Twenty years of West Nile virus spread and evolution in the Americas visualized by Nextstrain

J Hadfield, AF Brito, DM Swetnam, CBF Vogels… - PLoS …, 2019 - journals.plos.org
It has been 20 years since West Nile virus first emerged in the Americas, and since then,
little progress has been made to control outbreaks caused by this virus. After its first …

Sixteen novel lineages of SARS-CoV-2 in South Africa

H Tegally, E Wilkinson, RJ Lessells, J Giandhari… - Nature medicine, 2021 - nature.com
The first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in South
Africa was identified on 5 March 2020, and by 26 March the country was in full lockdown …

Evolution and epidemic spread of SARS-CoV-2 in Brazil

DS Candido, IM Claro, JG De Jesus, WM Souza… - Science, 2020 - science.org
Brazil currently has one of the fastest-growing severe acute respiratory syndrome
coronavirus 2 (SARS-CoV-2) epidemics in the world. Because of limited available data …

Relax, keep walking—a practical guide to continuous phylogeographic inference with BEAST

S Dellicour, MS Gill, NR Faria… - Molecular Biology …, 2021 - academic.oup.com
Spatially explicit phylogeographic analyses can be performed with an inference framework
that employs relaxed random walks to reconstruct phylogenetic dispersal histories in …

[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 …

Predicting the evolution of the Lassa virus endemic area and population at risk over the next decades

R Klitting, LE Kafetzopoulou, W Thiery, G Dudas… - Nature …, 2022 - nature.com
Lassa fever is a severe viral hemorrhagic fever caused by a zoonotic virus that repeatedly
spills over to humans from its rodent reservoirs. It is currently not known how climate and …

A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages

S Dellicour, K Durkin, SL Hong… - Molecular biology …, 2021 - academic.oup.com
Since the start of the COVID-19 pandemic, an unprecedented number of genomic
sequences of SARS-CoV-2 have been generated and shared with the scientific community …

[HTML][HTML] Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework

S Dellicour, S Lequime, B Vrancken, MS Gill… - Nature …, 2020 - nature.com
Computational analyses of pathogen genomes are increasingly used to unravel the
dispersal history and transmission dynamics of epidemics. Here, we show how to go beyond …

Phylogenetic analysis of migration, differentiation, and class switching in B cells

KB Hoehn, OG Pybus, SH Kleinstein - PLoS computational …, 2022 - journals.plos.org
B cells undergo rapid mutation and selection for antibody binding affinity when producing
antibodies capable of neutralizing pathogens. This evolutionary process can be intermixed …

Leveraging insect-specific viruses to elucidate mosquito population structure and dynamics

BD Hollingsworth, ND Grubaugh, BP Lazzaro… - PLoS …, 2023 - journals.plos.org
Several aspects of mosquito ecology that are important for vectored disease transmission
and control have been difficult to measure at epidemiologically important scales in the field …