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THE HUNT FOR COVID VARIANTS: HOW THE NEW OMICRON VARIANT WAS FOUND AND WHAT WE
KNOW SO FAR

TOPICS:COVID-19Infectious DiseasesThe ConversationVirology

By The Conversation November 29, 2021

Scientists find variants by sequencing samples from people that have tested
positive for the virus.

Since early in the COVID pandemic, the Network for Genomics Surveillance in
South Africa has been monitoring changes in SARS-CoV-2. This was a valuable tool
to understand better how the virus spread. In late 2020, the network detected a
new virus lineage, 501Y.V2, which later became known as the beta variant. Now a
new SARS-CoV-2 variant has been identified – B.1.1.529. The World Health
Organisation has declared it a variant of concern, and assigned it the name
Omicron. To help us understand more, The Conversation Africa’s Ozayr Patel asked
scientists to share what they know.

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 as early as 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 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. This is thanks to a central
repository of public sector laboratory results at the National Health Laboratory
Service, (NGS-SA), good linkages to private laboratories, the Provincial Health
Data Centre of the Western Cape Province, and state-of-the-art modeling
expertise.

In addition, South Africa has several laboratories that can grow and study the
actual virus and discover how far antibodies, formed in response to vaccination
or previous infection, are able to neutralize the new virus. This data will
allow us to characterize the new virus.

3d Variants of Covid-19 Virus (Sars-COV-2). Alpha, Beta, Gamma, Delta in white
background.

The beta variant spread much more efficiently between people compared to the
“wild type” or “ancestral” SARS-CoV-2 and caused South Africa’s second pandemic
wave. It was therefore classified as a variant of concern. During 2021, yet
another variant of concern called delta spread over much of the world, including
South Africa, where it caused a third pandemic wave.

Very recently, routine sequencing by Network for Genomics Surveillance member
laboratories detected a new virus lineage, called B.1.1.529, in South Africa.
Seventy-seven samples collected in mid-November 2021 in Gauteng province had
this virus. It has also been reported in small numbers from neighboring Botswana
and Hong Kong. The Hong Kong case is reportedly a traveler from South Africa.

The World Health Organisation has given B.1.1.529 the name Omicron and
classified it as a variant of concern, like beta and delta.

WHY IS SOUTH AFRICA PRESENTING VARIANTS OF CONCERN?

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 viral
variants.

The assumption is that some degree of “immune pressure” (which means an immune
response which is not strong enough to eliminate the virus yet exerts some
degree of selective pressure which “forces” the virus to evolve) creates the
conditions for new variants to emerge.

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, but much remains to be learned.

WHY IS THIS VARIANT 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, and the spike protein alone has over 30 mutations. This is
important, because the spike protein is what makes up most of the vaccines.

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 “daughter
of delta” or “grandson of beta” but rather represents a new lineage of
SARS-CoV-2.

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, albeit on a background of much relaxed non-pharmaceutical
interventions and 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 include individuals who had been
vaccinated. However, we have learned that the immune protection provided by
vaccination wanes over time and does not protect as much against infection but
rather against severe disease and death. 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, people who’ve
been infected already, 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 and, together with
non-pharmaceutical interventions, will go a long way towards helping the
healthcare system cope during the coming wave.

Written by:

 * Prof. 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 Programme,
   Professor, Department Medical Virology, University of Pretoria
 * Tulio de Oliveira, Director: KRISP – KwaZulu-Natal Research and Innovation
   Sequencing Platform, University of KwaZulu-Natal

This article was first published in The Conversation.


WE RECOMMEND

 1. COVID-19: The Older You Are, the More Antibodies You Have – Better
    Protection Against Delta Variant
    Mike ONeill, SciTechDaily, 2021
 2. COVID Delta and Delta Plus Variants Evade the Antibody Response
    Mike ONeill, SciTechDaily, 2021
 3. Delta-Like COVID-19 Variants Are Most Likely To Increase Pandemic Severity
    Mike ONeill, SciTechDaily, 2021
 4. COVID-19 VOCs – Especially Delta Variant – More Virulent Than Original
    Strain
    Mike ONeill, SciTechDaily, 2021
 5. New Research Explains Why Vaccinated People at Low Risk During COVID Delta
    Variant Surge
    Mike ONeill, SciTechDaily, 2021

 1. Variants of SARS-CoV-2
    Adam S. Lauring et al., Journal of American Medical Association, 2021
 2. Omicron: What we know so far — and what lies ahead
    Cathrine Scheepers et al., Genetic Literacy Project, 2021
 3. Covid-19: How many variants are there, and what do we know about them?
    Elisabeth Mahase, The BMJ, 2021
 4. Epidemiology Features and Effectiveness of Vaccination and
    Non-pharmaceutical Interventions of Delta and Lambda SARS-CoV-2 Variants
    Wenqing Bai et al., China CDC Weekly, 2021
 5. Be Sure: Bimekizumab versus Adalimumab in Plaque Psoriasis
    Richard B. Warren et al., NEJM, 2021

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