Hidden Viral Sequences in Public Sequencing Data and Warning for Future Emerging Diseases

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Long-read metagenomics using PromethION uncovers oral bacteriophages and their interaction with host bacteria

Koji Yahara et al.

Summary: This study utilizes PromethION for long-read metagenomic analysis, identifying hundreds of viral contigs in human saliva and shedding light on the interactions between bacteriophages and host bacteria.

NATURE COMMUNICATIONS (2021)

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Article Microbiology

Decoding the RNA viromes in rodent lungs provides new insight into the origin and evolutionary patterns of rodent-borne pathogens in Mainland Southeast Asia

Zhiqiang Wu et al.

Summary: This study provides a comprehensive description of the core viromes of rodents and insectivores from Mainland Southeast Asia, highlighting a high diversity of viruses in rodent species in this region. Through meta-transcriptomic analysis, novel viruses from different evolutionary lineages were identified, as well as a characterization of viruses related to known pathogens.

MICROBIOME (2021)

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Article Virology

Identification of novel avian and mammalian deltaviruses provides new insights into deltavirus evolution

Masashi Iwamoto et al.

Summary: The study identified novel deltaviruses in passerine birds, woodchucks, and white-tailed deer, shedding light on the origin of HDV from mammalian deltaviruses and interspecies transmission with passerine deltaviruses. The satellite-helper relationship between HDV and hepadnavirus was established after the divergence of the HDV lineage from non-HDV mammalian deltaviruses, as revealed by metaviromic and experimental analyses. Further surveillance for deltaviruses is deemed important based on the findings to enhance understanding of deltavirus evolution, diversity, and transmission.

VIRUS EVOLUTION (2021)

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Review Microbiology

Hepatitis E virus: host tropism and zoonotic infection

Bo Wang et al.

Summary: Hepatitis E virus (HEV) is an important but understudied pathogen that can cause acute viral hepatitis and, in some cases, chronic infection with other manifestations. Various strains of HEV from different animal species have been identified, with the ability to cross species barriers and infect humans through consumption of animal meat or direct contact. The discovery of animal HEV variants provides opportunities for developing useful animal models for research on HEV.

CURRENT OPINION IN MICROBIOLOGY (2021)

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Article Environmental Sciences

Bats and birds as viral reservoirs: A physiological and ecological perspective

Ghulam Nabi et al.

Summary: Birds and bats are well-known reservoirs of viruses, potentially carrying more zoonotic pathogens than other animals. Their adaptability to urban environments may increase the risk of viral spillover transmission, facilitating the emergence of novel viruses that could cause global pandemics. Their ecological interactions play a crucial role in this process.

SCIENCE OF THE TOTAL ENVIRONMENT (2021)

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Article Genetics & Heredity

Identification of a reptile lyssavirus in Anolis allogus provided novel insights into lyssavirus evolution

Masayuki Horie et al.

Summary: A lyssa-like virus named Anole Lyssa-like Virus 1 (ALLV-1) was discovered in Anolis allogus (Spanish flag anole), showing closer relation to lyssaviruses than Frog Lyssa-like Virus 1 (FLLV-1). The presence of the psi region in ALLV-1 genome suggests evolution divergence after the split from FLLV-1, providing novel insights into the evolution of lyssaviruses.

VIRUS GENES (2021)

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Article Microbiology

The new scope of virus taxonomy: partitioning the virosphere into 15 hierarchical ranks

Alexander E. Gorbalenya et al.

NATURE MICROBIOLOGY (2020)

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METAVIRALSPADES: assembly of viruses from metagenomic data

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BIOINFORMATICS (2020)

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Review Biotechnology & Applied Microbiology

A tool with many applications: vesicular stomatitis virus in research and medicine

Altar M. Munis et al.

EXPERT OPINION ON BIOLOGICAL THERAPY (2020)

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Review Microbiology

West Nile Virus: An Update on Pathobiology, Epidemiology, Diagnostics, Control and One Health Implications

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PATHOGENS (2020)

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Hepatitis A Virus and Hepatitis E Virus: Emerging and Re-Emerging Enterically Transmitted Hepatitis Viruses

Stanley M. Lemon et al.

COLD SPRING HARBOR PERSPECTIVES IN MEDICINE (2019)

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Article Virology

Expanding the RNA Virosphere by Unbiased Metagenomics

Yong-Zhen Zhang et al.

ANNUAL REVIEW OF VIROLOGY, VOL 6, 2019 (2019)

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Review Biology

A brief history of bird flu

Samantha J. Lycett et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2019)

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Global estimates of mammalian viral diversity accounting for host sharing

Colin J. Carlson et al.

NATURE ECOLOGY & EVOLUTION (2019)

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Novel Mammalian orthorubulavirus 5 Discovered as Accidental Cell Culture Contaminant

Brandi J. Feehan et al.

VIRUSES-BASEL (2019)

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Article Biochemistry & Molecular Biology

UFBoot2: Improving the Ultrafast Bootstrap Approximation

Diep Thi Hoang et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

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Article Biochemical Research Methods

fastp: an ultra-fast all-in-one FASTQ preprocessor

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BIOINFORMATICS (2018)

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Review Medicine, General & Internal

Parechovirus: an important emerging infection in young infants

Philip N. Britton et al.

MEDICAL JOURNAL OF AUSTRALIA (2018)

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Editorial Material Multidisciplinary Sciences

The Global Virome Project

Dennis Carroll et al.

