President-elect Joe Biden announced a plan on Friday for what will likely be his most pressing challenge when he takes the White House next week: fixing America’s messy Covid-19 vaccine rollout.

The plan builds on Biden’s $1.9 trillion economic stimulus proposal, which included a $400 billion Covid-19 plan, announced on Thursday. It seeks more support to states and lower levels of government, a greater expansion of vaccine eligibility, funding for more public health workers, a boost in vaccine production, better communication about the vaccines, an education and awareness campaign, and more. He promises 100 million vaccine doses delivered in his first 100 days in office.

Above all, the plan aims for something that President Donald Trump’s administration didn’t do with Covid-19 more broadly and the vaccine in particular: greater federal involvement. The Trump administration has repeatedly pushed against a bigger federal role — even characterizing more support for states so they can get shots in arms as a “federal invasion.” Biden has rejected that rhetoric, calling for a bigger role by the feds, and cementing it with his plan.

The stakes are as high as they’ve ever been. The country now averages 240,000 Covid-19 cases and more than 3,300 deaths each day. The American death toll is among the worst in the world, with the country now approaching a total of 400,000 dead. If the US had the same death rate per million people as Canada, over 230,000 more Americans would likely be alive today.

The vaccine is America’s — and the world’s — chance at fixing this mess. Experts say the country must vaccinate at least 70 percent of its population, and possibly more, to reach herd immunity and protect a sufficient amount of the population from the virus. Only then can outbreaks truly be curbed.

But the US has been slow in rolling out a vaccine. The Trump administration overpromised and underdelivered: It promised 40 million doses and 20 million people vaccinated by the end of 2020; two weeks into 2021, only 31 million does have been delivered and just 11 million Americans have received at least the first dose of a vaccine, according to federal data. The country is currently not on track to reach 70-plus percent vaccination rates by the end of the summer.

Biden’s immediate challenge is to clean this all up. His presidency may count on it — his handling of the country’s most pressing crisis will likely be what Americans judge him on over the next year.

More seriously, it’s a matter of life or death: With thousands of people dying each day, ending the epidemic in the US even days or weeks earlier than otherwise could save up to tens or hundreds of thousands of lives.

Here’s how Biden plans to do it.

What Biden’s vaccine plan does

Biden promises to leverage “the full strength of the federal government,” in partnership with state, local, and private organizations, for a truly national vaccine plan. You can read the full proposal here, but these are some of the key points:

• More federal work to get shots to people: Biden calls for more involvement by the federal government in getting vaccine doses to people. That includes new vaccination centers, mobile vaccination units in underserved communities, reimbursement of states’ National Guard deployments, and expanding vaccine availability in pharmacies. He also promises to target hard-to-reach, marginalized communities with extra support, particularly those that have been hit the hardest by Covid-19.
• Boost the supply of vaccines: Biden says he’ll make greater use of federal powers, such as the Defense Production Act, to boost the manufacture of vaccines and related supplies. He also says he’ll improve communication with states so they can better understand when and how much vaccine they can expect to get — addressing a big complaint from states today, as the Trump administration has often failed to inform them of even these basic details.
• Expanded vaccine eligibility: Biden calls for expanding vaccine eligibility to include everyone 65 and older as well as frontline essential workers, including teachers, first responders, and grocery store employees. Several states have already moved in this direction, but Biden promises more support and encouragement toward this objective.
• Mobilize a larger public health workforce: Building on his stimulus plan, Biden vows to hire and use a larger public health workforce to help deploy the vaccine across the country. He’ll also take other steps, like allowing retired medical professions who aren’t currently licensed under state law to help administer vaccines “with appropriate training.”
• Launch a national public education campaign: To help convince people to get vaccinated, Biden also plans to launch an education campaign “that addresses vaccine hesitancy and is tailored to meet the needs of local communities.”

All of that is on top of Biden’s broader Covid-19 plan, which promises $400 billion more funds to combat the coronavirus and, specifically, $20 billion more for vaccine efforts.

Biden’s plan hits many of the marks that I’ve heard from experts over the past few weeks as I’ve asked them about what’s going wrong with America’s vaccine rollout.

First, the plan has clear goals to address what supply chain experts call the “last mile” — the path vaccines take from storage to injection in patients — by making sure there’s enough staff, infrastructure, and planning to actually put shots in arms. Second, it takes steps to ensure that supply chain problems are fixed proactively, with careful monitoring and use of federal powers when needed to address bottlenecks. Last, but just as crucially, there’s a public education campaign to ensure that Americans actually want to get vaccinated when it’s their turn.

