For weeks, state officials have been blaming much of Pennsylvanias slow COVID-19 vaccine rollout on providers unnecessarily holding back doses to make sure people got second doses when needed.
In fact, they forcefully urged providers not to hold back doses, assuring them the second of the two required doses would be available when needed.
Yet on Wednesday, Acting Health Secretary Alison Beam announced providers since early January have been giving out second doses of the Moderna vaccine as first doses, characterizing it as a significant mistake. More than 100,000 people could be affected, Beam said.
Because of the error, Beam said up to 60,000 people could have to reschedule appointments, and up to 55,000 others might be delayed in getting their initial doses.
While not fully reconciling the apparent conflict in guidance, Beam laid out the details while also saying the state can adjust so that everyone gets their second dose within an acceptable time frame. There is no medical difference between the first and second doses, so the situation should provide no immediate health danger, she noted.
Beam refused to assign blame, although she suggested the state health department is at least partly responsible.
What we are working on is making sure our department, our communication, our transparency, our end of the bargain is improved upon, Beam said.
Beam said the problem only involves the Moderna vaccine, one of two vaccines distributed so far, with the other being the Pfizer vaccine.
She said the mistake began in early January, with the consequences compounding each week.
The state recently discovered the problem, she said, when the weekly request for second Moderna doses equaled the entire supply received so far.
Beam also said the mistake can be corrected with little or no harm. That can largely be accomplished by rescheduling appointments for second Moderna doses. While people generally receive their second dose within about 28 days, Beam said some could wait up to 42 days for their second dose, which would still fall under federal guidelines.
The Centers for Disease Control and Prevention has said the second Moderna doses are fully effective if given within 42 days of the first shot; there is limited research on its effectiveness beyond 42 days, the CDC said last week.
Beam said her department has found unused inventories around the state to help fill the void. She further expressed confidence the federal government will provide doses within the needed time frame. She said she expects the two sources will allow the 30,000 to 60,000 people who are affected to get their second dose within the appropriate time frame.
She further pledged the health department in conjunction with vaccine providers will make sure people are contacted and their appointments are rescheduled. She said appointments will need to be moved to the following week or at most two weeks from the original appointment.
In a strained briefing with news reporters, Bean didnt detail how the situation squares with the fact her department for weeks has been telling providers not to hold back second doses and assuring them a second dose, from a separate supply, will be available when needed.
However, she said the situation has been discussed with the new legislative task force formed to improve Pennsylvanias vaccine rollout and it agrees with the response she detailed. She said the task force, just formed last week, has met three times to improve communication and address issues with the vaccine rollout.
All of us are focusing on the path forward, and the fix directionally moving Pennsylvania forward as well, Beam said.
Beams further called the situation a stark reminder that right now, there is not enough vaccine for everyone who is eligible to get it.
Pennsylvania has so far given vaccine doses to about 1.7 million people, including about a half-million who have received the two doses needed to be fully protected.
This week it will receive 183,575 first doses, along with 143,275 second doses. The vaccine supply has been growing, although slowly, with this weeks allocation having increased by about 8,000 doses from last week, a state official said Wednesday.
In a separate news conference Wednesday afternoon, Gov. Tom Wolf said his administration will work to ensure those who need the second dose will get it. He also said theres no doubt that there will be other ways the vaccine rollout can improve in the future.
We will look for ways and find ways to make the system work even better, Wolf said.
State leaders announce a new fund aimed at improving access to the COVID-19 vaccine. Here are the top vaccine facts for Tuesday, Feb. 16.
Washington fund aims to boost COVID-19 vaccine equity in BIPOC, rural communities
Washington state leaders announced a new fund Monday aimed at improving access to the COVID-19 vaccine in communities disproportionately impacted by the virus.
"Now is the time to address these inequities," said Lilliane Ballesteros, executive director of the Latino Community Fund. "Now is the time to mobilize our collective resources quickly to those in need and those best position to help them. The vaccine initiative is, we think, a critical step forward for recovery."
VERIFY: Your COVID-19 shots didn't cause side effects, does that mean they didn't work?
Health officials have said mild to moderate side effects are expected and normal with the currently approved COVID-19 vaccines. In fact, doctors say it's a sign the immune system is responding to the shot.
But don't worry if you don't feel side effects from the shots. The VERIFY team spoke to doctors to explain why.
Biden administration increasing vaccine supplies to states, pharmacies
President Joe Bidens administration is increasing coronavirus vaccine supplies sent to states to 13.5 million doses per week.
