☆ 4.8 Review

A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations

FRONTIERS IN IMMUNOLOGY (2022)

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Article Oncology

SARS-CoV-2 Neutralization in Convalescent Plasma and Commercial Lots of Plasma-Derived Immunoglobulin

Andreas Volk et al.

Summary: Patients with immune deficiencies often receive antibodies from healthy donors as a first line of defense against infections. Research shows that plasma-derived immunoglobulin lots produced between December 2020 and June 2021 have increasing neutralizing activity against SARS-CoV-2 over time.

BIODRUGS (2022)

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Article Pharmacology & Pharmacy

Emerging mutations in the SARS-CoV-2 variants and their role in antibody escape to small molecule-based therapeutic resistance

Chiranjib Chakraborty et al.

Summary: This article discusses the clinical trials and mutations during the COVID-19 pandemic, identifying potential therapeutic candidates and explaining the impact of mutations in S-glycoprotein and RdRp on therapeutic drugs and antibodies.

CURRENT OPINION IN PHARMACOLOGY (2022)

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Editorial Material Medicine, General & Internal

Winter of Omicron-The Evolving COVID-19 Pandemic

Carlos del Rio et al.

JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION (2022)

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Article Virology

Omicron: Call for updated vaccines

Xingguang Li

Summary: The Omicron SARS-CoV-2 variant may have originated from a chronically infected patient vaccinated with mRNA or non-mRNA vaccines, highlighting the need for more effective one-dose vaccines to protect against new variants in the global fight against the pandemic.

JOURNAL OF MEDICAL VIROLOGY (2022)

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Article Multidisciplinary Sciences

Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies

Yunlong Cao et al.

Summary: The Omicron variant of SARS-CoV-2 contains 15 mutations in the receptor-binding domain, leading to evasion of over 85% of tested neutralizing antibodies. Different epitope groups of neutralizing antibodies are affected to varying degrees by single mutations of Omicron. Antibodies targeting the conserved region of sarbecovirus remain most effective against Omicron.

NATURE (2022)

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Article Hematology

Early high-titer convalescent plasma therapy in patients with moderate and severe COVID-19

Alieh Fazeli et al.

Summary: This study assessed the outcome of CCP therapy on patients with moderate and severe COVID-19 and investigated the association with variables such as antibody titer and transfusion time. The findings suggest that patients who received CCP with high antibody titers in the early stages of the disease had a lower mortality rate.

TRANSFUSION AND APHERESIS SCIENCE (2022)

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News Item Critical Care Medicine

Omicron variant and booster COVID-19 vaccines

Talha Khan Burki

LANCET RESPIRATORY MEDICINE (2022)

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Article Microbiology

Omicron SARS-CoV-2 Variant Spike Protein Shows an Increased Affinity to the Human ACE2 Receptor: An In Silico Analysis

Joseph Thomas Ortega et al.

Summary: This study evaluated the changes in the viral spike of SARS-CoV-2 Omicron variant and found an increased interaction with the human ACE2 receptor. This contributes to a better understanding of the impact of Omicron variant on virus pathogenicity.

PATHOGENS (2022)

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Article Immunology

Emergence of the E484K Mutation in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Lineage B.1.1.345 in Upstate New York

Emil Lesho et al.

Summary: A SARS-CoV-2 B.1.1.345 variant carrying the E484K mutation was detected in 4 patients with no apparent epidemiological association from a hospital network in upstate New York. An additional 11 B.1.1.345 variants from this region were identified between December 2020 and February 2021.

CLINICAL INFECTIOUS DISEASES (2022)

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Letter Infectious Diseases

De novo emergence of the mutation E484K in a SARS-CoV-2 B.1.1.7 lineage variant

Mikel Urrutikoetxea-Gutierrez et al.

ENFERMEDADES INFECCIOSAS Y MICROBIOLOGIA CLINICA (2022)

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Review Virology

Present variants of concern and variants of interest of severe acute respiratory syndrome coronavirus 2: Their significant mutations in S-glycoprotein, infectivity, re-infectivity, immune escape and vaccines activity

Chiranjib Chakraborty et al.

Summary: The study discusses the emergence of alarming SARS-CoV-2 variants globally, highlighting key properties, mutations, and clinical characteristics of both variant of concern (VOC) and variant of interest (VOI) variants. The comprehensive review offers updated information on these newly appearing variants to aid researchers in formulating strategies to control the COVID-19 pandemic.

REVIEWS IN MEDICAL VIROLOGY (2022)

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Article Geriatrics & Gerontology

A Paradigm Shift in the Combination Changes of SARS-CoV-2 Variants and Increased Spread of Delta Variant (B.1.617.2) across the World

Chiranjib Chakraborty et al.

Summary: This study developed a model to analyze the frequency and genetic characteristics of Delta variants across 28 countries. The analysis showed that Delta variants had the highest prevalence in Europe and the lowest prevalence in Australia. The study concluded that the high global prevalence of Delta variants can be attributed to their high infectivity rate.

AGING AND DISEASE (2022)

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Article Biochemistry & Molecular Biology

Recognition of the SARS-CoV-2 receptor binding domain by neutralizing antibodies

Meng Yuan et al.

Summary: Since the outbreak of COVID-19 pandemic, researchers from diverse biomedical and biological disciplines have collaborated to study the novel pandemic virus SARS-CoV-2. The focus has been on the antibody response to SARS-CoV-2, crucial for vaccine and therapeutic development. Most of the neutralizing antibodies for SARS-CoV-2 target the spike protein receptor binding domain (RBD).

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2021)

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Editorial Material Medicine, General & Internal

SARS-CoV-2 Brazil variants in Latin America: More serious research urgently needed on public health and vaccine protection

Chiranjib Chakraborty et al.

Summary: COVID-19 has not only caused a pandemic, but also created socio-economic chaos in Latin America. New variants of SARS-CoV-2, including the significant P.1 lineage with 17 mutations, are currently circulating in the region. Further research is needed to understand the virulence of these variants and their impact on vaccine efficacy.

ANNALS OF MEDICINE AND SURGERY (2021)

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Review Biotechnology & Applied Microbiology

D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity

Manojit Bhattacharya et al.

Summary: The COVID-19 pandemic has resulted in the emergence of numerous global variants of SARS-CoV-2, with the D614G mutation playing a key role in enhancing infectivity and immune evasion capabilities in these variants.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2021)

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Editorial Material Medicine, General & Internal

Genetic Variants of SARS-CoV-2-What Do They Mean?

Adam S. Lauring et al.

JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION (2021)

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News Item Multidisciplinary Sciences

COULD NEW COVID VARIANTS UNDERMINE VACCINES? LABS SCRAMBLE TO FIND OUT

Ewen Callaway

NATURE (2021)

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Article Medicine, General & Internal

A Randomized Trial of Convalescent Plasma in Covid-19 Severe Pneumonia

V. A. Simonovich et al.

Summary: There were no significant differences observed in clinical status or overall mortality between patients treated with convalescent plasma and those who received placebo in the treatment of severe Covid-19 pneumonia. The study results indicate that both groups had similar clinical outcomes and mortality rates after 30 days.

NEW ENGLAND JOURNAL OF MEDICINE (2021)

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Article Multidisciplinary Sciences

Learning the language of viral evolution and escape

Brian Hie et al.

Summary: Researchers used machine learning algorithms to model viral escape and identified patterns in escape mutations, showing that language models can accurately predict viral escape patterns similar to how words can change the meaning of a sentence. This study represents a promising conceptual bridge between natural language and viral evolution.

SCIENCE (2021)

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Article Multidisciplinary Sciences

Structure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escape

Paul-Albert Koenig et al.

Summary: In this study, new neutralizing nanobodies targeting the SARS-CoV-2 spike protein were developed, showing enhanced neutralizing activity through engineering technology and successfully suppressing the emergence of escape mutants. The findings suggest that nanobodies can neutralize through receptor binding competition and also render virions noninfectious.

