Table 4.

A list of positions with AA change in at least two host-jump branches leading to the sHCoVs. Where there was an AA insertion in the sHCoVs relative to the Wuhan-Hu-1 SARS-CoV-2 reference genome, we used the X.Y positional notation where X is the reference genome position and Y is nth sHCoV AA insertion. The positions at which there were no AA changes in branches other than the host-jump branches leading to the sHCoVs are in bold.

ORF	Positions Shared by Alpha sHCoVs 229E and NL63	Positions Shared by Beta sHCoVs OC43 and HKU1	Positions Shared between Alpha and Beta sHCoVs
Spike	769, 1009, 1210, and 1253	8.21, 8.27, 8.31, 146, 154, 257, 329, 463.11, 489, 490.5, 490.7, 490.9, 497, 504.51, 1135, 1181, and 1221	60, 74, 152, 162, 208, 271, 295, 321, 367, 441, 476, 580, 624, 628, 629, 641, 680, 684, 751, 776, 795, 817, 932, 939, 957, 975, 1061, 1071, 1076, 1101, 1104, 1116, 1124, 1142, 1153, 1154, 1165, 1170, 1171, 1174, 1185, 1192, 1224, 1225, 1226, 1227, 1228, and 1272
Nucleocapsid	158, 160, 205, 216, 236, 252.7, 366, and 402	32 and 373.3	37, 62, 125, 127, 166, 182, 208, 210, 212, 240, 241, 249, 256, 297, 321, 323, 354, 364, 365, 384, 389, 390, 392, and 394
Membrane	8, 11, 72, and 82	-	10, 12, 15, 188, and 222
Envelope	-	-	3, 26, 27, 66, 72, and 73