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DRC-2018-Viral Genome Characterization - Ebolavirus - Virological
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content="https://virological.org/t/drc-2018-viral-genome-characterization/230" /> <meta property="og:title" content="DRC-2018-Viral Genome Characterization" /> <meta name="twitter:title" content="DRC-2018-Viral Genome Characterization" /> <meta property="og:description" content="Dear all, I am sharing the linked statement on the name of Prof. Steve Ahuka-Mundeke, from INRB on the characterization of the ebolavirus genomes causing the outbreaks in the Democratic Republic of Congo. Thanks, -Gustavo Palacios Director, Center for Genome Sciences, USAMRIID -Prof. Steve Ahuka-Mundeke (amstev04@yahoo.fr) INRB, School of Medicine Kinshasa University https://drive.google.com/open?id=1Ih02T5z1cpqEgsBUsLtOIQhuEeb2Yh5Y INRB Statement From May 8th to July 25th, 2018, the De..." /> <meta name="twitter:description" content="Dear all, I am sharing the linked statement on the name of Prof. Steve Ahuka-Mundeke, from INRB on the characterization of the ebolavirus genomes causing the outbreaks in the Democratic Republic of Congo. Thanks, -Gustavo Palacios Director, Center for Genome Sciences, USAMRIID -Prof. Steve Ahuka-Mundeke (amstev04@yahoo.fr) INRB, School of Medicine Kinshasa University https://drive.google.com/open?id=1Ih02T5z1cpqEgsBUsLtOIQhuEeb2Yh5Y INRB Statement From May 8th to July 25th, 2018, the De..." /> <meta property="og:article:section" content="Ebolavirus" /> <meta property="og:article:section:color" content="0E76BD" /> <meta name="twitter:label1" value="Reading time" /> <meta name="twitter:data1" value="3 mins 🕑" /> <meta name="twitter:label2" value="Likes" /> <meta name="twitter:data2" value="2 ❤" /> <meta property="article:published_time" content="2018-08-10T03:01:47+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/drc-2018-viral-genome-characterization/230">DRC-2018-Viral Genome Characterization</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/9" class="badge-wrapper bullet" itemprop="item"> <span class='badge-category-bg' style='background-color: #0E76BD'></span> <span class='badge-category clear-badge'> <span class='category-name' itemprop='name'>Ebolavirus</span> </span> </a> <meta itemprop="position" content="1" /> </span> </div> </div> <div itemscope itemtype='http://schema.org/DiscussionForumPosting'> <meta itemprop='headline' content='DRC-2018-Viral Genome Characterization'> <link itemprop='url' href='https://virological.org/t/drc-2018-viral-genome-characterization/230'> <meta itemprop='datePublished' content='2018-08-10T03:01:47Z'> <meta itemprop='articleSection' content='Ebolavirus'> <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/gustavo_palacios'><span itemprop='name'>gustavo_palacios</span></a> </span> <link itemprop="mainEntityOfPage" href="https://virological.org/t/drc-2018-viral-genome-characterization/230"> <link itemprop="image" href="https://virological.org/uploads/default/original/1X/b884c4563fef52fa51199b5c6d205f4bdff555f8.png"> <span class="crawler-post-infos"> <time datetime='2018-08-10T03:01:47Z' class='post-time'> August 10, 2018, 3:01am </time> <meta itemprop='dateModified' content='2018-08-14T19:44:00Z'> <span itemprop='position'>1</span> </span> </div> <div class='post' itemprop='text'> <p>Dear all,<br> I am sharing the linked statement on the name of Prof. Steve Ahuka-Mundeke, from INRB on the characterization of the ebolavirus genomes causing the outbreaks in the Democratic Republic of Congo.