4.7 Review

The biological and clinical significance of emerging SARS-CoV-2 variants

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Article Immunology

Estimation of Secondary Household Attack Rates for Emergent Spike L452R Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants Detected by Genomic Surveillance at a Community-Based Testing Site in San Francisco

James Peng et al.

Summary: The prevalence of West Coast SARS-CoV-2 variants and their transmission rate showed a modest increase in a community testing setting in San Francisco during January 2021.

CLINICAL INFECTIOUS DISEASES (2022)

Review Immunology

Neutralizing Antibodies Against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants Induced by Natural Infection or Vaccination: A Systematic Review and Pooled Analysis

Xinhua Chen et al.

Summary: Emerging SARS-CoV-2 variants pose a threat to immunity, with varying reductions in neutralizing antibody titers. Vaccines induce neutralizing antibodies that can effectively neutralize the newer variants, but with significant reductions in neutralizing titers.

CLINICAL INFECTIOUS DISEASES (2022)

Article Health Care Sciences & Services

Household transmission of COVID-19 cases associated with SARS-CoV-2 delta variant (B.1.617.2): national case-control study

Hester Allen et al.

Summary: This study indirectly assessed the differences in transmissibility between the SARS-CoV-2 Delta variant and the previously dominant Alpha variant. The results showed that the Delta variant had a higher rate of household transmission, potentially explaining its success in displacing the Alpha variant as the dominant strain in England. Understanding the transmissibility of this variant is important for informing international infection prevention and control policies.

LANCET REGIONAL HEALTH-EUROPE (2022)

Article Biochemistry & Molecular Biology

T cell immunity to SARS-CoV-2 following natural infection and vaccination

Anthony T. DiPiazza et al.

Summary: SARS-CoV-2, transmitted via respiratory particles, has caused the COVID-19 pandemic with severe economic consequences. Cellular immunity plays a crucial role in limiting disease severity, emphasizing the importance of understanding the functional capacity and role of SARS-CoV-2-specific T cells for natural infection and vaccination responses.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2021)

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)

Article Infectious Diseases

Neutralisation of SARS-CoV-2 lineage P.1 by antibodies elicited through natural SARS-CoV-2 infection or vaccination with an inactivated SARS-CoV-2 vaccine: an immunological study

William M. Souza et al.

Summary: The study aimed to investigate whether isolates of wild-type P.1 lineage SARS-CoV-2 can escape from neutralising antibodies generated by a polyclonal immune response. The results showed that the neutralising capacity against the P.1 isolates was significantly lower than against the lineage B isolate, especially in individuals previously infected with SARS-CoV-2.

LANCET MICROBE (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)

Review Biochemistry & Molecular Biology

Adaptive immunity to SARS-CoV-2 and COVID-19

Alessandro Sette et al.

Summary: The adaptive immune system, consisting of B cells, CD4(+) T cells, and CD8(+) T cells, plays varying roles in different viral infections and vaccines. Studies are showing that CD4(+) T cells, CD8(+) T cells, and neutralizing antibodies all play a part in controlling SARS-CoV-2 in COVID-19 cases, emphasizing the importance of understanding adaptive immunity in combating the disease.
Article Biochemistry & Molecular Biology

COVID-19-neutralizing antibodies predict disease severity and survival

Wilfredo F. Garcia-Beltran et al.

Summary: Severe cases of COVID-19 show increased inflammatory markers, lymphopenia, pro-inflammatory cytokines, and high antibody levels. High neutralization potency is a predictor of survival. Patient sera can neutralize different strains, indicating cross-protection from reinfection.
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 Microbiology

D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization

Drew Weissman et al.

Summary: The D614G mutation in the spike protein of SARS-CoV-2 is not expected to hinder current vaccine development, as viruses with the G614 spike are more susceptible to neutralization, indicating that the mutation may not affect vaccine efficacy.

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 Medicine, General & Internal

Effect of Bamlanivimab as Monotherapy or in Combination With Etesevimab on Viral Load in Patients With Mild to Moderate COVID-19 A Randomized Clinical Trial

Robert L. Gottlieb et al.

Summary: The study showed that treatment with bamlanivimab and etesevimab was significantly associated with a reduction in SARS-CoV-2 viral load at day 11 in nonhospitalized patients with mild to moderate COVID-19, compared to placebo. However, bamlanivimab monotherapy did not show a significant reduction in viral load. Ongoing clinical trials will focus on assessing the clinical benefits of antispike neutralizing antibodies in COVID-19 patients.

JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION (2021)

Article Immunology

Antibody potency, effector function, and combinations in protection and therapy for SARS-CoV-2 infection in vivo

Alexandra Schafer et al.

Summary: The study shows that combined use of hu-mAbs is effective for prevention and therapy of SARS-CoV-2 infection, but in vivo protection is influenced by intact effector function.

JOURNAL OF EXPERIMENTAL MEDICINE (2021)

Article Medicine, General & Internal

Safety and efficacy of the ChAdOx1 nCoV-19 vaccine (AZD1222) against SARS-CoV-2: an interim analysis of four randomised controlled trials in Brazil, South Africa, and the UK

Merryn Voysey et al.

Summary: The ChAdOx1 nCoV-19 vaccine has been shown to have an acceptable safety profile and effectiveness against symptomatic COVID-19, with higher efficacy observed in the group that received a low dose followed by a standard dose.

LANCET (2021)

Article Biochemistry & Molecular Biology

Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult

Benoit Morel et al.

Summary: Inferring reliable phylogenies from virus sequence data is difficult due to the large number of sequences and low number of mutations; rooting the inferred phylogeny with external outgroups or applying novel computational methods is not credible; automatic classification of current sequences into subclasses for molecular species delimitation is also not possible due to sequences being too closely related.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

Article Multidisciplinary Sciences

Correlates of protection against SARS-CoV-2 in rhesus macaques

Katherine McMahan et al.

