Author: "Ben Gaunt" / Database: OpenAIRE - Searchworks@Jio Institute Digital Library Search Results

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1. Healthcare worker knowledge, attitudes, and beliefs regarding tuberculosis preventive therapy in rural South Africa: A content analysis using the consolidated framework for implementation research

Author: Brittney van de Water, Michael Wilson, Karl le Roux, Ben Gaunt, Sarah Gimbel, and Norma Ware
Abstract: Background: South African national tuberculosis (TB) guidelines, in accordance with the World Health Organization, recommend conducting routine household TB contact investigation with provision of TB preventive therapy (TPT) for those who qualify. However, implementation of TPT has been suboptimal in rural South Africa. We sought to identify barriers and facilitators to TB contact investigations and TPT management in rural Eastern Cape, South Africa to inform the development of an implementation strategy to launch a comprehensive TB program. Methods: We collected qualitative data through individual semi-structured interviews with 19 healthcare workers at a district hospital and four surrounding primary-care clinics referring to the hospital. The consolidated framework for implementation research (CFIR) was used to develop interview questions as well as guide deductive content analysis to determine potential drivers of implementation success or failure. Results: A total of 19 healthcare workers were interviewed. Identified common barriers included lack of provider knowledge regarding efficacy of TPT, lack of TPT documentation workflows for clinicians, and widespread community resource constraints. Facilitators identified included healthcare workers high interest to learn more about the effectiveness of TPT, interest in problem-solving logistical barriers in provision of comprehensive TB care (including TPT), and desire for clinic and nurse-led TB prevention efforts. Conclusion: The use of the CFIR, a validated implementation determinants framework, provided a systematic approach to identify barriers and facilitators to TB household contact investigation, specifically the provision and management of TPT in this rural, high TB burden setting. Specific resources – time, trainings, and evidence – are necessary to ensure healthcare providers feel knowledgeable and competent about TPT prior to prescribing it more broadly. Tangible resources such as improved data systems coupled with political coordination and funding for TPT programming are essential for sustainability.
Published: 2023
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2. Difference in mortality among individuals admitted to hospital with COVID-19 during the first and second waves in South Africa: a cohort study

Author: Waasila Jassat, Caroline Mudara, Lovelyn Ozougwu, Stefano Tempia, Lucille Blumberg, Mary-Ann Davies, Yogan Pillay, Terence Carter, Ramphelane Morewane, Milani Wolmarans, Anne von Gottberg, Jinal N Bhiman, Sibongile Walaza, Cheryl Cohen, Shaina Abdullah, Fiona Abrahams, Vincentius Adams, FHIMA ADNANE, Sonia Adoni, Dieketso Melitta Adoons, Veronique Africa, Dr Aguinaga, Susan Akach, Prisha Alakram Khelawon, George Aldrich, Olatunde Alesinloye, Mathale Biniki Aletta, Mametja Alice, Tebogo Aphane, Moherndran Archary, Felicity Arends, Shireen Arends, Munonde Aser, T Asmal, Mohammed Asvat, Theunis Avenant, Muvhali Avhazwivhoni, Magnolia Azuike, Johanna Baartman, Dlava Babalwa, Johan Badenhorst, Miranda Badenhorst, Badenhorst, Bianca Badripersad (CEO), Lalihla Badul, M Bagananeng, Mncedisi Bahle, Liezl Balfour, TC Baloyi, S Baloyi, Tinyiko Baloyi, Tshepo Mpho Baloyi, Thokozani Banda, Shimon Barit, Nicole Bartsch, Junaid Bayat, Siyabulela Bazana, Marlene Beetge, Nosindiso Bekapezulu, Rammala Belebele, Phala Bella, Zanenkululeko Belot, Lindi Gladys Bembe, Sonja Bensch, Gishma Beukes, Karla Bezuidenhout, Themba Bhembe, N.A BIKISHA, Ben Bilenge, Leesa Bishop, Baphamandla Biyela, Cyntheola Blaauw, Mark Blaylock, Nicola Bodley, Power Bogale, Sibongile Bokolo, Stefan Bolon, Mary Booysen, Eldereze Booysen, Lia Boretti, Paula Borges, Millicent Boshoga, Natasha Bosman, Lucinda Bosvark, Nicky Botes, Adele Botha, CHANTALL BOTHA, Jana Botha, MANDLAKAYISE IRVIN BOTHA, Alet Botha, Janet Bradbury, Zandisile Breakfast, Maria Breed, Molele Brenda, Moshito Brice, Jolene Britz, Amanda brown, Ms T Buchanan, Thozama Bucwa, Crystelle Burger, Ziyanda Busakwe, Nosiviwe Bushula, Zinhle Buthelezi, Dumsile Buthelezi, Thubelihle Buthelezi, Mpumelelo Basil Buthelezi, Fundiswa Lidwina Buthelezi, Nadia Bux, Christoff Buys, Anneline Buys, Ernestina Caka, Armando Sanchez Canal, Sithole Caroline, Monrick Casper, Shannon Cawood, Oratile Cebisa, Nothando Cele, Sboniso Cele, Sthembile Goodness Cele, Mkhacani Chauke, Pinkie Chauke, Nevil Chelin, Xiaohui Chen, Venmalla Chetty, Kerisse Chetty, Christinah Cheu, Vindana Chibabhai, Takudzwa Chirima, Mantwa ChisaleMabotja, CHARITY CHIVENGE, Ngoasheng Choene, Mbali Nosisa Choko, Martin Choshi, Sabbir Chowdhury, Anastacia Christoforou, S.L.S Chuene, T.S Chueu, Dale Cilliers, Vanessa Cilliers, Marcel Claassen, Jeané Cloete, Chantelle Coelho, Carol Coetzee, Hans Jurgens Coetzee, Christine Coetzee, Marelize Coetzee, Dane Coetzer, Sizwe Coka, Mr M Colane, Herkulaas Combrink, Songezo Conjwa, Colleen Contrad, Faith Cornelissen, Leezelle Cronje, Christine Crouse, Moshai D.A, Ms Mahabane D.I, Tshidi Dabi, Ziyanda Dandala, Ziyaad Dangor, Gildenhuys Daniel, Ngwana Daniel, Alfred Daumas, Madelein Dauth, Mongalo David, Wayne Davids, Nozuko Daweti, Halima Dawood, Wandisa Dayile, B DE BRUIN, Karin De Klerk, Tanya De la Rosa, Marice de Nysschen, Marie De vos, Darien De Wet, Mohith Debising, Darshan Deenadayalu, Babalwa Dekeda, Mofokeng Desiree, Annelise Deysel, Abram Dhlamini, Makgethwa Dhlala Diala, Mathapelo Diale, Bella Diketane, Nosisa Dingani, Siyabonga Diniso, Lesego Diphatse, Anele Diya, Zihloniphile Dladla, Nompumelelo Dladla, Mlungisi Dladla, Patience Dladla, Baphilie Dlamini, NONHLANHLA DLAMINI, Linda Dlamini, Nonzwakazi Dlamini, Wendy Dlamini, Ncomeka Dlamini, Siyabonga Dlamini, Nicodemus Dlamini, Lebohang Dlamini, Motshedise Dlamini, Babalwa Christine Dlava, Phikiwe Dlova, Lindiwe Dlozi, Maenetja Doreen, Vumile Doyi, Athini Doyi, Belinda Du Plessis, Johanna Aletta du Plessis, Mr. Eddie du Plessis, Nicolette du Plessis, Karin du Plessis, Briette du Toit, Narissa du Toit, Jabulile Dube, Athayanda Dubula, Msomi Duduzile, Sechaba Duiker, Unati Bongile Duma, Kholiwe Duma, Kella Dunne, Kholeka Dyantyi, Avile Dyantyi, Simphiwe Dyasi, CHAUKE DYONDZO, Phelisa Dyubhele, B.J Dywili, Letitia Edwards Edwards, Madie Eksteen, Tersia Ellis, Tia Ellis, Glenda Emmerson, Theusia Enslin, ODIMULA EPULE, Lana Erasmus, Mathonsi Erick, Lerato Etsane, Shimange Eunice, Zanele Fani, Mariette Ferreira, K.L Finger-Motsepe, Fabion Floris, Tseko Fobo, Keresemetse Fokotsane, Duduzile Emmelda Fokwana, Genevieve Marion Fords, Juanita Fortein, Christine Fouche, Rulandi Fourie, Andrew Frean, Ludwig Fredericks, Wandile Funda, Kabelo Funjwa, Martha Futhane, Amanda Futuse, Dora Gabaediwe, Nonhlanhla Gabuza, Janycke Galant, Zanele Gama, Thobile Gano, Emma Cora Gardiner, Henri Gastrow, Kelly Gate, Ben Gaunt, Rikhotso Gavaza, Thapelo Gayi, Nkosinathi Gcakasi, Nomusa Gcobo, Leon Geffen, S Geldenhuys, Jenny George, Martha Gerber, Zolisa Getyengana, Nkululo Gigi, Radha Gihwala, Mitchell Gilliland, Zandile Gloria, Elitia Glover, Ellen Gokailemang, Suseth Goosen, Maria Gopane, Thandazile Gosa - Lufuta, Bernadett Gosnell, Sharleen Gouws, Christina Govender, Raksha Govender, Pearl Govender, Sally Govender, Roxanne Govender, K Govender, Mrs Savie Govender, Rashika Govinden, Luphumlo Gqabuza, Nomthandazo Gqaji, Maneo Gqetywa, Caroline Green, Nathan Green, Neera Green, Hendrik Grobler, Pamela Groenwald, Daniel Grootboom, Beatrice Gumede, Nomonde Gumede, Simphiwe Gumede, Slindile Gumede, Ntombikayise Gumede, Zenande Gumede, Thandiswa Gxotiwe, Makhubela H.L, Nonhlanhla Hadebe, Skhumbuzo Hadebe, Christos Halkas, Ansie Hamer, Ebrahim Hamida, Juan Hammond, Sumayia Haniff, Annelise Hare, lorinda Hattingh, Thenjiwe Hendricks, Philip-George Henecke, Brends Henly-Smith, Glynis Herselman, Ansie Heymans, Chantel Heyns, Golekane Hlabahlaba, Lucky Hlabangwane, Simango Hlamarisa, Ntokozo Hlanzi, Hlengiwe Hlela, Katlego Hlokwe, Thembinkosi hlongwa, Anele Hlongwana, Themba Hlubi, Tozama Hobo, Nare Nathaniel Hopane, Mariska House, Catharina Hudson, Marinda Huysamen, Jezreen Indheren, Samantha Ingle, Gavin Isaacs, TS Thekiso Isaacs, Maringa Itumeleng, Karien J van Rensburg, Saloshni Jackson, Neziswa Jacob, Burton Jacobs, Tshireletso Jacobs, Gugulethu Jacobs, Mesadi Jaftha, Zimkhitha Jaji, Sibusiso Jali, Gcobisa James, Gillian January, Andiswa Jeke, Laurent Jeremiah, LS Jeremiah, Mubeen Jhetam, Maureen John, Chuene John, Thandiwe Jola, Yolande Jonas, Anovick Jonas, Amilcar Juggernath, eileen kaba, Venetia Kabo, Disebo Kadi, Karabo Kaizer, Moshaya Peter Kambule, Lorraine Kapp, Tshepo Kau, Nchabeleng Keneth, O Kgabi, Tebogo Audrey Kgafela, Vincent Kgakgadi, Isabella Kgaswe, Tsholofelo Kgathlane, Vuyelwa Julia Kgetha, Mmaselloane Kgomojoo, MR B Kgoro, Christinah Kgosiemang, Gloria Kgosiencho, Stephen Khambula, Ariffa Khan, Refemetswe Khanare, Ncamsile Khanyase, Nokwethemba Khanyile(Data Capturer), Fillip Kharatsi, Simangele Khawula, Themba Khohlakala, Letitia Khomo, Isabel khoza, Sinethemba Khoza, Nombulelo Khukule, Busisiwe Khumalo, Tracy Khumalo, Zinhle khumalo, Vuyelwa Khumalo, Delisile Khumalo, Lebohang Khumalo, Boitumelo Khumalo, Thuli Khumalo, Gugu Khumalo, Bongiwe Khuzwayo, Thembhelihle Khuzwayo, Hennie Kidson, Jesne Kistan, Gugu Klaas, Marilyn Klassen, Josehine Koeberg, Marizel Koen, Simphiwe Koena, Ina Kok, Imraan Kola, Karabo Kolokoto, Ramachandra Konar, Dr Kotsedi, Jaline Kotze, MARTINS KOUPIS CDS, Sr Helen Kritzinger, Marlize Kruger, Henk Kruger, Tlangelani Kubayi, Thabisile Kubeka, Nonjabulo Kubheka, Melusi Kubheka, Sibusiso Clifford Kubheka, Erol Kubheka, Monica Kumalo, Thulani Kunene, Siphilile Candy Kunene, Yvette Kunneke, R.P KUPA, Rachel Kutama, Nompumelelo Kwakwazi, Lwanele Kweyama, Maureen Labuschagne, Marina Labuschagne, Prabha Lakshman, Lungelo Lamani, Thembela Lamani, Naomi Langa, Khangelani Langeni, Aphelele Langeni, Nwabisa Hazel Langeni, Gena Langeveldt, Anchen Laubscher, Laetitia Le Roux, Magagane Leah, Collen Lebea, Sello Lebea, Viyella Phumla Cynthia Lebenya, Lorraine lebogang, PK LEBOHO, Chantel Lee, Kelebogile Rejoice Lefakane, Zandile Legoabe, Patrick Lekala, Motsitsi Lekhoaba, Tanki Shadrack Lekunutu, Galaletsang Lerefolo, Mrs N Letebele, Tsepo Patric Lethoba, Emission Letlalo, Ofentse Letlhage, D.S.V Letshufi, Dineo Fiona Letsoalo, Seleka Jones Letsoalo, Pennelope Letsoalo, Getrude Letwaba, Sobekwa Linda, Katleho Lipholo, Sabata Litabe, Harsha Lochan, Linda Lomax, Francina Lombaard, Elmarie Loots, Ariana Lourens, Celeste Louw, Rianna Louw, Zikhona Lubambo, Msebenzi Moises Lubambo, Gregory Ludada, Michael Lukas, Thembela Lungu, Nomvume Lupindo, Emmah Lusenga, Happiness Luthuli, Zoleka Sylvia Luvuno, Sr Gwangwa M.H, Mustafa Maarman, Buyisiwe Mabaso, Cynthia Mabaso, Morena Mabitle, Grace Mabogoane, Kgakgamatso Mabone, Rueben Mabuza, Velaphi Mabuza, Mogantla Madiseng, Thobile Madlala, Mashooase Madolo, Thabiso Madonsela, Lesetsa Madubanya, Amukelani Maepa, Namhla Mafumana, Caroline Mafumo, Pumeza Magadla, Viscah Magale, Nompumelelo Magaqa, Oberholzer Magda, Rakgoale Magdeline, Tswai Maggie, Bongeka Maginxa, Cathrine Maite Magoba, Caroline Magongwa, AGRETIA MAGUBANE, Agretia Ntombizodwa Magubane, R Magwai, Padmini Mahabeer, Elsie Mahadulula, Lungiswa Mahanjana, Amy Maharaj, Qedusiza Mahlambi, Yvonne Mahlangu, Lerato Mahlangu, Ntombifikile Mahlangu, Makhosazana Mahlangu, Mahlatsi Mahlangu, Penelope Mahlasela, Thosago Mahlatse, Regina Mahlobo, Dikhing Mahole, Adam Mahomed, Mapeu Debora Mahubane, Peter Mahume, Lehlogonolo Maifo, Vincent Maimane, Petunia Maimele, Phakoe Maine, Patricia Senyanyathi Mainongwane, Nomalungisa Majamani, Amahle Majozini, Noluthando Makalima, Nomfundo Makam, Khanyisa Makamba, R Makan, Mashiane Makarapa, Malesela Makgahlela, Mogoiwa David Makgisa, Makgoba Makgomo, MA Makgopa, Mabone Makhalema, Lindokuhle Lizo Makhanya, Philile Valentia Makhanya, Tolerance Makharaedzha, Nathi Makhathini, Elizabeth Makhesi, Cinile Makhubela, Nkululeko Freedom Makhunga, Nomalinge Makhupula, RR Makhura, Rangwato Makola, Zingisa Makuba, Asanda Makubalo, Lonwabo Makumsha, George Makuya, Levy Mmachuene Malaka, Themba Malangeni, ML MALATJI, Pelonomi Malebana-Metsing, Malek Malek, Luthando Malevu, Juanita Malgas, Dimakatso Malgas, Paul Makgasane Malope, Monyeki Malose, Katekani Maluleke, Kato Mambane, Nthabiseng Mamorobela, Kukami Manamela, Tshepo Manana, Sathiel Maneto, Aron Kabelo Manganye, Pheto Mangena, Anna Mangoale, TINOTENDA