Developers of COVID-19 vaccines may have a chance to do more than round up the usual suspects, that is, the bits of viral material that are used to help B cells recognize and respond to SARS-CoV-2. These bits have been known to correspond to parts of the infamous SARS-CoV-2 spike. Recently, other bits have come to light. Their functions are not so well known. However, according to a new study, these lesser-known bits can activate T cells. If these bits were to inform vaccine development, it would be possible to develop vaccines that could broaden the immune system’s response to COVID-19—and not just to those infections that are due to familiar SARS-CoV-2 variants, but also to those infections that will be due to variants that have yet to emerge.

The new study comes from Boston University’s National Emerging Infectious Diseases Laboratories (NEIDL) and the Broad Institute of MIT and Harvard. At these institutions, researchers have been paying attention to the “red flags” that appear during a SARS-CoV-2 infection and elicit responses from T cells—the killers the immune system dispatches to destroy infected cells. These red flags are peptides derived from viral proteins that are processed by a host cell, then presented in peptide fragments on the host cell surface by class I human leukocyte antigen (HLA-I).

The researchers examined the HLA-I immunopeptidome in two SARS-CoV-2-infected human cell lines, and they complemented this analysis with RNA-seq and global proteomics measurements. The results of this work appeared June 16 in the journal Cell, in an article titled, “Profiling SARS-CoV-2 HLA-I peptidome reveals T cell epitopes from out-of-frame ORFs.”

“We found HLA-I peptides derived not only from canonical ORFs, but also from internal out-of-frame ORFs in Spike and Nucleocapsid not captured by current vaccines,” the article’s authors wrote. “Some peptides from out-of-frame ORFs elicited T cell responses in a humanized mouse model and COVID-19 patients that exceeded responses to canonical peptides including some of the strongest epitopes reported to date. Whole proteome analysis of infected cells revealed that early expressed viral proteins contribute more to HLA-I presentation and immunogenicity.”

Based on the new information, “companies should reevaluate their vaccine designs,” said Mohsan Saeed, PhD, a NEIDL virologist and the co-corresponding author of the paper.

Saeed, who is also a Boston University School of Medicine assistant professor of biochemistry, performed experiments on human cells infected with coronavirus. He isolated and identified those missing pieces of SARS-CoV-2 proteins inside one of the NEIDL’s Biosafety Level 3 (BSL-3) labs. Saeed got involved after he was contacted by genetic sequencing experts at the Broad Institute, computational geneticists Pardis Sabeti, MD, PhD, and Shira Weingarten-Gabbay, PhD. They hoped to identify fragments of SARS-CoV-2 that activate the immune system’s T cells.

From the outset of the COVID-19 pandemic in early 2020, scientists around the world knew the identity of 29 proteins produced by SARS-CoV-2 virus in infected cells—viral fragments that now make up the spike protein in some coronavirus vaccines, such as the Moderna, Pfizer-BioNTech, and Johnson & Johnson vaccines. Later, scientists discovered another 23 proteins hidden inside the virus’ genetic sequence; however, the function of these additional proteins was a mystery until now. The new findings of Saeed and his collaborators reveal—unexpectedly and critically—that 25% of the viral protein fragments that trigger the human immune system to attack a virus come from these hidden viral proteins.

“It’s quite remarkable that such a strong immune signature of the virus is coming from regions [of the virus’ genetic sequence] that we were blind to,” said Weingarten-Gabby, the paper’s lead author and postdoctoral fellow in the Sabeti lab. “This is a striking reminder that curiosity-driven research stands at the basis of discoveries that can transform the development of vaccines and therapies.”

“Our discovery … can assist in the development of new vaccines that will mimic more accurately the response of our immune system to the virus,” Sabeti added.

T cells not only destroy infected cells but also memorize the virus’ flags so that they can launch an attack, stronger and faster, the next time the same or a different variant of the virus appears. That’s a crucial advantage, because the coronavirus appears to delay the cell’s ability to call in immune help.

“This virus wants to go undetected by the immune system for as long as possible,” Saeed explained. “Once it’s noticed by the immune system, it’s going to be eliminated, and it doesn’t want that.”

Based on the new findings, Saeed says, a new vaccine recipe, incorporating some of the newly discovered internal proteins making up the SARS-CoV-2 virus, would be effective in stimulating an immune response capable of tackling a wide swath of newly emerging coronavirus variants. And given the speed with which these variants continue to appear around the world, a vaccine that can provide protection against all of them would be a game changer.