☆ 4.7 Review

Clinical Characteristics, Transmissibility, Pathogenicity, Susceptible Populations, and Re-infectivity of Prominent COVID-19 Variants

AGING AND DISEASE (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 Biochemical Research Methods

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

Shaolei Teng et al.

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

BRIEFINGS IN BIOINFORMATICS (2021)

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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)

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Review Biochemistry & Molecular Biology

Structure and regulation of coronavirus genomes: state-of-the-art and novel insights from SARS-CoV-2 studies

Ilaria Manfredonia et al.

Summary: Coronaviruses are positive-sense single-stranded RNA viruses with the largest viral RNA genomes known to date. In addition to encoding viral proteins, certain regions of CoV genomes fold into stable structures that control various aspects of the virus life cycle. Recent discoveries from analyzing the SARS-CoV-2 genome have contributed to our understanding of CoV RNA structures.

BIOCHEMICAL SOCIETY TRANSACTIONS (2021)

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Article Biochemistry & Molecular Biology

Mutation-induced changes in the receptor-binding interface of the SARS-CoV-2 Delta variant B.1.617.2 and implications for immune evasion

Prabin Baral et al.

Summary: The surges of the more infectious Delta variant have intensified the health crisis, but current vaccines offer protection against it. However, the Delta variant can evade the immune system to some extent by reducing the receptivity of neutralizing antibodies.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2021)

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Article Medicine, General & Internal

Antibody Status and Incidence of SARS-CoV-2 Infection in Health Care Workers

S. F. Lumley et al.

Summary: In a longitudinal study of seropositive and seronegative health care workers undergoing asymptomatic and symptomatic SARS-CoV-2 testing, the presence of anti-spike or anti-nucleocapsid IgG antibodies was associated with a substantially reduced risk of SARS-CoV-2 reinfection in the ensuing 6 months.

NEW ENGLAND JOURNAL OF MEDICINE (2021)

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Article Public, Environmental & Occupational Health

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

Summer E. Galloway et al.

MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT (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 Infectious Diseases

Infection sustained by lineage B.1.1.7 of SARS-CoV-2 is characterised by longer persistence and higher viral RNA loads in nasopharyngeal swabs

Paolo Calistri et al.

Summary: A targeted surveillance in the Abruzzo region of Italy detected 313 persons affected by lineage B.1.1.7, with statistically significant differences in viral load and persistence compared to other lineages. In individuals infected with B.1.1.7 lineage, lower values of C-T associated with the detection of the N protein encoding gene and longer persistence of SARS-CoV-2 RNA in nasopharyngeal swabs were observed.

INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES (2021)

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Letter Virology

Genomic Characterization of a Novel SARS-CoV-2 Lineage from Rio de Janeiro, Brazil

Carolina M. Voloch et al.

JOURNAL OF VIROLOGY (2021)

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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)

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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)

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Review Cell Biology

COVID-19 vaccines: rapid development, implications, challenges and future prospects

Shivaji Kashte et al.

Summary: The COVID-19 pandemic has posed unprecedented challenges globally, leading to rapid development and distribution of vaccines to combat the virus. However, the accelerated development and Emergency Use Authorization of COVID-19 vaccines still raise many unanswered questions and challenges.

HUMAN CELL (2021)

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Letter Pediatrics

Effect of the new SARS-CoV-2 variant B.1.1.7 on children and young people

Sarah Brookman et al.

LANCET CHILD & ADOLESCENT HEALTH (2021)

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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.

CELL (2021)

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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)

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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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Article Biochemistry & Molecular Biology

Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations

Binquan Luan et al.

Summary: Recently emerged SARS-CoV-2 variants with mutations, such as N501Y, may enhance binding to hACE2. Molecular dynamics simulations show that Y501 in the mutated RBD can interact with Y41 and K353 in hACE2, potentially increasing the overall binding affinity by approximately 0.81 kcal center dot mol(-1). This binding dynamics may aid in designing more effective antibodies.

FEBS LETTERS (2021)

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Article Infectious Diseases

Early detection of P.1 variant of SARS-CoV-2 in a cluster of cases in Salvador, Brazil

Isadora Cristina de Siqueira et al.