<br> Thanks,</p> <p>-Gustavo Palacios<br> Director, Center for Genome Sciences, USAMRIID</p> <p>-Prof. Steve Ahuka-Mundeke (<a href="/cdn-cgi/l/email-protection#cfaea2bcbbaab9fffb8fb6aea7a0a0e1a9bd"><span class="__cf_email__" data-cfemail="7f1e120c0b1a094f4b3f061e17101051190d">[email protected]</span></a>)<br> INRB, School of Medicine Kinshasa University</p> <p><a href="https://drive.google.com/open?id=1Ih02T5z1cpqEgsBUsLtOIQhuEeb2Yh5Y" class="onebox" target="_blank" rel="noopener">https://drive.google.com/open?id=1Ih02T5z1cpqEgsBUsLtOIQhuEeb2Yh5Y</a></p> <h1> <a name="inrb-statement-1" class="anchor" href="#inrb-statement-1"></a>INRB Statement</h1> <p>From May 8th to July 25th, 2018, the Democratic Republic of the Congo faced its ninth Ebola<br> outbreak, which affected 54 people, including 33 deaths in the health zones of Bikoro, Iboko and<br> Wangata, in the Province of Equateur. Institut National de Recherche Biomedicale (INRB), in<br> collaboration with its partners, deployed 3 mobile laboratories on the 3 affected sites (Mbandaka,<br> Bikoro and Itipo) to contribute quickly and efficiently to control this epidemic. A total of 432 samples were collected from these 3 laboratories, of which 51 were positive in real-time RT-PCR. These came from the 38 confirmed cases for the whole period of the epidemic (8 May- 25 July 2018). On<br> July 10th, samples from the mobile laboratories arrived at INRB, and processing of samples and<br> sequencing began. Thus far 23 samples have been processed yielding 15 coding-complete<br> genomes that will be released shortly on GenBank as well. Initial phylogenetic analysis indicates<br> these genomes are closest to the 2014 DRC outbreak (Figure 1, blue labels). Further analysis will<br> need to be conducted on these preliminary findings as the main focus is to finish processing<br> available samples from the outbreak, which will be made available as soon as they are generated.<br> Unfortunately, on August 1st a new cluster of cases was discovered in the region of North<br> Kivu and confirmed at INRB. Samples were prepared for sequencing at INRB. Two full genome<br> sequences were obtained (Figure 1, red labels).</p> <p><strong>Figure 1</strong><br> <div class="lightbox-wrapper"><a class="lightbox" href="https://virological.org/uploads/default/original/1X/b884c4563fef52fa51199b5c6d205f4bdff555f8.png" data-download-href="https://virological.org/uploads/default/b884c4563fef52fa51199b5c6d205f4bdff555f8" title="INRB%20tree"><img src="https://virological.org/uploads/default/optimized/1X/b884c4563fef52fa51199b5c6d205f4bdff555f8_2_499x499.png" alt="INRB%20tree" data-base62-sha1="qkkiZSWbeFj3npGf2hfqE8QcDPy" width="499" height="499" srcset="https://virological.org/uploads/default/optimized/1X/b884c4563fef52fa51199b5c6d205f4bdff555f8_2_499x499.png, https://virological.org/uploads/default/optimized/1X/b884c4563fef52fa51199b5c6d205f4bdff555f8_2_748x748.png 1.5x, https://virological.org/uploads/default/optimized/1X/b884c4563fef52fa51199b5c6d205f4bdff555f8_2_998x998.png 2x" data-dominant-color="EEEEF1"><div class="meta"> <svg class="fa d-icon d-icon-far-image svg-icon" aria-hidden="true"><use href="#far-image"></use></svg><span class="filename">INRB%20tree</span><span class="informations">1950×1950 373 KB</span><svg class="fa d-icon d-icon-discourse-expand svg-icon" aria-hidden="true"><use href="#discourse-expand"></use></svg> </div></a></div></p> <p>The data confirms that the current EVD cases in Nord Kivu (July 30th and ongoing), DRC are caused by a distinct EBOV “strain” than the one causing the outbreak in Equateur province. Based on this findings, although both events are caused by the same ebolavirus species (EBOV), the outbreaks appear not to be connected. On that basis, the available vaccine should work against the new strain.