Covid strains combined to produce ‘persistent’ variant in the US, scientists say

Scientists have identified a “persistent” Covid variant in the US which emerged after two different strains of the virus combined to share characteristics.

Known as recombination, this process takes place when a person is co-infected with different Covid variants at the same time. It is a major driver of genetic evolution and common in coronaviruses.

After analysing the genetic make-up of a variant called B.1.628, researchers from Oxford University concluded that it emerged following a recombination event between two different strains (B.1.631 and B.1.634).

All three variants have been in co-circulation in the US and Mexico throughout 2021, leading scientists to believe that B.1.628 first appeared in North or Central America.

The paper, which has yet to be peer-reviewed, said its findings raise “important questions regarding the role and potential effects of recombination on the evolution of SARS-CoV-2 during the ongoing Covid-19 pandemic.”

Co-author Oliver Pybus, a professor of evolution and infectious disease at the University of Oxford, said B.1.628 was “persistent” in the US and warned that “recombination as a source of new and viable virus genetic diversity needs to be taken seriously”.

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.

But as the virus continues to spread and builds up greater genetic diversity, there are concerns that recombination events could become more pronounced and produce an offspring variant that carries concerning characteristics.

“Recombination happens when two different strains of virus infect the same cell, then exchange pieces of genetic material with each other - the virus offspring contain genetic material derived from both parental viruses,” said Professor Jonathan Ball, a virologist at the University of Nottingham.

“When you have lots of virus circulating, as now, you have lots of opportunities for recombination to take place.

“If the new combination of genetic elements renders the virus less fit then it will be quickly outcompeted. If not then the recombinant strain can persist. Sometimes the recombinant form might be fitter in which case it is likely to take off in much the same way that we have seen other variants dominate.

“The major difference is that recombination allows a virus to acquire lots of genetic changes at once and therefore has the potential to have a big impact on virus fitness.

“However, this is no way guaranteed. It is important to study the impact of any genetic changes on virus behaviour, especially changes that might affect transmissibility, disease severity or immune escape.”

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.

Professor Lawrence Young, a virologist at the University of Warwick, said recombination events are “clearly a cause for concern” and do have the “potential to be a source for a new super variant”.

However, he added, the dominance of Delta meant other merging variants are being given little opportunity to take hold. “Delta is such a strong and highly transmissible virus, it seems to almost wipe out everything else,” Prof Young said.

He said that the findings from the Oxford paper reinforce the need to “keep on with genomic surveillance” to monitor how the virus is continuing to evolve in different countries and populations, and to determine which new variants are likely to pose a threat.

“This is vital,” he added. “What we're seeing is rampant infection in the across Europe, you do worry about the whether the capacity for genomic surveillance is there for looking at all of this and certainly in those parts of the world where people are not fully protected.”