Evidence of long-lived founder virus in mother-to-child HIV transmission.

by Sivapragashini Danaviah, Tulio de Oliveira, Ruth Bland, Johannes Viljoen, Sureshnee Pillay, Edouard Tuaillon, Philippe Van de Perre, Marie-Louise Newell
Published 2015-01-01

Evaluation of miniaturized Illumina DNA preparation protocols for SARS-CoV-2 whole genome sequencing

by Sureshnee Pillay, James Emmanuel San, Derek Tshiabuila, Yeshnee Naidoo, Yusasha Pillay, Akhil Maharaj, Ugochukwu J. Anyaneji, Eduan Wilkinson, Houriiyah Tegally, Richard J. Lessells, Cheryl Baxter, Tulio de Oliveira, Jennifer Giandhari
Published 2023-01-01

Comparison of SARS-CoV-2 sequencing using the ONT GridION and the Illumina MiSeq

by Derek Tshiabuila, Jennifer Giandhari, Sureshnee Pillay, Upasana Ramphal, Yajna Ramphal, Arisha Maharaj, Ugochukwu Jacob Anyaneji, Yeshnee Naidoo, Houriiyah Tegally, Emmanuel James San, Eduan Wilkinson, Richard J. Lessells, Tulio de Oliveira
Published 2022-04-01

Evaluation of miniaturized Illumina DNA preparation protocols for SARS-CoV-2 whole genome sequencing.

by Sureshnee Pillay, James Emmanuel San, Derek Tshiabuila, Yeshnee Naidoo, Yusasha Pillay, Akhil Maharaj, Ugochukwu J Anyaneji, Eduan Wilkinson, Houriiyah Tegally, Richard J Lessells, Cheryl Baxter, Tulio de Oliveira, Jennifer Giandhari
Published 2023-01-01

Molecular Epidemiology of SARS-CoV-2 during Five COVID-19 Waves and the Significance of Low-Frequency Lineages

by Kathleen Subramoney, Nkhensani Mtileni, Jennifer Giandhari, Yeshnee Naidoo, Yajna Ramphal, Sureshnee Pillay, Upasana Ramphal, Akhil Maharaj, Derek Tshiabuila, Houriiyah Tegally, Eduan Wilkinson, Tulio de Oliveira, Burtram C. Fielding, Florette K. Treurnicht
Published 2023-05-01

Correction: Subramoney et al. Molecular Epidemiology of SARS-CoV-2 during Five COVID-19 Waves and the Significance of Low-Frequency Lineages. <i>Viruses</i> 2023, <i>15</i>, 1194

by Kathleen Subramoney, Nkhensani Mtileni, Jennifer Giandhari, Yeshnee Naidoo, Yajna Ramphal, Sureshnee Pillay, Upasana Ramphal, Akhil Maharaj, Derek Tshiabuila, Houriiyah Tegally, Eduan Wilkinson, Tulio de Oliveira, Burtram C. Fielding, Florette K. Treurnicht
Published 2023-07-01

SARS-CoV-2 spike protein diversity at an intra-host level, among SARS-CoV-2 infected individuals in South Africa, 2020 to 2022.

by Kathleen Subramoney, Nkhensani Mtileni, Ashlyn Davis, Jennifer Giandhari, Houriiyah Tegally, Eduan Wilkinson, Yeshnee Naidoo, Yajna Ramphal, Sureshnee Pillay, Upasana Ramphal, Andiswa Simane, Bhaveshan Reddy, Bonolo Mashishi, Nonhlanhla Mbenenge, Tulio de Oliveira, Burtram C Fielding, Florette K Treurnicht
Published 2023-01-01

Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic

by Sureshnee Pillay, Jennifer Giandhari, Houriiyah Tegally, Eduan Wilkinson, Benjamin Chimukangara, Richard Lessells, Yunus Moosa, Stacey Mattison, Inbal Gazy, Maryam Fish, Lavanya Singh, Khulekani Sedwell Khanyile, James Emmanuel San, Vagner Fonseca, Marta Giovanetti, Luiz Carlos Alcantara, Tulio de Oliveira
Published 2020-08-01

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

by Jennifer Giandhari, Sureshnee Pillay, Eduan Wilkinson, Houriiyah Tegally, Ilya Sinayskiy, Maria Schuld, José Lourenço, Benjamin Chimukangara, Richard Lessells, Yunus Moosa, Inbal Gazy, Maryam Fish, Lavanya Singh, Khulekani Sedwell Khanyile, Vagner Fonseca, Marta Giovanetti, Luiz Carlos Junior Alcantara, Francesco Petruccione, Tulio de Oliveira
Published 2021-02-01

