[SARS-CoV-2 infections in cats, dogs, and other animal species: Findings on infection and data from Switzerland]

INTRODUCTION

The pandemic with the novel coronavirus (SARS-CoV-2) has led to infections and deaths worldwide. Apart from humans, certain animal species are susceptible to the viral infection. Spillover between humans and animals is favored by close contact; thus, surveillance of animals is an important component to fight the pandemic from a One Health perspective. The Clinical Laboratory of the Vetsuisse Faculty Zurich has been investigating SARS-CoV-2 infections in animals since the beginning of the pandemic. In November 2020, the first SARS-CoV-2 positive Swiss cat was reported to the World Organisation for Animal Health (OIE-WAHIS). The cat showed respiratory signs and lived in a COVID-19 affected household. By now, over 500 natural SARS-CoV-2 infections have been recorded in animals worldwide. A prevalence study on SARS-CoV-2 infections in dogs and cats was carried out together with clinics from Germany and Italy during the first wave of the pandemic (March-July 2020). Among the tested 1137 animals, only one cat and one dog were positive. The prevalence of infection in dogs and cats presented to veterinary clinics was low, even in pandemic hotspot regions. However, recent studies that focused on animals in COVID-19 households found a higher prevalence of infection. A study is currently underway that specifically collects samples from pets from Swiss COVID-19 affected household and collects data on human-animal interaction.

Viral discovery as a tool for pandemic preparedness

Emerging diseases are frequently caused by novel or previously unrecognised zoonotic viral pathogens, which tend to originate in and emerge from wildlife. When human or animal cases are first recognised, molecular or serological diagnostic assays specific to them do not yet exist, causing a delay in the identification of an outbreak's aetiologic agent as well as its source. Preparing for the next virus to emerge is a major public health challenge, impeded by a poor understanding of the diversity of potential candidates that exist in wildlife reservoirs. Characterising the diversity of viruses in key wildlife species will help to reduce the time between detection and response in an outbreak situation, and inform public health strategies that reduce the risk of spillover from animal reservoirs. Pathogen discovery techniques such as consensus polymerase chain reaction (cPCR) and next-generation sequencing (NGS) have been used to identify known and novel viruses in animals and humans, but have not been widely used in surveillance programmes. Metagenomic studies have identified novel viruses, new strains of known viruses, and have characterised host microbiomes. While NGS represents an unbiased approach to viral sequence detection, it is constrained by lower sensitivity than conventional PCR, requires substantial bioinformatics capabilities, and is cost prohibitive and therefore not widely available in the regions of the world that are most vulnerable to zoonotic disease emergence. In contrast, consensus PCR uses standard and widely available technologies, has greater sensitivity than NGS, and has also been used to identify novel viruses in wildlife, livestock and humans, though it is limited to detecting target genetic sequences conserved across known groups of viruses. The use of cPCR, in combination, if possible, with NGS and serology, can offer a powerful approach to rapidly identifying aetiologic agents in an outbreak and characterising the virome of key wildlife known to carry zoonotic viruses. Here, the authors review pathogen discovery techniques currently being used in human and animal surveillance programmes and the challenges of using viral discovery to identify novel zoonotic pathogens.