Analysis of new highly mutated BA.2.87.1  variant

By Jesse Bloom, current as of Feb-2-2024, https://slides.com/jbloom/ba_2_87_1-sars2-variant

Summary

BA.2.87.1 is new highly mutated variant of SARS-CoV-2 recently reported by Tulio de Oliveira and colleagues in South Africa

 

So far only nine sequences have been identified, all in South Africa

 

Historically, most highly mutated variants never spread widely, but some do (eg, Omicron BA.1, Omicron BA.2, and BA.2.86's immediate descendant JN.1)

 

BA.2.87.1 is of scientific interest and merits experimental study and epidemiological monitoring. However, there is no current indication that it is of immediate public-health relevance.

Why is BA.2.87.1 being discussed?

Like other human coronaviruses, SARS-CoV-2 continually evolves. Some viral mutations erode antibody immunity, and this is one reason people are re-infected with coronaviruses every few years.

 

Most of the time, the evolution is gradual, with new viral variants having just one or a few mutations relative to their parent. 

 

But sometimes new variants appear with many mutations. Highly mutated variants probably evolve in chronic human infections.

 

Most highly mutated variants fizzle out, but a few have spread widely (eg, Omicron BA.1, Omicron BA.2, and BA.2.86's descendant JN.1)

 

BA.2.87.1 is a highly mutated variant, and so it is natural to ask if it will spread widely and have a public health impact

What will determine impact (if any) of BA.2.87.1?

Is it spreading rapidly? So far 9 sequences have been identified over ~2 months, all in South Africa. So BA.2.87.1 is transmitting some, but there is not currently evidence of rapid growth. We should monitor genomic data to see if it spreads more or fizzles.

 

Will it have increased antibody escape? This is best determined by experimental neutralization assays. But we can make an educated guess based on existing knowledge (see next slide).

 

Will it continue to evolve? All variants should be monitored for further evolution. For instance, BA.2.86 did not spread immediately, but its descendant JN.1 did.

 

Is it more or less pathogenic? Far too little data to even try to assess this. Question only really matters if it spreads widely.

Spike mutations in BA.2.87.1

Above are the spike mutations in:

  • BA.2 (an approximate ancestor of all current major variants)
  • XBB.1.5 (current vaccine strain)
  • JN.1 (current dominant variant)
  • BA.2.87.1 (newly discovered variant)

We can see that while BA.2.87.1 has a lot of RBD mutations, it is still less mutated in the RBD than JN.1. This is encouraging, as the RBD is the main target of neutralizing antibodies.

However, BA.2.87.1 does have a number of new deletions in the NTD. The effects of these need to be assessed in neutralization assays.

Additional information from others

(note a few of these threads have some errors in the specific spike mutations they list)