People get tested for covid-19 in Los Angeles Xinhua/Shutterstock (11701695a)
Two variants of the SARS-CoV-2 coronavirus that causes covid-19 have combined their genomes to form a heavily mutated hybrid version of the virus. The 鈥渞ecombination鈥 event was discovered in a virus sample in California, provoking warnings that we may be poised to enter a new phase of the pandemic.
The hybrid virus is the result of聽recombination of the highly transmissible B.1.1.7 variant discovered in the UK and the B.1.429 variant that originated in聽California and which may be聽responsible for a recent wave of聽cases in Los Angeles because it聽carries a mutation making it resistant to some antibodies.
The recombinant was discovered by Bette Korber at the in聽New Mexico, who told a meeting organised by the on 2聽February that she had seen 鈥減retty clear鈥 evidence of it in her聽database of US viral genomes.
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If confirmed, the recombinant would be the first to be detected in聽this pandemic. In December and January, two research groups independently reported that they聽hadn鈥檛 seen any evidence of聽recombination, even though it聽has long been expected as it is聽common in coronaviruses.
Unlike regular mutation, where changes accumulate one at a time, which is how variants such as B.1.1.7 arose, recombination can bring together multiple mutations in one go. Most of the time, these don鈥檛 confer any advantage to the virus, but occasionally they do.
Recombination can be of major evolutionary importance, according to Fran莽ois Balloux at University College London. It is considered by many to be how SARS-CoV-2 originated.
Recombination could lead to聽the emergence of new and even聽more dangerous variants, although it isn鈥檛 yet clear how much of a threat this first recombination event might pose.
Korber has only seen a single recombinant genome among thousands of sequences and it isn鈥檛 clear whether the virus is being transmitted from person to聽person or is just a one-off.
Recombination commonly occurs in coronaviruses because the enzyme that replicates their genome is prone to slipping off the RNA strand it is copying and then rejoining where it left off. If聽a聽host cell contains two different coronavirus genomes, the enzyme can repeatedly jump from one to聽the other, combining different elements of each genome to create聽a hybrid virus.
The recent emergence of multiple variants of the new coronavirus may have created the raw material for recombination because people can be infected with two different variants at once.
鈥淲e may be getting to the point聽when this is happening at聽appreciable rates,鈥 says at Temple University in Pennsylvania, who keeps an eye聽out for recombinants by comparing thousands of genome sequences uploaded to databases. He says there is still no evidence of聽widespread recombination, but that 鈥渃oronaviruses all recombine, so it鈥檚 a question of when, not if鈥.
The implications of the finding aren鈥檛 yet clear because very little is known about the recombinant鈥檚 biology. However, it does carry a聽mutation from B.1.1.7, called 螖69/70, which makes the UK virus聽more transmissible, and another from B.1.429, called L452R,聽which can confer resistance聽to antibodies.
鈥淭his kind of event could allow the virus to have coupled a more infectious virus with a more resistant virus,鈥 Korber said at the New York meeting.
Lucy van Dorp at University College London says that she hadn鈥檛 yet heard about the recombinant, but 鈥渨ould not be overly surprised if some cases start to be detected鈥.
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