Cécile Tran Kiem
Research Fellow, Imperial College London
The CEIRR CMC holds bi-monthly research seminars that feature leading researchers who develop state-of-the-art computational methods to better understand respiratory viruses. These events are designed to facilitate in-depth discussions and provide ample opportunity for questions from the audience, with each seminar lasting 1 hour and 30 minutes.
Title: SARS-CoV-2 saltational events are recurrent and trace to persistent human infections
SARS-CoV-2 evolution is characterized by gradual mutation accumulation but has been punctuated by rare yet impactful highly mutated variants. Whether such saltational jumps are a broad feature of SARS-CoV-2 evolution or rare anomalies remains unclear. We systematically investigate SARS-CoV-2 saltational evolution by developing a scalable framework to detect saltational events from 4.4 million high-quality viral genomes. Saltational events occurred at low but detectable rates during the pandemic and post-pandemic periods and across geographies. Their mutational signature closely matches that seen in persistent human infections but is inconsistent with the signatures of mink or deer infections. This points to persistent infection, rather than reverse zoonosis, as their primary source. While most saltational events lack evidence of onward transmission, those that do tend to carry mutations found in successful clades. Our work demonstrates that the emergence of highly mutated SARS-CoV-2 variants reflects a recurrent evolutionary process, with implications for preparedness.
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Note: CEIRR CMC events are open only to CEIRR participants. The meeting and discussion are confidential.