Towards an understanding of the avian virome

Abstract

The last two decades have seen the rise of viromics, the study of viral communities through the detection and characterization of virus genome sequences. Here we systematically review and summarize the scope and limitations of our current understanding of avian viromes, in both domesticated and wild-bird populations. We compare this viromic work to the broader literature on avian prokaryotic microbiomes, and highlight the growing importance of structured sampling and experimental design for testing explanatory hypotheses. We provide a number of recommendations for sample collection and preliminary data analysis to guide the development of avian viromics. Avian viromes have the potential to inform disease surveillance in poultry and improve our understanding of the risk of zoonotic viruses to human health.

Keywords: ecology; epidemiology; metagenomics; poultry; virus; wild birds.

Fig. 1.

Comparison of research effort between bird viromes and prokaryotic microbiomes. We conducted a bibliographic search of PubMed on 16 September 2019 using the Adjutant package in R. We retrieved papers on bird prokaryotic microbiomes using the search ‘(bird OR avian) AND (bact metagenomic OR 16S OR bact microbio)’ (1424 papers). We retrieved papers on bird viromes using the search ‘(bird OR avian) AND (virome OR vir metagenomic OR vir communit OR vir diversity OR vir composition)’ and supplemented this search by manual screening, resulting in 28 papers. We removed papers (i) that were non-research articles, (ii) whose samples were not taken from living birds, or (iii) that targeted one or few specific virus/prokaryote taxa. We consequently retained a total of 310 papers on bird microbiomes and viromes (full details in Tables S1 and S2). (a) The bar chart and values show the number of papers published each year on bird microbiomes (orange) and bird viromes (blue). (b) The top pie chart shows the total number of published virome and microbiome papers. The other pie charts show the number of papers structured by host type (middle) and by study objective (bottom, see main text for definition of ‘descriptive’ and ‘hypothesis evaluation’). Due to the small number of bird virome studies, the corresponding proportions should be interpreted with caution.

Fig. 2.

General workflow of VANA virome generation and analysis. The main difference between VANA metagenomics and metatranscriptomics is that the latter is based solely on RNA extraction, without DNA extraction or prior enrichment for viral particles.