Virome

Virome refers to the collection of nucleic acids, both RNA and DNA, that make up the viral community associated with a particular ecosystem or holobiont. The word is derived from virus and genome and first used by Forest Rohwer and colleagues to describe viral shotgun metagenomes.^[1] All macro-organisms have viromes that include bacteriophage and viruses, including humans. Viromes are important in the nutrient and energy cycling,^[2] development of immunity,^[3] and a major source of genes through lysogenic conversion.^[4]

In order to study the virome, virus-like particles are separated from cellular components, usually using a combination of filtration, density centrifugation, and enzymatic treatments to get rid of free nucleic acids.^[5] The nucleic acids are then sequenced and analyzed using metagenomic methods.

Fig1: Total number of host assignments to metagenomic viruses with three approaches.

Connections of host virus:

Fig3:Proportion of viral groups connected with predicted hosts at various taxonomic levels.

Viruses are the most abundant biological entities on Earth , but challenge in detecting , isolating, and classifying unknown viruses have prevented exhaustive surveys of the global virome.^[6] Over 5 Tb of metagenomic sequence data were analysed from 3,042 geographically diverse samples to assess the global distribution, phylogenetic diversity, and host specificity of viruses .^[6] Over 125,000 partial DNA viral genomes, including the largest phage yet identified, and increased the number of known viral genes by 16-fold were discovered.^[6] A suite of computational methods was used to identify putative host virus connections.^[6] The isolate viral host information was projected onto a group, resulting in host assignments for 2.4% of viral groups (Fig 1).^[6] Then the CRISPR–Cas prokaryotic immune system which holds a ‘library’ of genome fragments from phages (proto-spacers) that have previously infected the host.^[6] Spacers from isolate microbial genomes with matches to metagenomic viral contigs (mVCs) were identified for 4.4% of the viral groups and 1.7% of singletons .^[6]The hypothesis was explored that viral transfer RNA (tRNA) genes originate from their host.^[6] Viral tRNAs identified in 7.6% of the mVCs were matched to isolate genomes from a single species or genus.^[6]The specificity of tRNA-based host viral assignment was confirmed by CRISPR–Cas spacer matches showing a 94% agreement at the genus level.These approaches identified 9,992 putative host–virus associations enabling host assignment to 7.7% of mVCs .^[6] The majority of these connections were previously unknown, and include hosts from 16 prokaryotic phyla for which no viruses have previously been identified (Fig 2).^[6]It is assumed that most viruses specialize in infecting related hosts.^[6] However, this may be an artifact and viral generalists that infect hosts across taxonomic orders do exist.^[6] Most CRISPR spacer matches were from viral sequences to hosts within one species or genus .^[6]As viruses exploit the host transcription/translation machinery, the existence of viruses with a surprisingly broad range of hosts opens opportunities for identification of novel enzymes or regulatory sequences, with biotechnological applications .^[6]

History

Viromes were the first examples of shotgun community sequence,^[7] which is now known as metagenomics. In the 2000s, the Rohwer lab sequenced viromes from seawater,^[7][8] marine sediments,^[9] adult human stool,^[10] infant human stool,^[11] soil,^[12] and blood.^[13] This group also performed the first RNA virome with collaborators from the Genomic Institute of Singapore.^[14] From these early works, it was concluded that most of the genomic diversity is contained in the global virome and that most of this diversity remains uncharacterized.^[15] This view was supported by individual genomic sequencing project, particularly the mycobacterium phage.^[16]

References