Summary: Adoptive transfer of purified IgG from convalescent macaques protects naive macaques against SARS-CoV-2 infection, and cellular immune responses contribute to protection against rechallenge with SARS-CoV-2. The findings suggest that relatively low antibody titres are sufficient for protection against SARS-CoV-2 in macaques, while higher antibody titres are required for treatment of SARS-CoV-2 infection.

NATURE (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 Medicine, General & Internal

REGN-COV2, a Neutralizing Antibody Cocktail, in Outpatients with Covid-19

D. M. Weinreich et al.

Summary: Recent data indicate that complications and death from Covid-19 may be related to high viral loads. In this trial involving nonhospitalized patients, a cocktail of two neutralizing monoclonal antibodies (REGN-COV2) reduced viral load, with a greater effect in patients with no immune response or high viral load at baseline. Safety outcomes were similar between REGN-COV2 dose groups and the placebo group.

NEW ENGLAND JOURNAL OF MEDICINE (2021)

Article Multidisciplinary Sciences

Broad and potent activity against SARS-like viruses by an engineered human monoclonal antibody

C. Garrett Rappazzo et al.

Summary: The engineered antibody ADG-2 shows enhanced neutralization breadth and potency against a wide range of sarbecoviruses, providing complete protection in SARS and COVID-19 mouse models. Structural and biochemical studies reveal that ADG-2 targets a highly conserved epitope through a unique angle of approach.

SCIENCE (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 Multidisciplinary Sciences

Three-quarters attack rate of SARS-CoV-2 in the Brazilian Amazon during a largely unmitigated epidemic

Lewis F. Buss et al.

Summary: Research indicates that the attack rate of COVID-19 in Manaus, the capital of Amazonas state in northern Brazil, reached 66% in June 2020, rising to 76% by October, higher than the estimated attack rate of 29% in Sao Paulo, southeastern Brazil, during the same period.

SCIENCE (2021)

Review Virology

Structural Analysis of Neutralizing Epitopes of the SARS-CoV-2 Spike to Guide Therapy and Vaccine Design Strategies

Maxwell T. Finkelstein et al.

Summary: This review summarizes recent studies focusing on the development of monoclonal antibodies and vaccines against SARS-CoV-2. By studying the structural details of the virus, important information for the treatment and prevention of COVID-19 can be obtained.

VIRUSES-BASEL (2021)

Article Cell Biology

D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction

Sophie M-C Gobeil et al.

Summary: The study found that the mutation variant G614 of SARS-CoV-2 leads to significant changes in the protein structure, resulting in altered positioning ratio of RBD, which may have implications for vaccine design.

CELL REPORTS (2021)

Article Microbiology

The coronavirus proofreading exoribonuclease mediates extensive viral recombination

Jennifer Gribble et al.

Summary: Recombination is essential for coronavirus diversity and the emergence of new strains. The mechanisms of CoV recombination are not well understood, but studies have shown extensive and diverse recombination products in CoVs during replication. The nsp14-ExoN protein is crucial for native recombination in CoVs, highlighting its potential as a target for inhibitors to control SARS-CoV-2 and future emerging zoonotic CoVs.

PLOS PATHOGENS (2021)

Article Biology

Evidence for adaptive evolution in the receptor-binding domain of seasonal coronaviruses OC43 and 229e

Kathryn E. Kistler et al.

Summary: Seasonal coronaviruses, including OC43 and 229E, are undergoing adaptive evolution in regions of the viral spike protein exposed to human immune response, potentially leading to reinfection. This adaptive change may require continual vaccine updates for effective protection against these viruses.
Article Immunology

Epicutaneous immunization with modified vaccinia Ankara viral vectors generates superior T cell immunity against a respiratory viral challenge

Youdong Pan et al.

Summary: Studies have demonstrated that MVA vaccination through skin scarification generates a greater number of T cells with unique transcriptional characteristics, providing more effective protection against lethal respiratory virus challenges in mice.

NPJ VACCINES (2021)

Article Immunology

Comparison of Four SARS-CoV-2 Neutralization Assays

Lydia Riepler et al.

Summary: Neutralizing antibodies are crucial for protection against viruses like SARS-CoV-2. This study compared four different assays for detecting these antibodies and found that they were all robust and yielded comparable results, indicating their reliability.

VACCINES (2021)

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.
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.
Article Biochemistry & Molecular Biology

The antigenic anatomy of SARS-CoV-2 receptor binding domain

Wanwisa Dejnirattisai et al.

Summary: Antibodies play a crucial role in immune protection against SARS-CoV-2, with some being used as therapeutics. A study identified 377 human monoclonal antibodies, focusing on 80 that bind the virus spike, and found that most highly inhibitory antibodies can block the virus-receptor interaction. Novel binding modes of potent inhibitory antibodies were discovered, showing potential for prophylactic or therapeutic use in animal models.
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 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.
Article Biochemistry & Molecular Biology

Human neutralizing antibodies against SARS-CoV-2 require intact Fc effector functions for optimal therapeutic protection

Emma S. Winkler et al.

Summary: This study found that neutralizing human monoclonal antibodies in SARS-CoV-2-infected animals require Fc effector functions for optimal protection, reducing inflammation, improving respiratory mechanics, and being associated with diminished immune signaling and tissue repair.
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.
Article Microbiology

SARS-CoV-2 variant B.1.1.7 is susceptible to neutralizing antibodies elicited by ancestral spike vaccines

Xiaoying Shen et al.

Summary: Current COVID-19 vaccines target the ancestral SARS-CoV-2 spike, but the emerging B.1.1.7 variant with multiple spike mutations may impact some antibody therapies while posing no major concerns for vaccine efficacy or increased risk of reinfection.

CELL HOST & MICROBE (2021)

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)

Review Microbiology

The variant gambit: COVID-19's next move

Jessica A. Plante et al.

Summary: Despite the development of vaccines, COVID-19 caused by SARS-CoV-2 continues to be a global concern due to the emergence of new variants, raising worries about increased spread and potential impacts on immunity.

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 Microbiology

Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single supersite

Gabriele Cerutti et al.

