Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities
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Title
Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities
Authors
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Journal
BRIEFINGS IN BIOINFORMATICS
Volume -, Issue -, Pages -
Publisher
Oxford University Press (OUP)
Online
2020-10-09
DOI
10.1093/bib/bbaa297
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Note: Only part of the references are listed.- Pattern of early human-to-human transmission of Wuhan 2019 novel coronavirus (2019-nCoV), December 2019 to January 2020
- (2020) Julien Riou et al. Eurosurveillance
- Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR
- (2020) Victor M Corman et al. Eurosurveillance
- Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding
- (2020) Roujian Lu et al. LANCET
- A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster
- (2020) Jasper Fuk-Woo Chan et al. LANCET
- Viral load of SARS-CoV-2 in clinical samples
- (2020) Yang Pan et al. LANCET INFECTIOUS DISEASES
- An interactive web-based dashboard to track COVID-19 in real time
- (2020) Ensheng Dong et al. LANCET INFECTIOUS DISEASES
- A new coronavirus associated with human respiratory disease in China
- (2020) Fan Wu et al. NATURE
- A pneumonia outbreak associated with a new coronavirus of probable bat origin
- (2020) Peng Zhou et al. NATURE
- Emergence of a novel human coronavirus threatening human health
- (2020) Leo L. M. Poon et al. NATURE MEDICINE
- Detectable 2019-nCoV viral RNA in blood is a strong indicator for the further clinical severity
- (2020) Weilie Chen et al. Emerging Microbes & Infections
- Molecular and serological investigation of 2019-nCoV infected patients: implication of multiple shedding routes
- (2020) Wei Zhang et al. Emerging Microbes & Infections
- The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2
- (2020) Nature Microbiology
- The Incubation Period of Coronavirus Disease 2019 (COVID-19) From Publicly Reported Confirmed Cases: Estimation and Application
- (2020) Stephen A. Lauer et al. ANNALS OF INTERNAL MEDICINE
- Ethnic and socioeconomic differences in SARS-CoV-2 infection: prospective cohort study using UK Biobank
- (2020) Claire L. Niedzwiedz et al. BMC Medicine
- A Genomic Perspective on the Origin and Emergence of SARS-CoV-2
- (2020) Yong-Zhen Zhang et al. CELL
- The Architecture of SARS-CoV-2 Transcriptome
- (2020) Dongwan Kim et al. CELL
- A Global Effort to Define the Human Genetics of Protective Immunity to SARS-CoV-2 Infection
- (2020) Jean-Laurent Casanova et al. CELL
- Clinical characteristics of fatal and recovered cases of coronavirus disease 2019 (COVID-19) in Wuhan, China
- (2020) Yan Deng et al. CHINESE MEDICAL JOURNAL
- Metatranscriptomic Characterization of COVID-19 Identified A Host Transcriptional Classifier Associated With Immune Signaling
- (2020) Haocheng Zhang et al. CLINICAL INFECTIOUS DISEASES
- Quantitative Detection and Viral Load Analysis of SARS-CoV-2 in Infected Patients
- (2020) Fengting Yu et al. CLINICAL INFECTIOUS DISEASES
- Probable Pangolin Origin of SARS-CoV-2 Associated with the COVID-19 Outbreak
- (2020) Tao Zhang et al. CURRENT BIOLOGY
- The COVID-19 Host Genetics Initiative, a global initiative to elucidate the role of host genetic factors in susceptibility and severity of the SARS-CoV-2 virus pandemic
- (2020) EUROPEAN JOURNAL OF HUMAN GENETICS
- Connecting data, tools and people across Europe: ELIXIR’s response to the COVID-19 pandemic
- (2020) Niklas Blomberg et al. EUROPEAN JOURNAL OF HUMAN GENETICS
- SARS-CoV-2 Vaccines: Status Report
- (2020) Fatima Amanat et al. IMMUNITY
- A Review of Coronavirus Disease-2019 (COVID-19)
- (2020) Tanu Singhal INDIAN JOURNAL OF PEDIATRICS
- Pharmacologic Treatments for Coronavirus Disease 2019 (COVID-19)
- (2020) James M. Sanders et al. JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION
- Genomic characterization and phylogenetic analysis of SARS-COV-2 in Italy
- (2020) Gianguglielmo Zehender et al. JOURNAL OF MEDICAL VIROLOGY
- Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant
- (2020) Maria Pachetti et al. Journal of Translational Medicine
- Identifying SARS-CoV-2 related coronaviruses in Malayan pangolins