The question, of course, is if all of this can get implemented properly. As the US response to Covid-19 has floundered, a key question has been how much of the failure is attributable just to Trump versus bigger systemic problems, like the country’s size and sprawl, fractured health care system, and fragmented federalist government.

There’s also the question of whether Biden can get the congressional support needed for all these efforts. Democrats will control both houses of Congress. But more moderate wings of the party may scoff at the high price tag: Biden’s stimulus plan is estimated at $1.9 trillion and the Covid-19 plan alone (which is included in the bigger plan) at $400 billion. The cost of borrowing money is low, and Biden argues that the risk right now is doing too little instead of too much, but it remains to be seen if he gets enough backing in Congress.

If he pulls it off, though, Biden has a chance to show how much of a difference true federal leadership can make — and demonstrate how much the previous administration failed by refusing to embrace a larger role for itself.

Biden wants a federal role that Trump disavowed

At the core of Biden’s plan is a posture of more federal involvement that Trump has resisted at every step throughout the Covid-19 crisis.

This was clear in Biden’s broader Covid-19 plan, too: The ideas in the proposal aren’t at all new. Experts have called for expanding testing, preparing for mass vaccination efforts, supporting schools, providing emergency paid leave, and much more in the past year. Biden himself proposed many of these things last March. You can see many of these ideas in article after article in Vox and elsewhere, dating back to early 2020.

The Trump administration declined more aggressive steps, repeatedly taking a stance that it wasn’t the federal government’s proper role to get hands-on with the Covid-19 response. With protective equipment, Trump resisted using the Defense Production Act to get more masks, gloves, and other gear to health care workers. On testing, the Trump administration left the bulk of the task to local, state, and private actors, describing the federal government as merely a “supplier of last resort.” On tracing, the administration never had anything resembling a plan to make sure the country could track down the sick or exposed and help them isolate or quarantine.

This kind of hands-off, leave-it-to-the-states attitude culminated in the messy vaccine rollout. While there are many factors contributing to America’s slow vaccine efforts — including the country’s size, sprawl, and fragmented health care system — a key contributor is the lack of federal involvement. In effect, the Trump administration purchased tens of millions of doses of the vaccines, shipped them to the states, and then left the states to figure out the rest.

This was clear in the funding numbers. State organizations asked for $8 billion to build up vaccine infrastructure. The Trump administration provided $340 million. Only in December did Congress finally approve $8 billion for vaccine distribution, but experts say that money comes late, given that vaccination efforts are already well underway and the funds could’ve helped in the preparation stages.

When asked about the botched vaccine rollout, the Trump administration has stuck to its anti-federalist stance — arguing that it’s on states and localities to figure out how they can vaccinate more people. Brett Giroir, an administration leader on Covid-19 efforts, argued, “The federal government doesn’t invade Texas or Montana and provide shots to people.”

Characterizing greater federal support for Covid-19 efforts as a federal invasion is of course absurd, but it’s emblematic of the Trump administration’s approach to the crisis.

On vaccines, as with the coronavirus in general, Biden’s promise has long been that he’ll embrace a bigger role for the federal government. With his plan, Biden is putting some specific details to that end. The question now is if he can pull it off — if he gets the support he needs from Congress, and if the feds really can deliver what Biden has promised.

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There’s a reason why a new, more contagious variant of SARS-CoV-2 appeared first in the UK: The country does a lot of viral genetic sequencing. Since the start of the pandemic, researchers in the UK have uploaded 151,859 individual SARS-CoV-2 sequences to GISAID, an international platform for sharing viral genomic data. That’s the highest number of sequences shared by any country in the world.

If a more contagious strain of SARS-CoV-2 first evolved in the United States, scientists likely would not have noticed so quickly. Despite having a larger population than the UK, a sophisticated biomedical research industry, and tens of millions more cases of Covid-19, to date US labs have only uploaded 69,111 sequences, according to GISAID.

“It’s embarrassing, is all I can say,” Diane Griffin, a microbiologist and immunologist at Johns Hopkins, told Vox.

The US has lagged behind on so many aspects of pandemic response — from an initial lack of testing, to the current strained and clumsy rollout of the Covid-19 vaccines. Lack of genetic surveillance is just another. Without it, we’re kept in the dark: Scientists can’t see, clearly or quickly, how and if the virus is mutating in concerning ways. It also leaves us without another useful tool to deploy in contact tracing studies.

