The race between COVID vaccines and emerging variants

[gwb-trading]

I have outlined several times how the U.S. is in a race between vaccinations and COVID variants between now and June. Recently the race is not going well. COVID cases have been rising in the U.S. for two weeks. Most of this is attributed to spring break travel and governors loosening restrictions.

The reality is if the U.S. can maintain our restrictions, social distancing, mask wearing and other proper public health measures for a another 8 weeks or so then we would have likely defeated COVID from rising vaccinations. Unfortunately due to not maintaining proper discipline in many states cases appear to be on a brink of a surge and our path over the upcoming days is likely to mirror Europe.

Of particular concern are the new variants of COVID sweeping the U.S. which are both more infectious and more severe. Currently all three vaccines used in the U.S. are effective against most of these variants -- so rising vaccination defeats the variants as well.

The race between COVID vaccines and emerging variants
https://www.axios.com/coronavirus-variants-vaccines-c27dd1d5-6531-4c67-80c0-310705d6ff45.html

America is in a race to vaccinate people before the country is overwhelmed by variants that are spurring a fourth wave of COVID-19.

Why it matters: Spring is here, and when cases were dropping, hope was rising for a more normal summer. But experts warn this will only happen if people keep social distancing, wearing masks and getting vaccinated as soon as they can.

State of play: Growing evidence shows the three authorized vaccines currently offer protection against the variants, Larry Luchsinger, assistant member of the nonprofit New York Blood Center, tells Axios.

• But Luchsinger and several other experts warn vaccinations must speed up in the U.S. and globally before a more serious variant pops up that renders the first generation of vaccines ineffective.
• Experts aren't the only ones worried: A recent Harris poll finds a majority of Americans from all political parties are either "somewhat" or "very" concerned about the variants.

What's happening: Viruses constantly mutate, mostly without public health impact unless the changes converge on a trait that is advantageous to the virus. For the most part, those changes haven't made a big impact on SARS-CoV-2.

• None of the currently circulating variants have been labeled by the CDC as being of "high consequence," which would require serious medical countermeasures.

Yes, but: The agency is watching five "variants of concern" that can alter public health measures by having characteristics such as increased transmissibility, more severe disease or a higher death rate, and the ability to interfere with treatments or vaccine effectiveness.

• Those five variants, and the places they were originally detected, are: B.1.1.7 (U.K.), P.1 (Japan/Brazil), B.1.351 (South Africa), B.1.427 (California), and B.1.429 (California).

"The B.1.1.7 is a superspreader, in a way. It has a higher chance of spreading — about 50% to 70% more likely," says Ali Mokdad, professor of health metrics sciences at the IHME at the University of Washington.

• This variant is primarily responsible for the rise in several hotspots in New York, Michigan, Wisconsin and elsewhere, Mokdad tells Axios.
• B.1.1.7 tends to dominateother variants in a community, has been found to roughly double every 7–10 days, and is now about 26% of cases in the nation.
• Good news: The vaccines are effective against it. Bad news: It's more infectious and can cause worse complications or death. Plus, only about 150 million doses of COVID-19 vaccines have been given in the U.S. so far.
• "Basically, we're in a race against time, where we need to make sure everybody who's eligible to a vaccine has access and gets it in order to ensure that cases will keep falling all the way until the end of the summer," Mokdad says.

The California variants (B.1.427 and B.1.429) are about 20% more transmissible than the original SARS-CoV-2, "but the vaccines are still fantastic and are doing a really good job," says Stacia Wyman, a genomics researcher who leads thesequencing effort in UC Berkeley’s Innovative Genomics Institute.

• "But I'm a little bit worried because I feel like places have been opening up too early. Just because cases are going down, doesn't mean it's safe to eat inside next to someone or go to a bar," Wyman adds.

The South Africa and Brazil variants (B.1.351 and P.1) appear to render the current vaccines slightly less effective in experimental data. B.1.351 is also about 50% more transmissible, but the rate for P.1 is not yet known, per the CDC.

