Anna McCaffrey and J. Stephen Morrison. "New Variants Rattle the World." CSIS Commission on Strengthening America's Health Security, Center for Strategic and International Studies, January 22, 2021. Accessed December 21, 2023.

SARS-CoV-2 variants confer a new competitive edge to the virus and threaten to change the pandemic game fundamentally, at the very moment when many countries are facing runaway outbreaks and worsening economic and social crises.

Photo Credit: GARY RAMAGE/POOL/AFP via Getty Images


The emergence of new SARS-CoV-2 variants should come as no surprise. Yet, one year into the Covid-19 pandemic, world leaders are rattled as several new variants have taken hold in the United Kingdom, South Africa, Brazil, and now the United States. They confer a new competitive edge to the virus and threaten to change the pandemic game fundamentally, at the very moment when many countries are facing runaway outbreaks and worsening economic and social crises.

The United States is especially vulnerable and ill-equipped. Without a robust national genomic surveillance system, it is “flying blind” with limited visibility into how and where the virus is mutating and spreading. This is all unfolding as states are scrambling to get Covid-19 shots into arms while coping with a confused and chaotic vaccine introduction and an unrelenting surge that is bending health systems to a breaking point. The Biden administration is preparing to negotiate and implement its national Covid-19 strategy with a razor-thin margin in Congress.

Research on the new variants is just beginning and the full implications of their emergence remain unclear. One thing is clear: these new variants are generating new levels of anxiety and threatening to upend the best laid plans for Covid-19 prevention and control. They have created a sense of urgency and a renewed focus on the basics: expand genomic surveillance; achieve greater compliance in masking, social distancing, and avoidance of congregate settings; accelerate vaccination campaigns; and communicate to an anxious and skeptical public to win higher trust and confidence.

The Ground Shifts beneath Our Feet

Over the past year, SARS-CoV-2, the virus that causes the disease Covid-19, has infected at least 97 million people—the true number of infections is much higher. The U.S. Centers for Disease Control and Prevention (CDC) estimates that 30 percent of the U.S. public has been infected, roughly 100 million people. This explosive spread has given the virus nearly unlimited potential to mutate. While many mutations have had no meaningful effect, certain mutations have emerged that confer an advantage to the virus as it infects people and invades their cells. The fear is that those advantaged strains may become dominant, making outbreaks far more difficult and costly to control.

Scientists are most concerned about two types of mutations: those that increase the transmissibility of the virus (as is the case in the B.1.1.7 variant, which was originally detected in the United Kingdom) and those with “escape mutations” that allow the virus to avoid antibodies from therapeutics, vaccines, or prior infection (as is the case in the B.1.351 variant identified in South Africa and the P.1 variant identified in Brazil). (At time of writing, there is no standardized naming convention for coronavirus variants. We will use these three names—B.1.1.7, B.1.351, and P.1—in this paper.)

The B.1.1.7 variant, which is believed to increase transmission by up to 50 percent, has quickly become the dominant strain in the United Kingdom, leading to a runaway surge in cases and hospitalizations, pushing already strained hospitals to the brink. As of mid-January, one in fifty people in England had Covid-19, and nearly one in thirty in London.

The B.1.351 variant may be more resistant to existing Covid-19 therapies, including monoclonal antibodies and convalescent plasma. With relatively few effective Covid-19 therapies in the world’s arsenal, the emergence of a variant that can evade medicines is unsettling. New research also suggests that this variant might be able to reinfect those who have previously overcome mild Covid-19 infections.

A similar variant has emerged in the Amazonian capital of Manaus, Brazil, where an estimated 75 percent of the residents had Covid-19 by October 2020. But the city is experiencing an alarming resurgence, and the discovery of a new dominant variant, P.1, is leading experts to worry that it too is able to overcome natural immune protection.

If the B.1.351 and P.1 variants—or others with similar escape mutations—become more widespread, this could potentially lead to large numbers of recurring infections. Even more troubling, some new research indicates that vaccines may be less effective against these variants. These developments certainly do not justify any slow-down of vaccination efforts today—the Pfizer and Moderna vaccines are proven to induce strong immune responses—but they do indicate that we should be prepared to modify vaccines and therapies to respond to new variants in the future.

