Degree of danger not yet clear for Omicron COVID variant

Of the Network for Genomics Surveillance in South Africa

Since early in the COVID pandemic, the Network for Genomics Surveillance has been monitoring changes in SARS-CoV-2. This is a valuable tool in better understanding how the virus spreads.

In late 2020, the network detected a new virus lineage, 501Y.V2, which became known as the Beta Variant. Later, the Delta Variant displayed a level of contagion that soon made it the dominant strain around the world.

Now a potentially dangerous new SARS-CoV-2 variant has been identified — B.1.1.529. The World Health Organization has declared it a variant of concern, and assigned it the name Omicron, which stands for O in the Greek alphabet.

To help us understand more, The Conversation Africa’s Ozayr Patel asked scientists from the team to share what they know. Here’s what they had to say:

So, what’s the science behind the search?

Hunting for variants requires a concerted effort. South Africa and the UK were the first big countries to implement nationwide genomic surveillance efforts for SARS-CoV-2, beginning in April 2020.

Variant hunting, as exciting as that sounds, is performed through whole genome sequencing of samples that have tested positive for the virus.

This process involves checking every sequence obtained for differences compared to what we know is circulating in South Africa and the rest of the world. When we see multiple differences, this immediately raises a red flag and we investigate further to confirm what we’ve noticed.

Fortunately, South Africa is well set up for this. Thanks to a central repository of public sector laboratory results maintained by  the National Health Laboratory Service, good linkages to private laboratories, Western Cape Province’s Provincial Health Data Centre and state-of-the-art modeling expertise.

In addition, South Africa has several laboratories that can grow and study the actual virus. They can determine how far antibodies, formed in response to vaccination or previous infection, are able to neutralize new strains.

The Beta Variant spread much more efficiently between people compared to the “wild type” or “ancestral” SARS-CoV-2. And that caused a second wave in South Africa, leading to its classification as a variant of concern.

During 2021, another variant of concern,Delta, spread over much of the world. It touched off a third wave of infection in South Africa.

Very recently, routine sequencing by Network for Genomics Surveillance member laboratories detected a new virus lineage, called B.1.1.529. Seventy-seven samples collected in mid-November 2021 in Gauteng province belonged to this strain.

It has also been reported in small numbers from neighboring Botswana, and in Hong Kong. The Hong Kong case reportedly involves a traveler from South Africa.

So why are so many variants of concern first being detected in South Africa?

We do not know for sure. It certainly seems to be more than just the result of concerted efforts to monitor the circulating virus.

One theory is that people with highly compromised immune systems, and who experience prolonged active infection because they cannot clear the virus, may be the source of new variants.

The assumption is that some degree of “immune pressure” — an immune response not strong enough to eliminate the virus, but strong enough to exert some degree of selective pressure, forcing the virus to evolve — creates the conditions for new variants.

Despite an advanced antiretroviral treatment program for people living with HIV, numerous individuals in South Africa have advanced HIV disease and are not on effective treatment. Several clinical cases have been investigated that support this hypothesis for South Africa’s role in generating new COVID strains, but much remains to be learned.

Why is this variant so worrying?

The short answer is, we don’t know. The long answer is, B.1.1.529 carries certain mutations that are concerning. They have not been observed in this combination before.

Also, the spike protein alone displays more than 30 mutations. This is important, because the spike protein is what most vaccines target.

We can also say that B.1.1.529 has a genetic profile very different from other circulating variants of interest and concern. It does not seem to be a son of delta or grandson of beta, but rather an entirely new SARS-CoV-2 lineage.

Some of its genetic changes are known from other variants, and we know they can affect transmissibility or allow immune evasion, but many are new and have not been studied as yet. While we can make some predictions, we are still studying how far the mutations will influence its behavior.

We want to know about transmissibility, disease severity, and ability of the virus to “escape” the immune response in vaccinated or recovered people. We are studying this in two ways.

Firstly, careful epidemiological studies seek to find out whether the new lineage shows changes in transmissibility, ability to infect vaccinated or previously infected individuals, and so on.

At the same time, laboratory studies examine the properties of the virus. Its viral growth characteristics are compared with those of other virus variants and it is determined how well the virus can be neutralized by antibodies found in the blood of vaccinated or recovered individuals.

In the end, the full significance of the genetic changes observed in B.1.1.529 will become apparent when the results from all these different types of studies are considered. It is a complex, demanding and expensive undertaking, which will carry on for months, but indispensable to understand the virus better and devise the best strategies to combat it.

Do early indications point to this variant causing different symptoms or more severe disease?

There is no evidence for any clinical differences yet.

What is known is that cases of B.1.1.529 infection have increased rapidly in Gauteng, where the country’s fourth pandemic wave seems to be commencing. This suggests easy transmissibility.

However, this comes against a background of much relaxed non-pharmaceutical interventions and a low number of cases. So we cannot really tell yet whether B.1.1.529 is transmitted more efficiently than the previously prevailing variant of concern, delta.

COVID-19 is more likely to manifest as severe, often life-threatening disease in the elderly and chronically ill individuals. But the population groups often most exposed first to a new virus are younger, mobile and usually healthy people. If B.1.1.529 spreads further, it will take a while before its effects, in terms of disease severity, can be assessed.

Fortunately, it seems that all diagnostic tests that have been checked so far are able to identify the new virus.

Even better, it appears that some widely used commercial assays show a specific pattern: two of the three target genome sequences are positive, but the third one is not. It’s like the new variant consistently ticks two out of three boxes in the existing test.

This may serve as a marker for B.1.1.529, meaning we can quickly estimate the proportion of positive cases due to B.1.1.529 infection per day and per area. This is very useful for monitoring the virus’s spread almost in real time.

Are current vaccines likely to protect against the new variant?

Again, we do not know.

The known cases do include some individuals who had been vaccinated. However, we have learned the immune protection provided by vaccination wanes over time, and does not protect as much against infection as against severity of infection.

One of the epidemiological analyses that have commenced is looking at how many vaccinated people become infected with B.1.1.529.

The possibility that B.1.1.529 may evade the immune response is disconcerting. The hopeful expectation is that the high seroprevalence rates, found by several studies, would provide a degree of “natural immunity” for at least a period of time.

Ultimately, everything known about B.1.1.529 so far highlights that universal vaccination is still our best bet against severe COVID-19. Together with non-pharmaceutical interventions, that will go a long way toward helping the healthcare system cope during the coming wave.

From The Conversation, an online repository of lay versions of academic research findings found at https://theconversation.com/us . Used with permission .


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