• "The B.1.1.7 seems to be edging out the B.1.351 and the P.1 at least for now. Although they are concerning, they are not playing a big role in our epidemiology right now," Caitlin Rivers, senior scholar at the Johns Hopkins Center for Health Security, tells Axios.

Of note: Mutation E484K, nicknamed Eek, is also under close watch.

• It's "especially concerning" because it's popped up in different variants (B.1.351, B.1.1.28 and now B.1.1.7), can help the virus evade the immune system, and may become resistant to current vaccines and monoclonal antibody treatments, says Allison Greaney, graduate student researcher at Fred Hutchinson Cancer Research Center.

What's next: Strengthening the U.S. genomic surveillance strategy and contact-tracing programs is key, according to Rivers. The American Rescue Plan Act had $1.75 billion for surveillance that "will boost our capabilities," she says.

• Developing new technologies to explore the role a person's biomarkers or other characteristics play in leading to differing responses to the virus and its variants would be "a real leap of technology," Luchsinger says.
• Second-generation vaccines are already under development. For example, Moderna just started the Phase 1 clinical trial of its COVID-19 variant vaccine that aims to address key mutations from the South African variant.

The bottom line: "Summer could be very good for us, as long as we behave for the next couple of weeks" with social distancing, masking and getting vaccinated, Mokdad says.

Go deeper: Check out our new, live Coronavirus Variant Tracker.

 

[Cuddles]

the earth is only 6000 years old they said...
evolution is just a theory they said...
masks don't work they said...
a democratic hoax they said...

 

[gwb-trading]

In the race to stay ahead of COVID-19 variants, the US lags globally
https://www.usatoday.com/in-depth/n...-19-can-us-catch-up-tracking-them/7064761002/

The vaccines going in our arms today could become less effective later as the virus keeps mutating, a dilemma that demands scientists meticulously track variants to protect us.

But the United States lags well behind many other countries in employing the essential tool for keeping abreast of variants – gene sequencing – increasing the risk that a new variant could spread undetected.

So far this year, the United States ranks 33rd in the world for its rate of sequencing, falling between Burkina Faso and Zimbabwe, according to COVID CoV Genomic, led by researchers at Harvard and MIT. The top three nations – Iceland, Australia and New Zealand – sequenced at a rate between 55 and 95 times greater.

Sequencing happens behind the scenes when someone gets tested for the coronavirus. If the test is positive, the sample may be sent to another lab for sequencing, especially if the person has had COVID-19 before or has been vaccinated. That provides the genetic code of a virus, laying out for scientists a precise map for how to defeat it.

For arcane reasons, sequencing results in the U.S. go only to researchers, not to those who got tested. That could become a problem if the variant demands a different approach to treatment or proves resistant to existing vaccines.

Public laboratories in the United Kingdom, considered a model for tracking the virus, sequence a third of positive coronavirus tests, according to the COVID-19 Genomic UK Consortium. Through those efforts they discovered the B.1.1.7 variant first in September. On Dec. 14, scientists there reported this new variant was far more contagious and could be more lethal.

Until recently, only a minuscule fraction of samples in the U.S. were sequenced. Under the Biden administration, the Centers for Disease Control and Prevention is spending an additional $200 million on sequencing, quadrupling the rate of testing starting in mid-February.

Currently, the CDC tries to sequence at least 7,000 positive test samples a week, about 2% of new cases. Some say it needs to do more; a 2% rate could mean not catching new variants early enough.

“We’d really like to get that into double digits or more,” said Joel Sevinsky, founder of Theiagen Genomics, which helps public health officials track outbreaks.

By early January, laboratories in the U.S. had detected only 76 cases of the variant first detected in Britain. It was estimated at 5% of new cases. Since then, the variant has exploded. Last week, it made up an estimated 32% of new cases. Another fast-spreading variant, B.1.526 – which was first detected in New York – reached 36%, according to CoVariants.org.

Samuel Scarpino, director of the Emergence Epidemic Lab at Northeastern University in Boston, says he spends hours each day trying to track the U.K. variant but cannot say definitively how widespread it is in Massachusetts.

“And the reason I don't know that is because I've not found a representative publicly available data set, for example, that the CDC puts out on B.1.1.7,” he said. “There’s good evidence that what we’re doing now is not enough.”