FLORENCE MANGOZHO, Pariva Manickchund, Zandisile Mankayi, Arthur Manning, Kelebogile Manyaapelo Manyaapelo, Tabea Manyane, Zoliswa Manzana, Milton Manzini, Busisiwe Mapasa-Dube, Siboniso Maphumulo, Ntombifuthi Maphumulo, Sindy Maponya, Khomotso Mumsy Maponya, Napjadi Maponya, Lami Maqubela, Lizeka Maqubela, Vuyo Maqungo, Marisa Marais, Chantal Marais, Nondumiso Maramba, Annelize Mare, Madumetsa Maredi, Afikile Martins, Johanna Marule, Refilwe Marumo, NN Masakona, KEDIBONE VINCENTIA MASEHLA, Eric Maseko, Tshilidzi Maselesele, Mojalefa Maselo, M Maseloa, M.E Masemola, Thembi Masemola, Bella Mashaba, James Mashangwane, Mantebele Mashao, Shalom Mashego, Lerato Mashele, Ester Mashiane, Joyce Mashibini, J Mashilo, Tumi Mashiloane, Charity Mashishi, Ngazibini Mashiyi, Khomola Mashudu, aluwani masindi, Caroline Maslo, Nduduzo Masondo, Dumisile Masuku, Cry Matamela, Mirriam Matandela, Nontokozo Mathabela, T Mathabi, Keitumetse Mathe, Mathabo Mathebula, Catherine Mathebula, Mdungazi Andres Mathebula, Nqobizwe Mathenjwa, Jane Mathibe, Lebohang Mathibela, MAKWELA MATHILDA, Khakhu Mathiva, Mokgadi Alinah Mathobela, Fikile Pearl Mathonsi, KP Mathonsi, Katlego Mathosa, Noluvo Matiwane, Emma Matjeke, Bella Matjiane, Thabang Matjila, Sr Chidi Matlala, Petlo Matome, Nolusindiso Matoti, C. Matseliso, Dineo Matsemela, Phumeza Matsha, Gaalebale Prudence Matshediso, Motsumi Matshediso, Esther Matshela, Bongeka Mavuma, Pearl Mavundla, Nomthandazo Mavuso, Lovender Mawasha, Rebecca Mawelela, Nelisiwe Mazibuko, Phumlani Mazibuko, Lindiwe Mazubane, Bavumile Mbanjwa, Ayanda Mbasa, Nosimilo Mbatha, ZANELE MBATHA, Rudolph Zenzele Mbatha, Gift Mbedzi, Tatenda Trevor Mbizi, Khumbulani Mbonambi, Nondumiso Mboniswa, Nomfanelo Mbonisweni, Jody Mbuilu, Siyabonga Mbulawa, Zama Mbutho, Natasha Mbuzi, Nonkululeko Mchunu, Cyprian Mchunu, Nokuzola Mchunu, Masesi Thandeka Mchunu, Vuyokazi Mciteka, Solly Mdaka, Neho Mdakane, Siyabonga Mdediswa, Melusi Mdima, Nozipho Mdima Masondo, Siviwe Mdindana, Ntombizikhona Mdleleni, Sibusiso Mdletshe, Gcobisa Precious Mdoda, Ntombi Mdolo, Anele Mdontsane, Ruchikas Mehta, Philile Rittah Memela, Masande Methuse, Keatlaretse Metshile, Pheliswa Metuse, Anton Meyer, Gavin Meyer, Cameron Meyer, Sisonke Mfazwe, Andiswa Mfecane, Bongeka Mfecane, Nelisiwe Mfeka, Busisiwe Mgaga, Thandiwe Portia Mgauli, Thembekile Mgedezi, Vuyokazi Mgedezi, Kalipile Mgevane, Bongni Mgiba, Babalwa Mgoduka, PATRICK MHLABA, Zeldah Mhlaba, Ntombizodwa Mhlanga, Vangile Mhlinza, Nokuthula Mhlongo, sibongiseni Mhlongo, Unamandla Mhlotshana, Mabaso Mikateko, Helena Minnie, Karen Mintoor, Bongi Miyeni, Mabelane MJ, Rosy Mjethu, Gloria Mkhize, Mvuselelo Mkhize, Ntokozo Siyabonga Mkhize, Victoria Mkhize, Nomkhosi Mkhize, Nokuthula Mkhize, Mathini Mkhwanazi, Nolwandle Mkile, Kholofelo Mkise, Nokwandiso Mkiya, Pearl Mkongi, Mnonopheli Mkungeka, Hlomile Mlahleki, Nolukholo Mlibali, Sakhumzi mlungwana, Jonas Mmachele, Mashatole Mmateka, Molebatsi Mmokwa, Thembisa Mmutlane, Zanele Olive Mndebele, nonhlanhla mngomezulu, Noluthando Millicent Mnguni, Pumza Mngunyana, Nomxolisi Mngunyana, Ntombebongo Mngxekeza, ZENZELE MNISI, Hlengiwe Precious Mnqayi, PHUMZILE MNQAYI, Thabiso Mntungwa, Siya Mnyaka, Ntombikayise Mnyakeni, Vuyani Mnyamana, Nomzingisi Mnyipika, Koena Moabelo, Mmakgoshi Alseria Moatshe, Jennifer Mochaki-Senoge Mochaki-Senoge, Sharon Moche, Tebello Mocwagae, Koeikantse Modibane, Tebogo godfrey Modimoeng, Obakeng Modisa, Itumeleng Modisane, Olebogeng Modise, Makaepeaa Flovia Modjadji, Sharon Modupe, Maja Moeketsi, Ntswaki Moeketsi, Kereditse Kingsley Moeng, Naledi Nthabiseng Mofamere, Samuel Mofokeng, Thabo Mofokeng, Jonas Mofomme, VICKY MOGAKANE, Lehlohonolo Mogale, Audrey Mogapi, Thomas Mogashoa, Mphaka James Mogatla, Kgaladi Mogoale, Dikeledi Maggie Mohajane, Nkuba Mohapi, Mthoamihla Mohatsela, Irene Mohlala, Daphney Mohlala, Mpho Mohlamonyane, Bonolo Millord Mohutsiwa, Selemela Moipone, Tshepang Moisi, Nelly Mojalefa, Vuyo Moji, Buhle Mokangwana, Matloa Mokgabo, Manaka Mokgaetji, Jane Mokgaotsi, Neo Theodore Mokgoro, Thalitha Mokhatla, Lerato Lovedalia Mokhele, Sheila Mokhema, Mamoya Mokoena, Mojalefa Mokoena, Lleka Mokome, Cynthia Mokone, Ipeleng Mokono, Thabiso Mokonyama, Josiah Mokori, Dolores Mokuena, Danny Mokumo, Oddy Mokwena, Kgaogelo Mokwena, Kgantshi Sam Mokwena, Lebogang Mokwene, Thato Elliott Molate, Ditoche Molebalwa, Boingotlo Molefe, KGOPA STANLEY MOLEHE, Kgomotso Moleme, Sarah Moliane, FANYANA MOLOI, Retshepile Joseph Molorane, Glenda Tsholanang Molotsi, Lerato Molukanele, Joy Monareng, Thapelo Moncho, Modiadie Monica, Refilwe Monnane, Andile Monqo, Neo Montewa, Kgalalelo Montsioa, Reitumetse monyaki, Masekhobe Jeanett Monyane, Lipson Monyela, Yudeshan Moodley, Kriesen Moodley, Kaira Moodley, Boitumelo Donald Mooka, Prea Moonsamy, Simmi Moopanar, David Moore, Lineo Mophethe, Tshegohatso Moremedi, Kealeboga Moremong, nthangeni morgan, Egma Moripa, Lulamile Morris, Me. A.M. Mosala, Thabo Mosana, Alice Mosase, Yolanda Mose, Maponya Mosehlo, Mothusi Moseki, Mojalefa David Moshabe, Mbulelo Moshani, Pelisa Moshani, Ledwaba Mosima, Ezrom Mosima, M.P Mosoma, Lebohang Motaung, Mokete Motaung, Thozama Charmain Motaung Xhama, Purine Khethiwe Motha, Lerato Motimele, Boitumelo Motimeng, Shirley Motladiile, otsile Motlhabane, Joshua Motlhamme, Mandla Motloba, Kagiso Motse, Sophia Motshegoa, Edward Moutlana, Irma Mouton, Zanele Moya, Nomonde Moyake, Maja MP, Jenny Mpete, Luamba Meltha Mpfuni, Seputule Mphahlele Mphahlele, Mashadi Mphake, Ephraim Letlhogonolo Mphanya, Mashudu Mphaphuli, Tebogo Chwene Mphela, MS Mpontshane, Thabile Mqotyana, Babalwa Mqungquthu, Noluthando Busane Msane, Malusi Mseleku, Sibusiso Msibi, Mancele Msibi, Thulisile Msibi, Siyabonga Linda Msibi, Clement Nhlanhla Msiza, Lungelo Msomi, Mandlenkosi Mtatambi, Thembisa Mthathambi, December Mthembu, Nhlahla Mthembu, Fezile Mbali Mthembu, Lungiswa Mthembu, Nompumelelo Petunia Mthethwa, Khulekani Mthimkhulu, Lungani Percival Mthuli, Ashley Mthunzi, Xolani Sydney Mtolo, Nomonde Precious Mtolo, Linda Mtshali, Neliswa Mtwa, Fezeka Mtyobile, Kanyisa Mtyobile, Mpfariseni Mudau, Magwabeni Muemeleli, Isaac Mulaudzi, Rebecca Mulaudzi, Mhlelekedzeni Mulaudzi, Dakalo Rejoyce Muligwe, Blessing Muponda, Mmbangiseni Stella Mushadi, M Mushid, Konanani Muthaphuli, J Muthavhine, Mpho Muthika, Samkelisiwe Mvelase, Vusi Mvelase, LAURENT KAYUMBA MWEHU, Thabile Myaka, Magriet