With Omicron emerging as the fulcrum of the pandemic, concerns and renewed measures are being taken rapidly across the world. Amidst all the excitement India has also reported the presence of the newest variant of the coronavirus with two persons detected of having infection by it, in the state of Karnataka. Several aspects are being researched regarding the new strain, like its more transmissibility, the capability of evading the immune system (our defence mechanism to fight off any infection), the possibility of causing more severe disease amongst the infected and evasion of the vaccine protection by the strain.
All these concerns are welcome and are necessary, but at the same time, it is also important to not panic.
Shahid Jameel, an eminent virologist and the ex-head of the Indian SARS-CoV-2 Genomics Consortium (INSACOG), while speaking to NewsClick on various facets of the strain also appealed to keep away from being panic. “Continue with the Covid appropriate behaviour, but don’t panic”—he told us. Shahid Jameel also put forwarded some other points in this regard; “Enough numbers of Indians were exposed after the first two waves (about 930-950 million based on serosurveys), so severe (effects of the) disease would be minimal.”
He also has some advice to ramp up vaccination— “Increase vaccinations to cover as many as possible with two doses - for this, the government may consider giving Covishield doses 12 weeks apart (instead of 16 weeks now)”.
Jameel also shed some light on the molecular biology of the virus and its new strain, the Omicron. On being asked on what basis it is said that the newest variant of concern is more transmissible where confirmed results are still awaiting, the professor explained— “This is based on early results from South Africa. Over 200 confirmed sequences are now available but also results from a surrogate test called S gene target failure, in which the S gene fails to be detected in RT-PCR while two other genes of SARS-CoV-2 (N and orf1ab) are detected. So far, all such results turn out to be Omicron, so it’s a quicker surrogate test.”
Further, he commented on the transmissibility of the strain as— “At this time it is estimated to transmit about 30% faster than Delta. This may change as it spreads more.”
The rapidity with which a variant can transmit among populations may also be related to its ability in evading the immune system responses with other factors. A lot has been said in media about the possible immune system evasion by the strain, which, however, is not confirmatory yet. Prof. Jameel explained this point taking account of the molecular biology of the viral variant. He explained— “Those are only predictions at this time based on the mutation profile. All Covid vaccines generate a multi-target response to epitopes (regions/surfaces) within the receptor-binding domain (RBD) and N-terminal domain (NTD) of the Spike protein. Several of these are mutated in the Omicron spike. What we do not know is if binding affinity will not be affected, dip variably or be lost altogether. Since it is a multi-target response, my hunch is that vaccine effectiveness will dip but current vaccines will not become useless against Omicron. Lab neutralisation data should be available in another week or so.”
The RBD (Receptor binding domain) and the NTD (N terminal domain) are some of the portions lying in the spike protein of the coronavirus. The spike protein of the virus is essential in binding a viral particle to a human cell and to enter inside the cell.
Commenting on the possibility that Omicron might have been present in India even before it was detected and how it becomes visible, Jameel said— “Since all Covid cases cannot be sequenced, not finding it via sequencing doesn't mean it was not already there. Once the frequency crosses a threshold (which depends upon sequencing density), it will be seen.”
“I understand that India also does not use PCR tests with a spike gene target, so even S gene target failure, which was quickly used in South Africa, is missing for us. With increased airport surveillance and sequencing, it’s only a matter of time that we find it in India.”