The panzootic potential of SARS-CoV-2

Abstract

Each year, SARS-CoV-2 is infecting an increasingly unprecedented number of species. In the present article, we combine mammalian phylogeny with the genetic characteristics of isolates found in mammals to elaborate on the host-range potential of SARS-CoV-2. Infections in nonhuman mammals mirror those of contemporary viral strains circulating in humans, although, in certain species, extensive viral circulation has led to unique genetic signatures. As in other recent studies, we found that the conservation of the ACE2 receptor cannot be considered the sole major determinant of susceptibility. However, we are able to identify major clades and families as candidates for increased surveillance. On the basis of our findings, we argue that the use of the term panzootic could be a more appropriate term than pandemic to describe the ongoing scenario. This term better captures the magnitude of the SARS-CoV-2 host range and would hopefully inspire inclusive policy actions, including systematic screenings, that could better support the management of this worldwide event.

Keywords: SARS-CoV-2; evolution; mammals; mutations; panzootic.

Figure 1.

Diversity of SARS-CoV-2 in animals. The plot shows the distribution of SARS-CoV-2 variants of concern or interest and lineages assessed by full genome sequences obtained from infected animals worldwide across time. The lineages with frequency less than 0.005 have been collapsed into the “Other” category.

Figure 2.

(a) Global phylogeny of SARS-CoV-2 sequences obtained from infected animals. The maximum likelihood tree is rooted in the first genome of SARS-CoV-2 obtained from a human case in Wuhan, China. The branches are colored on the basis of the ancestral state reconstruction using PANGO lineages or variants as traits. (b) Continent specific phylogenetic reconstruction of SARS-CoV-2 sequences obtained from infected animals. The phylogenetic trees with branches are colored on the basis of variant of SARS-CoV-2 sequences and heatmap depicting host of origin (the infected animal from which the genome was obtained).

Figure 3.

SARS-CoV-2 mink (a and b) and deer (c and d) specific mutations. The percentage equals the number of samples that contain each mutation. The percentages of samples with mutation in the two species in different countries were compared with those of humans using a Bayesian approach with beta distribution β(n + 1, n – s + 1), where n is the total number of tested sequences in each species or country and s is the number of samples with mutation. Abbreviations: LCL, lower control limit; UCL, upper control limit.

Figure 4.

Stochastic character mapping of ACE2 receptor conservation with SARS-CoV-2 infection secondarily mapped at the tips. The orders are indicated around the outside. Our phylogeny was limited to just mammal families with DNA, and the data were time scaled using node dating (TopoFree_ND; Upham et al. 2019).