More Variants Emerge

As new variants emerge, it’s time to update our charts so you will know what’s coming and what to watch for.  In its summary released last week, the CDC made minor terminology revisions and made some roster changes on the line-up cards.  In this edition, we will highlight the changes and update our charts with the latest information.

Variants of High Consequence.  Now called Variants of High Consequence instead of Variants of High Concern, these SARS-CoV-2 strains cannot be detected by tests, are not treatable by current therapies, or are not protected by natural or vaccine induced immunity.  A strain that fits any of these categories must be reported to the WHO and CDC immediately.  Thankfully, this list is still blank.

Variants of Concern.  Variants of Concern have reduced detection by tests, reduced response to therapy, reduced immune protection, greater transmissibility, or more severe disease.  Although there have been no additions to this list, there have been noteworthy updates to our understanding of these variants.  For example, B.1.1.7, the UK Variant, and B.1.351, the South African Variant, remain at the top of the increased transmissibility list at 50%; however, as we predicted in January, B.1.1.7 is also now the most prevalent lineage of the virus in most regions of the U.S. except the west coast. The California Variants B.1.527 and B.1.529 are now considered the most resistant to therapy of all U.S. variants.

Variants of Interest.  Variants of Interest are U.S. variants with the potential to become Variants of Concern based in the mutations within the variant, even though they don’t fulfill criteria to be a Variant of Concern based on observation.  Two changes have occurred.  First, B.1.525 is now believed to have first originated in the U.K. and Nigeria, even it continues to be most prevalent in New York.  And second, since last writing, a new variant, B.1.526.1 has spun off the New York Variant B.1.526.  This gives us the opportunity to briefly explain the classification system I have been using.

Because SARS-CoV-2 mutates so quickly, new variants emerge rapidly.  The PANGO lineage system attempts to apply some order to this chaos.  Names begin with a letter designating a unique lineage, followed by a series of numbers separated by dots.  For example, the U.K. Variant B.1.1.7 is the seventh named variant of the B.1.1 lineage, and B.1.1 is the first named variant of the B.1 lineage, and so forth.  By looking at the name B.1.526.1 we know that this variant evolved from the New York Variant B.1.526, but that it has enough unique characteristics to merit its own name.  The variant’s family tree is embedded in the name.  For example, B.1.1 and B.1.526 are siblings, B.1.526.1 and B.1.1.7 are cousins, and B.1 and P.1 are from totally different families.  It’s a useful although not perfect system, and like everything in the pandemic, it continues to evolve.

Thousands of variants have been described.  The ones highlighted in the charts below are currently considered the most important in the U.S:

Variants of Concern
Variant	First Detection	Current U.S. Prevalence	Increased Transmission	Increased Severity	Reduced Detection by Tests	Resistance to Treatment
B.1.1.7	UK	44.7%	50%	●
P.1	Japan/Brasil	1.5%				●
B.1.351	South Africa	0.7%	50%			●
B.1.427	California	3.1%	20%			●
B.1.429	California	6.9%	20%			●

Variants of Interest
Variant	First Detection	Current U.S. Prevalence	Increased Transmission	Increased Severity	Reduced Detection by Tests	Resistance to Treatment
B.1.526	New York	6.9%				●
B.1.526.1	New York	3.6%				●
B.1.525	UK/Nigeria	0.3%				●
P.2	Brazil	0.3%				●