Hidden Viral Sequences in Public Sequencing Data and Warning for Future Emerging Diseases

Area of Science:

• Virology
• Genomics
• Public Health

Background:

• Emerging RNA viral diseases often originate from mammalian and avian reservoirs.
• Large-scale surveillance and novel virus discovery are crucial for controlling infectious diseases.
• Metagenomic analysis of deep-sequencing data is a powerful tool for unbiased virus identification.

Purpose of the Study:

• To screen publicly available mammalian and avian sequencing data for RNA viral infections.
• To discover novel viral genomes and assess their potential risk to human health.
• To demonstrate the utility of public sequencing data for viral surveillance.

Main Methods:

• Screened over 46,000 public deep-sequencing datasets from mammalian and avian samples.
• Utilized metagenomic analysis to identify viral sequences from 33 RNA viral families.
• Performed phylogenetic analysis to determine the relationship of novel viruses to known human pathogens.

Main Results:

• Identified approximately 900 hidden RNA viral infections across diverse animal hosts.
• Discovered six nearly complete viral genomes, including novel hepatovirus, hepeviruses, astrovirus, parechovirus, and pegivirus.
• Found five novel viruses with potential spread in natural host populations and identified viruses phylogenetically related to human pathogens.

Conclusions:

• Public sequencing data is a valuable, reusable resource for identifying known and novel viral infections.
• The discovery of potentially zoonotic viruses underscores the ongoing threat of emerging infectious diseases.
• Continuous metagenomic monitoring of public data is essential for pandemic preparedness and mitigation.