Summary: Three cases of severe COVID-19 caused by the SARS-CoV-2 P.1 lineage were reported in a familial cluster detected in Salvador, Bahia, Brazil, linked to travel by family members from Amazonas to Bahia in late December 2020. This highlights the cryptic transmission of the SARS-CoV-2 P.1 lineage across Brazil and emphasizes the importance of genomic surveillance in tracking the emergence of new variants of concern.

INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES (2021)

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Article Cell Biology

Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data

Abbas Khan et al.

Summary: The new variants of SARS-CoV-2 are more contagious and require further investigation on their interaction with the host receptor to identify new therapeutic options. Specific mutations in the Spike glycoprotein of the new variants may play a critical role in their unique pathogenicity.

JOURNAL OF CELLULAR PHYSIOLOGY (2021)

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Letter Infectious Diseases

The 501Y.V2 SARS-CoV-2 variant has an intermediate viral load between the 501Y.V1 and the historical variants in nasopharyngeal samples from newly diagnosed COVID-19 patients

Elisa Teyssou et al.

JOURNAL OF INFECTION (2021)

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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)

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Article Immunology

The effect of SARS-CoV-2 D614G mutation on BNT162b2 vaccine-elicited neutralization

Jing Zou et al.

Summary: The D614G mutation modestly reduced SARS-CoV-2 neutralization by sera elicited from BNT162b2 vaccine in mice, rhesus monkeys, and humans, but the vaccine efficacy was consistent with the 95% observed in clinical trials.

NPJ VACCINES (2021)

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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)

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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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Article Virology

Genomic analysis reveals a rapid spread and predominance of lambda (C.37) SARS-COV-2 lineage in Peru despite circulation of variants of concern

Carlos Padilla-Rojas et al.

Summary: The pandemic caused by SARS-Cov-2 has hit South America hard, with new variants raising concerns over evasion of vaccine protection, increased transmissibility, or higher virulence. Genomic surveillance in Peru revealed a significant rise of the lambda lineage, becoming predominant from January to April 2021, warranting close monitoring for potential variant of concern status.

JOURNAL OF MEDICAL VIROLOGY (2021)

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Letter Virology

A cluster of the new SARS-CoV-2 B.1.621 lineage in Italy and sensitivity of the viral isolate to the BNT162b2 vaccine

Serena Messali et al.

JOURNAL OF MEDICAL VIROLOGY (2021)

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Article Biochemistry & Molecular Biology

COVID-19 in Amazonas, Brazil, was driven by the persistence of endemic lineages and P.1 emergence

Felipe Gomes Naveca et al.

Summary: Analysis of circulating SARS-CoV-2 viruses during the first and second waves of COVID-19 in Amazonas, Brazil, shows successive lineage replacements led to predominance of the variant of concern P.1 and are associated with variable levels of social distancing.

NATURE MEDICINE (2021)

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Article Multidisciplinary Sciences

Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York

Anthony P. West et al.

Summary: Wide-scale SARS-CoV-2 genome sequencing is crucial for tracking viral evolution. The software tool Variant Database was developed to quickly examine spike mutations, and the emergence and spread of the B.1.526 lineage in New York has extended the second wave of COVID-19 cases.

NATURE COMMUNICATIONS (2021)

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Article Biochemical Research Methods

Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants

Natalia Teruel et al.

Summary: This study uses normal mode analysis to simulate the dynamics of the SARS-CoV-2 Spike protein, identifying mutations that can increase the open-state occupancy and potentially impact viral infectivity and evolutionary processes.

PLOS COMPUTATIONAL BIOLOGY (2021)

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Letter Anesthesiology

Preliminary data on severe SARS-CoV-2 infection caused by the 501Y.V2 variant

Guillaume Louis et al.

ANAESTHESIA CRITICAL CARE & PAIN MEDICINE (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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Review Biochemistry & Molecular Biology

Emerging SARS-CoV-2 Variants of Concern (VOCs): An Impending Global Crisis

Angel Yun-Kuan Thye et al.

Summary: The battle against the SARS-CoV-2 virus continues globally, with various clinically significant variants emerging, including Alpha, Beta, Delta, and Gamma. These variants possess key mutations on the spike protein, which contribute to increased transmissibility and evasion of the host immune response, leading to detrimental effects on public health.

BIOMEDICINES (2021)

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Article Infectious Diseases

Early detection of SARS-CoV-2 P.1 variant in Southern Brazil and reinfection of the same patient by P.2

Mariana Soares da Silva et al.

