Metagenomic Insights into the Sewage RNA Virosphere of a Large City

Characterisation of the sewage virome: comparison of NGS tools and occurrence of significant pathogens

(2020) Sandra Martínez-Puchol et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Coronavirus in water environments: Occurrence, persistence and concentration methods - A scoping review

(2020) Giuseppina La Rosa et al.   WATER RESEARCH

ICTV Virus Taxonomy Profile: Bromoviridae

(2019) Joseph Bujarski et al.   JOURNAL OF GENERAL VIROLOGY

Novel Picobirnaviruses in Respiratory and Alimentary Tracts of Cattle and Monkeys with Large Intra- and Inter-Host Diversity

(2019) Patrick C. Y. Woo et al.   Viruses-Basel

A Structure-Function Diversity Survey of the RNA-Dependent RNA Polymerases From the Positive-Strand RNA Viruses

(2019) Hengxia Jia et al.   Frontiers in Microbiology

Differential removal of human pathogenic viruses from sewage by conventional and ozone treatments

(2018) Hao Wang et al.   INTERNATIONAL JOURNAL OF HYGIENE AND ENVIRONMENTAL HEALTH

Seasonal and spatial dynamics of enteric viruses in wastewater and in riverine and estuarine receiving waters

(2018) Kata Farkas et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Comparative enteric viruses and coliphage removal during wastewater treatment processes in a sub-tropical environment

(2018) J.P.S. Sidhu et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Metagenomics for the study of viruses in urban sewage as a tool for public health surveillance

(2018) X. Fernandez-Cassi et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Extensive conservation of prokaryotic ribosomal binding sites in known and novel picobirnaviruses

(2018) Siddharth R. Krishnamurthy et al.   VIROLOGY

A decade of RNA virus metagenomics is (not) enough

(2018) Alexander L. Greninger   VIRUS RESEARCH

Viromic Analysis of Wastewater Input to a River Catchment Reveals a Diverse Assemblage of RNA Viruses

(2018) Evelien M. Adriaenssens et al.   mSystems

Quito's virome: Metagenomic analysis of viral diversity in urban streams of Ecuador's capital city

(2018) Laura Guerrero-Latorre et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Multiple divergent picobirnaviruses with functional prokaryotic Shine-Dalgarno ribosome binding sites present in cloacal sample of a diarrheic chicken

(2018) Ákos Boros et al.   VIROLOGY

Active Crossfire Between Cyanobacteria and Cyanophages in Phototrophic Mat Communities Within Hot Springs

(2018) Sergio Guajardo-Leiva et al.   Frontiers in Microbiology

ICTV virus taxonomy profile: Picobirnaviridae

(2018) Bernard Delmas et al.   JOURNAL OF GENERAL VIROLOGY

Predominance of Rotavirus G8P[8] in a City in Chile, a Country Without Rotavirus Vaccination

(2018) Yalda Lucero et al.   JOURNAL OF PEDIATRICS

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Detection of potentially novel paramyxovirus and coronavirus viral RNA in bats and rats in the Mekong Delta region of southern Viet Nam

(2017) A. Berto et al.   Zoonoses and Public Health

Viromes As Genetic Reservoir for the Microbial Communities in Aquatic Environments: A Focus on Antimicrobial-Resistance Genes

(2017) Stefano Colombo et al.   Frontiers in Microbiology

Discovery and genetic analysis of novel coronaviruses in least horseshoe bats in southwestern China

(2017) Lihua Wang et al.   Emerging Microbes & Infections

K-mer Content, Correlation, and Position Analysis of Genome DNA Sequences for the Identification of Function and Evolutionary Features

(2017) Aaron Sievers et al.   Genes

Risk management of viral infectious diseases in wastewater reclamation and reuse: Review

(2016) Daisuke Sano et al.   ENVIRONMENT INTERNATIONAL

Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses

(2016) François Enault et al.   ISME Journal

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices

(2016) Dinghua Li et al.   METHODS

Redefining the invertebrate RNA virosphere

(2016) Mang Shi et al.   NATURE

Human norovirus transmission and evolution in a changing world

(2016) Miranda de Graaf et al.   NATURE REVIEWS MICROBIOLOGY

W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis

(2016) Jana Trifinopoulos et al.   NUCLEIC ACIDS RESEARCH

Full Genome Characterization of Novel DS-1-Like G8P[8] Rotavirus Strains that Have Emerged in Thailand: Reassortment of Bovine and Human Rotavirus Gene Segments in Emerging DS-1-Like Intergenogroup Reassortant Strains

(2016) Ratana Tacharoenmuang et al.   PLoS One

Linking Virus Genomes with Host Taxonomy

(2016) Tomoko Mihara et al.   Viruses-Basel

Hyperexpansion of RNA Bacteriophage Diversity

(2016) Siddharth R. Krishnamurthy et al.   PLOS BIOLOGY

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

(2016) Daniel H. Huson et al.   PLoS Computational Biology

Increased detection of G3P[9] and G6P[9] rotavirus strains in hospitalized children with acute diarrhea in Bulgaria

(2015) Zornitsa Mladenova et al.   INFECTION GENETICS AND EVOLUTION

Common and unique features of viral RNA-dependent polymerases

(2014) Aartjan J. W. te Velthuis   CELLULAR AND MOLECULAR LIFE SCIENCES

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Relative abundance and treatment reduction of viruses during wastewater treatment processes — Identification of potential viral indicators

(2014) Masaaki Kitajima et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Epidemiology, Phylogeny, and Evolution of Emerging EntericPicobirnavirusesof Animal Origin and Their Relationship to Human Strains

(2014) Yashpal S. Malik et al.   Biomed Research International

Proposal for a unified norovirus nomenclature and genotyping

(2013) Annelies Kroneman et al.   ARCHIVES OF VIROLOGY

Detection of unusual G6 rotavirus strains in Italian children with diarrhoea during the 2011 surveillance season

(2013) Giovanni Ianiro et al.   JOURNAL OF MEDICAL VIROLOGY

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

A Novel Group of Avian Astroviruses in Wild Aquatic Birds

(2012) D. K. W. Chu et al.   JOURNAL OF VIROLOGY

High Variety of Known and New RNA and DNA Viruses of Diverse Origins in Untreated Sewage

(2012) T. F. F. Ng et al.   JOURNAL OF VIROLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Assessing the Diversity and Specificity of Two Freshwater Viral Communities through Metagenomics

(2012) Simon Roux et al.   PLoS One

Tracking Down Antibiotic-Resistant Pseudomonas aeruginosa Isolates in a Wastewater Network

(2012) Céline Slekovec et al.   PLoS One

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Raw Sewage Harbors Diverse Viral Populations

(2011) P. G. Cantalupo et al.   mBio

Bacteriophages and genetic mobilization in sewage and faecally polluted environments

(2011) Maite Muniesa et al.   Microbial Biotechnology

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Detection of rotavirus A in sewage samples using multiplex qPCR and an evaluation of the ultracentrifugation and adsorption-elution methods for virus concentration

(2010) Tulio M. Fumian et al.   JOURNAL OF VIROLOGICAL METHODS

Eukaryotic Viruses in Wastewater Samples from the United States

(2009) E. M. Symonds et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS