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253 results on '"Amoako, Daniel G."'

1. Standardized Phylogenetic Classification of Human Respiratory Syncytial Virus below the Subgroup Level

Author

Goya, Stephanie, Ruis, Christopher, Neher, Richard A., Meijer, Adam, Aziz, Ammar, Hinrichs, Angie S., von Gottberg, Anne, Roemer, Cornelius, Amoako, Daniel G., Acuna, Dolores, McBroome, Jakob, Otieno, James R., Bhiman, Jinal N., Everatt, Josie, Munoz-Escalante, Juan C., Ramaekers, Kaat, Duggan, Kate, Presser, Lance D., Urbanska, Laura, Venter, Marietjie, Wolter, Nicole, Peret, Teresa C.T., Salimi, Vahid, Potdar, Varsha, Borges, Vitor, and Viegas, Mariana

Subjects
Identification and classification, Research, Genetic aspects, Methods, Viral research, Phylogeny -- Research, Genomes -- Research, Respiratory syncytial virus -- Identification and classification -- Genetic aspects, Taxonomy (Biology) -- Methods, Phenetics -- Methods, Biology -- Identification and classification, Virus research
Abstract

Human respiratory syncytial virus (HRSV) is a leading cause of acute lower respiratory tract infection in children, elderly, and immunocompromised persons. In 2023, the US Food and Drug Administration and [...]

Published
2024
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5. Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa

Author

Tegally, Houriiyah, Moir, Monika, Everatt, Josie, Giovanetti, Marta, Scheepers, Cathrine, Wilkinson, Eduan, Subramoney, Kathleen, Makatini, Zinhle, Moyo, Sikhulile, Amoako, Daniel G., Baxter, Cheryl, Althaus, Christian L., Anyaneji, Ugochukwu J., Kekana, Dikeledi, Viana, Raquel, Giandhari, Jennifer, Lessells, Richard J., Maponga, Tongai, Maruapula, Dorcas, Choga, Wonderful, Matshaba, Mogomotsi, Mbulawa, Mpaphi B., Msomi, Nokukhanya, Naidoo, Yeshnee, Pillay, Sureshnee, Sanko, Tomasz Janusz, San, James E., Scott, Lesley, Singh, Lavanya, Magini, Nonkululeko A., Smith-Lawrence, Pamela, Stevens, Wendy, Dor, Graeme, Tshiabuila, Derek, Wolter, Nicole, Preiser, Wolfgang, Treurnicht, Florette K., Venter, Marietjie, Chiloane, Georginah, McIntyre, Caitlyn, O’Toole, Aine, Ruis, Christopher, Peacock, Thomas P., Roemer, Cornelius, Kosakovsky Pond, Sergei L., Williamson, Carolyn, Pybus, Oliver G., Bhiman, Jinal N., Glass, Allison, Martin, Darren P., Jackson, Ben, Rambaut, Andrew, Laguda-Akingba, Oluwakemi, Gaseitsiwe, Simani, von Gottberg, Anne, and de Oliveira, Tulio

Published
2022
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8. Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

Author

Viana, Raquel, Moyo, Sikhulile, Amoako, Daniel G., Tegally, Houriiyah, Scheepers, Cathrine, Althaus, Christian L., Anyaneji, Ugochukwu J., Bester, Phillip A., Boni, Maciej F., Chand, Mohammed, Choga, Wonderful T., Colquhoun, Rachel, Davids, Michaela, Deforche, Koen, Doolabh, Deelan, du Plessis, Louis, Engelbrecht, Susan, Everatt, Josie, Giandhari, Jennifer, Giovanetti, Marta, Hardie, Diana, Hill, Verity, Hsiao, Nei-Yuan, Iranzadeh, Arash, Ismail, Arshad, Joseph, Charity, Joseph, Rageema, Koopile, Legodile, Kosakovsky Pond, Sergei L., Kraemer, Moritz U. G., Kuate-Lere, Lesego, Laguda-Akingba, Oluwakemi, Lesetedi-Mafoko, Onalethatha, Lessells, Richard J., Lockman, Shahin, Lucaci, Alexander G., Maharaj, Arisha, Mahlangu, Boitshoko, Maponga, Tongai, Mahlakwane, Kamela, Makatini, Zinhle, Marais, Gert, Maruapula, Dorcas, Masupu, Kereng, Matshaba, Mogomotsi, Mayaphi, Simnikiwe, Mbhele, Nokuzola, Mbulawa, Mpaphi B., Mendes, Adriano, Mlisana, Koleka, Mnguni, Anele, Mohale, Thabo, Moir, Monika, Moruisi, Kgomotso, Mosepele, Mosepele, Motsatsi, Gerald, Motswaledi, Modisa S., Mphoyakgosi, Thongbotho, Msomi, Nokukhanya, Mwangi, Peter N., Naidoo, Yeshnee, Ntuli, Noxolo, Nyaga, Martin, Olubayo, Lucier, Pillay, Sureshnee, Radibe, Botshelo, Ramphal, Yajna, Ramphal, Upasana, San, James E., Scott, Lesley, Shapiro, Roger, Singh, Lavanya, Smith-Lawrence, Pamela, Stevens, Wendy, Strydom, Amy, Subramoney, Kathleen, Tebeila, Naume, Tshiabuila, Derek, Tsui, Joseph, van Wyk, Stephanie, Weaver, Steven, Wibmer, Constantinos K., Wilkinson, Eduan, Wolter, Nicole, Zarebski, Alexander E., Zuze, Boitumelo, Goedhals, Dominique, Preiser, Wolfgang, Treurnicht, Florette, Venter, Marietje, Williamson, Carolyn, Pybus, Oliver G., Bhiman, Jinal, Glass, Allison, Martin, Darren P., Rambaut, Andrew, Gaseitsiwe, Simani, von Gottberg, Anne, and de Oliveira, Tulio

Published
2022
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10. Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage

Author

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

Published
2022
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13. Omicron extensively but incompletely escapes Pfizer BNT162b2 neutralization

Author

Cele, Sandile, Jackson, Laurelle, Khoury, David S., Khan, Khadija, Moyo-Gwete, Thandeka, Tegally, Houriiyah, San, James Emmanuel, Cromer, Deborah, Scheepers, Cathrine, Amoako, Daniel G., Karim, Farina, Bernstein, Mallory, Lustig, Gila, Archary, Derseree, Smith, Muneerah, Ganga, Yashica, Jule, Zesuliwe, Reedoy, Kajal, Hwa, Shi-Hsia, Giandhari, Jennifer, Blackburn, Jonathan M., Gosnell, Bernadett I., Abdool Karim, Salim S., Hanekom, Willem, von Gottberg, Anne, Bhiman, Jinal N., Lessells, Richard J., Moosa, Mahomed-Yunus S., Davenport, Miles P., de Oliveira, Tulio, Moore, Penny L., and Sigal, Alex

Published
2022
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14. Genomic Characterization of Methicillin-Resistant and Methicillin-Susceptible Staphylococcus aureus Implicated in Bloodstream Infections, KwaZulu-Natal, South Africa: A Pilot Study.

Author

Hetsa, Bakoena A., Asante, Jonathan, Mbanga, Joshua, Ismail, Arshad, Abia, Akebe L. K., Amoako, Daniel G., and Essack, Sabiha Y.

