Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic

SW Attwood, SC Hill, DM Aanensen… - Nature Reviews …, 2022‏ - nature.com
Determining the transmissibility, prevalence and patterns of movement of severe acute
respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is central to our understanding …

A pseudovirus system enables deep mutational scanning of the full SARS-CoV-2 spike

B Dadonaite, KHD Crawford, CE Radford, AG Farrell… - Cell, 2023‏ - cell.com
A major challenge in understanding SARS-CoV-2 evolution is interpreting the antigenic and
functional effects of emerging mutations in the viral spike protein. Here, we describe a deep …

Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape

Y Turakhia, B Thornlow, A Hinrichs, J McBroome… - Nature, 2022‏ - nature.com
Accurate and timely detection of recombinant lineages is crucial for interpreting genetic
variation, reconstructing epidemic spread, identifying selection and variants of interest, and …

Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic

Y Turakhia, B Thornlow, AS Hinrichs, N De Maio… - Nature …, 2021‏ - nature.com
As the SARS-CoV-2 virus spreads through human populations, the unprecedented
accumulation of viral genome sequences is ushering in a new era of 'genomic contact …

Fitness effects of mutations to SARS-CoV-2 proteins

JD Bloom, RA Neher - Virus Evolution, 2023‏ - academic.oup.com
Abstract Knowledge of the fitness effects of mutations to SARS-CoV-2 can inform
assessment of new variants, design of therapeutics resistant to escape, and understanding …

Phylogenetic analysis of SARS-CoV-2 data is difficult

B Morel, P Barbera, L Czech… - Molecular biology …, 2021‏ - academic.oup.com
Numerous studies covering some aspects of SARS-CoV-2 data analyses are being
published on a daily basis, including a regularly updated phylogeny on nextstrain. org. Here …

A biochemical perspective of the nonstructural proteins (NSPs) and the spike protein of SARS CoV-2

FK Yoshimoto - The protein journal, 2021‏ - Springer
The global pandemic that shut down the world in 2020 was caused by the virus, SARS CoV-
2. The chemistry of the various nonstructural proteins (NSP3, NSP5, NSP12, NSP13 …

Co-infection with SARS-CoV-2 Omicron and Delta variants revealed by genomic surveillance

RJ Rockett, J Draper, M Gall, EM Sim, A Arnott… - Nature …, 2022‏ - nature.com
Co-infections with different variants of SARS-CoV-2 are a key precursor to recombination
events that are likely to drive SARS-CoV-2 evolution. Rapid identification of such co …

Want to track pandemic variants faster? Fix the bioinformatics bottleneck

EB Hodcroft, N De Maio, R Lanfear, DR MacCannell… - Nature, 2021‏ - nature.com
Want to track pandemic variants faster? Fix the bioinformatics bottleneck Skip to main content
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Evolution of the SARS-CoV-2 mutational spectrum

JD Bloom, AC Beichman, RA Neher… - Molecular Biology and …, 2023‏ - academic.oup.com
SARS-CoV-2 evolves rapidly in part because of its high mutation rate. Here, we examine
whether this mutational process itself has changed during viral evolution. To do this, we …