Summary: Structural analysis revealed that seven potent NTD-directed neutralizing antibodies target a common surface on NTD, forming a single supersite different from the recognition pattern of RBD-directed antibodies.

CELL HOST & MICROBE (2021)

Article Infectious Diseases

Tracking SARS-CoV-2 lineage B.1.1.7 dissemination: insights from nationwide spike gene target failure (SGTF) and spike gene late detection (SGTL) data, Portugal, week 49 2020 to week 3 2021

Vitor Borges et al.

Summary: The study found that the B.1.1.7 lineage of SARS-CoV-2 is highly disseminated in Portugal, with an estimated 89% increase per week. RT-PCR spike gene target late detection (SGTL) can be a useful tool to track the spread, showing higher viral loads in SGTL/SGTF samples without significant age distribution shifts.

EUROSURVEILLANCE (2021)

Article Biochemistry & Molecular Biology

The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization

Rafael Bayarri-Olmos et al.

Summary: A new variant discovered in minks has shown enhanced transmission capacity but does not affect immunity in previously infected individuals or vaccine models. The rise in frequency of this variant in mink farms may be due to a fitness advantage conferred by receptor adaptation rather than evading immune responses.

JOURNAL OF BIOLOGICAL CHEMISTRY (2021)

Article Immunology

S-Variant SARS-CoV-2 Lineage B1.1.7 Is Associated With Significantly Higher Viral Load in Samples Tested by TaqPath Polymerase Chain Reaction

Michael Kidd et al.

Summary: Analysis of recent test data shows that samples containing the SARS-CoV-2 variant B1.1.7 with mutation Delta 69/70 exhibit S gene target failure (SGTF) in ThermoFisher TaqPath RT-qPCR. Samples with SGTF profile are more likely to have higher viral loads, indicating higher infectivity and rapid spread of this variant.

JOURNAL OF INFECTIOUS DISEASES (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

SARS-CoV-2 spike D614G change enhances replication and transmission

Bin Zhou et al.

Summary: Research has shown that the D614G substitution in the spike protein of SARS-CoV-2 leads to increased binding and replication potential in humans, as well as significantly higher replication and transmissibility in different animal models, providing an explanation for the global prevalence of this variant in the COVID-19 pandemic.

NATURE (2021)

Article Multidisciplinary Sciences

Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies

Dami A. Collier et al.

Summary: The B.1.1.7 variant of SARS-CoV-2 exhibited reduced neutralization by vaccines and antibodies from recovered COVID-19 patients, with a more substantial loss seen when introducing the E484K mutation. This mutation poses a threat to the efficacy of the BNT162b2 vaccine.

NATURE (2021)

Article Multidisciplinary Sciences

Detection of a SARS-CoV-2 variant of concern in South Africa

Houriiyah Tegally et al.

Summary: The article describes a newly emerged lineage of SARS-CoV-2, 501Y.V2, characterized by eight mutations in the spike protein, which may result in increased transmissibility or immune escape. This lineage originated in South Africa and quickly became dominant in Eastern Cape, Western Cape, and KwaZuluNatal provinces within weeks.

NATURE (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

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)

Article Biochemistry & Molecular Biology

SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma

Constantinos Kurt Wibmer et al.

Summary: The SARS-CoV-2 virus in the B.1.351 variant discovered in South Africa can evade neutralization by most antibodies when expressed, but does not affect binding by convalescent plasma. This suggests the potential for reinfection with antigenically distinct variants and predicts reduced efficacy of spike-based vaccines.

NATURE MEDICINE (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 Biochemistry & Molecular Biology

Neutralization of SARS-CoV-2 spike 69/70 deletion, E484K and N501Y variants by BNT162b2 vaccine-elicited sera

Xuping Xie et al.

Summary: The study found that human sera from recipients of the BNT162b2 vaccine can neutralize SARS-CoV-2 viruses containing key spike mutations from the newly emerged UK and SA variants.

NATURE MEDICINE (2021)

Article Biochemical Research Methods

Engineering SARS-CoV-2 using a reverse genetic system

Xuping Xie et al.

Summary: Reverse genetic system for SARS-CoV-2 is essential for studying viruses, developing vaccines, and screening antiviral drugs. However, manipulating the system is complex due to the large size of the coronavirus genome and toxic genomic elements, requiring a meticulous six-step process. Mastering this system will accelerate COVID-19 research across different scientific fields.

NATURE PROTOCOLS (2021)

Letter Medicine, General & Internal

Serum Neutralizing Activity Elicited by mRNA-1273 Vaccine

Kai Wu et al.

NEW ENGLAND JOURNAL OF MEDICINE (2021)

Article Multidisciplinary Sciences

Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England

Nicholas G. Davies et al.

Summary: A new variant of SARS-CoV-2 has emerged in England, with a higher reproduction number and potential for large resurgences of COVID-19 cases. Without stringent control measures, it is projected that COVID-19 hospitalizations and deaths in England for the first 6 months of 2021 will exceed those in 2020. The variant has spread globally and exhibited similar transmission increases in Denmark, Switzerland, and the United States.

SCIENCE (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 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)

Article Virology

SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations

Frederic Grabowski et al.

Summary: The novel SARS-CoV-2 Variant of Concern (VOC)-202012/01, known as B.1.1.7, first identified in the UK in September 2020, has rapidly spread globally and is of concern due to its potential impact on vaccine effectiveness. The VOC has acquired significant mutations, including some that may compromise the binding of neutralizing antibodies, and it is essential to monitor its molecular evolution to understand its impact on the ongoing pandemic.

VIRUSES-BASEL (2021)

Article Multidisciplinary Sciences

Discrete SARS-CoV-2 antibody titers track with functional humoral stability

Yannic C. Bartsch et al.

Summary: The study reveals significant heterogeneity in antibody responses following SARS-CoV-2 infection, with limited decay of antibody titers over time. Observing neutralization, Fc-function, and SARS-CoV-2 specific T cell responses requires reaching a certain threshold of receptor-binding domain (RBD)-specific antibody titers, indicating a switch-like relationship between antibody titer and function.