Subjects
METHICILLIN-resistant staphylococcus aureus, WHOLE genome sequencing, METHICILLIN resistance, DRUG resistance in bacteria, STAPHYLOCOCCUS aureus, MICROCOCCACEAE
Abstract

Staphylococcus aureus is an opportunistic pathogen and a leading cause of bloodstream infections, with its capacity to acquire antibiotic resistance genes posing significant treatment challenges. This pilot study characterizes the genomic profiles of S. aureus isolates from patients with bloodstream infections in KwaZulu-Natal, South Africa, to gain insights into their resistance mechanisms, virulence factors, and clonal and phylogenetic relationships. Six multidrug-resistant (MDR) S. aureus isolates, comprising three methicillin-resistant S. aureus (MRSA) and three methicillin-susceptible S. aureus (MSSA), underwent whole genome sequencing and bioinformatics analysis. These isolates carried a range of resistance genes, including blaZ, aac(6′)-aph(2″), ant(9)-Ia, ant(6)-Ia, and fosB. The mecA gene, which confers methicillin resistance, was detected only in MRSA strains. The isolates exhibited six distinct spa types (t9475, t355, t045, t1265, t1257, and t7888) and varied in virulence gene profiles. Panton–Valentine leukocidin (Luk-PV) was found in one MSSA isolate. Two SCCmec types, IVd(2B) and I(1B), were identified, and the isolates were classified into four multilocus sequence types (MLSTs), with ST5 (n = 3) being the most common. These sequence types clustered into two clonal complexes, CC5 and CC8. Notably, two MRSA clones were identified: ST5-CC5-t045-SCCmec_I(1B) and the human-associated endemic clone ST612-CC8-t1257-SCCmec_IVd(2B). Phylogenomic analysis revealed clustering by MLST, indicating strong genetic relationships within clonal complexes. These findings highlight the value of genomic surveillance in guiding targeted interventions to reduce treatment failures and mortality. [ABSTRACT FROM AUTHOR]

Published
2024
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17. The unified proposal for classification of human respiratory syncytial virus below the subgroup level

Author

Goya, Stephanie, primary, Ruis, Christopher, additional, Neher, Richard A., additional, Meijer, Adam, additional, Aziz, Ammar, additional, Hinrichs, Angie S., additional, von Gottberg, Anne, additional, Roemer, Cornelius, additional, Amoako, Daniel G., additional, Acuna, Dolores, additional, McBroome, Jakob, additional, Otieno, James R., additional, Bhiman, Jinal N., additional, Everatt, Josie, additional, Munoz-Escalante, Juan C., additional, Ramaekers, Kaat, additional, Duggan, Kate, additional, Presser, Lance D., additional, Urbanska, Laura, additional, Venter, Marietjie, additional, Wolter, Nicole, additional, Peret, Teresa C. T., additional, Salimi, Vahid, additional, Potdar, Varsha, additional, Borges, Vitor, additional, and Viegas, Mariana, additional

Published
2024
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19. A Genomic Snapshot of Antibiotic-ResistantEnterococcus faecalis within Public Hospital Environments in South Africa

Author

Shobo, Christiana O., Amoako, Daniel G., Allam, Mushal, Ismail, Arshad, Essack, Sabiha Y., and Bester, Linda A.

Abstract

Enterococci are among the most common opportunistic hospital pathogens. This study used whole-genome sequencing (WGS) and bioinformatics to determine the antibiotic resistome, mobile genetic elements, clone and phylogenetic relationship of Enterococcus faecalis isolated from hospital environments in South Africa. This study was carried out from September to November 2017. Isolates were recovered from 11 frequently touched sites by patients and healthcare workers in different wards at 4 levels of healthcare (A, B, C, and D) in Durban, South Africa. Out of the 245 identified E. faecalis isolates, 38 isolates underwent whole-genome sequencing (WGS) on the Illumina MiSeq platform, following microbial identification and antibiotic susceptibility tests. The tet(M) (31/38, 82%) and erm(C) (16/38, 42%) genes were the most common antibiotic-resistant genes found in isolates originating from different hospital environments which corroborated with their antibiotic resistance phenotypes. The isolates harboured mobile genetic elements consisting of plasmids (n = 11) and prophages (n = 14) that were mostly clone-specific. Of note, a large number of insertion sequence (IS) families were found on the IS3 (55%), IS5 (42%), IS1595 (40%), and Tn3 transposons the most predominant. Microbial typing using WGS data revealed 15 clones with 6 major sequence types (ST) belonging to ST16 (n = 7), ST40 (n = 6), ST21 (n = 5), ST126 (n = 3), ST23 (n = 3), and ST386 (n = 3). Phylogenomic analysis showed that the major clones were mostly conserved within specific hospital environments. However, further metadata insights revealed the complex intraclonal spread of these E. faecalis major clones between the sampling sites within each specific hospital setting. The results of these genomic analyses will offer insights into antibiotic-resistantE. faecalis in hospital environments relevant to the design of optimal infection prevention strategies in hospital settings.

Published
2023
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22. Household Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 From Adult Index Cases With and Without Human Immunodeficiency Virus in South Africa, 2020–2021: A Case-Ascertained, Prospective, Observational Household Transmission Study

Author

Kleynhans, Jackie, primary, Walaza, Sibongile, additional, Martinson, Neil A, additional, Neti, Mzimasi, additional, von Gottberg, Anne, additional, Bhiman, Jinal N, additional, Toi, Dylan, additional, Amoako, Daniel G, additional, Buys, Amelia, additional, Ndlangisa, Kedibone, additional, Wolter, Nicole, additional, Genade, Leisha, additional, Maloma, Lucia, additional, Chewparsad, Juanita, additional, Lebina, Limakatso, additional, de Gouveia, Linda, additional, Kotane, Retshidisitswe, additional, Tempia, Stefano, additional, and Cohen, Cheryl, additional

Published
2022
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23. Antibiotic, Heavy Metal, and Biocide Concentrations in a Wastewater Treatment Plant and Its Receiving Water Body Exceed PNEC Limits: Potential for Antimicrobial Resistance Selective Pressure.

Author

Chukwu, Kelechi B., Abafe, Ovokeroye A., Amoako, Daniel G., Essack, Sabiha Y., and Abia, Akebe L. K.

Subjects
BODIES of water, SEWAGE disposal plants, DRUG resistance in microorganisms, HEAVY metals, WATER sampling, ANTIBIOTIC residues
Abstract

Although the rise in antimicrobial resistance has been attributed mainly to the extensive and indiscriminate use of antimicrobials such as antibiotics and biocides in humans, animals and on plants, studies investigating the impact of this use on water environments in Africa are minimal. This study quantified selected antibiotics, heavy metals, and biocides in an urban wastewater treatment plant (WWTP) and its receiving water body in Kwazulu-Natal, South Africa, in the context of the predicted no-effect concentrations (PNEC) for the selection of antimicrobial resistance (AMR). Water samples were collected from the WWTP effluent discharge point and upstream and downstream from this point. Heavy metals were identified and quantified using the United States Environmental Protection Agency (US EPA) method 200.7. Biocides and antibiotic residues were determined using validated ultra-high-performance liquid chromatography with tandem mass spectrometry-based methods. The overall highest mean antibiotic, metal and biocide concentrations were observed for sulfamethoxazole (286.180 µg/L), neodymium (Nd; 27.734 mg/L), and benzalkonium chloride (BAC 12) (7.805 µg/L), respectively. In decreasing order per sampling site, the pollutant concentrations were effluent > downstream > upstream. This implies that the WWTP significantly contributed to the observed pollution in the receiving water. Furthermore, most of the pollutants measured recorded values exceeding the recommended predicted no-effect concentration (PNEC) values, suggesting that the microbes in such water environments were at risk of developing resistance due to the selection pressure exerted by these antimicrobials. Further studies are required to establish such a relationship. [ABSTRACT FROM AUTHOR]

