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Review
Biochemistry & Molecular Biology
Daniele Focosi et al.
Summary: The first 2 years of the COVID-19 pandemic were characterized by recurrent mutations of SARS-CoV-2 Spike protein, and since Spring 2022, convergent evolution has led to the observation of different lineages acquiring additional mutations. These mutations have become increasingly prevalent, and the most likely reason for this is the selective pressure exerted by previous infection or vaccination. This accelerated evolution has caused the failure of all anti-Spike monoclonal antibodies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Virology
Romina Zambrana Montano et al.
Summary: This study aimed to investigate the introduction and diversification patterns of SARS-CoV-2 in Northwestern Argentina during the early stages of the COVID-19 pandemic. The results showed the presence of eight lineages in the first wave, which were later replaced by variants of concern and other lineages in the early second wave. The study also found that the evolutionary rate of one of the most prevalent lineages in the region was faster than that of another lineage.
Article
Virology
Carolina Torres et al.
Summary: This study aimed to investigate the dynamics of SARS-CoV-2 Omicron lineages during the third and fourth waves of COVID-19 in Argentina. The third wave was associated with lineage BA.1 and characterized by a high number of cases, rapid displacement of Delta, and low lineage diversity and clustering. In contrast, the fourth wave was longer but had a lower number of cases and was initially caused by BA.2 and later by BA.4/BA.5. Differential dynamics between the waves may be attributed to waning immunity, population gatherings, and boosted population with prior immunity or vaccination.
Article
Virology
Maria Antonieta Quispe-Ricalde et al.
Summary: SARS-CoV-2 Lambda variant has spread rapidly in Cusco, Peru, and the study aimed to understand its distribution and characterize its genomes. Phylogenetic analysis showed dominance of the Lambda lineage and no clustering of variants by district. Unvaccinated patients accumulated more new mutations, including mutations in ORF7a, NSP3, and deletions in S and ORF3a.
ARCHIVES OF VIROLOGY
(2023)
Article
Virology
Guy Shapira et al.
Summary: The clinical course of COVID-19 is affected by host factors, but viral evolution of SARS-CoV-2 during acute infection is limited and mostly unaffected by host characteristics. Variants of concern (VOCs), novel SARS-CoV-2 variants produced by evolutionary leaps, have significant alterations in a small subset of immunocompromised COVID-19 cases. In these cases, the viral genomes accumulate impactful and potentially adaptive mutations, but the transmissibility of such viruses remains unclear.
Article
Public, Environmental & Occupational Health
Jose Arturo Molina-Mora et al.
Frontiers in Public Health
(2023)
Article
Virology
Simone Kashima et al.
Summary: This study characterized the circulation of the SARS-CoV-2 Lambda variant in Sao Paulo State, Brazil. Among approximately 8000 newly sequenced genomes, seven Lambda isolates were identified, with three possibly due to contact transmission. Vaccinated patients showed mild symptoms, while one required hospitalization among those testing positive for Lambda variant.
JOURNAL OF MEDICAL VIROLOGY
(2022)
Article
Cell Biology
Izumi Kimura et al.
Summary: This study reveals the increased infectivity and antibody evasion mechanism of the SARS-CoV-2 Lambda variant using pseudoviruses. The spike protein of the Lambda variant is more infectious than other variants due to specific mutations, and the RSYLTPGD246-253N mutation is responsible for antibody evasion and enhanced infection.
Article
Virology
Marlena Stadtmueller et al.
Summary: This article conducted genomic epidemiology analysis on SARS-CoV-2 samples collected from a border region between Germany, Poland, and the Czech Republic to monitor the evolution of SARS-CoV-2 variants. A new B.1.1.7 sub-lineage with additional mutations was identified, which is the predominant variant in several European countries. This sub-lineage showed reduced sensitivity to vaccine-elicited antibodies and lower replication fitness. The wide spread of this sub-lineage was related to the pandemic waves in early 2021 in various European countries.
Review
Medicine, General & Internal
Suresh Thakur et al.
Summary: With the global increase in COVID-19 infections, the emergence of SARS-CoV-2 variants was inevitable. Mutations, especially in the spike protein, have been found to alter the transmissibility and virulence of the virus. The WHO has classified the variants with fitness-enhancing mutations into variants of concern, interest or under monitoring. These variants pose a significant threat as they exhibit higher transmissibility and immune evasion. This article reviews the mutational landscape of SARS-CoV-2 proteins and their impact on diagnostics, therapeutics, and vaccines, as well as the effectiveness of approved vaccines, antibody therapy, and convalescent plasma against the currently prevalent variants.
FRONTIERS IN MEDICINE
(2022)
Article
Genetics & Heredity
Zhiyuan Chen et al.
Summary: This study analyzed global SARS-CoV-2 genomic surveillance and genomic data, finding significant variations in surveillance and sequencing capabilities among different countries. It also identified heterogeneity in sequencing percentage, sequencing technologies, turnaround time, and completeness of released metadata across regions and income groups. Moreover, it revealed a lack of proactive sharing of sequences related to variant of concerns (VOCs) in public repositories by some countries. Urgent actions are required to enhance timely and full sharing of sequences, standardize metadata files, and support countries with limited sequencing and bioinformatics capacity.
Article
Multidisciplinary Sciences
Philip L. Tzou et al.