SCIENCE (2021)

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Article Infectious Diseases

A discernable increase in the severe acute respiratory syndrome coronavirus 2 R.1 lineage carrying an E484K spike protein mutation in Japan

Tsuyoshi Sekizuka et al.

Summary: Three waves of COVID-19 in Japan have been characterized by distinct PANGO lineages, with the E484K mutation in the spike protein of the R.1 lineage showing up to 40% predominance. It is essential to pay attention to potential variants to prevent the emergence of mutants, highlighting the importance of real-time genome surveillance in containing COVID-19 clusters.

INFECTION GENETICS AND EVOLUTION (2021)

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Article Virology

Intranasal Infection of Ferrets with SARS-CoV-2 as a Model for Asymptomatic Human Infection

Helen E. Everett et al.

Summary: The experiment showed that ferrets inoculated with SARS-CoV-2 exhibited subclinical infection from 2 to 21 days post-inoculation, with viral RNA peaking between days 4 to 6. Genomic analysis found a Y453F nucleotide substitution in samples from three animals. Viral RNA was also detected in environmental samples, particularly in ferret fur swabs.

VIRUSES-BASEL (2021)

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Article Multidisciplinary Sciences

Molecular determinants and mechanism for antibody cocktail preventing SARS-CoV-2 escape

Zhiqiang Ku et al.

Summary: Antibody cocktails are a promising approach to prevent SARS-CoV-2 escape, with a combination of antibodies CoV2-06 and CoV2-14 identified as effective in preventing viral escape and providing protection in mice, offering new insights for treating COVID-19.

NATURE COMMUNICATIONS (2021)

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Review Pharmacology & Pharmacy

SARS-CoV-2 protein drug targets landscape: a potential pharmacological insight view for the new drug development

Chiranjib Chakraborty et al.

Summary: This article explores the protein drug targets and drug discovery approaches for SARS-CoV-2, focusing on drug repurposing studies, design of viral entry inhibitors, and development of different enzymes. By conducting comprehensive literature searches, the structural landscape of viral and host proteins is illustrated, providing insights for understanding drug targets and structure-based drug discovery for SARS-CoV-2.

EXPERT REVIEW OF CLINICAL PHARMACOLOGY (2021)

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Review Biotechnology & Applied Microbiology

Perspective on therapeutic and diagnostic potential of camel nanobodies for coronavirus disease-19 (COVID-19)

Salma Bessalah et al.

Summary: Nanobodies, as a revolutionary therapy for COVID-19, have the potential to guide drug discovery efforts. Their small size and strong antigen affinity make them effective in treating and preventing SARS-CoV-2 infection, controlling disease transmission and development.

3 BIOTECH (2021)

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Article Biochemistry & Molecular Biology

SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape

Qianqian Li et al.

Summary: The 501Y.V2 variants of SARS-CoV-2 with multiple mutations are rapidly spreading from South Africa to other countries, showing reduced susceptibility to neutralizing antibodies and potential compromise of monoclonal antibodies and vaccines. Enhanced infectivity in murine ACE2-overexpressing cells suggests the possibility of transmission to mice.

CELL (2021)

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Article Biochemistry & Molecular Biology

Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera

Piyada Supasa et al.

Summary: Research on the UK-dominant variant B.1.1.7 shows that it is harder to neutralize than the parental virus, but widespread escape from antibodies or monoclonal antibodies has not been observed yet.

CELL (2021)

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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.

CELL (2021)

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Article Biochemistry & Molecular Biology

Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity

Wilfredo F. Garcia-Beltran et al.

Summary: New variants of SARS-CoV-2 show high resistance to vaccine neutralization, with some able to escape vaccine responses with just a few mutations, highlighting the importance of developing broadly protective measures against variants.

CELL (2021)

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Article Biochemistry & Molecular Biology

Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera

Daming Zhou et al.

Summary: The race to develop vaccines against SARS-CoV-2 variants, such as B.1.1.7, B.1.351, and P.1, is ongoing as these variants have mutations in the spike protein, potentially leading to immune escape. A structure-function analysis of B.1.351 revealed tighter ACE2 binding and widespread evasion from monoclonal antibody neutralization, particularly driven by the E484K mutation.

CELL (2021)

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Article Microbiology

Genomic monitoring of SARS-CoV-2 uncovers an Nsp1 deletion variant that modulates type I interferon response

Jing-wen Lin et al.

Summary: This study utilized an integrative approach to analyze mutations of the SARS-CoV-2 virus, identifying 35 recurrent variants of clinical importance, with one variant associated with severe clinical phenotypes. The findings suggest that mutations in Nsp1 may have implications for molecular diagnostics and drug design.

CELL HOST & MICROBE (2021)

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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)

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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)

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Article Biochemical Research Methods

A one-step real-time RT-PCR assay for simultaneous typing of SARS-CoV-2 mutations associated with the E484K and N501Y spike protein amino-acid substitutions

Serafeim C. Chaintoutis et al.

Summary: A one-step real-time RT-PCR assay has been developed to simultaneously detect SARS-CoV-2 mutations N501Y and E484K, showing high sensitivity and accuracy, serving as an effective pre-screening tool for rapid identification of emerging variants of the virus.

JOURNAL OF VIROLOGICAL METHODS (2021)

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Article Biochemistry & Molecular Biology

SARS-Cov-2 ORF3a: Mutability and function

Martina Bianchi et al.

Summary: This study analyzed the changes of SARS-CoV-2 ORF3a protein during the COVID-19 pandemic, identifying seventeen variants and determining their locations in the protein structure. The findings provide insights into virus biology and may guide the development of new therapeutic strategies.

INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES (2021)

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News Item Multidisciplinary Sciences

HEAVILY MUTATED OMICRON VARIANT PUTS SCIENTISTS ON ALERT

Ewen Callaway

NATURE (2021)

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Review Virology

Role of Toll-like receptors in the pathogenesis of COVID-19

Shaghayegh Khanmohammadi et al.

Summary: COVID-19 caused by SARS-CoV-2 has led to a pandemic. TLRs play a crucial role in activating the immune system in response to the virus, and could potentially be a target for controlling the infection. Understanding the mechanisms of TLR in COVID-19 may help in developing vaccines and treatments.

JOURNAL OF MEDICAL VIROLOGY (2021)

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Article Virology

SARS-CoV-2 Triggers an MDA-5-Dependent Interferon Response Which Is Unable To Control Replication in Lung Epithelial Cells

Antoine Rebendenne et al.

Summary: The study found that in lung cells, despite producing high levels of IFNs in response to SARS-CoV-2 infection, the IFN response was unable to control viral replication, contrary to what was observed in intestinal epithelial cells. The ambiguous interplay between viral replication and the timing of IFN responses needs to be further understood for guiding future therapeutic interventions.

JOURNAL OF VIROLOGY (2021)

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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)

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Article Biochemistry & Molecular Biology

Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies

Rita E. Chen et al.

Summary: The study analyzed antibody neutralization activity against a panel of authentic isolates and chimeric SARS-CoV-2 variants, showing significantly reduced neutralizing activity against the B.1.351 variant first identified in South Africa. Antibodies targeting the receptor-binding domain and N-terminal domain, monoclonal antibodies, convalescent sera, and mRNA vaccine-induced immune sera exhibited decreased inhibitory activity against viruses with an E484K spike mutation, suggesting a need for updated monoclonal antibodies or vaccine adjustments to prevent loss of protection against emerging variants.

NATURE MEDICINE (2021)

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Article Multidisciplinary Sciences

Omicron sparks a vaccine strategy debate

Jon Cohen

SCIENCE (2021)

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Article Multidisciplinary Sciences

Neutralization of SARS-CoV-2 lineage B.1.1.7 pseudovirus by BNT162b2 vaccine-elicited human sera

Alexander Muik et al.