myburgh, Zimkhitha Mzamo, Fezeka Mzawuziwa, Mfundo Lunga Mzini, Oscar Mzizana, Ntokozo Mzobe, Thokozile Mzobe, Zamaswazi Mzobe, Mtimkulu Mzwandile, Fathima Naby, KESHNEE NAICKER, Pregashnie Naicker, Saroja Naicker, Pershen Naicker, Saiyen Virgil Naicker, RIA NAIDOO, Sam Naidoo, Mergan Naidoo, KAMALAMBAL NAIDOO, Aroomugam Naidoo, Sivuyile Naku, Firdose Nakwa, Masoga Nancy, Rita Nathan, Maritsa Naude, Gcobisa Ncaza, Aviwe Ncaza, Relebohile Ncha, Yanelisa Ncoyini, Snothile Ncube, Mrs Ndaba, VUSUMUZI NDABA, Mmapula Ndaba, Siziwe Ndawonde, Ziphozihle Ndevu, NONHLANHLA FAITH NDHLOVU, Simphiwe Ndima, Sindisiwe Ndlela, Thobsile P Ndlela, Nobuhle Ndlovu, Nwabisa Ndlovu, Virginia Dipuo Ndlovu, Sombekhaya Ndlumbini, Khululiwe Nduli, Priscilla Nontokozo Nduli, Michael Ndwambi, Jeremy Nel, Rina Nel, Lizelle Nel, Ntsundeni florah Nemanashi, Usinkhangwe Nyaphophi Nemudivhiso, Joyce Nemutavhanani Nemutavhanani, Jabu Nene, Xolani Nene, David Netshilonga, Rendani Netsianda, Charmaine Newton, Vuyo Leroy Ngalo, Ncumisa Ngani, Thabisa Monica Ngcakaza, Thamela Ngcobo, Trulove Nonhlanhla Ngcobo, Richards Ngcobo, Gcinile Ngcobo, Guguletu Ngcobo, Thozama Ngetu, Pinkie Ngewu, Tshepo Ngobeni, Providence Ngobeni, Khanyisile Ngobeni, Prudence Ngobeni, Thembisile Ngobese, Tracy Ngomane, Nolusindiso Ngondo, Nokukhanya Ngubane, Sithembiso Ngubane, Ntombizodwa Praxedise Nguse, Tholakele Ngwane, Elizabeth Ngwasheng, Siphamandla Ngwenya, Gugu Ngwenya, Nomthandazo Ngwenya, Themba Ngwenya, Eva Ngwenya, Zintlanu Ngxola, Tshegofatso Nhabe, Jabulile Nhlabathi, Ishmael Nhlangwana, Sithembile Nhlapo, Matlala nick, Vicky Niemand, Carina Nienaber, Louise Nix, Chumisa Njikelana, Masiza Njomi, Lucia Nkabinde, M NKABINDE, Boitumelo Nkabiti, Gugu Nkabule, Mankopodi Nkadimeng, Nonkanyiso Nkanjeni, Palesa Portia Nkatlo, Bongani Nkewana, Audrey Nkhwashu, Ngokoana Nkoana, Mmathapelo Nkoane, M Nkogatse, Fezile Nkomo, Ntando Nkomo, Nontobeko Nkonyane, Sydney Nkosi, Ntombikayise Nkosi, Phumzile Nkosi, Ntombifuthi Nkosi, TINTSWALO NKOSI, ML Nkosi, Godfrey Nkosi, Amukelani Nkosi, Fikile Vinoliah Nkosi, Mbali Nkosi, Nomcebo Lucia Nkosi, Siphokazi Nkosi, Amanda Nkuhlu, Phumzile Nkumane, Malebo Nkuna, Wendy Nkwakwha, Sesi Noge, Elizabeth Nolte, Peko Nomawabo, Malibongwe Nombita, Nandipha Nophale, Jeanetta Nothnagel, Bongiwe Novokoza, Zanele Nqaphi, Thobekile Nqondo, Siphokazi Nqwelo, Nkoana NS, Sindiswa Ntabeni, Mr Ntabeni, mawethu Ntampula, Mthutuzeli Ntebe, MOKWABO NTELA, Hezekiah Ntimbane, Xolisa Ntintsilana, Patrick Ntleki, Zanele Ntobela, Bandile Ntombela, Zamaswazi Ntombela, Khonelihle Zandile Ntombela, Praisegod Samkelo Thobani Ntombela, Lindiwe Ntonintshi, Dipuo Ntseane, Thobeka Ntseane, Xolelwa Ntsham, Mbalenhle Ntshele, Amanda Ntshewula, Zinzi Ntsoko, Athini Ntsoto, Nomsa Ntuli, Nokwazi Ntuli, Nomvula Ntuli, Andrew Diffar Ntuli, Faith Ntuli, Margrit Nurnberger, Ntsikelelo Nxala, Sithandiwe Nxasane, Mr Thanda Nxumalo, Xolani Nyathi, Nontobeko Nyawula, Nhlakanipho Nzama, Maila Nkuneng Obed, Florence Ogwal, Maureen Olifant, Mr B Oliphant, Monota Olive, Kagisho Olyn, Raymond Omoighe, Phumeza One, Ratombo Oscar, Nkuna Owen, Mailula P, Nalini Padayachee, Vasaily Padayachy, Ntombizakhe Pakade, Mosiuoa Palime, Jane Palisa, Arifa Parker, Lesenyeho Parkies, Andy Parrish, Nilesh Patel, Anastasia Pather, Mkhombo Tsakani Patience, Marisa Patzke, Akhumzi Pawuli, Ntandokazi Pelako, Phaswana Sibasa Penrose, Litha Peppeta, Santosh Pershad, Makheda Pertunia, Nkuna Pertunia, Dane Perumal, Mongameli Peter, Justin Peters, Vatiswa Petlane, Harideen Petrus, Kgomotso Phahladira, Matebesi John Phakisa, R Phale, Livhuwani Phathela, Sekate Daniel Phillip, Beverly Phiri, Mapule Precious Phiri, Thapelo Phokane, Frank Phokoane, Moele Pholosho, Sekoro Phooko, Sekodi Geoffrey Phooko, Maponya Phutiane, Faiza Pillay, Melanie Pillay, Sayuri Pillay, CR Pillay, Zikhona Plaatjie, James Pootona, Samantha Potgieter, Marius Potgieter, Mulaudzi Mulatedzi Precious, Paul Janus Pretorius, Hans Prozesky, Mokhethi Pule, Jayshina Punwasi, Dot Putzier, Lutho Qankqiso, Siphokazi Qebedu, Phozisa Qhola, Ntombesithathu Qotoyi, Sipho Victor Qotso, Zanele Qwabe, Helena Rabie, Phoebe Rabothata, Christina Rachoene, Mteteleli Radana, Maria Radebe, Dr. Valentino Radebe, Nonkululeko Radebe, Ella Radinne, Sherly Raduvha, Shamintha Raghunath, Claudine Rajagopaul, Mary Rakgwale, Malumbete Michael Ralethe, Kenneth ralimo, Motlalepule Ramafoko, Maduvhahafani Ramagoma, Charlotte Raman, Dr Ramavhuya, Molly Rambally, Nivasha Ramdeen, Tanusha Ramdin, Sharita Rameshwarnath, Yeishna Ramkillawan, null Ramotlou, Faith Rampedi, Vijayluxmi Rampersad, Avhashoni Ramuima, Noluthando Ranone, Mabohlale Portia Rapasa, Mpharoane rapelang, Nika Raphaely, Lesiba Rashokeng, Caroline Rashopola, Tebogo Ratau, M RATAU, Mpfariseni David Ratshili, Elmari Rautenbach, Rofhiwa Ravele, Johannes Reachable, Peta Mmalahla Rebecca, Kessendri Reddy, Andrew Redfern, Robertha Reed, Mumsy Rees, Dr Reji, Gary Reubenson, Veena Rewthinarain, Paul Rheeder, Nkonayani Rhulani, Mufamadi Richard, J.S Rikhotso, Shatimone Beverley Rikhotso, Lavhelani Ndivhaleni Robert, Noncedo Roto, Gideon Ruder, Kapil Rugnath, Lizette Ruiters, Mina Ruiters, Sue Russell, Lynn Ruwiza, Molokoane RY, Mandy Saaiman, Emmanuel Sabela, Lerato Sadiq, Litha Saki, HYPPOLITE SALAMBWA, Menitha Samjowan, Nazlee Samodien, Rakgolele Samuel, Fakudze Sandile, Cekuse Sanelisiwe, Mandlankosi Sani, Simangele Sawuka, Lelani Schoeman, Magriet Scholts, Ronel Schroder, Mamotetekoane Sebalabala, Selwalenkwe Collet 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Sifumba, Sipho Sigcau, Lutho Sigila, Kayakazi Sihentshe, Bongani Sihlangu, Daisy Sikhakhane, Shaun Nhlanhla Sikhakhane, Mbali Siko, Sipho Sikonje, Khumbulekile Simanga, Nomsa Simango, Thulisile Simela, Ntombikayise Simelane, Sashah Singh, Marjorie Singh, Mrs Ragani Singh, Shash Singh, Anita Singh, Hitekani Sithole, Senzekile Sithole, Ntokozo Danielle Sithole, Koketso Maxwell Sithole, Jonnie Situma, Annie Sivraman, Katekani Siwela, Nonqubela Siyewuyewu, Maweya Sizeka, Nonceba Siziba, Andrew Skhosana, Khanyisile Skhosana, RORISANG SKHOSANA, Tandiwe Skoko, Sunet Slabbert, Ntombela Smangaliso, Christine Smedley, Lydia Smit, Natassia Smit, Lizelle Smit, Michelle Smit, Fasie Smith, Lizzie Smith, Sunell Smith, Cassius Smith, Stefan Smuts, Ayanda Sofe, Khobane Solomon, LJ Solomon, chauke Sombani, RICHARD SONGCA, Anga Sontamo, Supriya Soorju, Zubenathi Sopazi, Brian