COVID-19: Omicron's first image out, strain shows more than double the mutations of Delta

Scientists at Rome’s pretigious Bambino Gesu hospital on Sunday presented the first three-dimensional (3D) image of the new highly mutated coronavirus variant ‘Omicron’. The model also depicted Delta variant as the two variants of concern were compared side-by-side with respect to their mutations on the protein spike. “We can clearly see that the Omicron variant presents many more mutations than the Delta variant, concentrated above all in one area of the protein that interacts with human cells”, the team of researchers said in a statement issued on Sunday.

The image was produced “from the study of the sequences of this new variant made available to the scientific community” coming mainly “from Botswana, South Africa, and Hong Kong”, said the scientists.

“This does not automatically mean that these variations are more dangerous, just that the virus has further adapted to the human species by generating another variant,” the researchers said. “Other studies will tell us if this adaptation is neutral, less dangerous or more dangerous,” Scientists at Rome’s pretigious Bambino Gesu hospital  said in a statement. 

To determine the danger level and severity of Omicron, the WHO has asked the member states to enhance surveillance and sequencing efforts to better understand circulating variants, and submit complete genome sequences and associated metadata to a publicly available database, such as GISAID.

30 mutations concentrated on Spike (S) protein, half on receptor-binding domain

In the 3D image, one can see a large number of mutations particularly concentrated in the spike (S) protein. According to South African scientists, there are about 50 mutations in Omicron, 30 of those are concentrated on Spike protein, and half are found in the receptor-binding domain – the part that binds to the ACE2 receptor on human cells. As per the doctors in Bambino Gesu, the red dots in the image indicate areas with a “very high variability,” while the orange marks are the “high variability”, and the yellow dots represent the “medium variability.” 

The gray area depicts the parts that do not vary with the hypervirulent Delta variant that became the dominant strain worldwide. Meanwhile, the Green dots in the image are the parts of the S protein that depict the considerably lower level of difference between the Omicron and the Delta variant of the SARS-CoV-2 lineage. 

Deakin University epidemiologist Professor Catherine Bennett tells Australian news outlet news.com.au that the B. 1.1.529 variant stands out with respect to several mutations, more than 50, but the more important aspect to note is not the number of mutations but where many of these were located. “Usually a new variant only has a handful of important mutations,” she told the outlet, adding that generally the major change due to this is virus’ transmissibility.

But as far as Omicron is concerned, “more than 30 are in the spike region alone,” Prof Bennett said, “this is unusual”. Further, she explained that the mutations in the spike region could be concerning as “this is where the virus attaches to human cells, it’s also that part of the virus that vaccines focus on,” she told Australian news outlet news.com.au studying the image. This also means, explains Professor Bennett, that the variant has become so different from previous versions of the SARS-CoV-2 that our body’s immune system may fail to recognise it, or remember how to fight it, she stressed.