And it’s one this country ought to invest in, and get right, scientists say — at least before the next pandemic strikes.

How the US fails on testing viral genomes

Earlier this year, Griffin was on a committee making recommendations for a recent National Academies of Science report on the state of genomic surveillance in the US. Genomic surveillance is used, routinely, around the world to track flu, and to try to predict which flu vaccine strains will be most effective in a given season. Genetic sequencing tools are not a new technology, and the Academies wanted a report to survey how they were being deployed in the pandemic in the US. Genetic sequencing is of particular import when it comes to coronaviruses because they use RNA as their genetic code, and RNA viruses are known to mutate frequently.

The report, when it was published in July, outlined a bleak landscape of SARS-CoV-2 mutation tracking. It’s not just that the US isn’t collecting enough genome samples of the virus. It’s doing so in an unsystematic, patchwork way.

“Current sources of SARS-CoV-2 genome sequence data … are patchy, typically passive, reactive, uncoordinated, and underfunded in the United States,” the report concluded. And the data that did exist? The report found it was “inadequate to answer many of the pressing questions about the evolution and transmission of the virus.”

Early on in the pandemic — way back in March — the UK government invested £20 million ($27 million) to launch the COVID-19 Genomics UK (COG-UK) consortium, which coordinates the collection of this data from public health labs. The consortium also tracks viral genetic samples from health clinics, university research labs, and public health research facilities, to help generate a close-to-real-time snapshot of how the virus is changing in the country.

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It’s what allows researchers to generate maps like this one, which shows how the new, more contagious strain of the virus spread geographically in the country over time.

The rich genetic data, when paired with case reports, also guides researchers to ask and answer crucial questions, such as: Is this new variant more deadly than other ones? Scientists were able to quickly determine the answer is “no.” (That said, a more contagious virus can still end up killing more people than a more virulent one.)

The US Centers for Disease Control and Prevention does have a genetic surveillance program called SPHERES (SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology, and Surveillance), but it’s less well coordinated than the UK effort. Right now labs have to essentially raise their hands and volunteer to contribute. And the funding for their efforts isn’t consistent. That leads to a patchwork of surveillance across the country. “So you might know what’s going on in Boston, or New York City, but have no idea what’s going on in Iowa,” Griffin says.

“In other words,” says Stanford microbiologist David Relman, who also contributed to the National Academies report, “anybody who has the means and interest to engage in genomics is certainly encouraged to do so.” But genomic sequencing, he says, hasn’t been made a “mainstream central pillar of public health efforts.”

What we lose out on when we don’t collect genetic samples of circulating viruses

The National Academies report was published in July. Has the situation gotten much better since? “No,” Griffin says. There has been a little bit of positive movement: Recently, private genomics companies Illumina and Helix have started to help in the detection of new variants in the United States. Even so, James Lu, president of Helix, told MIT Technology Review the US still needs to go from sequencing a few hundred samples a day to around 7,000 per day.

Viral genomics surveillance doesn’t just allow researchers to spot new variants, it helps them learn crucial lessons about how the virus is spreading.

Scientists take advantage of the fact that viruses are constantly making copies of themselves. And every time they make a copy, they may make a little typo in their genetic code. Most of the time, these mutations are meaningless, but they occur at a regular rate. And that makes it possible to make a family tree of the virus. If one viral sample and another have similar typos, researchers can determine they are more closely related.

This can generate key insights.

“In the beginning of the pandemic, we got our hands on some of the first cases that were identified in Connecticut,” says Mary Petrone, a PhD student who works in a molecular biology lab at Yale. Using genomic data, Petrone and her colleagues were able to figure out whether these cases were introduced from abroad, or came from somewhere in the United States. The genetic data revealed that the viruses more closely resembled those circulating on the West Coast than strains from abroad. “It was telling us: there is actually domestic transmission going on,” she says.

Petrone’s lab delivered a key early insight into understanding the virus’s spread in the US. But it wasn’t like the CDC directed them to do so. “Our lab was actually originally set up to do this type of research for mosquito-borne viruses,” she says. “When the pandemic hit we switched over, because there was an urgent public health need to answer some of these questions. So we just happened to really to be set up to do this type of work.”

Setting up more labs to do this work could also help with contact tracing efforts, overall. “For example, if 10 college students test positive,” Julie Segre, a scientist at the National Human Genome Research Institute, writes in an email, “did they come to school already colonized [i.e. infected] or did they transmit the virus while at school.” Genetic evidence can help answer such a question and help prevent future outbreaks.

