Omicron: How was this new variant of SARS-CoV-2 identified, and what do we know about it?

Since the start of the Covid-19 pandemic, the South Africa Genomic Surveillance Network follows the evolution of the SARS-CoV-2 coronavirus. At the end of 2020, this precious tool, which allows us to understand the mode of propagation of the virus, had detected a new line of SARS-CoV-2, 501Y.V2, who was later baptized beta variant.

Today, a new variant has been identified: B.1.1.529. The World Health Organization said so "Variant of concern", and gave it the name Omicron.

To help us better understand the situation, Ozayr Patel of The Conversation Africa asked scientists to share what they know about this variant.

Where is scientific research?

"Tracking down new variants": exciting as this activity may seem, it is mainly based on the sequencing of the entire genome of the coronavirus, from samples that have tested positive. Chasing the new variants requires a concerted effort. South Africa and the United Kingdom were the first countries to establish a SARS-CoV-2 genomic surveillance through efforts nationally, from April 2020.

The process involves comparing each sequence obtained with those of strains that we know to be in circulation in South Africa and around the world. When multiple differences are found, the alarm bells are sounded, and research is deepened to confirm what was initially detected.

Fortunately, South Africa is well equipped for this activity. His National Health Laboratory Service (NGS-SA) centralizes the results of public sector laboratories, the links with private laboratories are good, and it has a cutting-edge modeling expertise, as well as Provincial Health Data Center of the Western Cape Province, whose main mission is to provide clinicians and those responsible for monitoring patients with the most relevant data.

In addition, South Africa has several laboratories capable of cultivating and studying viruses, which makes it possible to determine the extent to which antibodies produced in response to vaccination or a previous infection are able to neutralize the novel coronavirus. . All of these data will allow us to better characterize Omicron.

3D representations of Alpha, Beta, Gamma and Delta coronaviruses on a white background
3D representations of the Alpha, Beta, Gamma and Delta coronaviruses.
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At the time, the Beta variant had spread much more efficiently than the “wild” or “ancestral” SARS-CoV-2. It had been the source of the second pandemic wave in South Africa and was therefore categorized as a variant of concern, too. In 2021, another variant of concern has also spread across much of the world, including South Africa, where it caused a third pandemic wave : the Delta variant.

Very recently, the routine sequencing carried out by the member laboratories of the Genomic Surveillance Network made it possible to detect a new line of coronavirus in South Africa, named B.1.1.529. Seventy-seven samples collected in mid-November 2021 in Gauteng, South Africa's most urbanized province, contained the virus. The latter had also been reported from neighboring Botswana and Hong Kong in a small number of samples. In Hong Kong, this variant would have been imported by a traveler from South Africa.

The World Health Organization gave the variant B.1.1.529 the name ofOmicron, and classified it as a variant of concern, as Beta and Delta before it.

Why are worrying variants emerging in South Africa?

We don't know with absolute certainty, but that is for sure not only related to the significant coronavirus surveillance effort being carried out in the country.

One theory postulates that people with severely weakened immune systems who, because they cannot suppress it, experience prolonged infection with the SARS-CoV-2 coronavirus, could be the cause of the emergence of new variants.

According to this hypothesis, the immune system of these people would exert a certain degree of "immune pressure" which would create conditions conducive to the emergence of variants. In other words, their immune response would not be strong enough to eliminate the coronavirus, but would nevertheless exert on it a certain level of selective pressure which would "force" it to evolve.

In fact, in South Africa, many people are infected with HIV and are at an advanced stage of the disease. Indeed, despite the existence of a program aimed at distributing antiretroviral treatment, many HIV-positive people do not have effective care. Several clinical cases have been studied which confirm this hypothesis, but there is still a lot to learn.

Why is the emergence of this variant worrying?

The short answer is that we don't really know yet whether to worry about this emergence. The long answer is that B.1.1.529 does indeed carry certain mutations which are worrying. Its only Spike protein has more than 30, and the fact is that the mutations involved have never been seen in such a combination until now. This is what crystallizes the concerns, because the Spike protein is used in the composition of most vaccines (the antibodies of which current vaccines stimulate production could prove to be less effective against the Spike protein of B.1.1.529 - Omicron, if it is too different from that of the previous strains used to develop said vaccines, editor's note).