White House press secretary Jen Psaki says that represents a 57% increase from when Biden took office nearly a month ago on Jan. 20.
Psaki also says the administration is doubling, to 2 million doses per week, the amount of vaccine being sent to pharmacies across the country as part of a program to extend access into neighborhoods.
VERIFY: Fully vaccinated people can skip quarantine after COVID-19 exposure if they meet these conditions
As more and more Americans receive their COVID-19 vaccines, questions are popping up around what we can do safely when fully vaccinated.
The CDC is consistently releasing new guidance as they learn more about vaccine efficacy, including tips for quarantining after exposure to COVID-19. Some news outlets ran with misleading headlines on this, so the Verify team is here to give you all the context you need to stay safe.
How to get a COVID-19 vaccine in Washington
The Washington State Department of Health (DOH) released an online portal to check your eligibility for the COVID-19 vaccine. Use the Phase Finder tool to input personal information like age, health conditions and essential worker status to determine if it's your turn.
As of Jan. 18, Washington is vaccinating people in Phase 1A and the first tier of Phase 1B. That includes:
If you are eligible, find a list of vaccine providers on the DOH website and information on how to make an appointment.
Theres a lot of pent-up desire among seniors, and a sense of life running out, said Jeff Galak, a professor at Carnegie Mellon Universitys Tepper School of Business. Theres a theory called mortality salience: When your own mortality is brought to mind, behaviors change. Were going to see upgrades to better cabins on cruise ships, and booking of better hotels.
For travelers in their 60s, 70s and 80s, said Conor Goodwin, corporate marketing manager of Charlestowne Hotels, the ticking of the clock is another strong motivation to book as soon as an inoculation makes it safe.
The 65-plus demographic is losing out on their golden years and theyre understandably eager to get back out there, he said.
The Bristol Hotel in Virginia, which is part of Charlestownes portfolio, saw revenue from travelers over the age of 65 increase 179 percent between Dec. 13 and Jan. 22. The French Quarter Inn, in Charleston, S.C., which is also managed by Charlestowne, saw 11 percent more bookings from people over 65 between Jan. 10 and 28 compared Dec. 22 to Jan 9.
Some older travelers are even opting to finally book those big-ticket dream trips. Fernando Diez, who owns Quasar Expeditions, a luxury cruise operator in the Galpagos Islands, says that in December, when frontline health care workers were among the very first Americans to receive vaccines, he saw a wave of requests for trip information from doctors and nurses.
Since Jan. 1, however, 70 percent of his booking inquiries have come from guests over the age of 65 in previous years, that number was closer to 40 percent. Most inquiries are for travel from June onward.
Most of them say theyve been vaccinated, and theyre comfortable now traveling to a destination like Ecuador and the Galpagos, Mr. Diez said. The vaccination gives them the confidence to travel to a remote spot.
Boxes containing the Pfizer-BioNTech Covid vaccine are prepared to be shipped at the Pfizer Global Supply Kalamazoo manufacturing plant on December 13, 2020 in Portage, Michigan.
Morry Gash | Getty Images
The Biden administration is increasing the number of Covid-19 vaccine doses shipped to states weekly, sending out 13.5 million doses this week and doubling the number going to retail pharmacies, White House press secretary Jen Psaki said Tuesday.
As of last week, the administration was sending out 11 million doses to states every week. Overall, Psaki noted, the administration has increased the number of doses shipped weekly to states by 57% since President Joe Biden was inaugurated Jan. 20.
Psaki also announced that the White House is doubling the number of doses being shipped directly to retail pharmacies around the country, expanding it from 1 million doses sent to 6,500 pharmacies last week. Psaki said the White House will ship 2 million doses per week to stores going forward and plans to eventually expand to 40,000 stores nationwide.
"This program will expand access in neighborhoods across the country so that people can call and make an appointment and get their shot conveniently and quickly," she said. "This is a critical, critical part of our plan."
The administration has been announcing gradual increases in the amount of vaccine being distributed every week while opening up new distribution channels such as pharmacies, community health centers and federally run vaccination centers. After a slower-than-expected initial rollout of the vaccine, many states now say the lack of supply from the federal government is the biggest constraint.
The pace of vaccination across the country has picked up in recent weeks, and the difference between doses distributed and doses administered has narrowed. More than 52.8 million doses have been administered as of Sunday, according to data from the Centers for Disease Control and Prevention, out of 70 million doses delivered to states.
