Abstract
RNA viruses cause numerous emerging diseases, mostly due to transmission from mammalian and avian reservoirs. Large-scale surveillance of RNA viral infections in these animals is a fundamental step for controlling viral infectious diseases. Metagenomic analysis is a powerful method for virus identification with low bias and has substantially contributed to the discovery of novel viruses. Deep sequencing data have been accumulated in public databases in recent decades; however, only a small number of them have been examined for viral infections. Here, we screened for infections of 33 RNA viral families in publicly available mammalian and avian RNA-seq data and found over 900 hidden viral infections. We also discovered viral sequences in livestock, wild, and experimental animals: hepatovirus in a goat, hepeviruses in blind mole-rats and a galago, astrovirus in macaque monkeys, parechovirus in a cow, pegivirus in tree shrews, and seadornavirus in rats. Some of these viruses were phylogenetically close to human pathogenic viruses, suggesting the potential risk of causing disease in humans upon infection. Furthermore, the infections of five novel viruses were identified in several different individuals, indicating that their infections may have already spread in the natural host population. Our findings demonstrate the reusability of public sequencing data for surveying viral infections and identifying novel viral sequences, presenting a warning about a new threat of viral infectious disease to public health.
Importance Monitoring the spread of viral infections and identifying novel viruses capable of infecting humans through animal reservoirs are necessary to control emerging viral diseases. Massive sequencing data collected from various animals are publicly available, but almost all these data have not been investigated regarding viral infections. Here, we analyzed more than 46,000 public sequencing data and identified over 900 hidden RNA viral infections in mammalian and avian samples. Some viruses discovered in this study were genetically similar to pathogens that cause hepatitis, diarrhea, or encephalitis in humans, suggesting the presence of new threats to public health. Our study demonstrates the effectiveness of reusing public sequencing data to identify known and unknown viral infections, indicating that future continuous monitoring of public sequencing data by metagenomic analyses would help prepare and mitigate future viral pandemics.
Competing Interest Statement
The authors have declared no competing interest.
