The hunt for coronavirus variants

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The hunt for coronavirus variants

In News: 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, known as B.1.1.529.

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 they see multiple differences, this immediately raises a red flag and they investigate further to confirm what they’ve noticed.
• 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 neighbouring Botswana and Hong Kong. The Hong Kong case is reportedly a traveller from South Africa.

Whether B.1.1.529 will be classified as a variant of interest or of concern, like beta and delta, has not been decided by the World Health Organization yet.

Why is this variant worrying?

We still do not know but 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.
• 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 behaviour.

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. 
• 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?

• We do not know. The known cases include individuals who had been vaccinated. However we have learnt 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.
• 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.