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Acknowledgements This work was supported by the European Commission (Marie
Skłodowska-Curie Innovative Training Network “HONOURS”; grant agreement no. 721367),
the Swiss National Science Foundation (SNF; grants CRSII3_160780 and 310030_173085),
the German Research Council (DFG; grants SFB-TR84 (TRR 84/3, A07) and DR 772/7-2), the
Federal Ministry of Education and Research (BMBF; grant RAPID, 01KI1723A) and by core
funds of the University of Bern. We thank S. Vashee for the provision of the TAR vectors and
for discussions related to his herpesvirus work; J. Peters Zocher for her advice in generating
the figures; F. Suter-Riniker and P. Bittel for providing clinical samples; staff from the Next
Generation Sequencing platform (University of Bern); and M. Schweizer, P. Plattet, M.
Gerber, M. Friesland, M. Alves, N. Vielle, B. Zumkehr, M. Brügger and D. Brechbühl for
reagents, technical advice and helpful discussions. This study is dedicated to S. Kunz.
Author contributions V.T. and J.J. conceived the study. T.T.N.T., N.E. and F.L. performed most
of the experiments. P.V., H.S., K.S., J.P., S. Steiner, M.H., A.K., M.G., L.L., L.H., M.W., S.P., D.H.,
V.C., S.C.-P., S. Schröder, D.M., D.N., V.M.C., M.A.M., C.D. and R.D. did experimental work
and/or provided essential experimental systems and reagents. T.T.N.T., N.E., F.L., H.S., J.K.
and R.D. performed sequencing analyses, including computational analyses. V.T., J.J.,
T.T.N.T., F.L. and N.E. wrote the manuscript and made the figures. All authors read and
approved the final manuscript.
Competing interests The authors declare no competing interests.
Additional information
Supplementary information is available for this paper at https://doi.org/10.1038/s41586-020-
2294-9.
Correspondence and requests for materials should be addressed to J.J. or V.T.
Peer review information Nature thanks Luis Enjuanes, Stanley Perlman and Timothy Patrick
Sheahan for their contribution to the peer review of this work.
Reprints and permissions information is available at http://www.nature.com/reprints.
