Several concerns have been raised in respect to the new COVID variant Omicron, which was first detected in South Africa and was reported to the World Health Organization (WHO) on 24 November. The global health organization on Friday designated the newly discovered B.1.1.529 variant as Variant of Concern (VoC) and has now suggested that it could pose a “very high” global risk. 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.
Up until now, the SARs-COV-2 virus is known for its wide-ranging and unpredictable symptoms. From fever, fatigue, persistent cough to more severe illnesses including shortness of breath, chest pain and brain fog, people infected with COVID-19 have seen it all and even battled long haul symptoms.
The initial cases of infection were primarily reported among younger people under the age of 30, including kids, as per the South African doctor. Most of the patients complained of only mild symptoms and were not severely ill. Some complained of high body temperature, but somehow were cured on their own.
One of the most concerning aspects of the Omicron variant is that it has over 30 mutations in the spike protein, which helps it potentially develop an ‘immune-escape mechanism’. As is known, the spike protein is a compound that helps the virus to enter the host cell, making it more transmissible and infectious.
Most COVID vaccines on the other hand work towards eliminating these spike proteins. Having said that, mutations in the spike protein only make the new variant more difficult to detect and neutralize, which is why it could possibly render the available COVID vaccines less effective.
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.
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 most effective steps individuals can take to reduce the spread of the COVID-19 virus is to keep a physical distance of at least 1 metre from others; wear a well-fitting mask; open windows to improve ventilation; avoid poorly ventilated or crowded spaces; keep hands clean; cough or sneeze into a bent elbow or tissue, and get vaccinated when it’s their turn.
All the expert bodies have stressed that vaccination remains critical, especially to protect groups at high risk of hospitalization 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 sanitizing hands and surfaces regularly.
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