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

Rapid replacement of the Beta variant by the Delta variant in South Africa

Tegally H, Wilkinson E, Althaus C, Giovanetti M, San J, Giandhari J, Pillay S, Naidoo Y, Ramphal U, Msomi N, Mlisana K,...

medRxiv, 2021

The biological and clinical significance of emerging SARS- CoV-2 variants

Tao T, Tzou1 PL, Nouhin J, Gupta RK, de Oliveira T, Pond SLK, Fera D, Shafer RW

Nature Reviews Genetics, 2021

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

Wilkinson E, Giovanetti M, Tegally H, San EJ, Lessells R, Abdoul K. Sangare, Abdoul-Salam Ouedraogo, Abdul K. Sesay,...

Science, 2021

The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages

Martin DP, Weaver S, Tegally H, San EJ, Shank SD, Wilkinson E, Lucaci AG, Giandhari J, Naidoo S, Pillay Y, Singh L,...

Cell, 2021

Implementation of an efficient SARS-CoV-2 specimen pooling strategy for high throughput...

Singh L, Anyaneji UJ, Ndifon W, Turok N, Mattison SA, Lessells R, Sinayskiy I, San EJ, Tegally H, Barnett S, Lorimer T,...

Scientific Reports, 2021

Two doses of SARS-CoV-2 vaccination induce robust immune responses to emerging SARS-CoV-2...

Skelly DT, Harding AC, Gilbert-Jaramillo J, Knight ML, Longet S, Brown A, Adele S, Adland E, Brown H, Medawar...

Nature Communications, 2021

Reduced antibody cross-reactivity following infection with B.1.1.7 than with parental...

Faulkner N, Ng KW, Wu MY, Harvey R, Margaritis M, Paraskevopoulou S, Houlihan C, Hussain S, Greco M, Bolland W, Warchal...

Elife, 2021

HIV-1 and SARS-CoV-2: Patterns in the evolution of two pandemic pathogens.

Fischer W, Giorgi EE, Chakraborty S, Nguyen K, Bhattacharya T, Theiler J, Goloboff PA, Yoon H, Abfalterer W, Foley BT,...

Cell Host Microbe, 2021

Molecular surveillance of the on-going SARS-COV-2 epidemic in Ribeirao Preto City, Brazil

Slavov SN, Giovanetti M, Bezerra RS, Fonseca V, Santos EV, Rodrigues ES, Adelino T, Xavier J, Borges JS, Evaristo M,...

Infect Genet Evol, 2021

SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit...

Giovanetti M, Cella E, Benedetti F, Rife Magalis B, Fonseca V, Fabris S, Campisi G, Ciccozzi A, Angeletti S, Borsetti...

Communications Biology, 2021

Efficacy of NVX-CoV2373 Covid-19 Vaccine against the B.1.351 Variant

Shinde V, Bhikha S, Hoosain Z, Archary M, Bhorat Q, Fairlie L, Lalloo U, Masilela MSL, Moodley D, Hanley S, Fouche L,...

NEJM, 2021

Multiplex qPCR discriminates variants of concern to enhance global surveillance of...

Vogels CBF, Breban MI, Ott IM, Alpert T, Petrone ME, Watkins AE, Kalinich CC, Earnest R, Rothman JE, Goes de Jesus J,...

PLoS Biology, 2021

Genomic surveillance activities unveil the introduction of the SARS-CoV-2 B.1.525 variant...

Pereira F, Tosta S, Lima MM, Reboredo de Oliveira da Silva L, Nardy VB, Gomez MKA, Lima JG, Fonseca V, de Oliveira T,...

J Med Virol, 2021

Genomic evidence of SARS-CoV-2 reinfection case with the emerging B.1.2 variant in Brazil

Fonseca V, de Jesus R, Adelino T, Reis AB, de Souza BB, Ribeiro AA, Guimaraes NR, Livorati MTFP, Neto DFL, Kato RB,...

Journal of Infection, 2021

Transmission dynamics of SARS-CoV-2 within-host diversity in two major hospital outbreaks...

San JE, Ngcapu S, Kanzi AM, Tegally H, Fonseca V, Giandhari J, Wilkinson E, Nelson CW, Smidt W, Kiran AM, Chimukangara...

