NGS-SA: Publications and pre-prints of our genomics surveillance work

High Resolution analysis of Transmission Dynamics of Sars-Cov-2 in Two Major Hospital...

San EJ, Ngcapu S, Kanzi A, Tegally H, Fonseca V, Giandhari J, Wilkinson E, Chimukangara B, Pillay S, Singh L, Fish M,...

MedRxiv, 2020

Cost-effectiveness of public health strategies for COVID-19 epidemic control in South...

Reddy KP, Shebl FM, Foote JHA, Harling G, Scott JA, Panella C, Fitzmaurice KP, Flanagan C, Hyle EP, Neilan AM, Mohareb...

Lancet Global Health, 2020

Major new lineages of SARS-CoV-2 emerge and spread in South Africa during lockdown

Tegally H, Wilkinson E, Lessells R, Giandhari J, Pillay S, Msomi N, Mlisana K, Bhiman J, Allam M, Ismail A, Engelbrecht...

medRxiv, 2020

Unlocking the efficiency of genomics laboratories with robotic liquid-handling

Tegally H, San JE, Giandhari J, de Oliveira T

BMC Genomics, 2020

Accelerating genomics-based surveillance for COVID-19 response in Africa

Tessema SK, Inzaule SC, Christoffels A, Kebede Y, de Oliveira T, Ouma AEO, Happi CT, Nkengasong JN

Lancet Microbe, 2020

A genomics network established to respond rapidly to public health threats in South...

Msomi N, Mlisana K, Willianson C, Bhiman JN, Goedhals D, Engelbrecht S, Van Zyl G, Preiser W, Hardie D, Hsiao M, Mulder...

Lancet Microbe, 2020

Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate...

Pillay S, Giandhari J, Tegally H, Wilkinson E, Chimukangara B, Lessells R, Mattison S, Moosa Y, Gazy I, Fish M, Singh...

Genes, 2020

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

Giandhari J, Pillay S, Wilkinson E, Tegally H, Sinayskiy I, Schuld M, Lourenço J, Chimukangara B, Lessells R, Moosa Y,...

IJID, 2020

Protocol: Leveraging a demographic and health surveillance system for Covid-19...

Siedner MJ, Harling G, Derache A, Smit T, Khoza T, Gunda R, Mngomezulu T, Gareta D, Majozi N, Ehlers E, Dreyer J,...

Wellcome Open Research, 2020

Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2...

Mavian C, Pond SK, Marini S, Magalis BR, Vandamme A-M, Dellicour S, Scarpino SV, Houldcroft C, Villabona-Arenas J,...

Proceedings of the National Academy of Sciences (PNAS), 2020

Genome Detective Coronavirus Typing Tool for rapid identification and characterization of...

Cleemput S, Dumon W, Fonseca V, Abdool Karim W, Giovanetti M, Alcantara LCJ, Deforche K, de Oliveira T

Bioinformatics, 2020

Genome Detective: An Automated System for Virus Identification from High-throughput...

Vilsker M, Moosa Y, Nooij S, Fonseca V, Ghysens Y, Dumon K, Pauwels R, Alcantara LC, Vanden Eynden E, Vandamme AM,...

Bioinformatics, 2019