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GIANT DATA GAP. “The number and diversity of viral sequences that are identified in metagenomic data far exceeds that of experimentally characterized virus isolates.” https://lnkd.in/gbF24QP View in LinkedIn

TIP OF ICEBERG. “The number and diversity of viral sequences in reference databases are dwarfed by the sequences from their cellular hosts. As a result, 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.” https://lnkd.in/g35Hmrp View in LinkedIn

TWO DIMENSIONAL SNAPSHOT. “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.” https://lnkd.in/g35Hmrp View in LinkedIn

RNA VIRUSES are even more obscure because replication infidelity makes them mutate so fast, lacking the DNA polymerase proofreading mechanism of DNA viruses leading to huge mutant swarms. “Currently there are 5 orders and 47 families of RNA viruses recognised. There are also many unassigned species and genera.” https://lnkd.in/gG8F5cw View in LinkedIn

VIROME CONCEPT. “A different view of viruses has recently emerged, the virome, a name for the entire community of viruses found in a given biome.” Once again, the trend in biology today is about context. https://lnkd.in/g35Hmrp View in LinkedIn

NO COMMON THREADS. “Studying viral sequences means working at the edge of human knowledge. Even microbial genomics experts working on uncultivated microbes use the term “dark matter” when describing the viral sequences they find in metagenomes. While metagenomics expands our ability to detect viruses, a combination of small viral sequence databases and great diversity still means that many viral reads have no homology to known viruses.” https://lnkd.in/g35Hmrp View in LinkedIn

BACKLOG. The International Committee on Taxonomy of Viruses (ICTV). “In the current (2013) ICTV taxonomy, 7 orders have been established, the Caudovirales, Herpesvirales, Ligamenvirales, Mononegavirales, Nidovirales, Picornavirales, and Tymovirales. The committee does not formally distinguish between subspecies, strains, and isolates. In total there are 7 orders, 103 families, 22 subfamilies, 455 genera, about 2,827 species and over 4,000 types yet unclassified.” https://lnkd.in/eF3wTsF View in LinkedIn

VIRAL DARK MATTER. “Our understanding of viral diversity and virus–host interactions remains a major bottleneck in the development of predictive ecosystem models and unifying eco-evolutionary theories. This is because the lack of a universal marker gene for viruses hinders environmental survey capabilities, while the number of isolate viral genomes in databases remains limited: for comparison, more than 25,000 bacterial and archaeal host genomes are available in NCBI RefSeq (January 2015), whereas only 1,531 of their viruses were entirely sequenced and most (86%) of these derive from only 3 of 61 known host phyla.” https://lnkd.in/gQQCawV View in LinkedIn

GENE SOUP. “The estimated 10(28) viral infections in the ocean per day substantially affect marine systems by causing host mortality, facilitating horizontal gene transfer and influencing biogeochemical cycles via production of dissolved organic matter through cell lysis. An emerging paradigm is that viruses also possess auxiliary metabolic genes (AMGs) —‘host' genes that may be expressed to augment viral-infected host metabolism and facilitate production of new viruses.” https://lnkd.in/eTUuJwS View in LinkedIn

FRAGMENT FROM NATURE continues from last weekend on the theme of viral dark matter. We have virtually no grasp on the diversity or roles of viruses. When you consider that viruses are typically hybrid swarms of semispecies, reverting to Victorian classification systems might appear quaint at best. These little creatures continue to make fools of us humans. https://lnkd.in/gc5arxt View in LinkedIn