August 18, 2023

expert comment on new COVID variants

In light of reports on an uptick in COVID cases and on new variants of SARS-CoV-2, here are some comments from Professor Francois Balloux in case useful.

Prof Francois Balloux, Professor of Computational Systems Biology and Director, UCL Genetics Institute, UCL, said:

“There has been renewed interest in the media about SARS-CoV-2 variants. The first to attract attention was EG.5 / EG.5.1 (nicknamed Eris). The interest over it was largely unwarranted. EG.5 / EG.5.1 is a direct descendent of the XBB.1.9.2 sub-variant, and carries only one additional mutation in the spike protein. It is one of the myriad Omicron sub-lineages in circulation constantly jockeying for places.

“More recently the BA.2.86 variant has attracted attention, rightly so, as it is of far more interest. BA.2.86 is the most striking SARS-CoV-2 strain the world has witnessed since the emergence of Omicron. Even if is highly derived, BA.2.86 is still an Omicron sub-lineage strain, branching deep in the Omicron phylogeny next to BA.2 (the 2nd major Omicron variant) which emerged and spread globally in early 2022.

“There have been five genomes of BA.2.86 sequenced to date. One from Israel on July 31, and two from Denmark on July 24 and 31. More recently two others have been collected, one in the US and one in the UK.

“The five BA.2.86 genomes display some genetic diversity suggesting that the lineage has been circulation for months, but all five are located on a the same very long branch in the Omicron phylogenetic tree. Interestingly all >30 mutations on that long branch are found in the spike protein, which is the target of neutralising antibodies.

“The most plausible scenario is that the lineage acquired its mutations during a long term infection in a immunocompromised person over a year ago and then spread back into the community. BA.2.86 has since then probably been circulating in a region of the world with poor viral surveillance, and has now been repeatedly exported to other places in the world.

“Over the coming weeks we will see how well BA.2.86 will be faring relative to other Omicron subvariants. It is expected that BA.2.86 in part escaped prior immunity against re-infection provided by vaccination and previous infection. Nothing is known at this stage about its intrinsic transmissibility and virulence. A priori, it is not expected to behave differently from current Omicron strains in circulation. Even in the worst case scenario where BA.2.86 caused a major new wave of cases, we are not expecting to witness comparable levels of severe disease and death than we did earlier in the pandemic when the Alpha, Delta or Omicron variants spread.

“Most people on earth have now been vaccinated and/or infected by the virus. Even if people get reinfected by BA.2.86, immune memory will still allow their immune system to kick in and control the infection far more effectively. It remains that a large wave of infection by BA.2.86, or any future comparable variant, would be an unwelcome event.”

Declared interests

No conflicts of interest