SCIENCE (2018)

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Review Virology

A decade of RNA virus metagenomics is (not) enough

Alexander L. Greninger

VIRUS RESEARCH (2018)

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GGTREE: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data

Guangchuang Yu et al.

METHODS IN ECOLOGY AND EVOLUTION (2017)

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Article Biochemistry & Molecular Biology

metaSPAdes: a new versatile metagenomic assembler

Sergey Nurk et al.

GENOME RESEARCH (2017)

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Article Biotechnology & Applied Microbiology

ICTV Virus Taxonomy Profile: Picornaviridae

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JOURNAL OF GENERAL VIROLOGY (2017)

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Article Biotechnology & Applied Microbiology

ICTV Virus Taxonomy Profile: &ITHepeviridae&IT

Michael A. Purdy et al.

JOURNAL OF GENERAL VIROLOGY (2017)

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Correction Biotechnology & Applied Microbiology

The plasma virome of febrile adult Kenyans shows frequent parvovirus B19 infections and a novel arbovirus (Kadipiro virus) (vol 97, pg 3359, 2016)

Carolyne N. Ngoi et al.

JOURNAL OF GENERAL VIROLOGY (2017)

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Article Biotechnology & Applied Microbiology

ICTV Virus Taxonomy Profile: Flaviviridae

Peter Simmonds et al.

JOURNAL OF GENERAL VIROLOGY (2017)

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ModelFinder: fast model selection for accurate phylogenetic estimates

Subha Kalyaanamoorthy et al.

NATURE METHODS (2017)

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Astrovirus Pathogenesis

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VIRUSES-BASEL (2017)

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Astrovirus Biology and Pathogenesis

Valerie Cortez et al.

ANNUAL REVIEW OF VIROLOGY, VOL 4 (2017)

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Karen Clark et al.

NUCLEIC ACIDS RESEARCH (2016)

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Acute encephalopathy in an immunocompromised boy with astrovirus-MLB1 infection detected by next generation sequencing

Masanori Sato et al.

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Linking Virus Genomes with Host Taxonomy

Tomoko Mihara et al.

VIRUSES-BASEL (2016)

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Article Multidisciplinary Sciences

Novel highly divergent reassortant bat rotaviruses in Cameroon, without evidence of zoonosis

Claude Kwe Yinda et al.

SCIENTIFIC REPORTS (2016)

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Article Multidisciplinary Sciences

SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation

Wei Shen et al.

PLOS ONE (2016)

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Article Microbiology

Draft Genome Sequence of Goose Dicistrovirus

Alexander L. Greninger et al.

GENOME ANNOUNCEMENTS (2016)

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Article Microbiology

Genome Sequence of the Parainfluenza Virus 5 Strain That Persistently Infects AGS Cells

Elizabeth Wignall-Fleming et al.

GENOME ANNOUNCEMENTS (2016)

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Article Biochemical Research Methods

HISAT: a fast spliced aligner with low memory requirements

Daehwan Kim et al.

NATURE METHODS (2015)

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Article Microbiology

Discovery of a Novel Hepatovirus (Phopivirus of Seals) Related to Human Hepatitis A Virus

S. J. Anthony et al.

MBIO (2015)

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Article Microbiology

Non-Human Primates Harbor Diverse Mammalian and Avian Astroviruses Including Those Associated with Human Infections

Erik A. Karlsson et al.

PLOS PATHOGENS (2015)

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Article Biochemistry & Molecular Biology

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

Lam-Tung Nguyen et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

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Article Virology

Novel dicistrovirus from bat guano

Gabor Reuter et al.

ARCHIVES OF VIROLOGY (2014)

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Article Biotechnology & Applied Microbiology

Novel hepatitis E like virus found in Swedish moose

Jay Lin et al.

JOURNAL OF GENERAL VIROLOGY (2014)

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Article Biochemical Research Methods

STAR: ultrafast universal RNA-seq aligner

Alexander Dobin et al.

BIOINFORMATICS (2013)

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Article Biochemistry & Molecular Biology

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Kazutaka Katoh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

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Article Biochemical Research Methods

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

Anton Bankevich et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2012)

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Article Medicine, General & Internal

Zoonoses 1 Ecology of zoonoses: natural and unnatural histories

William B. Karesh et al.

LANCET (2012)

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BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata

Tanya Barrett et al.

NUCLEIC ACIDS RESEARCH (2012)

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Article Biochemistry & Molecular Biology

The Sequence Read Archive

Rasko Leinonen et al.

NUCLEIC ACIDS RESEARCH (2011)

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Article Biochemical Research Methods

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan et al.

BIOINFORMATICS (2010)

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Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

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Article Biochemical Research Methods

BLAST plus : architecture and applications

Christiam Camacho et al.

BMC BIOINFORMATICS (2009)

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Article Virology

Complete genome sequence of a highly divergent astrovirus isolated from a child with acute diarrhea

Stacy R. Finkbeiner et al.

VIROLOGY JOURNAL (2008)

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Article Virology

A bicistronic subgenornic mRNA encodes both the ORF2 and ORF3 proteins of hepatitis E virus

Judith Graff et al.

JOURNAL OF VIROLOGY (2006)

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Review Multidisciplinary Sciences

Global patterns of influenza A virus in wild birds

B Olsen et al.

SCIENCE (2006)

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Hidden Viral Sequences in Public Sequencing Data and Warning for Future Emerging Diseases

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