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Preliminary analysis of full genome sequences of 58 MPXV clade Ib cases from Kamituga and Kamanyola, South-Kivu , DRC - Evolution - Virological
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We sequenced MPX..." /> <meta property="og:article:section" content="MPXV" /> <meta property="og:article:section:color" content="0088CC" /> <meta property="og:article:section" content="Evolution" /> <meta property="og:article:section:color" content="12A89D" /> <meta name="twitter:label1" value="Reading time" /> <meta name="twitter:data1" value="1 mins 🕑" /> <meta name="twitter:label2" value="Likes" /> <meta name="twitter:data2" value="1 ❤" /> <meta property="article:published_time" content="2024-08-05T12:11:10+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/preliminary-analysis-of-full-genome-sequences-of-58-mpxv-clade-ib-cases-from-kamituga-and-kamanyola-south-kivu-drc/975">Preliminary analysis of full genome sequences of 58 MPXV clade Ib cases from Kamituga and Kamanyola, South-Kivu , DRC</a> </h1> <div class="topic-category" itemscope itemtype="http://schema.org/BreadcrumbList"> <span itemprop="itemListElement" itemscope itemtype="http://schema.org/ListItem"> <a href="/c/mpxv/evolution/48" class="badge-wrapper bullet" itemprop="item"> <span class='badge-category-bg' style='background-color: #0088CC'></span> <span class='badge-category clear-badge'> <span class='category-name' itemprop='name'>MPXV</span> </span> </a> <meta itemprop="position" content="1" /> </span> <span itemprop="itemListElement" itemscope itemtype="http://schema.org/ListItem"> <a href="/c/mpxv/evolution/48" class="badge-wrapper bullet" itemprop="item"> <span class='badge-category-bg' style='background-color: #12A89D'></span> <span class='badge-category clear-badge'> <span class='category-name' itemprop='name'>Evolution</span> </span> </a> <meta itemprop="position" content="2" /> </span> </div> </div> <div itemscope itemtype='http://schema.org/DiscussionForumPosting'> <meta itemprop='headline' content='Preliminary analysis of full genome sequences of 58 MPXV clade Ib cases from Kamituga and Kamanyola, South-Kivu , DRC'> <link itemprop='url' href='https://virological.org/t/preliminary-analysis-of-full-genome-sequences-of-58-mpxv-clade-ib-cases-from-kamituga-and-kamanyola-south-kivu-drc/975'> <meta itemprop='datePublished' content='2024-08-05T12:11:10Z'> <meta itemprop='articleSection' content='Evolution'> <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/b.oudemunnink'><span itemprop='name'>b.oudemunnink</span></a> </span> <link itemprop="mainEntityOfPage" href="https://virological.org/t/preliminary-analysis-of-full-genome-sequences-of-58-mpxv-clade-ib-cases-from-kamituga-and-kamanyola-south-kivu-drc/975"> <link itemprop="image" href="https://virological.org/uploads/default/original/2X/8/84d4bf861ac03ece0f346644934255ee547c194f.png"> <span class="crawler-post-infos"> <time datetime='2024-08-05T12:11:10Z' class='post-time'> August 5, 2024, 12:11pm </time> <meta itemprop='dateModified' content='2024-08-05T12:11:10Z'> <span itemprop='position'>1</span> </span> </div> <div class='post' itemprop='text'> <p><strong>Preliminary analysis of full genome sequences of 58 MPXV clade Ib cases from Kamituga and Kamanyola, South-Kivu , DRC</strong></p> <p>Recently, we showed that the MPXV outbreak in South Kivu is associated with a novel sub- lineage of clade I viruses (Murhula Masirika et al, 2024). The majority of these cases seem to be transmitted through heterosexual contact, with also person-to-person transmission within and outside the households. Here we provide an update of the ongoing sequencing effort. We sequenced MPXV genomes from samples during the current outbreak collected between October 2023 and May 2024. All samples were collected within a study protocol with ethics approval and informed consent in place.</p> <p>58 complete, or nearly complete, whole genome sequences were generated. Phylogenetic analysis and inspection of the mutation patterns revealed three potential clusters and two potential subclusters consisting of sequences of different collection dates including April/May 2024, suggesting several different and ongoing transmission chains. Research efforts are ongoing to link the genomic data with epidemiological metadata (<a href="https://www.medrxiv.org/content/10.1101/2024.05.10.24307057v1" rel="noopener nofollow ugc">https://www.medrxiv.org/content/10.1101/2024.05.10.24307057v1</a>).