The CDC has begun asking laboratories in each state to provide weekly samples, based on population, for it to analyze.

“Is it enough?” said Mark Pandori, director of the Nevada State Public Health Laboratory. “That’s a difficult question to answer; we don’t know.”

As more people get vaccinated, the rate of sequencing will increase if new coronavirus cases fall significantly. Last week, however, the number of U.S. cases rose, and some public health officials worry the U.K. variant could trigger another surge. They also are watching the New York variant, concerned that it may be resistant to vaccines.

In an emotional plea, CDC Director Rochelle Walensky urged all Americans to get vaccinated, saying she feared “impending doom.”

Until the entire world is vaccinated, there’s a chance the virus could mutate in ways that evade detection, treatments or vaccines. Keeping a close eye on variants gives vaccine makers a chance to stay ahead of the virus.

A study published this week in Lancet revealed that the AstraZeneca vaccine, not yet available in the U.S., is less effective against the variant first found in Britain.

The good news is that vaccine is 70% effective against symptomatic COVID-19 from the U.K. variant, compared to 80% for other variants. It’s only 28% effective in protecting against asymptomatic disease from the U.K.variant, though, so those who are vaccinated can still spread the disease.

Some existing vaccines are less effective against a variant that originated in South Africa, as clinical trials by Johnson & Johnson revealed. Its vaccine was only 57% effective in stopping symptomatic COVID-19 from that variant.

Pfizer just released new data on 800 volunteers in South Africa and found its vaccine was 100% effective against the variant. Moderna is injecting volunteers with an experimental booster to see if it will offer more protection.

Tracking changes helps with treatments, vaccines
Viruses survive by hijacking the body’s own genetic process to make more virus. The coronavirus is made up of RNA, the same thing our own DNA uses to keep our bodies functioning. When the virus invades a human cell, it can make the cell replicate the virus.

Sequencing took center stage with the Genome Project in 2000, a massive effort to map all of the genes in human DNA. Back then, sequencing genes cost up to $100 million. The price has since plummeted to a few dollars.

Knowing the genetic makeup of a virus has many advantages, including the ability to track changes in the virus and find effective treatments and vaccines.

The specimens come from people getting coronavirus tests at their local pharmacies or health care clinics. The virus is extracted from the swabs stuck up nostrils, which are sent to laboratories with special machines. The sequence itself is made up of only four letters: G, U, A, C, the building blocks of RNA. Scientists can tell when the virus failed to replicate itself exactly by noting differences in the sequence of those letters.

Problems can arise if the mutation changes the proteins on the surface of a virus. Those are the proteins that attach to human cells, allowing the virus to invade. If that protein changes, vaccines and treatments could be less effective.

The ability to sequence has increased dramatically in recent years. Faster technology led to a public-health breakthrough in 2014, when scientists from the Broad Institute at Harvard University used sequencing in West Africa, on early patients of Ebola. By understanding how the virus spread, it made it easier to stop that spread.

By 2018, all states had the ability to sequence. The CDC tests 7,000 samples annually from influenza tests to inform what goes into the annual flu shot.

The U.K. stepped up its sequencing efforts a year ago, soon learning that the coronavirus there was coming from France and Spain more than China, said Ewan Harrison, a deputy director at COVID-19 Genomics UK at the Wellcome Sanger Institute.

When the U.K. in December told the World Health Organization about its disturbing findings on the variant it first detected, the world closed its borders to the UK.

“That arguably saved lives,” Harrison said. “Now we’re at the point where we pretty much sequence everything we can lay our hands on.”

In the U.S., for years sequencing was largely left to state laboratories and wasn’t a high priority. Although technology for sequencing has improved dramatically in the past decade, some states are still catching up.

Data from GISAID – Global Initiative on Sharing All Influenza Data, a nonprofit database in Germany – indicates the proportion of new coronavirus cases sequenced by states since Feb. 1 has averaged 1.5%, ranging from 0.02% in Oklahoma to 9.7% in Hawaii.

Access to data limited for most scientists
Another problem in tracking variants is how the samples are selected.

