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Article
Multidisciplinary Sciences
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.
Article
Biochemistry & Molecular Biology
Laura A. VanBlargan et al.
Summary: The emergence of the B.1.1.529 Omicron variant raises concerns about the efficacy of antibody countermeasures. This study shows that some of the antibodies currently in clinical use may lose their ability to neutralize the Omicron variant.
Article
Multidisciplinary Sciences
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.
Article
Multidisciplinary Sciences
Louis du Plessis et al.
Summary: The study analyzed the genetic lineage structure of the early UK COVID-19 epidemic through genomic sampling, identifying that virus lineages introduced before the national lockdown tended to be larger and more dispersed. After the lockdown, lineage importation and regional diversity decreased, while lineage elimination depended on lineage size. The research emphasizes the impact of genetic perspective on transmission dynamics for COVID-19 epidemiology and control.
Article
Biochemistry & Molecular Biology
Lin Yang et al.
Summary: Research has found that most harmful mutations resulting in increased transmissibility have already been covered by existing mutations, and a possible enhancement in binding affinity at amino-acid position 498 of the RBD. A new calculation method based on entropy-enthalpy compensation rule suggests that all known structures comply with this rule, providing the driving force behind spontaneous protein-protein docking.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
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.
Review
Biochemistry & Molecular Biology
Fabio Arena et al.
Summary: Genetic variability of the virus may impact the reliability of diagnostic protocols, but most virus variants currently have minimal impact on the sensitivity of existing diagnostic protocols. However, to address the continuous emergence of new variants, protocols including multiple targets should be preferred in the future.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Editorial Material
Medicine, General & Internal
John P. Moore et al.
Summary: This article reviews the circulating SARS-CoV-2 genetic variants and the mechanisms of immunity by which they may escape vaccine-induced protection, proposing 6 measures to address these issues, including enhanced variant isolation and testing procedures, and continued adherence to mask-wearing and other established public health measures.
JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION
(2021)
Article
Multidisciplinary Sciences
Brona Brejova et al.
Summary: Sequencing the SARS-CoV-2 genome using long amplicons with PCR-tiling and nanopore sequencing on a MinION device outperforms the original short amplicon protocol. However, common issues with the PCR-tiling approach include uneven genome coverage, variable fractions of discarded sequencing reads, human and bacterial contamination, and the presence of reads from viral sub-genomic RNAs.
Article
Multidisciplinary Sciences
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.
Article
Multidisciplinary Sciences
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.
Article
Genetics & Heredity
Dave J. Baker et al.
Summary: CoronaHiT is a flexible sequencing method for SARS-CoV-2 genomes, suitable for rapid expansion of global sequencing efforts. In experiments, CoronaHiT demonstrated good performance on both nanopore and Illumina platforms.
Article
Virology
Matthew Cotten et al.
Summary: Efforts are being made globally to control the spread and evolution of SARS-CoV-2 by sequencing its genome, but a significant percentage of generated genomes each month have gaps, reducing their information content. This study identifies the frequencies and positions of these genome gaps and provides a new primer set and sequencing scheme to enhance the quality and coverage of the genomes.
Article
Microbiology
James J. Davis et al.
Summary: The ARTIC Network provides PCR primer sequences and recommendations for amplifying SARS-CoV-2 genomes. Comparing the V3 and V4 primer sets in sequencing clinical samples showed that the V4 primer set is critical for accurate sequencing of the SARS-CoV-2 spike region. The study highlights the importance of primer schemes in downstream analyses and the impact on publicly available SARS-CoV-2 sequencing data.
MICROBIOLOGY SPECTRUM
(2021)
Article
Multidisciplinary Sciences
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.
Article
Psychology, Biological
Edouard Mathieu et al.
Summary: An effective rollout of COVID-19 vaccines is crucial in ending the pandemic, and Our World in Data's vaccination dataset tracks the progress and scale of vaccine distribution globally, aiding policymakers and researchers in understanding the global vaccination efforts.
NATURE HUMAN BEHAVIOUR
(2021)
Article
Infectious Diseases
Jonathan Daniel Ip et al.
Summary: The study aimed to determine viral genome diversity in serial samples of COVID-19 patients by performing targeted deep sequencing of the spike gene using nanopore and Illumina sequencing. A patient with severe disease was found to have a spike protein amino acid mutation W152L, located within a neutralizing epitope. Monitoring of serial specimens is important in identifying hotspots of mutations, especially those occurring at neutralizing epitopes which may affect therapeutic efficacy of monoclonal antibodies.
CLINICAL MICROBIOLOGY AND INFECTION
(2021)
Letter
Medicine, General & Internal
Emma C. Wall et al.
Article
Infectious Diseases
Kit Man Chai et al.
Summary: Efficient vaccines against COVID-19 are urgently needed, with the spike protein of SARS-CoV-2 as a major target. A DNA vaccine delivery via electroporation showed promising results in inducing antibodies and neutralizing antibodies, especially with the ability to induce strong Th1-biased responses.
PLOS NEGLECTED TROPICAL DISEASES
(2021)
Article
Health Care Sciences & Services
Geraldine Rios et al.
Summary: This study implemented a nanopore RNA sequencing monitoring system in Nice to analyze SARS-CoV-2 variants in wastewater samples, revealing the diversity of sequences in different neighborhoods. Wastewater sequencing correctly identified lineages found in clinical samples, demonstrating its potential for tracking pathogen sequence diversity in current and future outbreaks.
LANCET REGIONAL HEALTH-EUROPE
(2021)
Article
Microbiology
Kayzad Nilgiriwala et al.
Summary: The study reports the genome sequences of SARS-CoV-2 variants from five COVID-19 patients in Mumbai, India, with 8 to 22 mutations identified. These variants belong to lineages previously associated with Indian variants.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2021)
Article
Virology
Matthew Cotten et al.
Summary: Global efforts to sequence the SARS-CoV-2 genome are hindered by gaps in approximately 19 to 43 per cent of monthly generated sequences. This study provides an alternative primer set and sequencing scheme to improve the quality and coverage of genomes, aiding in the development of effective control measures.
Article
Virology
Francisco Diez-Fuertes et al.
Summary: Whole-genome analysis of SARS-CoV-2 identified five large clades worldwide that emerged in 2019 and 2020. Spain had 62 independent introductions of the virus, with 19B being the most prevalent in the early stages, later replaced by G614-bearing viruses. The G614 variant showed enhanced infectivity, suggesting a fitness advantage and potential driving force for the variant shift observed in Spain.
JOURNAL OF VIROLOGY
(2021)
Article
Multidisciplinary Sciences
Fan Wu et al.
Article
Genetics & Heredity
Ci-Hong Liou et al.
MICROBIAL GENOMICS
(2020)
Review
Chemistry, Multidisciplinary
Yuan Huang et al.
ACTA PHARMACOLOGICA SINICA
(2020)
Article
Biochemistry & Molecular Biology
Mathieu Gand et al.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Article
Virology
Zhe Liu et al.
JOURNAL OF VIROLOGY
(2020)
Article
Chemistry, Multidisciplinary
Ming Wang et al.
Article
Virology
Jalees A. Nasir et al.
Article
Multidisciplinary Sciences
Rowena A. Bull et al.
NATURE COMMUNICATIONS
(2020)
Article
Biochemical Research Methods
Nikki E. Freed et al.
BIOLOGY METHODS & PROTOCOLS
(2020)
Article
Virology
John-Sebastian Eden et al.
Article
Multidisciplinary Sciences
Wei Shen et al.
