CDC Unveils New COVID Variant(s) Interactive Map Format

 The CDC's Old Format

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Over the past three days two previously undetected COVID variants have been reported in the United States for the first time (see Minnesota DOH Statement On 1st Detection Of Brazilian P.1. COVID Variant In the United States and South Carolina Dept Of Health Statement On 1st Detection of COVID Variant B.1.351 In The United States), joining the already widespread B.1.1.7 (aka `UK' variant), which has been detected in 26 states. 

Although not scheduled for an update until this evening, last night the CDC unveiled a new map format that now accommodates multiple variant types (see below).  Incidence (by state) is now color coded, and a variant-by-state table has been added. 

Given the likelihood of additional variants arriving (or emerging domestically) in the weeks and months ahead, this is a welcome and timely change.  After the break I'll have excerpts from the CDC's latest update on variants of concern. 

Emerging SARS-CoV-2 Variants

Updated Jan. 28, 2021 

Multiple SARS-CoV-2 variants are circulating globally. Several new variants emerged in the fall of 2020, most notably:

• In the United Kingdom (UK), a new variant of SARS-CoV-2 (known as 20I/501Y.V1, VOC 202012/01, or B.1.1.7) emerged with a large number of mutations. This variant has since been detected in numerous countries around the world, including the United States (US). In January 2021, scientists from UK reported evidence[1] that suggests the B.1.1.7 variant may be associated with an increased risk of death compared with other variants. More studies are needed to confirm this finding. This variant was reported in the US at the end of December 2020.

• In South Africa, another variant of SARS-CoV-2 (known as 20H/501Y.V2 or B.1.351) emerged independently of B.1.1.7. This variant shares some mutations with B.1.1.7. Cases attributed to this variant have been detected in multiple countries outside of South Africa. This variant was reported in the US at the end of January 2021. 

• In Brazil, a variant of SARS-CoV-2 (known as P.1) emerged that was first was identified in four travelers from Brazil, who were tested during routine screening at Haneda airport outside Tokyo, Japan. This variant has 17 unique mutations, including three in the receptor binding domain of the spike protein. This variant was detected in the US at the end of January 2021.

Scientists are working to learn more about these variants to better understand how easily they might be transmitted and the effectiveness of currently authorized vaccines against them. New information about the virologic, epidemiologic, and clinical characteristics of these variants is rapidly emerging.

CDC, in collaboration with other public health agencies, is monitoring the situation closely. CDC is working to detect and characterize emerging viral variants. Furthermore, CDC has staff available to provide technical support to investigate the epidemiologic and clinical characteristics of SARS-CoV-2 variant infections. CDC will communicate new information as it becomes available.

 

A more technical description of these variants follows:

Emerging Variants

B.1.1.7 lineage (a.k.a. 20I/501Y.V1 Variant of Concern (VOC) 202012/01)

This variant has a mutation in the receptor binding domain (RBD) of the spike protein at position 501, where the amino acid asparagine (N) has been replaced with tyrosine (Y). The shorthand for this mutation is N501Y. This variant also has several other mutations, including:

• 69/70 deletion: occurred spontaneously many times and likely leads to a conformational change in the spike protein

P681H: near the S1/S2 furin cleavage site, a site with high variability in coronaviruses. This mutation has also emerged spontaneously multiple times.

• This variant is estimated to have first emerged in the UK during September 2020.
• Since December 20, 2020, several countries have reported cases of the B.1.1.7 lineage, including the United States.
• This variant is associated with increased transmissibility (i.e., more efficient and rapid transmission).
• In January 2021, scientists from UK reported evidence[1] that suggests the B.1.1.7 variant may be associated with an increased risk of death compared with other variants.
• Early reports found no evidence to suggest that the variant has any impact on the severity of disease or vaccine efficacy.[2],[3],[4]

B.1.351 lineage (a.k.a. 20H/501Y.V2)

• This variant has multiple mutations in the spike protein, including K417T, E484K, N501Y. Unlike the B.1.1.7 lineage detected in the UK, this variant does not contain the deletion at 69/70.
• This variant was first identified in Nelson Mandela Bay, South Africa, in samples dating back to the beginning of October 2020, and cases have since been detected outside of South Africa, including the United States
• The variant also was identified in Zambia in late December 2020, at which time it appeared to be the predominant variant in the country.
• Currently there is no evidence to suggest that this variant has any impact on disease severity.
• There is some evidence to indicate that one of the spike protein mutations, E484K, may affect neutralization by some polyclonal and monoclonal antibodies.[4],[5]

P.1 lineage (a.k.a. 20J/501Y.V3)

• The P.1 variant is a branch off the B.1.1.28 lineage that was first reported by the National Institute of Infectious Diseases (NIID) in Japan in four travelers from Brazil, sampled during routine screening at Haneda airport outside Tokyo.
• The P.1 lineage contains three mutations in the spike protein receptor binding domain: K417T, E484K, and N501Y.
• There is evidence to suggest that some of the mutations in the P.1 variant may affect its transmissibility and antigenic profile, which may affect the ability of antibodies generated through a previous natural infection or through vaccination to recognize and neutralize the virus.
• A recent study reported on a cluster of cases in Manaus, the largest city in the Amazon region, in which the P.1 variant was identified in 42% of the specimens sequenced from late December.[5] In this region, it is estimated that approximately 75% of the population had been infected with SARS-CoV2 as of October 2020. However, since mid-December the region has observed a surge in cases. The emergence of this variant raises concerns of a potential increase in transmissibility or propensity for SARS-CoV-2 re-infection of individuals.

• This variant was identified in the United States at the end of January 2021.