Rapid Replacement of SARS-CoV-2 Variants by Delta and Subsequent Arrival of Omicron, Uganda, 2021

by Nicholas Bbosa, Deogratius Ssemwanga, Hamidah Namagembe, Ronald Kiiza, Jocelyn Kiconco, John Kayiwa, Tom Lutalo, Julius Lutwama, Alfred Ssekagiri, Isaac Ssewanyana, Susan Nabadda, Henry Kyobe-Bbosa, Jennifer Giandhari, Sureshnee Pillay, Upasana Ramphal, Yajna Ramphal, Yeshnee Naidoo, Derek Tshiabuila, Houriiyah Tegally, Emmanuel J. San, Eduan Wilkinson, Tulio de Oliveira, Pontiano Kaleebu
Published 2022-05-01

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

by Nokukhanya Msomi, Koleka Mlisana, Tulio de Oliveira, Nokukhanya Msomi, Koleka Mlisana, Carolyn Willianson, Jinal N. Bhiman, Dominique Goedhals, Susan Engelbrecht, Gert Van Zyl, Wolfgang Preiser, Diana Hardie, Marvin Hsiao, Nicola Mulder, Darren Martin, Alan Christoffels, Denis York, Jennifer Giandhari, Eduan Wilkinson, Sureshnee Pillay, Houriiyah Tegally, San Emmanuel James, Aquilah Kanzi, Richard John Lessells, Tulio de Oliveira
Published 2020-10-01

Molecular Epidemiology and Diversity of SARS-CoV-2 in Ethiopia, 2020–2022

by Abay Sisay, Derek Tshiabuila, Stephanie van Wyk, Abraham Tesfaye, Gerald Mboowa, Samuel O. Oyola, Sofonias Kifle Tesema, Cheryl Baxter, Darren Martin, Richard Lessells, Houriiyah Tegally, Monika Moir, Jennifer Giandhari, Sureshnee Pillay, Lavanya Singh, Yajna Ramphal, Arisha Maharaj, Yusasha Pillay, Akhil Maharaj, Yeshnee Naidoo, Upasana Ramphal, Lucious Chabuka, Eduan Wilkinson, Tulio de Oliveira, Adey Feleke Desta, James E. San
Published 2023-03-01

Genomic epidemiology of SARS-CoV-2 during the first four waves in Mozambique

by Nalia Ismael, Stephanie van Wyk, Houriiyah Tegally, Jennifer Giandhari, James Emmanuel San, Monika Moir, Sureshnee Pillay, Christian Utpatel, Lavanya Singh, Yeshnee Naidoo, Upasana Ramphal, Nédio Mabunda, Nuro Abílio, Paulo Arnaldo, Joicymara Xavier, Daniel Gyamfi Amoako, Josie Everatt, Yajna Ramphal, Arisha Maharaj, Leonardo de Araujo, Ugochukwu J. Anyaneji, Derek Tshiabuila, Sofia Viegas, Richard Lessells, Susan Engelbrecht, Eduardo Gudo, Ilesh Jani, Stefan Niemann, Eduan Wilkinson, Túlio de Oliveira
Published 2023-01-01

Genomic epidemiology of SARS-CoV-2 during the first four waves in Mozambique.

by Nalia Ismael, Stephanie van Wyk, Houriiyah Tegally, Jennifer Giandhari, James Emmanuel San, Monika Moir, Sureshnee Pillay, Christian Utpatel, Lavanya Singh, Yeshnee Naidoo, Upasana Ramphal, Nédio Mabunda, Nuro Abílio, Paulo Arnaldo, Joicymara Xavier, Daniel Gyamfi Amoako, Josie Everatt, Yajna Ramphal, Arisha Maharaj, Leonardo de Araujo, Ugochukwu J Anyaneji, Derek Tshiabuila, Sofia Viegas, Richard Lessells, Susan Engelbrecht, Eduardo Gudo, Ilesh Jani, Stefan Niemann, Eduan Wilkinson, Túlio de Oliveira
Published 2023-01-01