Summary: A new SARS-CoV-2 lineage B.1.1.7 has emerged in the UK, which is more transmissible and faster spreading than other strains. However, a study found that the BNT162b2 vaccine offers largely preserved protection against the B.1.1.7 lineage, despite some reduced neutralizing titers.

SCIENCE (2021)

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Review Immunology

Dual Nature of Type I Interferons in SARS-CoV-2-Induced Inflammation

Cecile King et al.

Summary: Inhibition of IFN-I by SARS-CoV-2 can worsen the disease and affect the immune response, but therapeutic boosting of IFN-I has a narrow time window for efficacy. Further research is needed to explore therapeutic approaches and vaccine design to counteract this limitation.

TRENDS IN IMMUNOLOGY (2021)

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Article Multidisciplinary Sciences

SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity

Seiya Ozono et al.

Summary: The naturally occurring mutations of SARS-CoV-2 spike protein can affect cell entry, with the D614G mutation resulting in increased cell entry and maintaining susceptibility to neutralization by antisera against prototypic viruses. Further global surveillance is needed to understand the transmissibility of SARS-CoV-2 among humans.

NATURE COMMUNICATIONS (2021)

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Review Materials Science, Multidisciplinary

Molecular recognition in the infection, replication, and transmission of COVID-19-causing SARS-CoV-2: an emerging interface of infectious disease, biological chemistry, and nanoscience

Prem Kumar et al.

Summary: The article reviews the mechanisms of infection, immune response, replication, and transmission of SARS-CoV-2, emphasizing the importance of the interface between chemistry, nanoscience, cell biology, immunology, and virology in addressing the challenges of COVID-19.

NPG ASIA MATERIALS (2021)

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Article Biology

The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types

Zharko Daniloski et al.

Summary: A novel variant of SARS-CoV-2 virus with mutation D614G has been found to be more effective at transducing human cells and showing increased infectivity in human cells compared to the wild-type variant.

ELIFE (2021)

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Letter Public, Environmental & Occupational Health

Immune evasion means we need a new COVID-19 social contract

Laetitia Atlani-Duault et al.

LANCET PUBLIC HEALTH (2021)

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Article Microbiology

SARS-CoV-2 Nonstructural Proteins 1 and 13 Suppress Caspase-1 and the NLRP3 Inflammasome Activation

Na-Eun Kim et al.

Summary: Viral infection-induced activation of inflammasome complexes has both positive and negative effects on the host, with coronaviruses encoding viroporins that are associated with inflammasome activation and disease severity. To establish primary replication, these viruses must evade inflammasome-mediated antiviral immune responses. The SARS-CoV-2 NSP1 and NSP13 have been identified as potent antagonists of the NLRP3 inflammasome, inhibiting caspase-1-mediated IL-1 beta activation.

MICROORGANISMS (2021)

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Article Biology

IFN signaling and neutrophil degranulation transcriptional signatures are induced during SARS-CoV-2 infection

Bruce A. Rosa et al.

Summary: The study discovered that genes associated with Interferon signaling, neutrophil degranulation, and innate immune pathways are induced in the lungs of macaques in response to SARS-CoV-2 infection, while genes related to collagen formation and regulation are reduced. Age is identified as a significant risk factor for poor prognosis and increased mortality in COVID-19.

COMMUNICATIONS BIOLOGY (2021)

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Article Biology

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

Rui Wang et al.

Summary: The study reveals the presence of four sub-strains and eleven top mutations in the United States, with five and eight concurrent mutations prevailing in two groups, while another group with three concurrent mutations gradually fading out. Additionally, it is found that female immune systems are more active than those of males in responding to SARS-CoV-2 infections.

COMMUNICATIONS BIOLOGY (2021)

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Article Microbiology

Overcoming Culture Restriction for SARS-CoV-2 in Human Cells Facilitates the Screening of Compounds Inhibiting Viral Replication

Santseharay Ramirez et al.

Summary: Efforts to combat the COVID-19 pandemic include repurposing existing antiviral drugs and screening their efficacy in different cell lines. In this study, serial passages of SARS-CoV-2 in human liver and lung cancer cells led to the selection of a more infective variant with spike protein mutations. The adapted virus showed less dependence on ACE2 and increased susceptibility to interferon, demonstrating the potential for antiviral drug screening efficacy across different cell lines.

ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2021)

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Article Biochemistry & Molecular Biology

SARS-CoV-2 variants B.1.351 and P.1 escape from neutralizing antibodies

Markus Hoffmann et al.

Summary: The emerging SARS-CoV-2 variants may exhibit resistance to existing neutralizing antibodies and treatments, which could have significant implications for pandemic containment efforts.

CELL (2021)

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Article Biochemistry & Molecular Biology

Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant

Xianding Deng et al.

Summary: A new SARS-CoV-2 variant named B.1.427/B.1.429 was identified in California, with increased transmissibility and carrying three mutations in spike protein, including L452R substitution. The variant emerged in May 2020 and became predominant in sequenced cases from September 2020 to January 2021. In vivo viral shedding was increased and antibody neutralization decreased, calling for further investigation.

CELL (2021)

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Letter Cell Biology

SARS-CoV-2 spike protein interacts with and activates TLR41

Yingchi Zhao et al.

CELL RESEARCH (2021)

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Letter Immunology

Bamlanivimab Treatment Leads to Rapid Selection of Immune Escape Variant Carrying the E484K Mutation in a B.1.1.7-Infected and Immunosuppressed Patient

Benedikt Lohr et al.

CLINICAL INFECTIOUS DISEASES (2021)

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Editorial Material Infectious Diseases

Severe acute respiratory syndrome coronavirus 2 escape mutants and protective immunity from natural infections or immunizations

Antonino Di Caro et al.

CLINICAL MICROBIOLOGY AND INFECTION (2021)

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Article Infectious Diseases

Novel SARS-CoV-2 variants: the pandemics within the pandemic

Erik Boehm et al.

Summary: Many new variants of SARS-CoV-2 have been identified as variants of concern/interest due to increased transmissibility, severity, immune escape, and reduced vaccine efficacy. These variants often share similar mutations, such as N501Y and E484K, which lead to partial immune escape, decreased vaccine efficacy, and potentially increased severity.

CLINICAL MICROBIOLOGY AND INFECTION (2021)

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Review Pharmacology & Pharmacy

The Drug Repurposing for COVID-19 Clinical Trials Provide Very Effective Therapeutic Combinations: Lessons Learned From Major Clinical Studies

Chiranjib Chakraborty et al.

Summary: The rapid spread of SARS-CoV-2 globally has highlighted the need for effective treatment options. Drug repurposing of existing medications has become a key strategy in managing COVID-19 patients. Clinical trials conducted across multiple countries have shown promising results in antiviral and immunotherapeutic treatments, indicating the importance of further research in this area.

FRONTIERS IN PHARMACOLOGY (2021)

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Editorial Material Medicine, Research & Experimental

D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin?

Chiranjib Chakraborty et al.

MOLECULAR THERAPY-NUCLEIC ACIDS (2021)

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Review Immunology

Effects of SARS-CoV-2 variants on vaccine efficacy and response strategies

Lianlian Bian et al.

Summary: The global spread of the SARS-CoV-2 pandemic has led to the emergence of several variants, posing challenges to vaccine efficacy. However, some vaccines have shown advantages in providing protection against certain variants. Response strategies have been proposed to address the challenges posed by emerging variants, including accelerating the rollout of current vaccines, enhancing vaccine immunogenicity, and developing next-generation vaccines targeting the variants.

EXPERT REVIEW OF VACCINES (2021)

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Article Biotechnology & Applied Microbiology

Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries

Rui Wang et al.

