Robust Virus-Specific Adaptive Immunity in COVID-19 Patients with SARS-CoV-2 Δ382 Variant Infection

Early induction of functional SARS-CoV-2 specific T cells associates with rapid viral clearance and mild disease in COVID-19 patients

(2021) Anthony T. Tan et al.   Cell Reports

Emergence of SARS-CoV-2 B.1.1.7 Lineage — United States, December 29, 2020–January 12, 2021

(2021) Summer E. Galloway et al.   MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT

COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas

(2021) Xianwen Ren et al.   CELL

Highly functional virus-specific cellular immune response in asymptomatic SARS-CoV-2 infection

(2021) Nina Le Bert et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants

(2021) Rui Wang et al.   Communications Biology

Increased resistance of SARS-CoV-2 variant P.1 to antibody neutralization

(2021) Pengfei Wang et al.   Cell Host & Microbe

Asymptomatic COVID‐19: disease tolerance with efficient anti‐viral immunity against SARS‐CoV‐2

(2021) Yi‐Hao Chan et al.   EMBO Molecular Medicine

Single-cell multi-omics analysis of the immune response in COVID-19

(2021) Emily Stephenson et al.   NATURE MEDICINE

Global dynamics of SARS-CoV-2 clades and their relation to COVID-19 epidemiology

(2021) Samira M. Hamed et al.   Scientific Reports

HLA-A*11:01:01:01, HLA-C*12:02:02:01-HLA-B*52:01:02:02, Age and Sex Are Associated With Severity of Japanese COVID-19 With Respiratory Failure

(2021) Seik-Soon Khor et al.   Frontiers in Immunology

SARS-CoV-2 N protein promotes NLRP3 inflammasome activation to induce hyperinflammation

(2021) Pan Pan et al.   Nature Communications

SARS-CoV-2 B.1.617.2 (Delta) Variant COVID-19 Outbreak Associated with a Gymnastics Facility — Oklahoma, April–May 2021

(2021) Kendra Dougherty et al.   MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT

SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India

(2021) Sarah Cherian et al.   Microorganisms

Genomic variance of the 2019‐nCoV coronavirus

(2020) Carmine Ceraolo et al.   JOURNAL OF MEDICAL VIROLOGY

Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China

(2020) Chaolin Huang et al.   LANCET

Clinical Characteristics of Coronavirus Disease 2019 in China

(2020) Wei-jie Guan et al.   NEW ENGLAND JOURNAL OF MEDICINE

Heightened Innate Immune Responses in the Respiratory Tract of COVID-19 Patients

(2020) Zhuo Zhou et al.   Cell Host & Microbe

Profile of IgG and IgM antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

(2020) Jiuxin Qu et al.   CLINICAL INFECTIOUS DISEASES

Could the D614 G substitution in the SARS-CoV-2 spike (S) protein be associated with higher COVID-19 mortality?

(2020) Muthukrishnan Eaaswarkhanth et al.   INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES

Neutrophil-to-lymphocyte ratio predicts critical illness patients with 2019 coronavirus disease in the early stage

(2020) Jingyuan Liu et al.   Journal of Translational Medicine

Two linear epitopes on the SARS-CoV-2 spike protein that elicit neutralising antibodies in COVID-19 patients

(2020) Chek Meng Poh et al.   Nature Communications

Longitudinal characteristics of lymphocyte responses and cytokine profiles in the peripheral blood of SARS-CoV-2 infected patients

(2020) Jing Liu et al.   EBioMedicine

Immune cell profiling of COVID-19 patients in the recovery stage by single-cell sequencing

(2020) Wen Wen et al.   Cell Discovery

Distinct Early Serological Signatures Track with SARS-CoV-2 Survival

(2020) Caroline Atyeo et al.   IMMUNITY

A single-cell atlas of the peripheral immune response in patients with severe COVID-19

(2020) Aaron J. Wilk et al.   NATURE MEDICINE

Discovery and Genomic Characterization of a 382-Nucleotide Deletion in ORF7b and ORF8 during the Early Evolution of SARS-CoV-2

(2020) Yvonne C. F. Su et al.   mBio

Geographic and Genomic Distribution of SARS-CoV-2 Mutations

(2020) Daniele Mercatelli et al.   Frontiers in Microbiology

Effects of a major deletion in the SARS-CoV-2 genome on the severity of infection and the inflammatory response: an observational cohort study

(2020) Barnaby E Young et al.   LANCET

The ORF6, ORF8 and nucleocapsid proteins of SARS-CoV-2 inhibit type I interferon signaling pathway

(2020) Jin-Yan Li et al.   VIRUS RESEARCH

Differential Expression of Viral Transcripts From Single-Cell RNA Sequencing of Moderate and Severe COVID-19 Patients and Its Implications for Case Severity

(2020) Teng Liu et al.   Frontiers in Microbiology

Impaired natural killer cell counts and cytolytic activity in patients with severe COVID-19

(2020) Mohammed Osman et al.   Blood Advances

Infection of human Nasal Epithelial Cells with SARS-CoV-2 and a 382-nt deletion isolate lacking ORF8 reveals similar viral kinetics and host transcriptional profiles

(2020) Akshamal M. Gamage et al.   PLoS Pathogens

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

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

The Membrane Protein of Severe Acute Respiratory Syndrome Coronavirus Functions as a Novel Cytosolic Pathogen-Associated Molecular Pattern To Promote Beta Interferon Induction via a Toll-Like-Receptor-Related TRAF3-Independent Mechanism

(2016) Yi Wang et al.   mBio

Globin mRNA reduction for whole-blood transcriptome sequencing

(2016) Kaarel Krjutškov et al.   Scientific Reports

High Secretion of Interferons by Human Plasmacytoid Dendritic Cells upon Recognition of Middle East Respiratory Syndrome Coronavirus

(2015) Vivian A. Scheuplein et al.   JOURNAL OF VIROLOGY

Severe Acute Respiratory Syndrome (SARS) Coronavirus ORF8 Protein Is Acquired from SARS-Related Coronavirus from Greater Horseshoe Bats through Recombination

(2015) Susanna K. P. Lau et al.   JOURNAL OF VIROLOGY

ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap

(2015) Tauno Metsalu et al.   NUCLEIC ACIDS RESEARCH

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

The 8ab protein of SARS-CoV is a luminal ER membrane-associated protein and induces the activation of ATF6

(2009) Shu-Chiun Sung et al.   VIROLOGY

From endoplasmic-reticulum stress to the inflammatory response

(2008) Kezhong Zhang et al.   NATURE

Transcriptional profiling of Vero E6 cells over-expressing SARS-CoV S2 subunit: Insights on viral regulation of apoptosis and proliferation

(2007) Yin-Shan Yeung et al.   VIROLOGY