Wildlife in Britain found free of SARS-CoV-2, but novel virus discovered in stoats

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Scientists in the United Kingdom have conducted a large-scale screening for sarbecoviruses and pan-coronaviruses in British Wildlife to investigate the occurrence of widespread spillover events. They have identified a novel minacovirus in stoats recently introduced to the Orkney Islands.

The study is currently available on the bioRxiv* preprint server.

Lack of detection of SARS-CoV-2 in British wildlife 2020-21 and first description of a stoat (Mustela erminea) MinacovirusStudy: Lack of detection of SARS-CoV-2 in British wildlife 2020-21 and first description of a stoat (Mustela erminea) Minacovirus. Image Credit: Stephan Morris / Shutterstock

*Important notice: bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Background

Coronaviruses are a diverse group of enveloped RNA viruses found in a wide range of vertebrate hosts, including humans and domestic dogs. Among different genera, alpha- and beta-coronaviruses are primarily responsible for causing infection in mammals.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative pathogen of coronavirus disease 2019 (COVID-19) pandemic, is a beta-coronavirus that is believed to have transmitted to humans from horseshoe bats (the natural hosts of the beta-coronavirus subgenus sarbecoviruses) via an intermittent host, such as racoon dog or Malayan pangolin.

Cross-species transmission of coronaviruses is significantly associated with repeated spillover events of SARS-CoV-2 into new hosts. One of the major outputs of spillover events is the establishment of new viral reservoirs. Higher susceptibility to SARS-CoV-2 spillover has been observed in many animals, including mink, ferrets, and hamsters.

Considering these predispositions, scientists have designed this study to detect the presence of coronavirus infections in wild animals present in Great Britain. Animals included in the study are known to have a higher susceptibility to SARS-CoV-2 infection.

Study design

The study was conducted on a total of 402 animals belonging to 14 species, primarily mustelids, and cricetid rodents. Oral, lung, rectal, or fecal samples collected from the animals during the COVID-19 pandemic were subjected to polymerase chain reaction (PCR) for the detection of viral RNA. Sarbecovirus-specific quantitative PCR and pan-coronavirus PCR assay for SARS-CoV-2 were conducted in the study.

High-throughput sequencing and genome analysis of virus-positive samples were conducted for the identification of specific viral strains. Moreover, phylogenetic analysis was conducted to understand genetic changes present in identified viral sequences.

Important observations

Sarbecovirus infection was not detected in any of the collected samples. However, coronavirus infection was detected in 57% of rectal samples collected from stoats. All stoat samples analyzed in the study were from the same population recently introduced to the Orkney Islands.

Genomic sequencing and phylogenetic analysis of the identified stoat sequences revealed that the novel virus is a member of the minacovirus subgroup of the alpha-coronavirus genus, which closely clusters to mink and mink and ferret coronaviruses.  

Genome annotation and organization of the sequence revealed a typical alpha-coronavirus genome containing 3’ and 5’ UTRs, a large open reading frame (ORF1ab) encoding 16 non-structural proteins, and genes encoding four structural proteins (spike, membrane, envelop, and nucleocapsid proteins).

The ORFs encoding accessory proteins showed close homology to the ORF 3c and 7b of feline coronavirus. Within these regions, a number of smaller potential ORFs were identified, which were possibly associated with other accessory proteins with homology to the ORF3 or 7 of other minacovirus and tegacovirus.     

Study significance

The study identifies a novel minacovirus related to mink and ferret alpha-coronaviruses in British Wildlife during the COVID-19 pandemic. However, no trace of widely circulating SARS-CoV-2 has been found in these wild animals. Furthermore, the study includes only a limited type of samples for most of the tested animal species. Thus, if SARS-CoV-2 infection is restricted to some specific tissues, there could be a possibility that the study have failed to detect low-level circulation of the virus in tested animals.

A high prevalence of this novel virus has been observed in stoats recently introduced in the Orkney Islands. Mink and ferret alpha-coronaviruses are known to cause various diseases, including diarrhea and a systemic inflammation similar to feline infectious peritonitis caused by a feline coronavirus in cats.

As mentioned by the scientists, future studies are required to understand the pathogenicity of this novel virus in stoats. Therefore, they have deposited the assembled minacovirus sequence in the NCBI GenBank database.

*Important notice: bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Journal reference:
Dr. Sanchari Sinha Dutta

Written by

Dr. Sanchari Sinha Dutta

Dr. Sanchari Sinha Dutta is a science communicator who believes in spreading the power of science in every corner of the world. She has a Bachelor of Science (B.Sc.) degree and a Master's of Science (M.Sc.) in biology and human physiology. Following her Master's degree, Sanchari went on to study a Ph.D. in human physiology. She has authored more than 10 original research articles, all of which have been published in world renowned international journals.

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