Biden announced last week that the U.S. has secured 100 million more doses of the Pfizer-BioNTech vaccine and 100 million more of the Moderna vaccine, increasing the total U.S. supply to 600 million doses. The Food and Drug Administration is also expected to authorize Johnson & Johnson's one-shot Covid-19 vaccine for emergency use as soon as later this month.
It's unlikely to be an immediate boon to supply, but will help ramp up the number of doses available to Americans in the late spring and summer. Dr. Anthony Fauci, White House health advisor, said Tuesday that by May the vaccine could be available to any American who wants it, slightly later than his previous forecast of opening up access to the vaccine in April.
"It may take until June, July and August to finally get everybody vaccinated," he said on CNN. "So when you hear about how long it's going to take to get the overwhelming proportion of the population vaccinated, I don't think anybody disagrees that that's going to be well to the end of the summer and we get into the early fall."
(CNN) As the Covid-19 pandemic continues to wreak havoc on the travel industry, countless destinations around the world are rolling out vaccines to their most vulnerable citizens.
Meanwhile, Denmark has announced plans to launch a coronavirus digital passport by the end of February that will act as documentation the holder has been fully vaccinated against Covid-19.
As a result, a number of destinations are choosing to either drop border restrictions for travelers who've been fully vaccinated, or ease them significantly.
From Cyprus to the Seychelles, here are seven destinations reopening to tourists who've received the Covid-19 vaccine.
Cyprus
Late last year, Cyprus official revealed plans to drop restrictions for vaccinated travelers.
ETIENNE TORBEY/AFP via Getty Images
Back in December, Cyprus became the first destination to announce plans to allow travelers who've been fully vaccinated to enter without having to go into quarantine.
In addition, visitors who provide proof that they've received both doses of a Covid-19 vaccine will be allowed to visit without providing a negative PCR test result on arrival.
While it was previously claimed that the new rules would come into effect on March 1, this not been confirmed by government officials as yet.
Currently travelers who are permitted to visit Cyprus have the option to either provide a negative PCR test taken within 72 hours before travel, or undergo a test on arrival.
They must then go into quarantine for two weeks in government-assigned accommodation. The isolation period can be shortened slightly if travelers undergo a molecular test on their tenth day of quarantine at their own expense and receive a negative result.
Estonia
EU travelers arriving in Estonia who are fully vaccinated do not have to quarantine.
Sean Gallup/Getty Images
The European country is also accepting those with vaccinations from nine suppliers across the world rather than just Moderna, Pfizer-BioNTech or Oxford-AstraZeneca, the three that have been approved by the European Union.
Only vaccination certificates produced in Estonian, Russian or English will be recognized and visitors who've previously had Covid will need to submit a doctor's certificate, as well as a recent PCR test indicating they are no longer infected with the virus.
Georgia
Visitors who provide evidence they are fully vaccinated will be exempt from quarantine in Georgia.
VANO SHLAMOV/AFP via Getty Images
Georgia, which sits at the crossroads between Asia and Europe, has also opted to lift restrictions for fully vaccinated travelers.
The Ministry of Foreign Affairs for Georgia recently announced that all visitors who've received two doses of any Covid-19 vaccine are permitted to enter the nation without producing a negative PCR test.
Non-vaccinated travelers must present a negative PCR test result taken within 72 hours of travel and are also required to take a second test "at their own expense" on day three of their stay.
Those who've traveled to the United Kingdom within 14 days of their visit must undergo a 12-day mandatory quarantine upon entry.
Iceland
In May, Iceland is ditching border restrictions for those who've had a full course of the Covid vaccine.
Maja Hitij/Bongarts/Getty Images
From May 1, fully vaccinated travelers from European Union countries, as well as Liechtenstein, Norway and Switzerland, can skip quarantine when they arrive in Iceland and will not be required to submit a negative PCR test.
Visitors who can provide a paper vaccination in Icelandic, Danish, Norwegian, Swedish or English proving they've had two doses of one of the three main Covid-19 vaccines will be exempt from border restrictions.
Non-vaccinated arrivals from destinations where travel to Iceland is permitted must take a Covid test on arrival, before going into quarantine for five to six days and taking a second test.
Exemptions will be made in some circumstances, such as those with a valid medical reason.
Poland
Poland has been allowing travelers to enter without going into quarantine since December 28.
