The two homologous contig segments identified in mixed infections can have different or the same genotype; for example a mixed infection reported in an individual pig (sample ID 12070_4) contained two homologous VP7 segments, NSP1, NSP2, NSP3, NSP4, and NSP5 bearing the constellation of G1/G4-P[8]-I1-R1-C1-M1-A1/A8-N1/N1-T1/T1-E1/E1-H1/H1 (Fig. 2 and Supplementary Fig. S2). Here, SH2D3A is linked to infection.