Journal
VIRUSES-BASEL
Volume 12, Issue 1, Pages -Publisher
MDPI
DOI: 10.3390/v12010107
Keywords
virome; livestock; deep sequencing; animal reservoir; zoonosis; one health; viral metagenomics; NGS; emerging infectious diseases; high-throughput sequencing
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Funding
- ZonMW TOP project [91217040]
- European Union's Horizon 2020 research and innovation programme (COMPARE) [643476]
- Marie Sklodowska-Curie Individual Fellowship - European Union's Horizon 2020 research and innovation programme [799417]
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A majority of emerging infectious diseases are of zoonotic origin. Metagenomic Next-Generation Sequencing (mNGS) has been employed to identify uncommon and novel infectious etiologies and characterize virus diversity in human, animal, and environmental samples. Here, we systematically reviewed studies that performed viral mNGS in common livestock (cattle, small ruminants, poultry, and pigs). We identified 2481 records and 120 records were ultimately included after a first and second screening. Pigs were the most frequently studied livestock and the virus diversity found in samples from poultry was the highest. Known animal viruses, zoonotic viruses, and novel viruses were reported in available literature, demonstrating the capacity of mNGS to identify both known and novel viruses. However, the coverage of metagenomic studies was patchy, with few data on the virome of small ruminants and respiratory virome of studied livestock. Essential metadata such as age of livestock and farm types were rarely mentioned in available literature, and only 10.8% of the datasets were publicly available. Developing a deeper understanding of livestock virome is crucial for detection of potential zoonotic and animal pathogens and One Health preparedness. Metagenomic studies can provide this background but only when combined with essential metadata and following the FAIR (Findable, Accessible, Interoperable, and Reusable) data principles.
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