SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes

Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69–V70, France, August to December 2020

(2021) Antonin Bal et al.   Eurosurveillance

Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies

(2021) Allison J. Greaney et al.   Cell Host & Microbe

Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence

(2021) Ester C Sabino et al.   LANCET

Emergence of a SARS-CoV-2 variant of concern with mutations in spike glycoprotein

(2021) Houriiyah Tegally et al.   NATURE

SARS-CoV-2 evolution during treatment of chronic infection

(2021) Steven A. Kemp et al.   NATURE

Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: A homology-based resolution

(2021) Irwin Jungreis et al.   VIROLOGY

Evidence for a novel overlapping coding sequence in POLG initiated at a CUG start codon

(2020) Yousuf A. Khan et al.   BMC GENETICS

Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding

(2020) Roujian Lu et al.   LANCET

A new coronavirus associated with human respiratory disease in China

(2020) Fan Wu et al.   NATURE

Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan

(2020) Jasper Fuk-Woo Chan 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 Architecture of SARS-CoV-2 Transcriptome

(2020) Dongwan Kim et al.   CELL

A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2

(2020) Alba Grifoni et al.   Cell Host & Microbe

Proteomics of SARS-CoV-2-infected host cells reveals therapy targets

(2020) Denisa Bojkova et al.   NATURE

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing

(2020) David E. Gordon et al.   NATURE

The proximal origin of SARS-CoV-2

(2020) Kristian G. Andersen et al.   NATURE MEDICINE

RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses: a first look

(2020) Ramya Rangan et al.   RNA

Direct RNA Sequencing for the Study of Synthesis, Processing, and Degradation of Modified Transcripts

(2020) Mattia Furlan et al.   Frontiers in Genetics

Emergence of SARS-CoV-2 through recombination and strong purifying selection

(2020) Xiaojun Li et al.   Science Advances

Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding

(2020) Tyler N. Starr 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

A putative new SARS-CoV protein, 3c, encoded in an ORF overlapping ORF3a

(2020) Andrew E. Firth   JOURNAL OF GENERAL VIROLOGY

New insights into the evolutionary features of viral overlapping genes by discriminant analysis

(2020) Angelo Pavesi   VIROLOGY

Characterisation of the transcriptome and proteome of SARS-CoV-2 reveals a cell passage induced in-frame deletion of the furin-like cleavage site from the spike glycoprotein

(2020) Andrew D. Davidson et al.   Genome Medicine

Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant

(2020) Leonid Yurkovetskiy et al.   CELL

Coding potential and sequence conservation of SARS-CoV-2 and related animal viruses

(2020) Rachele Cagliani et al.   INFECTION GENETICS AND EVOLUTION

The coding capacity of SARS-CoV-2

(2020) Yaara Finkel et al.   NATURE

Spike mutation D614G alters SARS-CoV-2 fitness

(2020) Jessica A. Plante et al.   NATURE

The UCSC SARS-CoV-2 Genome Browser

(2020) Jason D. Fernandes et al.   NATURE GENETICS

ORF8 and ORF3b antibodies are accurate serological markers of early and late SARS-CoV-2 infection

(2020) Asmaa Hachim et al.   NATURE IMMUNOLOGY

Characterization of accessory genes in coronavirus genomes

(2020) Christian Jean Michel et al.   Virology Journal

SARS-CoV-2 ORF3b Is a Potent Interferon Antagonist Whose Activity Is Increased by a Naturally Occurring Elongation Variant

(2020) Yoriyuki Konno et al.   Cell Reports

Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic

(2020) Chase W Nelson et al.   eLife

Case Study: Prolonged Infectious SARS-CoV-2 Shedding from an Asymptomatic Immunocompromised Individual with Cancer

(2020) Victoria A. Avanzato et al.   CELL

Persistence and Evolution of SARS-CoV-2 in an Immunocompromised Host

(2020) Bina Choi et al.   NEW ENGLAND JOURNAL OF MEDICINE

SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity

(2020) Lizhou Zhang et al.   Nature Communications

Pervasive generation of non-canonical subgenomic RNAs by SARS-CoV-2

(2020) Jason Nomburg et al.   Genome Medicine

The SARS-CoV-2 RNA–protein interactome in infected human cells

(2020) Nora Schmidt et al.   Nature Microbiology

A gene expression atlas of embryonic neurogenesis in Drosophila reveals complex spatiotemporal regulation of lncRNAs

(2019) Alexandra L. McCorkindale et al.   DEVELOPMENT

Regulation of Viral Infection by the RNA Modification N6-methyladenosine

(2019) Graham D. Williams et al.   Annual Review of Virology

Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci

(2019) Jonathan M. Mudge et al.   GENOME RESEARCH

Nextstrain: real-time tracking of pathogen evolution

(2018) James Hadfield et al.   BIOINFORMATICS

Attenuation of replication by a 29 nucleotide deletion in SARS-coronavirus acquired during the early stages of human-to-human transmission

(2018) Doreen Muth et al.   Scientific Reports

Origin and evolution of pathogenic coronaviruses

(2018) Jie Cui et al.   NATURE REVIEWS MICROBIOLOGY

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: 2019 update

(2018) Maximilian Haeussler et al.   NUCLEIC ACIDS RESEARCH

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

Most m6A RNA Modifications in Protein-Coding Regions Are Evolutionarily Unconserved and Likely Nonfunctional

(2017) Zhen Liu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Clustal Omega for making accurate alignments of many protein sequences

(2017) Fabian Sievers et al.   PROTEIN SCIENCE

Upstream ORFs are prevalent translational repressors in vertebrates

(2016) Timothy G Johnstone et al.   EMBO JOURNAL

Genomic insights into the Ixodes scapularis tick vector of Lyme disease

(2016) Monika Gulia-Nuss et al.   Nature Communications

Discovery of an essential nucleotidylating activity associated with a newly delineated conserved domain in the RNA polymerase-containing protein of all nidoviruses

(2015) Kathleen C. Lehmann et al.   NUCLEIC ACIDS RESEARCH

FRESCo: finding regions of excess synonymous constraint in diverse viruses

(2015) Rachel S Sealfon et al.   GENOME BIOLOGY

Accessory proteins of SARS-CoV and other coronaviruses

(2014) Ding Xiang Liu et al.   ANTIVIRAL RESEARCH

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

SARS-Coronavirus Open Reading Frame-9b Suppresses Innate Immunity by Targeting Mitochondria and the MAVS/TRAF3/TRAF6 Signalosome

(2014) Chong-Shan Shi et al.   JOURNAL OF IMMUNOLOGY

Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser

(2013) B. J. Raney et al.   BIOINFORMATICS

Non-canonical translation in RNA viruses

(2012) A. E. Firth et al.   JOURNAL OF GENERAL VIROLOGY

Partitioning the Genetic Diversity of a Virus Family: Approach and Evaluation through a Case Study of Picornaviruses

(2012) C. Lauber et al.   JOURNAL OF VIROLOGY

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

(2011) M. F. Lin et al.   BIOINFORMATICS

Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes

(2011) M. F. Lin et al.   GENOME RESEARCH

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH