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SARS-CoV-2: SARS-CoV-2 Recombination

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

What is Recombination?

Genetic Recombination

Recombination is the exchange of genetic material between two distinct organisms which produce an "offspring" that has a combination of traits that are not found in either parent.

Numerous RNA viruses (including coronaviruses) are capable of genetic recombination when at least two viral genomes are present in the same host cell. Recombination is thought to the be the major driving force of viral evolution. In coronaviruses especially, it is believed that recombination has created the broad genetic diversity of this family of viruses, including their ability to transmit from host to host (including cross-overs to other species), and even how many novel coronaviruses likely emerged.


Viral Recombinants

Recombinant viral variants can occur when a single person is infected with multiple distinct variants at the same time, allowing the two different variants to interact during replication. When their genetic materials mix they create a new hybrid, or a recombinant variant.

There's nothing inherently 'worse' about recombinant variants - they could be more or less fit than their parents, or have the same fitness. While recombinants are not necessarily "worse" than regular variant strains, sometimes recombination can bring together mutations that offer a big advantage to the virus in some way.

SARS-CoV-2 Recombinants

SARS-CoV-2 Recombinant Strains

Recombinant strains use a different naming system that begins with an X followed by sequential letters (XA, XB, XC....then XAA, XAB, etc.), and no numbers unless there is an unamibiguous descendant (ex. XB, XB.1). In most cases, there is a minimum of 50 sequences to design a novel recombinant linage, but exceptions arise if the recombinant has a particular novelty or significance, with unusual breakpoint and/or parental lineages.


"Deltacron"

The first recombinant variant that gained any sort of growth traction was the first "Deltacron". Delta and Omicron BA.1 co-circulated from November 2021 until February 2022 and eventually recombined to form a new recombinant variant. These recombinants were often referred to as "Deltacron". They were some of the earliest recombinants to be named by PANGOLIN.

Both the Delta variant and "Deltacron" were overtaken by BA.2 by February 2022, thus there was little co-circulation of Delta and BA.2 and no identified recombinants with those strains.

Recently there have been a handful of "Deltacron" recombinants resurfacing (XAY, XBC). This is likely due to patients with prolonged or latent infection with Delta that then got subsequently infected with Omicron, or potentially from Delta variants in animal reservoirs.

SARS-CoV-2 Recombinant Lineages

Notable SARS-CoV-2 Recombinant Lineages
Recombinant Hybrid Lineage
XC Alpha (B.1.1.7) and Delta (AY.29)
XD "Deltacron" Delta (AY.4) and Omicron (BA.1)
XE BA.1 and BA.2
XF Delta (AY.4) and Omcrion (BA.1)
XG BA.1 and BA.2
XAY AY.45 (Delta) & BA.4/BA.5 (Omicron)
XBB "Gryphon" BJ.1 (BA.2.10.1.1) and BM.1.1.1 (BA.2.75.3.1.1.1)
XBC B.1.617 (Delta) & BA.2 (Omicron)
XBF BA.5.2.3 and CJ.1
XBL* XBB.1 and BA.2.75

*XBL (XBB.1 and BA.2.75) is the first recombinant of a recombinant!!

Meet the Gryphon Family

What is XBB?

XBB* is a recombinant of two Omicron sublineages:

  • BJ.1 (BA.2.10) "Argus"
  • BM.1.1.1 (BA.2.75) "Mimas"

It first emerged in Singapore in the fall of 2022 and quickly began spreading across the globe. XBB.1 was first detected in the U.S. on September 15, 2022.

XBB was considered to be the most immune-evasive COVID variant so far, surpassing the immune-evasiveness of BA.5, which was dominant around the globe last summer, The ability of XBB to evade immunity is “extreme,” approaching the level of immune evasion shown by SARS, a coronavirus that infected thousands and caused nearly 800 deaths in the early 2000s.