NATURE COMMUNICATIONS (2021)

Article Medicine, General & Internal

Risk of mortality in patients infected with SARS-CoV-2 variant of concern 202012/1: matched cohort study

Robert Challen et al.

Summary: The study found that the mortality hazard ratio associated with infection with VOC-202012/1 compared with previously circulating variants was 1.64, indicating an increase in deaths from 2.5 to 4.1 per 1000 detected cases in comparatively low risk group of covid-19 patients in the community. This suggests that infection with VOC-202012/1 may lead to substantial additional mortality compared with previously circulating variants, impacting healthcare capacity planning and control policies.

BMJ-BRITISH MEDICAL JOURNAL (2021)

Article Cell Biology

The effect of spike mutations on SARS-CoV-2 neutralization

Chloe Rees-Spear et al.

Summary: The study found that emerging variants of the coronavirus may lead to reduced neutralization by antibodies induced by vaccines or previous infection, but some samples still retain effectiveness. This highlights the importance of real-time monitoring of emerging mutations and their impact on vaccine efficacy.

CELL REPORTS (2021)

Article Biochemistry & Molecular Biology

Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen

Oscar A. MacLean et al.

Summary: The study suggests that SARS-CoV-2 has undergone limited significant adaptation to humans, with evidence of moderate positive selection concentrated in the early phases of the pandemic. In contrast, bat Sarbecoviruses show evidence of significant positive selection and an adaptive depletion in CpG composition. This indicates that the progenitor of SARS-CoV-2 likely acquired efficient human-human transmission capabilities through evolutionary history in bats, leading to the emergence of a relatively generalist virus.

PLOS BIOLOGY (2021)

Article Immunology

SARS-CoV-2 mutations in MHC-I-restricted epitopes evade CD8(+) T cell responses

Benedikt Agerer et al.

Summary: The study identified nonsynonymous mutations in MHC-I-restricted CD8(+) T cell epitopes of SARS-CoV-2 virus isolates, which resulted in diminished MHC-I binding of mutant peptides. This led to decreased proliferation, IFN-gamma production, and cytotoxic activity of CD8(+) T cells, along with qualitative differences in the transcriptional response to mutant peptides. These findings highlight the ability of SARS-CoV-2 to evade CD8(+) T cell surveillance through point mutations in MHC-I-restricted viral epitopes.

SCIENCE IMMUNOLOGY (2021)

Article Biochemistry & Molecular Biology

N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2

Matthew McCallum et al.

Summary: The study identifies 41 human monoclonal antibodies that recognize the N-terminal domain of the SARS-CoV-2 spike protein and exhibit strong neutralizing activity. These antibodies inhibit cell-to-cell fusion, activate effector functions, and protect animals from virus challenge, highlighting the importance of NTD-specific neutralizing antibodies for protective immunity and vaccine development. Several SARS-CoV-2 variants with mutations in the NTD supersite suggest ongoing selective pressure on the virus.
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.
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.
Article Biochemistry & Molecular Biology

Antibody evasion by the P.1 strain of SARS-CoV-2

Wanwisa Dejnirattisai et al.

Summary: Ending the SARS-CoV-2 pandemic requires global vaccination. New virus strains with mutations impact antibody responses, but some variants are less resistant than others. A monoclonal antibody can neutralize different variants and partially restore neutralization potency for other public antibodies.
Article Microbiology

Infection- and vaccine-induced antibody binding and neutralization of the B.1.351 SARS-CoV-2 variant

Venkata Viswanadh Edara et al.

Summary: Despite reduced antibody titers against the B.1.351 variant, sera from infected and vaccinated individuals containing polyclonal antibodies to the spike protein could still neutralize SARS-CoV-2 B.1.351, suggesting that protective humoral immunity may be retained against this variant.

CELL HOST & MICROBE (2021)

Article Microbiology

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

Pengfei Wang et al.

Summary: The emerging Brazilian variant P.1 shows increased resistance to antibody neutralization, posing a threat to current antibody therapies, but has less impact on the effectiveness of protective vaccines.

CELL HOST & MICROBE (2021)

Article Immunology

Sera Neutralizing Activities Against Severe Acute Respiratory Syndrome Coronavirus 2 and Multiple Variants 6 Months After Hospitalization for Coronavirus Disease 2019

Maureen Betton et al.

Summary: After COVID-19 infection, levels of IgG antibodies and neutralization activity against SARS-CoV-2 decrease over time, but do not imply loss of neutralizing capacity; A few patients showed negative serological status 6 months post-infection; IgG levels correlate with neutralization and show a stronger correlation for anti-S antibodies.

CLINICAL INFECTIOUS DISEASES (2021)

Article Infectious Diseases

Case fatality risk of the SARS-CoV-2 variant of concern B.1.1.7 in England, 16 November to 5 February

Daniel J. Grint et al.

Summary: The SARS-CoV-2 B.1.1.7 VOC is spreading across Europe and poses a higher risk of death compared to non-VOC cases, with increased mortality in older individuals and those with comorbidities. This variant has the potential to spread faster and cause higher mortality than previous strains.

EUROSURVEILLANCE (2021)

Letter Medicine, General & Internal

Neutralizing Antibodies Against SARS-CoV-2 Variants After Infection and Vaccination

Venkata Viswanadh Edara et al.

Summary: This study investigates the neutralizing antibody response to 4 SARS-CoV-2 variants in individuals who have been infected or vaccinated.

JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION (2021)

Article Virology

Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K

Simone Di Giacomo et al.

Summary: In this study, analysis of more than 1,000,000 SARS-CoV-2 genomic sequences deposited on the GISAID public repository up to April 27, 2021, revealed a novel T478K mutation located on the SARS-CoV-2 Spike protein. The mutation has predominantly emerged in Mexico and the United States since January 2021, but has also been detected in several European countries.

JOURNAL OF MEDICAL VIROLOGY (2021)

Article Medicine, General & Internal

Impact and effectiveness of mRNA BNT162b2 vaccine against SARS-CoV-2 infections and COVID-19 cases, hospitalisations, and deaths following a nationwide vaccination campaign in Israel: an observational study using national surveillance data

Eric J. Haas et al.

