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SARS-CoV-2 in animals: susceptibility of animal species, risk for animal and public health, monitoring, prevention and control

EFSA Panel on Animal Health and Welfare (AHAW) et al. EFSA J. .

Abstract

The epidemiological situation of SARS-CoV-2 in humans and animals is continually evolving. To date, animal species known to transmit SARS-CoV-2 are American mink, raccoon dog, cat, ferret, hamster, house mouse, Egyptian fruit bat, deer mouse and white-tailed deer. Among farmed animals, American mink have the highest likelihood to become infected from humans or animals and further transmit SARS-CoV-2. In the EU, 44 outbreaks were reported in 2021 in mink farms in seven MSs, while only six in 2022 in two MSs, thus representing a decreasing trend. The introduction of SARS-CoV-2 into mink farms is usually via infected humans; this can be controlled by systematically testing people entering farms and adequate biosecurity. The current most appropriate monitoring approach for mink is the outbreak confirmation based on suspicion, testing dead or clinically sick animals in case of increased mortality or positive farm personnel and the genomic surveillance of virus variants. The genomic analysis of SARS-CoV-2 showed mink-specific clusters with a potential to spill back into the human population. Among companion animals, cats, ferrets and hamsters are those at highest risk of SARS-CoV-2 infection, which most likely originates from an infected human, and which has no or very low impact on virus circulation in the human population. Among wild animals (including zoo animals), mostly carnivores, great apes and white-tailed deer have been reported to be naturally infected by SARS-CoV-2. In the EU, no cases of infected wildlife have been reported so far. Proper disposal of human waste is advised to reduce the risks of spill-over of SARS-CoV-2 to wildlife. Furthermore, contact with wildlife, especially if sick or dead, should be minimised. No specific monitoring for wildlife is recommended apart from testing hunter-harvested animals with clinical signs or found-dead. Bats should be monitored as a natural host of many coronaviruses.

Keywords: SARS‐CoV‐2; control; mink; monitoring; prevention; public health; wildlife.

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Figures

Figure 1
Figure 1
Risk ranking matrix as in ECDC (2019)
Figure 2
Figure 2
Animal species that are susceptible to SARS‐CoV‐2 infection under experimental conditions based on seroconversion and/or detection of viral RNA and ability of further transmit SARS‐CoV‐2 virus (as of literature search carried out on 15 February 2022)

  1. Detection of viral RNA refers to either detection in at least two consecutive ante‐mortem respiratory samples, or any post‐mortem sample. A black cross indicates the absence of a feature, while a red check mark indicates the presence of a feature. Both signs mean disagreement among studies considered; ‘nd’ means that this feature was not determined. Please note that for some species for which extensive literature is available (e.g. ferrets and Syrian hamsters), only a selection of a few representative references were included.

Figure 3
Figure 3
Companion and farm animal species that have been reported as being susceptible to SARS‐CoV‐2 infection under field conditions based on seroconversion and/or detection of viral RNA and able to further transmit (based on the literature search carried out on 15 February 2022)
Figure 4
Figure 4
Zoo and wild animal species that are susceptible to SARS‐CoV‐2 infection under field conditions based on seroconversion and/or detection of viral RNA (based on literature search carried out on 15 February 2022)
Figure 5
Figure 5
Geographical distribution of SARS‐CoV‐2 outbreaks in mink establishments (green circles) and of mink establishments by country (grey areas) in Europe, from 1 February 2021 to 30 November 2022

  1. *: This designation is without prejudice to positions on status and is in line with United Nations Security Council Resolution 1,244 and the International Court of Justice Opinion on the Kosovo Declaration of Independence.

Figure 6
Figure 6
Distribution of SARS‐CoV‐2 reported outbreaks in mink establishments in the EU by month of confirmation and affected countries from February 2021 to November 2022

  1. Source: EC, EFSAThe vertical grey line indicates when the Commission Implementing Decision (EU) 2021/788 of 12 May 2021 laying down rules for the monitoring and reporting of infections with SARS‐CoV‐2 in certain animal species (OJ L 173, 17.5.2021, p. 6) entered into force.

