Recent Zoonotic Spillover and Tropism Shift of a Canine Coronavirus Is Associated with Relaxed Selection and Putative Loss of Function in NTD Subdomain of Spike Protein

Abstract

A canine coronavirus (CCoV) has now been reported from two independent human samples from Malaysia (respiratory, collected in 2017–2018; CCoV-HuPn-2018) and Haiti (urine, collected in 2017); these two viruses were nearly genetically identical. In an effort to identify any novel adaptations associated with this apparent shift in tropism we carried out detailed evolutionary analyses of the spike gene of this virus in the context of related Alphacoronavirus 1 species. The spike 0-domain retains homology to CCoV2b (enteric infections) and Transmissible Gastroenteritis Virus (TGEV; enteric and respiratory). This domain is subject to relaxed selection pressure and an increased rate of molecular evolution. It contains unique amino acid substitutions, including within a region important for sialic acid binding and pathogenesis in TGEV. Overall, the spike gene is extensively recombinant, with a feline coronavirus type II strain serving a prominent role in the recombinant history of the virus. Molecular divergence time for a segment of the gene where temporal signal could be determined, was estimated at around 60 years ago. We hypothesize that the virus had an enteric origin, but that it may be losing that particular tropism, possibly because of mutations in the sialic acid binding region of the spike 0-domain.

Conserved recombination patterns across coronavirus subgenera

“…2021 ; Vlasova et al. 2021 ; Zehr, Kosakovsky Pond, and Martin 2021 )), transmissible gastroenteritis virus, infecting pigs and feline coronavirus from cats ( Herrewegh et al. 1998 ; Decaro et al.…”

Emerging variants of canine enteric coronavirus associated with seasonal outbreaks of severe canine gastroenteric disease

“…Amino acid sequence alignment of the S1 NTD region (modified from Zehr et al [19]). The blue bar represents the area identified experimentally as being pertinent to sialic acid binding (a viral tropism determinant) in TGEV.…”

“…Sequence analysis by Zehr et al [19] identified multiple recombination events between CECoV and FCoV; temporal analysis suggested CCoV-HuPn-2018 may have diverged from a lineage most recently circulating in cats between 1846 and 1976 (95% HPD-Highest Posterior Density Interval), with a median estimate of 1957 [19]. The lack of similarity between 10/22 and CECoV-HuPn-2018 and lack of conserved deletions/unique substitutions between 7/20 and CECoV-HuPn-2018 putatively attributed to loosened sialic acid binding, suggests there is currently unlikely to be a zoonotic threat from these highly prevalent CECoV variants of interest.…”

“…The precise mechanism for such spillover events is not known but it is reasonable to speculate this will include spike gene mutations; indeed, replacement of the spike gene of the betacoronavirus mouse hepatitis virus (MHV) with that of feline coronavirus (FCoV), allowed the MHV recombinant to acquire permissiveness to cats [38]. Sequence analysis by Zehr et al [19] identified multiple recombination events between CECoV and FCoV; temporal analysis suggested CCoV-HuPn-2018 may have diverged from a lineage most recently circulating in cats between 1846 and 1976 (95% HPD—Highest Posterior Density Interval), with a median estimate of 1957 [19]. The lack of similarity between 10/22 and CECoV-HuPn-2018 and lack of conserved deletions/unique substitutions between 7/20 and CECoV-HuPn-2018 putatively attributed to loosened sialic acid binding, suggests there is currently unlikely to be a zoonotic threat from these highly prevalent CECoV variants of interest.…”

“…The emergence of new CECoV variants and its implications to canine health are discussed. In addition, recent evidence of variants of CECoV in human respiratory disease [19,20], suggests a need to better understand how this observed evolution might represent a new risk to human health. We further propose CECoV can provide an accessible model to study the mechanisms and consequences of endemic coronavirus population adaptation and evolution.…”