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‘A wakeup call’: How resilient new coronavirus variants could prolong the pandemic

Andrew Romano
·West Coast Correspondent
·12-min read

It’s no secret that ending the coronavirus pandemic requires two things: mitigation and vaccination.

But the urgency of doing both — and doing them as completely and quickly as possible — dramatically increased this week as news broke that the so-called South African variant had finally arrived in the United States, with South Carolina officials reporting on Thursday America’s first two known cases involving the B.1.351 strain.

Neither South Carolina patient had traveled or been in contact with the other, which is a strong indication that the South African variant is already spreading undetected in America.

“By the time someone has symptoms, gets a test, has a positive result and we get the sequence, our opportunity for doing real case control and contact tracing is largely gone,” said Dr. Rochelle Walensky, the new director of the Centers for Disease Control and Prevention, during Friday’s White House COVID-19 briefing. “We should be treating every case as if it’s a variant during this pandemic right now.”

At the same time, a raft of new data underscored why B.1.351’s arrival in the U.S. is cause for concern: It has an advantageous set of spike-protein mutations that allow it to partially evade the immune responses that protect against the original, “wild type” virus.

A CVS Health Corp. pharmacists administers a dose of the Moderna Covid-19 vaccine at the Covenant Place assisted living facility in Sumter, South Carolina on Jan. 26, 2021. (Micah Green/Bloomberg via Getty Images)
A CVS Health Corp. pharmacist administers a dose of the Moderna COVID-19 vaccine in Sumter, S.C., on Jan. 26. (Micah Green/Bloomberg via Getty Images)

On Thursday, Novavax announced that its new two-shot vaccine was nearly 90 percent effective in preventing infection during its U.K. trial but just 49 percent effective during a smaller study in South Africa, largely due to the dominance of the B.1.351 variant (which now accounts for nine out of 10 cases there).

Likewise, Johnson & Johnson revealed Friday that its new single-dose vaccine was 72 percent effective in the U.S. but only 57 percent effective in South Africa.

Laboratory studies show that the Pfizer and Moderna vaccines approved for emergency use in the U.S. also generate a weaker immune response against the South African variant.

So how worried should we be?

The temptation is to see the South African variant — and a similar Brazilian “mutant,” P.1, that seems to have evolved independently and also first surfaced in the U.S. earlier this week — as the start of a bleak new chapter in our seemingly never-ending war against the virus.

Like the much discussed U.K. variant (a.k.a. B.1.1.7), both of these strains seem to be more transmissible than earlier versions of the virus. But while studies show the U.K. variant isn’t necessarily better at dodging existing immunity than its predecessors, its mutant cousins are.

This, in turn, has led to fears that “we could still be battling the pandemic well into 2022,” as Newsweek’s David H. Freedman writes. Noting that “case rates are frighteningly high, few people have immunity and the vaccine rollout is grindingly slow,” Guterl spells out “the nightmare scenario: the virus mutates into a variant that renders current vaccines weakened or obsolete before the rollout reaches the 150 million or so people needed to achieve herd immunity.”

But the truth is, we’re a long way from that particular nightmare, and it’s a nightmare we have the ability to avoid.

The immediate threat isn’t that new variants will render vaccines obsolete. We're actually in good shape there. The more troubling issue is that these mutants may already have the power to reinfect people who were previously infected by an earlier strain of the virus.

Viruses don’t evolve new variants in a vacuum; they only mutate when they are actively infecting human cells. The more the virus spreads, the more such mutants will emerge — and the less we’ll be able to rely on natural immunity to layer atop vaccine-induced immunity and knock the wind out of the pandemic.

That’s why masking up and distancing may be more important now than ever — because it’s the one thing individual Americans can do to prevent new strains from replicating, evolving and eventually reinfecting people who would otherwise be immune.

Anthony Fauci, director of the National Institute of Allergy and Infectious Diseases, wears a protective mask while speaking to members of the media before an event on the Biden administration's Covid-19 response in the State Dining Room of the White House in Washington, D.C., U.S., on Thursday, Jan. 21, 2021. (Al Drago/Bloomberg via Getty Images)
Dr. Anthony Fauci. (Al Drago/Bloomberg via Getty Images)

“This is a wake-up call to all of us,” Dr. Anthony Fauci, the nation’s top infectious disease expert, said Friday. “Mutations occur because the virus has a playing field, as it were, to mutate. … The best way to prevent the evolution of a mutant is to prevent replication.”

