We further identify a notable variant at amino acid position 655 in Spike (H655Y), which was previously shown to confer escape from human monoclonal antibodies. Using domestic cats as a model, we show that SARS-CoV-2 consensus sequences remain largely unchanged over time within hosts, while dynamic sub-consensus diversity reveals processes of genetic drift and weak purifying selection. The evolutionary mechanisms by which SARS-CoV-2 viruses adapt to mammalian hosts and, potentially, undergo antigenic evolution depend on the ways genetic variation is generated and selected within and between individual hosts. Results were visualized using Matplotlib 3.3.2( ), Seaborn v0.10.0 ( ), and Baltic v0.1.0 ( ).
AC3D CONSTRAIN TO LINE CODE
Code to process sequencing data is available at and dependencies are available through Docker.
AC3D CONSTRAIN TO LINE PRO
Fig 1 was created by hand in Adobe Illustrator and S6 and S7 Figs were created using samtools command line tools, were visualized in JMP Pro 15 ( ), and were then edited for readability in Adobe Illustrator. Ĭode to replicate analyses and re-create most figures is available at. Derived data, analysis pipelines, and figures have been made available for easy replication of these results at a publicly-accessible GitHub repository.
AC3D CONSTRAIN TO LINE ARCHIVE
Source data after mapping have been deposited in the Sequence Read Archive (SRA) under bioproject PRJNA666926. Friedrich, Conceptualization, Funding acquisition, Investigation, Project administration, Supervision, Writing – original draft, Writing – review & editing 1, 5, * O’Connor, Funding acquisition, Investigation, Project administration, Supervision, Writing – original draft, Writing – review & editing, 2, 5 and Thomas C. Haj, Software, Writing – review & editing, 2 Masato Hatta, Conceptualization, Data curation, Writing – review & editing, 1, 3 Shiho Chiba, Conceptualization, Writing – review & editing, 1, 3 Tadashi Maemura, Conceptualization, Writing – review & editing, 1, 3 Yoshihiro Kawaoka, Conceptualization, Funding acquisition, Resources, Supervision, Writing – review & editing, 1, 3 Katia Koelle, Formal analysis, Methodology, Writing – review & editing, 6 David H. Weiler, Investigation, Writing – review & editing, 1, 5 Amelia K. Boehm, Investigation, Writing – original draft, Writing – review & editing, 1 Andrea M. Baker, Data curation, Software, Writing – review & editing, 2 Emma C. Hodcroft, Investigation, Resources, Visualization, Writing – review & editing, 4 David A. Halfmann, Conceptualization, Data curation, Investigation, Resources, Validation, Writing – review & editing, 1, 3 Emma B. Moreno, Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Project administration, Software, Validation, Visualization, Writing – original draft, Writing – review & editing, # 2 Peter J.
Braun, Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Project administration, Software, Validation, Visualization, Writing – original draft, Writing – review & editing, # 1 Gage K.
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