On Friday, the World Health Organization (WHO) classified a new variant of SARS-CoV-2, currently circulating in South Africa, as a ‘variant of concern’. It also named it Omicron.
The Network for Genomics Surveillance in South Africa (NGS-SA) had identified the variant on Monday. It had detected a group of related SARS-CoV-2 viruses, which belong to a lineage named B.1.1.529.
Early indications are that this variant is possibly even more transmissible than the highly infectious Delta variant, and that current vaccines may be less effective against it.
New variants continue to emerge as SARS-CoV-2 spreads, and the significance of each mutation becomes known after a period of time. But health authorities worldwide need to keep a constant watch to identify which ones are more important than others. It was as part of such an exercise that the NGS-SA detected B.1.1.529.
From what is known currently, B.1.1.529 has multiple spike protein mutations, and preliminary analysis suggests it is highly infectious. South Africa has reported a four-fold increase in new cases over the last two weeks, coinciding with the emergence of B.1.1.529.
On Thursday, the NGS-SA said B.1.1.529 has rapidly increased in Gauteng province, which includes Johannesburg and Pretoria, and may already be present in most provinces. The NGS-SA has said the sustained increase in cases is possibly fuelled by cluster outbreaks.
On the mutation profile of the new variant, the NGS-SA has said that B.1.1.529 has “very unusual constellations of mutations” — with 30 in the region that encodes the spike protein, which is responsible for the virus’s entry in human cells.
It has said that some of the mutations are well characterised with a known phenotypic impact, affecting transmissibility and immune evasion. Some of these mutations have already been detected in the Alpha and Delta variants. But many other mutations, the NGS-SA said, have been “rarely observed until now and not well characterised”. So, the full significance of these mutations remain uncertain at this point. “More investigations are underway to determine the possible impact of these mutations on the capacity of the virus to transmit more efficiently, to impact vaccine effectiveness and evade immune response, and/or to cause more severe or milder disease,” the Africa Centers for Disease Control (CDC) has said.
The NGS-SA has said that a cluster of mutations, known as H655Y + N679K + P681H, is associated with more efficient cell entry, indicating enhanced transmissibility.
There is also a deletion, nsp6, which is similar to a deletion in the Alpha, Beta, Gamma, and Lambda variants. The NGS-SA says this may be associated with evasion of innate immunity, and could enhance transmissibility.
Again, the new variant carries the mutations R203K+G204R — also seen in Alpha, Gamma and Lambda — and which are associated with increased infectivity.
The WHO said on Friday that its technical advisory group met to review the new variant and designated it as a variant of concern. This effectively means that Omicron has been demonstrated to be associated with one or more of the following changes: increase in transmissibility; and decrease in the effectiveness of diagnostics, vaccines, therapeutics.
Earlier in the day, Maria Van Kerkohove, Covid-19 Technical Lead at WHO, had said in a statement: “This variant has been detected and reported to us by our colleagues in South Africa. There are fewer than 100 whole-genome sequences that are available. We do not know very much about this yet. What we do know is that his variant has a large number of mutations. And the concern is that when you have so many mutations, it can have an impact on how the virus behaves.”
The National Institute for Communicable Diseases (NICD) of South Africa has said that currently, “no unusual symptoms” have been reported following infection with the B.1.1.529 variant. It has highlighted the fact that, as with other infectious variants such as Delta, some individuals are asymptomatic.
Omicron’s epidemiological and clinical correlation is not fully established. Without that, scientists cannot establish a direct linkage to any surge. South Africa has started to examine the immune escape potential of B.1.1.529 in a laboratory setting. This will also indicate the performance of current vaccines. It has also established a real-time system to monitor hospitalisation and the outcome associated with B.1.1.529. The data will reveal if the mutation is associated with disease severity, or if it may affect the performance of therapeutic medicines being administered in hospitals.
The South African NICD has said B.1.1.529 has a deletion within the S gene that allows for rapid identification of this variant.
“However, most other targets (including the N and RdRp genes) remain unaffected from specimens tested in over 100 specimens from testing laboratories in Gauteng so it is unlikely that overall PCR test sensitivity is affected. These PCR tests typically detect at least two different SARS-CoV-2 targets, which serves as a backup in the case of a mutation arising in one,” the NICD said.
All the expert bodies have stressed that vaccination remains critical, especially to protect groups at high risk of hospitalisation and death. Real-time data have shown that high vaccination rates also significantly reduce the strain on health systems.
The emergence of the new variant shows once again that the pandemic is far from over — and Covid-appropriate behaviour is critical for breaking the chain of transmission: masking, social distancing, good ventilation in all shared spaces, and washing or sanitising hands and surfaces regularly.
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