Evidence for a mouse origin of the SARS-CoV-2 Omicron variant
<i>&gt; Intermediate versions have gone largely undetected, thus resulting in an exceptionally long branch leading to the most recent common ancestor (MRCA) of Omicron in the phylogenetic tree. We hereafter refer to this long branch as Branch O.</i><p><i>&gt; We found that mutations accumulated in ORF S at a rate of ∼0.45 mutations per month on average. In sharp contrast, 27 mutations accumulated in ORF S in Branch O during the 18 months spanning May 2020–November 2021, equivalent to ∼1.5 mutations per month, or ∼3.3 times faster than the average rate of other variants</i><p><i>&gt; We found that the Omicron spike protein sequence was subjected to stronger positive selection than that of any reported SARS-CoV-2 variants known to evolve persistently in human hosts, suggesting a possibility of host-jumping</i><p>Although host jumping is undoubtedly occurring (eg infection has been serologically observed in white-tailed deer and other animals), I’m skeptical that it is the <i>primary</i> factor as this paper suggests.<p>Another possibility is that viral mutation rates are underestimated, and&#x2F;or infections are systematically underestimated. There is evidence of both in the literature.<p>Combined with enhanced selective pressure on the spike protein RBD due to mass vaccination campaigns, these are scientifically supported alternative explanations for the observations in OP.