</p> <h2> <a name="partners-and-collaborators-2" class="anchor" href="#partners-and-collaborators-2"></a>Partners and collaborators</h2> <p>This work is part of ongoing research collaborations between several partners:<br> Institut National de Recherche Biomédicale (INRB)<br> US Army Medical Research Institute of Infectious Diseases (USAMRIID)<br> Institut Pasteur de Dakar, Dakar, Senegal (IPD)<br> TransVIHMI (IRD, INSERM, University of Montpellier)</p> <h3> <a name="data-availability-3" class="anchor" href="#data-availability-3"></a>Data availability</h3> <p>Genome sequences for all samples had been shared with all local and international partners working in the DRC. The information reported here is being shared pre-publication to help the research and public health communities respond to the current Ebola virus disease outbreak. Please note though that this data is still based on work in progress and should be considered preliminary. Our analysis of this data is ongoing and a publication communicating our findings is in preparation. INRB will distribute these data to any entity or collaborator that needs it. Please communicate with Drs. Muyembe-Tamfum and Ahuka for further coordination.</p> <p>Prof. Jean-Jacques Muyembe Tamfum (INRB, School of Medicine Kinshasa University)<br> Prof. Steve Ahuka-Mundeke (INRB, School of Medicine Kinshasa University)<br> Dr. Gustavo Palacios (USAMRIID)<br> Dr. Michael Wiley (USAMRIID)<br> Dr. Amadou Sall (Institut Pasteur de Dakar, Dakar, Senegal)<br> Dr. Ousmane Faye (Institut Pasteur de Dakar, Dakar, Senegal)<br> Prof. Eric Delaporte (TransVIHMI (IRD, INSERM, University of Montpellier)<br> Dr. Martine Peeters (TransVIHMI (IRD, INSERM, University of Montpellier)</p> <p>Avenue de la Démocratie N°5345 – Kin/Gombe – B.P. 1197 – KINSHASA 1 – Tél. 898949 289 – 9913614 - 99 23123 – 081 5144285 E-mail : <a href="/cdn-cgi/l/email-protection#21484f5343534542615840494e4e0f4753"><span class="__cf_email__" data-cfemail="4b22253929392f280b322a232424652d39">[email protected]</span></a>, Site web : www.inrb.cd</p> </div> <div itemprop="interactionStatistic" itemscope itemtype="http://schema.org/InteractionCounter"> <meta itemprop="interactionType" content="http://schema.org/LikeAction"/> <meta itemprop="userInteractionCount" content="1" /> <span class='post-likes'>1 Like</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='2018-08-10T05:48:34Z' class='post-time'> August 10, 2018, 5:48am </time> <meta itemprop='dateModified' content='2018-08-10T05:48:34Z'> <span itemprop='position'>2</span> </span> </div> <div class='post' itemprop='text'> <p>Thanks Gus - very helpful and we’re starting to see some interesting clustering of the EBOV tree! Looking forward to seeing the data and manuscripts.</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='2018-08-10T17:28:35Z' class='post-time'> August 10, 2018, 5:28pm </time> <meta itemprop='dateModified' content='2018-08-10T17:28:35Z'> <span itemprop='position'>3</span> </span> </div> <div class='post' itemprop='text'> <p>Very interesting to see this. It would certainly seem that there are multiple co-circulating lineages in the non-human hosts. It is interesting that this all goes back to a single clade in 1976-1977. I wonder if perhaps habitat fragmentation of the reservoir has produced divergent lineages?</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/d.gatherer'><span itemprop='name'>d.gatherer</span></a> </span> <link itemprop="image" href="https://virological.org/uploads/default/original/1X/8e83956de4024106241ad531a755b5c6ab56d8e8.jpg"> <span class="crawler-post-infos"> <time itemprop='datePublished' datetime='2018-08-14T06:37:43Z' class='post-time'> August 14, 2018, 6:37am </time> <meta itemprop='dateModified' content='2018-08-14T06:37:43Z'> <span itemprop='position'>4</span> </span> </div> <div class='post' itemprop='text'> <p><div class="lightbox-wrapper"><a class="lightbox" href="https://virological.org/uploads/default/original/1X/8e83956de4024106241ad531a755b5c6ab56d8e8.jpg" data-download-href="https://virological.org/uploads/default/8e83956de4024106241ad531a755b5c6ab56d8e8" title="image"><img