LUDOVIC MARIN/AFP via Getty Images
Travelers from EU countries can visit Poland without undergoing its mandatory 10-day quarantine "on the basis of a certificate confirming vaccination against Covid-19."
Those who provide a negative SARSCoV2 test on arrival are also exempt as long as there's no more than 48 hours between the time they receive their test result and the time they cross the border.
Romania
Fully vaccinated visitors arrivijng in Romania can also avoid having to quarantine.
IONUT IORDACHESCU/AFP via Getty Images
All travelers arriving in Romania from permitted destinations who have been fully vaccinated from Covid have been exempt from quarantining on arrival since January 18.
The new rules were announced by the European's country's National Committee for Emergency Situations (CNSU), who stipulated that visitors and returning residents will need to show evidence that they've had two doses of the vaccine in order to avoid mandatory isolation.
The second dose must have been administered at least 10 days prior to their arrival.
Those who submit a PCR taken no fewer than 72 hours before entry must quarantine for 10 days.
The Seychelles
Vaccinated travelers can visit the Seychelles without having to isolate, but they are still required to submit a negative PCR test.
Yasuyoshi Chiba/AFP via Getty Images
Fully vaccinated visitors are now permitted to enter the remote destination situated off the coast of Tanzania without having to quarantine for 10 days.
However, those who've received a full course of any Covid-19 vaccine are still required to present a negative PCR test result taken within 72 hours of travel, as well as a certificate from their national health authority verifying that they've been fully vaccinated.
The 115-island nation is aiming to become the first nation to vaccinate its entire population after receiving a donation of 50,000 doses from the United Arab Emirates government.
President Wavel Ramkalawan hopes over 70% will be vaccinated by mid-March. Restrictions will be further relaxed if this target is reached, meaning those permitted to enter the Seychelles will only have to submit proof of a negative Covid-19 PCR test taken within 72 hours of travel.
Japan has formally approved its first COVID-19 vaccine and says it will start nationwide inoculations within days, but months behind the U.S. and many other countries
By MARI YAMAGUCHI Associated Press
February 14, 2021, 3:16 PM
3 min read
TOKYO -- Japan on Sunday formally approved its first COVID-19 vaccine and said it would start nationwide inoculations within days, but months behind the U.S. and many other countries.
Japans health ministry said it had approved the vaccine co-developed and supplied by Pfizer Inc.
The announcement comes after a government panel on Friday confirmed that final results of clinical testing done in Japan showed that the vaccine had an efficacy similar to what overseas tests showed.
Many countries began vaccinating their citizens late last year, and Pfizer's vaccine has been used elsewhere since December.
Under the current plan, about 20,000 front-line medical workers at hospitals in Japan will get their first shots beginning around Wednesday. About 3.7 million other medical workers will be next, followed by elderly people, who are expected to get their shots in April. By June, its expected that all others will be eligible.
Health ministry official Yuta Yamashita said inoculations can start as soon as a ministry panel on vaccination logistics gives the go-ahead.
The approval was granted in a special fast-track process for emergency use. It took two months compared to the usual one year in a country known for cautious and slow-moving approval processes.
Still, the rollout in Japan is months behind many other countries because the government had asked for clinical testing at home in addition to the multinational tests Pfizer conducted on more than 40,000 people from July to November. Many countries accepted Pfizer's results and moved ahead.
In a country where many people are skeptical about vaccines, Japan sought additional tests to address safety concerns. But the tests were conducted on only 160 people, and some question whether it was worth it to delay the rollout.
Vaccines are considered key to holding the delayed Tokyo Olympics this summer. Japan is expected to receive 144 million doses from Pfizer, 120 million from AstraZeneca and about 50 million from Moderna before the end of this year, enough to cover its population.
Vaccines being developed by Japan are still in the early stages, so the country must rely on imports. AstraZeneca applied for approval in Japan only recently, while Moderna hasnt applied yet. Japans reliance on the imports, many of them subject to EU export controls, is also causing concerns about supplies.
Shigeru Omi, the head of the government coronavirus task force, earlier this month cited a lack of global competitiveness of Japanese pharmaceuticals as a reason for the delayed rollout.
Follow Mari Yamaguchi on Twitter at https://www.twitrer.com/mariyamaguchi
"This is a very big and aggressive effort to address vaccine hesitancy in the Black community," Cuomo said.
The governor said he told county and city leaders on Tuesday that the vaccine distribution system, which he said "is no doubt confusing," needs to be fair.
"This is a precious resource. Everybody wants it. There's not enough," Cuomo said. "The best you can do is make sure that you were fair."
