A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa

Genomic-informed pathogen surveillance in Africa: opportunities and challenges

(2021) Seth C Inzaule et al.   LANCET INFECTIOUS DISEASES

SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma

(2021) Constantinos Kurt Wibmer et al.   NATURE MEDICINE

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

(2021) Houriiyah Tegally et al.   NATURE MEDICINE

Covid-19 deaths in Africa: prospective systematic postmortem surveillance study

(2021) Lawrence Mwananyanda et al.   BMJ-British Medical Journal

The first and second waves of the COVID-19 pandemic in Africa: a cross-sectional study

(2021) Stephanie J Salyer et al.   LANCET

Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant

(2021) Shabir A. Madhi et al.   NEW ENGLAND JOURNAL OF MEDICINE

Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7

(2021) Bo Meng et al.   Cell Reports

A novel coronavirus outbreak of global health concern

(2020) Chen Wang et al.   LANCET

A new coronavirus associated with human respiratory disease in China

(2020) Fan Wu et al.   NATURE

Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus–Infected Pneumonia

(2020) Qun Li et al.   NEW ENGLAND JOURNAL OF MEDICINE

Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus

(2020) Bette Korber et al.   CELL

COVID-19 in Egypt: Uncovered figures or a different situation?

(2020) Mohammed A Medhat et al.   Journal of Global Health

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

(2020) Andrew Rambaut et al.   Nature Microbiology

Lockdown measures in response to COVID-19 in nine sub-Saharan African countries

(2020) Najmul Haider et al.   BMJ Global Health

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

(2020) Erik Volz et al.   CELL

Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report

(2020) Jennifer Giandhari et al.   INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES

Renewing Felsenstein’s phylogenetic bootstrap in the era of big data

(2018) F. Lemoine et al.   NATURE

GISAID: Global initiative on sharing all influenza data – from vision to reality

(2017) Yuelong Shu et al.   Eurosurveillance

SERAPHIM: studying environmental rasters and phylogenetically informed movements

(2016) Simon Dellicour et al.   BIOINFORMATICS

Origin, imports and exports of HIV-1 subtype C in South Africa: A historical perspective

(2016) Eduan Wilkinson et al.   INFECTION GENETICS AND EVOLUTION

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

Phylogeography Takes a Relaxed Random Walk in Continuous Space and Time

(2010) P. Lemey et al.   MOLECULAR BIOLOGY AND EVOLUTION