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© FEMS 2020.A combination of favipiravir and zanamivir successfully cleared influenza B infection in a child who had undergone bone marrow transplant for X-linked severe combined immunodeficiency, with no recovery of T lymphocytes. Deep sequencing of viral samples illuminated the within-host dynamics of infection, demonstrating the effectiveness of favipiravir in this case. © The Author(s) 2020. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permi