- (2020) Tommy Tsan-Yuk Lam et al. NATURE
- The proximal origin of SARS-CoV-2
- (2020) Kristian G. Andersen et al. NATURE MEDICINE
- Spread of SARS-CoV-2 in the Icelandic Population
- (2020) Daniel F. Gudbjartsson et al. NEW ENGLAND JOURNAL OF MEDICINE
- Aerosol and Surface Stability of SARS-CoV-2 as Compared with SARS-CoV-1
- (2020) Neeltje van Doremalen et al. NEW ENGLAND JOURNAL OF MEDICINE
- Demographic science aids in understanding the spread and fatality rates of COVID-19
- (2020) Jennifer Beam Dowd et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Laboratory testing of SARS‐CoV, MERS‐CoV, and SARS‐CoV‐2 (2019‐nCoV): Current status, challenges, and countermeasures
- (2020) Ying Yan et al. REVIEWS IN MEDICAL VIROLOGY
- Supporting pandemic response using genomics and bioinformatics: A case study on the emergent SARS‐CoV‐2 outbreak
- (2020) Denis C. Bauer et al. Transboundary and Emerging Diseases
- Assay Techniques and Test Development for COVID-19 Diagnosis
- (2020) Linda J. Carter et al. ACS Central Science
- Evidence for host-dependent RNA editing in the transcriptome of SARS-CoV-2
- (2020) Salvatore Di Giorgio et al. Science Advances
- Making Sense of Mutation: What D614G Means for the COVID-19 Pandemic Remains Unclear
- (2020) Nathan D. Grubaugh et al. CELL
- Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus
- (2020) Bette Korber et al. CELL
- Tracing open data in emergencies: The case of the COVID‐19 pandemic
- (2020) Konstantinos Gkiouras et al. EUROPEAN JOURNAL OF CLINICAL INVESTIGATION
- Ion torrent-based nasopharyngeal swab metatranscriptomics in COVID-19
- (2020) Gubio S. Campos et al. JOURNAL OF VIROLOGICAL METHODS
- Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study
- (2020) Luke W Meredith et al. LANCET INFECTIOUS DISEASES
- Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling
- (2020) Rebecca J. Rockett et al. NATURE MEDICINE
- Ten recommendations for supporting open pathogen genomic analysis in public health
- (2020) Allison Black et al. NATURE MEDICINE
- First confirmed detection of SARS-CoV-2 in untreated wastewater in Australia: A proof of concept for the wastewater surveillance of COVID-19 in the community
- (2020) Warish Ahmed et al. SCIENCE OF THE TOTAL ENVIRONMENT
- Preliminary analysis of COVID-19 academic information patterns: a call for open science in the times of closed borders
- (2020) J. Homolak et al. SCIENTOMETRICS
- Nanopore Targeted Sequencing for the Accurate and Comprehensive Detection of SARS‐CoV‐2 and Other Respiratory Viruses
- (2020) Ming Wang et al. Small
- Multiple approaches for massively parallel sequencing of SARS-CoV-2 genomes directly from clinical samples
- (2020) Minfeng Xiao et al. Genome Medicine
- No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics
- (2020) Dannon Baker et al. PLoS Pathogens
- COVID-19 pandemic reveals the peril of ignoring metadata standards
- (2020) Lynn M. Schriml et al. Scientific Data
- Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic
- (2020) Maciej F. Boni et al. Nature Microbiology
- Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City Region
- (2020) Matthew T Maurano et al. GENOME RESEARCH
- Kinetics of viral load and antibody response in relation to COVID-19 severity
- (2020) Yanqun Wang et al. JOURNAL OF CLINICAL INVESTIGATION
- SARS-CoV-2 detection, viral load and infectivity over the course of an infection
- (2020) Kieran A. Walsh et al. JOURNAL OF INFECTION
- CoV3D: a database of high resolution coronavirus protein structures
- (2020) Ragul Gowthaman et al. NUCLEIC ACIDS RESEARCH
- ViruSurf: an integrated database to investigate viral sequences
- (2020) Arif Canakoglu et al. NUCLEIC ACIDS RESEARCH
- Disentangling primer interactions improves SARS-CoV-2 genome sequencing by multiplex tiling PCR
- (2020) Kentaro Itokawa et al. PLoS One
- First detection of SARS-CoV-2 in untreated wastewaters in Italy
- (2020) Giuseppina La Rosa et al. SCIENCE OF THE TOTAL ENVIRONMENT
- Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic
- (2020) Sureshnee Pillay et al. Genes
- Clinical metagenomics
- (2019) Charles Y. Chiu et al. NATURE REVIEWS GENETICS
- Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis
- (2019) Adrian Viehweger et al. GENOME RESEARCH