Summary: This study assessed the real-world effectiveness of the Pfizer-BioNTech mRNA COVID-19 vaccine BNT162b2 in Israel, showing high efficacy in preventing SARS-CoV-2 infections, hospitalizations, severe disease, and death. As vaccine coverage increased, there were marked declines in SARS-CoV-2 outcomes, indicating that COVID-19 vaccination can help control the pandemic.

LANCET (2021)

Article Medicine, General & Internal

Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 variant of concern 202012/01 (B.1.1.7): an exploratory analysis of a randomised controlled trial

Katherine R. W. Emary et al.

Summary: A post-hoc analysis was conducted on the efficacy of the ChAdOx1 nCoV-19 vaccine against the B.1.1.7 variant of SARS-CoV-2 in the UK. The vaccine showed reduced neutralisation activity against the B.1.1.7 variant in vitro, but still demonstrated efficacy against the B.1.1.7 variant of the virus.

LANCET (2021)

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)

Article Multidisciplinary Sciences

Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7

Nicholas G. Davies et al.

Summary: Studies have shown that the SARS-CoV-2 B.1.1.7 lineage is more transmissible and may cause more severe illness compared to pre-existing variants.

NATURE (2021)

Article Multidisciplinary Sciences

Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England

Erik Volz et al.

Summary: Genetic and testing data from England indicate that the SARS-CoV-2 variant B.1.1.7 has a transmission advantage over other lineages, showing a rapid expansion during autumn 2020. Analysis of S gene target failures (SGTF) in community-based diagnostic PCR testing suggests that B.1.1.7 is more transmissible than non-variant of concern lineages and has a significant transmission advantage, with a reproduction number 50% to 100% higher. Additionally, cases of B.1.1.7 appear to include a larger share of under 20-year-olds compared to non-variant cases.

NATURE (2021)

Article Biochemistry & Molecular Biology

Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies

Delphine Planas et al.

Summary: The ability of convalescent sera from individuals with coronavirus disease 2019 and those vaccinated with BNT162b2 to neutralize SARS-CoV-2 variants B1.1.7 and B.1.351 decreases, but increases after two vaccine doses. The study found that the B.1.1.7 and B.1.351 variants may have acquired partial resistance to neutralizing antibodies generated by natural infection or vaccination, particularly in individuals with low antibody levels. This suggests that the B.1.351 variant may pose a greater risk of infection in immunized individuals.

NATURE MEDICINE (2021)

Article Biochemistry & Molecular Biology

Neutralizing antibody levels are highly predictive of immune protection from symptomatic SARS-CoV-2 infection

David S. Khoury et al.

Summary: The level of neutralizing antibodies is closely related to immune protection against COVID-19, playing a crucial role in protecting against detected infection and severe infection. Studies have shown that neutralizing titers will decline over time after vaccination, leading to decreased protection against SARS-CoV-2 infection.

NATURE MEDICINE (2021)

Letter Medicine, General & Internal

Effectiveness of the BNT162b2 Covid-19 Vaccine against the B.1.1.7 and B.1.351 Variants

Laith J. Abu-Raddad et al.

NEW ENGLAND JOURNAL OF MEDICINE (2021)

Letter Medicine, General & Internal

Neutralization of SARS-CoV-2 Variants B.1.429 and B.1.351

Xiaoying Shen et al.

NEW ENGLAND JOURNAL OF MEDICINE (2021)

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)

Letter Medicine, General & Internal

Susceptibility of Circulating SARS-CoV-2 Variants to Neutralization

Guo-Lin Wang et al.

NEW ENGLAND JOURNAL OF MEDICINE (2021)

Letter Medicine, General & Internal

BNT162b2-Elicited Neutralization against New SARS-CoV-2 Spike Variants

Yang Liu et al.

NEW ENGLAND JOURNAL OF MEDICINE (2021)

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)

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)

Article Multidisciplinary Sciences

Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil

Nuno R. Faria et al.

Summary: A new variant of concern, P.1, with 17 mutations including three spike protein mutations associated with increased binding to human ACE2 receptors, emerged in Manaus, Brazil between November 2020 and January 2021. Molecular analysis suggests P.1 may be 1.7- to 2.4-fold more transmissible and that previous infection may provide 54 to 79% protection against P.1 infection compared to other lineages. Enhanced global genomic surveillance of such variants is crucial for pandemic response.

SCIENCE (2021)

Article Microbiology

A human coronavirus evolves antigenically to escape antibody immunity

Rachel T. Eguia et al.

Summary: This study investigates the evolution of human coronavirus 229E and finds that as the virus evolves, mutations in the spike protein can escape neutralization by antibodies in old human sera. The results suggest that viral evolution may impact immunity, highlighting the need for periodic updates to coronavirus vaccines.

PLOS PATHOGENS (2021)

Article Public, Environmental & Occupational Health

Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study

Mark S. Graham et al.

Summary: The study showed that the B.1.1.7 variant did not result in changes in COVID-19 symptoms or duration of illness, and there was no significant increase in reinfection rate compared to previous variants.

LANCET PUBLIC HEALTH (2021)

Article Immunology

SARS-CoV-2 genome-wide T cell epitope mapping reveals immunodominance and substantial CD8+ T cell activation in COVID-19 patients

Sunil Kumar Saini et al.

Summary: This study experimentally evaluated MHC class I-binding peptides covering the complete SARS-CoV-2 genome, revealing significant CD8(+) T cell recognition of SARS-CoV-2 epitopes in patients with COVID-19, coupled with strong activation features in these T cells. Compared to healthy individuals, patients with severe disease displayed larger populations of SARS-CoV-2-specific T cells.

SCIENCE IMMUNOLOGY (2021)

Article Multidisciplinary Sciences

Learning from HIV-1 to predict the immunogenicity of T cell epitopes in SARS-CoV-2

Ang Gao et al.

