Coronaviruses in farm animals: Epidemiology and public health implications

Abstract

Coronaviruses (CoVs) are documented in a wide range of animal species, including terrestrial and aquatic, domestic and wild. The geographic distribution of animal CoVs is worldwide and prevalences were reported in several countries across the five continents. The viruses are known to cause mainly gastrointestinal and respiratory diseases with different severity levels. In certain cases, CoV infections are responsible of huge economic losses associated or not to highly public health impact. Despite being enveloped, CoVs are relatively resistant pathogens in the environment. Coronaviruses are characterized by a high mutation and recombination rate, which makes host jumping and cross-species transmission easy. In fact, increasing contact between different animal species fosters cross-species transmission, while agriculture intensification, animal trade and herd management are key drivers at the human-animal interface. If contacts with wild animals are still limited, humans have much more contact with farm animals, during breeding, transport, slaughter and food process, making CoVs a persistent threat to both humans and animals. A global network should be established for the surveillance and monitoring of animal CoVs.

Keywords: Coronaviruses; domestic animals; host jump; public health; widespread.

FIGURE 1

Phylogenetic tree of different representative CoVs based on the Spike (S) protein gene (the strain responsible for the pandemic SARS‐CoV‐2 in humans is shown with the bolded character among the Betacoronavirus genus). The shown animals are hosts from where the corresponding CoVs were isolated. The sequences of all animal CoVs were downloaded from the National Center for Biotechnology Information (NCBI) GenBank database (https://www.ncbi.nlm.nih.gov/genbank/). The tree was constructed using the Neighbour‐Joining method (bootstrap resampling = 1,000 replicates and bootstrap values are indicated as % at branch points) (Saitou & Nei, 1987). The evolutionary distances were computed using the Maximum Composite Likelihood method (Tamura et al., 2004) and are in the units of the number of base substitutions per site. All positions containing either gaps or missing data were eliminated. There were a total of 2044 positions in the final dataset. Evolutionary analyses were made with MEGA7 (Kumar et al., 2016)

FIGURE 2

The map of the five continents, showing the countries where different animal coronaviruses were detected either using serological or molecular tools. The map was created in QGIS 3.12.2 (QGIS, 2018)