Origin and evolution of SARS-CoV-2

Article Multidisciplinary Sciences

Omicron extensively but incompletely escapes Pfizer BNT162b2 neutralization

Sandile Cele et al.

Summary: The study found that the Omicron variant has reduced neutralizing effectiveness in individuals vaccinated with Pfizer BNT162b2, but those who had previously been infected with SARS-CoV-2 showed better neutralization against Omicron.

NATURE (2022)

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Article Multidisciplinary Sciences

Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

Raquel Viana et al.

Summary: The SARS-CoV-2 epidemic in southern Africa has experienced three distinct waves, driven by different variants. The recently identified Omicron variant has rapidly spread in South Africa and to numerous countries, raising global concern.

NATURE (2022)

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Article Multidisciplinary Sciences

SARS-CoV-2 Omicron virus causes attenuated disease in mice and hamsters

Peter J. Halfmann et al.

Summary: The recent study by the SAVE/NIAID network shows that the B.1.1.529 Omicron variant causes milder lung disease in rodents, which is consistent with preliminary human clinical data.

NATURE (2022)

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Article Multidisciplinary Sciences

Viral infection and transmission in a large, well-traced outbreak caused by the SARS-CoV-2 Delta variant

Baisheng Li et al.

Summary: This article reports the first local transmission of the Delta variant in mainland China. Compared to A/B lineage infections during the first wave in China in early 2020, Delta infections had viral loads that were on average about 1000 times greater when they first tested positive, suggesting potentially faster viral replication and greater infectiousness during early infection. The transmission bottleneck size of the Delta variant was generally narrow, with 1-3 virions in most donor-recipient transmission pairs. However, transmission of minor intra-host variants resulted in at least 3 of the 34 substitutions identified in the outbreak, highlighting the contribution of intra-host variants to population-level viral diversity during rapid spread.

NATURE COMMUNICATIONS (2022)

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News Item Infectious Diseases

Research in brief

Sharmila Devi

LANCET INFECTIOUS DISEASES (2022)

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Article Multidisciplinary Sciences

Antibody evasion properties of SARS-CoV-2 Omicron sublineages

Sho Iketani et al.

Summary: The identification of the Omicron variant of SARS-CoV-2 in Botswana in November 2021 sparked concern due to the spike protein alterations that could potentially evade antibodies. Further studies showed that the Omicron sublineages, BA.1+R346K and BA.2, are antigenically similar to the wild-type virus and pose similar risks to the effectiveness of current vaccines. BA.2 also demonstrated resistance to many neutralizing monoclonal antibodies, highlighting the challenges in developing effective therapeutic options.

NATURE (2022)

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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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Editorial Material Medicine, General & Internal

Omicron SARS-CoV-2 variant: a new chapter in the COVID-19 pandemic

Salim S. Abdool Karim et al.

LANCET (2021)

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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)

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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)

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Letter Medicine, General & Internal

Neutralizing Activity of BNT162b2-Elicited Serum

Yang Liu et al.

NEW ENGLAND JOURNAL OF MEDICINE (2021)

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Article Multidisciplinary Sciences

Evidence for SARS-CoV-2 related coronaviruses circulating in bats and pangolins in Southeast Asia

Supaporn Wacharapluesadee et al.

Summary: A study identified a SARS-CoV-2-related coronavirus (SC2r-CoV), RacCS203, in Rhinolophus acuminatus bats from Thailand, with 91.5% genome similarity to SARS-CoV-2, and demonstrated that sera obtained from bats and Malayan pangolin can neutralize SARS-CoV-2.

NATURE COMMUNICATIONS (2021)

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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)

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Article Biochemistry & Molecular Biology

Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses

Hong Zhou et al.

Summary: A study in Yunnan province, China, found the existence of bat coronaviruses related to both SARS-CoV-2 and SARS-CoV, with RpYN06 virus being the closest relative of SARS-CoV-2. Ecological modeling predicted the co-existence of up to 23 Rhinolophus bat species, with the largest hot-spots extending from South Laos and Vietnam to southern China. The study highlights the remarkable diversity of bat coronaviruses at the local scale.

CELL (2021)

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Article Multidisciplinary Sciences

Lectins enhance SARS-CoV-2 infection and influence neutralizing antibodies

Florian A. Lempp et al.

Summary: The study reveals that C-type lectin receptors and other factors can serve as attachment receptors for SARS-CoV-2 infection, enhancing ACE2-mediated infection and modulating the neutralizing activity of antibodies.

NATURE (2021)

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Review Microbiology

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

William T. Harvey et al.

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

NATURE REVIEWS MICROBIOLOGY (2021)

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Article Microbiology

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

Chiranjib Chakraborty et al.

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

MBIO (2021)

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News Item Medicine, General & Internal

Covid-19: Delta variant is now UK's most dominant strain and spreading through schools

Ingrid Torjesen

BMJ-BRITISH MEDICAL JOURNAL (2021)

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Article Microbiology

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

Sarah Cherian et al.

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

MICROORGANISMS (2021)

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Article Multidisciplinary Sciences

After the pandemic: perspectives on the future trajectory of COVID-19

Amalio Telenti et al.

