4.7 Review

SARS-CoV-2 Entry Related Viral and Host Genetic Variations: Implications on COVID-19 Severity, Immune Escape, and Infectivity

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

First comprehensive computational analysis of functional consequences of TMPRSS2 SNPs in susceptibility to SARS-CoV-2 among different populations

Alireza Paniri et al.

Summary: This study aimed to investigate the impact of SNPs on TMPRSS2 function and structure, and found that 21 SNPs affected the function and structure of TMPRSS2. Particularly, some SNPs may influence protein folding, post-translational modifications, and miRNA profiles.

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2021)

Article Biochemical Research Methods

Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity

Shaolei Teng et al.

Summary: This study quantified the systemic effects of missense mutations on the SARS-CoV-2 spike protein, revealing that most mutations destabilize the protein while specific mutations can enhance stability. The research also identified crucial residues affecting the RBD-ACE2 interaction, providing potential target sites for drug and vaccine development against COVID-19.

BRIEFINGS IN BIOINFORMATICS (2021)

Article Multidisciplinary Sciences

Spike mutation D614G alters SARS-CoV-2 fitness

Jessica A. Plante et al.

Summary: The D614G substitution in the SARS-CoV-2 spike protein enhances viral replication and infectivity in human lung epithelial cells, primary airway tissues, and hamsters. This variant may increase transmission in the upper respiratory tract and doesn't seem to significantly reduce vaccine efficacy. Further research on therapeutic antibodies targeting the circulating G614 virus is recommended.

NATURE (2021)

Article Microbiology

Complete Mapping of Mutations to the SARS-CoV-2 Spike Receptor-Binding Domain that Escape Antibody Recognition

Allison J. Greaney et al.

Summary: Antibodies targeting the SARS-CoV-2 spike receptor-binding domain (RBD) are key in neutralizing antibody responses, and a deep mutational scanning method was used to assess the impact of all amino-acid mutations in the RBD on antibody binding with 10 human monoclonal antibodies. The study identified the clustered escape mutations in different surfaces of the RBD that correspond to structurally defined antibody epitopes, showing that even antibodies targeting the same surface can have distinct escape mutations.

CELL HOST & MICROBE (2021)

Article Infectious Diseases

Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020

Kathy Leung et al.

Summary: Two new lineages of SARS-CoV-2 with the N501Y mutation in the receptor-binding domain of the spike protein have spread rapidly in the United Kingdom. The 501Y lineage without amino acid deletion Delta 69/Delta 70 was estimated to be 10% more transmissible than the 501N lineage, while the 501Y lineage with amino acid deletion Delta 69/Delta 70 was estimated to be 75% more transmissible than the 501N lineage.

EUROSURVEILLANCE (2021)

Article Virology

Comparative insight into the genomic landscape of SARS-CoV-2 and identification of mutations associated with the origin of infection and diversity

Divya Mishra et al.

Summary: The study analyzed 2325 SARS-CoV-2 genomes from America, Europe, and Asia, identifying numerous nucleotide substitutions, particularly nonsynonymous, in key coding regions. The nucleotide substitutions, mutation patterns, and phylogenetic analyses revealed continent-specific differences in the virus strains, highlighting the importance of ORF9 and its potential role in viral assembly and pathogenesis. Furthermore, the spatial and temporal dynamics of SARS-CoV-2 mutations across continents were noted, along with the identification of highly conserved regions and potential siRNAs for antiviral therapy development.

JOURNAL OF MEDICAL VIROLOGY (2021)

Article Multidisciplinary Sciences

Loss of furin cleavage site attenuates SARS-CoV-2 pathogenesis

Bryan A. Johnson et al.

Summary: The genetic mutation in SARS-CoV-2 resulted in better fitness in some cells but lower replication capacity in human respiratory cell lines. Despite reducing disease symptoms, the Delta PRRA mutant provided protection against rechallenge with the wildtype SARS-CoV-2.

NATURE (2021)

Article Biochemistry & Molecular Biology

Human SARS CoV-2 spike protein mutations

Lalitha Guruprasad

Summary: Analyzing spike protein sequences from different regions globally, this study found that out of 10333 sequences, 8155 proteins had mutations. A total of 9654 mutations were observed, with 44 mutations in the RBD region.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2021)

Article Multidisciplinary Sciences

Prospective mapping of viral mutations that escape antibodies used to treat COVID-19

Tyler N. Starr et al.

Summary: Research has found that mutations in the receptor binding domain (RBD) of SARS-CoV-2 may potentially escape the action of the REGN-COV2 cocktail, providing important information for interpreting mutations observed during viral surveillance.

SCIENCE (2021)

Article Virology

Population-Specific ACE2 Single-Nucleotide Polymorphisms Have Limited Impact on SARS-CoV-2 Infectivity In Vitro

Mei Hashizume et al.

