Mutations that adapt SARS-CoV-2 to mustelid hosts do not increase fitness in the human airway.

Abstract

SARS-CoV-2 has a broad mammalian species tropism infecting humans, cats, dogs and farmed mink. Since the start of the 2019 pandemic several reverse zoonotic outbreaks of SARS-CoV-2 have occurred in mink, one of which reinfected humans and caused a cluster of infections in Denmark. Here we investigate the molecular basis of mink and ferret adaptation and demonstrate the spike mutations Y453F, F486L, and N501T all specifically adapt SARS-CoV-2 to use mustelid ACE2. Furthermore, we risk assess these mutations and conclude mink-adapted viruses are unlikely to pose an increased threat to humans, as Y453F attenuates the virus replication in human cells and all 3 mink-adaptations have minimal antigenic impact. Finally, we show that certain SARS-CoV-2 variants emerging from circulation in humans may naturally have a greater propensity to infect mustelid hosts and therefore these species should continue to be surveyed for reverse zoonotic infections.

SARS-CoV-2 variants of concern alpha, beta, gamma and delta have extended ACE2 receptor host ranges

“…This is evident in our data; the increase in mouse ACE2 receptor usage by delta spike, albeit to a lesser extent than the N501Y-containing VOCs, suggests that changes in host tropism are likely a combinatorial effect of different RBD mutations. We observed a similar trend during adaptation of SARS-CoV-2 in ferrets, with spike mutations Y453F, F486L and N501T leading to increased ferret ACE2 usage [10]. This mirrors the situation with natural infections in mink, a related mustelid, where a similar array of mutations has repeatedly arisen [28, 29], leading to severe restrictions on the farming of mink and the mass culling of animals.…”

“…To support these research endeavours, we and others have shown that the SARS-CoV-2 spike has a broad tropism for mammalian ACE2 proteins [7–9]. Using lentiviral pseudotyping combined with live virus experiments, we showed that SARS-CoV-2 can use a wide range of mammalian ACE2s, including dog, cat, cattle, sheep, pangolin and rabbit, but is restricted with rat, ferret and a subset of bat and bird receptors [7, 10].…”

“…This mirrors the situation with natural infections in mink, a related mustelid, where a similar array of mutations has repeatedly arisen [28,29], leading to severe restrictions on the farming of mink and the mass culling of animals. Importantly, these ferret or mink acquired mutations are unlikely to pose an increased threat to human populations, as these changes inhibit human ACE2 usage (Y453F) and/or have little antigenic impact [10].…”

“…If, for example, N501Y containing VOCs cause increased pathogenicity because they are now able to use mouse ACE2 more efficiently, this could complicate or potentially invalidate comparisons between WT D614-and VOC-based mouse data and more broadly correlations with human data, where the difference in human ACE2 usage is marginal. In addition, those animal models that endogenously express restricted ACE2s (ferret, mouse and rat) are likely to drive in-animal adaptation, as we witnessed with ferrets [10], which further complicates conclusions on viral phenotypes such as transmission potential. Fortunately, in hamsters, which have emerged as a highly tractable model for SARS-CoV-2, the situation appears less convoluted, as differences in hamster and human ACE2 usage between WT D614 and VOC pseudotypes look comparable (Fig.…”

Global landscape of the host response to SARS-CoV-2 variants reveals viral evolutionary trajectories

“…Wuhan-Hu-1-D614G with R203K/G204R was achieved by introducing mutations R203K (G28881A, G28882A) and G204R (G28883C). Reverse genetics (RG) derived viruses were generated essentially as previously described (76,77). Rescued RG SARS-CoV-2 viruses were sequenced using Oxford Nanopore as previously described (78).…”