Summary: The study reveals many mutations on the RBD of the S protein, with the majority strengthening the binding between the RBD and host ACE2, indicating an evolution towards more infectious variants. Additionally, certain mutations found in different variants may weaken the binding between the RBD and antibodies, potentially compromising existing vaccines and antibody therapies. The study also identifies potential vaccine escape mutations that could pose a threat to current vaccines and antibody treatments.

GENOMICS (2021)

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Article Medicine, General & Internal

Evidence for retained spike-binding and neutralizing activity against emerging SARS-CoV-2 variants in serum of COVID-19 mRNA vaccine recipients

Juan Manuel Carreno et al.

Summary: The study found that currently circulating viral variants, including Iota and Delta, show only minimal decreases in neutralization, while the Lambda sub-variant exhibits a significant reduction in neutralization, followed by Beta and Alpha (E484K). Overall, mRNA SARS-CoV-2 vaccines may still be effective against these viral variants, and receptor binding domain and spike binding antibody tests may retain specificity in the face of evolving SARS-CoV-2 diversity.

EBIOMEDICINE (2021)

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News Item Medicine, General & Internal

COVID-19 Vaccines vs Variants-Determining How Much Immunity Is Enough

Rita Rubin

Summary: Efficiency of COVID-19 vaccines against SARS-CoV-2 variants is still being studied.

JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION (2021)

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Article Biochemical Research Methods

A novel single nucleotide polymorphism assay for the detection of N501Y SARS-CoV-2 variants

M. Sandoval Torrientes et al.

Summary: The N501Y mutation in SARS-CoV-2 variants has been linked to increased transmission in strains from the UK, South Africa, and Brazil. A single nucleotide polymorphism discrimination assay was designed and validated for quick discrimination of N501Y variants, and successfully deployed in 757 nasopharyngeal swabs. This sensitive, specific, and simple method can be applied in any microbiology lab.

JOURNAL OF VIROLOGICAL METHODS (2021)

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Editorial Material Oncology

Preparation for the challenge of heavily mutated Omicron variant COMMENT

Yuanlin Song et al.

CLINICAL AND TRANSLATIONAL MEDICINE (2021)

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Article Multidisciplinary Sciences

Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma

Sandile Cele et al.

Summary: The study compared the neutralization of non-VOC and 501Y.V2 VOC variants using plasma from COVID-19 patients in South Africa. It found that plasma from individuals infected during the first wave effectively neutralized the first-wave virus variant, while plasma from those infected in the second wave effectively neutralized the 501Y.V2 variant.

NATURE (2021)

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Letter Medicine, General & Internal

New SARS-CoV-2 Variants - Clinical, Public Health, and Vaccine Implications

Salim S. Abdool Karim et al.

Summary: The emergence of SARS-CoV-2 variants, including B.1.1.7 (VOC-202012/01), 501Y.V2 (B.1.351), and P.1 (B.1.1.28.1), has raised concerns about worsening Covid-19 and potential escape from vaccine-induced immunity.

NEW ENGLAND JOURNAL OF MEDICINE (2021)

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Article Medicine, General & Internal

Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant

S. A. Madhi et al.

Summary: The ChAdOx1 nCoV-19 vaccine did not provide significant protection against mild-to-moderate Covid-19 caused by the B.1.351 variant, with an efficacy of 10.4%. The incidence of serious adverse events was balanced between the vaccine and placebo groups.

NEW ENGLAND JOURNAL OF MEDICINE (2021)

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Article Medicine, General & Internal

Efficacy of NVX-CoV2373 Covid-19 Vaccine against the B.1.351 Variant

V. Shinde et al.

Summary: The NVX-CoV2373 vaccine showed efficacy in preventing Covid-19, with higher vaccine efficacy observed among HIV-negative participants. Most infections were caused by the B.1.351 variant.

NEW ENGLAND JOURNAL OF MEDICINE (2021)

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Review Virology

Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines

Daniele Focosi et al.

Summary: The Spike protein serves as the target for antibody-based therapeutics and vaccines, but mutations in Spike could impact their efficacy. Monitoring mutations is crucial for adjusting the therapeutics inventory. Different clades exhibit varying mutation combinations, with a focus on the UK, South African, and Brazilian variants.

REVIEWS IN MEDICAL VIROLOGY (2021)

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Review Infectious Diseases

Immunobiology and nanotherapeutics of severe acute respiratory syndrome 2 (SARS-CoV-2): a current update

Ifeanyi Elibe Mba et al.

Summary: The emergence of SARS-CoV-2 has posed a significant global health challenge, sparking renewed interest in coronavirus research. The spike proteins, ACE2, and TMPRSS2 play crucial roles in viral infection, while pro-inflammatory proteins released upon viral entry further exacerbate the inflammatory state.

INFECTIOUS DISEASES (2021)

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Article Multidisciplinary Sciences

The SARS-CoV-2 Spike variant D614G favors an open conformational state

Rachael A. Mansbach et al.

Summary: The emergence of the G-form variant of COVID-19 has led to a more infectious strain with increased viral loads, likely due to changes in protein energetics favoring infection-capable states and enhanced exposure of the receptor binding domain. These findings are crucial for vaccine design.

SCIENCE ADVANCES (2021)

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Article Cell Biology

Distinct uptake, amplification, and release of SARS-CoV-2 by M1 and M2 alveolar macrophages

Jiadi Lv et al.

Summary: M1 alveolar macrophages facilitate the spread and replication of SARS-CoV-2, while M2 alveolar macrophages help degrade the virus to combat infection.

CELL DISCOVERY (2021)

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Article Genetics & Heredity

Extremes of age are associated with differences in the expression of selected pattern recognition receptor genes and ACE2, the receptor for SARS-CoV-2: implications for the epidemiology of COVID-19 disease

Stephen W. Bickler et al.

Summary: By analyzing genome-wide RNA-seq profiles from human dermal fibroblasts, it was found that extremes of age are associated with increased expression of certain genes that may interact with SARS-CoV-2 proteins. Therefore, assessing the expression of pattern recognition receptors (PRR) could provide a strategy for stratifying the risk of severe COVID-19 at both individual and population levels.

BMC MEDICAL GENOMICS (2021)

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Article Infectious Diseases

E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil

Patricia Aline Grohs Ferrareze et al.

Summary: The COVID-19 pandemic caused by SARS-CoV-2 has affected millions of people since 2019, with new lineages propagating and the virus adopting mechanisms to evade the immune system. The E484K mutation has been progressively found in Brazil since the second half of 2020, raising concerns about reinfection risk and vaccine effectiveness. Genomic and phylogenetic analyses showed over 40% of sequenced genomes in October 2020 from Brazilian samples had the E484K mutation, leading to insights about adaptive and purifying selection driving virus evolution.

INFECTION GENETICS AND EVOLUTION (2021)

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Review Infectious Diseases

Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic

Xue Li et al.

Summary: The mutations and variants of the SARS-CoV-2 virus have impact on its transmissibility and pathogenicity, enhancing its infectivity, transmissibility, and resistance to neutralization. Suggestions for prevention and control of the pandemic are being proposed.

INFECTION GENETICS AND EVOLUTION (2021)

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Review Biochemistry & Molecular Biology

Structural Evaluation of the Spike Glycoprotein Variants on SARS-CoV-2 Transmission and Immune Evasion

Mohd Zulkifli Salleh et al.

Summary: The emergence of SARS-CoV-2 has posed significant challenges worldwide, resulting in millions of deaths. Mutations in the spike (S) glycoprotein may impact vaccine efficacy. Variants such as Alpha, Beta, Gamma have mutations in their spike proteins that enhance viral fitness.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

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Article Biochemistry & Molecular Biology

Lessons Learned from Cutting-Edge Immunoinformatics on Next-Generation COVID-19 Vaccine Research

Chiranjib Chakraborty et al.

Summary: Immunoinformatics and bioinformatics approaches have significantly accelerated COVID-19 vaccine research, leading to the development of next-generation vaccines and a new direction in the field.