Summary: The study analyzed the impact of 8 SNPs found in specific populations on SARS-CoV-2 infection, revealing that except for one SNP causing reduced ACE2 expression, the other SNPs did not notably alter the interaction between ACE2 and the SARS-CoV-2 spike protein or the efficiency of viral cell entry.

VIRUSES-BASEL (2021)

Article Genetics & Heredity

Impact of Genetic Variability in ACE2 Expression on the Evolutionary Dynamics of SARS-CoV-2 Spike D614G Mutation

Szu-Wei Huang et al.

Summary: The D614G mutation in the SARS-CoV-2 spike protein has been shown to increase the virus's ability to bind to ACE2 receptors, leading to higher transmission efficiency. This mutation became prevalent in Europe and North America but not in China, possibly due to variations in human population genetics. The higher ACE2 expression in Asian populations compared to other populations suggests that genetic diversity plays a role in the adaptive evolution of SARS-CoV-2, impacting public health interventions during the pandemic.

GENES (2021)

Article Biochemistry & Molecular Biology

Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity

Emma C. Thomson et al.

Summary: SARS-CoV-2 virus can mutate and evade immunity, with mutations like N439K conferring resistance against neutralizing monoclonal antibodies and enhancing binding affinity to hACE2 receptor. Despite similar in vitro replication fitness and clinical outcomes compared to wild type, N439K mutation highlights the importance of ongoing molecular surveillance for guiding vaccine and therapeutic development and usage.
Article Microbiology

Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization

Zhuoming Liu et al.

Summary: The study found that antibodies targeting the SARS-CoV-2 spike protein have escape mutations, different monoclonal antibodies have unique resistance profiles, some mutants are resistant to multiple antibodies while some variants can escape neutralization by convalescent sera. Comparing antibody-mediated mutations with circulating SARS-CoV-2 sequences revealed substitutions that may weaken neutralizing immune responses in some individuals, warranting further investigation.

CELL HOST & MICROBE (2021)

Article Microbiology

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

Allison J. Greaney et al.

Summary: The evolution of SARS-CoV-2 may impact the recognition of the virus by human antibody-mediated immunity, with mutations affecting antibody binding varying significantly among individuals and within the same individual over time. Despite this variability, mutations that greatly reduce antibody binding usually occur at specific sites in the RBD, with E484 being the most crucial. These findings can inform surveillance efforts for SARS-CoV-2 evolution in the future.

CELL HOST & MICROBE (2021)

Article Biochemistry & Molecular Biology

In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2-Spike RBD Interface

Bruno O. Villoutreix et al.

Summary: The SARS-CoV-2 virus exploits ACE2 as a receptor for cell invasion, with certain mutations potentially enhancing its transmission capabilities and pathogenicity through effects on ACE2 binding. The UK strain may exhibit higher affinity for ACE2, while the transmission level of the South African strain could be influenced by the N501Y substitution.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

Letter Medicine, General & Internal

Emergence of a Novel SARS-CoV-2 Variant in Southern California

Wenjuan Zhang et al.

Summary: The research focused on sequencing and phylogenetic analyses of SARS-CoV-2 isolates from symptomatic patients at Cedar-Sinai Medical Center in November-December 2020, providing insights into a surge in cases and hospitalizations during that period.

JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION (2021)

Letter Infectious Diseases

Introduction of Brazilian SARS-CoV-2 484K.V2 related variants into the UK

Oliver T. R. Toovey et al.

JOURNAL OF INFECTION (2021)

Editorial Material Medicine, General & Internal

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

Ester C. Sabino et al.

LANCET (2021)

Article Multidisciplinary Sciences

Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7

Pengfei Wang et al.

Summary: The COVID-19 pandemic has had global repercussions, with promising vaccines and monoclonal antibody therapies. However, newly detected variants of SARS-CoV-2 present challenges to these treatment options.

NATURE (2021)

Article Multidisciplinary Sciences

mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants

Zijun Wang et al.

Summary: Volunteers who received the Moderna or Pfizer-BioNTech vaccine showed high levels of antibodies and memory B cell responses against SARS-CoV-2, with activity similar to individuals who had recovered from natural infection. However, their efficacy against specific SARS-CoV-2 variants was reduced, indicating a potential need for periodic updates to mRNA vaccines to maintain clinical efficacy.

NATURE (2021)

Article Multidisciplinary Sciences

SARS-CoV-2 evolution during treatment of chronic infection

Steven A. Kemp et al.

Summary: Chronic infection with SARS-CoV-2 can lead to viral evolution and increased resistance to neutralizing antibodies in immunosuppressed individuals treated with convalescent plasma. During convalescent plasma therapy, there were significant shifts in the viral population structure and sensitivity, suggesting strong selection pressure on the virus during treatment.