Why are these variants emerging now? Scientists believe that some variants first emerged in patients with chronic infections, or those who were immunocompromised. As these patients remained ill over the course of several months, the virus had extended opportunities to replicate and mutate. The continued spread of Covid-19 throughout the year—and the winter surges across many parts of the Americas and Europe—then allowed these new variants to become dominant in certain geographies.

We should expect the emergence of new variants to accelerate into the future, as the virus has more opportunities to infect, mutate, and evolve.

Will Variants Push the United States Deeper into Catastrophe?

As of January 22, 144 cases of the B.1.1.7 variant had been confirmed across 20 U.S. states, accounting for less than 0.5 percent of new cases. (The B.1.351 and P.1. strains have not yet been detected in the United States.) But the true number of B.1.1.7 cases is likely much higher, and the CDC has warned that it expects the B.1.1.7 strain to become the dominant strain in the United States by March.

That is potentially terrible news for the United States, which is experiencing uncontrolled spread across the country and has already suffered over 410,000 deaths. New cases, hospitalizations, and deaths are hitting record highs every day. The week before Joe Biden was inaugurated, the country reported 23,259 deaths, 25 percent more deaths than any other week since the beginning of the pandemic.

While the B.1.1.7 variant is not more fatal, it may be up to 50 percent more transmissible than strains currently circulating. Because the baseline in the United States is already astronomically high, a more transmissible variant could drive cases and hospitalizations up rapidly, further overwhelming hospitals that are already at capacity, potentially leading to many more deaths.

Even before the emergence of these new variants, the Biden administration faced a herculean task. The country is reeling from the failed, seditious January 6 attack on the U.S. Capitol, President Trump was impeached for inciting insurrection, and many lawmakers continue to contest the results of the 2020 presidential election. The country is arguably the most polarized and divided it has been since the Civil War. The economy is buckling under the weight of the pandemic, with over 1 million workers filing unemployment claims in the first week of 2021.

All the while, the virus continues to burn through the country, as many people continue to gather indoors and in large groups and refuse to wear masks or social distance. The national vaccine rollout thus far has been utterly calamitous, as the Trump administration left states to manage distribution without providing sufficient resources or technical guidance. No one in the Trump White House or elsewhere had a plan for the last mile of moving vaccines from delivery drop off sites to the arms of citizens.

The variants are accelerants and amplifiers. They leave the U.S. government with even less time to respond to the growing Covid-19 crisis—and the cascade of crises it has generated—both at home and abroad.

How Should the United States Respond?

It is clear that the Biden administration is cognizant of this new dimension and is incorporating it into its Covid-19 strategy. The recently released National Strategy for the Covid-19 Response and Pandemic Preparedness includes “increasing surveillance for variants and emerging threats” as a top priority, and the administration has called for “funding to dramatically increase our country’s sequencing, surveillance, and outbreak analytics capacity.” A national genomic surveillance system is a vital next step in addressing the threat posed by new and emerging strains. The expanded U.S. system will need to be integrated with global genomic surveillance efforts—many of which are similarly rudimentary and in need of modernization.

A more proactive way to stay out in front of new variants is to vaccinate as many people as possible before new variants can become dominant. The more people are vaccinated, the less the virus is able to circulate and the more difficult it will be for new variants to take hold. But given the CDC projections that the B.1.1.7 strain could become dominant by March and the current bottlenecks in the administration of vaccines in the United States, this will be an uphill battle. And if B.1.1.7 becomes the dominant strain, a greater percentage of the population—possibly more than 85 percent—will need to be immunized to stop the more transmissible Covid-19 from spreading. This pushes the herd immunity threshold higher, requiring an even more expansive and comprehensive vaccination effort.

An accelerated vaccination campaign will nevertheless remain central to mitigating the spread of the B.1.1.7 variant and others that may emerge, as reflected in the Biden administration’s plan for a whole-of-government vaccination effort. However, there are risks involved.

The Biden administration has announced that in an effort to accelerate the vaccination effort, it will release nearly all available doses of Covid-19 vaccines, only holding back a “small reserve and monitoring supply to ensure that everyone receives the full regimen as recommended by the FDA.” But if vaccine manufacturing does not keep pace, there is a risk that the time between the first and second doses will extend beyond the three to four weeks used in the Pfizer and Moderna clinical trials, respectively.

