Virus Metagenomics in Farm Animals: A Systematic Review

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.

Keywords: NGS; animal reservoir; deep sequencing; emerging infectious diseases; high-throughput sequencing; livestock; one health; viral metagenomics; virome; zoonosis.

Figure 1

Flow chart of systematic review. The procedures were adapted from the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines.

Figure 2

An overview of study design and data (and metadata) availability of 120 included publications. Each column represents one paper, and numbers refer to the list of references (Supplementary Materials). Rows describe data fields extracted from the papers as follows (from top to bottom): study rationale, sequencing platforms, sample sizes, availability of sequencing data in public repository, availability of animal age description, availability of farm type description, indication of whether filtration was performed, indication of whether nuclease treatment was performed during sample preparation, nucleic acid extraction strategy, type of nucleic acid extracted, indication of whether nucleic acid amplification was performed, indication of whether sample pooling was performed in same/different farms, and mention of technical controls for validating sequencing results. Categories and color codes for each data field are indicated in the figure legend. Gray boxes indicate that the technique was not performed, or the information was not specified. mNGS = metagenomic Next-Generation Sequencing. SRA = Sequence Read Archive. ENA = European Nucleotide Archive. NA = nucleic acid.

Figure 3

(A) Geographical origin of included studies stratified by World Health Organization (WHO) regions. (B) An overview of sequencing platforms. (C) An overview of sample sizes.

Figure 4

Types of specimens tested in different farm animals by number of papers, stratified by reported health conditions. Categories per variable are color-coded as shown in the legend. GI = gastrointestinal. A version of Y-axis as frequency (%) can be found in Supplementary Materials Figure S2.

Figure 5

An overview of virus families found in different farm animals in included studies, stratified by reported health conditions. The bars are color-coded by host range of the viruses as shown in the figure legend. GI = gastrointestinal. Y axis shows proportion of studies that found the viruses specified.

Figure 6

Frequencies of virus genera of top three most abundant virus families stratified by health conditions. (A) Picornaviridae. (B) Parvoviridae. (C) Astroviridae. Color code is based on host range and adapted from Figure 5.