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Update to observations about putative APOBEC3 deaminase editing in the light of new genomes from USA - Evolution - Virological
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And another one from USA from 2021 splitting the long branch to the global 2022 lineage.</p> <p><div class="lightbox-wrapper"><a class="lightbox" href="https://virological.org/uploads/default/original/2X/6/67d728910278d18d196bfe0f7a5733e07bfb53f1.png" data-download-href="https://virological.org/uploads/default/67d728910278d18d196bfe0f7a5733e07bfb53f1" title="HPXV_APOBEC_tree"><img src="https://virological.org/uploads/default/optimized/2X/6/67d728910278d18d196bfe0f7a5733e07bfb53f1_2_690x485.png" alt="HPXV_APOBEC_tree" data-base62-sha1="eOC9zgItnbCh7JlhcAnILSo95Yt" width="690" height="485" srcset="https://virological.org/uploads/default/optimized/2X/6/67d728910278d18d196bfe0f7a5733e07bfb53f1_2_690x485.png, https://virological.org/uploads/default/optimized/2X/6/67d728910278d18d196bfe0f7a5733e07bfb53f1_2_1035x727.png 1.5x, https://virological.org/uploads/default/original/2X/6/67d728910278d18d196bfe0f7a5733e07bfb53f1.png 2x" data-dominant-color="F6F6F7"><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">HPXV_APOBEC_tree</span><span class="informations">1280×900 166 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> <blockquote> <p><strong>Figure 1</strong> | Orange dots denote <code>GA</code> → <code>AA</code> mutations, blue dots denote <code>TC</code> → <code>TT</code> mutations (both predicted APOBEC3 dinucleotide mutations), cyan dots are other <code>G</code> → <code>A</code> or <code>C</code> → <code>T</code> mutations, and grey dots are other mutations.</p> </blockquote> <p>All of these genomes exhibit the same pattern of having a predominance of likely APOBEC3 deaminase induced mutations.</p> <p>A substantial number of the 2022 genomes have unique or shared APOBEC3 mutations confirming this mechanism as being the likely source of most genetic single nucleotide variation in humans within this lineage of MPXV.</p> <p>If these APOBEC3 edits are specifically indicative of replication in humans as opposed to another host species then this would confirm this entire clade to be representative of the emergence of a human epidemic by 2017.</p> <p>New USA genomes:</p> <div class="md-table"> <table> <thead> <tr> <th>accession</th> <th>name</th> <th>reference</th> </tr> </thead> <tbody> <tr> <td>ON676708</td> <td>MPXV_USA_2021_MD</td> <td><a href="https://www.ncbi.nlm.nih.gov/nuccore/ON676708">Gigante et al, 2022, CDC</a></td> </tr> <tr> <td>ON674051</td> <td>MPXV_USA_2022_FL001</td> <td><a href="https://www.ncbi.nlm.nih.gov/nuccore/ON674051">Gigante et al, 2022, CDC</a></td> </tr> <tr> <td>ON676707</td> <td>MPXV_USA_2021_TX</td> <td><a href="https://www.ncbi.nlm.nih.gov/nuccore/ON676707">Gigante et al, 2022, CDC</a></td> </tr> <tr> <td>ON675438</td> <td>MPXV_USA_2022_VA001</td> <td><a href="https://www.ncbi.nlm.nih.gov/nuccore/ON675438">Gigante et al, 2022, CDC</a></td> </tr> </tbody> </table> </div> </div> <div itemprop="interactionStatistic" itemscope itemtype="http://schema.org/InteractionCounter"> <meta itemprop="interactionType" content="http://schema.org/LikeAction"/> <meta itemprop="userInteractionCount" content="2" /> <span class='post-likes'>2 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 class='crawler-linkback-list' itemscope itemtype='http://schema.org/ItemList'> <div itemprop='itemListElement' itemscope itemtype='http://schema.org/ListItem'> <a itemprop='url' href="https://pando.tools/t/monkeypox-virus-genome-sequences-from-multiple-lesions-indicates-co-infection-of-a-uk-returning-traveller/873">Monkeypox virus genome sequences from multiple lesions indicates co-infection of a UK returning traveller</a> <meta 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