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Yunlong Cao et al.
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Summary: Following the identification of SARS-CoV-2 as the cause of COVID-19, efforts have been made to study the genetic diversity within hosts through quasispecies analysis. Research in Victoria, Australia found quasispecies diversity in 68% of samples, with a majority being nonsynonymous variants, particularly in the spike glycoprotein and ORF1a genes. Shared variants among samples suggested host-to-host transmission, with implications for the virus's epidemiology.
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Rafael Bayarri-Olmos et al.
Summary: The alpha/B.1.1.7 SARS-CoV-2 variant showed an eightfold increase in affinity towards human angiotensin-converting enzyme-2 (ACE-2), leading to faster disease progression and severity in transgenic hACE2 mice compared to earlier isolates. The N501Y substitution in the receptor-binding domain also resulted in a minor but significant increase in evasion potential of ACE-2/RBD antibody neutralization, suggesting its role in the higher transmission rate and severity of the B.1.1.7 variant.
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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.
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Delphine Planas et al.
Summary: The ability of convalescent sera from individuals with coronavirus disease 2019 and those vaccinated with BNT162b2 to neutralize SARS-CoV-2 variants B1.1.7 and B.1.351 decreases, but increases after two vaccine doses. The study found that the B.1.1.7 and B.1.351 variants may have acquired partial resistance to neutralizing antibodies generated by natural infection or vaccination, particularly in individuals with low antibody levels. This suggests that the B.1.351 variant may pose a greater risk of infection in immunized individuals.
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Andrew L. Valesano et al.
Summary: This study found that the within-host genetic diversity of SARS-CoV-2 is low and does not vary over time. While shared variation across individuals is generally limited, there are instances of intrahost variants shared among individuals who are unlikely to be related by transmission, indicating limited utility for predicting future lineages.
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Sung Hee Ko et al.
Summary: The study revealed that SARS-CoV-2 can rapidly adapt genetically in response to humoral immunity, potentially leading to delayed viral clearance in the acute phase of infection. Tracking the virus evolution within infected individuals can provide insights into COVID-19 pathogenesis and guide antiviral interventions.
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Ben Jackson et al.
Summary: The study identified multiple independent origins of recombinant SARS-CoV-2 viruses in the United Kingdom, showing similarities to the B.1.1.7 variant but also some unique features. Evidence suggested that these viruses have the capability of transmission.
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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
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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.
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Lynda Rocheleau et al.
Summary: The SARS-CoV-2 virus is constantly evolving, with a variety of genetic variants observed in infected individuals. Research has identified a high-frequency viral sublineage that may be involved in intrahost disease cytopathic effects.
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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.
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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.
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Tiantian Liu et al.
Summary: The research compared seven different SARS-CoV-2 WGS library protocols and found significant differences in mappability, genome coverage, sensitivity, reproducibility, and precision, with certain protocols requiring important trimming steps for accurate variant calling. The study results provide guidance for choosing appropriate WGS protocols to study SARS-CoV-2 and its evolution.
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Bryce Kille et al.
Summary: Recent advances in sequencing technology have made it affordable and practical to sequence genomes at high depth-of-coverage, allowing researchers to discover low-frequency variants. LoFreq is a state of the art algorithm for low-frequency variant detection, but has a relatively long runtime and could benefit from a simplified interface for more efficient operation.
2021 IEEE INTERNATIONAL PARALLEL AND DISTRIBUTED PROCESSING SYMPOSIUM WORKSHOPS (IPDPSW)
(2021)
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Simon Pollett et al.
Summary: The study evaluated recombination in the evolution of human coronaviruses, finding evidence of recombination events in SARS-CoV-2, SARS-CoV-1, and other coronaviruses. Recombination breakpoints were more likely to occur in the non-ORF1 region of the genome containing structural genes, significantly affecting the temporal structure of the data. The findings underscore the importance of genomic surveillance to detect recombination, especially in SARS-CoV-2, which could potentially lead to immune evasion.
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Nicholas Stoler et al.
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