The good news is that our existing vaccines should still help with that, despite the dire headlines. Is 49 percent or 57 percent efficacy as encouraging as 72 or 90 percent efficacy? Of course not. But there are two reasons why it isn’t an emergency, either.

The first is that a less effective vaccine isn’t the same thing as an ineffective vaccine — especially in the midst of a raging pandemic, when your main objective is to slow the spread of the virus while preventing as many hospitalizations and deaths as possible.

As Fauci noted Friday, Johnson & Johnson’s phase III clinical trial showed that its vaccine is actually “85 percent effective” in preventing “severe disease,” with “no hospitalizations or deaths in the vaccine group” across every country that participated in the study — including South Africa.

“This really tells us that we have now a value-added additional vaccine candidate,” Fauci said, emphasizing the positive worldwide impact that a cheap, easily transportable, single-dose vaccine could have. “The results are really very encouraging.”

Meanwhile, the Novavax vaccine was 60 percent effective at protecting HIV-negative South African trial participants against symptoms of COVID-19 — probably a better benchmark than the more widely reported 49 percent figure, given that HIV is far less prevalent in most other countries.

As for the even more effective Moderna and Pfizer vaccines, they come with a considerable amount of wiggle room. While studies have yet to determine how well they guard against B.1.351, Fauci explained earlier this week that scientists have seen only a “moderate diminution” in the ability of their antibodies to neutralize the South African variant in a lab — a decrease that was still “well within the cushion of protection.” In other words, these vaccines probably won’t end up being 95 percent effective against South African-style mutants, but they can still save a lot of lives.

A vial of the Phase 3 Novavax coronavirus vaccine is seen ready for use in the trial at St. George's University hospital in London Wednesday, Oct. 7, 2020. (Alastair Grant/AP)
A vial of the Phase 3 Novavax coronavirus vaccine. (Alastair Grant/AP)

Which brings us to the second reason not to stress about vaccines becoming useless: They too can “evolve.” As Fauci pointed out, mRNA “platforms” in particular are relatively simple to adjust and the federal government is already collaborating with the drug companies on updated shots that can be tailored to combat troubling mutations and rolled out as necessary in the coming months.

“As the virus uses its devices to evade pressure, particularly immunological pressure, we will continue to see the evolution of mutants,” Fauci said. “That means that we, as a government, the companies, all of us that are in this together, will have to be nimble, to be able to adjust readily, to make versions of the vaccine that are specifically directed to whatever mutation is actually prevalent at any given time.”

Moderna, Novavax and Johnson & Johnson have already said that they are developing booster shots to protect against the South African variant, and on Friday senior White House COVID-19 adviser Andy Slavitt confirmed that “contingency planning” was underway to ensure “sufficient manufacturing capacity and enough space in our contracts to be able to make adjustments on the fly.”

But while the alarm over vaccines may be excessive, the emerging evidence that both the South African and Brazilian variants have the potential to reinfect people who survived a first infection isn’t getting the attention it deserves.

The example of Manaus is especially unsettling. Last spring, a huge COVID-19 surge overwhelmed hospitals in this Brazilian city, ultimately infecting an estimated 76 percent of the population. The wave eventually subsided. Cases fell. Control measures were relaxed, and for seven months hospitalizations remained low. Scientists and government officials speculated that the city had achieved herd immunity. “Manaus will be the first Brazilian city to defeat the COVID-19 pandemic,” wrote a group of researchers from the Federal University of Amazonas.

Then came late December. Cases began to climb again. By mid-January, they had surpassed the highs of the spring. As the Washington Post recently reported, “Even in a city as traumatized as Manaus, the horror has been unlike anything doctors have seen. The oxygen quickly ran out. Dozens of hospital patients have died of asphyxiation. Scores more, unable to get care, have died at home. Every half-hour, one doctor said, a funeral procession rumbled toward the cemetery.”