What needs to happen: coordination, and money

And it’s not necessarily cheap or easy work to do. While the technology that sequences the viral genomes has become relatively inexpensive in recent years (a plug-in USB sequencer will set you back around $1,500), it still takes a lot of skilled lab work to prep samples for analysis. “You definitely don’t need a PhD to be able to do it,” Petrone says. “But you do need to be pretty well trained in molecular biology in the lab. There are a lot of steps where you can contaminate your samples. It can be quite expensive to do.”

Petrone’s lab can do full genome sequencing; that is, they can read every letter of a virus’s genetic code. But not all labs would need to do that to contribute to a surveillance effort. For instance, Petrone’s group is working on a simpler test that can identify the more contagious B117 variant that first was detected in the UK. “That is something you’d be able to run in a clinic,” she says.

But creating a widespread surveillance network for the new variant would require a lot more coordination than what’s currently taking place.

That’s why the US government needs to be more proactive on this, and help set up a nationwide network for genomic data. And that may be coming. According to STAT, the incoming Biden Administration plans to scale up the country’s genomic sequencing efforts as part of a $415 billion emergency Covid-19 spending package it will ask Congress to approve. (Perhaps also auspicious: Biden has selected Eric Lander, a geneticist who co-led the Human Genome Project, to lead the White House Office of Science and Technology Policy, which will be elevated to a Cabinet-level position.)

For a robust genetic surveillance network to be most useful, it needs to be backed up with other rich datasets too. New variants pop up all the time. What matters is whether those variants are linked to worse health outcomes, more reinfections, or faster spread.

“We would ideally have access to good, consistent data about each sample — at the least, geographical location, but more would be better,” Adam Felsenfeld, director of genome sciences at the National Human Genome Research Institute, writes in an email. If possible, too, “one would need details about the medical record of the patients,” he writes, to try to determine if genetic changes in the virus correspond to different disease courses. Again, this would take coordination, as researchers would need informed consent from people to collect this personal data.

A network of viral genome surveillance isn’t just needed for this pandemic, but for future ones too.

“This won’t be the last pandemic,” Griffin says. “If we could get the infrastructure right and get the approach right, then you have things in place you could activate” … for the next time.

For the nearly 100 million people around the world who’ve been infected with the coronavirus, new science offers some comfort: Reinfections appear to be rare, and you may be protected from Covid-19 for at least five months.

The study, the largest of its kind, followed more than 20,000 health workers in the UK, regularly testing them for infection and antibodies. Between June and November, the researchers — from Public Health England (PHE) — found 44 potential reinfections out of the 6,614 participants who had tested positive for antibodies or had a previous positive PCR or antibody test when they joined the study. Meanwhile, of the 14,000-plus people who had tested negative for the virus at the start of the study, there were 409 new infections.

Only two of the 44 potential reinfections were designated “probable” and the rest were considered “possible,” “based on the amount of confirmatory evidence available,” according to the health agency. Fifteen people — or 34 percent — had symptoms.

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So if all 44 reinfections are real, that translates to an 83 percent lower risk of reinfection compared to health workers who never had the virus. If only two are confirmed, that rate of protection goes up to 99 percent. Either way, it suggests natural immunity might provide a similar level of protection as the approved Covid-19 vaccines.

But as with the vaccines, it’s not yet clear how long immunity after an infection lasts. Antibodies may fade after five months or last much longer, something the researchers behind the ongoing study, which will run for a total of 12 months, plan to investigate.

“This [new] study does provide some comfort that naturally acquired antibodies are pretty effective in preventing reinfections,” Akiko Iwasaki, an immunobiologist at Yale University, told Vox. The findings also square with another paper on health workers, published in the New England Journal of Medicine in December: Researchers found people who had Covid-19 antibodies were better protected from the virus for six months than people who did not.

Iwasaki added, “You can also interpret these data to mean that protection against reinfection is not complete — especially for people who had Covid during the first wave, say in March-April 2020.”

People who had the virus may still be able to pass it on if reinfected

The good news for individuals who have had Covid-19 also comes with a warning about the risk they can still pose to other people. While antibodies might protect against a second case of Covid-19 in most people, “early evidence from the next stage of the study suggests that some of these individuals carry high levels of virus and could continue to transmit the virus to others,” PHE warned in its press release.

“We now know that most of those who have had the virus, and developed antibodies, are protected from reinfection, but this is not total,” Susan Hopkins, a senior medical adviser at PHE and the study lead, said in a statement, “and we do not yet know how long protection lasts.”

