Paired SARS-CoV-2 spike protein mutations observed during ongoing SARS-CoV-2 viral transfer from humans to minks and back to humans

Abstract

A mutation analysis of SARS-CoV-2 genomes collected around the world sorted by sequence, date, geographic location, and species has revealed a large number of variants from the initial reference sequence in Wuhan. This analysis also reveals that humans infected with SARS-CoV-2 have infected mink populations in the Netherlands, Denmark, United States, and Canada. In these animals, a small set of mutations in the spike protein receptor binding domain (RBD), often occurring in specific combinations, has transferred back into humans. The viral genomic mutations in minks observed in the Netherlands and Denmark show the potential for new mutations on the SARS-CoV-2 spike protein RBD to be introduced into humans by zoonotic transfer. Our data suggests that close attention to viral transfer from humans to farm animals and pets will be required to prevent build-up of a viral reservoir for potential future zoonotic transfer.

Keywords: Bioinformatics; Mink; Mutation; Next-generation sequencing; SARS-CoV-2; Zoonotic.

Fig. 1

A: Illustration of positions of mutation variants described on the SARS-CoV-2 spike glycoprotein for the N-terminal domain (NTD), receptor binding domain (RBD), and receptor binding motif (RBM). B: Left: Crystal Structure (PDB ID: 7A98) of SARS-CoV-2 receptor binding domain (green) in complex with ACE2 (teal) with residues highlighted in red. Right: Interaction of highlighted residues (red) with ACE2 (teal). Interaction denoted with magenta clouds.

Fig. 2

Total mutation counts stratified by mutation, location, and species (human and mink). Dates reported for human samples from the Netherlands are predominately submission dates, in contrast to the reported collection dates seen in meta data associated with sequences submitted from other countries.

Fig. 3

Cumulative counts for mutation F486L individually and in pairs with L452M or Q314K in the Netherlands.

Fig. 4

The phylogeny uses maximum likelihood with ultrafast bootstrapping till convergence and likelihood testing to generate the tree; shown if meeting high certainty threshold. Distinct, significant groupings were detected between all combinations of mutations, as opposed to a mixture of mutation type. Branch lengths to help determine differentiation or relationships are shown to scale at 0.003.

Supplementary Fig. S1

ACE2 Sequence Alignment