9/3/2021 What we now know about how to fight the delta variant of COVID, by J. Stacey Klutts, M.D., Tampa Bay Times
Klutts is Special Assistant to the National Director of Pathology and Lab Medicine for the entire Veterans Affairs system, with a specific role in advising on elements of COVID testing for the system.
- 1. Like Gorilla Glue. The delta variant (lineage B.1.617.2) has a particular collection of mutations in the spike protein (that knob-like projection you see in renderings of the virus) that make it extremely effective in attaching to human cells and gaining entry. If the original COVID strains were covered in syrup, this variant is covered in ultrafast-drying Gorilla Super Glue (industrial strength).
- 2. 1,000 times higher. There are two recent publications which demonstrate that the viral loads in the back of the throats of infected patients are 1,000 times higher with the delta than with previous variants. I can tell you from data in my own labs, that is absolutely true. We are seeing viral signals we never saw last year using the exact same assays.
- 3. Much more infectious. This much higher load plus the ultra “stickiness” of the delta strains for adhering to human cells makes it remarkably more infectious than previous strains. You may have heard of R0 (Pronounced R naught) which is, in a nutshell, the number of people to which an infected person would be expected to transmit the virus. Early versions of the virus had a 2 to 2.5 R0 value. So one infected person would infect two or so people on average. Delta has an R0 of about eight! In the infectious disease world, that’s almost unheard of. Chickenpox and measles are about all we have ever seen that spread that efficiently from human to human. This changes the story line completely from earlier in the pandemic and makes this surge, in many ways, like a completely different pandemic event.
- 4. Five days. There is another recent publication out of Singapore with data that confirms something we suspected. I will explain more about the “why” on this below when I talk about vaccines, but the gist is this: The viral loads in the throats of vaccinated persons who become infected with delta rises at identical rates as in unvaccinated persons, but only for the first few days. After five days or so, the viral loads in the vaccinated person start to quickly drop whereas those in the unvaccinated person persist. This key set of observations is important for several reasons relating to vaccinated persons serving as vectors for spread (see below).
- 5. Young people. This pandemic, Round 2, is primarily being observed in younger patients than in Round 1. Our children’s hospitals are even already filling up or full. Because of the delta viral dynamics, it is much more capable of causing severe disease in a larger swath of the population. You spew enough of any human pathogen on someone without immunity, and it’s not going to end well. This sets up very poorly for the beginning of the school year — which has already started in Florida — and it scares me. Check that. It is actually terrifying. I sure hope we have vaccines for the 5- to 11-year-olds soon.
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6. Vaccines work! Speaking of vaccines. Are they working? Yes! They are absolutely doing their expected job. We know a lot about vaccines for upper respiratory viruses, as we have been giving the population one every year for decades (influenza). To explain all of this, I need to provide some biological context. When you get a vaccine as a “shot,” the “antigen” in the vaccine leads to formation of an antibody response. You probably knew that. What’s important, though, is that it primarily leads to a specific Immunoglobulin G (IgG) response. That’s the antibody type that circulates around in really high numbers in the blood, is located some in tissues and is more easily detectable by blood tests, etc.
What that shot does not do is produce an Immunoglobulin A (IgA) antibody response to the virus at the surface of the throat mucosa. That’s the antibody type that could prevent the virus from ever binding in the first place. As such, in a vaccinated person, the virus can still attach like it’s about to break into the house, but it doesn’t realize that there is an armed homeowner on the other side of the door. When that virus is detected, the IgG beats it up and clears it before the person gets very ill (or ill at all). (Sidebar: Anyone ever had their kid — or themselves — get the “Flumist” vaccine as their annual flu booster? The idea there is to introduce the antigens at the surface of the throat mucosa leading to that IgA response that will prevent infection from happening at all. Sounds good and still has a place, but it isn’t quite as effective overall as the shot.)
- 7. Preventing disease and death. The COVID-19 vaccines are designed to prevent disease/death through that IgG response (though it does also reduce infections somewhat). How good are the vaccines at doing all of this with delta? The Centers for Disease Control and Prevention has just released data addressing that very question. Punchline: They’re remarkably good! The vaccine shows an 8-fold reduction in the development of any symptomatic disease secondary to delta. For hospitalization, it is a 25-fold reduction. That’s 25 times! Remarkable. For death, it is also 25 times! This is a very effective pharmaceutical class when looking at overall efficacy toward the intended/expected purpose. When looking at the very tiny side effect profile, I’d personally consider it one of the best overall pharmaceuticals on the market in any class of drugs.