Soqasha, Bongiwe Sosibo, Ntsika Sotsaka, Mandy Soula, Simon Spoor, Sarah Stacey, Asanda Stali, Mutele Mmboniseni Stephina, Myra Steup, Sinoxolo Steven, AW Stevens, Vincent Stevens, Dewald Steyn, Bianca Steyn, Pat Stocks, Henk Stolk, Alida Stoltz, Renate Strehlau, Anneke Stroebel, Loraine Strydom, Jean-Marie Strydom, Anton Strydom, Ursula Strydom, Midhu Sunnyraj, Nwabisa Swana, Winnie Swanepoel, Suzan Swanepoel, Elsie Swartbooi, Estley Swartz Swartz, Casandra Syce, Shihambi T.E, Joyce Tabane, NE Tabane, Mrs Tawana, Ntene Tebello, Siphosetu Wiseman Tembe, Samantha Terblanche, Ntombifuthi Thabede, Nkhumeleni Thabelo, Sibusiso Thabethe, Lekhanya Thabo George, Keorapetse Thare, Makofane Thebogo, Lerato Thekiso, Lloyd Theko, Celimphilo Zandi Themba, Danie Theron, Henda Theron, Ilze Theron, Thandiwe Thingathinga, M.M THLABADIRA, Dikeledi Thoka, Zanele Thokwana, Gustav Thom, Mamphot Joel Thubakgale, Theodora Thwala, P Thys, Monethi Tieho, Matodzi Timothy, Ndlovu Tintswalo, Babalwa Tivana, Molefi Tladi, Bongiwe Tokota, Simthandile Toni, Ariel Torres, Mande Toubkin, Marinda Tsatsi, Khanyisile Tshabalala, Nozibele Tshamase, Gontse Tshefu, Makgoga Tshegofatjo, Given Tshikomba, Thapelo Tshilo, Lerato Tshira, S.T Tshirado, Maipfi Tshisikule, G Tsoke, N TSOKE, Alatha Tsoko, Mosele Tsotetsi, SANDEVA TSUBELLA, Noxolo Tuswa, Maipato Tutse, Nomayenzeke Tutu, Sphephelo Twala, Nhlanhla Twala, Simphiwe Twala, John Ubisi, Tefo Unathi, A Van Aswegen, Marietjie van der Merwe, Trudie van der Merwe, Patience van der Plank, Elmarie van der Spuy, Linda Van Der Westhuizen, Adele Van Der Westhuizen, Talana van der Westhuizen, Mene van der Westhuyzen, Thea Van Dyk, Ingrid van Heerden, Ryno van Jaarsveld, M Van Lill, Heidi van Niekerk, Ben van Niekerk, Amanda van Rensburg, Judy van Schallwyk, Zeitschke Yarnrich Van Sensie, Magda van Vuuren, Cloete van Vuuren, Olga Funiswa Vandu, Mandisa Vane, Lucia VanZyl, Ebrahim Variava, Mariam Veerus, Nokhwezi Velapi, Sebina Veleko, Z. Velezantsi, Retha Venter, Corlia Vergottini, Inga Vermeulen, Liabara Lufuluvhi Vidah, Bongani Vilakazi, Treasure N Vilakazi, Mbalenhle Precious Vilakazi, Karen Viljoen, Werner Viljoen, Zuretha Volschenk, Angelo Vos, Matlala VV, Jacques Walters, Kate Webb, John Welsh, D WESSELS, Judy Wheller, Fundile White, Priscilla White, Carmen Whyte, Ansie Willemse, Sape William, Daniel Williams, Kamielah Williams, Mercia Williams, Anne Williamson, Cherade Wilson, Boipelo Wolff, Michelle Wray, Ntombizonke B Xaba, Thabang Jabulani Xaba, Thanks Xiniwe, Mtshali Xoliswa, Funokwakhe Xulu, Gibson Xulu, Sandlakazi Yam, NM Zakhura, Mashela Zareloa, Sive Zinto, Dyibeni Zinziswa, Lulamile Ziselo, Zakhele Zitha, Emmanuel Zitha, Anele Zokufa, Innocent Zondi, Sikhumbuzo Bernard Zondi, Sbuyi Zondi, Thulani Zondi, Wandiswa Zongola, Liesl Zühlke, Zandile Zulu, LUNGELO ZULU, Thandeka Zulu, Slindili Zulu, Nkosinathi Zulu, Angel Zuma, precious Zungu, Pamela Zungu, Melusi Zungu, Priscilla Zungu, Bongo Lihle Zwakala, Antonia Zwane, Promise Zwane, Muziwendoda Zwane, Hlengiwe Priscila Zwane, and Nomgcobo Zwane
Subjects: Coronavirus disease 2019 (COVID-19), SARS-CoV-2, business.industry, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Incidence (epidemiology), COVID-19, Articles, General Medicine, Odds ratio, Logistic regression, Wave period, South Africa, Humans, Medicine, Prospective cohort study, business, Demography, Cohort study
Abstract: Background The first wave of COVID-19 in South Africa peaked in July, 2020, and a larger second wave peaked in January, 2021, in which the SARS-CoV-2 501Y.V2 (Beta) lineage predominated. We aimed to compare in-hospital mortality and other patient characteristics between the first and second waves. Methods In this prospective cohort study, we analysed data from the DATCOV national active surveillance system for COVID-19 admissions to hospital from March 5, 2020, to March 27, 2021. The system contained data from all hospitals in South Africa that have admitted a patient with COVID-19. We used incidence risk for admission to hospital and determined cutoff dates to define five wave periods: pre-wave 1, wave 1, post-wave 1, wave 2, and post-wave 2. We compared the characteristics of patients with COVID-19 who were admitted to hospital in wave 1 and wave 2, and risk factors for in-hospital mortality accounting for wave period using random-effect multivariable logistic regression. Findings Peak rates of COVID-19 cases, admissions, and in-hospital deaths in the second wave exceeded rates in the first wave: COVID-19 cases, 240·4 cases per 100 000 people vs 136·0 cases per 100 000 people; admissions, 27·9 admissions per 100 000 people vs 16·1 admissions per 100 000 people; deaths, 8·3 deaths per 100 000 people vs 3·6 deaths per 100 000 people. The weekly average growth rate in hospital admissions was 20% in wave 1 and 43% in wave 2 (ratio of growth rate in wave 2 compared with wave 1 was 1·19, 95% CI 1·18–1·20). Compared with the first wave, individuals admitted to hospital in the second wave were more likely to be age 40–64 years (adjusted odds ratio [aOR] 1·22, 95% CI 1·14–1·31), and older than 65 years (aOR 1·38, 1·25–1·52), compared with younger than 40 years; of Mixed race (aOR 1·21, 1·06–1·38) compared with White race; and admitted in the public sector (aOR 1·65, 1·41–1·92); and less likely to be Black (aOR 0·53, 0·47–0·60) and Indian (aOR 0·77, 0·66–0·91), compared with White; and have a comorbid condition (aOR 0·60, 0·55–0·67). For multivariable analysis, after adjusting for weekly COVID-19 hospital admissions, there was a 31% increased risk of in-hospital mortality in the second wave (aOR 1·31, 95% CI 1·28–1·35). In-hospital case-fatality risk increased from 17·7% in weeks of low admission (8000 admissions; aOR 1·24, 1·17–1·32). Interpretation In South Africa, the second wave was associated with higher incidence of COVID-19, more rapid increase in admissions to hospital, and increased in-hospital mortality. Although some of the increased mortality can be explained by admissions in the second wave being more likely in older individuals, in the public sector, and by the increased health system pressure, a residual increase in mortality of patients admitted to hospital could be related to the new Beta lineage. Funding DATCOV as a national surveillance system is funded by the National Institute for Communicable Diseases and the South African National Government.