All identified XBB subvariants: XBB* Subvariant Collection #144 (covSPECTRUM - maintained by Tsh Huang)


Who's Who in the XBB ("Gryphon") Family
  • Gryphon = XBB* (recombinant of BJ.1 ["Argus"] & BM.1.1.1["Mimas"])
  • Hippogryph = XBB.1 (child of XBB Gryphon)
  • Kraken = XBB.1.5 (child of Hippogryph)
  • Hyperion = XBB.1.9.1 (descendant of Hippogryph, but not Kraken)
  • Arcturus = XBB.1.16 (descendant of Hippogryph, but not Kraken)
  • Acrux = XBB.2.3 (descendant of XBB Gryphon)
  • Bellatrix = FY.4 (alias XBB.1.22.1)
  • Eris = EG.1.5 (descendant of Arcturus)
  • Fornax = FL.1.5.1 (descendant of Hyperion)

 

"Gryphon" (XBB)

XBB was dubbed "Gryphon" by evolutionary biologist Ryan Gregory in early October 2022, and since its emergence it quickly began to dominant the SARS-CoV-2 viral landscape. Today the vast majority of circulating variants across the globe are descendants of XBB (aka the "Gryphon Family").

 
"Hippogryph" (XBB.1)

XBB.1 was the first descendant of XBB. It was first detected in the U.S. on September 15, 2022. It has spawned several notable descendants: Kraken, Hyperion, and Arcturus.

 
"Kraken" (XBB.1.5)

XBB.1.5 (nicknamed "Kraken" by Ryan Gregory), first appeared in December 2022 in New York.

In mid-December 2022 the CDC failed to report XBB.1.5 as a new breakout lineage (>1% circulation) in their weekly Nowcast for several weeks, simply showing XBB circulating at around 20%. On December 31, 2022 the weekly Nowcast reported that XBB.1.5 was circulating at 40% across the U.S. and that the prior week (12/24/22), suddenly had XBB .1.5 being reported at circulating at 20%!

Not only is "Kraken" even more immune evasive than XBB ("Gryphon"), but it has much better (bad) binding affinity to ACE2.

By early 2023 "Kraken" took control in the U.S., and accounted for nearly 100% of circulating variants in the Northeast. By late-February 2023 it accounted for more than 75% of circulating variants across the U.S. and was the dominant variant in all 10 HHS regions. By early-March 2023 XBB.1.5 was nearing 90% of all circulating variants in the U.S., and nearly 40% of circulating variants globally.

On March 15, 2023, the WHO updated their variant designation system, removing Omicron (B.1.1.529) from their list of Variants of Concern (VOC), and added Kraken (XBB.1.5) as a Variant of Interest (VOI), under their new system.

 
"Hyperion" (XBB.1.9.1)

XBB.1.9.1 was the first variant to receive a nickname using the new system: "Hyperion", after a moon of Saturn. XBB.1.9.1 (Hyperion) is the 1st descendant of the 9th descendant of the first descendant of XBB. It is not descended from XBB.1.5 (Kraken).

XBB.1.9.1 is the first variant to have an increased transmission advantage of XBB.1.5 (Kraken). It was first detected in Southeast Asia in January 2023. By late January it was circulating globally at over 1% and by mid-February over 4% globally. It first appeared on CDC Nowcast on February 27th. It has also been increasing in the United Kingdom and Europe.

 
"Arcturus" (XBB.1.16)

XBB.1.16 first appeared in early March 2023 with significant growth advantage in India and quickly began causing a surge of infections and hospitalizations. It was named Arcturus on March 13, 2023.

 
"Acrux" (XBB.2.3)

XBB2.3 first appeared in late December 2022 in India, but did not experience significant growth advantage until March 2023, likely as the Arcturus surge in India began slowing. It is now the fasting growing XBB variant and carries the highly evasive mutation S:T478K from the very deadly Delta variant. It was named Acrux on April 29, 2023.

 
"Bellatrix" (FY.4)

FY.4 is the alias of XBB.1.22.1.4. It first appeared in March 2023 in Kenya with significant growth advantage. It was named Bellatrix on May 24, 2023.

 
"Eris" (EG.5.1)

EG.1.5 is alias of XBB.1.9.2.5 It first appeared in March 2023 in China and has since spread to over 50 countries.  It was named Eris on August 4, 2023. The WHO upgraded Eris from a "variant under monitoring" to a "Variant of Interest" on August 10, 2023.

 
"Fornax" (FL.1.5.1)

FL.1.5.1 is alias of XBB.1.9.1.1.5. It first appeared in April 2023. It was named on August 11, 2023.