Published
2023
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26. The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

Author

Tegally, Houriiyah, primary, San, James E., additional, Cotten, Matthew, additional, Tegomoh, Bryan, additional, Mboowa, Gerald, additional, Martin, Darren P., additional, Baxter, Cheryl, additional, Moir, Monika, additional, Lambisia, Arnold, additional, Diallo, Amadou, additional, Amoako, Daniel G., additional, Diagne, Moussa M., additional, Sisay, Abay, additional, Zekri, Abdel-Rahman N., additional, Barakat, Abdelhamid, additional, Gueye, Abdou Salam, additional, Sangare, Abdoul K., additional, Ouedraogo, Abdoul-Salam, additional, Sow, Abdourahmane, additional, Musa, Abdualmoniem O., additional, Sesay, Abdul K., additional, Lagare, Adamou, additional, Kemi, Adedotun-Sulaiman, additional, Abar, Aden Elmi, additional, Johnson, Adeniji A., additional, Fowotade, Adeola, additional, Olubusuyi, Adewumi M., additional, Oluwapelumi, Adeyemi O., additional, Amuri, Adrienne A., additional, Juru, Agnes, additional, Ramadan, Ahmad Mabrouk, additional, Kandeil, Ahmed, additional, Mostafa, Ahmed, additional, Rebai, Ahmed, additional, Sayed, Ahmed, additional, Kazeem, Akano, additional, Balde, Aladje, additional, Christoffels, Alan, additional, Trotter, Alexander J., additional, Campbell, Allan, additional, Keita, Alpha Kabinet, additional, Kone, Amadou, additional, Bouzid, Amal, additional, Souissi, Amal, additional, Agweyu, Ambrose, additional, Gutierrez, Ana V., additional, Page, Andrew J., additional, Yadouleton, Anges, additional, Vinze, Anika, additional, Happi, Anise N., additional, Chouikha, Anissa, additional, Iranzadeh, Arash, additional, Maharaj, Arisha, additional, Batchi-Bouyou, Armel Landry, additional, Ismail, Arshad, additional, Sylverken, Augustina, additional, Goba, Augustine, additional, Femi, Ayoade, additional, Sijuwola, Ayotunde Elijah, additional, Ibrahimi, Azeddine, additional, Marycelin, Baba, additional, Salako, Babatunde Lawal, additional, Oderinde, Bamidele S., additional, Bolajoko, Bankole, additional, Dhaala, Beatrice, additional, Herring, Belinda L., additional, Tsofa, Benjamin, additional, Mvula, Bernard, additional, Njanpop-Lafourcade, Berthe-Marie, additional, Marondera, Blessing T., additional, Khaireh, Bouh Abdi, additional, Kouriba, Bourema, additional, Adu, Bright, additional, Pool, Brigitte, additional, McInnis, Bronwyn, additional, Brook, Cara, additional, Williamson, Carolyn, additional, Anscombe, Catherine, additional, Pratt, Catherine B., additional, Scheepers, Cathrine, additional, Akoua-Koffi, Chantal G., additional, Agoti, Charles N., additional, Loucoubar, Cheikh, additional, Onwuamah, Chika Kingsley, additional, Ihekweazu, Chikwe, additional, Malaka, Christian Noël, additional, Peyrefitte, Christophe, additional, Omoruyi, Chukwuma Ewean, additional, Rafaï, Clotaire Donatien, additional, Morang’a, Collins M., additional, Nokes, D. James, additional, Lule, Daniel Bugembe, additional, Bridges, Daniel J., additional, Mukadi-Bamuleka, Daniel, additional, Park, Danny, additional, Baker, David, additional, Doolabh, Deelan, additional, Ssemwanga, Deogratius, additional, Tshiabuila, Derek, additional, Bassirou, Diarra, additional, Amuzu, Dominic S.Y., additional, Goedhals, Dominique, additional, Grant, Donald S., additional, Omuoyo, Donwilliams O., additional, Maruapula, Dorcas, additional, Wanjohi, Dorcas Waruguru, additional, Foster-Nyarko, Ebenezer, additional, Lusamaki, Eddy K., additional, Simulundu, Edgar, additional, Ong’era, Edidah M., additional, Ngabana, Edith N., additional, Abworo, Edward O., additional, Otieno, Edward, additional, Shumba, Edwin, additional, Barasa, Edwine, additional, Ahmed, El Bara, additional, Kampira, Elizabeth, additional, Fahime, Elmostafa El, additional, Lokilo, Emmanuel, additional, Mukantwari, Enatha, additional, Cyril, Erameh, additional, Philomena, Eromon, additional, Belarbi, Essia, additional, Simon-Loriere, Etienne, additional, Anoh, Etilé A., additional, Leendertz, Fabian, additional, Taweh, Fahn M., additional, Wasfi, Fares, additional, Abdelmoula, Fatma, additional, Takawira, Faustinos T., additional, Derrar, Fawzi, additional, Ajogbasile, Fehintola V, additional, Treurnicht, Florette, additional, Onikepe, Folarin, additional, Ntoumi, Francine, additional, Muyembe, Francisca M., additional, Ngiambudulu, Francisco, additional, Zongo Ragomzingba, Frank Edgard, additional, Dratibi, Fred Athanasius, additional, Iyanu, Fred-Akintunwa, additional, Mbunsu, Gabriel K., additional, Thilliez, Gaetan, additional, Kay, Gemma L., additional, Akpede, George O., additional, George, Uwem E., additional, van Zyl, Gert, additional, Awandare, Gordon A., additional, Schubert, Grit, additional, Maphalala, Gugu P., additional, Ranaivoson, Hafaliana C., additional, Lemriss, Hajar, additional, Omunakwe, Hannah E, additional, Onywera, Harris, additional, Abe, Haruka, additional, Karray, Hela, additional, Nansumba, Hellen, additional, Triki, Henda, additional, Adje Kadjo, Herve Albéric, additional, Elgahzaly, Hesham, additional, Gumbo, Hlanai, additional, mathieu, Hota, additional, Kavunga-Membo, Hugo, additional, Smeti, Ibtihel, additional, Olawoye, Idowu B., additional, Adetifa, Ifedayo, additional, Odia, Ikponmwosa, additional, Boubaker, Ilhem Boutiba-Ben, additional, Ssewanyana, Isaac, additional, Wurie, Isatta, additional, Konstantinus, Iyaloo S, additional, Afiwa Halatoko, Jacqueline Wemboo, additional, Ayei, James, additional, Sonoo, Janaki, additional, Lekana-Douki, Jean Bernard, additional, Makangara, Jean-Claude C., additional, Tamfum, Jean-Jacques M., additional, Heraud, Jean-Michel, additional, Shaffer, Jeffrey G., additional, Giandhari, Jennifer, additional, Musyoki, Jennifer, additional, Uwanibe, Jessica N., additional, Bhiman, Jinal N., additional, Yasuda, Jiro, additional, Morais, Joana, additional, Mends, Joana Q., additional, Kiconco, Jocelyn, additional, Sandi, John Demby, additional, Huddleston, John, additional, Odoom, John Kofi, additional, Morobe, John M., additional, Gyapong, John O., additional, Kayiwa, John T., additional, Okolie, Johnson C., additional, Xavier, Joicymara Santos, additional, Gyamfi, Jones, additional, Kofi