This paper reports on mpox cases in South Africa in 2024, finding that the virus was reintroduced and transmitted locally, clustering with known outbreak variants.

bioRxiv · Nov 7, 2024 · PreprintMicrobiology

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

Eduan Wilkinson, Marta Giovanetti, Houriiyah Tegally, James Emmanuel San, Richard J. Lessells, Diego F. Cuadros, Darren Patrick Martin, David A. Rasmussen, Abdel‐Rahman N. Zekri, Abdoul Karim Sangaré, Abdoul–Salam Ouédraogo, Abdul Karim Sesay, Priscilla Abechi, Adedotun-Sulaiman Kemi, Adewunmi M. Olubusuyi, , Gabriel K. Mbunsu

This study uses genomic data from 8746 SARS-CoV-2 genomes across 33 African countries to show that most epidemics were initiated by European importations and later driven by local transmission and mobility, leading to the spread of variants of concern.

Science · Oct 9, 2021Peer-reviewedGenetic & Genomic Medicine

Mapping the drivers of within-host pathogen evolution using massive data sets

Duncan S. Palmer, Isaac Turner, Sarah J. Fidler, John Frater, Dominique Goedhals, Philip Goulder, Kuan‐Hsiang Gary Huang, Annette Oxenius, Rodney Phillips, Roger Shapiro, Cloete van Vuuren, Angela Ruth McLean, Gil McVean

The paper develops a Bayesian method to detect host influences on pathogen evolution using large datasets, demonstrating improved precision in identifying HLA-induced selection in HIV-1.

Nature Communications · Jul 9, 2019Peer-reviewedGenetics

PhyloPi: an affordable, purpose built phylogenetic pipeline for the HIV drug resistance testing facility

Phillip Armand Bester, Andrie de Vries, Stephanus Riekert, Kim Steegen, Gert Uves van Zyl, Dominique Goedhals

PhyloPi provides an affordable phylogenetic pipeline for HIV drug resistance testing, enabling sample swap detection and genetic diversity analysis using a Raspberry Pi.

PLoS ONE · Mar 5, 2019Peer-reviewedBioinformatics