Summary: The Stanford Coronavirus Resistance Database (CoV-RDB) collects and curates published data on the neutralizing susceptibility of SARS-CoV-2 variants and spike mutations to antibodies. The database provides an interactive interface for displaying neutralization data at different levels of granularity and offers a sequence analysis program to assist users in determining mutation-detection thresholds.
Article
Immunology
Jiri Zahradnik et al.
Summary: This study examines the evolutionary patterns of SARS-CoV-2 and finds that certain mutations have independently emerged in multiple lineages, indicating their adaptive advantage. The omicron variant introduces new mutations, potentially due to their synergistic nature. Most of the mutations in the S protein cluster in specific functional domains and favor improvements in ACE2 affinity. Furthermore, all amino acids reachable by single nucleotide changes has been explored, while mutations requiring two nucleotide changes are increasing rapidly. These findings highlight the importance of understanding the mutation landscape for the future evolution of SARS-CoV-2.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Immunology
Bingjie Hu et al.
Summary: This study identifies key changes in the spike protein of the Omicron variant that contribute to its virological characteristics and pathogenicity.
EMERGING MICROBES & INFECTIONS
(2022)
Article
Cell Biology
Alexandre Bolze et al.
Summary: This study reports the sequencing of 74,348 SARS-CoV-2 positive samples collected in the United States, showing that the Delta variant became the dominant variant by September 2021 and had a higher viral load compared to the Alpha variant.
CELL REPORTS MEDICINE
(2022)
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
Immunology
Saathvik R. Kannan et al.
Summary: The study revealed differences in the mutational profile between Delta and Delta Plus variants, with Delta Plus having more high-prevalence mutations and unique signature mutations. Structural analysis showed that these mutations can weaken the interactions between the virus and antibodies.
JOURNAL OF AUTOIMMUNITY
(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
Microbiology
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)
Editorial Material
Medicine, General & Internal
Ester C. Sabino et al.
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
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
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
Medicine, General & Internal
Carolina Torres et al.
Summary: Argentina conducted surveillance on SARS-CoV-2 variants, identifying Gamma and Lambda as the main variants, along with Alpha, Zeta, Epsilon, and more recently Delta. These variants predominated in different regions, with the emergence of Delta towards the end of the second wave, replacing Gamma and Lambda.
FRONTIERS IN MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Chantal B. F. Vogels et al.
Summary: With the emergence of SARS-CoV-2 variants with increased transmissibility and immune escape, targeted surveillance is urgently needed. The B.1.1.7 variant can be detected by a specific deletion in the spike gene, but other variants like B.1.351 and P.1 cannot. An open-source PCR assay targeting a deletion in the ORF1a gene has been designed and validated to enhance surveillance for these variants.
Article
Virology
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)
Review
Biochemistry & Molecular Biology
Bas B. Oude Munnink et al.
Summary: This review summarizes the current knowledge on key viral mutations and variants, emphasizing the need for a systematic approach to link global genomic surveillance with timely assessment of the phenotypic characteristics of novel variants in preparation for the next phase of the pandemic.
News Item
Medicine, General & Internal
Ingrid Torjesen
BMJ-BRITISH MEDICAL JOURNAL
(2021)
Article
Cell Biology
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.
Article
Virology
Aine O'Toole et al.
Summary: The global virus genomics community has responded unprecedentedly to the SARS-CoV-2 pandemic, leading to significant advances in 'real-time' generation and sharing of genomic data. The development of new analytical methods, such as pangolin, has been necessary to handle the rapid growth in virus genome data production. Pangolin has processed nearly two million virus genomes, aiding in SARS-CoV-2 genomic epidemiology and providing researchers with valuable information about the pandemic's transmission lineages.
Article
Biochemistry & Molecular Biology
Jiahui Chen et al.
JOURNAL OF MOLECULAR BIOLOGY
(2020)
Article
Biochemical Research Methods
Nikki E. Freed et al.
BIOLOGY METHODS & PROTOCOLS
(2020)
Article
Biochemistry & Molecular Biology
Diep Thi Hoang et al.
MOLECULAR BIOLOGY AND EVOLUTION
(2018)
Article
Evolutionary Biology
Andrew Rambaut et al.
SYSTEMATIC BIOLOGY
(2018)
Article
Virology
Marc A. Suchard et al.
Article
Biochemical Research Methods
Subha Kalyaanamoorthy et al.
Article
Multidisciplinary Sciences
Stefan Elbe et al.
Article
Biochemistry & Molecular Biology
Filip Bielejec et al.
MOLECULAR BIOLOGY AND EVOLUTION
(2016)
Article
Virology
Andrew Rambaut et al.
Article
Biochemistry & Molecular Biology
Lam-Tung Nguyen et al.
MOLECULAR BIOLOGY AND EVOLUTION
(2015)
Article
Biochemistry & Molecular Biology
Kazutaka Katoh et al.
MOLECULAR BIOLOGY AND EVOLUTION
(2013)
Article
Multidisciplinary Sciences
Robert Schmieder et al.
Article
Biochemical Research Methods
Heng Li et al.
Article
Evolutionary Biology
Stephane Guindon et al.
SYSTEMATIC BIOLOGY
(2010)
Article
Biochemistry & Molecular Biology
Alexei J. Drummond et al.
Article
Biochemistry & Molecular Biology
AJ Drummond et al.
MOLECULAR BIOLOGY AND EVOLUTION
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