Bonney, Joseph Humphrey, additional, Nyandwi, Joseph, additional, Everatt, Josie, additional, Farah, Jouali, additional, Nakaseegu, Joweria, additional, Ngoi, Joyce M., additional, Namulondo, Joyce, additional, Oguzie, Judith U., additional, Andeko, Julia C., additional, Lutwama, Julius J., additional, O’Grady, Justin, additional, Siddle, Katherine J, additional, Victoir, Kathleen, additional, Adeyemi, Kayode T., additional, Tumedi, Kefentse A., additional, Carvalho, Kevin Sanders, additional, Mohammed, Khadija Said, additional, Musonda, Kunda G., additional, Duedu, Kwabena O., additional, Belyamani, Lahcen, additional, Fki-Berrajah, Lamia, additional, Singh, Lavanya, additional, Biscornet, Leon, additional, de Oliveira Martins, Leonardo, additional, Chabuka, Lucious, additional, Olubayo, Luicer, additional, Deng, Lul Lojok, additional, Ochola-Oyier, Lynette Isabella, additional, Mine, Madisa, additional, Ramuth, Magalutcheemee, additional, Mastouri, Maha, additional, ElHefnawi, Mahmoud, additional, Mbanne, Maimouna, additional, Matsheka, Maitshwarelo I., additional, Kebabonye, Malebogo, additional, Diop, Mamadou, additional, Momoh, Mambu, additional, Lima Mendonça, Maria da Luz, additional, Venter, Marietjie, additional, Paye, Marietou F, additional, Faye, Martin, additional, Nyaga, Martin M., additional, Mareka, Mathabo, additional, Damaris, Matoke-Muhia, additional, Mburu, Maureen W., additional, Mpina, Maximillian, additional, Claujens Chastel, Mfoutou Mapanguy, additional, Owusu, Michael, additional, Wiley, Michael R., additional, Tatfeng, Mirabeau Youtchou, additional, Ayekaba, Mitoha Ondo’o, additional, Abouelhoda, Mohamed, additional, Beloufa, Mohamed Amine, additional, Seadawy, Mohamed G, additional, Khalifa, Mohamed K., additional, Dellagi, Mohammed Koussai, additional, Matobo, Mooko Marethabile, additional, Kane, Mouhamed, additional, Ouadghiri, Mouna, additional, Salou, Mounerou, additional, Mbulawa, Mphaphi B., additional, Saibu, Mudashiru Femi, additional, Mwenda, Mulenga, additional, Kaba, Muluken, additional, Phan, My V.T., additional, Abid, Nabil, additional, Touil, Nadia, additional, Rujeni, Nadine, additional, Ismael, Nalia, additional, Top, Ndeye Marieme, additional, Dia, Ndongo, additional, Mabunda, Nédio, additional, Hsiao, Nei-yuan, additional, Silochi, Nelson Boricó, additional, Saasa, Ngonda, additional, Bbosa, Nicholas, additional, Murunga, Nickson, additional, Gumede, Nicksy, additional, Wolter, Nicole, additional, Sitharam, Nikita, additional, Ndodo, Nnaemeka, additional, Ajayi, Nnennaya A., additional, Tordo, Noël, additional, Mbhele, Nokuzola, additional, Razanajatovo, Norosoa H, additional, Iguosadolo, Nosamiefan, additional, Mba, Nwando, additional, Kingsley, Ojide C., additional, Sylvanus, Okogbenin, additional, Peter, Okokhere, additional, Femi, Oladiji, additional, Testimony, Olumade, additional, Ogunsanya, Olusola Akinola, additional, Fakayode, Oluwatosin, additional, Ogah, Onwe E., additional, Faye, Ousmane, additional, Smith-Lawrence, Pamela, additional, Ondoa, Pascale, additional, Combe, Patrice, additional, Nabisubi, Patricia, additional, Semanda, Patrick, additional, Oluniyi, Paul E., additional, Arnaldo, Paulo, additional, Quashie, Peter Kojo, additional, Bejon, Philip, additional, Dussart, Philippe, additional, Bester, Phillip A., additional, Mbala, Placide K., additional, Kaleebu, Pontiano, additional, Abechi, Priscilla, additional, El-Shesheny, Rabeh, additional, Joseph, Rageema, additional, Aziz, Ramy Karam, additional, Essomba, René Ghislain, additional, Ayivor-Djanie, Reuben, additional, Njouom, Richard, additional, Phillips, Richard O., additional, Gorman, Richmond, additional, Kingsley, Robert A., additional, Audu, Rosemary, additional, Carr, Rosina A.A., additional, Kabbaj, Saâd El, additional, Gargouri, Saba, additional, Masmoudi, Saber, additional, Sankhe, Safietou, additional, Mohamed, Sahra Isse, additional, Mhalla, Salma, additional, Hosch, Salome, additional, Kassim, Samar Kamal, additional, Metha, Samar, additional, Trabelsi, Sameh, additional, Lemriss, Sanaâ, additional, Agwa, Sara Hassan, additional, Mwangi, Sarah Wambui, additional, Doumbia, Seydou, additional, Makiala-Mandanda, Sheila, additional, Aryeetey, Sherihane, additional, Ahmed, Shymaa S., additional, Ahmed, Sidi Mohamed, additional, Elhamoumi, Siham, additional, Moyo, Sikhulile, additional, Lutucuta, Silvia, additional, Gaseitsiwe, Simani, additional, Jalloh, Simbirie, additional, Andriamandimby, Soafy, additional, Oguntope, Sobajo, additional, Grayo, Solène, additional, Lekana-Douki, Sonia, additional, Prosolek, Sophie, additional, Ouangraoua, Soumeya, additional, van Wyk, Stephanie, additional, Schaffner, Stephen F., additional, Kanyerezi, Stephen, additional, Ahuka-Mundeke, Steve, additional, Rudder, Steven, additional, Pillay, Sureshnee, additional, Nabadda, Susan, additional, Behillil, Sylvie, additional, Budiaki, Sylvie L., additional, van der Werf, Sylvie, additional, Mashe, Tapfumanei, additional, Aanniz, Tarik, additional, Mohale, Thabo, additional, Le-Viet, Thanh, additional, Velavan, Thirumalaisamy P., additional, Schindler, Tobias, additional, Maponga, Tongai, additional, Bedford, Trevor, additional, Anyaneji, Ugochukwu J., additional, Chinedu, Ugwu, additional, Ramphal, Upasana, additional, Enouf, Vincent, additional, Nene, Vishvanath, additional, Gorova, Vivianne, additional, Roshdy, Wael H., additional, Karim, Wasim Abdul, additional, Ampofo, William K., additional, Preiser, Wolfgang, additional, Choga, Wonderful T., additional, Ahmed, Yahaya Ali, additional, Ramphal, Yajna, additional, Bediako, Yaw, additional, Naidoo, Yeshnee, additional, Butera, Yvan, additional, de Laurent, Zaydah R., additional, Ouma, Ahmed E.O., additional, von Gottberg, Anne, additional, Githinji, George, additional, Moeti, Matshidiso, additional, Tomori, Oyewale, additional, Sabeti, Pardis C., additional, Sall, Amadou A., additional, Oyola, Samuel O., additional, Tebeje, Yenew K., additional, Tessema, Sofonias K., additional, de Oliveira, Tulio, additional, Happi, Christian, additional, Lessells, Richard, additional, Nkengasong, John, additional, and Wilkinson, Eduan, additional

