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Article ; Online: Atypical Divergence of SARS-CoV-2 Orf8 from Orf7a within the Coronavirus Lineage Suggests Potential Stealthy Viral Strategies in Immune Evasion.

Neches, Russell Y / Kyrpides, Nikos C / Ouzounis, Christos A

2021 Volume 12, Issue 1

Abstract: Orf8, one of the most puzzling genes in the SARS lineage of coronaviruses, marks a unique and striking difference in genome organization between SARS-CoV-2 and SARS-CoV-1. Here, using sequence comparisons, we unequivocally reveal the distant sequence ... ...

Abstract	Orf8, one of the most puzzling genes in the SARS lineage of coronaviruses, marks a unique and striking difference in genome organization between SARS-CoV-2 and SARS-CoV-1. Here, using sequence comparisons, we unequivocally reveal the distant sequence similarities between SARS-CoV-2 Orf8 with its SARS-CoV-1 counterparts and the X4-like genes of coronaviruses, including its highly divergent "paralog" gene Orf7a, whose product is a potential immune antagonist of known structure. Supervised sequence space walks unravel identity levels that drop below 10% and yet exhibit subtle conservation patterns in this novel superfamily, characterized by an immunoglobulin-like beta sandwich topology. We document the high accuracy of the sequence space walk process in detail and characterize the subgroups of the superfamily in sequence space by systematic annotation of gene and taxon groups. While SARS-CoV-1 Orf7a and Orf8 genes are most similar to bat virus sequences, their SARS-CoV-2 counterparts are closer to pangolin virus homologs, reflecting the fine structure of conservation patterns within the SARS-CoV-2 genomes. The divergence between Orf7a and Orf8 is exceptionally idiosyncratic, since Orf7a is more constrained, whereas Orf8 is subject to rampant change, a peculiar feature that may be related to hitherto-unknown viral infection strategies. Despite their common origin, the Orf7a and Orf8 protein families exhibit different modes of evolutionary trajectories within the coronavirus lineage, which might be partly attributable to their complex interactions with the mammalian host cell, reflected by a multitude of functional associations of Orf8 in SARS-CoV-2 compared to a very small number of interactions discovered for Orf7a.
MeSH term(s)	Animals ; COVID-19/immunology ; COVID-19/virology ; Databases, Genetic ; Evolution, Molecular ; Genome, Viral ; Humans ; Immune Evasion ; Phylogeny ; SARS-CoV-2/genetics ; SARS-CoV-2/immunology ; Sequence Alignment ; Viral Proteins/genetics ; Viral Proteins/immunology
Chemical Substances	ORF7a protein, SARS-CoV-2 ; ORF8 protein, SARS-CoV-2 ; Viral Proteins
Language	English
Publishing date	2021-01-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mBio.03014-20
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Thesis ; Online: Prediction of Ecological Function in the Microbiome Using Machine Learning on the Graph Spectra of Coevolving Subnetworks

Neches, Russell Y.

2017

Abstract: ... to Phuket, Thailand aboard the S/Y Indigo V. An inventory the surface water population of bacterioplankton ...