In other words, even if you’ve had Covid-19, while you’re unlikely to get really sick again anytime soon, you should still consider yourself a potential risk of spreading it to others if you catch the virus again and are asymptomatic. That means continuing to take precautions — like mask-wearing and social distancing, Iwasaki added. And it’s one reason why immunologists have said people who’ve already been infected with the virus should still plan to get the vaccine when their turn comes.

So there’s still a lot more to learn about immunity after Covid-19: How will the new coronavirus variants affect it? Lab data from South Africa, where the 501Y.V2 variant has been spreading, suggests it might be able to escape antibodies produced by prior infections in some people.

Who is most likely to have a strong immune response? We do have some evidence that different individuals mount different antibody responses after Covid-19 infections, but the PHE researchers found no statistically significant difference in rates of protection between people who reported symptoms and those who did not. It’s also possible factors like gender and disease severity influence the strength of a person’s immune response.

For now, though, the research suggests that survivors of the virus might just help us get to herd immunity faster — if their immunity lasts long enough. But given the virus has only been known to humans for a little over a year, it may take a while to authoritatively answer the question.

The number of confirmed Covid-19 deaths in the United States has now surpassed 400,000, and that devastating toll is set to grow in the coming weeks with the US still averaging more than 3,300 deaths every single day.

In just the 11 months since the country’s first confirmed death from Covid-19, the disease has killed as many Americans as US soldiers who died during four years of World War II.

That figure is also almost surely an undercount. The number of excess deaths during the Covid-19 pandemic (the number of deaths that have occurred in excess of what would ordinarily be expected based on long-running trends) is closer to 500,000, according to some recent estimates. Some of the additional 100,000 deaths may not be from the coronavirus — they could, instead, be people who couldn’t get adequate medical care because health systems have been strained by the pandemic — but experts think a substantial portion probably are uncounted Covid-19 deaths.

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Regardless, the loss of human life over the past year has been extraordinary. The US has by far the most confirmed Covid-19 deaths in the world and nearly doubles the toll in Brazil, the second-hardest-hit country. Even when adjusting for population, America ranks 11th in the world in Covid-19 deaths per million people.

And even now, nearly a year into the pandemic, deaths are piling up faster and faster, rather than slowing down. It took about three months from the first confirmed Covid-19 death in the US in late February for the country to hit 100,000 deaths. Another four months elapsed before the country reached 200,000 deaths in late September. But then things picked up speed during the winter surge: The US added 100,000 more deaths in less than two months, and from there, it took a little more than a month to go from 300,000 to 400,000 deaths.

What went so wrong? Vox’s German Lopez explained at the beginning of this month:

The primary answer lies in President Donald Trump and Republican leaders in Congress, who have collectively abdicated the federal government’s role in addressing the outbreak or even acknowledging its severity. From Trump’s borderline denialist messaging on Covid-19 to Congress’s inability to pass broader economic relief, the country has been left in a place where states, local governments, and the public have to fend for themselves — and none of them have the resources to deal with the coronavirus on their own.

Trump and his allies have also actively worked to sideline the Centers for Disease Control and Prevention, crippling the agency’s ability to provide guidance to states and others that have now been left out on their own.

At the same time, there are serious structural issues that hindered states’ and the public’s ability to act. Experts have long argued that the US’s public health infrastructure is underresourced and ill prepared for a serious crisis, and the pandemic has exposed this many times over: Nearly a year into the pandemic, no state has capacities for testing and contact tracing that most experts would consider adequate.

President-elect Joe Biden is coming into the White House promising to pass a big bill allocating more funding for the Covid-19 response and to fix the nation’s troubled vaccine rollout. More precautions and more vaccinations could help reduce the loss of life going forward.

But America’s failures in the pandemic have already exacted an awful cost: at least 400,000 lives lost.

We knew it was going to be a long, dark winter. But unfortunately, it’s now looking even more grim. Just as the first coronavirus vaccines began rolling out in the US and countries around the world in December — offering hope for the end of the Covid-19 pandemic — two fast-spreading variants of the SARS-CoV-2 virus were discovered in the United Kingdom and South Africa.

Within a matter of weeks, the new variants replaced other versions of the virus in some regions. Scientists say these variants help explain the recent peak in cases in the UK and South Africa that have forced new and tough social distancing measures. They’re also proliferating around the world. As of January 17, the UK variant had been found in 60 countries, and the South Africa variant in 23, according to the World Health Organization.