src="https://virological.org/uploads/default/optimized/1X/8e83956de4024106241ad531a755b5c6ab56d8e8_2_690x388.jpg" alt="image" data-base62-sha1="kkJIurIeKnYJv7OsKawSsn8XqE8" width="690" height="388" srcset="https://virological.org/uploads/default/optimized/1X/8e83956de4024106241ad531a755b5c6ab56d8e8_2_690x388.jpg, https://virological.org/uploads/default/optimized/1X/8e83956de4024106241ad531a755b5c6ab56d8e8_2_1035x582.jpg 1.5x, https://virological.org/uploads/default/original/1X/8e83956de4024106241ad531a755b5c6ab56d8e8.jpg 2x" data-dominant-color="E3EFE7"><div class="meta"> <svg class="fa d-icon d-icon-far-image svg-icon" aria-hidden="true"><use href="#far-image"></use></svg><span class="filename">image</span><span class="informations">1200×675 133 KB</span><svg class="fa d-icon d-icon-discourse-expand svg-icon" aria-hidden="true"><use href="#discourse-expand"></use></svg> </div></a></div></p> <p>Yes, reservoir habitat fragmentation - one east, one west, one central</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_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/arambaut'><span itemprop='name'>arambaut</span></a> </span> <span class="crawler-post-infos"> <time itemprop='datePublished' datetime='2018-08-14T19:59:28Z' class='post-time'> August 14, 2018, 7:59pm </time> <meta itemprop='dateModified' content='2018-08-14T19:59:28Z'> <span itemprop='position'>5</span> </span> </div> <div class='post' itemprop='text'> <p>Also evident is the apparently reduced rate of evolution in the lineages leading to the DRC outbreaks in 2014, 2017 and 2018 as first described for the 2014 by Tommy Lam, Eddie Holmes & Yi Guan in <a href="http://jvi.asm.org/content/early/2015/07/16/JVI.01226-15">http://jvi.asm.org/content/early/2015/07/16/JVI.01226-15</a> . It would seem now that just two ‘latency’ periods are need parsimoniously, one in the branch leading to the MRCA of Boende-Lokolia/2014 and Bikoro/2018 and another in the branch leading to MRCA of Likati/2017 and Mangina/2018.</p> <p>Could this be a form of latency in the non-human animal host, related to that seen in survivors in West Africa (i.e., <a href="http://advances.sciencemag.org/content/2/4/e1600378">http://advances.sciencemag.org/content/2/4/e1600378</a>, <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5189159/">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5189159/</a>)?</p> </div> <div itemprop="interactionStatistic" itemscope itemtype="http://schema.org/InteractionCounter"> <meta itemprop="interactionType" content="http://schema.org/LikeAction"/> <meta itemprop="userInteractionCount" content="1" /> <span class='post-likes'>1 Like</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/VincentMunster'><span itemprop='name'>VincentMunster</span></a> </span> <span class="crawler-post-infos"> <time itemprop='datePublished' datetime='2018-08-20T22:20:22Z' class='post-time'> August 20, 2018, 10:20pm </time> <meta itemprop='dateModified' content='2018-08-20T22:20:22Z'> <span itemprop='position'>6</span> </span> </div> <div class='post' itemprop='text'> <p>I don’t think this is habitat fragmentation per se, but more loosely connected populations of the host reservoir. We are currently working on some satellite telemetry studies to understand more of the spatial movements of bats in Congo. Rather than habitat fragmentation, it looks like there are more sub populations of hosts (of the same species) and this would drive the evolution of slightly different lineages of EBOV. It would be of interest to see if we can merge some host (and pathogen) ecology with some of the photodynamic analyses.</p> <p>to an more extreme extend, you see similar dynamics with avian influenza, where separation of the same species on two different continents (mallards) drives the evolution of different lineages of H7 and H7 viruses.