Abstract	Chapter 1. We propose a method for predicting the ecological function of host-associated microbes using neural networks trained on a feature space of labeled ecological interactions from the literature. The feature space is constructed over the Laplacian spectral density distributions of the networks formed by linking the phylogenies of the host and microbial clades through their ecological associations. A classifier trained on 51 interactions with known ecology and 100 simulated controls was used predict the ecological function in the microbimes of 14 species of wild-caught cichlid fish from the Lake Tanganyika adaptive radiation observed using 16S rRNA sequencing. Chapter 2. Genomic patterns of divergence are examined using whole-genome resequencing of three sympatric cichlid species pairs with similar functional and ecological differentiation but different ages, revealing a signature of genomic divergence. Regions of elevated relative differentiation exhibit increased absolute differentiation. We detect a signature of convergent evolution across all three species pairs. Our results suggest that functional phenotypic differentiation is associated with a signature of genomic divergence. Chapter 3. We show that evolutionary innovations can result in competitive inferiority and extinction. The modified pharyngeal jaws of cichlid fishes and several marine fish, a classic example of evolutionary innovation, are not universally beneficial. Analysis of dietary evolution across marine fish lineages reveals that the innovation compromises access to predator niches. This competitive inferiority shaped the adaptive radiation of cichlids in Lake Tanganyika and played a pivotal, previously unrecognized role in the mass extinction of cichlid fishes in Lake Victoria after Nile perch invasion. Chapter 4. We map protein sequences from the Global Ocean Survey to protein families and use non-negative matrix factorization (NMF) to approximate linear combinations of ecological components with characteristic functional and site profiles. We identify functional signatures, estimate functional distance between sites, and find that an NMF-filtered measure is more strongly correlated with environmental distance than a comparable PCA-filtered measure. We find that functional distance is more strongly correlated with environmental distance than geographic distance in agreement with prior studies. Chapter 5. We describe the unique technical, logistical, organizational, and ethical issues from the 2013 Indigo V Indian Ocean Expedition research cruise from Cape Town, South Africa, to Phuket, Thailand aboard the S/Y Indigo V. An inventory the surface water population of bacterioplankton was collected and basic measurements of ocean physics and chemistry were tabulated. Chapter 6. We report on the microbial diversity across the Indian Ocean and a lagoon in the Chagos Archipelago. The community within the lagoon differed from adjacent community despite constant water exchange, driven by photosynthetic cyanobacterium Synechococcus. Enrichment of photosynthesis-related transcripts and nutrient cycling indicate influence of primary production on community structure. A five-fold diurnal increase in viral transcripts within the lagoon suggests concomitant bacteriophage influence. Chapter 7. We present a novel ChIP-seq workflow for archaea using Halobacterium salinarum sp. NRC-1 and map binding sites of natively expressed transcription factors. Relative to ChIP-Chip and qPCR, it improves spatial resolution and reduces cost. Chapter 8. Pique is a user-friendly, freely licensed ChIP-Seq peak finding application for bacterial and archaeal ChIP-Seq experiments. Output is provided in standardized file formats for manual curation and data exploration. Chapter 9. With appropriate handling, 3D printers produce sterile components from non-sterile thermoplastic feedstock without post-fabrication treatment. Chapter 10. We present a method for fabricating single-use microtiter plates with volumes calibrated for each sample, allowing the use of multichannel pipettes for general liquid handling operations. Many custom plates can be 3D printed simultaneously, resulting in substantial savings in cost and time. Chapter 11. The growth kinetics of 48 strains of building-associated bacteria were measured aboard the International Space Station. One strain, Bacillus safensis JPL-MERTA-8-2, grew 60% better in microgravity.
Keywords	Ecology\|Applied Mathematics\|Evolution and Development
Subject code	333
Language	ENG
Publishing date	2017-01-01 00:00:01.0
Publisher	University of California, Davis
Publishing country	us
Document type	Thesis ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Recombination should not be an afterthought.

Neches, Russell Y / McGee, Matthew D / Kyrpides, Nikos C

Nature reviews. Microbiology

2020 Volume 18, Issue 11, Page(s) 606

MeSH term(s)	Betacoronavirus/genetics ; COVID-19 ; Coronavirus Infections/virology ; Genome, Viral ; Humans ; Pandemics ; Phylogeny ; Pneumonia, Viral/virology ; Reassortant Viruses ; SARS-CoV-2
Keywords	covid19
Language	English
Publishing date	2020-09-21
Publishing country	England
Document type	Journal Article
ZDB-ID	2139054-X
ISSN	1740-1534 ; 1740-1526
ISSN (online)	1740-1534
ISSN	1740-1526
DOI	10.1038/s41579-020-00451-1
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Article: Recombination should not be an afterthought

Neches, Russell Y / McGee, Matthew D / Kyrpides, Nikos C

Nat Rev Microbiol

Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #885524
Database	COVID19

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Article ; Online: Genomic adaptation of giant viruses in polar oceans.

Meng, Lingjie / Delmont, Tom O / Gaïa, Morgan / Pelletier, Eric / Fernàndez-Guerra, Antonio / Chaffron, Samuel / Neches, Russell Y / Wu, Junyi / Kaneko, Hiroto / Endo, Hisashi / Ogata, Hiroyuki

Nature communications

2023 Volume 14, Issue 1, Page(s) 6233

Abstract: Despite being perennially frigid, polar oceans form an ecosystem hosting high and unique biodiversity. Various organisms show different adaptive strategies in this habitat, but how viruses adapt to this environment is largely unknown. Viruses of phyla ... ...