“It’s scary, isn’t it?” said Richard Lessells, a University of KwaZulu-Natal infectious disease specialist in Durban, South Africa, who co-discovered the South Africa variant. “I’m a Scotsman so talking about my emotions doesn’t come to me naturally but I have a lot of anxiety at the moment.”

All viruses mutate as they move through populations, and until recently, the mutations in SARS-CoV-2 weren’t cause for much concern. (A mutation is a change in the genetic makeup of a virus while a variant is a virus that has a suite of mutations that alter how it behaves.)

B.1.1.7 in the UK and 501Y.V2 in South Africa each have a startling number of changes in the virus’s spike protein, the part that fits into the receptor in human cells, allowing it to infect people — and these changes may be why the new variants are seemingly more contagious than earlier versions of the already contagious virus. (There’s already increasing alarm over variants that have emerged in California and Brazil — and these are just the ones we know about right now.)

While there’s no evidence they cause more severe disease, more cases mean further stress on hospitals and, after that, a rising death rate.

And some researchers have another, pressing worry: These mutations could render the current Covid-19 vaccines less effective. Or they could mean the virus eventually “escapes” them all together. That’s why doctors, virologists, and other health researchers are calling on officials to “vaccinate 24/7 like it’s an emergency,” as Scripps Research scientist Eric Topol said on Twitter. “Because it is.

While vaccine manufacturers like Pfizer and BioNTech say their technologies can readily adapt to changes in the virus, we’re still learning about how the shots will work in this new context — and the mutations in South Africa’s 501Y.V2 are causing particular concern.

As the virus continues to spread and more people are infected, the likelihood of even more dangerous mutations happening rises. So too does the threat the mutations pose to the vaccines. So, without drastic countermeasures, the variants could herald a new, potentially even more difficult, chapter in the pandemic.

Why the new Covid-19 variants are different — and more worrisome — when it comes to the vaccines

Scientists have warned that it was always possible the coronavirus could evolve to evade the Covid-19 vaccines that have been approved so far. The arrival of the UK and South Africa variants may be a step in that direction, increasing the odds of the vaccines becoming less effective over time.

In SARS-CoV-2, the main mutations scientists care about are on the spike protein of the virus — the part that allows it to enter human cells. This is also the protein that Covid-19 vaccines currently available in the US (from Moderna and Pfizer/BioNTech) are designed to imitate. About 4,000 mutations in the SARS-CoV-2 spike protein have been detected at various points in the pandemic. Most haven’t altered the function of the virus and haven’t stirred worry.

In rare cases, a mutation, or several at the same time, lead to changes that give the virus a greater advantage. And that appears to be what’s happening with the UK and South Africa mutation.

The UK variant, B.1.1.7, contains 23 mutations in the genome of the virus while the South Africa variant, 501Y.V2, has at least 21 mutations, with some overlap between the two. In both cases, the changes seem to have increased the fitness of the virus, or its ability to propagate.

“[With genomic sequencing in South Africa] we can show quite clearly there were lots of different lineages circulating prior to October,” Lessells said. “Within the course of just a few weeks, this new lineage — 501Y.V2 — became almost the only lineage you’re detecting.” The story is similar in England, where one in 50 people were infected with Covid-19 as of the new year.

The fact that these mutations became so dominant so quickly suggests that they may be more contagious. Scientists in South Africa think the variant that emerged there is about 50 percent more transmissible, and one estimate suggested the UK variant is up to 70 percent more transmissible.

There could also be other more familiar variables that are driving the spread of these new variants, like holiday travel. Scientists still have to complete experiments in animals to pinpoint differences in transmissibility between these mutations and earlier versions of the virus — and to what extent shifts in peoples’ behavior might also explain the growth in cases.

But they’ve already zeroed in on concerning changes in the virus that are relevant to vaccine effectiveness. With the South Africa variant, for example, one change of particular interest is the E484K mutation in the receptor-binding domain of the virus where it latches on to human cells.

“The E484K mutation has been shown to reduce antibody recognition,” said Francois Balloux, a professor of computational systems biology at the University College London, in a statement. This means it can help the virus “bypass immune protection provided by prior infection or vaccination.”

Researchers have demonstrated how this might happen in cell culture and small human experiments. One, described in a pre-print paper (and therefore not yet peer-reviewed) on Biorxiv, looked at several generations of SARS-CoV-2 challenged with antibody-rich plasma from a Covid-19 convalescent patient and watched to see what happened. At first, the antibodies seemed to beat back the virus. But as the virus mutated, eventually making the E484K substitution, it started to proliferate in spite of the presence of the antibodies.