Summary: This article discusses the future patterns of SARS-CoV-2 infection, the development of variants, and the implications for vaccine deployment. It suggests that the virus may become endemic fueled by pockets of susceptible individuals and waning immunity. Effective surveillance and response are crucial to prevent new epidemic or pandemic patterns.

NATURE (2021)

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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)

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Article Multidisciplinary Sciences

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

Peng Zhou et al.

NATURE (2020)

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Article Medicine, General & Internal

A Novel Coronavirus from Patients with Pneumonia in China, 2019

Na Zhu et al.

NEW ENGLAND JOURNAL OF MEDICINE (2020)

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Article Medicine, General & Internal

Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus-Infected Pneumonia

Qun Li et al.

NEW ENGLAND JOURNAL OF MEDICINE (2020)

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Article Multidisciplinary Sciences

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

Daniel Wrapp et al.

SCIENCE (2020)

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Review Hematology

Hematological findings and complications of COVID-19

Evangelos Terpos et al.

AMERICAN JOURNAL OF HEMATOLOGY (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

Forty years with coronaviruses

Susan R. Weiss

JOURNAL OF EXPERIMENTAL MEDICINE (2020)

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Article Multidisciplinary Sciences

Virological assessment of hospitalized patients with COVID-2019

Roman Woelfel et al.

NATURE (2020)

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Review Medicine, General & Internal

Prevalence of Asymptomatic SARS-CoV-2 Infection A Narrative Review

Daniel P. Oran et al.

ANNALS OF INTERNAL MEDICINE (2020)

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Article Infectious Diseases

SARS-CoV-2 infection in farmed minks, the Netherlands, April and May 2020

Nadia Oreshkova et al.

EUROSURVEILLANCE (2020)

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Article Biochemistry & Molecular Biology

Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus

Bette Korber et al.

CELL (2020)

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Editorial Material Medicine, General & Internal

Airborne Transmission of SARS-CoV-2 Theoretical Considerations and Available Evidence

Michael Klompas et al.

JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION (2020)

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Article Microbiology

A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology

Andrew Rambaut et al.

NATURE MICROBIOLOGY (2020)

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Article Infectious Diseases

Comparing SARS-CoV-2 with SARS-CoV and influenza pandemics

Eskild Petersen et al.

LANCET INFECTIOUS DISEASES (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

Evolution and epidemic spread of SARS-CoV-2 in Brazil

Darlan S. Candido et al.

SCIENCE (2020)

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Article Multidisciplinary Sciences

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

Hongjing Gu et al.

SCIENCE (2020)

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Article Virology

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

Sebastian Duchene et al.

VIRUS EVOLUTION (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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News Item Multidisciplinary Sciences

Coronaviruses closely related to the pandemic virus discovered in Japan and Cambodia

Smriti Mallapaty

NATURE (2020)

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Letter Medicine, General & Internal

Persistence and Evolution of SARS-CoV-2 in an Immunocompromised Host

Bina Choi et al.

NEW ENGLAND JOURNAL OF MEDICINE (2020)

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Article Multidisciplinary Sciences

Evidence of exposure to SARS-CoV-2 in cats and dogs from households in Italy

E. Patterson et al.

NATURE COMMUNICATIONS (2020)

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Article Microbiology

A planarian nidovirus expands the limits of RNA genome size

Amir Saberi et al.

PLOS PATHOGENS (2018)

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Article Microbiology

Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus

Ben Hu et al.

PLOS PATHOGENS (2017)

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Article Medicine, General & Internal

Middle East respiratory syndrome

Alimuddin Zumla et al.

LANCET (2015)

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Article Virology

Thinking Outside the Triangle: Replication Fidelity of the Largest RNA Viruses

Everett Clinton Smith et al.

ANNUAL REVIEW OF VIROLOGY, VOL 1 (2014)

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Article Medicine, General & Internal

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

Ali Moh Zaki et al.

NEW ENGLAND JOURNAL OF MEDICINE (2012)

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Review Biochemistry & Molecular Biology

Coronaviruses An RNA proofreading machine regulates replication fidelity and diversity

Mark R. Denison et al.

RNA BIOLOGY (2011)

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Review Virology

Recombination, Reservoirs, and the Modular Spike: Mechanisms of Coronavirus Cross-Species Transmission

Rachel L. Graham et al.

JOURNAL OF VIROLOGY (2010)

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Article Multidisciplinary Sciences

Bats are natural reservoirs of SARS-like coronaviruses

WD Li et al.

SCIENCE (2005)

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Article Multidisciplinary Sciences

Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human

HD Song et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

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Article Immunology

Coronaviridae and SARS-associated coronavirus strain HSR1

E Vicenzi et al.

EMERGING INFECTIOUS DISEASES (2004)

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Article Multidisciplinary Sciences

Isolation and characterization of viruses related to the SARS coronavirus from animals in Southern China

Y Guan et al.

SCIENCE (2003)

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Article Medicine, General & Internal

A novel coronavirus associated with severe acute respiratory syndrome

TG Ksiazek et al.

NEW ENGLAND JOURNAL OF MEDICINE (2003)

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Article Medicine, General & Internal

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

C Drosten et al.

NEW ENGLAND JOURNAL OF MEDICINE (2003)

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Origin and evolution of SARS-CoV-2

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