Omicron: its transmissibility, its virulence and its ability to escape vaccines

Thanks to the experts, we are always learning a little more about the characteristics of this Omicron variant, as the government confirms the tightening of border measures and advises Canadians against traveling abroad in an attempt to curb its spread. What about the transmissibility, virulence, and ability of this coronavirus variant to evade vaccines?

Omicron, the first Covid-19 variant to be elevated to a variant of concern (VP) by the World Health Organization (WHO) in just a few days, appeared on the Lancet laboratory's radar on November 8 in South Africa, although it is suspected that it had been in circulation for some time.

Thanks to their excellent genomic surveillance system, South African health authorities reported its presence early on. Unlike other variants, Omicron can be detected using a PCR test without requiring whole genome sequencing, allowing its spread to be quickly followed.

As of 23 & nbsp; November, 1,100 cases of the variant (73% of all positive cases) were detected in Gauteng province, South Africa, compared to 10 cases recorded in early November. By December 3, Omicron had officially overtaken the Delta variant in the country.

The effective reproduction rate (the number of people infected by a single individual) for Omicron is estimated to be over six, while that for Delta has been estimated to be around five and that for a highly contagious disease like chickenpox is nine.

Where did Omicron spread?

The Omicron variant is confirmed on all continents except in Antarctica. The cases reported outside South Africa so far appear to be mainly travel-related and mainly involve people who have been vaccinated. However, there are already fears of community spread.

Projections from many countries predict that Omicron's cases will soon overtake Delta's. Ontario's Chief Medical Officer of Health reported on December 12 that Omicron cases represent 10% of all positive cases in the province, confirming that the variant is highly transmissible, even with a reduced level of disease. 'social activities (75% of pre-pandemic levels).

How is Omicron different from other variants?

Variants appear as a result of changes or errors, called mutations, in the sequence of the virus genome (the set of genetic instructions virus).

The Omicron variant has many more mutations than other variants in its S gene – this one encodes the virus's spike protein, which is the key that allows the virus to access our cells. Omicron has accumulated 50 mutations, 32 of which are in the S gene. By comparison, the Alpha variant has 9 in its S gene, and the Delta, 9 to 13.

These last two are more transmissible than the original version, respectively 50% and 100%, and to some extent compromise the protection offered by the vaccine.

It is too early to fully understand the Omicron variant. Because proteins are made up of chains of amino acids, mutations in the S gene lead to amino acid substitutions that lead to changes in the spike protein. The number of amino acid substitutions in Omicron's S protein, and the overlap with those seen in other variants of concern (VP) and variants of interest (VI), make its spike protein appear overloaded.

Omicron spike protein exhibits six unique amino acid substitutions that have not been seen in other VPs, seven present in one or more VPs, three that appear in all current VPs, and the other substitutions are many. less present in the other variants. The three substitutions common to all VPs are associated with immune escape and increased transmissibility and infection capacity.

Is Omicron a “super-variant”?

As a scientist, I am baffled by this variant. How did his spike protein accumulate 32 amino acid substitutions in what appears to be a very short period of time and fit so many substitutions into a single protein? Has this protein become the perfect key to accessing our cells and, at the same time, hiding from our antibodies? Does Omicron cause more serious infections?

It won't be easy to understand when and how Omicron evolved, but it is certain that the mutations it has acquired leave scientists perplexed.

The number of amino acid substitutions in its spike protein is considerable. Proteins are quite flexible in their ability to accept these substitutions, which makes them more effective. But this often happens to the detriment of the microbe (virus, in this case), as substitutions require energy and resources.

First, for every useful mutation, a compensatory mutation must take place in the gene so that the structure of the protein remains intact.

Second, the existence of so many mutations in the S gene would require modifications to the virus's replication machinery to allow so many errors. However, these modifications could have harmful consequences on the replication of the virus.

Finally, the virus depends on the host's resources to make its proteins, such as certain host RNA molecules (transfer RNA) and amino acids. These resources, and others, may not meet the demand of the virus and cause it to malfunction. In other words, the mutated virus may run into a supply and demand problem.

Thus, a “super-mutated” S gene is likely to compromise the overall adaptive value of the virus; another element must therefore be less efficient to allow the production of a super-mutated S gene. This loss of fitness is normal in the microbial world. For example, the resistance of bacteria to antimicrobials is caused by the use of antibiotics. However, in the absence of these, bacteria often lose this resistance because it is energy-intensive.

This suggests that Omicron may be more transmissible (as current data shows) than Delta, while causing a less severe infection. Data from South Africa and cases identified around the world suggest that Omicron has not been linked to serious illness and death.

Do vaccines and post-infection immunity protect against Omicron?

Current vaccines have been designed to protect against infection with Covid-19, that is, to prevent the hospitalization and death. However, they offer more, as they can reduce infections by up to 80% (for mRNA vaccines) and slow down transmission.

It is not known whether the Omicron variant can evade immunity, whether induced by natural infection or a vaccine. However, a study that has not yet been peer reviewed shows that the rate of reinfection with Omicron is much higher than that recorded during the Beta and Delta waves in South Africa.

This report suggests that the immunity acquired by infections with Beta or Delta variants may not protect against Omicron. This finding could explain the rapid increase in Omicron cases in South Africa, where a large part of the population was infected during waves of the Alpha, Beta and Delta variants.

There is insufficient data to draw a conclusion about the protection offered by vaccine immunity against Omicron. The vaccination rate in South Africa is around 25%. Cases of post-immunization infections with the Omicron variant around the world suggest that this variant could bypass vaccines when it comes to infection.

An infection can be asymptomatic or mild. Vaccines are very likely to protect against severe forms of Covid-19, as recent reports (not yet peer reviewed) from South Africa indicate.

In light of numerous reports of the weakening of neutralizing antibodies induced by the vaccine (or by natural infection) over time, many countries, including Canada, are rushing to administer booster doses and increase vaccination coverage in order to protect their population against a possible resurgence of the disease.

Clinical studies and real data have shown that booster doses protect against infection and the severe form of the disease . A recent report from Pfizer shows that administering a third dose could alter the transmission path of Omicron. -in-the-near-future “> What will happen to Omicron in the near future?

Many laboratories around the world are currently evaluating Omicron for its transmissibility, virulence, the severity of the disease it causes, and its ability to evade vaccine protection. For now, we can only wait for the results.

Here in Canada, we must continue to increase immunization coverage to 90% and more for the eligible population. The vaccines work!

Approval of vaccines for children aged five to eleven will undoubtedly further increase immunization coverage and change the transmission trajectory of Omicron.

At the same time, we must maintain measures sanitary: face coverings (actual data shows they reduce the spread of the virus by 53%), distancing (Covid-19 is an airborne disease), hand hygiene and reduction of large gatherings, especially at 'inside.

Finally, and just as important, the emergence of the Omicron variant reminds us, once again, how essential it is to help developing countries with their immunization campaigns. The virus will continue to undermine the progress rich countries have made through vaccination as long as it finds fertile ground to evolve somewhere in the world.

Dasantila Golemi-Kotra, Professor, Biology , York University, Canada

This article is republished from The Conversation under a Creative Commons license. Read the original article.