INTERNATIONAL JOURNAL OF PEPTIDE RESEARCH AND THERAPEUTICS (2021)

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Article Microbiology

Mutation-Specific SARS-CoV-2 PCR Screen: Rapid and Accurate Detection of Variants of Concern and the Identification of a Newly Emerging Variant with Spike L452R Mutation

Huanyu Wang et al.

Summary: A PCR-based detection method has been developed by the research team to identify different variants of SARS-CoV-2, with same-day reporting and demonstrated 100% concordance with whole-genome sequencing results. This method offers a rapid screening approach for early detection of newly emerging variants.

JOURNAL OF CLINICAL MICROBIOLOGY (2021)

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Article Virology

SARS-CoV-2 B.1.617 Indian variants: Are electrostatic potential changes responsible for a higher transmission rate?

Stefano Pascarella et al.

Summary: Lineage B.1.617+, also known as G/452R.V3 and denoted by WHO as delta and kappa, is a newly described SARS-CoV-2 variant first identified in India in October 2020. Three sublineages, B.1.617.1 (kappa), B.1.617.2 (delta), and B.1.617.3, have been identified, with their potential impact on the current pandemic under investigation. This variant with 13 amino acid changes, including E484Q, L452R, and P681R, is characterized by a significant alteration in the surface electrostatic potential of the spike protein receptor-binding domain, particularly noticeable in the delta sublineage. The enhanced electrostatic potential change may facilitate the interaction between the B.1.617+ RBD and the ACE2 receptor, potentially increasing virus transmission.

JOURNAL OF MEDICAL VIROLOGY (2021)

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Article Multidisciplinary Sciences

SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape

Tyler N. Starr et al.

Summary: An ideal therapeutic anti-SARS-CoV-2 antibody should have resistance to viral escape, activity against diverse sarbecoviruses, and provide high protection through viral neutralization and effector functions. Studies have found a trade-off between in vitro neutralization potency and breadth of sarbecovirus binding in SARS-CoV-2 antibodies targeting the RBD, but identified some antibodies with exceptional sarbecovirus breadth and resistance to SARS-CoV-2 escape.

NATURE (2021)

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Review Microbiology

SARS-CoV-2 variants, spike mutations and immune escape

William T. Harvey et al.

Summary: The evolution of SARS-CoV-2 has been characterized by the emergence of mutations and variants that impact virus characteristics. Manufacturers are preparing for possible updates to vaccines in response to changes in the virus population, and it is crucial to monitor genetic and antigenic changes alongside experiments to understand the impacts of mutations.

NATURE REVIEWS MICROBIOLOGY (2021)

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Article Multidisciplinary Sciences

Natural killer-cell immunoglobulin-like receptors trigger differences in immune response to SARS-CoV-2 infection

Roberto Littera et al.

Summary: The study found that the KIR2DS2/HLA C1 functional unit has a strong protective effect against adverse outcomes of COVID-19. This marker, combined with other factors such as age, sex, and autoimmune diseases, could provide highly informative insights into disease progression and enable timely interventions to reduce mortality associated with severe forms of SARS-CoV-2 infection.

PLOS ONE (2021)

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Editorial Material Virology

SARS-CoV-2 Variants: A Synopsis of In Vitro Efficacy Data of Convalescent Plasma, Currently Marketed Vaccines, and Monoclonal Antibodies

Daniele Focosi et al.

Summary: This study summarizes the in vitro evidence of efficacy for convalescent plasma, approved vaccines and monoclonal antibodies against various SARS-CoV-2 variants, providing guidance for treating physicians while awaiting real-world clinical efficacy.

VIRUSES-BASEL (2021)

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Article Virology

Rise and Fall of SARS-CoV-2 Lineage A.27 in Germany

Sebastien Calvignac-Spencer et al.

Summary: The frequency of the SARS-CoV-2 lineage A.27 in Germany has been increasing, with most genomes identified in laboratories from Baden-Wuerttemberg. The A.27 lineage exhibits mutational patterns typical of VOIs/VOCs, potentially leading to immune escape and higher transmissibility. While the relative abundance of A.27 in Germany has declined since the end of February, other variants such as B.1.1.7 and B.1.617.2 are on the rise.

VIRUSES-BASEL (2021)

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Article Microbiology

Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants

Chiranjib Chakraborty et al.

Summary: The study analyzes the evolutionary patterns, geographical distributions, and transmission patterns of multiple emerging SARS-CoV-2 variants, as well as their impact on public health, including mutations within each lineage. The B.1.1.7 lineage shows the highest transmission frequency, and critical mutations (such as E484K, K417T/N, N501Y, and D614G) may affect vaccine efficacy. The findings will help in strategizing future pandemic planning, developing next-generation vaccines, and planning vaccination programs globally.

MBIO (2021)

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Article Multidisciplinary Sciences

Mapping mutations to the SARS-CoV-2 RBD that escape binding by different classes of antibodies

Allison J. Greaney et al.

Summary: The study found that although the human immune system can produce antibodies that target diverse RBD epitopes, in practice, the polyclonal response to infection tends to be skewed towards a single class of antibodies targeting an epitope that is already undergoing rapid evolution.

NATURE COMMUNICATIONS (2021)

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Article Microbiology

Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies

Marta Alenquer et al.

Summary: Understanding the evolution of SARS-CoV-2 and host immunity is crucial in controlling COVID-19 pandemics. Mutations in the spike protein can impact antibody and ACE2 binding, requiring monitoring of SARS-CoV-2 evolution and dynamics. Identifying signatures in SARS-CoV-2 that make the virus resistant to neutralizing antibodies is critical for the development of therapies, vaccines, and diagnostics.

PLOS PATHOGENS (2021)

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Article Biology

Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics

Michael Barton et al.

Summary: The study analyzed the effects of mutations in the Spike protein of SARS-CoV-2 on its interaction with ACE2, finding that most mutations increased affinity with ACE2. Two ACE2 mutations were also found to enhance binding with the Spike protein.

ELIFE (2021)

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Article Biology

N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2

Fang Tian et al.

Summary: Research indicates that the N501Y mutation in SARS-CoV-2 variants strengthens its interaction with ACE2, leading to an increased transmission rate, highlighting the need for close monitoring of future mutations in the virus' RBD.

ELIFE (2021)

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Article Microbiology

In vitro Characterization of Fitness and Convalescent Antibody Neutralization of SARS-CoV-2 Cluster 5 Variant Emerging in Mink at Danish Farms

Ria Lassauniere et al.

Summary: In addition to humans, SARS-CoV-2 can also infect various animals, with mink being particularly susceptible. The rapid spread of SARS-CoV-2 in mink farms in Denmark led to concerns over virus mutations and transmission back to humans.

FRONTIERS IN MICROBIOLOGY (2021)

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Review Microbiology

Acute Infection of Viral Pathogens and Their Innate Immune Escape

Kul Raj Rai et al.

Summary: Viral infections can cause widespread diseases in humans, requiring robust immune responses to prevent potentially fatal acute viral infections. While innate immunity plays a crucial role in viral clearance, it can also contribute to disease progression through immune-mediated host tissue injury.

FRONTIERS IN MICROBIOLOGY (2021)

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Review Immunology

SARS-CoV-2 Vaccines Based on the Spike Glycoprotein and Implications of New Viral Variants

Daniel Martinez-Flores et al.

Summary: COVID-19, caused by SARS-CoV-2, affects the respiratory system and has resulted in over 2 million deaths worldwide. Vaccines targeting the S glycoprotein have been developed, but the emergence of new variants could impact their effectiveness.

FRONTIERS IN IMMUNOLOGY (2021)

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Review Immunology

From COVID-19 to Cancer mRNA Vaccines: Moving From Bench to Clinic in the Vaccine Landscape

Chiranjib Chakraborty et al.

