The emergence, genomic diversity and global spread of SARS-CoV-2

J Li, S Lai, GF Gao, W Shi - Nature, 2021 - nature.com
Since the first cases of COVID-19 were documented in Wuhan, China in 2019, the world has
witnessed a devastating global pandemic, with more than 238 million cases, nearly 5 million …

Testing at scale during the COVID-19 pandemic

TR Mercer, M Salit - Nature Reviews Genetics, 2021 - nature.com
Assembly and publication of the severe acute respiratory syndrome coronavirus 2 (SARS-
CoV-2) genome in January 2020 enabled the immediate development of tests to detect the …

The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2

JE Pekar, A Magee, E Parker, N Moshiri, K Izhikevich… - Science, 2022 - science.org
Understanding the circumstances that lead to pandemics is important for their prevention.
We analyzed the genomic diversity of severe acute respiratory syndrome coronavirus 2 …

Imprinted antibody responses against SARS-CoV-2 Omicron sublineages

YJ Park, D Pinto, AC Walls, Z Liu, A De Marco… - Science, 2022 - science.org
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron sublineages carry
distinct spike mutations resulting in escape from antibodies induced by previous infection or …

[HTML][HTML] SARS-CoV-2 breakthrough infections elicit potent, broad, and durable neutralizing antibody responses

AC Walls, KR Sprouse, JE Bowen, A Joshi, N Franko… - Cell, 2022 - cell.com
Although infections among vaccinated individuals lead to milder COVID-19 symptoms
relative to those in unvaccinated subjects, the specificity and durability of antibody …

[HTML][HTML] Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding

TN Starr, AJ Greaney, SK Hilton, D Ellis, KHD Crawford… - cell, 2020 - cell.com
The receptor binding domain (RBD) of the SARS-CoV-2 spike glycoprotein mediates viral
attachment to ACE2 receptor and is a major determinant of host range and a dominant target …

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 dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology

A Rambaut, EC Holmes, Á O'Toole, V Hill… - Nature …, 2020 - nature.com
The ongoing pandemic spread of a new human coronavirus, SARS-CoV-2, which is
associated with severe pneumonia/disease (COVID-19), has resulted in the generation of …

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 …

Temporal detection and phylogenetic assessment of SARS-CoV-2 in municipal wastewater

A Nemudryi, A Nemudraia, T Wiegand, K Surya… - Cell Reports …, 2020 - cell.com
SARS-CoV-2 has recently been detected in feces, which indicates that wastewater may be
used to monitor viral prevalence in the community. Here, we use RT-qPCR to monitor …