Fig. 1

Transmission signatures conserved in SIV, SHIV, and HIV-1. a An alignment of two sequence logos representing Env sequences from an SIVsmE660 stock/inoculum (top) and the T/F (bottom) viruses establishing infections in four animals. The diagram illustrates the signature scanning protocol on one SIVsmE660 trial highlighting four signature sites: i.e., sites where the amino acid preference in the donor residue differs significantly from that of the T/F based on a Fisher Exact test. See our previous published work for statistical details of signature scanning in 11 other trials [3]. b Sequence logos tracking the signature residues in 170 T/F viruses from SIVsmE660, SIVmac251, SHIV-BaL, and HIV-1 (A, B, C, D, A1D). c An alignment of the donor (top) and T/F sequences from the study by Oberle et al. Sequence logos were generated using WebLogo software [16, 17]