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SARS-CoV-2: Variant Soup

Information and resources on SARS-CoV-2 (the virus that causes COVID-19)


For the most up-to-date information on the global trends of COVID-19 variants and mutations, check Cornelius Roemer's monthly SARS-CoV-2 Variant Reports on GitHub.

Latest Update: April 27, 2023


XBB descendants continue growing across the globe. In sequences collected at the beginning of April, less than 15% were non-XBB*, about half the proportion a month earlier (30% beginning of March).

At the start of April, there was particularly little non-XBB* left in the USA (<5%). China had the highest proportion of non-XBB* (~75%) though XBB* is quickly making inroads there as well. Japan and South Korea also still have sizeable non-XBB* proportions.

Spike mutation S:486P is now present in the vast majority of XBB*: less than 5% of XBB* do not have 486P.

The major XBB* sublineages are currently:

  • XBB.1.5*
  • XBB.1.9.1*
  • XBB.1.9.2*
  • XBB.2.3*
  • XBB.1.16*

XBB.1.16* has grown to dominance in India and is increasing globally. The extra advantage over XBB.1.5*-like lineages appears to be mutation S:478R (in addition to 486P). As seen with 486P, 478R has arisen multiple times within XBB and appears to predictably confer a growth advantage in the lineages that acquire it (the more beneficial a mutation, the more often it arises independently, recall 346T in BA.5).

While XBB.1.16* is currently the most prominent XBB lineage with both 486P and 478R, other such lineages could in the mid-term replace it.

India, where XBB.1.16* has been dominant since end of February, has seen a steep rise in confirmed cases which have grown by a factor of 100 since the start of February. It is difficult to say to which extent this wave is driven by XBB.1.16* and to which extent it is a seasonal effect: a strikingly similar pattern (40-fold growth from beginning of February to end of April) was seen at exactly the same time of year in 2021. Back then, the wave coincided with the emergence of Delta. So the answer is possibly both effects matter: emergence of new variant and seasonal effects.

A comprehensive discussion of XBB.1.16, including clinical properties, can be found in the recent WHO Risk Assessment from April 17.

Mutations to Watch in XBB

In addition to 486P and 478R, a number of other Spike mutations have been observed repeatedly in XBB*. While some, like 456L, did not initially appear to confer a significant growth advantage, growth (dis)advantages conferred by mutations can change over time, as population immunity builds against a variant. Recently, 456L has started to appear independently and grow in frequency. What is currently only a slight growth advantage (~20% per week) could grow in the future.

Besides 456L, mutations 403K and 521S have been observed to increase in share and are part of a number of lineages. This list is not exhaustive.



Remaining Non-XBB Diversity

In particular for vaccine variant selection, it is important to keep an eye on remaining non-XBB diversity (~15%): the fewer non-XBB there are, the more obvious and less risky a switch to XBB (or sublineage thereof) is.

The non-XBB diversity can be broken down roughly into (share is always with collection date beginning of April):

  • BA.2.75* (Nextstrain clade 22D, mostly BN.1* and CH.1.1*)
    • ~5%, decreasing steadily at ~10-20% per week
    • Most common in South Korea (BN.1*, ~40%) and Europe (CH.1.1, ~5-10%)
  • BQ.1* (Nextstrain clade 22E, mostly BQ.1.1*)
    • 4%, decreasing at 20-30% per week
    • Most common in Canada (10%) and Japan (10%)
  • BA.5* excluding BQ.1* (Nextstrain clade 22B, mostly BA.5.2.48* and BF.7*)
    • ~3%, decreasing at 10-20% per week
    • Most common in China (BA.5.2.48, BF.7.14*, 70%) and Japan (BF*, 25%)
  • BA.2* excluding BA.2.75* (Nextstrain clade 21L, mostly BA.2.3.20)
    • 0.2%, decreasing slowly at 5-15% per week
    • Most common in Philippines (no recent data, but was 50% in February, particularly CM.8.1), Japan (1%) and India (0.5%)
  • recombinants similar to BA.2.75* and/or XBB*
    • 1%, decreasing at 10-20% per week
    • Most common in Australia (XBF, 5%)
  • XBC* (Delta-Omicron recombinant)
    • 0.3%, potentially increasing at 10-20% per week
    • Most common in Australia (XBC.1.6, 10%) and Philippines (no recent data, but known to be common in February at 10%)
  • XAY* (Delta-Omicron recombinant)
    • 0.1%, ~steady
    • Most common in Denmark (1%, XAY.2) and Germany (1%, XAY.1.1)

While the future is most likely to look like XBB*, it is possible that BA.2.75* may play a role (potentially through recombination with XBB, like recently designated XCC). There is a small but non-zero chance, that a more divergent lineage may emerge from XBC, XAY or BA.2.3.20

Emerging Variants to Watch

Emerging Omicron Sub-Variants of Concern

Most of the hundreds of sub-variants that have descended from Omicron have not picked up traction to spread globally. However, certain mutations can increase the risk of a variant spreading globally. Below are sub-variants that have been identified as concerning for global spread.

PANGO Lineage Lineage or Alias Concerns
XBF BA.5.2 & CJ.1 (BA.5 & BA.2) BA.2 & BA.5 recombinant
DS.1 BN.1.3 (BA.2) Most immune evasive +  High ACE-binding affinity
XBL XBB.1 & BA.2.75 XBB/BA.2.75 recombinant
DN.1.1.1 BQ.1 (BA.5) Exceptional ACE-binding affinity
XBB.1.5.13 XBB.1.5  
DV.1 CH.1.1.1 (BA.2.75)  
EG.1 XBB.  
EK.2 XBB. Even better ACE2 binding without losing immune escape than XBB.1.5
EL.1 XBB.  
EM.1 XBB. Growth advantage
XBC.1.6 XBC.1*  

Highlighted covSPECTRUM Collections
  • Collection #24 - This collection keeps track of recent designated lineages - daily updated
  • Collection #25 - SARSCoV2 Lineages of Interest and Concern - Maintained by Rajlabn
  • Collection #71 - Designated Omicron lineages including recombinant lineages involving Omicron - Maintained by @alurqu
  • Collection #144 - XBB* Subvariants - Maintained by Tsh Huang
  • Collection #151 - A list of new and emerging lineages of the SARS-CoV-2 virus that may be worth watching - Maintained by @CawsonEthan
  • Collection #155 - Top variants - Maintained by aviczhl2
Immune Escape & ACE2 Binding Affinity of SARS-CoV-2 Omicron Variants

Last Updated: February 28, 2023

Red Box = Zone of Concern (high immune escape and high ACE2 binding affinity)

Image source: Raj Rajnarayanan @RajlabN