January 10, 2022

expert reaction to reports of a new variant of SARS-CoV-2 that combines characteristics of the delta and omicron variants

There have been reports of a delta and omicron SARS-CoV-2 variant hybrid detected in Cyprus.

Dr Jeffrey Barrett, Director of the COVID-19 Genomics Initiative at the Wellcome Sanger Institute, said:

“This is almost certainly not a biological recombinant of the Delta and Omicron lineages. The apparent Omicron mutations are located precisely and exclusively in a section of the sequence encoding the spike gene (amino acids 51 to 143) affected by a technological artifact in certain sequencing procedures. We published a technical description of this issue last year https://wellcomeopenresearch.org/articles/6-305/v1.”

Prof Ewan Birney, Deputy Director General of EMBL, said:

“Viruses change their sequence in two ways; by changing single bases (letters) like a spelling mistake, called mutation, and by swapping chunks from different variants which have differences due to previous mutations – like a whole sentence or stanza, called recombination. Think of it as a swap of a verse from Scot’s to the English translation of some of Rabbie Burn’s poetry – still recognisably the same poem, but very obviously changing from Scot’s to English. Recombination in Coronaviruses is rare, SARS-CoV-2 included, though they do happen. Detecting recombination requires detecting a likely swap of a section of the virus (spotting a section of English translation in the middle of Scot’s poem). This is complicated because the vast majority of viral sequencing also happens in chunks, where the scientists design specific chunks to be amplified before sequencing. These chunks are then matched on a scaffold of the original SARS-CoV-2 sequence, and differences called against that. In the case of many of the deltacron sequences, a proposed recombination of Delta and Omicron, the recombination are precisely coincident with some the scientist designed chunks. It is as if the English translation was precisely characters 200 to 250, knowing that laboratory system handles things in 50 letter chunks. This is strongly suggestive of a co-infection event or a laboratory contamination, many of which are very subtle and complex to track. Currently therefore scientists worldwide are carefully considering the possibility of the Deltacron variants, but a key first step is to confirm if this recombination has actually occurred or if the findings are due to a sequencing artifact when looking at both Omicron and Delta.”

All our previous output on this subject can be seen at this weblink:

www.sciencemediacentre.org/tag/covid-19

Declared interests

Prof Ewan Birney: “I am a consultant and shareholder of Oxford Nanopore which makes sequencing devices.”

None others received.