Coronavirus Research Tracking - Omicron special - 6 December
Omicron reports and studies that have appeared in the last 3 days
A short update that highlights papers or reports on the Omicron variant that have come out over the last few days.
As noted in the 3 Dec. tracker, there is still a high level of uncertainty about transmissibility and immune evasion of this variant, which will take several weeks to investigate.
The Research Tracker is prepared by Dr Robert Hickson for the Science Media Centre.
Omicron overview
A news report in Nature summarised what was known up to 2 December. Another news item in Nature noted that border bans came too late, and more research is needed to understand when and how travel restrictions work best for countries with pours borders.
Case reports from Gauteng Province, South Africa
A report on 42 early cases of assumed Omicron infections in South Africa notes that 70% did not require oxygen. In previous infection waves there were a higher proportion of more severe cases early on. Cases, with less clinical details, of another 124 patients suspected of having an Omicron variant infection in the last month were also generally mild, with hospitalisation associated with other causes. This may indicate Omicron severity is lower, but it is too early to reach that conclusion.
Over half of the cases were unvaccinated, although vaccination status in some is unknown. Ages of the patients are not reported, apart from one of the cases being a child. The results are included in a news item, and have not been peer reviewed.
UK Technical Briefing
The UK Health Security Agency has published a technical briefing on the Omicron variant. Based on current sequences there is little diversity in Omicron, indicating a recent emergence and rapid spread.
Modelling and analyses indicate that mutations in the Omicron variant are highly likely to affect the binding of antibodies.
Of 22 cases identified in the UK by 30 November, none have required hospitalisation. Fourteen were known to be fully vaccinated.
The briefing also identifies the large number of studies underway in the UK looking at this variant.
Omicron’s spike protein structure indicates it is likely to bind more strongly to human cells
Structural analysis indicates that the receptor binding domain of the Omicron variant binds more strongly to the ACE2 receptor than the Delta variant. This may lead to higher transmissibility, although this has not yet been demonstrated. The paper has not yet been peer reviewed.
One mutation may have been acquired from another source
A three amino acid insertion (ins214EPE) found in the Omicron variant has not been seen in other variants. All of the other mutations (substitutions or deletions) have been found in other SARS-CoV-2 genomes. This paper suggests the insertion may have been acquired by recombination with another virus, possibly a human coronavirus, infecting the same human cells, or from a human genome transcript in the infected cell.
The paper does not conclude what the original source is. The paper has not yet been peer reviewed.
An analysis in October found that other insertions in SARS-CoV-2 show strong similarity to RNA transcripts from host cells, suggesting incorporation of short sequences may occur. The insertions are all very short, so it is difficult to determine their origins. The analysis has not been peer reviewed.