</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/m_wiley'><span itemprop='name'>m_wiley</span></a> </span> <span class="crawler-post-infos"> <time itemprop='datePublished' datetime='2018-10-22T19:22:58Z' class='post-time'> October 22, 2018, 7:22pm </time> <meta itemprop='dateModified' content='2018-10-23T00:43:24Z'> <span itemprop='position'>7</span> </span> </div> <div class='post' itemprop='text'> <p>We just released 32 sequences from the Bikoro and Beni outbreak on GenBank that we are calling, Tumba and Ituri, respectively. Publications are hopefully not too far behind. I attached a link to download the sequences as it might take a few days for them to show up on GenBank. Enjoy</p> <p><strong>Data availability</strong><br> Genome sequences for all samples are available here: <a href="https://drive.google.com/open?id=1_1c3lIukzMFXwiAdVv_nd1_7UGzGzZ9M" rel="nofollow noopener">https://drive.google.com/open?id=1_1c3lIukzMFXwiAdVv_nd1_7UGzGzZ9M</a></p> <p><strong>Partners and collaborators</strong><br> This work is part of ongoing research collaborations between several partners:<br> Prof. Jean-Jacques Muyembe Tamfum (INRB, School of Medicine Kinshasa University)<br> Prof. Steve Ahuka-Mundeke (INRB, School of Medicine Kinshasa University)<br> Dr. Gustavo Palacios (USAMRIID)<br> Dr. Michael Wiley (USAMRIID)<br> Dr. Amadou Sall (Institut Pasteur de Dakar, Dakar, Senegal)<br> Dr. Ousmane Faye (Institut Pasteur de Dakar, Dakar, Senegal)<br> Prof. Eric Delaporte (TransVIHMI (IRD, INSERM, University of Montpellier)<br> Dr. Martine Peeters (TransVIHMI (IRD, INSERM, University of Montpellier)</p> <p><strong>Statement on continuing work and analyses prior to publication</strong><br> These genomes are being shared pre-publication. Please note though that this data is still based on work in progress and should be considered preliminary. Our analyses of this data is ongoing and a publication communicating our findings on these and other published genomes is in preparation. If you intend to use these sequences prior to our publication, please communicate with Drs. Muyembe-Tamfum and Ahuka for coordination.</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_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/c_pratt'><span itemprop='name'>c_pratt</span></a> </span> <link itemprop="image" href="https://virological.org/uploads/default/original/1X/bc19a7ac49a3d3c632fe021131675c2e60788f23.png"> <span class="crawler-post-infos"> <time itemprop='datePublished' datetime='2019-01-29T21:58:09Z' class='post-time'> January 29, 2019, 9:58pm </time> <meta itemprop='dateModified' content='2019-01-29T21:58:09Z'> <span itemprop='position'>8</span> </span> </div> <div class='post' itemprop='text'> <p>The Nord-Kivu/Ituri EVD outbreak is continuing in the Democratic Republic of the Congo (DRC). As of 22 January 2019, there have been a total of 713 EVD cases (664 confirmed and 49 probable), including 439 deaths.</p> <p>Following on from our previous release of 16 EBOV/”Ituri” sequences, we now make available an additional 72 sequences, bringing the total to 88. The sequences are available at the link below, and will shortly be released on GenBank:</p> <p><a href="https://drive.google.com/open?id=1_1c3lIukzMFXwiAdVv_nd1_7UGzGzZ9M" class="onebox" target="_blank" rel="noopener nofollow ugc">https://drive.google.com/open?id=1_1c3lIukzMFXwiAdVv_nd1_7UGzGzZ9M</a></p> <p>Please see below for a haplotype network analysis of the sequence data. All data has been shared with the DRC MoH.