Published
2022
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27. Household transmission of SARS-CoV-2 from adult index cases living with and without HIV in South Africa, 2020-2021: a case-ascertained, prospective observational household transmission study

Author

Kleynhans, Jackie, primary, Walaza, Sibongile, additional, Martinson, Neil A., additional, Neti, Mzimasi, additional, Gottberg, Anne von, additional, Bhiman, Jinal N., additional, Toi, Dylan, additional, Amoako, Daniel G., additional, Buys, Amelia, additional, Ndlangisa, Kedibone, additional, Wolter, Nicole, additional, Genade, Leisha, additional, Maloma, Lucia, additional, Chewparsad, Juanita, additional, Lebina, Limakatso, additional, de Gouveia, Linda, additional, Kotane, Retshidisitswe, additional, Tempia, Stefano, additional, and Cohen, Cheryl, additional

Published
2022
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28. Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function

Author

Martin, Darren P., primary, Lytras, Spyros, additional, Lucaci, Alexander G., additional, Maier, Wolfgang, additional, Grüning, Björn, additional, Shank, Stephen D., additional, Weaver, Steven, additional, MacLean, Oscar A., additional, Orton, Richard J., additional, Lemey, Philippe, additional, Boni, Maciej F., additional, Tegally, Houriiyah, additional, Harkins, Gordon W., additional, Scheepers, Cathrine, additional, Bhiman, Jinal N., additional, Everatt, Josie, additional, Amoako, Daniel G., additional, San, James Emmanuel, additional, Giandhari, Jennifer, additional, Sigal, Alex, additional, Williamson, Carolyn, additional, Hsiao, Nei-yuan, additional, von Gottberg, Anne, additional, De Klerk, Arne, additional, Shafer, Robert W., additional, Robertson, David L., additional, Wilkinson, Robert J., additional, Sewell, B. Trevor, additional, Lessells, Richard, additional, Nekrutenko, Anton, additional, Greaney, Allison J., additional, Starr, Tyler N., additional, Bloom, Jesse D., additional, Murrell, Ben, additional, Wilkinson, Eduan, additional, Gupta, Ravindra K., additional, de Oliveira, Tulio, additional, and Kosakovsky Pond, Sergei L., additional

Published
2022
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31. Selection analysis identifies clusters of unusual mutational changes in Omicron lineage BA.1 that likely impact Spike function

Author

Martin, Darren P, Lytras, Spyros, Lucaci, Alexander G, Maier, Wolfgang, Grüning, Björn, Shank, Stephen D, Weaver, Steven, MacLean, Oscar A, Orton, Richard J, Lemey, Philippe, Boni, Maciej F, Tegally, Houriiyah, Harkins, Gordon W, Scheepers, Cathrine, Bhiman, Jinal N, Everatt, Josie, Amoako, Daniel G, San, James Emmanuel, Giandhari, Jennifer, Sigal, Alex, NGS-SA, Williamson, Carolyn, Hsiao, Nei-Yuan, von Gottberg, Anne, De Klerk, Arne, Shafer, Robert W, Robertson, David L, Wilkinson, Robert J, Sewell, B Trevor, Lessells, Richard, Nekrutenko, Anton, Greaney, Allison J, Starr, Tyler N, Bloom, Jesse D, Murrell, Ben, Wilkinson, Eduan, Gupta, Ravindra K, de Oliveira, Tulio, and Pond, Sergei L Kosakovsky

Subjects
Model organisms, Human Biology & Physiology, FOS: Clinical medicine, Immunology, Infectious Disease
Abstract

Among the 30 non-synonymous nucleotide substitutions in the Omicron S-gene are 13 that have only rarely been seen in other SARS-CoV-2 sequences. These mutations cluster within three functionally important regions of the S-gene at sites that will likely impact (i) interactions between subunits of the Spike trimer and the predisposition of subunits to shift from down to up configurations, (ii) interactions of Spike with ACE2 receptors, and (iii) the priming of Spike for membrane fusion. We show here that, based on both the rarity of these 13 mutations in intrapatient sequencing reads and patterns of selection at the codon sites where the mutations occur in SARS-CoV-2 and related sarbecoviruses, prior to the emergence of Omicron the mutations would have been predicted to decrease the fitness of any virus within which they occurred. We further propose that the mutations in each of the three clusters therefore cooperatively interact to both mitigate their individual fitness costs, and, in combination with other mutations, adaptively alter the function of Spike. Given the evident epidemic growth advantages of Omicron over all previously known SARS-CoV-2 lineages, it is crucial to determine both how such complex and highly adaptive mutation constellations were assembled within the Omicron S-gene, and why, despite unprecedented global genomic surveillance efforts, the early stages of this assembly process went completely undetected.

Published
2022
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32. Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function

Author

Martin, Darren P, Lytras, Spyros, Lucaci, Alexander G, Maier, Wolfgang, Grüning, Björn, Shank, Stephen D, Weaver, Steven, MacLean, Oscar A, Orton, Richard J, Lemey, Philippe, Boni, Maciej F, Tegally, Houriiyah, Harkins, Gordon, Scheepers, Cathrine, Bhiman, Jinal N, Everatt, Josie, Amoako, Daniel G, San, James Emmanuel, Giandhari, Jennifer, Sigal, Alex, Williamson, Carolyn, Hsiao, Nei-yuan, von Gottberg, Anne, De Klerk, Arne, Shafer, Robert W, Robertson, David L, Wilkinson, Robert J, Sewell, B Trevor, Lessells, Richard, Nekrutenko, Anton, Greaney, Allison J., Starr, Tyler N., Bloom, Jesse D., Murrell, Ben, Wilkinson, Eduan, Gupta, Ravindra K, de Oliveira, Tulio, and Kosakovsky Pond, Sergei L

Subjects
SARS-CoV-2, Mutation, Spike Glycoprotein, Coronavirus, COVID-19, Humans, Article
Abstract

Among the 30 non-synonymous nucleotide substitutions in the Omicron S-gene are 13 that have only rarely been seen in other SARS-CoV-2 sequences. These mutations cluster within three functionally important regions of the S-gene at sites that will likely impact (i) interactions between subunits of the Spike trimer and the predisposition of subunits to shift from down to up configurations, (ii) interactions of Spike with ACE2 receptors, and (iii) the priming of Spike for membrane fusion. We show here that, based on both the rarity of these 13 mutations in intrapatient sequencing reads and patterns of selection at the codon sites where the mutations occur in SARS-CoV-2 and related sarbecoviruses, prior to the emergence of Omicron the mutations would have been predicted to decrease the fitness of any genomes within which they occurred. We further propose that the mutations in each of the three clusters therefore cooperatively interact to both mitigate their individual fitness costs, and adaptively alter the function of Spike. Given the evident epidemic growth advantages of Omicron over all previously known SARS-CoV-2 lineages, it is crucial to determine both how such complex and highly adaptive mutation constellations were assembled within the Omicron S-gene, and why, despite unprecedented global genomic surveillance efforts, the early stages of this assembly process went completely undetected.

