A model of the spike protein of the novel coronavirus. Photo: NIAID/Flickr, CC BY 2.0
- The Pasteur Institute in Paris has reported that it has sequenced a genome that appears to be a combination of those of the omicron and delta variants.
- Such recombinant variants won’t necessarily be more transmissible or more lethal than either of the two ‘parent’ variants – it’s possible, but not a rule.
- Recombination happens only when two different variants simultaneously enter the same cell in an individual’s body. If they enter different cells, they can’t recombine.
New Delhi: In little more than two years of the pandemic, there have been five ‘variants of concern’. Now, the Pasteur Institute in Paris has reported that it has sequenced a genome that appears to be a combination of those of the omicron and delta variants.
In response to the report, Jeremy Kamil, a US-based virologist, tweeted a thread with more details on March 8.
First solid evidence for a Delta #Omicron recombinant virus 🦠 has been shared by @institutpasteur via @GISAID; Accession: EPI_ISL_10819657 — includes the raw sequencing reads! @WHO @doctorsoumya @RickABright @DrTedros @g20org 🧵
— Jeremy Kamil 🇺🇦 (@macroliter) March 8, 2022
The variant in question had been circulating in France since January 2022, according to the country’s genome-sequencing consortium. In fact, Denmark and the Netherlands had also reported similar genomes in samples obtained from their populations.
The WHO has now taken note of the Pasteur Institute’s finding.
It hasn’t been common for the genomes of new strains of the novel coronavirus to be a combination of those of other variants. Such ‘mixtures’ are called recombinations. A recombination occurs when a person is infected by two variants of the same virus at the same time.
The resulting recombinant variant won’t necessarily be more transmissible or more lethal than either of the two ‘parent’ variants. This is because there is no rule that only the worst parts[footnote]From humans’ point of view[/footnote] of the variants will recombine. It is obviously possible – but it is not a rule.
Second, recombination happens only when both the two variants enter the same cell in an individual’s body. If they enter different cells, they won’t be able to recombine. This is why recombinant variants are rare.
This requirement also implies another condition: recombinant strains can arise only when two variants are circulating at the same time. For example, there was a time in late 2021 and early 2022 when the omicron variant was spreading rapidly – but hadn’t completely displaced the delta variant.
Third, once the two variants have recombined, there is no guarantee that the recombinant strain will spread in the population. This can only happen if the person (whose body hosts the recombinant) transmits the viral particles to someone else.
In a press conference on March 9, the WHO’s COVID-19 technical lead Maria Van Kerkhove said the body was aware of the Pasteur Institute’s report. She added that the new recombinant strain was present in France, Denmark and the Netherlands in “very low levels”.
“We have not seen any change in the epidemiology with this recombinant, we haven’t seen any change in severity but there are many studies that are underway,” she added.
A scientist working at a facility part of the Indian SARS-CoV-2 Genomics Consortium – better known as INSACOG – said Indian scientists had also recorded a delta-omicron recombinant earlier. (He wished to remain anonymous because he wasn’t authorised to talk to the press.)
A recombinant strain has also been reported from Cyprus.
Rare though they may be, recombination is also natural. It has happened with the flu virus, for example, as well as between other strains of the novel coronavirus.
Scientists from China reported a recombination of the beta and the delta variants on January 20, 2022. In Equatorial Guinea, scientists reported a recombination of the beta and the delta strains in the same month, and claimed it was the first known instance.
A recombinant is of value in public health only when its transmission and the severity of its infection are known. And so far there have been no indications that the newly reported delta-omicron recombinant is more transmissible or deadlier.
In fact, focusing on the recombinant itself may obscure the more important thing here: the discovery of new recombinant strains. We can make such discoveries only if we don’t lower our guards, especially on testing and genome sequencing.
As Kerkhove put it:
“It’s really critical that we have testing and it’s really critical that we have sequencing, that we have good geographic representation of sequencing around the world and that the systems that have been put in place for surveillance, for testing, for sequencing right now be reinforced, that they are not taken apart.”