</p> <p><div class="lightbox-wrapper"><a class="lightbox" href="https://virological.org/uploads/default/original/1X/bc19a7ac49a3d3c632fe021131675c2e60788f23.png" data-download-href="https://virological.org/uploads/default/bc19a7ac49a3d3c632fe021131675c2e60788f23" title="image"><img src="https://virological.org/uploads/default/optimized/1X/bc19a7ac49a3d3c632fe021131675c2e60788f23_2_642x500.png" alt="image" data-base62-sha1="qQ0Jg0fsbPA3JY0ZBRV9TBjL3Ef" width="642" height="500" srcset="https://virological.org/uploads/default/optimized/1X/bc19a7ac49a3d3c632fe021131675c2e60788f23_2_642x500.png, https://virological.org/uploads/default/original/1X/bc19a7ac49a3d3c632fe021131675c2e60788f23.png 1.5x, https://virological.org/uploads/default/original/1X/bc19a7ac49a3d3c632fe021131675c2e60788f23.png 2x" data-dominant-color="F1F0EF"><div class="meta"> <svg class="fa d-icon d-icon-far-image svg-icon" aria-hidden="true"><use href="#far-image"></use></svg><span class="filename">image</span><span class="informations">749×583 68.1 KB</span><svg class="fa d-icon d-icon-discourse-expand svg-icon" aria-hidden="true"><use href="#discourse-expand"></use></svg> </div></a></div></p> <p><strong>Figure 1</strong> . A median-joining haplotype network drawn using POPArt 1,2. Vertices are coloured by health zone as indicated in the key.</p> <p><a class="attachment" href="https://virological.org/uploads/default/original/1X/d9d286ba3108303ae3d87e92db3c97379798e183.pdf">haplotype_network.pdf</a> (186.6 KB)</p> <p><b>Partners and collaborators</b><br> This work is part of ongoing research collaborations between several partners:</p> <p>Prof. Jean-Jacques Muyembe Tamfum (INRB, School of Medicine Kinshasa University)<br> Prof. Steve Ahuka-Mundeke (INRB, School of Medicine Kinshasa University)<br> Dr. Placide Mbala-Kingebeni (INRB, TransVIHMI (IRD, INSERM, University of Montpellier), School of Medicine Kinshasa University)</p> <p>Dr. Gustavo Palacios (USAMRIID)<br> Dr. Michael Wiley (USAMRIID, University of Nebraska Medical Center)<br> Dr. Amadou Sall (Institut Pasteur de Dakar, Dakar, Senegal)<br> Dr. Ousmane Faye (Institut Pasteur de Dakar, Dakar, Senegal)<br> Prof. Eric Delaporte (TransVIHMI (IRD, INSERM, University of Montpellier))<br> Dr. Martine Peeters (TransVIHMI (IRD, INSERM, University of Montpellier))</p> <p><strong>Statement on continuing work and analyses prior to publication</strong><br> These genomes are being shared pre-publication. Please note that this data is based on work in progress and should be considered preliminary. Our analyses of this data is ongoing and a publication communicating our findings on these and other published genomes is in preparation. If you intend to use these sequences prior to our publication, please communicate with Drs. Muyembe-Tamfum and Ahuka for coordination.</p> <p><strong>References</strong></p> <ol> <li> <p>Bandelt, H., Forster, P., & Röhl, A. (1999). Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution, 16(1), 37–48.</p> </li> <li> <p><a href="http://popart.otago.ac.nz" rel="noopener nofollow ugc">http://popart.otago.ac.nz</a></p> </li> </ol> </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='2019-01-30T07:09:17Z' class='post-time'> January 30, 2019, 7:09am </time> <meta itemprop='dateModified' content='2019-01-30T07:09:17Z'> <span itemprop='position'>9</span> </span> </div> <div class='post' itemprop='text'> <p>This is interesting but are there any dates for these sequences? The network doesn’t provide a time-line here which makes it hard to interpret. Would it be possible to post a table of sampling dates for these data?</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_10' 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> <link itemprop="image" href="https://virological.org/uploads/default/original/1X/df3228ba8e8ac6e74f69eb30334b6d7c81438630.jpeg"> <span class="crawler-post-infos"> <time itemprop='datePublished' datetime='2019-01-30T10:51:00Z' class='post-time'> January 30, 2019, 10:51am </time> <meta itemprop='dateModified' content='2019-01-30T18:44:21Z'> <span itemprop='position'>10</span> </span> </div> <div class='post' itemprop='text'> <p>To get an idea of the timescale on this, I crudely highlighted the sequences currently on genbank with their dates (in July & August). By the way, MAN028 (MK007336) seems to be missing from the median-joining tree?