Summary: The article describes an early case of P.1 primary infection in Southern Brazil in late November 2020, followed by a reinfection with P.2 variant in March 2021. Genomic analysis confirmed significant genetic differences between the two infections, indicating the spread and prominence of the P.1 variant in the region.

REVISTA DO INSTITUTO DE MEDICINA TROPICAL DE SAO PAULO (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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Letter Immunology

Novel SARS-CoV-2 Variant in Travelers from Brazil to Japan

Takahisa Fujino et al.

Summary: Different variants of SARS-CoV-2 with higher transmission potential have been emerging globally, including one found in travelers from Brazil to Japan in January 2021, which carries an additional set of mutations.

EMERGING INFECTIOUS DISEASES (2021)

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Article Immunology

Human neutralising antibodies elicited by SARS-CoV-2 non-D614G variants offer cross-protection against the SARS-CoV-2 D614G variant

Cheryl Yi-Pin Lee et al.

Summary: The study found that antibodies induced by infection with either the D614 or G614 variants of SARS-CoV-2 can neutralize both variants with similar efficacy, although the neutralizing antibody capacity may decrease in the later phase of infection. This suggests that the D614G mutation does not impact the neutralization capacity of antibodies elicited by either variant.

CLINICAL & TRANSLATIONAL IMMUNOLOGY (2021)

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Article Multidisciplinary Sciences

Wuhan seafood market may not be source of novel virus spreading globally

Jon Cohen

SCIENCE (2020)

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Article Biochemistry & Molecular Biology

Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein

Alexandra C. Walls et al.

CELL (2020)

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Article Biochemistry & Molecular Biology

SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor

Markus Hoffmann et al.

CELL (2020)

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Article Immunology

Predicting Infectious Severe Acute Respiratory Syndrome Coronavirus 2 From Diagnostic Samples

Jared Bullard et al.

CLINICAL INFECTIOUS DISEASES (2020)

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Article Multidisciplinary Sciences

Cell entry mechanisms of SARS-CoV-2

Jian Shang et al.

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

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Article Multidisciplinary Sciences

Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor

Jun Lan et al.

NATURE (2020)

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Article Multidisciplinary Sciences

Structural basis of receptor recognition by SARS-CoV-2

Jian Shang et al.

NATURE (2020)

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Letter Biochemistry & Molecular Biology

The proximal origin of SARS-CoV-2

Kristian G. Andersen et al.

NATURE MEDICINE (2020)

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Article Public, Environmental & Occupational Health

Vaccine Efficacy Needed for a COVID-19 Coronavirus Vaccine to Prevent or Stop an Epidemic as the Sole Intervention

Sarah M. Bartsch et al.

AMERICAN JOURNAL OF PREVENTIVE MEDICINE (2020)

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Article Biochemistry & Molecular Biology

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

Tyler N. Starr et al.

CELL (2020)

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Article Biochemistry & Molecular Biology

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

Qianqian Li et al.

CELL (2020)

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Article Biochemistry & Molecular Biology

Mutations Strengthened SARS-CoV-2 Infectivity

Jiahui Chen et al.

JOURNAL OF MOLECULAR BIOLOGY (2020)

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Editorial Material Medicine, Research & Experimental

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

Giovanni Salvatori et al.

JOURNAL OF TRANSLATIONAL MEDICINE (2020)

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Article Biochemistry & Molecular Biology

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

Leonid Yurkovetskiy et al.

CELL (2020)

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Article Multidisciplinary Sciences

Enhanced receptor binding of SARS-CoV-2 through networks of hydrogen-bonding and interactions

Yingjie Wang et al.

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

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Article Biochemistry & Molecular Biology

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

Victoria A. Avanzato et al.

CELL (2020)

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Article Multidisciplinary Sciences

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

Yixuan J. Hou et al.

SCIENCE (2020)

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Review Microbiology

Origin and evolution of pathogenic coronaviruses

Jie Cui et al.

NATURE REVIEWS MICROBIOLOGY (2019)

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Article Microbiology

Newly Emerging Mutations in the Matrix Genes of the Human Influenza A(H1N1)pdm09 and A(H3N2) Viruses Reduce the Detection Sensitivity of Real-Time Reverse Transcription-PCR

Ji-Rong Yang et al.

JOURNAL OF CLINICAL MICROBIOLOGY (2014)

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