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8. So, you’re vaccinated? First of all, a sincere, heart-felt thank you! But you may now ask, so why do I again need to wear a mask? We talked about disease, hospitalizations and death above, but what about infections themselves? The vaccines are now estimated to provide a 3-times reduction in infection. For reasons that I tried to make clear above, it isn’t surprising that the vaccine is less effective at preventing infection vs. preventing disease. We are indeed seeing detectable virus, at high levels, in asymptomatic, vaccinated persons when we test them prior to procedures, etc. We have a few that are mildly symptomatic, too.
While we now understand that the virus fades from the back of the throat pretty quickly in a vaccinated person, we also know that an infected, vaccinated person can transmit this very infectious virus to others for at least a couple of days. So, as before, you are being asked to wear a mask to primarily protect others.
We need you again to interrupt the transmission cycle of the virus, as you don’t know when you might be infectious. The vaccine alone cannot interrupt this cycle when there is a lot of virus in the community within unprotected persons.
9. What’s next? I live and practice in Iowa, and I see the tsunami wave on the horizon. It’s typical for respiratory viruses to begin in the southern United States (where it is hot and everyone clusters indoors in the air conditioning to escape the heat) and then creep north to affect those areas when it gets colder (and people go inside because it’s getting colder). If you live in the north and are not vaccinated, it is not too late, but it’s getting damn close. It’s also time to start wearing masks in public again (ugh...I hate it, too).
Those of you in the south, particularly in Florida, know that the tsunami is already on your shores. If you weren’t already off the beach, you might be in trouble. However, if you are there and haven’t yet been affected, run like hell to metaphorical higher ground — get vaccinated, wear a mask.
I beg of you, watch that wave and don’t ignore it. I have zero political agenda (I hate politics). I’m just a nerdy scientist and physician who loves you all, and I certainly don’t want to see a mass of my friends grieving — or dead — because I didn’t yell loud enough to get you and your families off that beach. So, run! (to your pharmacy ... driving is allowed). You don’t want any part of this thing without vaccine on board.
Dr. J. Stacey Klutts is a clinical associate professor of pathology and clinical microbiology at the University of Iowa and is the chief of the Pathology and Laboratory Service for the Central Iowa VA Health Care System. He is the past president of the Academy of Clinical Laboratory Physicians and Scientists (ACLPS) and chairs the National VA Clinical Microbiology Council in addition to his national roles referenced above. This is adapted from a Facebook post with permission of the author.
7/30/2021 How Contagious Are Chickenpox, Measles As CDC Document Reveals Delta Variant's R0, by Aristos Georgiou, Newsweek
7/29/2021 ‘The war has changed’: Internal CDC document urges new messaging, warns delta infections likely more severe, by Yasmeen Abutaleb, Carolyn Y. Johnson and Joel Achenbach, The Washington Post
A person working in partnership with the CDC on investigations of the delta variant, who spoke on the condition of anonymity because they were not authorized to speak, said the data came from a July 4 outbreak in Provincetown, Mass. Genetic analysis of the outbreak showed that people who were vaccinated were transmitting the virus to other vaccinated people. The person said the data was “deeply disconcerting” and a “canary in the coal mine” for scientists who had seen the data.
Matthew Seeger, a risk communication expert at Wayne State University in Detroit, said a lack of communication about breakthrough infections has proved problematic. Because public health officials had emphasized the great efficacy of the vaccines, the realization that they aren’t perfect may feel like a betrayal.
7/29/2021 'The War Has Changed: Delta Strain Equally Contagious in Vaccinated Cases, Masks a Must, CDC Says, by Daniel Villareal, Newsweek
Symptomatic breakthrough infections seem to be happening among 0.0098 percent of all fully vaccinated people, according to an ABC News study of cases reported by the CDC last week. Put another way, out of 156 million fully vaccinated Americans, 153,000 contracted symptomatic COVID last week, the CDC reported.
7/27/2021 Tennessee evangelical pastor demands churchgoers ditch their masks: ‘Don’t believe this delta variant nonsense’, by Jaclyn Peiser, The Washington Post
If “you start showing up [with] all these masks and all this nonsense, I will ask you to leave,” Locke, 45, told scores of Global Vision Bible Church parishioners during his sermon on Sunday. His statement was followed by cheers and applause.
“I am not playing these Democrat games up in this church,” he added.
Tennessee recently reported that 98 percent of people who died of covid and 97 percent of covid hospitalizations are among the unvaccinated.
4/28/2021 Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021, by Tjede Funk, et al
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