Summary: mRNA vaccines have emerged as a significant type of therapeutic, especially with the recent approval of COVID-19 mRNA vaccines. These vaccines have sparked interest in the pharmaceutical and biotechnology industries, offering new hope for the future of medicine.

FRONTIERS IN IMMUNOLOGY (2021)

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Article Public, Environmental & Occupational Health

Effectiveness of Pfizer-BioNTech and Moderna Vaccines in Preventing SARS-CoV-2 Infection Among Nursing Home Residents Before and During Widespread Circulation of the SARS-CoV-2 B.1.617.2 (Delta) Variant — National Healthcare Safety Network, March 1–August 1, 2021

Srinivas Nanduri et al.

MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT (2021)

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Article Immunology

SARS-CoV-2 variants of concern partially escape humoral but not T- cell responses in COVID-19 convalescent donors and vaccinees

Daryl Geers et al.

Summary: This study suggests that some variants might partially escape humoral immunity induced by SARS-CoV-2 infection or BNT162b2 vaccination, but the S-specific CD4(+) T-cell activation is not affected by the mutations in the B.1.1.7 and B.1.351 variants.

SCIENCE IMMUNOLOGY (2021)

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Article Immunology

Asian-Origin Approved COVID-19 Vaccines and Current Status of COVID-19 Vaccination Program in Asia: A Critical Analysis

Chiranjib Chakraborty et al.

Summary: This paper analyzed the Asian-origin COVID-19 vaccines and vaccination program status in Asia till March 2021 under three sections. The analysis includes the mapping of approved vaccines, evaluation of vaccination programs, and factors affecting the vaccination program, aiming to assist the successful implementation of COVID-19 vaccination program in Asia.

VACCINES (2021)

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Article Microbiology

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

Sarah Cherian et al.

Summary: Genomic epidemiology and whole genome sequencing were used to investigate the transmission and evolution of the SARS-CoV-2 virus during the global pandemic. The study identified new variants B.1.617.1 and B.1.617.2 in India, responsible for the second wave of COVID-19 in Maharashtra, with B.1.617.2 designated as a VOC delta and B.1.617.1 as a variant of interest kappa. Monitoring of these and emerging variants in India is crucial for public health.

MICROORGANISMS (2021)

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Article Geriatrics & Gerontology

A Next-Generation Vaccine Candidate Using Alternative Epitopes to Protect against Wuhan and All Significant Mutant Variants of SARS-CoV-2: An Immunoinformatics Approach

Manojit Bhattacharya et al.

Summary: Newly emerging significant SARS-CoV-2 variants pose a serious threat to the world and require an effective vaccine that can target these variants. Through computational tools and methods, we identified key epitopes on SARS-CoV-2 variants to develop a next-generation peptide vaccine.

AGING AND DISEASE (2021)

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Review Biochemistry & Molecular Biology

The Genetic Variant of SARS-CoV-2: Would it matter for Controlling the Devastating Pandemic?

Shuxin Guo et al.

Summary: The COVID-19 pandemic is still not under control, with vaccination for herd immunity being a major hope. However, emerging genetic variants may potentially undermine vaccine efficacy, especially those that can escape vaccine protection. It is crucial to focus on developing new vaccines targeting these concerning variants.

INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES (2021)

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Letter Biochemistry & Molecular Biology

N501Y mutation imparts cross-species transmission of SARS-CoV-2 to mice by enhancing receptor binding

Zubiao Niu et al.

SIGNAL TRANSDUCTION AND TARGETED THERAPY (2021)

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Letter Infectious Diseases

Serum sample neutralisation of BBIBP-CorV and ZF2001 vaccines to SARS-CoV-2 501Y.V2

Baoying Huang et al.

LANCET MICROBE (2021)

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Article Health Care Sciences & Services

Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany

Bjoern Jensen et al.

Summary: The study indicates that treatment of SARS-CoV-2 with bamlanivimab in immunocompromised patients may result in the rapid development of immune escape variants, which could have significant implications for the effectiveness of vaccination and antibody-based therapies.

LANCET REGIONAL HEALTH-EUROPE (2021)

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Letter Geriatrics & Gerontology

All Nations Must Prioritize the COVID-19 Vaccination Program for Elderly Adults Urgently

Chiranjib Chakraborty et al.

AGING AND DISEASE (2021)

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Article Immunology

Immunological mechanisms of vaccine-induced protection against COVID-19 in humans

Manish Sadarangani et al.

Summary: Most COVID-19 vaccines aim to induce immune responses, particularly neutralizing antibodies (NAbs), against the spike protein of the virus. mRNA vaccines have shown efficacy after just one dose, while adenovirus vaccines elicit polyfunctional antibodies and strong T cell responses. These findings suggest that protection may not solely rely on NAbs but also involve other immune effector mechanisms.

NATURE REVIEWS IMMUNOLOGY (2021)

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Letter Infectious Diseases

SARS-CoV-2 spike E484K mutation reduces antibody neutralisation

Sonia Jangra et al.

LANCET MICROBE (2021)

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Article Infectious Diseases

Extensive genetic diversity with novel mutations in spike glycoprotein of severe acute respiratory syndrome coronavirus 2, Bangladesh in late 2020

S. Z. Afrin et al.

Summary: In Bangladesh, COVID-19 has been prevalent with nearly 500,000 confirmed cases in late 2020. Genetic investigation of SARS-CoV-2 in Bangladesh revealed diverse mutations in the spike protein, with the D614G mutation being present in all samples and 53 novel mutations discovered as of January 2021. These mutations are functionally linked to viral transmission and pathogenic capacity.

NEW MICROBES AND NEW INFECTIONS (2021)

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Article Medicine, Research & Experimental

Immunoinformatics Approach for the Identification and Characterization of T Cell and B Cell Epitopes towards the Peptide-Based Vaccine against SARS-CoV-2

Chiranjib Chakraborty et al.

Summary: Immunoinformatics plays a significant role in epitope identification and vaccine designing, particularly for targeting T cell and B cell epitopes against SARS-CoV-2. This review article discusses the importance of adaptive immunity and key points for utilizing immunoinformatics in vaccine designing, as well as summarizes current studies on infectious pathogens and related diseases. Additionally, it covers the identification and characterization of potential T cell and B cell epitopes for designing vaccines against SARS-CoV-2.

ARCHIVES OF MEDICAL RESEARCH (2021)

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Article Chemistry, Multidisciplinary

Immune evasion of SARS-CoV-2 variants of concern is driven by low affinity to neutralizing antibodies

Matheus V. F. Ferraz et al.

Summary: Immune evasion of SARS-CoV-2 variants is primarily attributed to decreased cross-reactivity of previously elicited antibodies, with increased affinity to hACE2 playing a smaller role. The affinity between antibodies and variants is influenced by the remodeling of electrostatic surface potential of the Spike RBDs. The P.3 variant is considered a putative VOC.

CHEMICAL COMMUNICATIONS (2021)

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Review Public, Environmental & Occupational Health

SARS-CoV-2 mutations: the biological trackway towards viral fitness

Parinita Majumdar et al.

Summary: The outbreak of pneumonia-like respiratory disorder in China and its global spread resulted in a public health emergency, putting the SARS-CoV-2 virus in the spotlight. Betacoronaviruses, known for their high mutation rate, recombination, and interspecies transmission, have shown considerable mutations in different proteins, with single-nucleotide substitutions being predominant. Specific mutations in spike glycoprotein and RNA-dependent RNA polymerase have emerged as dominant globally, posing challenges for therapeutics and vaccines.

EPIDEMIOLOGY AND INFECTION (2021)

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Review Urology & Nephrology

Evolution of SARS-CoV-2: Review of Mutations, Role of the Host Immune System

Helene Banoun

Summary: The article emphasizes on the mutations that have occurred in the virus since the beginning of the COVID-19 pandemic, as well as the cross-reactivity between common cold coronaviruses and SARS-CoV-2 in a majority of the population. Important evolutionary mutations have emerged in genes encoding proteins that interact with the host immune system, such as viral polymerase. The relationship between cross-reactivity and viral mutations may partly explain the evolution of the pandemic until the summer of 2020.