The senior author on the study, Rino Rappuoli, a professor of vaccines research at Imperial College and chief scientist at GSK, told Vox that when he and his colleagues first ran the experiment, they didn’t know how relevant their findings would be. “But when the South Africa and UK variants came along, we looked at [our data] and saw that, in real life, the first steps of what we saw in vitro are happening.” (GSK has a Covid-19 vaccine in clinical trials with the drugmaker Sanofi.)

Other scientists are coming to similar conclusions. In a second preprint, researchers tracked how mutations altered the effectiveness of the antibody response in people who had the virus. They also found E484K has antibody evasion capabilities. A third, also in test tubes involving survivor plasma from donors in South Africa, showed that antibodies from a prior infection were totally ineffective against the new variant in about half of the donors.

A couple of caveats here: These studies are in vitro, involving the specimens from Covid-19 survivors, rather than antibodies from someone who received a vaccine. We don’t yet know how people in clinical studies who got a vaccine will respond to the new variants.

Still, Rappuoli said, the findings are cause for concern nonetheless. “If given enough time under immune pressure, this virus has the possibility to escape.”

Another preprint study, from researchers in Brazil, recently provided an alarming example of how this could play out. The paper documents the case of a 45-year-old Covid-19 patient with no co-morbidities: months after her first bout with the illness, she was reinfected with a version of SARS-CoV-2 that had the E484K mutation — and experienced more severe illness the second time around. It’s limited evidence, but it suggests that surviving an earlier SARS-CoV-2 infection isn’t a guarantee of protection against variants with this mutation.

“The finding of the E484K, in an episode of SARS-CoV-2 reinfection might have major implications for public health policies, surveillance and immunization strategies,” the authors wrote.

Researchers are racing to figure out how vaccines work against the variants

So what does this mean for the vaccine rollout effort? Will pharmaceutical companies have to tweak their existing vaccines to fight the new variants?

“It is one of the key questions that we are trying to find answers to at the moment, and we have groups around the country working around the clock to get a better understanding of this,” said Lessells. “This also involves collaboration with other groups around the world, with groups running the vaccine trials, with vaccine developers.”

Rappuoli said even if there’s no evidence yet showing the variants can outsmart the immune response created by vaccines, “we should be prepared that at some point in the future that may happen,” he added. For Fred Hutch Cancer Research Center scientist Trevor Bedford, that point could come as early as autumn this year:

Vineet Menachery, a coronavirus researcher at the University of Texas Medical Branch, said the laboratory experiments on SARS-CoV-2 variants represent “the worst-case scenario.”

The currently available vaccines in the US — from Pfizer/BioNTech and Moderna — help the immune system target multiple areas of the spike protein, so the virus would have to change drastically to completely escape the immune response generated by the vaccines. He called the odds of this happening “unlikely but not impossible.”

The diversity of immune responses at the population level gives University of Utah evolutionary virologist Stephen Goldstein some comfort, too. “Our immune systems have evolved to deal with antigenic drift — or the selection of different variants of circulating viruses,” he said. “I’m not worried vaccine efficacy is going to fall off a cliff and go from 95 percent to zero.”

The incoming Centers for Disease Control and Prevention director, Rochelle Walensky, also took comfort in the very high rate of protection the vaccines already have. “The efficacy of the vaccine is so good and so high, that we have a little bit of a cushion,” Walensky said in a January 19 interview with JAMA.

And if the vaccines do turn out to be less effective against the new variants, vaccine developers say they’ll be up for the challenge of adapting them. That’s because the new platforms they’re using can be modified easily to counter new threats.

Vaccine developers say they can adapt their technologies fast

The Pfizer/BioNTech vaccine and the Moderna vaccine both use a molecule called mRNA as their platform to deliver instructions for making the spike protein of SARS-CoV-2. Meanwhile, the vaccine developed by the University of Oxford and AstraZeneca that recently received approval in the UK (but not yet in the US) uses a reprogrammed version of another virus, an adenovirus, to shuttle DNA that codes for the SARS-CoV-2 spike protein.

Human cells then read that DNA or mRNA genetic information and manufacture the spike protein themselves, allowing the immune system to use it for target practice. An advantage of using this approach is that vaccine developers only need to modify DNA or mRNA to tweak the vaccine, something they can do quickly and easily if necessary.

