The COVID-19 variant hunters: keeping the virus under surveillance
As COVID-19 crossed borders and took root around the world, it wasn’t a matter of IF the virus causing it would mutate — it was when. We spoke to Professor Sharon Peacock, the Executive Director and Chair of the COVID-19 Genomics UK Consortium, to find out more about the hunt for COVID-19’s viral variants and why it’s so important to our daily lives.
Viruses evolve and change over time. This is true of SARS-CoV-2: the virus that causes COVID-19. Whenever genetic information is copied, mistakes can happen, especially when copied millions of times. So, when people catch COVID-19 and the virus begins replicating inside our cells, there’s always that small chance of a mutation — like a typo in the genetic code.
Most of the time these mutations have no consequence. But a very small number could give the virus an advantage, like making it better at infecting people, dodging our immune system, or causing more severe illness. That’s when controlling the pandemic becomes more problematic.
Gathering the experts
Before COVID-19, the UK did not have a viral genomics surveillance system in place to track an active pandemic. The COVID-19 Genomics UK Consortium (COG-UK) was formed in March 2020, bringing together public health agencies, the NHS, and leading scientists from academic institutions across the UK. It’s the largest sequencing effort ever undertaken for a single viral pathogen. By mid-November 2020, COG-UK had sequenced over 100,000 viral genomes and the number generated by the UK is now over 1.4 million.
The team at COG-UK have generated genomes to track the virus since the early days of the pandemic, keeping a close eye on how it is evolving and spotting new variants.
“A constant watch on the genetic changes help us understand the virus is in its evolutionary journey, so that we can adapt our own interventions if needs be, and in particular, vaccines,” describes Professor Sharon Peacock.
“We need to monitor for variants and consider each mutation to decide if they are worrying based on everything that we know so far. The difficulty is that mutations arise all the time. Most of them are not worrisome — but particularly early on, spotting mutations that could be linked to a change in the way that the virus behaved and interacted with us was like finding a needle in a haystack.”
Hunting the variants
Polymerase chain reaction tests — more commonly known as PCR — are the gold standard for determining whether that annoying sore throat or cough is COVID-19, or whether you’ve got one of the many other respiratory infections in circulation. What PCR tests look for is simply the presence of genetic material from the virus. But very early on in the pandemic, scientists deciphered the full genome of the original SARS-CoV-2 virus from Wuhan, which provides much more information.
Scientists can compare genomes to see whether the virus has evolved into a variant. This repeated cycle of testing and sequencing to compare genomes is the basis of genomic surveillance.
“Genomic surveillance is essential, both in the short and long term, to track the emergence and spread of variants. We need unbiased surveillance when we sequence the virus from a random proportion of the population, as well as targeted surveillance of particular groups. For example, sequencing virus from people coming into the country can detect variants that have emerged in places with limited or no sequencing.”
Deciding when to act
As most mutations don’t change the virus enough to cause us problems, there have been many different variants identified through genomic surveillance that are just recorded but not pursued. Only a very small number of all the variants identified have been named as ‘Variants of Concern’ by the World Health Organization (WHO).
“Alpha was first detected in Kent and is more transmissible than the original virus from Wuhan. Beta and Gamma, first detected in South Africa and Brazil respectively, are more transmissible than the original virus and Beta, in particular, has some degree of immune evasion.
“The Delta variant of concern was first detected in India but has now spread globally and has largely replaced other circulating variants. Delta is more transmissible than Alpha and demonstrates a degree of immune evasion.”
Omicron is the latest Variant of Concern to emerge, having been classified by the WHO on 26 November 2021. First reported by South Africa, Omicron has already been detected in a growing number of countries — including cases in the UK.
The new Omicron variant is the most mutated to date, with around 50 mutations across the genome — more than 30 of which are in the spike protein gene. These spikes are what the virus uses to get inside our cells to make more copies, and are also what our immune systems are trained to recognise by the current COVID-19 vaccines.
“Omicron has mutations that in other variants have been associated with increased transmissibility and partial immune system evasion. Evidence so far points to greater transmissibility than Delta, but our understanding is limited, and urgent studies are underway to confirm this and to understand more about immunity and disease severity.”
“Although the full significance of this variant is not known, rapid action is being taken internationally on travel restrictions. There are enough red flags to take a precautionary approach and act rapidly to slow its spread whilst waiting for new evidence.”
Facing future unknowns
In late 2002, a respiratory disease called SARS emerged. SARS and COVID-19 are both caused by coronaviruses, but not the same virus — reflected by the very different outcomes of the resulting pandemics. Although there are some similarities, the virus causing COVID-19 has only been known in humans since 2019.
“We’ve only been studying the SARS-CoV-2 virus for just over 18 months, and it’s not clear what the evolutionary trajectory of this will be. We don’t know if we’ve seen the worst of the variants, or if new variants will emerge that are even more transmissible, or have greater immune evasion, or both. Surveillance helps us to capture these changes, and adapt our responses such as vaccine modification, if needed.”
Although life has moved on from lockdowns and school closures for now, the pandemic is still ongoing. That’s why it’s still important to hunt down new variants quickly once they emerge to give us the best chance of containing them.
“Genome data has become an essential part of business as usual for the public health responses to infectious diseases. This will undoubtedly include detecting, tracking, and managing the next novel virus to emerge with pandemic potential.”
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