SARS-CoV-2 intra-host evolution during prolonged infection in an immunocompromised patient
Erika Quaranta, Alice Fusaro, Edoardo Giussani, Valeria D’Amico, Maria Varotto, Matteo Pagliari, Maria Teresa Giordani, Maira Zoppelletto, Francesca Merola, Antonio Antico, Paola Stefanelli, Calogero Terregino, Isabella Monne
Abstract
OBJECTIVES: Intra-host SARS-CoV-2 evolution during chronic infection in immunocompromised hosts has been suggested as being the possible trigger of the emergence of new variants. METHODS: Using a deep sequencing approach, we investigated the SARS-CoV-2 intra-host genetic evolution in a patient with HIV over a period of 109 days. RESULTS: Sequencing of nasopharyngeal swabs at three time points demonstrated dynamic changes in the viral population, with the emergence of 26 amino acid mutations and two deletions, 57% of them in the Spike protein. Such a combination of mutations has never been observed in other SARS-CoV-2 lineages detected so far. CONCLUSION: Our data confirm that persistent infection in certain immunocompromised individuals for a long time may favor the dangerous emergence of new SARS-CoV-2 variants with immune evasion properties.