Abstract	Despite being perennially frigid, polar oceans form an ecosystem hosting high and unique biodiversity. Various organisms show different adaptive strategies in this habitat, but how viruses adapt to this environment is largely unknown. Viruses of phyla Nucleocytoviricota and Mirusviricota are groups of eukaryote-infecting large and giant DNA viruses with genomes encoding a variety of functions. Here, by leveraging the Global Ocean Eukaryotic Viral database, we investigate the biogeography and functional repertoire of these viruses at a global scale. We first confirm the existence of an ecological barrier that clearly separates polar and nonpolar viral communities, and then demonstrate that temperature drives dramatic changes in the virus-host network at the polar-nonpolar boundary. Ancestral niche reconstruction suggests that adaptation of these viruses to polar conditions has occurred repeatedly over the course of evolution, with polar-adapted viruses in the modern ocean being scattered across their phylogeny. Numerous viral genes are specifically associated with polar adaptation, although most of their homologues are not identified as polar-adaptive genes in eukaryotes. These results suggest that giant viruses adapt to cold environments by changing their functional repertoire, and this viral evolutionary strategy is distinct from the polar adaptation strategy of their hosts.
MeSH term(s)	Giant Viruses/genetics ; Genome, Viral/genetics ; Ecosystem ; Oceans and Seas ; Phylogeny ; DNA Viruses/genetics ; Genomics ; Viruses/genetics ; Eukaryota/genetics
Language	English
Publishing date	2023-10-12
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-41910-6
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Article ; Online: Genomic adaptation of giant viruses in polar oceans

Lingjie Meng / Tom O. Delmont / Morgan Gaïa / Eric Pelletier / Antonio Fernàndez-Guerra / Samuel Chaffron / Russell Y. Neches / Junyi Wu / Hiroto Kaneko / Hisashi Endo / Hiroyuki Ogata

Nature Communications, Vol 14, Iss 1, Pp 1-

2023 Volume 12

Abstract: Abstract Despite being perennially frigid, polar oceans form an ecosystem hosting high and unique biodiversity. Various organisms show different adaptive strategies in this habitat, but how viruses adapt to this environment is largely unknown. Viruses of ...

Abstract	Abstract Despite being perennially frigid, polar oceans form an ecosystem hosting high and unique biodiversity. Various organisms show different adaptive strategies in this habitat, but how viruses adapt to this environment is largely unknown. Viruses of phyla Nucleocytoviricota and Mirusviricota are groups of eukaryote-infecting large and giant DNA viruses with genomes encoding a variety of functions. Here, by leveraging the Global Ocean Eukaryotic Viral database, we investigate the biogeography and functional repertoire of these viruses at a global scale. We first confirm the existence of an ecological barrier that clearly separates polar and nonpolar viral communities, and then demonstrate that temperature drives dramatic changes in the virus–host network at the polar–nonpolar boundary. Ancestral niche reconstruction suggests that adaptation of these viruses to polar conditions has occurred repeatedly over the course of evolution, with polar-adapted viruses in the modern ocean being scattered across their phylogeny. Numerous viral genes are specifically associated with polar adaptation, although most of their homologues are not identified as polar-adaptive genes in eukaryotes. These results suggest that giant viruses adapt to cold environments by changing their functional repertoire, and this viral evolutionary strategy is distinct from the polar adaptation strategy of their hosts.
Keywords	Science ; Q
Subject code	551
Language	English
Publishing date	2023-10-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online ; Research data: (with research data) Evaluating genomic divergence and parallelism in replicate ecomorphs from young and old cichlid adaptive radiations.

McGee, Matthew D / Neches, Russell Y / Seehausen, Ole

Molecular ecology

2016 Volume 25, Issue 1, Page(s) 260–268

Abstract: Comparative genomic studies of closely related species typically focus on single species pairs at one given stage of divergence. That makes it difficult to infer the continuum of evolutionary process during speciation and beyond. Here, we use whole- ... ...

Abstract	Comparative genomic studies of closely related species typically focus on single species pairs at one given stage of divergence. That makes it difficult to infer the continuum of evolutionary process during speciation and beyond. Here, we use whole-genome resequencing to examine genomic patterns of divergence in three sympatric cichlid species pairs with very similar functional and ecological differentiation, but different ages. We find a strong signature of increasing genomic divergence with time in both the mitochondrial genome and the nuclear genome. In contrast to many other systems, we find that in these cichlids, regions of elevated relative differentiation also exhibit increased absolute differentiation. We detect a signature of convergent evolution in a comparison of outlier regions across all three species pair comparisons, but the extent of it is modest, and regions that are strongly divergent in any one pair tend to be only slightly elevated in the other pairs, consistent with a repeatable but polygenic basis of traits that characterize the ecomorphs. Our results suggest that strong functional phenotypic differentiation, as seen in all three species pairs, is generally associated with a clear signature of genomic divergence, even in the youngest species pair.
MeSH term(s)	Animals ; Biological Evolution ; Cichlids/classification ; Cichlids/genetics ; Genetic Speciation ; Genome, Mitochondrial ; Lakes ; Phenotype ; Sympatry
Language	English
Publishing date	2016
Publishing country	England
Document type	Journal Article
ZDB-ID	1126687-9
ISSN	1365-294X ; 0962-1083 ; 0962-1083
ISSN (online)	1365-294X
ISSN	0962-1083
DOI	10.1111/mec.13463
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Global Biogeography of the Soil Virosphere

Graham, Emily B. / Camargo, Antonio P / Wu, Ruonan / Neches, Russell Y / Nolan, Matt / Paez-Espino, David / Copeland, Alex / Kyrpides, Nikos / Jansson, Janet K. K. / McDermott, Jason E / Hofmockel, Kirsten S / Soil Virosphere Consortium

bioRxiv

Abstract: Historically neglected by microbial ecologists, soil viruses are now thought to be critical to global biogeochemical cycles. However, our understanding of their global distribution, activities, and interactions with the soil microbiome remains limited. ... ...