NEPHRON (2021)

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Article Cell Biology

Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016

Tyler N. Starr et al.

Summary: The study mapped mutations to the SARS-CoV-2 spike receptor-binding domain that escape binding by certain monoclonal antibodies. These mutations are concentrated in specific lineages of SARS-CoV-2. The authors suggest diversifying the epitopes targeted by antibodies and antibody cocktails to make them more resilient to SARS-CoV-2 antigenic evolution.

CELL REPORTS MEDICINE (2021)

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Article Microbiology

Developmental Status of the Potential Vaccines for the Mitigation of the COVID-19 Pandemic and a Focus on the Effectiveness of the Pfizer-BioNTech and Moderna mRNA Vaccines

Rashed Noor

Summary: Researchers have made progress in studying the genomics of SARS-CoV-2, its similarities with SARS-CoV-1 and MERS-CoV, and the host immune evasion mechanisms of SARS-CoV-2, leading to intensive global efforts on vaccine development. The mRNA-1273 vaccine has shown to be the most effective through clinical trials, with a 95% positive outcome. However, concerns remain regarding the sustainability of vaccine efficacy against emerging variants of SARS-CoV-2.

CURRENT CLINICAL MICROBIOLOGY REPORTS (2021)

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Review Immunology

Ongoing Clinical Trials of Vaccines to Fight against COVID-19 Pandemic

Chiranjib Chakraborty et al.

Summary: Following the outbreak of COVID-19, the global community is urgently seeking treatments and vaccines, including those targeting SARS-CoV-2. Various vaccines are currently in different stages of development, including some repurposed vaccines. Research on COVID-19 vaccines has received significant attention worldwide.

IMMUNE NETWORK (2021)

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Review Oncology

The Therapeutic Potential of Nanobodies

Ivana Jovcevska et al.

BIODRUGS (2020)

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Letter Critical Care Medicine

Clinical predictors of mortality due to COVID-19 based on an analysis of data of 150 patients from Wuhan, China

Qiurong Ruan et al.

INTENSIVE CARE MEDICINE (2020)

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Article Virology

Development of epitope-based peptide vaccine against novel coronavirus 2019 (SARS-COV-2): Immunoinformatics approach

Manojit Bhattacharya et al.

JOURNAL OF MEDICAL VIROLOGY (2020)

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Article Virology

COVID-2019: The role of the nsp2 and nsp3 in its pathogenesis

Silvia Angeletti et al.

JOURNAL OF MEDICAL VIROLOGY (2020)

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Article Medicine, General & Internal

Clinical Characteristics of Coronavirus Disease 2019 in China

W. Guan et al.

NEW ENGLAND JOURNAL OF MEDICINE (2020)

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Article Microbiology

We shouldn't worry when a virus mutates during disease outbreaks

Nathan D. Grubaugh et al.

NATURE MICROBIOLOGY (2020)

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Review Immunology

Mechanisms of Natural Killer Cell Evasion Through Viral Adaptation

Mathieu Mancini et al.

ANNUAL REVIEW OF IMMUNOLOGY, VOL 38 (2020)

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Editorial Material Medicine, Research & Experimental

Extensive Partnership, Collaboration, and Teamwork is Required to Stop the COVID-19 Outbreak

Chiranjib Chakraborty et al.

ARCHIVES OF MEDICAL RESEARCH (2020)

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Article Biochemistry & Molecular Biology

Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19

Daniel Blanco-Melo et al.

CELL (2020)

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Article Microbiology

Identification of Human Single-Domain Antibodies against SARS-CoV-2

Yanling Wu et al.

CELL HOST & MICROBE (2020)

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Editorial Material Immunology

Functional exhaustion of antiviral lymphocytes in COVID-19 patients

Meijuan Zheng et al.

CELLULAR & MOLECULAR IMMUNOLOGY (2020)

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Article Immunology

Dysregulation of Immune Response in Patients With Coronavirus 2019 (COVID-19) in Wuhan, China

Chuan Qin et al.

CLINICAL INFECTIOUS DISEASES (2020)

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Article Infectious Diseases

Could the D614G substitution in the SARS-CoV-2 spike (S) protein be associated with higher COVID-19 mortality?

Muthukrishnan Eaaswarkhanth et al.

INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES (2020)

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Article Medicine, Research & Experimental

Clinical and immunological features of severe and moderate coronavirus disease 2019

Guang Chen et al.

JOURNAL OF CLINICAL INVESTIGATION (2020)

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Review Immunology

Targeting potential drivers of COVID-19: Neutrophil extracellular traps

Betsy J. Barnes et al.

JOURNAL OF EXPERIMENTAL MEDICINE (2020)

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Article Multidisciplinary Sciences

Effectiveness of convalescent plasma therapy in severe COVID-19 patients

Kai Duan et al.

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

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Article Infectious Diseases

Evolutionary analysis of SARS-CoV-2: how mutation of Non-Structural Protein 6 (NSP6) could affect viral autophagy

Domenico Benvenuto et al.

JOURNAL OF INFECTION (2020)

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Article Immunology

Characteristics of Peripheral Lymphocyte Subset Alteration in COVID-19 Pneumonia

Fan Wang et al.

JOURNAL OF INFECTIOUS DISEASES (2020)

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Letter Virology

Consider TLR5 for new therapeutic development against COVID-19

Chiranjib Chakraborty et al.

JOURNAL OF MEDICAL VIROLOGY (2020)

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Editorial Material Virology

COVID-19: Consider IL-6 receptor antagonist for the therapy of cytokine storm syndrome in SARS-CoV-2 infected patients

Chiranjib Chakraborty et al.

JOURNAL OF MEDICAL VIROLOGY (2020)

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Article Medicine, Research & Experimental

Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant

Maria Pachetti et al.

JOURNAL OF TRANSLATIONAL MEDICINE (2020)

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Article Medicine, Research & Experimental

COVID-19: Loss of bridging between innate and adaptive immunity?

Vishal U. S. Rao et al.

MEDICAL HYPOTHESES (2020)

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Article Microbiology

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Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19

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A Novel Synonymous Mutation of SARS-CoV-2: Is This Possible to Affect Their Antigenicity and Immunogenicity?

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Emergence of Drift Variants That May Affect COVID-19 Vaccine Development and Antibody Treatment

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PATHOGENS (2020)

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Antiviral activities of type I interferons to SARS-CoV-2 infection

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ANTIVIRAL RESEARCH (2020)

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Immunoinformatics-guided design of an epitope-based vaccine against severe acute respiratory syndrome coronavirus 2 spike glycoprotein

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COMPUTERS IN BIOLOGY AND MEDICINE (2020)

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Review Biochemistry & Molecular Biology

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Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding

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

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Acute SARS-CoV-2 Infection Impairs Dendritic Cell and T Cell Responses

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The Lung Macrophage in SARS-CoV-2 Infection: A Friend or a Foe?