Published: 2021
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3. Risk factors for COVID-19-related in-hospital mortality in a high HIV and tuberculosis prevalence setting in South Africa: a cohort study

Author: Waasila Jassat, Cheryl Cohen, Stefano Tempia, Maureen Masha, Susan Goldstein, Tendesayi Kufa, Pelagia Murangandi, Dana Savulescu, Sibongile Walaza, Jamy-Lee Bam, Mary-Ann Davies, Hans W Prozesky, Jonathan Naude, Ayanda T Mnguni, Charlene A Lawrence, Hlengani T Mathema, Jarrod Zamparini, John Black, Ruchika Mehta, Arifa Parker, Perpetual Chikobvu, Halima Dawood, Ntshengedzeni Muvhango, Riaan Strydom, Tsholofelo Adelekan, Bhekizizwe Mdlovu, Nirvasha Moodley, Eunice L Namavhandu, Paul Rheeder, Jacqueline Venturas, Nombulelo Magula, Lucille Blumberg, Shaina Abdullah, Fiona Abrahams, Vincentius Adams, Fhima Adnane, Sonia Adoni, Dieketso Melitta Adoons, Veronique Africa, D Aguinaga, Susan Akach, Prisha Alakram Khelawon, George Aldrich, Olatunde Alesinloye, Mathale Biniki Aletta, Mametja Alice, Tebogo Aphane, Moherndran Archary, Felicity Arends, Shireen Arends, Munonde Aser, T Asmal, Mohammed Asvat, Theunis Avenant, Muvhali Avhazwivhoni, Magnolia Azuike, Johanna Baartman, Dlava Babalwa, Johan Badenhorst, Miranda Badenhorst, Bianca Badripersad, Lalihla Badul, M Bagananeng, Mncedisi Bahle, Liezl Balfour, T C Baloyi, S Baloyi, Tinyiko Baloyi, Tshepo Mpho Baloyi, Thokozani Banda, Shimon Barit, Nicole Bartsch, Junaid Bayat, Siyabulela Bazana, Marlene Beetge, Nosindiso Bekapezulu, Rammala Belebele, Phala Bella, Zanenkululeko Belot, Lindi Gladys Bembe, Sonja Bensch, Gishma Beukes, Karla Bezuidenhout, Themba Bhembe, N A Bikisha, Ben Bilenge, Leesa Bishop, Baphamandla Biyela, Cyntheola Blaauw, Mark Blaylock, Nicola Bodley, Power Bogale, Sibongile Bokolo, Stefan Bolon, Mary Booysen, Eldereze Booysen, Lia Boretti, Paula Borges, Millicent Boshoga, Natasha Bosman, Lucinda Bosvark, Nicky Botes, Adele Botha, Chantall Botha, Jana Botha, Chantall botha, Mandlakayise Irvin Botha, Alet Botha, Janet Bradbury, Zandisile Breakfast, Maria Breed, Molele Brenda, Moshito Brice, Jolene Britz, Amanda Brown, T Buchanan, Thozama Bucwa, Crystelle Burger, Ziyanda Busakwe, Nosiviwe Bushula, Zinhle Buthelezi, Dumsile Buthelezi, Thubelihle Buthelezi, Mpumelelo Basil Buthelezi, Fundiswa Lidwina Buthelezi, Nadia Bux, Christoff Buys, Anneline Buys, Ernestina Caka, Armando Sanchez Canal, Sithole Caroline, Monrick Casper, Shannon Cawood, Oratile Cebisa, Nothando Cele, Sboniso Cele, Sthembile Goodness Cele, Mkhacani Chauke, Pinkie Chauke, Nevil Chelin, Xiaohui Chen, Venmalla Chetty, Kerisse Chetty, Christinah Cheu, Vindana Chibabhai, Takudzwa Chirima, Mantwa ChisaleMabotja, Charity Chivenge, Ngoasheng Choene, Mbali Nosisa Choko, Martin Choshi, Sabbir Chowdhury, Anastacia Christoforou, S L S Chuene, T S Chueu, Dale Cilliers, Vanessa Cilliers, Marcel Claassen, Jeané Cloete, Chantelle Coelho, Carol Coetzee, Hans Jurgens Coetzee, Christine Coetzee, Marelize Coetzee, Dane Coetzer, Sizwe Coka, M Colane, Herkulaas Combrink, Songezo Conjwa, Colleen Contrad, Faith Cornelissen, Leezelle Cronje, Christine Crouse, Tshidi Dabi, Ziyanda Dandala, Ziyaad Dangor, Gildenhuys Daniel, Ngwana Daniel, Alfred Daumas, Madelein Dauth, Mongalo David, Wayne Davids, Nozuko Daweti, Wandisa Dayile, B De Bruin, Karin De Klerk, Tanya De la Rosa, Marice de Nysschen, Marie De vos, Darien De Wet, Mohith Debising, Darshan Deenadayalu, Babalwa Dekeda, Mofokeng Desiree, Annelise Deysel, Abram Dhlamini, Makgethwa Dhlala Diala, Mathapelo Diale, Bella Diketane, Nosisa Dingani, Siyabonga Diniso, Lesego Diphatse, Anele Diya, Zihloniphile Dladla, Nompumelelo Dladla, Mlungisi Dladla, Patience Dladla, Baphilie Dlamini, Nonhlanhla Dlamini, Linda Dlamini, Nonzwakazi Dlamini, Wendy Dlamini, Ncomeka Dlamini, Siyabonga Dlamini, Nicodemus Dlamini, Lebohang Dlamini, Motshedise Dlamini, Babalwa Christine Dlava, Phikiwe Dlova, Lindiwe Dlozi, Maenetja Doreen, Vumile Doyi, Athini Doyi, Belinda Du Plessis, Johanna Aletta du Plessis, Eddie du Plessis, Nicolette du Plessis, Karin du Plessis, Briette du Toit, Narissa du Toit, Jabulile Dube, Athayanda Dubula, Msomi Duduzile, Sechaba Duiker, Unati Bongile Duma, Kholiwe Duma, Kella Dunne, Kholeka Dyantyi, Avile Dyantyi, Simphiwe Dyasi, Chauke Dyondzo, Phelisa Dyubhele, B J Dywili, Letitia Edwards, Madie Eksteen, Tersia Ellis, Tia Ellis, Glenda Emmerson, Theusia Enslin, Odimula Epule, Lana Erasmus, Mathonsi Erick, Lerato Etsane, Shimange Eunice, Zanele Fani, Mariette Ferreira, K L Finger-Motsepe, Fabion Floris, Tseko Fobo, Keresemetse Fokotsane, Duduzile Emmelda Fokwana, Genevieve Marion Fords, Juanita Fortein, Christine Fouche, Rulandi Fourie, Andrew Frean, Ludwig Fredericks, Wandile Funda, kabelo funjwa, Martha Futhane, Amanda Futuse, Dora Gabaediwe, Nonhlanhla Gabuza, Janycke Galant, Zanele Gama, Thobile Gano, Emma Cora Gardiner, Henri Gastrow, Kelly Gate, Ben Gaunt, Rikhotso Gavaza, Thapelo Gayi, Nkosinathi Gcakasi, Nomusa Gcobo, Leon Geffen, S Geldenhuys, Jenny George, Martha Gerber, Zolisa Getyengana, Nkululo Gigi, Radha Gihwala, Mitchell Gilliland, Zandile Gloria, Elitia Glover, Ellen Gokailemang, Suseth Goosen, Maria Gopane, Thandazile Gosa-Lufuta, Bernadett Gosnell, Sharleen Gouws, Christina Govender, Raksha Govender, Pearl Govender, Sally Govender, Roxanne Govender, K Govender, Savie Govender, Rashika Govinden, Luphumlo Gqabuza, Nomthandazo Gqaji, Maneo Gqetywa, Caroline Green, Nathan Green, Neera Green, Hendrik Grobler, Pamela Groenwald, Daniel Grootboom, Beatrice Gumede, Nomonde Gumede, Simphiwe Gumede, Slindile Gumede, Ntombikayise Gumede, Zenande Gumede, Thandiswa Gxotiwe, Makhubela H L, Nonhlanhla Hadebe, Skhumbuzo Hadebe, Christos Halkas, Ansie Hamer, Ebrahim Hamida, Juan Hammond, Sumayia Haniff, Annelise Hare, lorinda Hattingh, Thenjiwe Hendricks, Philip-George Henecke, Brends Henly-Smith, Glynis Herselman, Ansie Heymans, Chantel Heyns, Golekane Hlabahlaba, Lucky Hlabangwane, Simango Hlamarisa, Ntokozo Hlanzi, Hlengiwe Hlela, Katlego Hlokwe, Thembinkosi Hlongwa, Anele Hlongwana, Themba Hlubi, Tozama Hobo, Nare Nathaniel Hopane, Mariska House, Catharina Hudson, Marinda Huysamen, Jezreen Indheren, Samantha 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Caroline Magongwa, Agretia Magubane, Agretia Ntombizodwa Magubane, R Magwai, D I Mahabane, Padmini Mahabeer, Elsie Mahadulula, Lungiswa Mahanjana, Amy Maharaj, Qedusiza Mahlambi, Yvonne Mahlangu, Lerato Mahlangu, Ntombifikile Mahlangu, Makhosazana Mahlangu, Mahlatsi Mahlangu, Penelope Mahlasela, Thosago Mahlatse, Regina Mahlobo, Dikhing Mahole, Adam Mahomed, Mapeu Debora Mahubane, Peter Mahume, Lehlogonolo Maifo, Vincent Maimane, Petunia Maimele, Phakoe Maine, Patricia Senyanyathi Mainongwane, Nomalungisa Majamani, Amahle Majozini, Noluthando Makalima, Nomfundo Makam, Khanyisa Makamba, R Makan, Mashiane Makarapa, Malesela Makgahlela, Mogoiwa David Makgisa, Makgoba Makgomo, M A Makgopa, Mabone Makhalema, Lindokuhle Lizo Makhanya, Philile Valentia Makhanya, Tolerance Makharaedzha, Nathi Makhathini, Elizabeth