Can Coronaviruses Steal Genes from the Host as Evidenced in Western European Hedgehogs by EriCoV Genetic Characterization?

Abstract

Due to their need for living cells, viruses have developed adaptive evolutionary strategies to survive and perpetuate in reservoir hosts that play a crucial role in the ecology of emerging pathogens. Pathogenic and potentially pandemic betacoronaviruses arose in humans in 2002 (SARS-CoV, disappeared in July 2003), 2012 (MERS-CoV, still circulating in Middle East areas), and 2019 (SARS-CoV-2, causing the current global pandemic). As universally recognized, bats host ancestors of the above-mentioned zoonotic viruses. However, hedgehogs have been recently identified in Europe and Asia as possible reservoirs of MERS-CoV-like strains classified as Erinaceus coronavirus (EriCoV). To elucidate the evolution and genetics of EriCoVs, NGS (next generation sequencing) and Sanger sequencing were used to examine fecal samples collected in Northern Italy in 2018/2019 from 12 hedgehogs previously found EriCoV-positive by RT-PCR. By sequence analysis, eight complete EriCoV genomes, obtained by NGS, showed a high phylogenetic correlation with EriCoV strains previously reported in Eurasia. Interestingly, eight viral strains presented an additional ORF encoding for the CD200 ortholog located between the genes encoding for the Spike and the ORF3a proteins. The CD200 ortholog sequences were closely similar to the host CD200 protein but varying among EriCoVs. The result, confirmed by Sanger sequencing, demonstrates for the first time that CoVs can acquire host genes potentially involved in the immune-modulatory cascade and possibly enabling the virus to escape the host defence.

Machine-learning prediction of hosts of novel coronaviruses requires caution as it may affect wildlife conservation

“…Thirdly, while we agree that the sometimes close associations between hedgehogs and humans could provide a theoretical risk of zoonotic transfers (for hedgehog rehabilitators, hedgehog researchers and those provisioning hedgehogs in their gardens), De Sabato et al 5 estimate that EriCoV originated between 190 and 1447 years ago, and in spite of its long history and high prevalence in hedgehogs, has not yet been recorded to have infected any other host, including humans. Furthermore, our research on methicillin-resistant Staphylococcus aureus (MRSA) indicates that the risk of zoonotic transfers between humans and hedgehogs appears, in practice, to be low 13 .…”

“…Many species of wildlife carry host-specific genetically distinct strains of coronaviruses which cannot infect humans. The coronavirus previously detected in hedgehogs is called EriCoV [2][3][4][5] . The prevalence of EriCoV in hedgehogs appears to be rather high, ranging from 10.8% in Great Britain 3 to 50% in France 6 to 58.3% in Italy 2 , and 58.9% in Germany 4 .…”

“…1), it is not intuitive that such coinfection would have been deemed likely -the only predisposing factor being the occasional close association to humans (a factor which, if necessary, might be rather easily regulated to ensure that the risk of exposure from feeding garden hedgehogs was low). Nevertheless, it is relevant to keep in mind that the absence of evidence for SARS-CoV-2 and wildlife strains of coronaviruses other than EriCoV infecting hedgehogs does not necessarily reflect reality, as it simply may have not been detected yet, in spite of a range of studies investigating this [2][3][4][5]14 .…”

Homology‐based classification of accessory proteins in coronavirus genomes uncovers extremely dynamic evolution of gene content

“…As a consequence, a number of studies have contributed to widen our knowledge of CoV distribution and genetic diversity. Whereas bats have remained the main focus of field surveys, and probably represent the major natural reservoir of alphaCoVs and betaCoVs, other small mammals such as rodents and shrews are increasingly recognized to host a large variety of coronaviruses (Annan et al, 2013;Anthony et al, 2017;Corman et al, 2015;Corman, Ithete, et al, 2014;Corman, Kallies, et al, 2014;De Sabato et al, 2020;Hu et al, 2017;Lam et al, 2020;Latinne et al, 2020;Lau et al, 2015;Li et al, 2021;Tao et al, 2017;Tsoleridis et al, 2016Tsoleridis et al, , 2019Wang et al, 2015Wang et al, , 2020Wang, Fu et al, 2017;Wang, Lin et al, 2017;Yang et al, 2014;Zhou et al, 2021). Also, wild birds are known to host a substantial diversity of deltaCoVs and gammaCoVs (Wille & Holmes, 2020).…”

Can the European Hedgehog (Erinaceus europaeus) Be a Sentinel for One Health Concerns?

“…Over the last two decades, it has become more than clear that potentially zoonotic betacoronaviruses can represent massive public health threats, such as those related to Middle East respiratory syndrome coronavirus (MERS-CoV), or more recently and globally with severe acute respiratory syndrome coronavirus (SARS-CoV-2). Recent findings of MERS-related CoVs in hedgehogs from Germany [39], France [24], and Great Britain [40] suggest that E. europaeus represents a wild reservoir of betacoronaviruses named as Erinaceus CoVs (EriCoVs) [12,41]. In 2020, a study that analysed virological and epidemiological data of COVID-19 outbreaks in Wuhan, China, comparing it with SARS-2002 and MERS-2012 outbreaks concluded that, among other findings, the responsible agent was genetically close to SARS-related viruses isolated from bats.…”