Virus Evolution, 2021

Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2

O'Toole A, Hill V, Pybus OG, Watts A, Bogoch II, Khan K, Messina JP, COVID-19 Genomics UK (COG-UK) consortium, Network...

Wellcome Open Res, 2021

SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse

Konings F, Perkins MD, Kuhn JH, Pallen MJ, Alm EJ, Archer BN, Barakat A, Bedford T, Bhiman JN, Caly L, Carter LL,...

Nature Microbiology, 2021

Persistent SARS-CoV-2 infection and intra-host evolution in association with advanced HIV...

Karim F, Moosa MYS, Gosnell BI, Cele S, Giandhari J, Pillay S, Tegally H, Wilkinson E, San JE, Msomi N, Mlisana K, Khan...

medRxiv, 2021

Cross-Reactive Neutralizing Antibody Responses Elicited by SARS-CoV-2 501Y.V2 (B.1.351)

Moyo-Gwete T, Madzivhandila M, Makhado Z, Ayres F, Mhlanga D, Oosthuysen B, Lambson EB, Kgagudi P, Tegally H, Iranzadeh...

NEJM, 2021

Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa

Engelbrecht S, Delaney K, Kleinhans B, Wilkinson E, Tegally H, Stander T, van Zyl G, Preiser W, de Oliveira T

Viruses, 2021

Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma.

Cele S, Gazy I, Jackson L, Hwa SH, Tegally H, Lustig G, Giandhari J, Pillay S, Wilkinson E, Naidoo Y, Karim F, Ganga Y,...

Nature, 2021

A novel variant of interest of SARS-CoV-2 with multiple spike mutations detected through...

de Oliveira T, Lutucuta S, Nkengasong J, Morais J, Paixao JP, Neto Z, Afonso P, Miranda J, David K, Ingles L, Amilton P...

medRxiv, 2021

Appropriate names for COVID-19 variants

Karim SSA, de Oliveira T, Loots G

Science, 2021

Safety and efficacy of the ChAdOx1 nCoV-19 (AZD1222) Covid-19 vaccine against the B.1.351...

Madhi SA, Baillie VL, Cutland CL, Voysey M, KoenAL, Fairlie L, Padayachee SD, Dheda K, Barnabas SL, Bhorat QE, Briner...

NEJM, 2021

Voices of Biotech Research

Annabi N, Baker M, Boettiger A, Chakraborty D, Chen Y, Corbett K, Correia B, Dahlman J, de Oliveira T, Ertuerk A, Yanik...

Nature Biotechnology, 2021

Emergence of a SARS-CoV-2 variant of concern with mutations in spike glycoprotein

Tegally H, Wilkinson E, Giovanetti M, Iranzadeh A, Fonseca V, Giandhari J, Doolabh D, Pillay S, San E, Msomi N, Mlisana...

Nature, 2021

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

Wibmer CK, Ayres F, Hermanus T, Madzivhandila M, Kgagudi P, Oosthuysen B, Lambson BE, de Oliveira T, Vermeulen M, van...

Nature Medicine, 2021

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

Tegally H, Wilkinson E, Lessells R, Giandhari J, Pillay S, Msomi N, Mlisana K, Bhiman J, Gottberg A, Walaza S, Fonseca...

Nature Medicine, 2021

Escape of SARS-CoV-2 501Y.V2 variants from neutralization by convalescent plasma

Cele S, Gazy I, Jackson L, Hwa S-H, Tegally H, Lustig G, Giandhari J, Pillay S, Wilkinson E, Naidoo Y, Karim F, Ganga...

medRxiv, 2021

Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus...

Tegally H, Wilkinson E, Giovanetti M, Iranzadeh A, Fonseca V, Giandhari J, Doolabh D, Pillay S, San E, Msomi N, Mlisana...

medRxiv, 2020

Reduced efficacy of HIV-1 integrase inhibitors in patients with drug resistance mutations...

Siedner MJ, Moorhouse MA, Simmons B, de Oliveira T, Lessells R, Giandhari J, Kemp SA, Chimukangara B, Akpomiemie G,...

Nature Communications, 2020

HIV infection alters SARS-CoV-2 responsive immune parameters but not clinical outcomes in...

Karim F, Gazy I, Cele S, Zungu Y, Krause R, Bernstein M, Ganga Y, Rodel H, Mthabela N, Mazibuko M, Khan K, Muema D,...

medRxiv, 2020

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

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