NATURE (2021)

Article Biochemistry & Molecular Biology

Sixteen novel lineages of SARS-CoV-2 in South Africa

Houriiyah Tegally et al.

Summary: The study identified 16 new lineages of SARS-CoV-2 in South Africa between March and August 2020, with unique mutations not found elsewhere. Three lineages (B.1.1.54, B.1.1.56, and C.1) dominated during the country's first wave, accounting for approximately 42% of all infections. The C.1 lineage, with 16 nucleotide mutations including the D614G spike protein change, became the most geographically widespread by August 2020. Genomic surveillance played a crucial role in identifying the 501Y.V2 variant in South Africa in December 2020.

NATURE MEDICINE (2021)

Article Multidisciplinary Sciences

Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape

Kevin R. McCarthy et al.

Summary: The translation above discusses zoonotic pandemics caused by animal viruses spilling over into highly susceptible human populations, specifically focusing on the evolution of coronaviruses in human hosts and the impact of recurrent deletions in the spike glycoprotein on antibody epitopes. These studies help understand the antigenic evolution and adaptive evolution of SARS-CoV-2.

SCIENCE (2021)

Article Biochemistry & Molecular Biology

Site-specific characterization of SARS-CoV-2 spike glycoprotein receptor-binding domain

Aristotelis Antonopoulos et al.

Summary: This study analyzed the glycosylation structure of the novel coronavirus SARS-CoV-2 and identified complex-type N-glycans as well as a single site of O-glycosylation within the receptor-binding domain.

GLYCOBIOLOGY (2021)

Review Biochemistry & Molecular Biology

Novel coronavirus disease (COVID-19) pandemic: A recent mini review

Muhammad Fayyaz ur Rehman et al.

Summary: COVID-19, caused by a novel coronavirus, is a global pandemic that is ongoing. Despite the repurposing of several drugs, no specific antiviral medication has been approved for treatment yet.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2021)

Article Multidisciplinary Sciences

A pneumonia outbreak associated with a new coronavirus of probable bat origin

Peng Zhou et al.

NATURE (2020)

Article Multidisciplinary Sciences

Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation

Daniel Wrapp et al.

SCIENCE (2020)

Article Biochemistry & Molecular Biology

Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2

Qihui Wang et al.

Article Medicine, General & Internal

SARS-CoV-2 viral spike G614 mutation exhibits higher case fatality rate

Manuel Becerra-Flores et al.

INTERNATIONAL JOURNAL OF CLINICAL PRACTICE (2020)

Article Multidisciplinary Sciences

Cell entry mechanisms of SARS-CoV-2

Jian Shang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Editorial Material Virology

DC/L-SIGNs of hope in the COVID-19 pandemic

Adam Brufsky et al.

JOURNAL OF MEDICAL VIROLOGY (2020)

Editorial Material Oncology

TMPRSS2 and COVID-19: serendipity or Opportunity for Intervention?

Konrad H. Stopsack et al.

CANCER DISCOVERY (2020)

Article Environmental Sciences

The Expression and Polymorphism of Entry Machinery for COVID-19 in Human: Juxtaposing Population Groups, Gender, and Different Tissues

Behrooz Darbani

INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH (2020)

Article Medicine, General & Internal

Clinical impact of COVID-19 on patients with cancer (CCC19): a cohort study

Nicole M. Kuderer et al.

LANCET (2020)

Article Biochemistry & Molecular Biology

A Multibasic Cleavage Site in the Spike Protein of SARS-CoV-2 Is Essential for Infection of Human Lung Cells

Markus Hoffmann et al.

MOLECULAR CELL (2020)

Article Multidisciplinary Sciences

Structural basis of receptor recognition by SARS-CoV-2

Jian Shang et al.

NATURE (2020)

Article Biochemistry & Molecular Biology

Genetic variants that influence SARS-CoV-2 receptor TMPRSS2 expression among population cohorts from multiple continents

Lalu Muhammad Irham et al.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2020)

Article Biochemistry & Molecular Biology

Interaction of the spike protein RBD from SARS-CoV-2 with ACE2: Similarity with SARS-CoV, hot-spot analysis and effect of the receptor polymorphism

Houcemeddine Othman et al.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2020)

Article Genetics & Heredity

Genetic variability in the expression of the SARS-CoV-2 host cell entry factors across populations

Lourdes Ortiz-Fernandez et al.

GENES AND IMMUNITY (2020)

Article Biochemistry & Molecular Biology

The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity

Qianqian Li et al.

Article Biochemistry & Molecular Biology

Mutations Strengthened SARS-CoV-2 Infectivity

Jiahui Chen et al.

JOURNAL OF MOLECULAR BIOLOGY (2020)

Article Biochemistry & Molecular Biology

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

Leonid Yurkovetskiy et al.