Abstract	Historically neglected by microbial ecologists, soil viruses are now thought to be critical to global biogeochemical cycles. However, our understanding of their global distribution, activities, and interactions with the soil microbiome remains limited. Here, we present the Global Soil Virus (GSV) Atlas, a comprehensive dataset from 2,953 soils that comprises 616,935 uncultivated virus genomes (UViGs) and 38,508 unique viral operational taxonomic units (vOTUs). Rarefaction curves from the GSV Atlas indicate that most soil viral diversity remains unexplored, further underscored by high spatial turnover and low rates of shared vOTUs across samples. By examining genes associated with biogeochemical functions, we also demonstrate the viral potential to impact soil carbon and nutrient cycling. This study represents the most extensive characterization of soil viral diversity to date and provides a foundation for developing testable hypotheses regarding the role of the virosphere in the soil microbiome and global biogeochemistry.
Keywords	covid19
Language	English
Publishing date	2023-11-05
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2023.11.02.565391
Database	COVID19

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Article ; Online: IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata.

Camargo, Antonio Pedro / Nayfach, Stephen / Chen, I-Min A / Palaniappan, Krishnaveni / Ratner, Anna / Chu, Ken / Ritter, Stephan J / Reddy, T B K / Mukherjee, Supratim / Schulz, Frederik / Call, Lee / Neches, Russell Y / Woyke, Tanja / Ivanova, Natalia N / Eloe-Fadrosh, Emiley A / Kyrpides, Nikos C / Roux, Simon

Nucleic acids research

2022 Volume 51, Issue D1, Page(s) D733–D743

Abstract: Viruses are widely recognized as critical members of all microbiomes. Metagenomics enables large-scale exploration of the global virosphere, progressively revealing the extensive genomic diversity of viruses on Earth and highlighting the myriad of ways ... ...

Abstract	Viruses are widely recognized as critical members of all microbiomes. Metagenomics enables large-scale exploration of the global virosphere, progressively revealing the extensive genomic diversity of viruses on Earth and highlighting the myriad of ways by which viruses impact biological processes. IMG/VR provides access to the largest collection of viral sequences obtained from (meta)genomes, along with functional annotation and rich metadata. A web interface enables users to efficiently browse and search viruses based on genome features and/or sequence similarity. Here, we present the fourth version of IMG/VR, composed of >15 million virus genomes and genome fragments, a ≈6-fold increase in size compared to the previous version. These clustered into 8.7 million viral operational taxonomic units, including 231 408 with at least one high-quality representative. Viral sequences in IMG/VR are now systematically identified from genomes, metagenomes, and metatranscriptomes using a new detection approach (geNomad), and IMG standard annotation are complemented with genome quality estimation using CheckV, taxonomic classification reflecting the latest taxonomic standards, and microbial host taxonomy prediction. IMG/VR v4 is available at https://img.jgi.doe.gov/vr, and the underlying data are available to download at https://genome.jgi.doe.gov/portal/IMG_VR.
MeSH term(s)	Databases, Genetic ; Genome, Viral ; Metadata ; Metagenomics ; Software
Language	English
Publishing date	2022-11-17
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkac1037
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Article: On the intrinsic sterility of 3D printing.

Neches, Russell Y / Flynn, Kaitlin J / Zaman, Luis / Tung, Emily / Pudlo, Nicholas

PeerJ

2016 Volume 4, Page(s) e2661

Abstract: 3D printers that build objects using extruded thermoplastic are quickly becoming commonplace tools in laboratories. We demonstrate that with appropriate handling, these devices are capable of producing sterile components from a non-sterile feedstock of ... ...

Abstract	3D printers that build objects using extruded thermoplastic are quickly becoming commonplace tools in laboratories. We demonstrate that with appropriate handling, these devices are capable of producing sterile components from a non-sterile feedstock of thermoplastic without any treatment after fabrication. The fabrication process itself results in sterilization of the material. The resulting 3D printed components are suitable for a wide variety of applications, including experiments with bacteria and cell culture.
Language	English
Publishing date	2016-12-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.2661
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