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Article
Medicine, General & Internal
Yang Pan et al.
Summary: Due to the national zero-COVID strategy in China, there were no local transmissions of SARS-CoV-2 in Beijing before December 2022. However, imported cases have been frequently detected. With the recent increase in COVID-19 cases in China, there are concerns about the emergence of novel variants. This study analyzes viral genome sequences in Beijing to provide important information for the global response to the pandemic.
Article
Infectious Diseases
Li Li et al.
Summary: This study describes the epidemiological and clinical characteristics of imported COVID-19 cases in Beijing and assesses the effectiveness of screening strategies. The combination of RT-PCR and chest CT is found to be an effective strategy for screening imported cases.
BMC INFECTIOUS DISEASES
(2022)
Article
Biochemistry & Molecular Biology
Zhen Cui et al.
Summary: The Omicron variant of SARS-CoV-2 is spreading rapidly worldwide due to its increased fitness, with spike structures that maintain stability for receptor recognition but compromise viral fusion efficiency. By altering amino acids and structures, it evades recognition by most antibodies, facilitating immune escape. The research sheds light on conserved regions for the development of broad-spectrum vaccines.
Review
Virology
Dandan Tian et al.
Summary: The Omicron variant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in Botswana in November 2021 and has since become the dominant strain in many countries. With a high number of mutations, it presents new challenges for preventing and controlling COVID-19. This review aims to provide a scientific reference by analyzing and summarizing the biological characteristics, epidemic features, immune escape, and vaccine reactivity of the Omicron variant.
JOURNAL OF MEDICAL VIROLOGY
(2022)
Article
Virology
Shailendra K. Saxena et al.
Summary: Omicron is the latest variant of concern of SARS-CoV-2, with more mutations compared to the previous Delta variant. Fifteen of these mutations are located in the receptor-binding domain of the spike glycoprotein, which may affect transmissibility, infectivity, antibody neutralization, and vaccine efficacy. The study provides insights into the mutational hotspots of Omicron and its global impact on transmission, testing, and immunity.
JOURNAL OF MEDICAL VIROLOGY
(2022)
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.
Letter
Infectious Diseases
Weifeng Yuan et al.
JOURNAL OF INFECTION
(2022)
Article
Medicine, General & Internal
Yahui Feng et al.
Summary: This study reported how the Chinese mainland battled its first omicron wave in Tianjin and successfully suppressed the outbreak within a month by identifying cases through mass PCR testing and dynamically adjusting quarantine policies. Nearly two-thirds of the cases had no or mild symptoms, and the research found that it might be possible to predict the timing of viral clearance based on clinical features.
Article
Biochemistry & Molecular Biology
Junxian Ou et al.
Summary: This study identifies multiple recombination events between Omicron variants and other variants of concern, suggesting the important roles of co-infection and genome recombination in the ongoing evolution of SARS-CoV-2. The study also characterizes core mutations of Omicron subvariants and their associations with other variants. Additionally, recombination events between Omicron and Delta variants are observed.
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2022)
Letter
Cell Biology
Jun Lan et al.
Article
Virology
Marta Giovanetti et al.
Summary: The COVID-19 epidemic in Brazil was initially driven by the Gamma variant, but was later replaced by the Delta variant. Unlike in other countries, the rapid spread of Delta in Brazil did not lead to a significant increase in cases and deaths, which may be attributed to the combination of early vaccination campaign and natural immunity from prior infection with the Gamma variant. The study highlights the importance of strengthening genomic monitoring on a national level to detect the emergence and spread of other variants of concern.
Article
Biochemistry & Molecular Biology
Erik Volz et al.
Summary: The study suggests a positive selection for the SARS-CoV-2 spike protein variant D614G in the UK, but no evidence of differences in COVID-19 mortality or clinical severity in patients infected with this variant. 614G is associated with higher viral load and younger age of patients compared to 614D.
Article
Multidisciplinary Sciences
Claudia Alteri et al.
Summary: The Lombardy region of Italy was heavily affected early in the SARS-CoV-2 pandemic. Using whole genome sequencing, researchers found multiple virus introductions into the region with transmission occurring before the first case was detected.
NATURE COMMUNICATIONS
(2021)
Article
Microbiology
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)
Article
Multidisciplinary Sciences
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.
Article
Multidisciplinary Sciences
Mahesh S. Dhar et al.
Summary: Delhi experienced multiple severe outbreaks in 2020, reaching a seropositivity rate of >50% by 2021. The Delta variant's high transmissibility and immune evasion led to a surge in cases in Delhi.
Article
Biology
Petr Danecek et al.
Summary: SAMtools and BCFtools are widely used tools for processing high-throughput sequencing data, with a history of 12 years of continuous development and improvement. These packages have been utilized in various software projects and genomic pipelines and are freely available on GitHub.
Article
Biochemistry & Molecular Biology
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
Cell Biology
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)
Article
Biochemistry & Molecular Biology
Ivica Letunic et al.
Summary: The Interactive Tree Of Life is an online tool for displaying, manipulating, and annotating phylogenetic and other trees. The latest version 5 introduces a new tree display engine and several new features, such as a new dataset type and expanded annotation options. Users can now also manually annotate trees by hand, providing more flexibility and control.
NUCLEIC ACIDS RESEARCH
(2021)
Editorial Material
Public, Environmental & Occupational Health
Ying Liu et al.
Summary: The Delta variant is rapidly replacing other strains of SARS-CoV-2, with a higher R-0 value of 5.08 compared to the ancestral strain's 2.79. Increasing vaccine coverage and strengthening public health measures are now more urgent than ever to control the spread of the virus.
JOURNAL OF TRAVEL MEDICINE
(2021)
Letter
Biochemistry & Molecular Biology
Jasdeep Singh et al.
Article
Public, Environmental & Occupational Health
Srinivas Nanduri et al.
MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT
(2021)
Article
Microbiology
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.
Letter
Immunology
Daniele Focosi et al.
Summary: This report demonstrates a novel mutation, Q493R, of the SARS-CoV-2 spike protein that confers resistance to both bamlanivimab and etesivimab, isolated from a patient who had received treatment with these drugs.
EMERGING INFECTIOUS DISEASES
(2021)
Article
Multidisciplinary Sciences
Peng Zhou et al.
Article
Multidisciplinary Sciences
Daniel Wrapp et al.
Article
Biochemistry & Molecular Biology
Alexandra C. Walls et al.
Article
Multidisciplinary Sciences
Jun Lan et al.
Article
Biochemical Research Methods
Shifu Chen et al.
Article
Biochemistry & Molecular Biology
Kazutaka Katoh et al.
MOLECULAR BIOLOGY AND EVOLUTION
(2013)
Article
Multidisciplinary Sciences
Morgan N. Price et al.
