4/6/2021 As Variants Have Spread, Progress Against the Virus in U.S. Has Stalled, by Lauren Leatherby, The New York Times
The country’s vaccine rollout has sped up since the first doses were administered in December, recently reaching a rolling average of more than three million doses per day. And new U.S. cases trended steeply downward in the first quarter of the year, falling by almost 80 percent from mid-January through the end of March.
But during that period, states also rolled back virus control measures, and now mobility data shows a rise in people socializing and traveling.
Amid all this, more-contagious variants have been gaining a foothold, and new cases are almost 20 percent higher than they were at the lowest point in March. The B.1.526 variant, which first appeared in New York City in samples from November, appears in two forms: one with a mutation that may help the virus evade antibodies and another that may help it bind more tightly to human cells.
4/1/2021 Michigan Confirms First Case Of The Brazil Variant, by Allen Lengel, Deadline Detroit
The news came on the same day the state reported 6,036 new Covid cases and 49 deaths.
4/1/2021 Michigan's 1st case of Brazil COVID-19 variant identified in Bay County, by Christina Hall, Detroit Free Press
This is the second new variant of COVID-19 to be identified in Bay County since last week, said Joel Strasz, the county's public health officer, adding, "The rise of these new variants definitely impact the progress we have made this year with vaccinations."
3/30/2021 The Fourth Surge Is Upon Us. This Time, It’s Different., by Zeynep Tufekci, The Atlantic
The twists and turns of a pandemic can be hard to predict, but this most recent increase was almost inevitable: A more transmissible and more deadly variant called B.1.1.7 has established itself at the precise moment when many regions are opening up rapidly by lifting mask mandates, indoor-gathering restrictions, and occupancy limits on gyms and restaurants.
3/26/2021
4) One Brazil @obscovid19br study puts #P1 transmission at 2.5x faster than old
common strain. This 150% increase is much faster than even #B117 if it holds up.
As ever, if it's a tweet, click it to follow the thread.
3/17/2021
SARS-CoV-2 Variants, updated Mar. 16, 2021, CDC
2/26/2021 Worst fears of Denmark CDC coming true, B117 will be the dominant #SARSCoV2 variant, by Dr Erid Feigl-Ding
2) The steady inevitable March of #B117 replacing the old strain is as constant as time. B117 will replace older less contagious common strains - and it certainly has. Denmark Data is best because they now genetically sequence 100% of all cases!!!
3) Denmark cases surge is now very different than before - a lot more reports of children not seen before. Here is an outbreak of #B117.
4) The global decline in cases **HAS NOW REVERSED**. Cases are once again on the rise worldwide, especially in Europe where #B117 is most common and surging.
5) I warned about this divergence - old strain pandemic is ending. But new #B117 led pandemic is on the rise. And we didn’t see it / it was hard to see because of the initial B117 growing in the underbelly of an overall decline.
TWO DIFFERENT #COVID19 PANDEMICS—Many think with cases dropping that pandemic is nearly over. But truth is, there are now 2 different #SARSCoV2 pandemics diverging—old strain is waning, while the more contagious #B117 strain is dominating. We will be soon slammed very hard.
Here is what is going to happen... currently R is ~0.9 in many places, but with the more infectious #B117, the R will jump 50% approximately. And it is inevitable (all CDC and Danish models say this) that B117 will take over as the reigning dominant variant soon... and when that happens, what worked before to keep the pandemic contained at R of 0.9 will no longer work. Here is the model for Alberta, by @GosiaGasperoPhD. The B117 dotted red line will soon dominate and drive a new surge in latter half of March and April.
The solution to defeating the #B117 is to chase a #ZeroCovid approach and slam the R even lower to below 0.7.... but optimally 0.6 or less. So that even when the #B117 arises, it will keep R under 1 (0.6*1.5=0.9). And by keeping R at 0.6 now—we will have buffer room for B117. And again Denmark CDC agrees with that assessment. Their model for R of 0.8 shows it is insufficient to defeat #B117. But its model for R 0.7 shows it can be enough. The problem is that of the declining states, only 1 state is under R 0.7... which is Wyoming (figure below sorted from lowest to highest R). Every other state’s R is over 0.7. Thus while they would yield decreases now—they won’t once #B117 takes over.
2/22/2021 Coronavirus Mutations: A Visual Guide to New, More-Infectious Variants, by Alberto Cervantes and Josh Ulick, The Wall Street Journal
2/20/2021 National and Subnational estimates for the United States of America
Danish scientists have been extremely worried and anxious about the growing #B117 underbelly despite case drop. They knew it was coming. And they kept warning the world.
Denmark even more worried than ever about new #B117 variant—B117 cases increasing 70% a week **despite strict lockdown**, says Denmark’s CDC genome sequencing *every single case in the country* for mutation. By contrast, United States sequencing 0.3%.
