Before America’s first stay-at-home orders, before school and business closings, before overwhelmed hospitals and the confirmation that the world is facing a deadly pandemic, scientists at the University of Pittsburgh were hard at work on research that could prove key to stopping the COVID-19 pandemic.

The virus arrived at Pitt in mid-February. It came not in an infected person, but in a vial, stuffed inside a plastic bag, sealed inside a cylinder, packed in dry ice, encased in Styrofoam, and sheathed in cardboard.

The highly secure delivery was made to the Biosafety Level 3 laboratory in the University of Pittsburgh’s Center for Vaccine Research (CVR), where Paul Duprex, the center’s director, and colleagues Amy Hartman, William Klimstra, Anita McElroy and Doug Reed were poised to begin work on interventions and vaccines. They had met with safety colleagues just 10 days before to launch their first COVID-19 task force, which has met every week since.

Pitt was one of the first institutions in the country to receive the virus directly from the Centers for Disease Control and Prevention—and it is specially equipped to take it on. With support from the National Institute of Allergy and Infectious Diseases within the National Institutes of Health, the CVR’s facilities are specifically designed to handle this kind of high-stakes work, and its staff have years of experience working in biocontainment. Pitt also has a legacy of tackling vaccine challenges, including, of course, Jonas Salk’s work on the polio vaccine in the 1950s.

The CVR’s focus quickly shifted to combating the virus. By mid-March, Duprex, the Jonas Salk Chair for Vaccine Research, and his team had earned further support. They were part of a $4.9 million grant to develop and test a COVID-19 vaccine as members of a three-way partnership with Institut Pasteur in Paris and Themis Bioscience, a biotech company based in Vienna. Awarded by the Coalition for Epidemic Preparedness Innovations, the grant was a big vote of confidence from an organization known as a leader in vaccine development.

So, how do scientists quickly develop a vaccine amid an active and evolving pandemic?

“We can use what we know about viruses and look for the weak points,” says Duprex.

The researchers’ efforts are zeroed in on perhaps the most visually notable component of the pathogen as it’s depicted in computer-generated renderings seen so often in the press: the parts that look like little red knobs sticking out of a gray sphere.

These are spike proteins, a feature of all coronaviruses. Research has shown that they can induce immunity by prompting the generation of antibodies, which fight the virus and build a person’s resistance to future infection.

To create a vaccine using spike proteins, Duprex has applied his expertise in measles, the “most infectious human virus on earth,” he says. A safe and effective measles vaccine already exists and has been successfully adapted to tackle other viruses. Duprex and his colleagues are genetically engineering the measles vaccine to include minuscule pieces of novel coronavirus spike proteins. The intended result: a vaccine candidate that may provide protection from SARS-CoV-2, the virus that causes COVID-19.

https://www.pittmag.pitt.edu/news/emergency-response

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 in a Feb. 4 paper 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, 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 co-evolutionary 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, 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.”

Additional authors on the study include Linda Rennick and Sham Nambulli of Pitt; Lindsey Robinson-McCarthy, formally Harvard Medical School and now working as a virologist at UPMC Hillman Cancer Center; and William Bain and Ghady Haidar of Pitt and UPMC.

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

https://www.cvr.pitt.edu/news/how-coronavirus-variants-could-outsmart-vaccines

PITTSBURGH — A firearm has been recovered at Carrick High School after it went into lockdown Tuesday, a Pittsburgh Public Schools spokesperson said.

A student is in custody and facing charged related to the incident, the spokesperson said.

A search with canine through the building by City and School Police lead to the discovery of the firearm. It was confiscated.

The reports of a possible gun in the building came from social media, the spokesperson said.

The spokesperson also said the incident is under investigation by school and city police and as an added precaution, Pittsburgh Carrick will operate on a modified lockdown tomorrow, Wednesday, January 12. A modified lockdown means that no one is permitted in or out of the building without a prior appointment.

Families were notified of the incident, according to the spokesperson.

https://www.wpxi.com/news/top-stories/social-media-reports-about-gun-lead-lockdown-pittsburghs-carrick-high-school/HAW6UVBKZND6JPYFBDVTIHGXA4/

If PCR tests don’t work for Covid does that mean they don’t work for HIV?

https://www.uofmhealth.org/health-library/hw4961