He said Erie County is one area that needs more mass vaccination sites.
"Look at the fairness and correct for the fairness," Cuomo said. "If Cheektowaga is low, open up a site in Cheektowaga. If the East Side of Buffalo is low, open up a site in the East Side of Buffalo."
The Native American Community Services vaccination center will be one of 13 new pop-up centers at community centers, public housing complexes and cultural centers around the state. It opens Saturday,but appointments are already filled, according to the governor's office.
Cuomo said 43,000 people have received first doses of the vaccine at the 91 earlier pop-up sites in largely Black areas, including some in Western New York.
Appointments at the Delavan-Grider Community Center and the other sites announced Wednesday in Rochester, Albany and Yonkers initially will be reserved for members of the community in which the sites are located. Community engagement efforts will be used to help and encourage community members sign up for appointments. More scheduling information, opening dates and hours of operation will be made available in the coming days, according to the governor.
Some of the biggest coronavirus vaccine manufacturers say they are not selling shots to provincial governments because they only want to deal with one contract per country at a time.
This comes as premiers in Alberta and Manitoba join arms in calling for a Plan B interprovincial task force to secure their own vaccine supplies following delays in deliveries to the federal government, and a lack of clarity from the federal government around the terms of those crucial contracts.
During the pandemic, we are committed to bringing this vaccine to help meet the public health need and only plan to sell the vaccine to the Government of Canada, said Christina Antoniou, director of corporate affairs for Pfizer.
The federal governments National Operations Centre is responsible for distributing the vaccine to each of the provinces, and we are working closely with them to support their efforts.
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In order the (sic) optimally address the pandemic situation worldwide, Pfizer decided to have one agreement per country, Antoniou added.
The idea was to limit the number of contractual agreements during the pandemic phase. As such, we have one contract for Canada. That will be the case until we have delivered on the full contract.
Global News reached out to Pfizer, Moderna, AstraZeneca and Johnson & Johnson following comments by Manitoba Premier Brian Pallister during an interview with Global News last week.
Pallister said the federal governments contracts with those major vaccine suppliers forbid those companies from selling vaccines to the provinces in separate deals.
Theyve all told us that they are not going to sell to us because thats part of the deal they made with the federal government, he said. To me, thats blocking.
Manitoba government officials provided Global News with records of their outreach to the four vaccine suppliers, which show the companies rebuffing requests from provincial officials to negotiate contracts.
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None of the responses from the vaccine companies in those emails stated that they were prohibited from entering into separate contracts with the provinces because of their federal contract.
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One official from the Manitoba governments procurement team appeared to paraphrase a response received from Janssen, the subsidiary of Johnson & Johnson that is developing the coronavirus vaccine.
Talked with Janssen, direction from them is they are only working with one entity per country PHAC, said the official, whose name was redacted in the records provided to Global News. They will not (sic) entertain working with us for additional vaccines once we receive volumes from Feds. They only want to engage with PHAC.
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An email that appeared to come from Moderna said the company wasnt interested in separate deals.
Modernas position on this remains the same as shared on our call last Friday, said an official in the email, whose name was redacted in the records provided to Global News. We are currently fully committed to the government of Canada to bring as many doses possible to Canada in 2021.
Another email that appeared to come from an official at AstraZeneca Canadas Mississauga location offered a similar response, noting their vaccine candidate remains under review by Health Canada.
Our commitment is to fulfill the supply requested by the Federal Government post Health Canada regulatory approval, said the official, whose name was redacted in the records.
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Unfortunately at this time we are still unable to respond to your specific provincial request.
The response that appeared to come from Pfizer was brief: The situation has not changed and contracts with individual provinces are not currently possible.
Pfizer was the only company to respond to Global News questions by deadline.
Any responses received by Moderna, AstraZeneca or Johnson & Johnson will be included once received.
Global News asked Pallisters office whether the provincial government had received any responses from the vaccine companies that specifically said the federal contracts prohibited them from selling to the provinces, as Pallister had indicated in his interview.
Olivia Billson, spokesperson for the premier, said the province is being blocked from buying vaccines from those companies if the companies are not taking orders until they fulfill the federal contracts.
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Manitoba has reached out repeatedly to COVID-19 vaccine suppliers since late last year on our own initiative to secure a direct supply of vaccines for Manitobans, she said in an email.