2/18/2021 Nextstrain, retweeted by the Covid-19 Genomics (COG-UK) Consortium
About Nextstrain
2/24/2021 Research Futures: The Sequencing and Tracking Of Phylogeny in COVID-19, University of Portsmouth
As the virus passes from person to person, mutations can occur that can be monitored and traced to identify chains of infection. Working as part of the COVID-19 Genomics UK Consortium (COG-UK), Dr Robson and his team work with NHS sites across the South and Lighthouse Labs throughout the UK to help with infection control processes and to provide a UK-wide database of viral genomes. The UK leads this field by a wide margin, and these data are used to track and trace novel variants of concern.
2/22/2021 How to Vaccinate the World, BBC, 28 minutes
Professor Emma Thomson (twitter: @emcat1 ) joined the panel of experts on @BBCRadio4’s How to Vaccinate the World, to discuss sequencing #SARSCoV2 & why monitoring global #COVID19 infection is vital for vaccine effectivenessMicrobe
2/22/2021 Introducing the COG-UK Mutation Explorer (COG-UK-ME), Covid-19 Genomics Consortium (COG-UK)
COG-UK-ME is an open-access dashboard that provides access to data on #SARSCoV2 mutations and variants of interest Microbe
Explore COG-UK-ME: http://sars2.cvr.gla.ac.uk/cog-uk/
Read our explainer blog: https://bit.ly/3smW51X
2/21/2021 Officials confirm the first case of the South Africa variant in a New York resident, by Mihir Zaveri, The New York Times
The variant, known as B.1.351, was originally identified in South Africa in December, and has since been found in dozens of other countries and at least nine states, including California, Texas and Virginia. The variant carries mutations that help it latch on more tightly to human cells and that may help the virus evade some antibodies.
Two weeks ago, South Africa halted the use of the AstraZeneca-Oxford vaccine after evidence emerged that it did not protect participants in a clinical trial from mild or moderate illness caused by the variant.
2/21/2021 Virus variants deliver fresh blow to Europe’s open borders, by Matina Stevis-Gridneff, The New York Times
Thousands of people in Austria and the Czech Republic commute daily to jobs in Germany, and after the new checks came into force, long lines began to form. By the end of the week, business groups were writing desperate letters asking Germany to ease or lift the restrictions.
2/18/2021 Coronavirus Variants and Mutations, by Jonathan Corum and Carl Zimmer, The New York Times
After its discovery in December, coronaviruses from the B.1.1.7 lineage quickly emerged in other countries and surged at an exponential rate. It is doubling in the United States every ten days. Preliminary evidence suggests that B.1.1.7 is about 35 percent more deadly than other variants. But testing suggests that vaccines still work well against it.
Lineages covered in this assemblage of reports:
B.1.1.1.7 aka 20I/501Y.V1
B.1.351 aka 20H/501Y.V2
P.1 aka 20J/501Y.V3
D614G Spike Mutation
N501Y Spike Mutation
E484K Spike Mutation
L452R Spike Mutation
Q677 Spike Mutation
CAL.20C Variant
On the NYTimes site, this diagram and dozens more from the report are actually readable
2/14/2021 7 Virus Variants Found in U.S. Carrying the Same Mutation, by Carl Zimmer, The New York Times
It’s difficult to answer even basic questions about the prevalence of these seven lineages because the United States sequences genomes from less than 1 percent of coronavirus test samples.
1/19/2021 As Coronavirus Mutates, the World Stumbles Again to Respond, by Matt Apuzzo, Selam Gebrekidan and Apoorva Mandavilli, The New York Times
“We do know how to dial down the transmission of the virus by a lot with our behavior,” said Carl T. Bergstrom, an evolutionary biologist at the University of Washington in Seattle. “We’ve got a lot of agency there.”
1/16/2021 Why the New Covid-19 Variants Could Be More Infectious, by Daniela Hernandez and Alberto Cervantes, The Wall Street Journal
The Receptor Binding Domain isn’t the only portion of the spike protein that is affected in the two variants found in the U.K. and South Africa.
1/6/2021 U.S. Is Blind to Contagious New Virus Variant, Scientists Warn, by Carl Zimmer, The New York Times
It’s not too late to curb the contagious variant’s spread in the U.S., experts say — but only with a national program for genetic sequencing.
Britain has sequenced 146,463 coronavirus genomes since March, nearly half of all the sequenced coronavirus genomes in the world.
Over the past month, American researchers have only sequenced a few hundred genomes a day, according to GISAID, an international database where researchers share new genomes from coronaviruses. And just a few states have been responsible for most of the effort. California is in the lead, with 8,896 genomes. In North Dakota, which has had more than 93,500 cases so far, researchers haven’t sequenced a single genome.
1/6/2021