</p> <p><div class="lightbox-wrapper"><a class="lightbox" href="https://virological.org/uploads/default/original/1X/df3228ba8e8ac6e74f69eb30334b6d7c81438630.jpeg" data-download-href="https://virological.org/uploads/default/df3228ba8e8ac6e74f69eb30334b6d7c81438630" title="image"><img src="https://virological.org/uploads/default/optimized/1X/df3228ba8e8ac6e74f69eb30334b6d7c81438630_2_656x500.jpeg" alt="image" data-base62-sha1="vQtWmh9rKLZnul1Zc87fAJUsFBm" width="656" height="500" srcset="https://virological.org/uploads/default/optimized/1X/df3228ba8e8ac6e74f69eb30334b6d7c81438630_2_656x500.jpeg, https://virological.org/uploads/default/optimized/1X/df3228ba8e8ac6e74f69eb30334b6d7c81438630_2_984x750.jpeg 1.5x, https://virological.org/uploads/default/optimized/1X/df3228ba8e8ac6e74f69eb30334b6d7c81438630_2_1312x1000.jpeg 2x" data-dominant-color="EFF0F0"><div class="meta"> <svg class="fa d-icon d-icon-far-image svg-icon" aria-hidden="true"><use href="#far-image"></use></svg><span class="filename">image</span><span class="informations">2058×1568 457 KB</span><svg class="fa d-icon d-icon-discourse-expand svg-icon" aria-hidden="true"><use 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_11' 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/c_pratt'><span itemprop='name'>c_pratt</span></a> </span> <link itemprop="image" href="https://virological.org/uploads/default/original/1X/29f4c84e433c3ad40d9a2c89fca5d4c534b8329c.jpeg"> <span class="crawler-post-infos"> <time itemprop='datePublished' datetime='2019-03-01T21:05:25Z' class='post-time'> March 1, 2019, 9:05pm </time> <meta itemprop='dateModified' content='2019-03-01T21:05:25Z'> <span itemprop='position'>11</span> </span> </div> <div class='post' itemprop='text'> <p>The Nord-Kivu/Ituri EVD outbreak is continuing in the Democratic Republic of the Congo (DRC). As of 1st March 2019, there have been a total of 888 EVD cases (823 confirmed and 65 probable), including 555 deaths.</p> <p>Following on from our previous release of 88 EBOV/”Ituri” sequences, we now make available an additional 54 sequences, bringing the total to 142. Please see previous posts for information on partners involved in the sequencing effort and data statement. The sequences are available at the link below, and will shortly be released on GenBank:</p> <p><a href="https://drive.google.com/open?id=1_1c3lIukzMFXwiAdVv_nd1_7UGzGzZ9M" class="onebox" target="_blank" rel="noopener nofollow ugc">https://drive.google.com/open?id=1_1c3lIukzMFXwiAdVv_nd1_7UGzGzZ9M</a></p> <p>Please see below for a haplotype network analysis of the sequence data. A flipbook separating the network by week, to add a time aspect to the analysis, is available at the above link. All data have been shared with the DRC MoH.</p> <p><div class="lightbox-wrapper"><a class="lightbox" href="https://virological.org/uploads/default/original/1X/29f4c84e433c3ad40d9a2c89fca5d4c534b8329c.jpeg" data-download-href="https://virological.org/uploads/default/29f4c84e433c3ad40d9a2c89fca5d4c534b8329c" title="Haplotype_Network_2019-03-01"><img src="https://virological.org/uploads/default/optimized/1X/29f4c84e433c3ad40d9a2c89fca5d4c534b8329c_2_647x500.jpeg" alt="Haplotype_Network_2019-03-01" data-base62-sha1="5Za1fRF9yD4JeQas8nQIxcWMV7C" width="647" height="500" srcset="https://virological.org/uploads/default/optimized/1X/29f4c84e433c3ad40d9a2c89fca5d4c534b8329c_2_647x500.jpeg, https://virological.org/uploads/default/optimized/1X/29f4c84e433c3ad40d9a2c89fca5d4c534b8329c_2_970x750.jpeg 1.5x, https://virological.org/uploads/default/optimized/1X/29f4c84e433c3ad40d9a2c89fca5d4c534b8329c_2_1294x1000.jpeg 2x" data-dominant-color="E6E6E3"><div class="meta"> <svg class="fa d-icon d-icon-far-image svg-icon" aria-hidden="true"><use href="#far-image"></use></svg><span class="filename">Haplotype_Network_2019-03-01</span><span class="informations">2200×1700 397 KB</span><svg class="fa d-icon d-icon-discourse-expand svg-icon" aria-hidden="true"><use href="#discourse-expand"></use></svg> </div></a></div></p> <p><a class="attachment" href="https://virological.org/uploads/default/original/1X/92f51047e097d6b105ab5507cfb8468da073adee.pdf">Haplotype_Network_2019-03-01.pdf</a> (74.0 KB)</p> <p><strong>Figure 1</strong> . A median-joining haplotype network drawn using POPArt. Vertices are coloured by health zone as indicated in the key.