Interferon alpha inducible protein 6 (IFI6) and interferon-induced transmembrane proteins (IFITM1 and IFITM3), were significantly associated with infection status and upregulated in spleen and thymus of Dual compared to Control and MB.<h4>Conclusion</h4>Downregulation of ECM components may cause degradation of the ECM and contribute to increased viral spread due to co-infection. Here, IFITM3 is linked to infection.