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The Virome Hunters Diversity Was—And Still Is to This Day— Mostly Uncharacterized

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The Virome Hunters Diversity Was—And Still Is to This Day— Mostly Uncharacterized NEWS FEATURE Virus images: colematt / iStock Getty Images Plus The virome hunters diversity was—and still is to this day— mostly uncharacterized. Scientists have since Ambitious efforts to catalog viruses across the globe may facilitate expanded their analyses into other many environments, as well as animal and human our understanding of viral communities and ecology, boost viromes. Indeed, a pure metagenomic analysis infectious disease diagnostics and surveillance, and spur new of human fecal samples revealed a previously unknown virus that represents a large part therapeutics. Charles Schmidt investigates. of the dark matter—as much as 90%—of the human gut virome. Dubbed the crAssphage by Robert Edwards and collaborators from In July, scientists from UC Davis and Columbia and our questions about the viral world are San Diego State because it was pieced together University announced they had isolated a new profound,” says Edward Holmes, a virologist by tool they invented called cross assembly species of the Ebola virus from bats roosting and professor at the University of Sydney in analysis (although its origin in stool seems to inside houses in Sierra Leone. Dubbed Bombali Australia. Along with new species, investigators have been in the minds of the researchers), it after the district where the bats were captured, are turning up vast stretches of what they call was called “one of the most striking feats of this new species is the first Ebola virus to have dark matter—viral sequences unlike any seen metagenomics at that time” by Eugene Koonin its initial identification in an animal host previously. They’re using sophisticated bioin- at US National Center for Biotechnology rather than from a sick person. According to formatics to characterize viral RNA and DNA Information (NCBI). Koonin’s group Tracey Goldstein, associate director of the One and its various functions, and findings have collaborated with Edwards’ to characterize Health Institute at the University of California, shown already that viruses can play essential as this family of phage and annotate some of the Davis, who led the team behind the research, well as harmful roles in human health. Ideally, 80% of the 100kb genome that didn’t align with it isn’t yet clear whether Bombali can infect virome research will lead to biomedical payoffs, known viral known viral proteins3. people in the field, although it has been shown such as new therapies, vaccines, and opportuni- Characterizing viromes, however, is compli- to infect cultured human cells1. ties to head off new disease outbreaks. cated by the lack of a shared genetic marker The discovery of Bombali is notable for among viruses analogous to the 16S ribosomal another reason: it was detected as a result of A new high-throughput era RNA gene in bacteria. All bacteria contain a sequencing the entire virome of bats that had During the 2000s, genomic sequencing version of that gene, allowing scientists to tested positive for Ebola in a consensus PCR- combined with advances in high-resolution identify a particular species on the basis of based assay1. This new approach to virology, microscopy ushered in the modern era its unique 16S signature. Viral identification which takes advantage of high-throughput of virome research. The first uncultured relies instead on multiple markers associated genomic technologies like next genera- viral genome was sequenced in 2002 by with different taxonomic groups and on the tion sequencing, is a novel adjunct to other Forest Rowher at San Diego State University way the sequences match up with those from approaches for identifying emerging viral from seawater samples collected off the known viruses in genomic repositories, such as pathogens before they ‘spill over’ into humans. California coast2. More than 65% of the the NCBI’s Genome database. These are early days. “We know of only a viral sequences in those samples had never David Paez Espino, a bioinformaticist at minuscule fraction of the viruses out there, been seen before, reflecting how viral the US Department of Energy’s Joint Genome 916 VOLUME 36 NUMBER 10 OCTOBER 2018 NATURE BIOTECHNOLOGY NEWS FEATURE Institute (JGI) in Walnut Creek, California, 800,000 explains that scientists can isolate a viral frac- ×16-fold ×2-fold ×3-fold tion in a sample by filtering it or by extracting 700,000 and sequencing the entire microbial nucleic 600,000 acid content. Applying metagenomic methods Unique viral sequences will home in on the genomes of DNA viruses 500,000 alone, whereas metatranscriptomic methods Total viral sequences 400,000 will reveal the sequences of both viral DNA number Total and viral RNA. Paez Espino explains that the 300,000 analytical approaches are continually evolving, but as metagenomic methods came first—and 200,000 DNA is inherently more stable than RNA— viral DNA sequences still predominate in 100,000 microbial databases. But metatranscriptomic 0 analyses