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 …

Ebola virus disease

ST Jacob, I Crozier, WA Fischer, A Hewlett… - Nature reviews Disease …, 2020 - nature.com
Ebola virus disease (EVD) is a severe and frequently lethal disease caused by Ebola virus
(EBOV). EVD outbreaks typically start from a single case of probable zoonotic transmission …

Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans

BB Oude Munnink, RS Sikkema, DF Nieuwenhuijse… - science, 2021 - science.org
Animal experiments have shown that nonhuman primates, cats, ferrets, hamsters, rabbits,
and bats can be infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV …

Resurgence of Ebola virus in 2021 in Guinea suggests a new paradigm for outbreaks

AK Keita, FR Koundouno, M Faye, A Düx, J Hinzmann… - Nature, 2021 - nature.com
Seven years after the declaration of the first epidemic of Ebola virus disease in Guinea, the
country faced a new outbreak—between 14 February and 19 June 2021—near the …

[HTML][HTML] Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore

JR Tyson, P James, D Stoddart, N Sparks… - BioRxiv, 2020 - ncbi.nlm.nih.gov
Genome sequencing has been widely deployed to study the evolution of SARS-CoV-2 with
more than 90,000 genome sequences uploaded to the GISAID database. We published a …

Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study

LW Meredith, WL Hamilton, B Warne… - The Lancet infectious …, 2020 - thelancet.com
Background The burden and influence of health-care associated severe acute respiratory
syndrome coronavirus 2 (SARS-CoV-2) infections is unknown. We aimed to examine the …

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples

J Quick, ND Grubaugh, ST Pullan, IM Claro, AD Smith… - Nature protocols, 2017 - nature.com
Genome sequencing has become a powerful tool for studying emerging infectious diseases;
however, genome sequencing directly from clinical samples (ie, without isolation and …

[PDF][PDF] Genomic sequencing of SARS-CoV-2: a guide to implementation for maximum impact on public health, 8 January 2021

World Health Organization - 2021 - apps.who.int
The year 2020 was a turning point in history and in global health. The COVID-19 pandemic
has highlighted the potential for deadly epidemic-prone diseases to overwhelm our …

Patterns of within-host genetic diversity in SARS-CoV-2

G Tonkin-Hill, I Martincorena, R Amato, ARJ Lawson… - elife, 2021 - elifesciences.org
Monitoring the spread of SARS-CoV-2 and reconstructing transmission chains has become
a major public health focus for many governments around the world. The modest mutation …

Virus genomes reveal factors that spread and sustained the Ebola epidemic

G Dudas, LM Carvalho, T Bedford, AJ Tatem, G Baele… - Nature, 2017 - nature.com
Abstract The 2013–2016 West African epidemic caused by the Ebola virus was of
unprecedented magnitude, duration and impact. Here we reconstruct the dispersal …