Vaccine suppliers have clearly indicated to our government that they are unable to take any orders from us at this time until they fulfill federal orders. That is fact, effectively blocking us from securing vaccines on our own accord.
The federal government has not released the details of any of its contracts with the major vaccine suppliers, despite repeated urging from premiers and opposition parties to be more transparent.
Procurement Minister Anita Anand said the government is bound by confidentiality clauses in those contracts, and has been trying to get vaccine companies to loosen those terms.
So far, she said, those efforts have been unsuccessful.
2021 Global News, a division of Corus Entertainment Inc.
The coronavirus SARS-CoV-2 has constantly evolved since it was first detected in humans over a year ago. Viruses replicate exceedingly fast, and each time they do, there's a small chance they mutate. This is par for the course, if you're a virus.
But in the last few weeks, scientists have been investigating SARS-CoV-2 variants with a handful of mutations arising much faster than expected. Normally, we'd expect to see one to two largely inconsequential genetic changes in the coronavirus every few months. New variants are emerging with a constellation of mutations, all at the same time.
In December 2020, the UK announced a variant of coronavirus, and two other variants were later detected in South Africa and Brazil. There is, for the time being, no reason to fear these variants or how the coronavirus is mutating -- scientists and the World Health Organization suggest that our current protective measures of social distancing and masking up work just as well against them. However, scientists are closely monitoring and evaluating them because they could worsen the pandemic if they are more transmissible or can evade our immune system and vaccines.
From the lab to your inbox. Get the latest science stories from CNET every week.
Epidemiologists, virologists and immunologists are now tasked with understanding how these mutations in the new variants may change the virus and how our bodies respond to them. Mutations could change SARS-CoV-2 in such a way that it may even be able to evade the immune response generated by vaccines. Preliminary research shows current vaccines should be able to deal with the three most concerning variants, but data continues to roll in. On Sunday, South Africa temporarily halted the use of the AstraZeneca-Oxford vaccine after a small clinical trial found it didn't protect shot recipients from a fast-moving variant of the virus first discovered in the country.
Scientists can see the virus evolving in real time and are in a race to describe how this evolution might affect our immunity and, down the line, treatments and vaccines. Here, we're sharing everything we know about COVID-19 variants and the various esoteric ways scientists discuss mutations and evolution.
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6:55
The coronavirus is an RNA virus, which means its complete genetic sequence, or genome, is a single-stranded template (humans and other mammals, by contrast, use double-stranded DNA). The template of SARS-CoV-2 is made up of four bases -- denoted by the letters a, c, u and g -- in a specific sequence, about 30,000 letters long.
The template provides instructions on how to build all the proteins that make a new coronavirus particle. To replicate, SARS-CoV-2 needs to take over a host cell and use it as a factory, hijacking the machinery within. Once it sneaks into a cell, it needs to read the RNA template.
Critical to this process is an enzyme known as an RNA-dependent RNA polymerase, or RdRp. It has one job, and it's terrible at it. "This is an enzyme that makes a huge amount of mistakes when replicating," says Roger Frutos, a molecular microbiologist at the French Agricultural Research Centre for International Development, or CIRAD. The RdRp introduces errors during replication, producing new viruses with slightly different templates. Changes in the template are known as mutations.
Mutations often have little effect on a virus, but sometimes they change the template so much they cause changes in the virus' physical structure. "A mutant doesn't mean it's like 10 times scarier or 10 times deadlier," says Tyler Starr, a computational biologist at the Fred Hutchinson Cancer Research Center. "Mutations have incremental effects."
This could be a bad thing for SARS-CoV-2, creating a useless zombie virus. Sometimes, it might confer an advantage, like allowing the virus to bind more tightly to a host cell or helping it evade the immune response.
Scientists and researchers spot mutations by sequencing SARS-CoV-2 isolated from patients, looking at the entire 30,000 letters of its genome. They compare this with the earliest viruses on record, those detected in Wuhan, China, patients back in December 2019, and see how they've changed. "We never see viruses now that look exactly like what was in Wuhan," says Stuart Turville, an immunovirologist at the Kirby Institute in Australia.
If researchers see that a mutation is becoming more prevalent in a population, there's a chance it may have changed the characteristics of SARS-CoV-2.
Any mutations to the coronavirus genome results in variants of the virus, but some are more concerning than others. In late 2020, three variants were identified with mutations that may make SARS-CoV-2 more transmissible or, in the case of one variant, more deadly.
