Recombination alters the furin cleavage site in novel bat-borne HKU5-CoV-2 coronavirus

Yeh, T.-Y.; Tsai, V.; Liao, S. M.; Hong, C.-E.; Kuo, F.-Y.; Wang, Y. C.; Feehley, M. C.; Feehley, P. J.; Lai, Y.-C.; Contreras, G. P.

doi:10.1101/2025.04.17.649446

bioRxiv · 10.1101/2025.04.17.649446

Recombination alters the furin cleavage site in novel bat-borne HKU5-CoV-2 coronavirus

Yeh, T.-Y.·Tsai, V.·Liao, S. M.·Hong, C.-E.·Kuo, F.-Y.·Wang, Y. C.·Feehley, M. C.·Feehley, P. J.·Lai, Y.-C.·Contreras, G. P.

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Abstract

HKU5-CoV-2 is a new bat-infecting coronavirus phylogenetically related to MERS-CoV. It has recently been confirmed that HKU5-CoV-2 can enter human cells and organoids in vitro via the ACE2 receptor, raising concerns about its pandemic potential due to zoonotic spillover. Whether recombination has an influence on HKU5-CoV-2 is completely unclear to date. Here we report the first evidence of HKU5-CoV-2 viral recombination, in association with mutations at the receptor binding domain (RBD) and S1/S2 furin cleavage site (FCS) of the spike protein. Using linkage disequilibrium and haploblock analysis, we identified that 167 recombination hotspots and 27 haploblocks. SNP23016/23043/23064/23156/23193/23285 at the RBD and SNP23833/23847 at the FCS are recombinant hotspots. Our results suggest that recombination may lead to the substitution at RBD residue 498 (Thr498Val/Val498Thr, Thr498Ile/Ile498Thr), which Thr498 directly contacts the ACE2 receptor. Recombination also causes Ser723 deletion/insertion and Ser729Ala substitution at the FCS. These mutations could affect host tropism and change furin cleavage activity. Our results indicate that recombination has played a critical role in HKU5-CoV-2 evolution and infectivity.

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Yeh, T.-Y., Tsai, V., Liao, S. M., Hong, C.-E., Kuo, F.-Y., Wang, Y. C., Feehley, M. C., Feehley, P. J., Lai, Y.-C., Contreras, G. P.. 2025-04-18. Recombination alters the furin cleavage site in novel bat-borne HKU5-CoV-2 coronavirus. https://doi.org/10.1101/2025.04.17.649446

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