Virus Metagenomics in Farm Animals: A Systematic Review.

Kirsty T T Kwok,Marion P G Koopmans,My V T Phan,David F Nieuwenhuijse

doi:10.3390/v12010107

Kirsty T T Kwok, Marion P G Koopmans + Show 2 more

Open Access

https://doi.org/10.3390/v12010107

Copy DOI

Journal: Viruses	Publication Date: Jan 16, 2020
Citations: 47	License type: CC BY 4.0

Affiliation: Erasmus University Rotterdam, Erasmus MC

Abstract

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.

Highlights

Emerging infectious diseases (EIDs) are responsible for a substantial burden of mortality and morbidity globally, and a majority of EIDs (60.3%) are caused by zoonotic pathogens [1,2,3]
2349 records were excluded for the following reasons: no Metagenomic Next-Generation Sequencing (mNGS) was performed, studied animals were wild animals or were not cattle, small ruminants, poultry, and/or pigs, records were not written in English, records did not contain original findings, or records were conference abstracts
Full text of 132 remaining records were assessed for eligibility, and 120 records were included for data extraction (Supplementary Materials)

Summary

Introduction

Emerging infectious diseases (EIDs) are responsible for a substantial burden of mortality and morbidity globally, and a majority of EIDs (60.3%) are caused by zoonotic pathogens [1,2,3]. This, in turn, facilitates disease transmissions within herds and between livestock and humans by increasing livestock population and density [3]. In 2003, there was an outbreak of a highly pathogenic avian influenza A subtype H7N7 in humans linked to multiple commercial poultry farms in the Netherlands [15]. Two years later, another highly pathogenic avian influenza A H5N1 virus emerged in Asia in 2005, probably as a result of frequent mixing between

Objectives

Methods

Results

Conclusion