CDC: Updated COVID Variants Interactive Map & National Genomic Surveillance Dashboard

SARS-CoV2  Variants of Concern - ECDC

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In the 72 hours since our last update from the CDC (see HERE) states have reported another 109 COVID variants; or at least another 109 belonging to the three lineages (B.1.1.7, B.1.351 & P.1) of greatest concern currently being monitored by CDC's interactive map. 

I make the distinction because the California's CAL.20C (aka ` L452R') variant - which made headlines 2 weeks ago (see PrePrint: Emergence of a novel SARS-CoV-2 strain (CAL.20C) in Southern California, USA) - is not currently tracked. 

 

Nor, apparently is Brazil's P.2 variant - which according to yesterday's Los Angeles Times - has been detected in California along with several other states.  Little, however, is known about the potential impact of this variant. 

Genomic testing in the United States is highly limited, and often takes an extra week or two after samples are collected. While testing is being ramped up, currently the state doing the most testing (as a percentage of positive cases) is Washington, sequencing just over 2% of their COVID cases. 

The following  interactive map from the CDC's National Genomic Surveillance Dashboard is one of several graphics on this page showing the extent of genomic testing in the United States.  

While Washington sequences roughly 1 in 50 cases, and Oregon a little over 1 in 100 . . . some states have sequenced as few as 1 or 2 out of every 10,000 cases since the pandemic began.  Florida and California - which lead the nation in the number of B.1.1.7 variants reported - fall in the middle of the pack. 

Which means we are still far from seeing the full picture. States who continue to report few or no variants may simply not be looking very hard. 

The latest update (below) from the CDC, as of Tuesday night (Feb 2nd), shows 546 variants detected across 33 states. 

The emerging variants CDC is closely monitoring have mutations in the virus genome that alter the characteristics and cause the virus to act differently in ways that are significant to public health (e.g., causes more severe disease, spreads more easily between humans, requires different treatments, changes the effectiveness of current vaccines). It’s important to understand that genetic mutations are expected, and some variants can spread and become predominant while others subside.

To maintain a limited number of colors and allow for an easier comparison between states, the data ranges have changed from 1-40 to 1-50.

*The cases identified above are based on a sampling of SARS-CoV-2-positive specimens and do not represent the total number of B.1.1.7, B.1.351, and P.1 lineage cases that may be circulating in the United States and may not match numbers reported by states, territories, tribes, and local officials.

†Numbers will be updated on Sunday, Tuesday, and Thursday by 7:00 pm. 

While there are a lot of unanswered questions about the impact of these (and other) emerging variants - including concerns over diminished vaccine effectiveness - the CDC briefly describes what is known about these variants on their New Variants of the Virus that Causes COVID-19 page.

Multiple variants of the virus that causes COVID-19 are circulating globally:

• The United Kingdom (UK) identified a variant called B.1.1.7 with a large number of mutations in the fall of 2020. This variant spreads more easily and quickly than other variants. In January 2021, experts in the UK reported that this variant may be associated with an increased risk of death compared to other variant viruses, but more studies are needed to confirm this finding. It has since been detected in many countries around the world. This variant was first detected in the US at the end of December 2020.
• In South Africa, another variant called B.1.351 emerged independently of B.1.1.7. Originally detected in early October 2020, B.1.351 shares some mutations with B.1.1.7. Cases caused by this variant have been reported in the US at the end of January 2021.
• In Brazil, a variant called P.1 emerged that was first identified in travelers from Brazil, who were tested during routine screening at an airport in Japan, in early January. This variant contains a set of additional mutations that may affect its ability to be recognized by antibodies. This variant was first detected in the US at the end of January 2021.

These variants seem to spread more easily and quickly than other variants, which may lead to more cases of COVID-19. An increase in the number of cases will put more strain on health care resources, lead to more hospitalizations, and potentially more deaths.

 

So far, studies suggest that antibodies generated through vaccination with currently authorized vaccines recognize these variants. This is being closely investigated and more studies are underway.

 

Rigorous and increased compliance with public health mitigation strategies, such as vaccination, physical distancing, use of masks, hand hygiene, and isolation and quarantine, is essential to limit the spread of the virus that causes COVID-19 and protect public health.