Summary: A physics-based learning model was used to predict the immunogenicity of CTL epitopes derived from SARS-CoV-2, showing that only some epitopes are immunogenic, with spike protein epitopes being less likely to provide broad immune coverage. Additionally, some immunogenic SARS-CoV-2 CTL epitopes were found to be identical to those of seasonal coronaviruses, suggesting existing CTL immunity against COVID-19 in some individuals prior to infection.

ISCIENCE (2021)

Article Rheumatology

Immunogenicity and safety of the BNT162b2 mRNA COVID-19 vaccine in adult patients with autoimmune inflammatory rheumatic diseases and in the general population: a multicentre study

Victoria Furer et al.

Summary: Vaccination with mRNA BNT162b2 vaccine showed reduced immunogenicity in patients with AIIRD compared to the general population, with risk factors including older age and treatment with glucocorticoids, rituximab, mycophenolate mofetil (MMF), and abatacept. However, most patients maintained stable disease activity post-vaccination.

ANNALS OF THE RHEUMATIC DISEASES (2021)

Article Biochemistry & Molecular Biology

Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum

Chang Liu et al.

Summary: Recent study examined the neutralizing ability of monoclonal antibodies, convalescent and vaccine sera against the Indian variants B.1.617.1 and B.1.617.2, showing that the neutralization of these variants is reduced compared to the ancestral strains, without widespread antibody escape as seen in other variants like B.1.351.
Review Biochemistry & Molecular Biology

Tackling COVID-19 with neutralizing monoclonal antibodies

Davide Corti et al.

Summary: Monoclonal antibodies have revolutionized the treatment of several human diseases, including cancer, autoimmunity, and infectious diseases. Lessons learned from the COVID-19 pandemic have paved the way for the development of more monoclonal antibody-based therapeutics.
Article Biochemistry & Molecular Biology

The monoclonal antibody combination REGEN-COV protects against SARS-CoV-2 mutational escape in preclinical and human studies

Richard Copin et al.

Summary: Monoclonal antibodies against SARS-CoV-2 are clinically validated therapeutic options against COVID-19. Studies show that non-competing antibody combinations in REGEN-COV provide protection against all current variants of concern and prevent the emergence of new variants.
Review Microbiology

SARS-CoV-2 human T cell epitopes: Adaptive immune response against COVID-19

Alba Grifoni et al.

Summary: This review summarizes recent studies on SARS-CoV-2 T cell epitopes, highlighting the significant correlation between epitope number and antigen size. It also presents an analysis of 1,400 different reported SARS-CoV-2 epitopes and identifies discrete immunodominant regions of the virus and more prevalently recognized epitopes.

CELL HOST & MICROBE (2021)

Article Microbiology

SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity

Chihiro Motozono et al.

Summary: Research has shown that certain mutations in SARS-CoV-2 variants can escape HLA-restricted cellular immunity, increase affinity for host cells, promote viral replication, and potentially affect the evolution of viral phenotypes.

CELL HOST & MICROBE (2021)

Article Microbiology

A single dose of the SARS-CoV-2 vaccine BNT162b2 elicits Fc-mediated antibody effector functions and T cell responses

Alexandra Tauzin et al.

Summary: A single dose of the BNT162b2 mRNA vaccine can be up to 90% effective, with boosted humoral and T cell responses in previously infected individuals. Therefore, spacing doses may help vaccinate more people in conditions of limited vaccine supply.

CELL HOST & MICROBE (2021)

Review Microbiology

Antibody and B cell responses to SARS-CoV-2 infection and vaccination

Katharina Roltgen et al.

Summary: Human immune responses to SARS-CoV-2 have made significant progress in understanding the nature of antibody responses and their role in protecting against infection or modulating the severity of COVID-19, aiding in the development of effective vaccines. However, important questions remain unanswered regarding the duration and effectiveness of antibody responses, immunity differences between infection and vaccination, cellular basis for serological findings, and the potential impact of viral variants on current immunity.

CELL HOST & MICROBE (2021)

Article Immunology

Affinity maturation of SARS-CoV-2 neutralizing antibodies confers potency, breadth, and resilience to viral escape mutations

Frauke Muecksch et al.

Summary: This study examined the development of antibodies following infection with the coronavirus, finding that evolved antibodies had increased affinity and neutralization potency, altered mutational pathways for viral resistance, and restricted neutralization escape options. These findings suggest that increasing antibody diversity through prolonged or repeated antigen exposure may improve protection against diversifying populations of the virus and other pandemic threat coronaviruses.

IMMUNITY (2021)

Article Immunology

Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species

Ruoke Wang et al.

Summary: Research shows that the South African B.1.351 variant exhibits the highest resistance to current monoclonal antibodies and convalescent plasma from COVID-19-infected individuals, and the molecular basis for this resistance and potential antibody escape has been identified.

IMMUNITY (2021)

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)

Article Microbiology

Evaluation of Cell-Based and Surrogate SARS-CoV-2 Neutralization Assays

Anton M. Sholukh et al.

Summary: This study compared five neutralization assays using plasma samples from convalescent individuals with mild to moderate COVID-19. The cell-based assays showed high correlation and can be used for valid cross-study comparisons.

JOURNAL OF CLINICAL MICROBIOLOGY (2021)

Article Immunology

SARS-CoV-2 B.1.617 Mutations L452R and E484Q Are Not Synergistic for Antibody Evasion

Isabella A. T. M. Ferreira et al.

Summary: The SARS-CoV-2 B.1.617 variant from India with key mutations L452R and E484Q shows reduced sensitivity to neutralizing antibodies elicited by the BNT162b2 mRNA vaccine, similar to the effect of L452R or E484Q mutations alone.

JOURNAL OF INFECTIOUS DISEASES (2021)

Article Biochemistry & Molecular Biology

Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants

Charlie Laffeber et al.

Summary: Different mutations in new variants of SARS-CoV-2 have varying effects on receptor binding affinity, viral transmission, and immune evasion, highlighting the importance of global viral genome surveillance and functional characterization.

