A new comment on Omicron SARS-CoV-2 variant has been published on The Lancet by South African researchers of Centre for the AIDS Programme of Research in Durban South Africa.
The Authors highlight that the first sequenced omicron case was reported from Botswana on Nov 11, 2021, and a few days lateranother sequenced case was reported from Hong Kong in a traveller from South Africa. Several sequences fromSouth Africa followed, after initial identification that the new variant was associated with an S-gene target failure
on a specific PCR assay because of a 69–70del deletion, similar to that observed with the alpha variant.
The earliest known case of omicron in South Africa was a patient diagnosed with COVID-19 on Nov 9, 2021, although it is probable that there were unidentified cases in several countries across the world before then.
In South Africa, the mean number of 280 COVID-19 cases per day in the week before the detection of omicron increased to 800 cases per day in the following week, partly attributed to increased surveillance. COVID-19 cases are increasing rapidly in the Gauteng province of South Africa; the early doubling time in the fourth wave is higher than that of the previous three waves.
For the Authors, Omicron has some deletions and more than 30 mutations, several of which (eg, 69–70del, T95I, G142D/143–145del, K417N, T478K, N501Y, N655Y, N679K, and P681H) overlap with those in the alpha, beta, gamma, or delta VoCs. These deletions and mutations are known to lead to increased transmissibility, higher viral binding
affinity, and higher antibody escape. Some of the other omicron mutations with known effects confer
increased transmissibility and affect binding affinity. Importantly, the effects of most of the remaining
omicron mutations are not known, resulting in a high level of uncertainty.
Regarding clinical presentation the Authors conclude that at this stage, the available anecdotal data from clinicians at the front lines in South Africa suggest that patients with omicron are younger people with a clinical presentation similar to that of past variants. Although no alarming clinical concerns have been raised thus far, this anecdotal information should be treated with caution given that severe COVID-19 cases typically present several weeks after the initial symptoms associated with mild disease.
Regarding immune escape for the Authors in the absence of data on observational vaccine effectiveness and antibody-neutralisation studies on vaccines sera, preliminary data from the national PCR testing programme could provide some clues. Data on positive PCR tests in people with previous positive tests suggest an increase in cases of reinfection in South Africa, keeping with the immune-escape mutations present in omicron.
In consideration of the fact that most COVID-19 vaccines have remained effective in preventing severe COVID-19, hospitalisation, and death, for all previous variants, because this efficacy might be more dependent on T-cell immune responses than antibodies, the Authors suggest the same for Omicron.
The Authors conclude that extrapolations based on known mutations and preliminary observations, which should be interpreted with caution, indicate that omicron might spread faster and might escape antibodies more readily than previous variants, thereby increasing cases of reinfection and cases of mild breakthrough infections in people who are vaccinated. On the basis of data from previous VoCs, people who are vaccinated are likely to have a much lower risk of severe disease from omicron infection.
A combination prevention approach of vaccination and public health measures is expected to remain an effective strategy.