Avian Flu Diary: CDC U.S. Variant Update: B.1.1.7 Dominates While P.1 & B.1.617.2 Continue To Rise

Global Spread of COVID Variant B.1.617.2 - Credit CDC

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The CDC released their latest bi-weekly analysis (current as of 05/08/21) of COVID variant spread and frequency in the United States late yesterday, and it continues to show the B.1.1.7 variant remains dominant and continues increase its share, albeit not as rapidly as the latecomers P.1. and B.1.617.2.

The B.1.427/B.1.429 (aka `California') variants - which once held sway in the western United States (particularly in California and Arizona) - continue to recede, with both states reporting less than 10% of recent samples matching.

While most of the other variants on the watch list continue to give ground to B.1.1.7, there are two notable exceptions:

the P.1 variant has increased its national share from 5.0% to 6.8% over the past two weeks. Illinois (21.1%), Massachusetts (13.4%), Indiana (10.3%), and California (10.0%) all report detections in the double digits, while Florida drops to 5th place and comes in at 9.6%.

the B.1.617.x lineages - which were only added to the CDC's tracking list two weeks ago - have shown rapid growth with B.1.617.2 going from .5% to 1.3% in this latest report, in increase of 260%. While still relatively minor players, there are concerns they may be even more transmissible than B.1.1.7, and may become the next dominant strain.

The following chart shows the progression of variant share in the United States over the past 3 months. B.1.1.7 has been the biggest performer, but we've seen reports from the UK and India suggesting the B.1.617.2 variant can be quickly overtaken by B.1.617.2.

Excerpts from the CDC's latest update follow:

Variant Proportions

Estimated Proportions of SARS-CoV-2 Lineages

The data below show the estimated biweekly proportions of the most common SARS-CoV-2 lineages circulating in the United States, based on greater than 175,000 sequences collected through CDC’s national genomic surveillance since Dec 20, 2020 and grouped in 2-week intervals. Data are subject to change over time and will be updated as more data become available. Variant proportions are adjusted using statistical weighting to correct for the non-random sampling of sequencing data over time and across states and to provide more representative national estimates.

Nowcast weighted estimates that predict proportions for more recent time intervals are added when “Nowcast On” is selected in the dashboard controls below.

This expected trend is shown by using the CDC's `Nowcast' option, that projects what the numbers will be two weeks after the the surveillance cut-off date. In this case, while B.1.1.7 gains additional ground (increasing by roughly 5%), P.1 is expected to grow by more than 40%, and B.1.617.2 to have doubled.

The CDC's most current (May 8th) breakdown of variant proportions follows:

While the World Health organization and the UK's PHE have both recently elevated the B.1.617.2 variant to a VOC (Variant of Concern), it remains a VOI (Variant of Interest) here in the United States.

SARS-CoV-2 Variant Classifications and Definitions
Updated May 25, 2021
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Key Points:

Genetic variants of SARS-CoV-2 have been emerging and circulating around the world throughout the COVID-19 pandemic.

Viral mutations and variants in the United States are routinely monitored through sequence-based surveillance, laboratory studies, and epidemiological investigations.

A US government interagency group developed a Variant Classification scheme that defines three classes of SARS-CoV-2 variants:

Variant of Interest
Variant of Concern
Variant of High Consequence

The B.1.1.7, B.1.351, P.1, B.1.427, and B.1.429 variants circulating in the United States are classified as variants of concern.

To date, no variants of high consequence have been identified in the United States.

Laboratory studies suggest specific monoclonal antibody treatments may be less effective for treating cases of COVID-19 caused by variants with the L452R or E484K substitution in the spike protein.

L452R is present in B.1.526.1, B.1.427, and B.1.429.

E484K is present in B.1.525, P.2, P.1, and B.1.351, but only some strains of B.1.526 and B.1.1.7.

Viruses constantly change through mutation. A variant has one or more mutations that differentiate it from other variants in circulation. As expected, multiple variants of SARS-CoV-2 have been documented in the United States and globally throughout this pandemic. To inform local outbreak investigations and understand national trends, scientists compare genetic differences between viruses to identify variants and how they are related to each other.