#15,892
For the first 11 months of 2020, COVID variants were viewed as primarily of academic interest. While thousands had been identified - with the exception of the D614G `European' variant which emerged in early 2020 that appeared to have increased transmissibility over the `Asian' lineage - none had demonstrated any truly `game changing' qualities.
For the most part, COVID appeared functionally stable over most of 2020, despite some anecdotal reports from places like South Africa.
In mid-December, just as the first COVID vaccines were rolling out, the UK Health Secretary Announced A New COVID Variant - now dubbed B.1.1.7 - was rapidly gaining ground in Southeast England, and initial estimates suggested it was 30%-40% more transmissible than the `wild type' COVID that had circulated for most of 2020.
Since then, we've seen evidence that this B.1.1.7 variant is not only more transmissible, it also causes more severe illness, and carries a 67% higher mortality risk (see Eurosurveillance: Case fatality risk of the SARS-CoV-2 variant of concern B.1.1.7 in England).
It has also spread globally (see CDC map below), and has now been reported in nearly 100 countries.
Since then other variants of concern (VOCs) have emerged and have been identified, including B.1.351, P.1, B.1.427, and B.1.429 - along with a small number of variants of interest VOIs (including B.1.526, B.1.527, and P.2) - all of which continue to evolve and spread globally.
Overnight the CDC updated their COVID Variant Map, and their breakdown of variants by states. Once again Florida leads the nation with 2351 B.1.1.7 variants detected, along with 49 P.1 variants, and 15 B.1.351. Michigan and California come in second and third.
All of these number are substantial undercounts and should be viewed as representing trends, not actual conditions on the ground.
Variant Proportions in the U.S.
Updated Mar. 31, 2021
CDC’s national genomic surveillance program identifies new and emerging SARS-CoV-2 variants to determine implications for COVID-19 diagnostics, treatments, or vaccines authorized for use in the United States. Monitoring the spread of emerging variants in the United States relies on widespread, rapid sequencing. To accelerate sequencing in the United States, CDC has contracted with commercial diagnostic laboratories, and, in partnership with the Association of Public Health Laboratories (APHL), has implemented the National SARS-CoV-2 Strain Surveillance (NS3) program to provide a comprehensive and population-based US surveillance system.
Based on these data, sequences with similar genetic changes associated with important epidemiological and biological events are grouped into lineages*, and the proportion of lineages circulating in the United Stated are tracked and characterized to determine if they are considered variants of concern (VOC) or variants of interest (VOI). Most of the lineages identified through genomic surveillance do not fall into either of these categories. These data, along with data from many other sources, are used to inform national and state public health actions related to variants.
*A viral lineage is a group of viruses defined by a founding variant and its descendants. Names are assigned to SARS-CoV-2 lineages using manual and automated methods. Lineage designations are based on phylogenetic grouping followed by the identification of shared, common mutations.
The above chart illustrates how - since the first week of January - 3 variants (B.1.1.7, B.1.526, B.1.429) have emerged and now make up the bulk of cases in the United States. The B.1.1.7 variant, which barely registered on January 1st, appears on track to become the dominant COVID variant in the U.S. in the next few weeks.
Testing for variants remains limited, and the data generally lags behind by several weeks, so the picture today could be markedly different from what is depicted above for mid-March. From the above chart, however, it is apparent that B.1.429 and B.1.526 are also gaining ground.
The prevalence of each variant varies by state, with the `California variants' not surprising leading the pack in California, while the B.1.1.7 variants are surging in places like Florida, Minnesota and Michigan.
The data below is only current as of February 27, 2021, and so big swings have undoubtedly occurred over the past 30 days.
Variant proportions are based on representative CDC sequence data (NS3 + CDC-funded contract sequencing) collected over a four-week period ending February 27, 2021. Proportions are only shown for states for which CDC has 300 sequences from specimens collected during this timeframe.
Last fall, none of these VOCs were on our radar, and since the these viruses continue to evolve, it is fair to say that six months from now we may be looking at an entirely different set of COVID concerns.
Some of these variants are more likely to be controlled by our current crop of vaccines than others, and as more people are immunized, that could alter their individual trajectories. Not all of these VOCs are destined to be contenders.
While we are making substantial progress against COVID-19, and the continued roll out of vaccines will undoubtedly save many lives, the pandemic we face today is in many ways far more complex than what emerged a little over a year ago.
As tired as we all are of lockdowns, social distancing, and other restrictions . . . we should not expect this virus to give up without throwing a few more surprises our way.