Figure 7
Figure 7
Phylogenetic analysis of SARS‐CoV‐2 Animal sequences along with the human clade‐specific reference genomes

  1. The tree is constructed using Animal sequences from GISAID EpiCoV, using Nextclade tool by including clade specific reference genomes from Nextclade (link). Human reference genomes are coloured Lavender blue in the tree, whereas the colouring patterns for Animal sequences are based on their hosts. Mainly, mink sequences (yellow), companion animals – cats, dogs and hamsters (shades of blue), wild cats – lions, tigers, mainland Asian tiger, leopard cats, fishing cat and bear cats (shades of orange) and white‐tailed deer (green).

Figure 8
Figure 8
Phylogenetic analysis of SARS‐CoV‐2 sequences from mink along with the human clade‐specific reference genomes and other animal sequences (not marked). Clusters are coloured by country of reporting.

  1. The tree is constructed using Animal sequences from GISAID EpiCoV, using Nextclade tool by including clade specific reference genomes from Nextclade (link).

Figure 9
Figure 9
Phylogenetic analysis of SARS‐CoV‐2 sequences from cats (blue dots) along with the human clade‐specific reference genomes and other animal sequences (not marked)

  1. The tree is constructed using Animal sequences from GISAID EpiCoV, using Nextclade tool by including clade‐specific reference genomes from Nextclade (link).

Figure 10
Figure 10
Phylogenetic analysis of SARS‐CoV‐2 sequences from dogs (light blue dots) along with the human clade‐specific reference genomes and other animal sequences (not marked)

  1. The tree is constructed using Animal sequences from GISAID EpiCoV, using Nextclade tool by including clade‐specific reference genomes from Nextclade (link).

Figure 11
Figure 11
Phylogenetic analysis of SARS‐CoV‐2 sequences from hamster (dark blue dots) along with the human clade‐specific reference genomes and other animal sequences (not marked)

  1. The tree is constructed using Animal sequences from GISAID EpiCoV, using Nextclade tool by including clade‐specific reference genomes from Nextclade (link).

Figure 12
Figure 12
Phylogenetic analysis of SARS‐CoV‐2 sequences from wild animals along with the human clade‐specific reference genomes

  1. The tree is constructed using Animal sequences from GISAID EpiCoV, using Nextclade tool by including clade‐specific reference genomes from Nextclade (link).

Figure 13
Figure 13
Phylogenetic analysis of SARS‐CoV‐2 animal sequences from white‐tailed deer along with the human clade‐specific reference genomes. Clusters are coloured by the hunting season.

  1. The tree is constructed using Animal sequences from GISAID EpiCoV, using Nextclade tool by including clade‐specific reference genomes from Nextclade (link).

Figure 14
Figure 14
Diagram of transmission pathways of SARS‐CoV‐2 in mink
Figure 15
Figure 15
Diagram of transmission pathways of SARS‐CoV‐2 between dogs or cats and humans
Figure 16
Figure 16
Diagram of transmission pathways of SARS‐CoV‐2 between hamsters and humans
Figure 17
Figure 17
Diagram of transmission pathways of SARS‐CoV‐2 between white‐tailed deer (or other wildlife species with high susceptibility to infection and potential for sustained infectivity) and humans
Figure 18
Figure 18
Diagram of transmission pathways of SARS‐CoV‐2 between zoo animals and humans
Figure 19
Figure 19
Number of weekly confirmed COVID‐19 cases reported from EU/EEA countries

  1. The proportion of the circulating variant viruses was estimated from the SARS‐CoV‐2 sequences submitted to GISAID EpiCov database based on the collection date of the submissions. The average proportions of variants were plotted for the EU/EEA countries. Omicron variants are depicted based on its sublineages (BA.1–BA.5) in the figure, ‘other’ indicates the lineages that are other than Alpha, Beta, Gamma, Delta and Omicron. In the pre‐Alpha period, ‘other’ includes ancestral lineages belonging to nextclade A and B clades whereas now during Omicron circulation, ‘other’ includes recombinants and unassigned lineages.

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