JOURNAL OF MOLECULAR BIOLOGY (2021)

Editorial Material Public, Environmental & Occupational Health

Neutralization of Beta and Delta variant with sera of COVID-19 recovered cases and vaccinees of inactivated COVID-19 vaccine BBV152/Covaxin

Pragya D. Yadav et al.

JOURNAL OF TRAVEL MEDICINE (2021)

Article Multidisciplinary Sciences

Age-related immune response heterogeneity to SARS-CoV-2 vaccine BNT162b2

Dami A. Collier et al.

Summary: Elderly individuals, especially those above eighty, show lower immune responses and neutralization abilities against variants of concern after the first vaccine dose, but this improves after the second dose. They have higher frequencies of spike-specific memory B cells but reduced somatic hypermutation of class-switched cells. Production of interferon-gamma and interleukin-2 by SARS-CoV-2 spike-specific T cells is lower in older participants, predominantly by CD4 T cells.

NATURE (2021)

Article Multidisciplinary Sciences

Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization

Delphine Planas et al.

Summary: The SARS-CoV-2 B.1.617 Delta variant, first identified in India in 2020, has become dominant in some regions and is spreading to many countries. This variant shows resistance to certain monoclonal antibodies and antibodies in convalescent sera, as well as reduced neutralization by some COVID-19 vaccines. Administration of two doses of the vaccine is needed for a neutralizing response against the Delta variant.

NATURE (2021)

Article Multidisciplinary Sciences

SARS-CoV-2 mRNA vaccines induce persistent human germinal centre responses

Jackson S. Turner et al.

Summary: SARS-CoV-2 mRNA vaccines induce a persistent germinal centre B cell response in humans, leading to the generation of robust humoral immunity, especially more significant in individuals previously infected with the virus.

NATURE (2021)

Article Multidisciplinary Sciences

BNT162b2-elicited neutralization of B.1.617 and other SARS-CoV-2 variants

Jianying Liu et al.

Summary: Serum samples from individuals vaccinated with the BNT162b2 vaccine can neutralize various SARS-CoV-2 variants, indicating mass immunization as a central strategy to end the global COVID-19 pandemic.

NATURE (2021)

Article Multidisciplinary Sciences

Spread of a SARS-CoV-2 variant through Europe in the summer of 2020

Emma B. Hodcroft et al.

Summary: A variant of SARS-CoV-2, 20E (EU1), was identified in Spain in early summer 2020 and later spread across Europe. Despite not showing increased transmissibility, the variant's success can be attributed to rising incidence in Spain, resumption of travel, and lack of effective screening and containment measures. Travel played a significant role in introducing the variant multiple times to European countries during the summer, undermining local efforts to prevent SARS-CoV-2 infection.

NATURE (2021)

Article Multidisciplinary Sciences

Naturally enhanced neutralizing breadth against SARS-CoV-2 one year after infection

Zijun Wang et al.

Summary: Despite challenges posed by COVID-19 variants, convalescent individuals receiving mRNA vaccines exhibit robust and long-lasting immune responses against circulating SARS-CoV-2 variants, providing hope for effective control of the pandemic.

NATURE (2021)

Article Biochemistry & Molecular Biology

CD8+ T cells contribute to survival in patients with COVID-19 and hematologic cancer

Erin M. Bange et al.

Summary: In patients with cancer and COVID-19, those with hematologic cancer show impaired immune responses compared to solid cancer patients. CD8 T cells play a crucial role in survival, even in the presence of limited humoral responses. The presence of SARS-CoV-2-specific T cell responses in hematologic cancer patients suggests a potential therapeutic target.

NATURE MEDICINE (2021)

Article Biochemistry & Molecular Biology

Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2-mRNA-vaccinated individuals

Talia Kustin et al.

Summary: Breakthrough SARS-CoV-2 infections post-vaccination may be caused by B.1.1.7 or B.1.351 variants, indicating the importance of robust vaccination. Reduced vaccine effectiveness against these variants was observed in the study, highlighting the need for continued surveillance and enhanced vaccination efforts.

NATURE MEDICINE (2021)

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)

Article Medicine, General & Internal

Safety and Efficacy of NVX-CoV2373 Covid-19 Vaccine

Paul T. Heath et al.

Summary: The NVX-CoV2373 vaccine demonstrated an efficacy of 89.7% in a phase 3 trial with over 15,000 participants, with mild and transient reactogenicity. It showed high efficacy against the B.1.1.7 variant and a low incidence of adverse events.

NEW ENGLAND JOURNAL OF MEDICINE (2021)

Letter Medicine, General & Internal

Infection and Vaccine-Induced Neutralizing-Antibody Responses to the SARS-CoV-2 B.1.617 Variants

Venkata-Viswanadh Edara et al.

NEW ENGLAND JOURNAL OF MEDICINE (2021)

Article Medicine, General & Internal

SARS-CoV-2 Variants and Vaccines

Philip R. Krause et al.

NEW ENGLAND JOURNAL OF MEDICINE (2021)

Article Multidisciplinary Sciences

SARS-CoV-2 immune evasion by the B.1.427/B.1.429 variant of concern

Matthew McCallum et al.

Summary: The novel CAL.20C (B.1.427/B.1.429) variant carries spike protein mutations, resulting in reduced neutralizing titers in vaccinated individuals and convalescent individuals. The L452R mutation reduces neutralizing activity in RBD-specific monoclonal antibodies, while the S13I and W152C mutations lead to the total loss of neutralization in NTD-specific antibodies due to antigenic supersite remodeling.

SCIENCE (2021)

Article Multidisciplinary Sciences

Durability of mRNA-1273 vaccine-induced antibodies against SARS-CoV-2 variants

Amarendra Pegu et al.

Summary: The study assessed the impact of SARS-CoV-2 variants on antibody responses induced by the mRNA vaccine over 7 months, showing that most individuals maintained binding and functional antibodies against variants, with B.1.351 having the lowest antibody recognition.

SCIENCE (2021)

Article Cell Biology

Antibodies elicited by mRNA-1273 vaccination bind more broadly to the receptor binding domain than do those from SARS-CoV-2 infection

Allison J. Greaney et al.

