Phylogenetic Diversity of Animal Oral and Gastrointestinal Viromes Useful in Surveillance of Zoonoses

Abstract

Great emphasis has been placed on bacterial microbiomes in human and animal systems. In recent years, advances in metagenomics have allowed for the detection and characterization of more and more native viral particles also residing in these organisms. The digestive tracts of animals and humans-from the oral cavity, to the gut, to fecal excretions-have become one such area of interest. Next-generation sequencing and bioinformatic analyses have uncovered vast phylogenetic virome diversity in companion animals, such as dogs and cats, as well as farm animals and wildlife such as bats. Zoonotic and arthropod-borne illnesses remain major causes of worldwide outbreaks, as demonstrated by the devastating COVID-19 pandemic. This highlights the increasing need to identify and study animal viromes to prevent such disastrous cross-species transmission outbreaks in the coming years. Novel viruses have been uncovered in the viromes of multiple organisms, including birds, bats, cats, and dogs. Although the exact consequences for public health have not yet become clear, many analyses have revealed viromes dominated by RNA viruses, which can be the most problematic to human health, as these genomes are known for their high mutation rates and immune system evasion capabilities. Furthermore, in the wake of worldwide disruption from the COVID-19 pandemic, it is evident that proper surveillance of viral biodiversity is crucial. For instance, gut viral metagenomic analysis in dogs has shown close relationships between the highly abundant canine coronavirus and human coronavirus strains 229E and NL63. Future studies and vigilance could potentially save many lives.

Keywords: COVID-19; metagenomics; microbiome; pandemic prevention; periodontitis; surveillance; virome; zoonoses.

Figure 1

Zoonotic transfer of pathogens occurs when close contact encourages species-jumping transmission between animals—such as domestics, wildlife, or livestock—and humans. This transmission can be in the form of vector intermediates, ingestion of contaminated food or drinks, or the inhalation of droplets.

Figure 2

Schematic of the Illumina sequencing technology commonly used in metagenomic analyses of viromes.

Figure 3

Dominant oral cavity viruses, including lytic bacteriophages (e.g., Myoviridae and Siphoviridae) that aid in immune protection, as well as pathogenic eukaryotic viruses (e.g., Herpesviridae) that threaten dysbiosis.

Figure 4

Oral and GI viromes share some common dominant members, but greater overall diversity is observed in the GI virome compared to the oral virome.

Figure 5

Suggested methods to reduce future pandemic risks from animal and human reservoirs.