Using Metagenomics to Characterize an Expanding Virosphere
Yong-Zhen Zhang,Yong-Zhen Zhang,Mang Shi,Mang Shi,Mang Shi,Edward C. Holmes,Edward C. Holmes,Edward C. Holmes +7 more
TLDR
How metagenomics has changed the authors' understanding of RNA viruses and present some of the remaining challenges, including characterization of the "dark matter" of divergent viral genomes are discussed.About:
This article is published in Cell.The article was published on 2018-03-08 and is currently open access. It has received 191 citations till now. The article focuses on the topics: Metagenomics.read more
Citations
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The Enhancement of Plant Disease Resistance Using CRISPR/Cas9 Technology.
Virginia Maria Grazia Borrelli,Vittoria Brambilla,Peter M. Rogowsky,Adriano Marocco,Alessandra Lanubile +4 more
TL;DR: Recently, CRISPR/Cas9 has largely overtaken the other genome editing technologies due to the fact that it is easier to design and implement, has a higher success rate, and is more versatile and less expensive.
Journal ArticleDOI
Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing.
Gareth Trubl,Ho Bin Jang,Simon Roux,Joanne B. Emerson,Natalie Solonenko,Dean R. Vik,Lindsey M. Solden,Jared Ellenbogen,Alexander T. Runyon,Benjamin Bolduc,Ben J. Woodcroft,Scott R. Saleska,Gene W. Tyson,Kelly C. Wrighton,Matthew B. Sullivan,Virginia I. Rich +15 more
TL;DR: These findings suggest that these soil viruses have distinct ecology, impact host-mediated biogeochemistry, and likely impact ecosystem function in the rapidly changing Arctic.
Journal ArticleDOI
Viral zoonotic risk is homogenous among taxonomic orders of mammalian and avian reservoir hosts
TL;DR: It is shown that the proportion of viruses that infect humans varies minimally across reservoir taxonomic orders, which supports a host-neutral explanation for observed variation in the number of zoonoses among animal groups, such that traits of animal orders are unlikely to produce viruses that disproportionately threaten humans.
Journal ArticleDOI
Evolution and ecology of plant viruses.
Pierre Lefeuvre,Darren P. Martin,Santiago F. Elena,Santiago F. Elena,Dionne N. Shepherd,Philippe Roumagnac,Arvind Varsani,Arvind Varsani +7 more
TL;DR: This Review focuses on the origins of plant viruses and the evolution of interactions between these viruses and both their hosts and transmission vectors, and identifies currently unknown aspects of plant virus ecology and evolution that should be resolvable in the near future through viral metagenomics.
Journal ArticleDOI
A planarian nidovirus expands the limits of RNA genome size.
Amir Saberi,Anastasia A. Gulyaeva,John L. Brubacher,Phillip A. Newmark,Alexander E. Gorbalenya,Alexander E. Gorbalenya +5 more
TL;DR: The evolutionary analysis suggests that PSCNV diverged early from multi-ORF nidoviruses, and acquired additional genes, including those typical of large DNA viruses or hosts, e.g. Ankyrin and Fibronectin type II, which might modulate virus-host interactions.
References
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Journal ArticleDOI
Redefining the invertebrate RNA virosphere
Mang Shi,Xian-Dan Lin,Jun-Hua Tian,Liangjun Chen,Xiao Chen,Ci-Xiu Li,Xin-Cheng Qin,Jun Li,Jian-Ping Cao,John-Sebastian Eden,Jan P. Buchmann,Wen Wang,Jianguo Xu,Edward C. Holmes,Edward C. Holmes,Yong-Zhen Zhang +15 more
TL;DR: A view of the RNA virosphere is presented that is more phylogenetically and genomically diverse than that depicted in current classification schemes and provide a more solid foundation for studies in virus ecology and evolution.
Journal ArticleDOI
Consensus statement: Virus taxonomy in the age of metagenomics
Peter Simmonds,Michael J. Adams,Mária Benkő,Mya Breitbart,J. Rodney Brister,Eric B. Carstens,Andrew J. Davison,Eric Delwart,Eric Delwart,Alexander E. Gorbalenya,Alexander E. Gorbalenya,Balázs Harrach,Roger Hull,Andrew M. Q. King,Eugene V. Koonin,Mart Krupovic,Jens H. Kuhn,Elliot J. Lefkowitz,Max L. Nibert,Richard J. Orton,Marilyn J. Roossinck,Sead Sabanadzovic,Matthew B. Sullivan,Curtis A. Suttle,Curtis A. Suttle,Robert B. Tesh,René van der Vlugt,Arvind Varsani,F. Murilo Zerbini +28 more
TL;DR: The rationale for why metagenomic sequence data should, and how it can, be incorporated into the ICTV taxonomy is considered, and present proposals that have been endorsed by the Executive Committee of the ITV.
Book
The Evolution and Emergence of RNA Viruses
TL;DR: The evolution and emergence of hantaviruses is more complex than previously anticipated, and may serve as a realistic model for other viral groups.
Journal ArticleDOI
The discovery, distribution, and evolution of viruses associated with Drosophila melanogaster
Claire L. Webster,Fergal M Waldron,Shaun Robertson,Daisy Crowson,Giada Ferrari,Juan F. Quintana,Jean-Michel Brouqui,Elizabeth H. Bayne,Ben Longdon,Amy H. Buck,Brian P. Lazzaro,Jewelna Akorli,Penelope R. Haddrill,Darren J. Obbard +13 more
TL;DR: The results provide an essential evolutionary and ecological context for host–virus interaction in Drosophila, and the newly reported viral sequences will help develop D. melanogaster further as a model for molecular and evolutionary virus research.
Journal ArticleDOI
Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families
TL;DR: Overall, it is shown that cross-species transmission plays a major role in virus evolution, with all the virus families studied here having the potential to jump host species, and that increased sampling will likely reveal more instances of host jumping.
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