Transmission electron micrograph of a SARS-CoV-2 virus particle isolated from a patient sample and cultivated in cell culture.
Enlarge / Transmission electron micrograph of a SARS-CoV-2 virus particle isolated from a patient sample and cultivated in cell culture.

Researchers in France have reported the first compelling genetic evidence of a recombinant SARS-CoV-2 virus that contains elements of both the omicron coronavirus variant and the delta variant. However, health experts at the World Health Organization and elsewhere have been quick to note that such a recombinant virus is expected to arise and, so far, there’s no reason to be worried about the hybrid.

The delta-omicron recombinant—a combination of the delta AY.4 subvariant’s backbone and the omicron BA.1 subvariant’s spike protein—has been circulating at very low levels since at least early January 2022 in France. Researchers have also reported a smattering of cases in Denmark, Germany, and the Netherlands. So far, epidemiology data on the recombinant’s spread does not raise any red flags, and the variant does not appear to cause more severe disease, according to WHO technical lead Maria Van Kerkhove, who addressed the variant in a press briefing this week. However, researchers are in the process of conducting more studies on the recombinant and will be monitoring it closely, as the organization does with other new variants, she noted.

Coronaviruses are known to recombine, and researchers fully expected that such recombinant SARS-CoV-2 viruses would crop up from time to time. Generally, recombination can happen when two variants infect one person at the same time and invade the same cells. In this scenario, the cellular machinery that viruses hijack to make clones of themselves can sometimes abruptly switch from translating the genetic code of one of the variants to the code of the other, resulting in a mosaic virus.

Viral merger

It’s particularly unsurprising that a recombinant of delta and omicron popped up, given that omicron gained global dominance while delta transmission was still very high in many places. That situation provided the two highly transmissible viruses plenty of opportunities to cross paths. Additionally, it’s easier for researchers to identify delta-omicron hybrids. Genetic monitoring has ramped up significantly amid the pandemic, making detection more efficient. And the two variants are relatively distinct from each other, making delta-omicron recombinants far easier to pick out than recombinants of past variants, which had more in common with each other. All of those factors make it more likely that there will be reports of delta-omicron recombinants.

Still, detecting when recombination happens can be tricky. Some genetic-sequencing efforts can easily appear to detect recombinant viruses if there’s a co-infection without recombination or if there’s contamination in laboratory procedures. Some form of contamination was suspected to be the case in a report from January of a recombinant SARS-CoV-2 virus detected by researchers at the University of Cyprus. But in the case of the virus detected in France, researchers are more confident that it’s truly a recombinant virus because the quality of sequence data is better and researchers were able to grow the recombinant virus in laboratory cell cultures.

While confirmation of a delta-omicron recombinant may sound alarming, virologists have pointed out that recombination isn’t like creating a super-variant progeny that contains only the most dangerous aspects of its menacing parent variants. Like most mutations, most recombination isn’t advantageous to the virus. And so far, there’s no indication that the delta-omicron recombinant identified will take off and become the next globally dominant variant.

However, the possibility for dangerous recombinants is yet another reason to remain vigilant amid the pandemic virus to try to keep transmission low. The lower the transmission, the fewer opportunities there are for variants to emerge and recombine. That means we should be sticking with proven methods to reduce transmission, namely staying up to date on vaccination and taking health precautions like mask-wearing and physical distancing when the risk of transmission is high.

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