How SARS-CoV-2 mutates to escape antibody binding

February 03, 2021

PITTSBURGH, Feb. 3, 2020 - In a recurring pattern of evolution, SARS-CoV-2 evades immune responses by selectively deleting small bits of its genetic sequence, according to new research from the University of Pittsburgh School of Medicine.

Since these deletions happen in a part of the sequence that encodes for the shape of the spike protein, the formerly neutralizing antibody can't grab hold of the virus, the researchers report today in Science. And because the molecular "proofreader" that usually catches errors during SARS-CoV-2 replication is "blind" to fixing deletions, they become cemented into the variant's genetic material.

"You can't fix what's not there," said study senior author Paul Duprex, Ph.D., director of the Center for Vaccine Research at the University of Pittsburgh. "Once it's gone, it's gone, and if it's gone in an important part of the virus that the antibody 'sees,' then it's gone for good."

Ever since the paper was first submitted as a preprint in November, the researchers watched this pattern play out, as several variants of concern rapidly spread across the globe. The variants first identified in the United Kingdom and South Africa have these sequence deletions.

Duprex's group first came across these neutralization-resistant deletions in a sample from an immunocompromised patient, who was infected with SARS-CoV-2 for 74 days before ultimately dying from COVID-19. That's a long time for the virus and immune system to play "cat and mouse," and gives ample opportunity to initiate the coevolutionary dance that results in these worrisome mutations in the viral genome that are occurring all over the world.

Then, Duprex enlisted the help of lead author Kevin McCarthy, Ph.D., assistant professor of molecular biology and molecular genetics at Pitt and an expert on influenza virus--a master of immune evasion--to see whether the deletions present in the viral sequences of this one patient might be part of a larger trend.

McCarthy and colleagues pored through the database of SARS-CoV-2 sequences collected across the world since the virus first spilled over into humans.

When the project started, in the summer of 2020, SARS-CoV-2 was thought to be relatively stable, but the more McCarthy scrutinized the database, the more deletions he saw, and a pattern emerged. The deletions kept happening in the same spots in the sequence, spots where the virus can tolerate a change in shape without losing its ability to invade cells and make copies of itself.

"Evolution was repeating itself," said McCarthy, who recently started up a structural virology lab at Pitt's Center for Vaccine Research. "By looking at this pattern, we could forecast. If it happened a few times, it was likely to happen again."

Among the sequences McCarthy identified as having these deletions was the so-called "U.K. variant"--or to use its proper name, B.1.1.7. By this point, it was October 2020, and B.1.1.7 hadn't taken off yet. In fact, it didn't even have a name, but it was there in the datasets. The strain was still emerging, and no one knew then the significance that it would come to have. But McCarthy's analysis caught it in advance by looking for patterns in the genetic sequence.

Reassuringly, the strain identified in this Pittsburgh patient is still susceptible to neutralization by the swarm of antibodies present in convalescent plasma, demonstrating that mutational escape isn't all or nothing. And that's important to realize when it comes to designing tools to combat the virus.

"Going after the virus in multiple different ways is how we beat the shapeshifter," Duprex said. "Combinations of different antibodies, combinations of nanobodies with antibodies, different types of vaccines. If there's a crisis, we'll want to have those backups."

Although this paper shows how SARS-CoV-2 is likely to escape the existing vaccines and therapeutics, it's impossible to know at this point exactly when that might happen. Will the COVID-19 vaccines on the market today continue to offer a high level of protection for another six months? A year? Five years?

"How far these deletions erode protection is yet to be determined," McCarthy said. "At some point, we're going to have to start reformulating vaccines, or at least entertain that idea."
-end-
Additional authors on the study include Linda Rennick, Ph.D., Sham Nambulli, Ph.D., of Pitt; Lindsey Robinson-McCarthy, Ph.D., formally Harvard Medical School and now working as a virologist at UPMC Hillman Cancer Center; and William Bain, M.D., and Ghady Haidar, M.D., of Pitt and UPMC.

Funding for this study was provided by the Richard King Mellon Foundation, Hillman Family Foundation and UPMC Immune Transplant and Therapy Center.

To read this release online or share it, visit https://www.upmc.com/media/news/020321-mccarthy-duprex-deletions.

About the University of Pittsburgh School of Medicine

As one of the nation's leading academic centers for biomedical research, the University of Pittsburgh School of Medicine integrates advanced technology with basic science across a broad range of disciplines in a continuous quest to harness the power of new knowledge and improve the human condition. Driven mainly by the School of Medicine and its affiliates, Pitt has ranked among the top 10 recipients of funding from the National Institutes of Health since 1998. In rankings recently released by the National Science Foundation, Pitt ranked fifth among all American universities in total federal science and engineering research and development support.

Likewise, the School of Medicine is equally committed to advancing the quality and strength of its medical and graduate education programs, for which it is recognized as an innovative leader, and to training highly skilled, compassionate clinicians and creative scientists well-equipped to engage in world-class research. The School of Medicine is the academic partner of UPMC, which has collaborated with the University to raise the standard of medical excellence in Pittsburgh and to position health care as a driving force behind the region's economy. For more information about the School of Medicine, see http://www.medschool.pitt.edu.

http://www.upmc.com/media

Contact: Erin Hare
Mobile: 412-738-1097
E-mail: HareE@upmc.edu

Contact: Ana Gorelova
Mobile: 412-491-9411
E-mail: GorelovaA@upmc.edu

University of Pittsburgh

Related Antibodies Articles from Brightsurf:

Scientist develops new way to test for COVID-19 antibodies
New research details how a cell-free test rapidly detects COVID-19 neutralizing antibodies and could aid in vaccine testing and drug discovery efforts.

Mussels connect antibodies to treat cancer
POSTECH research team develops innovative local anticancer immunotherapy technology using mussel protein.

For an effective COVID vaccine, look beyond antibodies to T-cells
Most vaccine developers are aiming solely for a robust antibody response against the SARS-CoV-2 virus, despite evidence that antibodies are not the body's primary protective response to infection by coronaviruses, says Marc Hellerstein of UC Berkeley.

Children can have COVID-19 antibodies and virus in their system simultaneously
With many questions remaining around how children spread COVID-19, Children's National Hospital researchers set out to improve the understanding of how long it takes pediatric patients with the virus to clear it from their systems, and at what point they start to make antibodies that work against the coronavirus.

The behavior of therapeutic antibodies in immunotherapy
Since the late 1990s, immunotherapy has been the frontline treatment against lymphomas where synthetic antibodies are used to stop the proliferation of cancerous white blood cells.

Re-engineering antibodies for COVID-19
Catholic University of America researcher uses 'in silico' analysis to fast-track passive immunity

Seroprevalence of antibodies to SARS-CoV-2 in 10 US sites
This study estimates how common SARS-CoV-2 antibodies are in convenience samples from 10 geographic sites in the United States.

Neutralizing antibodies in the battle against COVID-19
An important line of defense against SARS-CoV-2 is the formation of neutralizing antibodies.

Three new studies identify neutralizing antibodies against SARS-CoV-2
A trio of papers describes several newly discovered human antibodies that target the SARS-CoV-2 virus, isolated from survivors of SARS-CoV-2 and SARS-CoV infection.

More effective human antibodies possible with chicken cells
Antibodies for potential use as medicines can be made rapidly in chicken cells grown in laboratories.

Read More: Antibodies News and Antibodies Current Events
Brightsurf.com is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to Amazon.com.