Gravediggers carry the coffin of a COVID-19 victim at the Nossa Senhora Aparecida cemetery in Manaus, Amazonas state, Brazil, on January 22, 2021, amid the novel coronavirus pandemic. (Marcio James/AFP via Getty Images)
Gravediggers carry the coffin of a COVID-19 victim in Manaus, Amazonas state, Brazil, on Jan. 22. (Marcio James/AFP via Getty Images)

“How can you have 76 percent of people infected and, at the same time, have an epidemic that’s bigger than the first?" asked one Brazilian epidemiologist.

The answer may have come on Jan. 10 with the discovery of P.1., the new Brazilian variant. Its mutations resembled the strain from South Africa, but it appeared to have arisen independently. A second variant (P.2) was soon detected as well. Both were linked to reinfection in individuals. In December, according to researchers, P.1 accounted for 42 percent of the cases sampled in Manaus; in January, that number skyrocketed to 85 percent.

It’s unclear how much of Manaus’s second surge can be attributed solely to reinfection; other factors — including increased transmissibility, an overestimation of the city’s initial infection rate and the natural waning of immunity — could be playing a part as well.

But the risk is apparent. When B.1.351 became dominant in South Africa late last year, triggering another massive surge, participants who received a placebo in Novavax’s vaccine trial caught the disease at the same rate whether or not they had experienced an earlier infection, implying that “prior infection with COVID-19 may not completely protect against subsequent infection by the South Africa escape variant,” as Novavax wrote in a news release.

“It has global implications,” Shabir Madhi, the lead investigator of the South African Novavax trial, told the Wall Street Journal. “The immunity that was induced by the prototype virus is not protective [against the new variant].”

For Americans, at least, the implications are stark. For now, U.S. cases are falling 15 to 20 percent each week; hard-hit places such as California are relaxing restrictions. But as Walensky warned Friday, we’re still averaging 160,000 cases per day — a rate four times higher than over the summer.

Mutants emerge when — and where — infections run wild. This doesn’t just mean South Africa, Brazil and the U.K. It probably means the U.S. too. In December, researchers discovered a unique California variant with five spike-protein mutations. Named CAL.20C, it first surfaced over the summer but now accounts for at least half of all samples in Los Angeles — and may have been supercharging a winter resurgence in the city that seemed much harder to contain than previous waves. Other homegrown variants are likely spreading without our knowledge: As of late December, the U.S. had analyzed only 0.3 percent of its reported COVID-19 cases for genetic changes, a lower rate than 42 other countries.

“You can be almost certain that as long as a lot of virus is circulating in the community, there will be the evolution of mutants,” Fauci said Friday, alluding to Los Angeles and other U.S. cities. “Because that’s what viruses do.”

A notice inviting patrons to social distance is seen in the outdoor seating area of The Abbey Food & Bar on January 29, 2021 in West Hollywood, California. (Valerie Macon/AFP via Getty Images)
A notice inviting patrons to social distance is seen in the outdoor seating area of the Abbey Food & Bar on Friday in West Hollywood, Calif. (Valerie Macon/AFP via Getty Images)

On Friday, Walensky said the CDC had “scaled up surveillance dramatically just in the last 10 days,” collaborating with seven universities to cover thousands of samples per week while also asking every state to sequence at least 750 samples on its own.

The bottom line, however, is that B.1.351 and P.1 are likely a preview of things to come. More transmissible and evasive strains will continue to emerge as long as the virus continues to spread unchecked.

As vaccines roll out, they can and will help combat these variants, in both their current and future iterations.

But the factor that will determine whether these vaccines benefit from a head start on the path to herd immunity, or whether that goal keeps receding into the distance, is whether Americans can keep taking the necessary precautions — including masking up, distancing and gathering outdoors — to slow the spread of dangerous variants before they become dominant.

According to one respected forecasting model, America’s current trajectory of cases and vaccinations could produce a kind of combined herd immunity — roughly 35 percent of the population protected by inoculation and another 35 percent protected by infection — by mid-July. But if reinfection starts to erode America’s broad existing foundation of natural immunity, who knows how much longer the pandemic might drag on — and how many more people might die.

“What we’re saying, collectively, is let’s not be such polite hosts to this virus,” Slavitt warned at the end of Friday’s briefing. “Let’s turn the tide and [act] like other countries who do everything possible to shut out the growth of this virus and make sure it’s not welcome.”

The more committed we are to such measures, the easier it will be for vaccines to do their job in the months ahead — and the sooner we can return to something like normal.


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