Article Medicine, General & Internal

Genomewide Association Study of Severe Covid-19 with Respiratory Failure

David Ellinghaus et al.

NEW ENGLAND JOURNAL OF MEDICINE (2020)

Article Multidisciplinary Sciences

Adaptation of SARS-CoV-2 in BALB/c mice for testing vaccine efficacy

Hongjing Gu et al.

SCIENCE (2020)

Article Multidisciplinary Sciences

The major genetic risk factor for severe COVID-19 is inherited from Neanderthals

Hugo Zeberg et al.

NATURE (2020)

Article Multidisciplinary Sciences

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

Lizhou Zhang et al.

NATURE COMMUNICATIONS (2020)

Article Multidisciplinary Sciences

SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo

Yixuan J. Hou et al.

SCIENCE (2020)

Article Immunology

High Contagiousness and Rapid Spread of Severe Acute Respiratory Syndrome Coronavirus 2

Steven Sanche et al.

EMERGING INFECTIOUS DISEASES (2020)

Article Public, Environmental & Occupational Health

Genome-Wide Identification and Characterization of Point Mutations in the SARS-CoV-2 Genome

Jun-Sub Kim et al.

OSONG PUBLIC HEALTH AND RESEARCH PERSPECTIVES (2020)

Review Virology

Coronavirus envelope protein: current knowledge

Dewald Schoeman et al.

VIROLOGY JOURNAL (2019)

Review Cardiac & Cardiovascular Systems

The renin-angiotensin system: going beyond the classical paradigms

Robson Augusto Souza Santos et al.

AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY (2019)

Review Pharmacology & Pharmacy

Accessory proteins of SARS-CoV and other coronaviruses

Ding Xiang Liu et al.

ANTIVIRAL RESEARCH (2014)

Review Immunology

The physiological role of DC-SIGN: A tale of mice and men

Juan J. Garcia-Vallejo et al.

TRENDS IN IMMUNOLOGY (2013)

Review Genetics & Heredity

Rules of Engagement: Molecular Insights from Host-Virus Arms Races

Matthew D. Daugherty et al.

ANNUAL REVIEW OF GENETICS, VOL 46 (2012)

Article Medicine, General & Internal

Isolation of a Novel Coronavirus from a Man with Pneumonia in Saudi Arabia

Ali Moh Zaki et al.

NEW ENGLAND JOURNAL OF MEDICINE (2012)

Article Physiology

Ectodomain shedding of angiotensin converting enzyme 2 in human airway epithelia

Hong Peng Jia et al.

AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY (2009)

Review Genetics & Heredity

DC-SIGN and L-SIGN: the SIGNs for infection

Ui-Soon Khoo et al.

JOURNAL OF MOLECULAR MEDICINE-JMM (2008)

Article Medical Laboratory Technology

Correlation of angiotensin-converting enzyme 2 gene polymorphisms with stage 2 hypertension in Han Chinese

Wenquan Niu et al.

TRANSLATIONAL RESEARCH (2007)

Article Medicine, General & Internal

Promoter variation in the DC-SIGN-encoding gene CD209 is associated with tuberculosis

LB Barreiro et al.

PLOS MEDICINE (2006)

Article Genetics & Heredity

Homozygous L-SIGN (CLEC4M) plays a protective role in SARS coronavirus infection

VSF Chan et al.

NATURE GENETICS (2006)

Article Genetics & Heredity

A variant in the CD209 promoter is associated with severity of dengue disease

A Sakuntabhai et al.

NATURE GENETICS (2005)

Review Medicine, General & Internal

The renin-angiotensin-aldosterone system and the kidney: Effects on kidney disease

UC Brewster et al.

AMERICAN JOURNAL OF MEDICINE (2004)

Article Biochemistry & Molecular Biology

C-type lectins L-SIGN and DC-SIGN capture and transmit infectious hepatitis C virus pseudotype particles

PY Lozach et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2004)

Article Virology

The nucleoprotein is required for efficient coronavirus genome replication

F Almazán et al.

JOURNAL OF VIROLOGY (2004)

Article Biochemistry & Molecular Biology

Exploring the structure and function of zinc metallopeptidases: old enzymes and new discoveries

AJ Turner

BIOCHEMICAL SOCIETY TRANSACTIONS (2003)

Article Medicine, General & Internal

Identification of a novel coronavirus in patients with severe acute respiratory syndrome

C Drosten et al.

NEW ENGLAND JOURNAL OF MEDICINE (2003)

Review Medicine, General & Internal

Aspects of gene polymorphisms in cardiovascular disease: the renin-angiotensin system

M Carluccio et al.

EUROPEAN JOURNAL OF CLINICAL INVESTIGATION (2001)