To understand how viruses hijack our cells—and to design better vaccines—we need to know which proteins are encoded in viral genomes. However, many microproteins remain obscured by conventional definitions of coding regions. These hidden proteins make up the viral ‘dark proteome’

In 2021, we showed that unannotated proteins in #SARSCoV2 were preferentially presented on the MHC-I complex and elicited stronger T cell responses. Yet they remained invisible during the first five months of the pandemic—a lifetime in pandemic response. www.cell.com/cell/fulltex...

Why is that? Identifying coding regions requires growing the virus in cells—but figuring out how to grow it (which receptors it uses, needed host factors, etc) can take months to years. Some viruses can't be cultured at all, and dangerous ones require scarce high-containment labs

MPRP doesn’t require culturing viruses—we go straight from genome to ORF discovery, quickly, safely, and at scale. We built on ribosome profiling developed by @nickingolia.bsky.social and @jswlab.bsky.social and combined it with oligo synthesis to measure ribosome footprints on 15,000 sequences

MPRP works across diverse viral families. We observed striking similarity in ribosome footprints on certain annotated and non-canonical ORFs between MPRP and virus-infected cells—including a newly revealed internal ORF in #flu and a well-studied ribosome stalling site in #HCMV

MPRP boosts our #PandemicPreparedness by revealing which proteins a new virus encodes—before we even know how to culture it. It bridges the gap until full ribosome profiling is possible and provides the scientific community with functional insights in just a few weeks

OK, but what do these new ORFs do? Like in #SARSCoV2, peptides from microproteins detected by MPRP were presented on MHC-I in cells infected with #HCMV and #VACV — suggesting a role in antiviral immunity

We also detected hundreds of potential upstream ORFs (uORFs) in the 5’UTRs of viral genes that regulate viral protein translation. These uORFs respond to cellular changes that mimic viral infection, providing clues about the complex spatiotemporal regulation of viral gene expression

There’s so much to discover in this new universe of viral proteins—we’re just beginning to scratch the surface!! I’m continuing the journey into the dark proteome in my new lab at @harvardmed.bsky.social and excited for what lies ahead