SARS-CoV-2 variants from COVID-19 positive cases in the Free State province, South Africa from July 2020 to December 2021

by Peter Mwangi, Javan Okendo, Javan Okendo, Milton Mogotsi, Ayodeji Ogunbayo, Olusesan Adelabu, Hlengiwe Sondlane, Makgotso Maotoana, Lutfiyya Mahomed, Molefi Daniel Morobadi, Molefi Daniel Morobadi, Sabeehah Vawda, Sabeehah Vawda, Anne von Gottberg, Anne von Gottberg, Jinal Bhiman, Jinal Bhiman, Houriiyah Tegally, Eduan Wilkinson, Jennifer Giandhari, Sureshnee Pillay, Yeshnee Naidoo, Upasana Ramphal, Tulio de Oliveira, Tulio de Oliveira, Tulio de Oliveira, Armand Bester, Armand Bester, Dominique Goedhals, Dominique Goedhals, Dominique Goedhals, Martin Nyaga
Published 2022-09-01

Omicron BA.4/BA.5 escape neutralizing immunity elicited by BA.1 infection

by Khadija Khan, Farina Karim, Yashica Ganga, Mallory Bernstein, Zesuliwe Jule, Kajal Reedoy, Sandile Cele, Gila Lustig, Daniel Amoako, Nicole Wolter, Natasha Samsunder, Aida Sivro, James Emmanuel San, Jennifer Giandhari, Houriiyah Tegally, Sureshnee Pillay, Yeshnee Naidoo, Matilda Mazibuko, Yoliswa Miya, Nokuthula Ngcobo, Nithendra Manickchund, Nombulelo Magula, Quarraisha Abdool Karim, Anne von Gottberg, Salim S. Abdool Karim, Willem Hanekom, Bernadett I. Gosnell, COMMIT-KZN Team, Richard J. Lessells, Tulio de Oliveira, Mahomed-Yunus S. Moosa, Alex Sigal
Published 2022-08-01

Author Correction: Omicron BA.4/BA.5 escape neutralizing immunity elicited by BA.1 infection

by Khadija Khan, Farina Karim, Yashica Ganga, Mallory Bernstein, Zesuliwe Jule, Kajal Reedoy, Sandile Cele, Gila Lustig, Daniel Amoako, Nicole Wolter, Natasha Samsunder, Aida Sivro, James Emmanuel San, Jennifer Giandhari, Houriiyah Tegally, Sureshnee Pillay, Yeshnee Naidoo, Matilda Mazibuko, Yoliswa Miya, Nokuthula Ngcobo, Nithendra Manickchund, Nombulelo Magula, Quarraisha Abdool Karim, Anne von Gottberg, Salim S. Abdool Karim, Willem Hanekom, Bernadett I. Gosnell, COMMIT-KZN Team, Richard J. Lessells, Tulio de Oliveira, Mahomed-Yunus S. Moosa, Alex Sigal
Published 2022-10-01

Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage

by Cathrine Scheepers, Josie Everatt, Daniel G. Amoako, Houriiyah Tegally, Constantinos Kurt Wibmer, Anele Mnguni, Arshad Ismail, Boitshoko Mahlangu, Bronwen E. Lambson, Darren P. Martin, Eduan Wilkinson, James Emmanuel San, Jennifer Giandhari, Nelia Manamela, Noxolo Ntuli, Prudence Kgagudi, Sandile Cele, Simone I. Richardson, Sureshnee Pillay, Thabo Mohale, Upasana Ramphal, Yeshnee Naidoo, Zamantungwa T. Khumalo, Gaurav Kwatra, Glenda Gray, Linda-Gail Bekker, Shabir A. Madhi, Vicky Baillie, Wesley C. Van Voorhis, Florette K. Treurnicht, Marietjie Venter, Koleka Mlisana, Nicole Wolter, Alex Sigal, Carolyn Williamson, Nei-yuan Hsiao, Nokukhanya Msomi, Tongai Maponga, Wolfgang Preiser, Zinhle Makatini, Richard Lessells, Penny L. Moore, Tulio de Oliveira, Anne von Gottberg, Jinal N. Bhiman
Published 2022-04-01

Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 [version 1; peer review: 2 approved]