Published
2022

35. Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

Author

Viana, Raquel, primary, Moyo, Sikhulile, additional, Amoako, Daniel G, additional, Tegally, Houriiyah, additional, Scheepers, Cathrine, additional, Althaus, Christian L, additional, Anyaneji, Ugochukwu J, additional, Bester, Phillip A, additional, Boni, Maciej F, additional, Chand, Mohammed, additional, Choga, Wonderful T, additional, Colquhoun, Rachel, additional, Davids, Michaela, additional, Deforche, Koen, additional, Doolabh, Deelan, additional, Engelbrecht, Susan, additional, Everatt, Josie, additional, Giandhari, Jennifer, additional, Giovanetti, Marta, additional, Hardie, Diana, additional, Hill, Verity, additional, Hsiao, Nei-Yuan, additional, Iranzadeh, Arash, additional, Ismail, Arshad, additional, Joseph, Charity, additional, Joseph, Rageema, additional, Koopile, Legodile, additional, Pond, Sergei L Kosakovsky, additional, Kraemer, Moritz UG, additional, Kuate-Lere, Lesego, additional, Laguda-Akingba, Oluwakemi, additional, Lesetedi-Mafoko, Onalethatha, additional, Lessells, Richard J, additional, Lockman, Shahin, additional, Lucaci, Alexander G, additional, Maharaj, Arisha, additional, Mahlangu, Boitshoko, additional, Maponga, Tongai, additional, Mahlakwane, Kamela, additional, Makatini, Zinhle, additional, Marais, Gert, additional, Maruapula, Dorcas, additional, Masupu, Kereng, additional, Matshaba, Mogomotsi, additional, Mayaphi, Simnikiwe, additional, Mbhele, Nokuzola, additional, Mbulawa, Mpaphi B, additional, Mendes, Adriano, additional, Mlisana, Koleka, additional, Mnguni, Anele, additional, Mohale, Thabo, additional, Moir, Monika, additional, Moruisi, Kgomotso, additional, Mosepele, Mosepele, additional, Motsatsi, Gerald, additional, Motswaledi, Modisa S, additional, Mphoyakgosi, Thongbotho, additional, Msomi, Nokukhanya, additional, Mwangi, Peter N, additional, Naidoo, Yeshnee, additional, Ntuli, Noxolo, additional, Nyaga, Martin, additional, Olubayo, Lucier, additional, Pillay, Sureshnee, additional, Radibe, Botshelo, additional, Ramphal, Yajna, additional, Ramphal, Upasana, additional, San, James E, additional, Scott, Lesley, additional, Shapiro, Roger, additional, Singh, Lavanya, additional, Smith-Lawrence, Pamela, additional, Stevens, Wendy, additional, Strydom, Amy, additional, Subramoney, Kathleen, additional, Tebeila, Naume, additional, Tshiabuila, Derek, additional, Tsui, Joseph, additional, van Wyk, Stephanie, additional, Weaver, Steven, additional, Wibmer, Constantinos K, additional, Wilkinson, Eduan, additional, Wolter, Nicole, additional, Zarebski, Alexander E, additional, Zuze, Boitumelo, additional, Goedhals, Dominique, additional, Preiser, Wolfgang, additional, Treurnicht, Florette, additional, Venter, Marietje, additional, Williamson, Carolyn, additional, Pybus, Oliver G, additional, Bhiman, Jinal, additional, Glass, Allison, additional, Martin, Darren P, additional, Rambaut, Andrew, additional, Gaseitsiwe, Simani, additional, von Gottberg, Anne, additional, and de Oliveira, Tulio, additional

Published
2021
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38. Household Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 From Adult Index Cases With and Without Human Immunodeficiency Virus in South Africa, 2020–2021: A Case-Ascertained, Prospective, Observational Household Transmission Study.

Author

Kleynhans, Jackie, Walaza, Sibongile, Martinson, Neil A, Neti, Mzimasi, Gottberg, Anne von, Bhiman, Jinal N, Toi, Dylan, Amoako, Daniel G, Buys, Amelia, Ndlangisa, Kedibone, Wolter, Nicole, Genade, Leisha, Maloma, Lucia, Chewparsad, Juanita, Lebina, Limakatso, Gouveia, Linda de, Kotane, Retshidisitswe, Tempia, Stefano, and Cohen, Cheryl

Subjects
HOME environment, SARS-CoV-2, SCIENTIFIC observation, COVID-19, CONFIDENCE intervals, VIRAL load, RISK assessment, INFECTIOUS disease transmission, DESCRIPTIVE statistics, RESEARCH funding, T cells, ODDS ratio, HIV, LONGITUDINAL method
Abstract

Background In South Africa, 19% of adults are living with human immunodeficiency virus (HIV; LWH). Few data on the influence of HIV on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) household transmission are available. Methods We performed a case-ascertained, prospective household transmission study of symptomatic adult index SARS-CoV-2 cases LWH and not living with HIV (NLWH) and their contacts from October 2020 to September 2021. Households were followed up 3 times a week for 6 weeks to collect nasal swabs for SARS-CoV-2 testing. We estimated household cumulative infection risk (HCIR) and duration of SARS-CoV-2 positivity (at a cycle threshold value <30 as proxy for high viral load). Results HCIR was 59% (220 of 373), not differing by index HIV status (60% LWH vs 58% NLWH). HCIR increased with index case age (35–59 years: adjusted OR [aOR], 3.4; 95% CI, 1.5–7.8 and ≥60 years: aOR, 3.1; 95% CI, 1.0–10.1) compared with 18–34 years and with contacts' age, 13–17 years (aOR, 7.1; 95% CI, 1.5–33.9) and 18–34 years (aOR, 4.4; 95% CI, 1.0–18.4) compared with <5 years. Mean positivity was longer in cases LWH (adjusted hazard ratio, 0.4; 95% CI,.1–.9). Conclusions Index HIV status was not associated with higher HCIR, but cases LWH had longer positivity duration. Adults aged >35 years were more likely to transmit and individuals aged 13–34 to be infected SARS-CoV-2 in the household. As HIV infection may increase transmission, health services must maintain HIV testing and antiretroviral therapy initiation. [ABSTRACT FROM AUTHOR]

Published
2023
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39. Phenotypic and Genomic Insights into Biofilm Formation in Antibiotic-Resistant Clinical Coagulase-Negative Staphylococcus Species from South Africa.

Author

Asante, Jonathan, Abia, Akebe L. K., Anokwah, Daniel, Hetsa, Bakoena A., Fatoba, Dorcas O., Bester, Linda A., and Amoako, Daniel G.

