Extended Data Fig. 8: EVEscape later in a pandemic: using pandemic data and capturing epistatic shifts.
From: Learning from prepandemic data to forecast viral escape
a) Incorporating pandemic sequences in EVE training data results in a greater distinction between the distributions of escape and non-escape mutation EVE scores. b) Histogram of epistatic shift values between Wuhan and BA.2 strain EVE models for all single mutations, calculated as linear regression residuals. Convergent mutations that arise multiple times in Omicron lineages (mutations at sites 346, 444, 452, 460, and 486) are highlighted on the left. Wastewater mutations seen mid-202144 that were rarely seen clinically in patients, and so likely epistatic, are highlighted on the right. c) Max epistatic shift magnitudes of mutations at sites mutated in BA.2 shows high epistatic shifts concentrated in the RBD. d) Large epistatic shifts for mutations on Wuhan and BA.2 strains are concentrated at sites proximal to BA.2 mutations.