The variants are described by a number of names, which makes things a little confusing, but scientists refer to them by their lineage, giving them a letter-based descriptor based on their ancestry. They are:
These will not be the last variants of SARS-CoV-2 that arise, and scientists continue to track changes in the genome. Any changes can be useful for genomic epidemiologists to assess transmission dynamics and patterns, in turn helping inform public health units to alter their response to any emerging threats. "We are watching all the time," says Catherine Bennett, chair in epidemiology at Deakin University in Australia.
But why are these three variants of particular concern? They share common characteristics that early analysis suggests may enable them to spread more easily or evade the immune response. This seems to result from, at least partially, how these mutants change the structure of the SARS-CoV-2 spike protein, which enables the virus to hijack cells and turn them into factories.
Could coronavirus variants change the efficacy of our vaccines? Scientists are trying to figure that out.
Each SARS-CoV-2 particle is covered with spikes. Infiltration of a cell requires the club-like projections to lock onto a protein on the surface of a human cell known as ACE2, which facilitates viral entry.
But the viral protrusions are also recognized by the human immune system. When immune cells detect the SARS-CoV-2 spike, they begin pumping out antibodies to prevent it from locking on to ACE2, or send other cells in to destroy the virus. Antibodies also attach to the spike and can effectively prevent it from attaching to a cell. This puts the spike under extreme evolutionary pressure. Mutations that change the spike and help it evade immune cells or antibodies or lock onto ACE2 more strongly can provide a survival advantage.
The variants listed above all share mutations in a region of the spike known as the receptor binding domain, which directly contacts ACE2. If mutations cause structural changes in the RBD, it might bind to ACE2 differently and could, for example, prevent the immune system from recognizing it as dangerous.
Here's where things get a little confusing, but it's important to understand how scientists denote specific mutations and why you're seeing all these numbers and letters flying around.
Remember that each RNA genome (the template) contains four molecular bases denoted by the letters a, c, u and g. When this template is read, every three-letter combination or "codon" (GAU, for instance) corresponds to an amino acid. A chain of amino acids becomes a protein.
But here's the confusing bit: Amino acids are also denoted by a single-letter code, unrelated to the RNA template letters. The amino acid alanine, for instance, is A. Aspartic acid is D. Glycine is G.
Why is this important? Because scientists discuss and study coronavirus mutations at the amino acid level.
For example, we've already seen one SARS-CoV-2 variant arise and come to dominate across the world.
Sometime in early 2020, the coronavirus picked up a mutation that resulted in an increase in infectivity. A mutation in the RNA template flipped an "a" to a "g," which caused a different amino acid to form in the RBD of the spike. This change was beneficial for the virus, and now it's the dominant form we see across the world.
The mutation is known as D614G. This notation, letter-number-letter, corresponds to a change in the amino acid at position 614, from aspartic acid (D) to glycine (G).
Confusing? Definitely. Important? Absolutely. This naming convention is important to understand important mutations in the three new COVID-19 variants.
Strengthening lockdowns in the UK has helped curb the spread of the variant, B.1.1.7
There are a number of mutations in all three variants across the RNA genome, but let's focus on the spike here. B.1.1.7 has eight mutations in its spike, B.1.351 has seven and P.1 has 10. Not all of these mutations are the same, but some overlap -- that is, the virus has evolved similar mutations in different locations across the world, a process known as "convergent evolution."
There are three mutations, all found in the RBD of the spike, which may affect the virus or how our antibodies respond to an infection:
Scientists are only just beginning to understand how these individual changes may benefit SARS-CoV-2 and if they're increasing its infectivity and transmissibility or making them more prone to evading the immune response. There's emerging evidence that, alone, they may not be significant changes -- but when found in combination with other mutations, they may facilitate more worrying differences from "original" SARS-CoV-2.
N501Y is found in all variants and is one of the mutations scientists are most interested in.
The change from an asparagine (N) to a tyrosine (Y) has been shown to increase SARS-CoV-2's ability to bind to ACE2 and, in mice, increase its infectivity. It's currently unknown whether this one change would elicit any changes in the mortality or morbidity of COVID-19. However, the change does not seem to impact the ability for the Pfizer/BioNTech vaccine to stimulate antibodies, according to preliminary research published on preprint server bioRxiv. That's good news.
In addition to N501Y, the B.1.351 and the P.1 variants have two more mutations: E484K and K417N/T, both of which change how sensitive the virus is to antibodies. These changes are slightly more concerning.