Subjects
STAPHYLOCOCCUS, MICROBIAL sensitivity tests, BIOFILMS, BETA lactamases, PHENOTYPES, CONGO red (Staining dye), NUCLEOTIDE sequencing
Abstract

The work aims to investigate biofilm formation and biofilm/adhesion-encoding genes in coagulase-negative staphylococci (CoNS) species recovered from blood culture isolates. Eighty-nine clinical CoNS were confirmed using the VITEK 2 system, and antibiotic susceptibility testing of isolates was conducted using the Kirby-Bauer disk diffusion method against a panel of 20 antibiotics. Isolates were qualitatively screened using the Congo red agar medium. Quantitative assays were performed on microtiter plates, where the absorbances of the solubilised biofilms were recorded as optical densities and quantified. In all, 12.4% of the isolates were strong biofilm formers, 68.5% had moderate biofilm capacity, and 17.9% showed weak capacity. A subset of 18 isolates, mainly methicillin-resistant S. epidermidis, were investigated for adherence-related genes using whole-genome sequencing and bioinformatics analysis. The highest antibiotic resistance rates for strongly adherent isolates were observed against penicillin (100%) and cefoxitin (81.8%), but the isolates showed no resistance to linezolid (0.0%) and tigecycline (0.0%). The icaABC genes involved in biofilm formation were detected in 50% of the screened isolates. Other adherence-related genes, including autolysin gene atl (88.8%), elastin binding protein gene ebp (94.4%), cell wall-associated fibronectin-binding protein gene ebh (66.7%), clumping factor A gene clfA (5.5%), and pili gene ebpC (22.2%) were also found. The insertion sequence IS256, involved in biofilm formation, was found in 10/18 (55.5%) screened isolates. We demonstrate a high prevalence of biofilm-forming coagulase-negative staphylococci associated with various resistance phenotypes and a substantial agreement between the possession of biofilm-associated genes and the biofilm phenotype. [ABSTRACT FROM AUTHOR]

Published
2023
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41. A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa

Author

Wilkinson, Eduan, primary, Giovanetti, Marta, additional, Tegally, Houriiyah, additional, San, James E., additional, Lessells, Richard, additional, Cuadros, Diego, additional, Martin, Darren P., additional, Rasmussen, David A., additional, Zekri, Abdel-Rahman N., additional, Sangare, Abdoul K., additional, Ouedraogo, Abdoul-Salam, additional, Sesay, Abdul K., additional, Priscilla, Abechi, additional, Kemi, Adedotun-Sulaiman, additional, Olubusuyi, Adewunmi M., additional, Oluwapelumi, Adeyemi O. O., additional, Hammami, Adnène, additional, Amuri, Adrienne A., additional, Sayed, Ahmad, additional, Ouma, Ahmed E. O., additional, Elargoubi, Aida, additional, Ajayi, Nnennaya A., additional, Victoria, Ajogbasile F., additional, Kazeem, Akano, additional, George, Akpede, additional, Trotter, Alexander J., additional, Yahaya, Ali A., additional, Keita, Alpha K., additional, Diallo, Amadou, additional, Kone, Amadou, additional, Souissi, Amal, additional, Chtourou, Amel, additional, Gutierrez, Ana V., additional, Page, Andrew J., additional, Vinze, Anika, additional, Iranzadeh, Arash, additional, Lambisia, Arnold, additional, Ismail, Arshad, additional, Rosemary, Audu, additional, Sylverken, Augustina, additional, Femi, Ayoade, additional, Ibrahimi, Azeddine, additional, Marycelin, Baba, additional, Oderinde, Bamidele S., additional, Bolajoko, Bankole, additional, Dhaala, Beatrice, additional, Herring, Belinda L., additional, Njanpop-Lafourcade, Berthe-Marie, additional, Kleinhans, Bronwyn, additional, McInnis, Bronwyn, additional, Tegomoh, Bryan, additional, Brook, Cara, additional, Pratt, Catherine B., additional, Scheepers, Cathrine, additional, Akoua-Koffi, Chantal G., additional, Agoti, Charles N., additional, Peyrefitte, Christophe, additional, Daubenberger, Claudia, additional, Morang’a, Collins M., additional, Nokes, D. James, additional, Amoako, Daniel G., additional, Bugembe, Daniel L., additional, Park, Danny, additional, Baker, David, additional, Doolabh, Deelan, additional, Ssemwanga, Deogratius, additional, Tshiabuila, Derek, additional, Bassirou, Diarra, additional, Amuzu, Dominic S. Y., additional, Goedhals, Dominique, additional, Omuoyo, Donwilliams O., additional, Maruapula, Dorcas, additional, Foster-Nyarko, Ebenezer, additional, Lusamaki, Eddy K., additional, Simulundu, Edgar, additional, Ong’era, Edidah M., additional, Ngabana, Edith N., additional, Shumba, Edwin, additional, El Fahime, Elmostafa, additional, Lokilo, Emmanuel, additional, Mukantwari, Enatha, additional, Philomena, Eromon, additional, Belarbi, Essia, additional, Simon-Loriere, Etienne, additional, Anoh, Etilé A., additional, Leendertz, Fabian, additional, Ajili, Faida, additional, Enoch, Fakayode O., additional, Wasfi, Fares, additional, Abdelmoula, Fatma, additional, Mosha, Fausta S., additional, Takawira, Faustinos T., additional, Derrar, Fawzi, additional, Bouzid, Feriel, additional, Onikepe, Folarin, additional, Adeola, Fowotade, additional, Muyembe, Francisca M., additional, Tanser, Frank, additional, Dratibi, Fred A., additional, Mbunsu, Gabriel K., additional, Thilliez, Gaetan, additional, Kay, Gemma L., additional, Githinji, George, additional, van Zyl, Gert, additional, Awandare, Gordon A., additional, Schubert, Grit, additional, Maphalala, Gugu P., additional, Ranaivoson, Hafaliana C., additional, Lemriss, Hajar, additional, Anise, Happi, additional, Abe, Haruka, additional, Karray, Hela H., additional, Nansumba, Hellen, additional, Elgahzaly, Hesham A., additional, Gumbo, Hlanai, additional, Smeti, Ibtihel, additional, Ayed, Ikhlas B., additional, Odia, Ikponmwosa, additional, Ben Boubaker, Ilhem Boutiba, additional, Gaaloul, Imed, additional, Gazy, Inbal, additional, Mudau, Innocent, additional, Ssewanyana, Isaac, additional, Konstantinus, Iyaloo, additional, Lekana-Douk, Jean B., additional, Makangara, Jean-Claude C., additional, Tamfum, Jean-Jacques M., additional, Heraud, Jean-Michel, additional, Shaffer, Jeffrey G., additional, Giandhari, Jennifer, additional, Li, Jingjing, additional, Yasuda, Jiro, additional, Mends, Joana Q., additional, Kiconco, Jocelyn, additional, Morobe, John M., additional, Gyapong, John O., additional, Okolie, Johnson C., additional, Kayiwa, John T., additional, Edwards, Johnathan A., additional, Gyamfi, Jones, additional, Farah, Jouali, additional, Nakaseegu, Joweria, additional, Ngoi, Joyce M., additional, Namulondo, Joyce, additional, Andeko, Julia C., additional, Lutwama, Julius J., additional, O’Grady, Justin, additional, Siddle, Katherine, additional, Adeyemi, Kayode T., additional, Tumedi, Kefentse A., additional, Said, Khadija M., additional, Hae-Young, Kim, additional, Duedu, Kwabena O., additional, Belyamani, Lahcen, additional, Fki-Berrajah, Lamia, additional, Singh, Lavanya, additional, Martins, Leonardo de O., additional, Tyers, Lynn, additional, Ramuth, Magalutcheemee, additional, Mastouri, Maha, additional, Aouni, Mahjoub, additional, el Hefnawi, Mahmoud, additional, Matsheka, Maitshwarelo I., additional, Kebabonye, Malebogo, additional, Diop, Mamadou, additional, Turki, Manel, additional, Paye, Marietou, additional, Nyaga, Martin M., additional, Mareka, Mathabo, additional, Damaris, Matoke-Muhia, additional, Mburu, Maureen W., additional, Mpina, Maximillian, additional, Nwando, Mba, additional, Owusu, Michael, additional, Wiley, Michael R., additional, Youtchou, Mirabeau T., additional, Ayekaba, Mitoha O., additional, Abouelhoda, Mohamed, additional, Seadawy, Mohamed G., additional, Khalifa, Mohamed K., additional, Sekhele, Mooko, additional, Ouadghiri, Mouna, additional, Diagne, Moussa M., additional, Mwenda, Mulenga, additional, Allam, Mushal, additional, Phan, My V. T., additional, Abid, Nabil, additional, Touil, Nadia, additional, Rujeni, Nadine, additional, Kharrat, Najla, additional, Ismael, Nalia, additional, Dia, Ndongo, additional, Mabunda, Nedio, additional, Hsiao, Nei-yuan, additional, Silochi, Nelson B., additional, Nsenga, Ngoy, additional, Gumede, Nicksy, additional, Mulder, Nicola, additional, Ndodo, Nnaemeka, additional, Razanajatovo, Norosoa H, additional, Iguosadolo, Nosamiefan, additional, Judith, Oguzie, additional, Kingsley, Ojide C., additional, Sylvanus, Okogbenin, additional, Peter, Okokhere, additional, Femi, Oladiji, additional, Idowu, Olawoye, additional, Testimony, Olumade, additional, Chukwuma, Omoruyi E., additional, Ogah, Onwe E., additional, Onwuamah, Chika K., additional, Cyril, Oshomah, additional, Faye, Ousmane, additional, Tomori, Oyewale, additional, Ondoa, Pascale, additional, Combe, Patrice, additional, Semanda, Patrick, additional, Oluniyi, Paul E., additional, Arnaldo, Paulo, additional, Quashie, Peter K., additional, Dussart, Philippe, additional, Bester, Phillip A., additional, Mbala, Placide K., additional, Ayivor-Djanie, Reuben, additional, Njouom, Richard, additional, Phillips, Richard O., additional, Gorman, Richmond, additional, Kingsley, Robert A., additional, Carr, Rosina A. A., additional, El Kabbaj, Saâd, additional, Gargouri, Saba, additional, Masmoudi, Saber, additional, Sankhe, Safietou, additional, Lawal, Salako B., additional, Kassim, Samar, additional, Trabelsi, Sameh, additional, Metha, Samar, additional, Kammoun, Sami, additional, Lemriss, Sanaâ, additional, Agwa, Sara H. A., additional, Calvignac-Spencer, Sébastien, additional, Schaffner, Stephen F., additional, Doumbia, Seydou, additional, Mandanda, Sheila M., additional, Aryeetey, Sherihane, additional, Ahmed, Shymaa S., additional, Elhamoumi, Siham, additional, Andriamandimby, Soafy, additional, Tope, Sobajo, additional, Lekana-Douki, Sonia, additional, Prosolek, Sophie, additional, Ouangraoua, Soumeya, additional, Mundeke, Steve A., additional, Rudder, Steven, additional, Panji, Sumir, additional, Pillay, Sureshnee, additional, Engelbrecht, Susan, additional, Nabadda, Susan, additional, Behillil, Sylvie, additional, Budiaki, Sylvie L., additional, van der Werf, Sylvie, additional, Mashe, Tapfumanei, additional, Aanniz, Tarik, additional, Mohale, Thabo, additional, Le-Viet, Thanh, additional, Schindler, Tobias, additional, Anyaneji, Ugochukwu J., additional, Chinedu, Ugwu, additional, Ramphal, Upasana, additional, Jessica, Uwanibe, additional, George, Uwem, additional, Fonseca, Vagner, additional, Enouf, Vincent, additional, Gorova, Vivianne, additional, Roshdy, Wael H., additional, Ampofo, William K., additional, Preiser, Wolfgang, additional, Choga, Wonderful T., additional, Bediako, Yaw, additional, Naidoo, Yeshnee, additional, Butera, Yvan, additional, de Laurent, Zaydah R., additional, Sall, Amadou A., additional, Rebai, Ahmed, additional, von Gottberg, Anne, additional, Kouriba, Bourema, additional, Williamson, Carolyn, additional, Bridges, Daniel J., additional, Chikwe, Ihekweazu, additional, Bhiman, Jinal N., additional, Mine, Madisa, additional, Cotten, Matthew, additional, Moyo, Sikhulile, additional, Gaseitsiwe, Simani, additional, Saasa, Ngonda, additional, Sabeti, Pardis C., additional, Kaleebu, Pontiano, additional, Tebeje, Yenew K., additional, Tessema, Sofonias K., additional, Happi, Christian, additional, Nkengasong, John, additional, and de Oliveira, Tulio, additional

