Research Topic

Virus discovery by metagenomics: the (im)possibilities

About this Research Topic

Over the last one hundred years, the discovery of new viruses has been a gradual process. Viruses were described one by one using a suite of techniques such as electron microscopy and viral culture. Investigators were usually interested in a disease state within an organism, and expeditions in viral ecology ...

Over the last one hundred years, the discovery of new viruses has been a gradual process. Viruses were described one by one using a suite of techniques such as electron microscopy and viral culture. Investigators were usually interested in a disease state within an organism, and expeditions in viral ecology were rare. The advent of metagenomics using high-throughput sequencing has revolutionized not only the rate of virus discovery, but also the nature of the discoveries. For example, many more diseases can now be attributed to viral agents, non-pathogenic viral commensals are ubiquitous, and the description of environmental viromes is making progress.

This accelerated rate of virus discovery comes both with fantastic possibilities and with significant risks. Presently, the genomic era defines the viral universe by characterizing genotypes, but these genotypes are rarely associated with a phenotype and/or a physical entity. Moreover, state of the art taxonomic classification of viruses recognizes only several thousand viral species, a large fraction of which infect humans. This stands in sharp contrast with the diversity of the cellular organisms on which all viruses depend for their replication.

In this Frontiers in Virology Research Topic on Virus Discovery by Metagenomics, we will discuss how metagenomic and bioinformatic approaches have been used to discover, classify and characterize novel viruses. Difficult questions must be confronted and controls set in place. Like in the California Gold Rush, great discoveries in viral metagenomics can only be made by recognizing and addressing the most significant pitfalls.

What experimental approaches and analysis pipelines exist for viral metagenomics? When can we be satisfied that we have identified a novel viral genome? Are the current rules of what is accepted as a viral genome outdated? How severely does viral genomic recombination threaten reliable assembly? How can we annotate or understand the functions of new viral genes? How do we determine the role of a newly discovered virus in higher order processes? How can the metagenomic approach be implemented in a clinical setting? What does the composition of a host-associated viral community tell us about the health status of this host? How stable is viral community composition across time and space? And of course: what pearls from the viral universe have we already discovered by using metagenomics?

For this Research Topic, we solicit original research papers from both experimental and bioinformatic groups. Moreover, we will also reserve some space for reviews and perspectives that address the questions listed above or other hot topics from the frontiers of the field of virus discovery by metagenomics.


Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

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