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FRONTIERS IN IMMUNOLOGY (2020)

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Impaired NLRP3 inflammasome activation/pyroptosis leads to robust inflammatory cell death via caspase-8/RIPK3 during coronavirus infection

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Hepatitis E Virus: How It Escapes Host Innate Immunity

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Editorial Material Medicine, Research & Experimental

SARS-CoV-2 SPIKE PROTEIN: an optimal immunological target for vaccines

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JOURNAL OF TRANSLATIONAL MEDICINE (2020)

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Letter Infectious Diseases

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LANCET INFECTIOUS DISEASES (2020)

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Innate immune evasion bySARS-CoV-2: Comparison withSARS-CoV

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REVIEWS IN MEDICAL VIROLOGY (2020)

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Antibody cocktail to SARS-CoV-2 spike protein prevents rapid mutational escape seen with individual antibodies

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NATURE COMMUNICATIONS (2020)

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Critical Role of Type III Interferon in Controlling SARS-CoV-2 Infection in Human Intestinal Epithelial Cells

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Emerging of a SARS-CoV-2 viral strain with a deletion in nsp1

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Type I Interferon Susceptibility Distinguishes SARS-CoV-2 from SARS-CoV

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Review Medicine, Research & Experimental

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Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants

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SARS-CoV-2 Orf6 hijacks Nup98 to block STAT nuclear import and antagonize interferon signaling

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Structural Basis of SARS-CoV-2 and SARS-CoV Antibody Interactions

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Induction of the Antiviral Immune Response and Its Circumvention by Coronaviruses

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Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function

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Covid-19: Perspectives on Innate Immune Evasion

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Temporal signal and the phylodynamic threshold of SARS-CoV-2

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Antagonism of Type I Interferon by Severe Acute Respiratory Syndrome Coronavirus 2

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Versatile and multivalent nanobodies efficiently neutralize SARS-CoV-2

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Immunoinformatics approach to understand molecular interaction between multi-epitopic regions of SARS-CoV-2 spike-protein with TLR4/MD-2 complex

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Serum interleukin-6 is an indicator for severity in 901 patients with SARS-CoV-2 infection: a cohort study

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SARS-CoV-2 evades immune detection in alveolar macrophages

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The trinity of COVID-19: immunity, inflammation and intervention

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Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in COVID-19 patients

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ORF3a mutation associated with higher mortality rate in SARS-CoV-2 infection

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Viral Infection of Human Natural Killer Cells

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Severe acute respiratory syndrome coronavirus ORF3a protein activates the NLRP3 inflammasome by promoting TRAF3-dependent ubiquitination of ASC

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Porcine Reproductive and Respiratory Syndrome Virus nsp11 Antagonizes Type I Interferon Signaling by Targeting IRF9

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Middle East Respiratory Syndrome Coronavirus-Encoded Accessory Proteins Impair MDA5-and TBK1-Mediated Activation of NF-κB

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Middle East Respiratory Syndrome Coronavirus NS4b Protein Inhibits Host RNase L Activation

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Middle East respiratory syndrome coronavirus M protein suppresses type I interferon expression through the inhibition of TBK1-dependent phosphorylation of IRF3

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SARS Coronavirus Papain-Like Protease Inhibits the TLR7 Signaling Pathway through Removing Lys63-Linked Polyubiquitination of TRAF3 and TRAF6

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The Relationship between dN/dS and Scaled Selection Coefficients

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Rotavirus NSP1 Protein Inhibits Interferon-Mediated STAT1 Activation

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Enterovirus 2APro Targets MDA5 and MAVS in Infected Cells

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Mechanisms and Implications of Age-Associated Impaired Innate Interferon Secretion by Dendritic Cells: A Mini-Review

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Vaccinia virus immune evasion: mechanisms, virulence and immunogenicity

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Cleavage of Interferon Regulatory Factor 7 by Enterovirus 71 3C Suppresses Cellular Responses

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The C Proteins of Human Parainfluenza Virus Type 1 Block IFN Signaling by Binding and Retaining Stat1 in Perinuclear Aggregates at the Late Endosome

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Structural basis for Marburg virus VP35-mediated immune evasion mechanisms

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Impact of immune escape mutations on HIV-1 fitness in the context of the cognate transmitted/founder genome

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Viral fitness: definitions, measurement, and current insights

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Expanding roles for CD4+ T cells in immunity to viruses

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Barriers to mucosal transmission of immunodeficiency viruses

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Respiratory epithelial cells in innate immunity to influenza virus infection

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CELL AND TISSUE RESEARCH (2011)

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Correlates of Protection Induced by Vaccination

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Immune Escape Mutations Detected Within HIV-1 Epitopes Associated With Viral Control During Treatment Interruption

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Viral Mutation Rates

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JOURNAL OF VIROLOGY (2010)

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Editorial Material Biology

The population genetics of mutations: good, bad and indifferent

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PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2010)

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Immunity and immunopathology to viruses: what decides the outcome?

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Virus interaction with the apical junctional complex

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FRONTIERS IN BIOSCIENCE-LANDMARK (2009)

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Innate immunity to virus infection

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IMMUNOLOGICAL REVIEWS (2009)

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The roles of TLRs, RLRs and NLRs in pathogen recognition

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INTERNATIONAL IMMUNOLOGY (2009)

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Severe Acute Respiratory Syndrome Coronavirus M Protein Inhibits Type I Interferon Production by Impeding the Formation of TRAF3•TANK•TBK1/IKKε Complex

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JOURNAL OF BIOLOGICAL CHEMISTRY (2009)

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Antagonism to and Intracellular Sequestration of Human Tetherin by the Human Immunodeficiency Virus Type 2 Envelope Glycoprotein

Anna Le Tortorec et al.

JOURNAL OF VIROLOGY (2009)

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Review Biochemistry & Molecular Biology

Dendritic cells and cytokines in human inflammatory and autoimmune diseases

Patrick Blanco et al.

CYTOKINE & GROWTH FACTOR REVIEWS (2008)

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Functions of natural killer cells

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NATURE IMMUNOLOGY (2008)

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Multiple Dendritic Cell Populations Activate CD4+ T Cells after Viral Stimulation

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PLOS ONE (2008)

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Article Microbiology

Stable cytotoxic T cell escape mutation in hepatitis C virus is linked to maintenance of viral fitness

Luke Uebelhoer et al.

PLOS PATHOGENS (2008)

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Recognition of microorganisms and activation of the immune response

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NATURE (2007)

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Hepatitis C virus nonstructural protein 5A modulates the toll-like receptor-MyD88-dependent signaling pathway in macrophage cell lines

Takayuki Abe et al.

JOURNAL OF VIROLOGY (2007)

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Review Pharmacology & Pharmacy

A target on the move: Innate and adaptive immune escape strategies of hepatitis C virus

R Thimme et al.

ANTIVIRAL RESEARCH (2006)

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Review Biochemistry & Molecular Biology

Pathogen recognition and innate immunity

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CELL (2006)

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Article Immunology

HIV-1-specific CD8+ T cell responses and viral evolution in women and infants

V Sanchez-Merino et al.

JOURNAL OF IMMUNOLOGY (2005)

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Article Immunology

Vaccinia virus protein Toll-like-interleukin-1 A46R targets multiple receptor adaptors and contributes to virulence

J Stack et al.

JOURNAL OF EXPERIMENTAL MEDICINE (2005)

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Review Virology

T cell response in hepatitis C virus infection

C Neumann-Haefelin et al.

JOURNAL OF CLINICAL VIROLOGY (2005)

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Induction of suppressor of cytokine signaling-3 by herpes simplex virus type 1 contributes to inhibition of the interferon signaling pathway

S Yokota et al.

JOURNAL OF VIROLOGY (2004)

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Article Virology

STAT3 ubiquitylation and degradation by mumps virus suppress cytokine and oncogene signaling

CM Ulane et al.

JOURNAL OF VIROLOGY (2003)

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Viral immune evasion:: a masterpiece of evolution

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IMMUNOGENETICS (2002)

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Review Rheumatology

The instructive role of dendritic cells on T-cell responses

Federica Sallusto et al.

ARTHRITIS RESEARCH & THERAPY (2002)

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Review Pathology

Viral escape mechanisms - escapology taught by viruses

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INTERNATIONAL JOURNAL OF EXPERIMENTAL PATHOLOGY (2001)

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Observation of antigen-dependent CD8+ T-cell/dendritic cell interactions in vivo

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CELLULAR IMMUNOLOGY (2001)

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The evolution of RNA viruses: A population genetics view

A Moya et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2000)

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Review Gastroenterology & Hepatology

Clinical relevance of hepatitis B viral mutations

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HEPATOLOGY (2000)

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