by Áine O'Toole, Verity Hill, Oliver G. Pybus, Alexander Watts, Issac I. Bogoch, Kamran Khan, Jane P. Messina, The COVID-19 Genomics UK (COG-UK) consortium, Network for Genomic Surveillance in South Africa (NGS-SA), Brazil-UK CADDE Genomic Network, Houriiyah Tegally, Richard R. Lessells, Jennifer Giandhari, Sureshnee Pillay, Kefentse Arnold Tumedi, Gape Nyepetsi, Malebogo Kebabonye, Maitshwarelo Matsheka, Madisa Mine, Sima Tokajian, Hamad Hassan, Tamara Salloum, Georgi Merhi, Jad Koweyes, Jemma L. Geoghegan, Joep de Ligt, Xiaoyun Ren, Matthew Storey, Nikki E. Freed, Chitra Pattabiraman, Pramada Prasad, Anita S. Desai, Ravi Vasanthapuram, Thomas F. Schulz, Lars Steinbrück, Tanja Stadler, Swiss Viollier Sequencing Consortium, Antonio Parisi, Angelica Bianco, Darío García de Viedma, Sergio Buenestado-Serrano, Vítor Borges, Joana Isidro, Sílvia Duarte, João Paulo Gomes, Neta S. Zuckerman, Michal Mandelboim, Orna Mor, Torsten Seemann, Alicia Arnott, Jenny Draper, Mailie Gall, William Rawlinson, Ira Deveson, Sanmarié Schlebusch, Jamie McMahon, Lex Leong, Chuan Kok Lim, Maria Chironna, Daniela Loconsole, Antonin Bal, Laurence Josset, Edward Holmes, Kirsten St. George, Erica Lasek-Nesselquist, Reina S. Sikkema, Bas Oude Munnink, Marion Koopmans, Mia Brytting, V. Sudha rani, S. Pavani, Teemu Smura, Albert Heim, Satu Kurkela, Massab Umair, Muhammad Salman, Barbara Bartolini, Martina Rueca, Christian Drosten, Thorsten Wolff, Olin Silander, Dirk Eggink, Chantal Reusken, Harry Vennema, Aekyung Park, Christine Carrington, Nikita Sahadeo, Michael Carr, Gabo Gonzalez, SEARCH Alliance San Diego, National Virus Reference Laboratory, SeqCOVID-Spain, Danish Covid-19 Genome Consortium (DCGC), Communicable Diseases Genomic Network (CDGN), Dutch National SARS-CoV-2 surveillance program, Division of Emerging Infectious Diseases (KDCA), Tulio de Oliveira, Nuno Faria, Andrew Rambaut, Moritz U. G. Kraemer
Published 2021-05-01

Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch [version 2; peer review: 3 approved]

by Áine O'Toole, Verity Hill, Oliver G. Pybus, Alexander Watts, Issac I. Bogoch, Kamran Khan, Jane P. Messina, The COVID-19 Genomics UK (COG-UK) consortium, Network for Genomic Surveillance in South Africa (NGS-SA), Brazil-UK CADDE Genomic Network, Houriiyah Tegally, Richard R. Lessells, Jennifer Giandhari, Sureshnee Pillay, Kefentse Arnold Tumedi, Gape Nyepetsi, Malebogo Kebabonye, Maitshwarelo Matsheka, Madisa Mine, Sima Tokajian, Hamad Hassan, Tamara Salloum, Georgi Merhi, Jad Koweyes, Jemma L. Geoghegan, Joep de Ligt, Xiaoyun Ren, Matthew Storey, Nikki E. Freed, Chitra Pattabiraman, Pramada Prasad, Anita S. Desai, Ravi Vasanthapuram, Thomas F. Schulz, Lars Steinbrück, Tanja Stadler, Swiss Viollier Sequencing Consortium, Antonio Parisi, Angelica Bianco, Darío García de Viedma, Sergio Buenestado-Serrano, Vítor Borges, Joana Isidro, Sílvia Duarte, João Paulo Gomes, Neta S. Zuckerman, Michal Mandelboim, Orna Mor, Torsten Seemann, Alicia Arnott, Jenny Draper, Mailie Gall, William Rawlinson, Ira Deveson, Sanmarié Schlebusch, Jamie McMahon, Lex Leong, Chuan Kok Lim, Maria Chironna, Daniela Loconsole, Antonin Bal, Laurence Josset, Edward Holmes, Kirsten St. George, Erica Lasek-Nesselquist, Reina S. Sikkema, Bas Oude Munnink, Marion Koopmans, Mia Brytting, V. Sudha rani, S. Pavani, Teemu Smura, Albert Heim, Satu Kurkela, Massab Umair, Muhammad Salman, Barbara Bartolini, Martina Rueca, Christian Drosten, Thorsten Wolff, Olin Silander, Dirk Eggink, Chantal Reusken, Harry Vennema, Aekyung Park, Christine Carrington, Nikita Sahadeo, Michael Carr, Gabo Gonzalez, SEARCH Alliance San Diego, National Virus Reference Laboratory, SeqCOVID-Spain, Danish Covid-19 Genome Consortium (DCGC), Communicable Diseases Genomic Network (CDGN), Dutch National SARS-CoV-2 surveillance program, Division of Emerging Infectious Diseases (KDCA), Tulio de Oliveira, Nuno Faria, Andrew Rambaut, Moritz U. G. Kraemer
Published 2021-09-01