</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_12' 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/c_pratt'><span itemprop='name'>c_pratt</span></a> </span> <span class="crawler-post-infos"> <time itemprop='datePublished' datetime='2019-03-01T21:10:40Z' class='post-time'> March 1, 2019, 9:10pm </time> <meta itemprop='dateModified' content='2019-03-01T21:10:40Z'> <span itemprop='position'>12</span> </span> </div> <div class='post' itemprop='text'> <p>MAN028 was initally left out as there was no epi data available for that sample. Since then we have been including the unknowns. We shall include MAN028 in the next update.</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_13' 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/c_pratt'><span itemprop='name'>c_pratt</span></a> </span> <link itemprop="image" href="https://virological.org/uploads/default/original/1X/86b7fbb38a8bf5a3008a0d26c4969c9f37683f3b.png"> <span class="crawler-post-infos"> <time itemprop='datePublished' datetime='2019-05-23T21:01:19Z' class='post-time'> May 23, 2019, 9:01pm </time> <meta itemprop='dateModified' content='2019-05-23T21:01:19Z'> <span itemprop='position'>13</span> </span> </div> <div class='post' itemprop='text'> <p>The Nord-Kivu/Ituri EVD outbreak is continuing, with 1,866 cases (1,778 confirmed and 88 probable) as of 22 May 2019. The latest haplotype network is shown below (sequence IDs from samples > 6 months old removed for clarity). The network consists of 223 genome sequences, which are available at the link below.</p> <p><div class="lightbox-wrapper"><a class="lightbox" href="https://virological.org/uploads/default/original/1X/86b7fbb38a8bf5a3008a0d26c4969c9f37683f3b.png" data-download-href="https://virological.org/uploads/default/86b7fbb38a8bf5a3008a0d26c4969c9f37683f3b" title="image"><img src="https://virological.org/uploads/default/optimized/1X/86b7fbb38a8bf5a3008a0d26c4969c9f37683f3b_2_690x357.png" alt="image" data-base62-sha1="jdMa7w6Q5FRgXSV0A1fRqnMEe4H" width="690" height="357" srcset="https://virological.org/uploads/default/optimized/1X/86b7fbb38a8bf5a3008a0d26c4969c9f37683f3b_2_690x357.png, https://virological.org/uploads/default/optimized/1X/86b7fbb38a8bf5a3008a0d26c4969c9f37683f3b_2_1035x535.png 1.5x, https://virological.org/uploads/default/optimized/1X/86b7fbb38a8bf5a3008a0d26c4969c9f37683f3b_2_1380x714.png 2x" data-dominant-color="F0EEEA"><div class="meta"> <svg class="fa d-icon d-icon-far-image svg-icon" aria-hidden="true"><use href="#far-image"></use></svg><span class="filename">image</span><span class="informations">1745×905 225 KB</span><svg class="fa d-icon d-icon-discourse-expand svg-icon" aria-hidden="true"><use href="#discourse-expand"></use></svg> </div></a></div></p> <p><a class="attachment" href="https://virological.org/uploads/default/original/1X/32cb9c6efb2deb5657ce4d0e5d19be83eb94d68f.pdf">Haplotype_Network_2019-05-02_LabID-v3.pdf</a> (303.8 KB)</p> <p>Sequence data:<br> <a href="https://drive.google.com/drive/folders/1_1c3lIukzMFXwiAdVv_nd1_7UGzGzZ9M" class="inline-onebox" rel="noopener nofollow ugc">DRC_outbreak_sequences - Google Drive</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="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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