Makhesi, Cinile Makhubela, Nkululeko Freedom Makhunga, Nomalinge Makhupula, R R Makhura, Rangwato Makola, Zingisa Makuba, Asanda Makubalo, Lonwabo Makumsha, George Makuya, Levy Mmachuene Malaka, Themba Malangeni, M L Malatji, Pelonomi Malebana-Metsing, Malek Malek, Luthando Malevu, Juanita Malgas, Dimakatso Malgas, Paul Makgasane Malope, Monyeki Malose, Katekani Maluleke, Kato Mambane, Nthabiseng Mamorobela, Kukami Manamela, Tshepo Manana, Sathiel Maneto, Aron Kabelo Manganye, Pheto Mangena, Anna Mangoale, Tinotenda Florence Mangozho, Pariva Manickchund, Zandisile Mankayi, Arthur Manning, Kelebogile Manyaapelo Manyaapelo, Tabea Manyane, Zoliswa Manzana, Milton Manzini, Busisiwe Mapasa-Dube, Siboniso Maphumulo, Ntombifuthi Maphumulo, Sindy Maponya, Khomotso Mumsy Maponya, Napjadi Maponya, Lami Maqubela, Lizeka Maqubela, Vuyo Maqungo, Marisa Marais, Chantal Marais, Nondumiso Maramba, Annelize Mare, Madumetsa Maredi, Afikile Martins, Johanna Marule, Refilwe Marumo, N N Masakona, Kedibone Vincentia Masehla, Eric Maseko, Tshilidzi Maselesele, Mojalefa Maselo, M Maseloa, M E Masemola, Thembi Masemola, Bella Mashaba, James Mashangwane, Mantebele Mashao, Shalom 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Tatenda Trevor Mbizi, Khumbulani Mbonambi, Nondumiso Mboniswa, Nomfanelo Mbonisweni, Jody Mbuilu, Siyabonga Mbulawa, Zama Mbutho, Natasha Mbuzi, Nonkululeko Mchunu, Cyprian Mchunu, Nokuzola Mchunu, Masesi Thandeka Mchunu, Vuyokazi Mciteka, Solly Mdaka, Neho Mdakane, Siyabonga Mdediswa, Melusi Mdima, Nozipho Mdima Masondo, Siviwe Mdindana, Ntombizikhona Mdleleni, Sibusiso Mdletshe, Gcobisa Precious Mdoda, Ntombi Mdolo, Anele Mdontsane, Ruchikas Mehta, Philile Rittah Memela, Masande Methuse, Keatlaretse Metshile, Pheliswa Metuse, Anton Meyer, Gavin Meyer, Cameron Meyer, Sisonke Mfazwe, Andiswa Mfecane, Bongeka Mfecane, Nelisiwe Mfeka, Busisiwe Mgaga, Thandiwe Portia Mgauli, Thembekile Mgedezi, Vuyokazi Mgedezi, Kalipile Mgevane, Bongni Mgiba, Babalwa Mgoduka, Patrick Mhlaba, Zeldah Mhlaba, Ntombizodwa Mhlanga, Vangile Mhlinza, Nokuthula Mhlongo, sibongiseni Mhlongo, Unamandla Mhlotshana, Mabaso Mikateko, Helena Minnie, Karen Mintoor, Bongi Miyeni, Mabelane M J, Rosy Mjethu, Gloria Mkhize, Mvuselelo Mkhize, Ntokozo Siyabonga Mkhize, Victoria Mkhize, Nomkhosi Mkhize, Nokuthula Mkhize, Mathini Mkhwanazi, Nolwandle Mkile, Kholofelo Mkise, Nokwandiso Mkiya, Pearl Mkongi, Mnonopheli Mkungeka, Hlomile Mlahleki, Nolukholo Mlibali, Sakhumzi Mlungwana, Jonas Mmachele, Mashatole Mmateka, Molebatsi Mmokwa, Thembisa Mmutlane, Zanele Olive Mndebele, Nonhlanhla Mngomezulu, Noluthando Millicent Mnguni, Pumza Mngunyana, Nomxolisi Mngunyana, Ntombebongo Mngxekeza, Zenzele Mnisi, Hlengiwe Precious Mnqayi, Phumzile Mnqayi, Thabiso Mntungwa, Siya Mnyaka, Ntombikayise Mnyakeni, Vuyani Mnyamana, Nomzingisi Mnyipika, Koena Moabelo, Mmakgoshi Alseria Moatshe, Jennifer Mochaki-Senoge, Sharon Moche, Tebello Mocwagae, Koeikantse Modibane, Tebogo godfrey Modimoeng, Obakeng Modisa, Itumeleng Modisane, Olebogeng Modise, Makaepeaa Flovia Modjadji, Sharon Modupe, Maja Moeketsi, Ntswaki Moeketsi, Kereditse Kingsley Moeng, Naledi Nthabiseng Mofamere, Samuel Mofokeng, Thabo Mofokeng, Jonas 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Ndaba, Siziwe Ndawonde, Ziphozihle Ndevu, Nonhlanhla Faith Ndhlovu, Simphiwe Ndima, Sindisiwe Ndlela, Thobsile P Ndlela, Nobuhle Ndlovu, Nwabisa Ndlovu, Virginia Dipuo Ndlovu, Sombekhaya Ndlumbini, Khululiwe Nduli, Priscilla Nontokozo Nduli, Michael Ndwambi, Jeremy Nel, Rina Nel, Lizelle Nel, Ntsundeni florah Nemanashi, Usinkhangwe Nyaphophi Nemudivhiso, Joyce Nemutavhanani Nemutavhanani, Jabu Nene, Xolani Nene, David Netshilonga, Rendani Netsianda, Charmaine Newton, Vuyo Leroy Ngalo, Ncumisa Ngani, Thabisa Monica Ngcakaza, Thamela Ngcobo, Trulove Nonhlanhla Ngcobo, Richards Ngcobo, Gcinile Ngcobo, Guguletu Ngcobo, Thozama Ngetu, Pinkie Ngewu, Tshepo Ngobeni, Providence Ngobeni, Khanyisile Ngobeni, Prudence Ngobeni, Thembisile Ngobese, Tracy Ngomane, Nolusindiso Ngondo, Nokukhanya Ngubane, Sithembiso Ngubane, Ntombizodwa Praxedise Nguse, Tholakele Ngwane, Elizabeth Ngwasheng, Siphamandla Ngwenya, Gugu Ngwenya, Nomthandazo Ngwenya, Themba Ngwenya, Eva Ngwenya, Zintlanu Ngxola, 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Steven, AW Stevens, Vincent Stevens, Dewald Steyn, Bianca Steyn, Pat Stocks, Henk Stolk, Alida Stoltz, Renate Strehlau, Anneke Stroebel, Loraine Strydom, Jean-Marie Strydom, Anton Strydom, Ursula Strydom, Midhu Sunnyraj, Nwabisa Swana, Winnie Swanepoel, Suzan Swanepoel, Elsie Swartbooi, Estley Swartz Swartz, Casandra Syce, Shihambi T E, Joyce Tabane, N E Tabane, Mrs Tawana, Ntene Tebello, Siphosetu Wiseman Tembe, Samantha Terblanche, Ntombifuthi Thabede, Nkhumeleni Thabelo, Sibusiso Thabethe, Lekhanya Thabo George, Keorapetse Thare, Makofane Thebogo, Lerato Thekiso, Lloyd Theko, Celimphilo Zandi Themba, Danie Theron, Henda Theron, Ilze Theron, Thandiwe Thingathinga, M M Thlabadira, Dikeledi Thoka, Zanele Thokwana, Gustav Thom, Mamphot Joel Thubakgale, Theodora Thwala, P Thys, Monethi Tieho, Matodzi Timothy, Ndlovu Tintswalo, Babalwa Tivana, Molefi Tladi, Bongiwe Tokota, Simthandile Toni, Ariel Torres, Mande Toubkin, Marinda Tsatsi, Khanyisile Tshabalala, Nozibele Tshamase, Gontse Tshefu, Makgoga Tshegofatjo, Given Tshikomba, Thapelo Tshilo, Lerato Tshira, S T Tshirado, Maipfi Tshisikule, G Tsoke, N TSOKE, Alatha Tsoko, Mosele Tsotetsi, Sandeva Tsubella, Noxolo Tuswa, Maipato Tutse, Nomayenzeke Tutu, Sphephelo Twala, Nhlanhla Twala, Simphiwe Twala, John Ubisi, Tefo Unathi, A Van Aswegen, Marietjie van der Merwe, Trudie van der Merwe, Patience van der Plank, Elmarie van der Spuy, Linda Van Der Westhuizen, Adele Van Der Westhuizen, Talana van der Westhuizen, Mene van der Westhuyzen, Thea Van Dyk, Ingrid van Heerden, Ryno van Jaarsveld, M Van Lill, Heidi van Niekerk, Ben van Niekerk, Amanda van Rensburg, Judy van Schallwyk, Zeitschke Yarnrich Van Sensie, Magda van Vuuren, Cloete van Vuuren, Olga Funiswa Vandu, Mandisa Vane, Lucia VanZyl, Ebrahim Variava, Mariam Veerus, Nokhwezi Velapi, Sebina Veleko, Z Velezantsi, Retha Venter, Corlia Vergottini, Inga Vermeulen, Liabara Lufuluvhi Vidah, Bongani Vilakazi, Treasure N Vilakazi, Mbalenhle Precious Vilakazi, Karen Viljoen, Werner Viljoen, Zuretha Volschenk, Angelo Vos, Matlala V V, Jacques Walters, Kate Webb, John Welsh, D Wessels, Judy Wheller, Fundile White, Priscilla White, Carmen Whyte, Ansie Willemse, Sape William, Daniel Williams, Kamielah Williams, Mercia Williams, Anne Williamson, Cherade Wilson, Boipelo Wolff, Michelle Wray, Ntombizonke B Xaba, Thabang Jabulani Xaba, Thanks Xiniwe, Mtshali Xoliswa, Funokwakhe Xulu, Gibson Xulu, Sandlakazi Yam, NM Zakhura, Mashela Zareloa, Sive Zinto, Dyibeni Zinziswa, Lulamile Ziselo, Zakhele Zitha, Emmanuel Zitha, Anele Zokufa, Innocent Zondi, Sikhumbuzo Bernard Zondi, Sbuyi Zondi, Thulani Zondi, Wandiswa Zongola, Liesl Zühlke, Zandile Zulu, Lungelo Zulu, Thandeka Zulu, Slindili Zulu, Nkosinathi Zulu, Angel Zuma, Precious Zungu, Pamela Zungu, Melusi Zungu, Priscilla Zungu, Bongo Lihle Zwakala, Antonia Zwane, Promise Zwane, Muziwendoda Zwane, Hlengiwe Priscila Zwane, and Nomgcobo Zwane