Published
2021
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42. Rapid replacement of the Beta variant by the Delta variant in South Africa

Author

Tegally, Houriiyah, primary, Wilkinson, Eduan, additional, Althaus, Christian L., additional, Giovanetti, Marta, additional, San, James Emmanuel, additional, Giandhari, Jennifer, additional, Pillay, Sureshnee, additional, Naidoo, Yeshnee, additional, Ramphal, Upasana, additional, Msomi, Nokukhanya, additional, Mlisana, Koleka, additional, Amoako, Daniel G., additional, Everatt, Josie, additional, Mohale, Thabo, additional, Nguni, Anele, additional, Mahlangu, Boitshoko, additional, Ntuli, Noxolo, additional, Khumalo, Zamantungwa T., additional, Makatini, Zinhle, additional, Wolter, Nicole, additional, Scheepers, Cathrine, additional, Ismail, Arshad, additional, Doolabh, Deelan, additional, Joseph, Rageema, additional, Strydom, Amy, additional, Mendes, Adriano, additional, Davis, Michaela, additional, Mayaphi, Simnikiwe H., additional, Ramphal, Yajna, additional, Maharaj, Arisha, additional, Karim, Wasim Abdool, additional, Tshiabuila, Derek, additional, Anyaneji, Ugochukwu J., additional, Singh, Lavanya, additional, Engelbrecht, Susan, additional, Fonseca, Vagner, additional, Marais, Kruger, additional, Korsman, Stephen, additional, Hardie, Diana, additional, Hsiao, Nei-yuan, additional, Maponga, Tongai, additional, van Zyl, Gert, additional, Marais, Gert, additional, Iranzadeh, Arash, additional, Martin, Darren, additional, Alcantara, Luiz Carlos Junior, additional, Bester, Phillip Armand, additional, Nyaga, Martin M., additional, Subramoney, Kathleen, additional, Treurnicht, Florette K., additional, Venter, Marietjie, additional, Goedhals, Dominique, additional, Preiser, Wolfgang, additional, Bhiman, Jinal N., additional, Gottberg, Anne von, additional, Williamson, Carolyn, additional, Lessells, Richard J., additional, and de Oliveira, Tulio, additional

Published
2021
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