</p> <p>During the course of this MPXV outbreak we observe an accumulation of APOBEC3 mutations indicative of human-to-human transmission. Most APOBEC3 mutations were observed in cluster A, that includes the two sequences from cases from Kamanyola, bordering Rwanda. These two cases are not directly linked to each other and show up to 10 unique mutations, suggestion considerable transmission prior to their detection.</p> <p><div class="lightbox-wrapper"><a class="lightbox" href="https://virological.org/uploads/default/original/2X/8/84d4bf861ac03ece0f346644934255ee547c194f.png" data-download-href="https://virological.org/uploads/default/84d4bf861ac03ece0f346644934255ee547c194f" title="Picture 1"><img src="https://virological.org/uploads/default/optimized/2X/8/84d4bf861ac03ece0f346644934255ee547c194f_2_600x500.png" alt="Picture 1" data-base62-sha1="iX4PSZCV7APOIGUBj2qI9ooSjsH" width="600" height="500" srcset="https://virological.org/uploads/default/optimized/2X/8/84d4bf861ac03ece0f346644934255ee547c194f_2_600x500.png, https://virological.org/uploads/default/optimized/2X/8/84d4bf861ac03ece0f346644934255ee547c194f_2_900x750.png 1.5x, https://virological.org/uploads/default/original/2X/8/84d4bf861ac03ece0f346644934255ee547c194f.png 2x" data-dominant-color="ECECEC"><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">Picture 1</span><span class="informations">941×783 405 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>Figure 1: Zoom-in of phylogenetic tree specific for the currently shared and newly sequenced clade Ib sequences. Left panel shows the phylogenetic tree with colored tips indicating health area of originating patient. Proposed clusters are shown by shading and annotated by markings on the right side of the tree. Middle panel shows linking mutations, present in two or more cases. Right panel shows unique mutations. Differences from the majority rule consensus are highlighted in color. Mutations with characteristic APOBEC3 signature are marked with a black box. Positions that were masked by manual curation or due to too little coverage are indicated with “N”. Ambiguous nucleotides are marked in purple.</p> <p>Contacts:<br> For more information on the ongoing studies, sequences and data analysis, please contact Leandre Murhula Masirika <a href="/cdn-cgi/l/email-protection#c0aca5a1aea4b2a5adb5b2a8b5aca180a7ada1a9aceea3afad"><span class="__cf_email__" data-cfemail="a2cec7c3ccc6d0c7cfd7d0cad7cec3e2c5cfc3cbce8cc1cdcf">[email protected]</span></a> , Bas Oude Munnink <a href="/cdn-cgi/l/email-protection" class="__cf_email__" data-cfemail="05672b6a70616068706b6b6c6b6e456077647668707668662b6b69">[email protected]</a> and Marion Koopmans <a href="/cdn-cgi/l/email-protection" class="__cf_email__" data-cfemail="34591a5f5b5b4459555a47745146554759414759571a5a58">[email protected]</a></p> <p>Authors and Funding:<br> Sequencing and data analysis were made possible by funding provided by the GREAT-LIFE consortium and South-Kivu government public health team supporting data collection.</p> <p>The following individuals are involved in this work:</p> <p>DRC: Leandre Murhula Masirika, Justin Bengehya Mbiribindi, Freddy Belesi Siangoli<br> Rwanda : Pacifique Ndishimye, Jean Claude Udahemuka, Jean Pierre Musabyimana<br> Denmark: Frank M. Aarestrup<br> Netherlands: David F. Nieuwenhuijse, Leonard Schuele, Marjan Boter, Bas B. Oude Munnink, Marion Koopmans<br> United Kingdom: Trudie Lang</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/arambaut'><span itemprop='name'>arambaut</span></a> </span> <span class="crawler-post-infos"> <time itemprop='datePublished' datetime='2024-08-09T10:04:38Z' class='post-time'> August 9, 2024, 10:04am </time> <meta itemprop='dateModified' content='2024-08-09T10:04:38Z'> <span itemprop='position'>2</span> </span> </div> <div class='post' itemprop='text'> <p>Hi Bas & Leandre,</p> <p>Great to see this. One recommendation for the tree - use the <code>-czb</code> option in IQTree2 to collapse the very short branches (that are actually zero mutations). It cleans up the tree for the interpretation.</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> </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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