Viral Anarchy

#17,639

Although there were certainly variants in the mix from the beginning, for the first year of the COVID  pandemic we mainly dealt with the European variant (D614G) which appeared in early 2020.  The first major shift began in November in the UK (see CDC Update On New COVID Variant In The UK', and would be dubbed the `Alpha Variant'. 

In early January 2021, Denmark's SSI warned that the B.1.1.7 (Alpha) COVID variant was on track become the dominant COVID lineage in Denmark by the end of February.

 

By late February, Denmark's SSI also warned of increased hospitalizations linked to the B.1.1.7 variant (see SSI: COVID Variant B.1.1.7 Now Dominant In Denmark - Increases Risk of Hospitalization 64%).

In other parts of the world, other variants emerged, but most remained local threats.  Delta was the exception, and by mid-summer 2021, it was dominant throughout most of the world (see UK PHE Technical Briefing On COVID Variant B.1.617.2 (Delta). 

Delta reigned until the end of the year, but a new - highly divergent - Omicron variant dethroned Delta, and caused the biggest wave of the pandemic.  Luckily, Omicron proved to be less severe than Delta. 

And for the first year of Omicron, we saw an orderly (albeit, rapid) procession of similar variants, notable for their ability to evade previous immunity, but not (with the aid of vaccines) as severe as pre-Omicron waves. 

The CDC Nowcast from late August of 2022 (see below) featured 1 hugely dominant variant (BA.5), and a short list (n=3) of rising and falling competitors (BA.4.6, BA.4, BA.2.12.1).  

At that time, Omicron BA.5 seemed so well entrenched (90%), that there were few qualms about rolling out a new BA.5 based booster shot that fall.  But 3 months later BA.5 had been supplanted by BQ.1, and 30 days later, BQ.1 was on the decline as the first of the XBB (recombinant) variants began to surge. 

By the first week of the new year, the CDC was tracking 13 COVID variants in the United States (up from 4 in August), and BA.5 had dropped to less than 5% of cases in the country. 

By the end of April (see CDC Nowcast: Recombinants Rule), XBB variants were in full control, and in May the WHO Recommended Switching To A Monovalent XBB 1.5 based COVID Vaccine this fall. 

But evolution never stops. In fact, as we've seen for the past 3+ years with COVID, it continues to accelerate.  

The more diversity, the more genetic building blocks there are from which to assemble or spin off new variants. Which is why, the most recent CDC Nowcast is tracking  - not 13 - but 23 (*) COVID variants in the United States . 

Over the past 12 months we've seen a 6-fold increase in the number of circulating variants in the United States. But, as you'll notice, I put an asterisk on the number 23.  For while it isn't showing up yet in the CDC Nowcast, the CDC - and the world - are tracking a new - highly divergent - BA.2.86 variant. 

CDC Initial Risk Assessment On COVID BA.2.86

PAHO Technical Document & Statement On COVID EG.5 and BA.2.86

UKHSA Risk Initial Risk Assessment & Update on BA.2.86

Right now, we don't know how much of an impact BA.2.86 will have.  We only know that it represents the biggest evolutionary leap in the SARS-CoV-2 virus since the emergence of Omicron in late 2021.  

Granted, it may not be able to compete with the currently rising EG.5, or the next XBB variant to emerge. Or it may need to pick up additional mutations before it can become competitive.  Or, it could be the next `big' thing.

Only time will tell. 

Hopes that COVID would settle into a docile, `seasonal' COVID virus - one that we can mitigate with yearly vaccines, and build community immunity against - seem further away than ever.  

Instead of `One variant to rule them all', we've got viral anarchy. 

And while BA.2.86 is the latest big leap in COVID's evolution, it isn't necessarily the last one we'll see. Particularly given the continual spillover of SARS-CoV-2 into non-human hosts. 

And I'd be remiss if I didn't mention that we are seeing a similar (albeit, slower) pattern of evolution in HPAI H5 viruses; global spread, followed by the emergence of dozens of new genotypes (aka variants).

Predicting what influenza, COVID, or avian flu will do in the future is a mug's game.  There are too many variables, and too little reliable information, to do more than hazard a guess. 

But if patterns and trends mean anything, we should not assume that COVID or HPAI H5 will go quietly into the night.