The recombinant 鈥渄eltacron鈥� variant of the coronavirus has left many people unsure about the future of the pandemic, amid fears it could combine the delta variant鈥檚 virulence with omicron鈥檚 transmissibility. Recombination, which is essentially the viral version of sex, occurs when a single cell is simultaneously infected with two related viruses, whose genetic material could mix as they replicate.
Dozens of potential recombinant SARS-CoV-2 variants have been identified in recent weeks. So, why are these emerging and how worried should we be?
Recombination can occur when a viral genome is arranged in several segments, like that of a flu virus. When new flu viruses are assembled, they may take on some segments from one variant and other segments from a second variant if it is present.
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In contrast, the genome of the SARS-CoV-2 virus is composed of a single strand of RNA. Recombinants form when the enzyme that copies the RNA releases one strand during the replication process, grabs another strand and resumes copying, in a process called .
This can lead to major genetic mistakes, resulting in viruses that can鈥檛 replicate. It can also generate recombinant viruses with an advantageous mix of mutations, such as those that improve transmissibility.
In animals, recombination has played a pivotal role in the evolution of the many coronavirus strains. In humans, SARS-CoV-2 probably began recombining very early in the pandemic.
When existing variants differ by just a few mutations, it can be unclear whether a new variant with a mix of those mutations arose via recombination or if the mutations were independently acquired. Recombination is also difficult for sequencing laboratories to detect. Extra work is needed to rule out co-infections and sample contamination.
The arrival of omicron, which has more than 50 unique mutations, has made it easier to spot recombinants. It is like trying to decipher if two students have cheated: if they make the same spelling mistake on one word, it could be a coincidence, but if they misspell 10 words in the same way, someone has probably been copying.
The first omicron wave, caused by the BA.1 subvariant of omicron, began when the delta variant was still widespread in many countries. High case numbers mean many people would have been infected with delta and BA.1 simultaneously, creating more opportunities for recombination.
Several delta-BA.1 recombinants, known as 鈥渄eltacron鈥�,聽have been detected, but just two have been studied sufficiently for researchers : XD and XF.
XF hasn鈥檛 been sequenced anywhere in the world since February and may have quickly died out, as most new variants do. XD is still present in parts of Europe but is expected to have reduced transmissibility relative to the omicron subvariant BA.2. 鈥淚鈥檇 be surprised if it managed to compete with BA.2,鈥� says at Imperial College London.
BA.2 has overtaken BA.1 in many countries. Along with the relaxation of restrictions, this has triggered a second omicron wave. Many people will therefore be simultaneously infected with BA.1 and BA.2. This has created recombinants, of which six have been named: XE, XG, XH, XJ, XK and XL.
So how worried should we be? With flu, recombination can create much more dangerous viruses. Animal flu strains often kill a large proportion of the people they infect, but rarely spread from person to person.
The recombination of human and animal flu viruses could produce a strain that readily spreads between people, while remaining lethal, potentially causing a pandemic far worse than that of covid-19.
By contrast, the SARS-CoV-2 virus recombinants that have been identified are mixes of variants that have already spread widely in people, many of whom have some degree of covid-19 immunity. These recombinants aren鈥檛 expected to differ considerably from the variants they evolved from. Even viral offspring usually resemble their parents.
An entirely new variant with novel mutations and the ability to evade past immunity would probably pose a greater threat than recombinants, and may be evolving unseen.
According to the UK鈥檚 Scientific Advisory Group for Emergencies, the is a SARS-CoV-2 variant recombining with one of the human common cold coronaviruses, or an animal coronavirus, to produce something unexpected and dangerous.
While that is possible, says Peacock, it isn鈥檛 thought to be likely to happen. The more distantly related, the less likely viruses are to recombine into a functioning pathogen.
