Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic
Determining the transmissibility, prevalence and patterns of movement of severe acute
respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is central to our understanding …
respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is central to our understanding …
Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck
The evolutionary mechanisms by which SARS-CoV-2 viruses adapt to mammalian hosts
and, potentially, undergo antigenic evolution depend on the ways genetic variation is …
and, potentially, undergo antigenic evolution depend on the ways genetic variation is …
[PDF][PDF] Mutation rates and selection on synonymous mutations in SARS-CoV-2
The COVID-19 pandemic has seen an unprecedented response from the sequencing
community. Leveraging the sequence data from more than 140,000 SARS-CoV-2 genomes …
community. Leveraging the sequence data from more than 140,000 SARS-CoV-2 genomes …
Mutational signatures and heterogeneous host response revealed via large-scale characterization of SARS-CoV-2 genomic diversity
To dissect the mechanisms underlying the inflation of variants in the Severe Acute
Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) genome, we present a large-scale …
Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) genome, we present a large-scale …
Controlling long-term SARS-CoV-2 infections can slow viral evolution and reduce the risk of treatment failure
D Van Egeren, A Novokhodko, M Stoddard, U Tran… - Scientific reports, 2021 - nature.com
The rapid emergence and expansion of novel SARS-CoV-2 variants threatens our ability to
achieve herd immunity for COVID-19. These novel SARS-CoV-2 variants often harbor …
achieve herd immunity for COVID-19. These novel SARS-CoV-2 variants often harbor …
SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission
The COVID-19 pandemic has sparked an urgent need to uncover the underlying biology of
this devastating disease. Though RNA viruses mutate more rapidly than DNA viruses, there …
this devastating disease. Though RNA viruses mutate more rapidly than DNA viruses, there …
Perspectives: SARS-CoV-2 spike convergent evolution as a guide to explore adaptive advantage
Viruses rapidly co-evolve with their hosts. The 9 million sequenced SARS-CoV-2 genomes
by March 2022 provide a detailed account of viral evolution, showing that all amino acids …
by March 2022 provide a detailed account of viral evolution, showing that all amino acids …
LACE: Inference of cancer evolution models from longitudinal single-cell sequencing data
D Ramazzotti, F Angaroni, D Maspero… - Journal of …, 2022 - Elsevier
The rise of longitudinal single-cell sequencing experiments on patient-derived cell cultures,
xenografts and organoids is opening new opportunities to track cancer evolution, assess the …
xenografts and organoids is opening new opportunities to track cancer evolution, assess the …
Large-scale analysis of SARS-CoV-2 synonymous mutations reveals the adaptation to the human codon usage during the virus evolution
Many large national and transnational studies have been dedicated to the analysis of
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) genome, most of which …
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) genome, most of which …
[HTML][HTML] The race to understand immunopathology in COVID-19: Perspectives on the impact of quantitative approaches to understand within-host interactions
The COVID-19 pandemic has revealed the need for the increased integration of modelling
and data analysis to public health, experimental, and clinical studies. Throughout the first …
and data analysis to public health, experimental, and clinical studies. Throughout the first …