In a January 19 preprint, BioNTech and Pfizer found the UK’s variant may not pose as much of a threat to their vaccine: Antibodies in blood samples from people who got the shot appeared to work against the B.1.1.7’s mutations, making it “unlikely” the variant will escape the vaccine. If a stronger viral foe comes along, BioNTech’s chief executive Ugur Sahin told the FT, “we could manufacture a new vaccine within six weeks.”

These new vaccines would not necessarily require developers to go through every regulatory hurdle again, former FDA chief scientist Jesse Goodman told Vox in December. Instead, new versions of Covid-19 vaccines could end up going through an approval process similar to vaccines for seasonal influenza — with some initial testing but stopping short of massive clinical trials. That means revised Covid-19 vaccines could potentially roll out quickly.

Lessells was cautiously optimistic for another reason: Even if the current vaccines stop working as well as earlier clinical trials suggested, he said, “There are many vaccines in development. So as we learn more about this virus, the vaccine developers also learn from that, and different vaccines may be developed.”

But while it may be possible to alter the vaccine to adapt to new mutations, it’s not ideal: It would require expensive changes in the vaccine production process and eat up valuable time that could be used to inoculate more people during a devastating pandemic.

“From a cost and manufacturing perspective, it would put us far, far behind,” said Anna Durbin, a vaccine researcher and a professor of international health at the Johns Hopkins School of Public Health.

Now’s the time to drive down case numbers and vaccinate

That’s why researchers and health officials are hoping to drive down case numbers and rapidly build up herd immunity with the existing vaccines while also getting ready for changes to the virus that may lay ahead.

To track mutations and understand how they may impact vaccine effectiveness, governments also need to invest more in genomic sequencing, Lessells said. And right now, “there’s a lot of variability around the world in how much sequencing is being done and how people are using sequencing.”

Inadequate sequencing of SARS-CoV-2 genomes may create blind spots where new mutations could be lurking. Infectious disease experts told Stat’s Helen Branswell that the US doesn’t sequence enough and may be unaware of how widespread the UK variant is because of that. According to Lessells, the UK sequences about 10 percent of its cases — on the high end of sequencing volume globally — while the number in South Africa is closer to 1 percent.

Of course, there’s another way to prevent dangerous mutations from arising: preventing cases from happening at all through mask-wearing, social distancing, rapid testing, and treating and isolating infected people. The virus can’t mutate if it’s not replicating inside lots of people.

“The bottom line hasn’t changed: We need to suppress the amount of viral transmission as much as we can,” Goldstein said. Vaccines are a part of that suppression effort, but social distancing and masks are too. According to Salim Abdool Karim, chief adviser on Covid-19 to the South African government, social distancing measures in the country appeared to be bending the curve. “Outbreaks grow exponentially and you’re not going to vaccinate at an exponential rate,” he added. “But you can bring outbreaks down to a rate where they are not growing exponentially.”

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For now, the emergence of the worrisome mutations is a reminder that, despite our collective fatigue, there’s still a long road ahead, Lessells said.

“We keep passing these milestones — going into a new year, having Christmas — and thinking that the virus is going to suddenly do something different because we are celebrating or whatever. Of course, that’s not the case. We are still in the early days. We are still learning about this virus.”

People who are pregnant are now eligible to get the coronavirus vaccine in more than 40 states — typically ahead of their lower-risk peers. And more than 60,000 of them have already rolled up their sleeves, according to the Centers for Disease Control and Prevention.

Although the Covid-19 vaccines authorized in the US were not studied in pregnancy, early data is now starting to emerge suggesting — as researchers expected — that the vaccines are likely safe during pregnancy and confer protection not only to the recipient but also, potentially, the baby.

“It’s all very positive,” says Stephanie Gaw, a maternal-fetal medicine specialist at the University of California San Francisco Medical Center, of the findings so far.

There have been many reasons to suspect the vaccines should be safe in pregnancy, including the lack of major adverse events reported so far, solid studies in animals, and a good understanding of how the vaccines work in the body (they don’t contain live virus, and they are quickly broken down). “The data that we’re collecting on it so far has no red flags,” Anthony Fauci, the top US infectious disease doctor, said in February.

Meanwhile, new research, published March 25 in the American Journal of Obstetrics and Gynecology, found that the vaccines offer strong immune protection for people who are pregnant, just like their non-pregnant peers.

Preliminary research also suggests vaccines might provide some protection to newborns, who are unlikely to have their own approved Covid-19 vaccine anytime soon (and are also vulnerable to more severe illness). The new AJOG paper joins other early findings that antibodies to Covid-19 generated by pregnant mothers after receiving their vaccines were passed through the placenta to the fetus.