Viral sequence identification SOP with VirSorter2 v3

Guo, Jiarong; Vik, Dean; Pratama, Akbar Adjie; Roux, Simon; Sullivan, Matthew

doi:10.17504/protocols.io.bwm5pc86

Cited by 29 publications

(22 citation statements)

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“…The quality of viral contigs predicted from all three tools was assessed with CheckV v0.8.1 [50], and resulting trimmed viral sequences were annotated with DRAM v1.3 [51]. Annotated viral sequences were manually curated following the selection criteria outlined by Guo et al [52]. Additionally, viral sequences with the most confident prediction scores from DeepVirFinder (with corresponding viral scores ≥ 0.95, 𝑝 ≤ 0.05, and length ≥ 10 kb) and from VIBRANT (with corresponding quality scores of "high quality draft" or "complete circular", and length ≥ 10 kb) were retained.…”

Section: Recovery Of Viral Populationsmentioning

confidence: 99%

Ecological and evolutionary patterns of virus-host interactions throughout a grassland soil depth profile

Muscatt

Cook

Millard

et al. 2022

Preprint

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Background:Soil microbes play pivotal roles in global carbon cycling, however the fundamental interactions between microbes and their infecting viruses remain unclear. This is exacerbated with soil depth, where the patterns of viral dispersal, ecology, and evolution are markedly underexplored. To investigate viral communities across soil depth, we leveraged a publicly available metagenomic data set sampled from grassland soil in northern California.Results:10,196 non-redundant vOTUs were recovered from soil sampled from 20 cm to 120 cm below the surface. Viral prevalence was high throughout the soil depth profile, with viruses infecting dominant soil phyla, includingActinomycetota. Contrary to leading hypotheses, lysogeny did not dominate in the soil viral communities. Viral diversity was investigated at both the population-level (i.e., macro diversity) and strain-level (i.e., micro diversity) to reveal diverse ecological and evolutionary patterns of virus-host interactions in surface and subsurface soil.Conclusions:By investigating viral micro diversity in soil for the first time, we have uncovered patterns of antagonistic co-evolution across both surface and subsurface soils. Furthermore, we have provided evidence of soil viruses augmenting the remineralisation of soil carbon. While we continue to yield a more comprehensive understanding of soil viral ecology, our work appeals to future researchers to continue to investigate subsurface viral communities.

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Section: Recovery Of Viral Populationsmentioning

confidence: 99%

Ecological and evolutionary patterns of virus-host interactions throughout a grassland soil depth profile

Muscatt

Cook

Millard

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…1.2.2 (84) using default parameters. Viral contigs were subsequently conservatively manually curated using custom scripts and supervised screening based on combinations of viral and host gene counts from CheckV , hallmark gene counts from VirSorter2 , contig score, and gene-level annotations from DRAMv following previously benchmarked protocols (85) to remove potential false positive predictions (broadly screening for enrichment in viral-like or viral hallmark genes; depletion in host genes), retaining 12,843 total contigs from metagenomes, and 214 total contigs from metatranscriptomes. Manually curated dsDNA, ssDNA, and RNA viral sequences were clustered at 95% minimum sequence identity within coassembly using CD-HIT-EST ver.…”

Section: Methodsmentioning

confidence: 99%

Top-heavy trophic structure within benthic viral dark matter

Cissell

McCoy

2022

Preprint

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Viruses exert considerable influence on microbial population dynamics and community structure, with cascading effects on ecosystem-scale biogeochemical cycling and functional trajectories. Creating broadly generalizable theory on viral trophic ecology requires further inquiry into historically unexplored microbial systems that currently lack empirically demonstrated patterns in viral infectivity, such as structurally complex benthic communities. This becomes increasingly relevant considering recently proposed revisions to the fundamental mechanisms that modulate the strength and direction viral trophic linkages. Here, we employed deep longitudinal multiomic sequencing to characterize the viral assemblage (including ssDNA, dsDNA, and dsRNA viruses) and profile lineage-specific host-virus interactions within benthic cyanobacterial mats sampled from Bonaire, Caribbean Netherlands, over a complete diel time-series, and reconstruct patterns in intra-mat trophic structure. We recovered 11,020 unique viral populations spanning at least 10 viral families across the orders Caudovirales, Petitvirales, and Mindivirales, with evidence for extensive genomic novelty from reference and environmental viral sequences. Analysis of coverage ratios of viral sequences and computationally predicted hosts spanning 15 phyla and 21 classes revealed virus:host abundance and activity ratios consistently exceeding 1:1, with overall power-law scaling indicating an increasingly top-heavy intra-mat trophic structure with significant top-down pressure. Diel activity of cyanophages showed clear temporal patterns that seem to follow host physiological condition. These data generate important hypotheses concerning taxon-dependent variation in the relative contribution of top-down vs. bottom-up forcing in driving mat community dynamics, and establish a useful database of viral sequences from this previously unexplored system toward the generation of generalizable trans-system theory on viral trophic ecology.

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“…Reads were reassembled using metaplasmidSPAdes (Antipov et al, 2019) to look for contigs with overlapping ends, indicative of circular genomic regions, commonly viral or plasmid in origin. To remove potential viruses, putative plasmids identified as viral by VirSorter2 v2.2.3 (Guo, Bolduc, et al, 2021) and CheckV v0.8.1 (Nayfach et al, 2021) as outlined in their best practice protocol (Guo, Vik, et al, 2021) or identified as viral from Kaiju or Kraken2 were discarded. Putative non-viral plasmids were then checked against PlasClass v1st/Nov/2021 (Pellow et al, 2020) and any contig with a score of less than 0.5 was discarded as a false positive, as outlined in Pellow et al (2020).…”

Section: Methodsmentioning

confidence: 99%

The Diversity and Ubiquity of Antibiotic Resistance Genes in Finfish Culture Ponds in Bangladesh

Bell

Thornber

Chaput

et al. 2022

Preprint

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In Bangladesh, fish provide over 60% of animal-source food with 56.2% of this coming from aquaculture produced predominantly in rural freshwater ponds. Increasing demand for fish products is driving intensification and resulting in higher disease prevalence, posing a risk to food security.Biosecurity is often absent in rural aquaculture practices in Bangladesh and antibiotics are commonly used to treat and prevent disease outbreaks. Antibiotics are often administered incorrectly -a key factor associated with the development of antimicrobial resistance (AMR). AMR can be disseminated rapidly within microbial ecosystems via mobile genetic elements, posing a risk for humans and animals infected with AMR pathogens as treatments with antibiotics become ineffective. Early AMR detection and understanding of the spread of antimicrobial resistant genes (ARGs) in rural

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Viral sequence identification SOP with VirSorter2 v3

Abstract: This protocol shows how to use VirSorter2, checkV, DRAMv and some manual curation criteria for viral sequence identification.

Cited by 29 publications

References 0 publications

Ecological and evolutionary patterns of virus-host interactions throughout a grassland soil depth profile

Ecological and evolutionary patterns of virus-host interactions throughout a grassland soil depth profile

Top-heavy trophic structure within benthic viral dark matter

The Diversity and Ubiquity of Antibiotic Resistance Genes in Finfish Culture Ponds in Bangladesh

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