are taking hold at places like the JGI, August 2016 August 2017 August 2018 according to Paez Espino, because they provide Figure 1 Growth rate of virus identification and microbial host prediction. Growth over time in the so much more information about the virome— total and unique number of viral sequences in the January 2018 release of the IMG database. The not just sequences, but also expression pat- first data point represents a 16-fold increase in the number of species in comparison to the number of terns. Moreover, scientists are motivated to previously identified viruses. Subsequent points are twofold and threefold higher, respectively (image sequence RNA viruses because they account by David Paez Espino, JGI). for roughly half the entire viral world. “Most of big infectious diseases, such as Zika, Ebola Microbial Genomes (IMG) and Microbiomes pathogenicity begins. In her own laboratory, and influenza, are caused by RNA viruses,” database. Those viral contigs currently add up Goldstein starts by evaluating whether pro- Paez Espino adds. to 750,000 total sequences (428,000 unique) teins from a particular virus bind to human cell Simon Roux, a research scientist at the JGI’s owing to the continuous addition of new receptors, as was demonstrated with Bombali. facility in Berkeley, California, adds that ana- samples submitted by the JGI and the NCBI If they do, then researchers will try to grow the lytical methods used in virome research each and are deposited into the IMG/VR, a database virus in cell culture, test whether it causes dis- have their inherent limitations. For instance, of cultured and uncultured DNA viruses and ease symptoms in experimental animals, and scientists still can’t purify the viral content in retroviruses. look for antibodies against the virus in people a given sample completely. Some may be lost who live near where it was discovered. during filtration, for example. And the short Into the wild Several other large-scale efforts are now reads that one gets from sequencing often Goldstein’s team and many other groups are expanding on PREDICT. The Global Virome have uncertain origins: they could be viral or leveraging virome research with the aim of Project (GVP) is setting out to discover derived from some other microbe. To con- intercepting disease pandemics before they roughly 1.2 million new zoonotic viruses in firm their sources, scientists stitch the reads occur. The new Bombali finding is only the animals over the next ten years6. The project together into ‘contigs’, or longer sequences that latest to emerge from the PREDICT project, will depend heavily on the development and may have recognizable functions. According a global effort to discover new viral threats use of low-cost sequencing tools designed for to Roux, that process requires bioinformatic in wildlife with the potential to spill over developing countries. Peter Daszak, president algorithms that look for features unique to into human populations. Funded by the US of the New York–based EcoHealth Alliance, a viruses that other microbes don’t share. For Agency for International Development and nonprofit organization that works on global instance, newly formed viruses—but not other based at the University of California, Davis, infectious disease issues, is among those direct- microbes—come wrapped in a protein capsid PREDICT—which launched in 2009—relies ing the project. The GVP’s goal, he says, is to that can give away their identity. And microbial on PCR and next-generation sequencing to go from being reactive to proactive in the way sequences that look completely unlike anything characterize viromes in bats, rodents and pri- health officials confront zoonotic pathogens. seen previously are often assumed to be viral mates, three taxonomic groups that account Should the GVP succeed, he adds, then it will simply because they are so novel. “Say you’ve for a high proportion of zoonotic viral dis- have accumulated a database of all the high- gotten ten genes in your contig, and one looks eases. According to Goldstein, PREDICT risk viruses that threaten human populations. like it encodes for a capsid, and the other nine scientists have sampled more than 70,000 Run by the US Department of Defense, genes are totally new and we have no idea what animals and people in over 30 countries the PREEMPT project has a complementary they’re doing,” Roux says. “That’s what you’d with high zoonotic disease risks, and the focus on the biological mechanisms under- expect with a new virus genome.” researchers have reported on the discovery lying viral spillover into humans. According Although bacterial genomes greatly out- of 1,000 virus species with the potential to to Jim Gimlett, a program manager in the numbered their viral counterparts in micro- infect human beings5. To further character- Department of Defense’s Defense Advanced bial databases until recently, the number of ize those viruses, PREDICT researchers will Research Projects Agency, PREEMPT focuses published viral sequences is rapidly grow- isolate them or, if need be, synthesize them to on known classes of dangerous viruses, such as ing (Fig.
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