If manufacturing or supply chain problems result in delays in the administration of the second dose, we could enter unknown territory in terms of vaccine efficacy and safety. Immunity from the first dose could wane, and some people could lose contact with the health system as the timing of their second dose remains uncertain. If a large proportion of the U.S. population remains only partially immunized (with one dose) for an extended period of time as the virus continues to circulate widely, this could theoretically selectively pressure the virus to evolve resistance to existing vaccines.

Today, 27 percent of the public is hesitant to get a Covid-19 vaccine, a major barrier to achieving herd immunity. The first month of vaccination efforts in the United States, beset by both supply and demand problems and compounded by abrupt changes in national guidance and policy, did little to raise public confidence and trust. If the U.S. government tries to stay ahead of the variants by modifying its vaccination guidance further, hesitancy and mistrust could worsen.

Back to the Future

The identification of new variants has reminded us of several things we already knew, with a new sense of urgency and clarity.

The variants remind us that SARS-Cov2 is a novel virus, and much of its science is still unknown. It moves with remarkable speed, and is an exceptionally pernicious foe. Even as our understanding of the virus and our biotechnology evolves, so too will the virus evolve. It continues to deliver shocks that throw us off balance. We should be prepared to pivot our vaccine and therapeutic development and distribution efforts to respond to novel variants—even before they have emerged.

An uncoordinated, patchwork genomic surveillance system is now recognized to be an intolerable hazard. Once again, we face dangerous blind spots in our national infrastructure. We need to be able to stay ahead of the variants and make the necessary policy changes in real time. If we do not know what we are fighting, we will lose.

The variants remind us that we need to get back to basics, but with a new ferocity and determination. The fundamental behavioral interventions—masking, social distancing, and avoidance of indoor gatherings—remain the single best weapon we possess in the fight against Covid-19, yet our political pathologies divide us over their use and prevent us from maximizing their potential. Somehow, the Biden administration will need to find a way to unify the public behind these essential behaviors.

Once again, our nation stumbles, creating greater vulnerabilities. The United States’ sluggish, confused, and chaotic vaccination program was itself a shock, and is now an open door to new variants. The Biden administration is rightfully prioritizing a more cohesive national effort, but it will need to ensure that manufacturing keeps pace with expanded distribution, so as to avoid gaps between doses that provide variants another opening.

People remain confused. The variants remind us of the need for a national communications campaign that will bolster public confidence and trust in vaccines and in science. We cannot repeat with vaccines the mistakes made with masks, when public officials failed to explain why masks went from being discouraged to required, generating widespread confusion and mistrust. As we struggle to be nimble in tracking and mitigating new variants of the virus, we will need to communicate far more clearly and effectively to the U.S. public.

Inequities are deadly. The variants remind us of both the injustice and the danger of a bifurcated world, marked by deep divisions between the vaccinated and the unvaccinated, defined along racial, ethnic, socioeconomic, and geographic lines. Wherever the virus continues to spread unabated, there is the potential for a new variant to emerge that can overcome natural immunity, vaccines, and therapies—everywhere. Even as the United States struggles to get its own outbreak under control, it will need to use its influence and assets to support efforts by low- and middle-income countries to track, detect, and control spread. We cannot protect the American people without addressing the global threat.

Anna McCaffrey is a fellow for Global Health Security with the Global Health Policy Center at the Center for Strategic and International Studies (CSIS) in Washington, D.C. J. Stephen Morrison is senior vice president and director of the Global Health Policy Center at CSIS.

Commentary is produced by the Center for Strategic and International Studies (CSIS), a private, tax-exempt institution focusing on international public policy issues. Its research is nonpartisan and nonproprietary. CSIS does not take specific policy positions. Accordingly, all views, positions, and conclusions expressed in this publication should be understood to be solely those of the author(s).

© 2021 by the Center for Strategic and International Studies. All rights reserved.

Next Article

Immunizing the World in a Novel Pandemic

The novel coronavirus pandemic disrupted years of progress against vaccine-preventable diseases and created several new obstacles to sustaining access to global immunization. As the world surpasses 100 million cases of Covid-19, how are efforts such as the Access to Covid-19 Tools Accelerator’s COVAX Facility working to secure global collaboration, to ensure access to Covid-19 vaccines for all affected populations, and to begin to turn the tide of the pandemic?