Nevada's Pandori said her state started sequencing in April 2020, not to track variants but to track how the virus spread. When there is a COVID-19 cluster, sequencing can tell whether two people who had contact with one another are carrying the identical virus.

In Cambridge, England, an outbreak of coronavirus affected six dialysis patients at a hospital last April. An analysis using sequencing determined the virus wasn’t spreading at the hospital but on the bus bringing patients from their homes. Harrison said the hospital stopped the spread by changing the way patients were transported.

In the U.K., all samples sequenced are uploaded into a public database. While identities are protected, the rest is open and accessible, allowing any scientist to thoroughly analyze it.

The same is not true in the U.S., or many other countries. Instead, most data about samples are uploaded to GISAID. To encourage scientists to share their data without losing the right to publish their own analysis first, GISAID has strict rules that make it hard to access and share data on gene sequences.

Users also are limited to downloading only 10,000 records at a time. For precise detail, they have to look at each record individually. Then, they are prohibited from sharing the genetic data itself, protecting the intellectual property rights of the scientists who submitted it.

What’s more, the data in GISAID is not random, so without a fuller understanding of how it was collected, the results of any analysis could be biased. Some laboratories may have tested samples from a specific location to trace the origins of a cluster, for example. Some may be specifically testing samples believed to be a variant.

That’s one reason the CDC created its own database in February called National SARS-CoV-2 Strain Surveillance. The federal agency is talking not just to public health directors but also to large private laboratories to encourage them to submit samples in a uniform manner, said Duncan MacCannell, chief science officer for the CDC office that oversees sequencing.

MacCannell said the CDC has a good sense of how widespread variants are nationally, but it’s more difficult to draw conclusions at the state level because the numbers are so small.

“The volume of data that’s being collected every week needs to increase,” he said.

Scarpino at Northeastern University said it’s critical to have adequate data to track the virus at the state and local levels.

“COVID is a local disease,” he said. “It’s not enough to say we know what’s going on in Massachusetts. We need to know what’s going on in Boston. We need to know in the counties, you know, even in the neighborhoods.”

Catching variants of concern early is key
Greater sequencing also would improve the chances of catching a new variant of concern early.

One approach would be to sequence all positive samples from anyone previously infected with COVID-19 or fully vaccinated, said Kelly Wroblewski, director of the infectious disease program at the Association of Public Health Laboratories. That’s becoming a common protocol.

Wroblewski, however, is less concerned than some others about the current state of sequencing.

“I think we can always improve, we can always do more, but I don't have, like, the same urgent concern that we need to catch up,” Wroblewski said. “I think we're heading in the right direction.”

In the U.K., Harrison said he can foresee a day when sequencing will replace testing as a more accurate way to keep ahead of the disease.

When the coronavirus replicates in the body, it can make mistakes and change its structure. The changes more likely to survive are those more resistant to the immune response. That means the longer the virus spreads, the more likely variants will emerge that foil the vaccines.

“As we go further and further into the pandemic, as more and more people have immunity either from being exposed to the virus or from getting vaccinated, I think that's going to put increasing amounts of pressure on the virus to escape (vaccines) through mutation,” said Luca Giurgea, an infectious disease researcher at the National Institutes of Health.

Matthew Memoli, a director at the Laboratory of Infectious Diseases at NIH, said more resistant variants can be the result.

“And when they become dominant, if they’re compatible with the virus continuing to replicate, it becomes a problem,” Memoli said.

Giurgea and Memoli are working together on a new type of vaccine that the virus can’t escape through mutation: a universal coronavirus vaccine. They say they cannot yet predict when it might be available.

 

[Cuddles]

are anti-masker clowns still arguing that physical barriers don't block physical viruses and unleashing vax-resistant mutations on us? At what point do we run out of patience and start quarantining them like China does?

 

[jem]

All of sudden walls work for lefties?


Come on... stop it with the bullshit and starting bringing data and science.
Have you seen all the charts with the masks mandates failing.
You think that is a fluke?

iMasks do no protect the wearer.... I have presented studies from the CDC and Denmark on that... with control groups.

