Scientists warn of different Covid variants combining and sharing traits as infections rise

Scientists have warned of the possibility of Covid variants combining and sharing characteristics as infections surge and the virus is given more opportunity to diversify.

These “recombination” events have been recorded intermittently throughout the pandemic so far – but experts fear they could become more frequent and create new variants of concern.

“It’s something that could happen on a larger scale,” said Emma Thomson, a professor in infectious diseases at Glasgow University’s Centre for Virus Research. “We need to be very aware of that and looking out for it with the sequencing.”

In the UK, where case rates have reached record highs in people aged 20 to 29, the sequencing of positive tests from people arriving in from amber-listed countries has dropped from 61 per cent in March to just 3 per cent more recently, potentially allowing Covid variants to enter into Britain unchecked.

Limited genomic monitoring by other countries could also prevent scientists from properly tracking the virus’ evolution and how often variants are merging with one another, experts say.

Dr Stephen Griffin, a virologist at Leeds University, said the process of recombination was “very complicated, but it’s going to be driven by poor government policy” in allowing the continued spread of the virus in countries such as the UK and US.

The Sars-CoV-2 virus has been evolving through the gradual accumulation of random mutations in its spike protein. This has led to the creation of highly transmissible or immune-evading variants.

Recombination events – which occur when two variants infect the same host – are rare but far more likely to generate a series of major changes during the process of viral replication within cells.

In the early days of the pandemic, due to the limited genetic diversity of Sars-CoV-2 at the time, recombination was seen as largely inconsequential, with similar-looking variants exchanging much of the same genetic coding between each other.

“It has happened, but it hasn’t happened in such a way that it’s caused, as far as I’m aware, a major advantage to the virus,” said Prof Thomson.

But as the virus continues to spread – particularly in countries where it is given free rein to do so – it will build up genetic diversity that could make recombination more pronounced, and produce an offspring variant that carries concerning characteristics.

Lawrence Young, a virologist at Warwick University, said the degree to which recombination events are contributing to the emergence of new variants is “controversial”, arguing that they appear to have arisen largely through recurrent mutations.

“But we can’t rule out recombination in individuals infected with different variants – a phenomenon that has recently been reported and may be more common than we think,” he said.

Researchers recently reported that an unvaccinated 90-year-old woman in Belgium had been infected with two different variants of the Covid-19 virus at the same time, in what was one of the first documented cases of its kind.

Dr Julian Tang, a respiratory virologist at Leicester University, said that recombination occurs in coronaviruses “quite frequently”. But, so far, “we haven’t seen a lot of that”.

“You don’t see many cases of people getting infected by different variants at the same time as the virus is expanding in new populations that haven’t been infected before,” he added.

“But as you go forward like you do with flu, where we’ll get multiple seasons of Covid-19 stacking on top of each other, with these variants circulating, you’ll see more incidents of recombination due to individuals being infected by two or more different variants.”

However, he said that the data on recombination remains limited at this stage, and urged against “scaremongering”.

Earlier this year, research conducted by a team at Warwick University identified one virus sequence in the UK that appeared to have been a recombinant of Alpha and another lesser-known variant.

In South Africa, too, they found two examples of variants that were “very unlikely to have arisen through recurrent mutation alone,” suggesting they were the by-products of recombination.

As more genome sequence data accumulates and the genetic diversity of Sars-CoV-2 increases, it may be possible to shed more light on the role that recombination has in generating dangerous variants, said Prof Young.

Prof Thomson said it is imperative to continue expanding genomic surveillance networks and sequencing cases.

The researchers at Warwick University said this would enable the early detection of new recombinant variants and help identify parts of the Sars-CoV-2 genome that are more likely to reshuffle and be exchanged during a recombination event.