- Metagenomic Nanopore Sequencing of Influenza Virus Direct from Clinical Respiratory Samples
- (2019) Kuiama Lewandowski et al. JOURNAL OF CLINICAL MICROBIOLOGY
- Phylogenetic surveillance of travel-related Zika virus infections through whole-genome sequencing methods
- (2019) Kimia Kamelian et al. Scientific Reports
- Making multi-omics data accessible to researchers
- (2019) Ana Conesa et al. Scientific Data
- Nextstrain: real-time tracking of pathogen evolution
- (2018) James Hadfield et al. BIOINFORMATICS
- The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update
- (2018) Enis Afgan et al. NUCLEIC ACIDS RESEARCH
- RNA epitranscriptomics: Regulation of infection of RNA and DNA viruses by N 6 -methyladenosine (m6 A)
- (2018) Brandon Tan et al. REVIEWS IN MEDICAL VIROLOGY
- A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection
- (2018) Norman Goodacre et al. mSphere
- Whole genome sequencing, variant analysis, phylogenetics, and deep sequencing of Zika virus strains
- (2018) Susmita Shrivastava et al. Scientific Reports
- Assessment of metagenomic Nanopore and Illumina sequencing for recovering whole genome sequences of chikungunya and dengue viruses directly from clinical samples
- (2018) Liana E. Kafetzopoulou et al. Eurosurveillance
- ArrayExpress update – from bulk to single-cell expression data
- (2018) Awais Athar et al. NUCLEIC ACIDS RESEARCH
- GISAID: Global initiative on sharing all influenza data – from vision to reality
- (2017) Yuelong Shu et al. Eurosurveillance
- Shotgun metagenomics, from sampling to analysis
- (2017) Christopher Quince et al. NATURE BIOTECHNOLOGY
- Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist’s Perspective - Not Only Size Matters!
- (2017) John Vollmers et al. PLoS One
- Real-time, portable genome sequencing for Ebola surveillance
- (2016) Joshua Quick et al. NATURE
- SARS and MERS: recent insights into emerging coronaviruses
- (2016) Emmie de Wit et al. NATURE REVIEWS MICROBIOLOGY
- The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog)
- (2016) Jacqueline MacArthur et al. NUCLEIC ACIDS RESEARCH
- The FAIR Guiding Principles for scientific data management and stewardship
- (2016) Mark D. Wilkinson et al. Scientific Data
- The Theory and Practice of Genome Sequence Assembly
- (2015) Jared T. Simpson et al. Annual Review of Genomics and Human Genetics
- The European Genome-phenome Archive of human data consented for biomedical research
- (2015) Ilkka Lappalainen et al. NATURE GENETICS
- Tools and data services registry: a community effort to document bioinformatics resources
- (2015) Jon Ison et al. NUCLEIC ACIDS RESEARCH
- The International Nucleotide Sequence Database Collaboration
- (2015) Guy Cochrane et al. NUCLEIC ACIDS RESEARCH
- Exome Sequencing: Current and Future Perspectives
- (2015) Amanda Warr et al. G3-Genes Genomes Genetics
- The Epitranscriptome and Innate Immunity
- (2015) Mary A. O’Connell et al. PLoS Genetics
- Continuous and Discontinuous RNA Synthesis in Coronaviruses
- (2015) Isabel Sola et al. Annual Review of Virology
- Global health and the US Centers for Disease Control and Prevention
- (2014) Anne Schuchat et al. LANCET
- NCBI Viral Genomes Resource
- (2014) J. Rodney Brister et al. NUCLEIC ACIDS RESEARCH
- Assembly of viral genomes from metagenomes
- (2014) Saskia L. Smits et al. Frontiers in Microbiology
- Viral Quasispecies Evolution
- (2012) E. Domingo et al. MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
- ViPR: an open bioinformatics database and analysis resource for virology research
- (2011) Brett E. Pickett et al. NUCLEIC ACIDS RESEARCH
- The Open Knowledge Foundation: Open Data Means Better Science
- (2011) Jennifer C. Molloy PLOS BIOLOGY
- Microbial Metagenomics: Beyond the Genome
- (2010) Jack A. Gilbert et al. Annual Review of Marine Science
- Assembly algorithms for next-generation sequencing data
- (2010) Jason R. Miller et al. GENOMICS
- A Metagenomic Analysis of Pandemic Influenza A (2009 H1N1) Infection in Patients from North America
- (2010) Alexander L. Greninger et al. PLoS One
- The role of programmed-1 ribosomal frameshifting in coronavirus propagation
- (2008) Ewan et al. Frontiers in Bioscience-Landmark
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