Coronavirus protein interaction mapping in bat and human cells identifies molecular and genetic switches for immune evasion and replication

Batra, J.; Rutkowska, M.; Zhou, Y.; Ye, C.; Adavikolanu, R.; Young, J. M.; Anand, D.; Verma, S.; Gordon, M.; Malpotra, S.; Cupic, A.; Kehrer, T.; Moen, J. M.; Winters, D. M.; Rojc, A.; Mena, I.; Aslam, S.; Martinez-Romero, C.; Conde Vinas, I.; Khalil, Z.; Farrugia, K.; Banerjee, A.; Tussia-Cohen, D.; Dos Santos, M.; Maji, S.; Muralidharan, M.; Foussard, H.; Chen, I. P.; Fuchs, R.; San Felipe, C.; Zuliani-Alvarez, L.; Choudhury, P.; Obernier, K.; Gracias, S.; Suryawanshi, R.; Ibanez, C.; Juste, J.; Pache, L.; Taha, T. Y.; Jouvenet, N.; Verba, K. A.; Fraser, J. S.; Demeret, C.; Stroud, R. M.; va

doi:10.1101/2025.07.26.666918

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bioRxiv · 10.1101/2025.07.26.666918

Coronavirus protein interaction mapping in bat and human cells identifies molecular and genetic switches for immune evasion and replication

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Abstract

Coronaviruses, including SARS-CoV-2, can cause severe disease in humans, whereas reservoir hosts like Rhinolophus bats remain asymptomatic. To investigate how host-specific protein-protein interactions (PPIs) influence infection, we generated comparative PPI maps for SARS-CoV-2 and its bat-origin relative RaTG13 using affinity purification-mass spectrometry (AP-MS) in human and Rhinolophus ferrumequinum (RFe) bat cells. This approach identified both conserved and virus- and host-specific interactions that regulate infection dynamics. Notably, SARS-CoV-2 required a non-synonymous mutation in nucleocapsid to replicate in bat cells expressing human ACE2 and TMPRSS2. Analysis of the viral protein Orf9b revealed differential interactions with mitochondrial proteins Tom70 and MTARC2. A single residue difference in Orf9b between SARS-CoV-2 and RaTG13 functions as a molecular switch, weakening Tom70 binding and immune evasion in human cells while enhancing interaction with the bat-specific restriction factor MTARC2. These findings demonstrate how a single-residue substitution can reshape virus-host interactions and contribute to immune evasion and host adaptation.

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Batra, J., Rutkowska, M., Zhou, Y., Ye, C., Adavikolanu, R., Young, J. M., Anand, D., Verma, S., Gordon, M., Malpotra, S., Cupic, A., Kehrer, T., Moen, J. M., Winters, D. M., Rojc, A., Mena, I., Aslam, S., Martinez-Romero, C., Conde Vinas, I., Khalil, Z., Farrugia, K., Banerjee, A., Tussia-Cohen, D., Dos Santos, M., Maji, S., Muralidharan, M., Foussard, H., Chen, I. P., Fuchs, R., San Felipe, C., Zuliani-Alvarez, L., Choudhury, P., Obernier, K., Gracias, S., Suryawanshi, R., Ibanez, C., Juste, J., Pache, L., Taha, T. Y., Jouvenet, N., Verba, K. A., Fraser, J. S., Demeret, C., Stroud, R. M., va. 2025-07-28. Coronavirus protein interaction mapping in bat and human cells identifies molecular and genetic switches for immune evasion and replication. https://doi.org/10.1101/2025.07.26.666918

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