Summary: Vaccine-elicited antibodies have more focused neutralizing activity on the RBD of the SARS-CoV-2 spike protein, while infection-elicited antibodies have broader binding across epitopes; hence, single RBD mutations have less impact on neutralization by vaccine sera.

SCIENCE TRANSLATIONAL MEDICINE (2021)

Article Immunology

Evidence for antibody as a protective correlate for COVID-19 vaccines

Kristen A. Earle et al.

Summary: The study found a strong correlation between antibody titers and efficacy when assessing different COVID-19 vaccines, supporting the use of post-immunization antibody titers as the basis for establishing a correlate of protection for COVID-19 vaccines.

VACCINE (2021)

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)

Article Microbiology

B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies

Hao Zhou et al.

Summary: A new SARS-CoV-2 variant B.1.526 has been identified in New York City and is spreading rapidly, but current evidence suggests that vaccine-elicited antibodies and Regeneron therapeutic monoclonal antibodies remain effective in combating the B.1.526 variant.
Article Microbiology

Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes

Takuya Tada et al.

Summary: Convalescent-phase sera and antibodies elicited by Pfizer BNT162b2 vaccination can still neutralize several SARS-CoV-2 variants effectively, while Regeneron monoclonal antibodies may be less effective against certain variants, suggesting the need for continued surveillance for potential new variants.
Article Cell Biology

SARS-CoV-2 variant B.1.617 is resistant to bamlanivimab and evades antibodies induced by infection and vaccination

Markus Hoffmann et al.

Summary: The emergence of the B.1.617 variant in India may be responsible for the sharp increase in COVID-19 cases and deaths. B.1.617 shows increased efficiency in entering cells and evades antibody responses, contributing to its rapid spread.

CELL REPORTS (2021)

Article Cell Biology

Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7

Bo Meng et al.

Summary: The Delta H69N70 mutation in SARS-CoV-2 spike protein increases infectivity and partially rescues immune escape mutations that impair infectivity. Continued surveillance and research on deletions with functional effects are necessary.

CELL REPORTS (2021)

Article Biology

Reduced antibody cross-reactivity following infection with B.1.1.7 than with parental SARS-CoV-2 strains

Nikhil Faulkner et al.

Summary: The study found that antibodies elicited by infection with the B.1.1.7 variant exhibited significantly reduced recognition and neutralization of parental strains or the South Africa variant B.1.351, indicating an asymmetric heterotypic immunity induced by SARS-CoV-2 variants.
Article Cell Biology

Impact of SARS-CoV-2 variants on the total CD4+ and CD8+ T cell reactivity in infected or vaccinated individuals

Alison Tarke et al.

Summary: The study showed that SARS-CoV-2 variants do not significantly disrupt total T cell reactivity, although decreases in response frequency of 10%-22% were observed under certain assay/VOC combinations. This underscores the importance of actively monitoring T cell responses in the context of SARS-CoV-2 evolution.

CELL REPORTS MEDICINE (2021)

Letter Infectious Diseases

SARS-CoV-2 spike E484K mutation reduces antibody neutralisation

Sonia Jangra et al.

LANCET MICROBE (2021)

Article Cell Biology

Cross-reactive coronavirus antibodies with diverse epitope specificities and Fc effector functions

Andrea R. Shiakolas et al.

Summary: Research identifies antibodies from a recovered SARS-CoV donor sample that cross-react with the spike proteins of highly pathogenic SARS-CoV and SARS-CoV-2, as well as other coronaviruses. These antibodies mediate phagocytosis in vitro and reduce hemorrhagic pathology in murine lungs in vivo.

CELL REPORTS MEDICINE (2021)

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)

Article Immunology

The first 12 months of COVID-19: a timeline of immunological insights

Thiago Carvalho et al.

Summary: The timeline of major scientific discoveries during the first year of the COVID-19 pandemic highlights the collaborative efforts that led to rapid progress in understanding the immune response to SARS-CoV-2. It showcases the unprecedented convergence of research efforts on COVID-19 and identifies gaps in knowledge for future investigations.

NATURE REVIEWS IMMUNOLOGY (2021)

Article Biochemistry & Molecular Biology

Functional importance of the D614G mutation in the SARS-CoV-2 spike protein

Cody B. Jackson et al.

Summary: The D614G spike mutation in SARS-CoV-2 virus leads to more efficient infection of cells and animals, without affecting the affinity of the S protein for ACE2. This mutation is significant in the current global pandemic.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2021)

Article Cell Biology

Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases

Alison Tarke et al.

Summary: By studying T cell responses in 99 convalescent COVID-19 cases, we identified various HLA-restricted epitopes derived from SARS-CoV-2 and observed distinct patterns of immunodominance. The epitopes were combined into megapools to facilitate the identification and quantification of virus-specific CD4(+) and CD8(+) T cells.

CELL REPORTS MEDICINE (2021)

Article Multidisciplinary Sciences

Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans

Bas B. Oude Munnink et al.

Summary: Animal experiments have shown that various animals can be infected by SARS-CoV-2, with evidence of animal-to-human transmission within mink farms. Investigation into mink farm outbreaks revealed that the virus was initially introduced by humans and has since evolved, causing transmission between mink farms. Despite enhanced biosecurity measures and culling, transmission occurred between farms in three large clusters with unknown modes of transmission, resulting in a high percentage of infections among mink farm residents and employees.

SCIENCE (2021)

Review Microbiology

Coronavirus biology and replication: implications for SARS-CoV-2

Philip V'kovski et al.

Summary: This review discusses key aspects of coronavirus biology and their implications for SARS-CoV-2 infections, treatment, and prevention strategies. Understanding virus-host interactions at the molecular level is crucial for developing effective intervention strategies. Summarizing the discoveries of SARS-CoV-2 infection and comparing it with other coronaviruses will support future preparedness and combat strategies.

NATURE REVIEWS MICROBIOLOGY (2021)

Article Multidisciplinary Sciences

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

Daniel Wrapp et al.

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