We can also state that the genetic profile of B.1.1.529 is very different from that of other circulating variants, whether classified as "of interest" or "of concern" by the WHO. He does not appear to be "daughter of Delta" or "grandson of Beta", but rather to belong to a new line of SARS-CoV-2.

Some of its genetic changes have been identified in other variants, and we know that they may affect transmissibility or allow immune evasion, but many are new and have not yet been studied. While we can make various predictions, we are still investigating to what extent these mutations will influence its behavior.

The most essential characteristics to be determined are the transmissibility of this variant, its propensity to cause severe forms of the disease, and its ability to "evade" the immune response of those vaccinated or cured following natural infection by others. variants. We study these points in two ways. First of all, careful epidemiological studies are carried out, in order to know if the new line does indeed present differences compared to the previous ones in terms of transmissibility, ability to infect people who have been vaccinated or previously infected, etc.

In addition to this epidemiological approach, work carried out in the laboratory aims to determine the properties of this new variant. Its growth characteristics are compared with those of other variants, and tests are carried out to find out how well the virus can be neutralized by antibodies present in the blood of vaccinated or cured individuals.

Ultimately, the real significance of the genetic changes observed in B.1.1.529 will become apparent when the results of all these studies are taken into account. This is a complex, demanding and expensive endeavor that will go on for months, but is essential to better understand the Omicron variant and to develop the most effective strategies to combat it.

Does this variant cause different symptoms or more serious disease?

There is as yet no evidence of any clinical difference in the disease caused by this variant. What is known is that cases of infection with the B.1.1.529 virus have increased rapidly in Gauteng, where the country's fourth pandemic wave seems to start. This suggests facilitated transmissibility, which however concerns a small number of cases and occurs in the context of non-pharmaceutical interventions (barrier gestures, etc.) which are much more flexible than before. We therefore cannot yet fully say that B.1.1.529 is transmitted more efficiently than the variant of concern Delta, which prevailed previously.

Covid-19 is more likely to cause serious, often fatal, forms in the elderly and chronically ill. But in a population, the groups that are usually initially most exposed to a new virus are younger people, who are more mobile and generally in good health. If B.1.1.529 does spread further, it will take some time to assess its effects in terms of disease severity.

Fortunately, it appears that the diagnostic tests that have been shown to be effective so far are also able to identify this new viral variant. Better still, it seems that certain widely used commercial tests give in the presence of B.1.1.529 a specific pattern: two of the three target genomic sequences are positive, but the third is not. It is as if this new variant systematically ticks two out of three boxes. This pattern can serve as a marker for B.1.1.529, which means that we can quickly estimate the proportion of positive cases due to infection with Omicron, on a daily basis and in each geographic area. This is very useful for following the spread of the virus in near real time.

Are current vaccines likely to protect against the new variant?

Again, we don't know. People who had been vaccinated were also among the known cases of infection. But we have learned since the deployment of vaccination that the immune protection it provides weakens over time, and that vaccines do not protect so much against infection as against severe forms of disease and death. subsequent. One of the ongoing epidemiological analyzes aims to determine how many vaccinated people have been infected with the B.1.1.529 variant.

The possibility that the Omicron variant may escape the immune response is worrying. Corn several studies found that seroprevalence rates, which indicate how many people have already been infected with the SARS-CoV-2 coronavirus, are high. It is hoped that this will provide them with some degree of "natural immunity" against this variant as well, for some time at least.

Ultimately, what we know about Omicron so far seems to indicate that our best asset in the fight against Covid-19 and severe forms remains to vaccinate as many people as possible. In parallel with the establishment non-pharmaceutical interventions, this approach will help health systems cope with the looming wave.

Teacher. Wolfgang Preiser, Head: Division of Medical Virology, Stellenbosch University; Cathrine Scheepers, Senior Medical Scientist, University of the Witwatersrand; Jinal bhiman, Principal Medical Scientist at National Institute for Communicable Diseases (NICD), National Institute for Communicable Diseases; Marietjie Venter, Head: Zoonotic, Arbo and Respiratory Virus Program, Professor, Department Medical Virology, University of Pretoria et Tulio de Oliveira, Director: KRISP - KwaZulu-Natal Research and Innovation Sequencing Platform, University of KwaZulu-Natal

This article is republished from The Conversation under Creative Commons license. Read theoriginal article.

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