="url">Terms of Service </a> </span> </li> <li itemscope itemtype='http://schema.org/SiteNavigationElement'> <span itemprop='name'> <a href='/privacy' itemprop="url">Privacy Policy </a> </span> </li> </ul> </nav> <p class='powered-by-link'>Powered by <a href="https://www.discourse.org">Discourse</a>, best viewed with JavaScript enabled</p> </footer> <div class="buorg"><div>Unfortunately, <a href="https://www.discourse.org/faq/#browser">your browser is unsupported</a>. 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