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.
Highlights
The development and adoption of high-throughput sequencing technologies has led to studies of microbial and viral communities being undertaken across an increasing range of host species [1]
The viromes of wild birds are relevant to poultry, as many important pathogens of domesticated birds originate from wild-bird populations, most notably avian influenza A viruses
Almost all avian virome studies reported multiple new virus species, mostly from the Picornaviridae (n=17), Parvoviridae (7), Circoviridae (6), Caliciviridae (5) and Reoviridae (4) families. Some of these viruses could belong to new genera and potentially could infect birds. These results indicate that we do not yet have a clear idea of the range and diversity of viruses that infect poultry, and our knowledge of viruses infecting wild birds is even scanter
Summary
The development and adoption of high-throughput sequencing technologies has led to studies of microbial and viral communities (microbiomes and viromes) being undertaken across an increasing range of host species [1]. Studies of bird populations are common, in part due to their potential relevance to the poultry industry. Poultry flock populations are often high-d ensity and genetically homogenous, potentially rendering them susceptible to outbreaks of viral infectious disease, and dysbiosis of their viromes and microbiomes may impact poultry health and growth. These situations can result in substantial economic losses to the poultry industry and contribute to food insecurity. The viromes of wild birds are relevant to poultry, as many important pathogens of domesticated birds originate from wild-bird populations, most notably avian influenza A viruses. We survey the scope and limitations of our current understanding of avian viromes, and we provide recommendations for the future development of this important topic
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