Masks have been failing in real life because breath around them and they get dirty and most people touch them.


What is causing these problems is locking down just as the healthy could be starting to get immunity to each of the variants.

We should be protecting the high risk better.
What our govts are doing is voodoo and quackery.

are anti-masker clowns still arguing that physical barriers don't block physical viruses and unleashing vax-resistant mutations on us? At what point do we run out of patience and start quarantining them like China does?

 

[gwb-trading]

As expected and predicted over a month ago...

UK variant is now the dominant coronavirus strain in the US, says CDC chief
https://www.cnn.com/2021/04/07/us/uk-variant-dominant-coronavirus-strain/index.html

The coronavirus variant first identified in the United Kingdom is now the most common strain of coronavirus in the United States, US Centers for Disease Control and Prevention Director Dr. Rochelle Walensky said Wednesday.

"Based on our most recent estimates from CDC surveillance, the B.1.1.7 variant is now the most common lineage circulating in the United States," Walensky said at the White House COVID-19 Response Team briefing.

Studies have suggested that the UK variant is more contagious than the original strain, is possibly more dangerous and associated with a higher risk of death.

There are currently 16,275 confirmed cases of the B.1.1.7 variant in the United States, according to the CDC.
The country's daily rate of new cases rose over most of the last four weeks. Part of that is due to the spread of B.1.1.7 and other concerning variants, Walensky said this week.

Last month, evidence was mounting that the variant was possibly already dominant across the US. At the time, the CDC declined to say if the variant was dominant -- but predicted it would be within a few weeks.

 

[wrbtrader]

As expected and predicted over a month ago...

UK variant is now the dominant coronavirus strain in the US, says CDC chief
https://www.cnn.com/2021/04/07/us/uk-variant-dominant-coronavirus-strain/index.html

The coronavirus variant first identified in the United Kingdom is now the most common strain of coronavirus in the United States, US Centers for Disease Control and Prevention Director Dr. Rochelle Walensky said Wednesday.

"Based on our most recent estimates from CDC surveillance, the B.1.1.7 variant is now the most common lineage circulating in the United States," Walensky said at the White House COVID-19 Response Team briefing.

Studies have suggested that the UK variant is more contagious than the original strain, is possibly more dangerous and associated with a higher risk of death.

There are currently 16,275 confirmed cases of the B.1.1.7 variant in the United States, according to the CDC.
The country's daily rate of new cases rose over most of the last four weeks. Part of that is due to the spread of B.1.1.7 and other concerning variants, Walensky said this week.

Last month, evidence was mounting that the variant was possibly already dominant across the US. At the time, the CDC declined to say if the variant was dominant -- but predicted it would be within a few weeks.

The number of vaccinations needs to stay ahead of these Covid variants to continue the decrease in Covid infections because the variants is mainly targeting more younger adults.

My girlfriend said the last 3 people at her hospital that checked in with illness / then tested positive Covid...they tested positive for the variant and they were between the age of 25 - 40 years of age.

wrbtrader

 

[Nine_Ender]

The number of vaccinations needs to stay ahead of these Covid variants to continue the decrease in Covid infections because the variants is mainly targeting more younger adults.

My girlfriend said the last 3 people at her hospital that checked in with illness / then tested positive Covid...they tested positive for the variant and they were between the age of 25 - 40 years of age.

wrbtrader

The very people in Jem's "low risk group" that he wants operating like there is no Covid risk at all. It's become comical how badly Jem assessed Covid in 2020 and how it's all come out since. No doubt he's frantically trying to rewrite his narrative to match.

 

[Tsing Tao]

are anti-masker clowns still arguing that physical barriers don't block physical viruses and unleashing vax-resistant mutations on us? At what point do we run out of patience and start quarantining them like China does?

Some of us aren't anti-mask, but anti-mask mandate. The former works, the latter never does.

But keep believing in the flat earth stuff.

 

[gwb-trading]

Some of us aren't anti-mask, but anti-mask mandate. The former works, the latter never does.

But keep believing in the flat earth stuff.

Mask mandates work. Anyone who believes otherwise is engaged in fantasy and fiction.