The two mutations are in regions of the RBD that antibodies can bind to. Researchers are concerned about E484K in particular and mutations at this site can reduce the neutralizing ability of antibodies more than 10 times. This could have the greatest impact on generating immunity, according to a preprint paper published on Jan. 4. Another preprint, published on Jan. 26, points to E484K as a key mutation in diminishing antibody activity against COVID-19. Worryingly, the mutation appears in 100% of cases infected with the P.1 variant -- and scientists are concerned it's allowing for a significant number of reinfections in Brazil.
The amino acid change at 417 is also interesting. In the South African B.1.351 variant, it's K417N. In the P.1 variant it's K417T. The amino acid change is different, but it appears to result in a similar effect -- improving evasion from antibodies. Preliminary studies reveal that position K417 is an important target of neutralizing antibodies, too, suggesting that both mutations could help the virus evade vaccine-mediated and naturally acquired immunity.
The UK government has also seen the E484K mutation in at least 43 cases, according to a recent technical briefing and the BBC.
These are merely three of the many mutations scientists are finding in the new variants -- how they all fit together in reality is much more complicated, and many more mutations that change SARS-CoV-2 are waiting to be discovered. For instance, a paper published on Jan. 28 in Cell discusses the N439K variant and its ability to evade antibodies.
Fortunately, scientists can get ahead of these variants by studying mutations that may occur in SARS-CoV-2. This is central to work performed by Starr and some of his colleagues at the Fred Hutchinson Cancer Research Center. "We've been generating these maps where we just survey all the possible mutations that could occur in the RBD," Starr says.
When a new variant arises, other researchers can look to these maps and see how the mutation affects the biochemical properties of the virus. Does it bind better? Worse? Is it more likely to evade the immune system? Starr explains this work has allowed for mapping how mutations might avoid treatments, like those used by Regeneron or Eli Lilly and can inform surveillance and response to emerging variants.
Maps like these, produced by the Bloom lab at the Fred Hutchinson Cancer Research Center, guide research on mutations. At significant sites in the RBD, the team analyzes how mutants change the binding affinity. Blue is increased affinity, red is decreased. The N501Y mutant is a deep blue, showing how this mutant has increased binding affinity to ACE2.
Presently, there's not enough evidence to suggest the variants are causing more significant mortality or more severe disease -- which means public health advice is largely unchanged. Wearing masks, social distancing and good hand and respiratory hygiene are the best way to prevent the spread of the disease. The coronavirus has not mutated to overcome these measures.
A more pressing question is how the variants and their mutations could affect vaccines and treatments and whether they'll increase the rate of reinfection. Vaccines stimulate immunity by showing the body a harmless version of the virus, which can produce antibodies that roam our inner halls looking for invaders. These antibodies may not be adept at catching and neutralizing variants, as explained above -- but researchers don't have a great handle on the data at present.
Even so, vaccine manufacturers have begun to plan for variants that negatively affect the immune response. A report in Science on Jan. 26 highlights Moderna's efforts to look ahead and potentially change the formulation of their mRNA vaccine and provide "booster" shots that could protect against new variants that may arise.
On Jan. 28, biotech firm Novavax released news of results from late-stage clinical trials of its own vaccine candidate. The trial was conducted on patients in both the UK and South Africa, with mixed results. In the UK, Novavax claims its vaccine had around 89.3% efficacy, but in South Africa, where the more evasive variant is circulating, this efficacy dropped to 60%. This result is concerning and makes an urgent case to evaluate our current vaccines against the newly emerged variants.
Additionally, if the variants infect someone who has previously been infected by COVID-19, there's a chance the immune system will not mount an adequate response and block infection. There's limited data on this, though the P.1 variant has been detected in a case of reinfection in Brazil. The patient was exposed to an earlier variant of SARS-CoV-2, but then acquired P.1 and scientists believe they may have gone through a second period where they were able to transmit the disease again. More work is required to fully understand this phenomenon.
Ultimately, COVID-19 continues to spread across the globe and more new infections means more opportunities for SARS-CoV-2 to evolve. The virus can't evolve without us -- indeed, it can't survive without us. The simplest way to prevent new variants from emerging is preventing the virus from spreading at all. Our efforts will need to be focused on speeding up the vaccine rollout across the globe and continuing to practice the distancing and hygiene measures we're already adept at.
The information contained in this article is for educational and informational purposes only and is not intended as health or medical advice. Always consult a physician or other qualified health provider regarding any questions you may have about a medical condition or health objectives.