Subjects: Male, Pediatrics, medicine.medical_specialty, Tuberculosis, Epidemiology, Immunology, HIV Infections, Comorbidity, Disease, Cohort Studies, South Africa, Risk Factors, Virology, Diabetes mellitus, Prevalence, Humans, Medicine, Hospital Mortality, Asthma, SARS-CoV-2, business.industry, Public health, COVID-19, Articles, Odds ratio, medicine.disease, Infectious Diseases, Anti-Retroviral Agents, Female, business, Cohort study
Abstract: Summary Background The interaction between COVID-19, non-communicable diseases, and chronic infectious diseases such as HIV and tuberculosis is unclear, particularly in low-income and middle-income countries in Africa. South Africa has a national HIV prevalence of 19% among people aged 15–49 years and a tuberculosis prevalence of 0·7% in people of all ages. Using a nationally representative hospital surveillance system in South Africa, we aimed to investigate the factors associated with in-hospital mortality among patients with COVID-19. Methods In this cohort study, we used data submitted to DATCOV, a national active hospital surveillance system for COVID-19 hospital admissions, for patients admitted to hospital with laboratory-confirmed SARS-CoV-2 infection between March 5, 2020, and March 27, 2021. Age, sex, race or ethnicity, and comorbidities (hypertension, diabetes, chronic cardiac disease, chronic pulmonary disease and asthma, chronic renal disease, malignancy in the past 5 years, HIV, and past and current tuberculosis) were considered as risk factors for COVID-19-related in-hospital mortality. COVID-19 in-hospital mortality, the main outcome, was defined as a death related to COVID-19 that occurred during the hospital stay and excluded deaths that occurred because of other causes or after discharge from hospital; therefore, only patients with a known in-hospital outcome (died or discharged alive) were included. Chained equation multiple imputation was used to account for missing data and random-effects multivariable logistic regression models were used to assess the role of HIV status and underlying comorbidities on COVID-19 in-hospital mortality. Findings Among the 219 265 individuals admitted to hospital with laboratory-confirmed SARS-CoV-2 infection and known in-hospital outcome data, 51 037 (23·3%) died. Most commonly observed comorbidities among individuals with available data were hypertension in 61 098 (37·4%) of 163 350, diabetes in 43 885 (27·4%) of 159 932, and HIV in 13 793 (9·1%) of 151 779. Tuberculosis was reported in 5282 (3·6%) of 146 381 individuals. Increasing age was the strongest predictor of COVID-19 in-hospital mortality. Other factors associated were HIV infection (adjusted odds ratio 1·34, 95% CI 1·27–1·43), past tuberculosis (1·26, 1·15–1·38), current tuberculosis (1·42, 1·22–1·64), and both past and current tuberculosis (1·48, 1·32–1·67) compared with never tuberculosis, as well as other described risk factors for COVID-19, such as male sex; non-White race; underlying hypertension, diabetes, chronic cardiac disease, chronic renal disease, and malignancy in the past 5 years; and treatment in the public health sector. After adjusting for other factors, people with HIV not on antiretroviral therapy (ART; adjusted odds ratio 1·45, 95% CI 1·22–1·72) were more likely to die in hospital than were people with HIV on ART. Among people with HIV, the prevalence of other comorbidities was 29·2% compared with 30·8% among HIV-uninfected individuals. Increasing number of comorbidities was associated with increased COVID-19 in-hospital mortality risk in both people with HIV and HIV-uninfected individuals. Interpretation Individuals identified as being at high risk of COVID-19 in-hospital mortality (older individuals and those with chronic comorbidities and people with HIV, particularly those not on ART) would benefit from COVID-19 prevention programmes such as vaccine prioritisation as well as early referral and treatment. Funding South African National Government.
Published: 2021
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4. Molecular IgE sensitization profiles of urban and rural children in South Africa

Author: Jordache Ramjith, Nonhlanhla Lunjani, Wisdom Basera, Ben Gaunt, Irene Mittermann, Carol Hlela, Avumile Mankahla, Michael Levin, Heidi E. Facey‐Thomas, Sabine Flicker, Maresa Botha, Rudolf Valenta, Pia Gattinger, Claudia L. Gray, Jon Genuneit, and Sheron Dzoro
Subjects: Allergy, Immunology, Immunoglobulin E, medicine.disease_cause, Dermatitis, Atopic, Mice, South Africa, 03 medical and health sciences, 0302 clinical medicine, Allergen, Animals, Humans, Immunology and Allergy, Medicine, 030212 general & internal medicine, Child, Ige sensitization, Sensitization, House dust mite, biology, business.industry, Atopic dermatitis, Allergens, biology.organism_classification, medicine.disease, Women's cancers Radboud Institute for Health Sciences [Radboudumc 17], medicine.anatomical_structure, 030228 respiratory system, Pediatrics, Perinatology and Child Health, biology.protein, Rural area, business, Food Hypersensitivity
Abstract: Item does not contain fulltext BACKGROUND: Allergens can act as disease-triggering factors in atopic dermatitis (AD) patients. The aim of the study was to elucidate the molecular IgE sensitization profile in children with and without AD living in urban and rural areas of South Africa. METHODS: Specific IgE reactivity was assessed in 166 Black South African children aged 9-38 months using a comprehensive panel of microarrayed allergens. According to clinical characterization children fell in four groups, urban AD cases (n = 32), urban controls (non-AD, n = 40), rural cases (n = 49) and rural controls (non-AD, n = 45). RESULTS: IgE reactivity to at least one of the allergens was detected in 94% of urban and 86% of rural AD children. House dust mite (HDM; 81% urban, 74% rural AD) and animal-derived allergens (50% urban, 31% rural AD) were the most frequently recognized respiratory allergens, whereas IgE to pollen allergens was almost absent. Urban AD children showed significantly higher frequency of IgE reactivity (50%) to mouse lipocalin, Mus m 1, than rural AD children (12%). The most frequently recognized food allergens were from egg (63% urban, 43% rural AD), peanut (31% vs 41%), and soybean (22% vs 27%), whereas milk sensitization was rare. α-gal-specific IgE almost exclusively occurred in rural children (AD: 14%, non-AD: 49%). CONCLUSION: Molecular allergy diagnosis detects frequent IgE sensitization to HDM, animal but not pollen allergens and to egg, peanut, and soy, but not milk allergens in African AD children. Urban AD children reacted more often to Mus m 1, whereas α-gal sensitization is more common in rural children likely due to parasite exposure.
Published: 2020
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5. Cryptic pathogen-sugar interactions revealed by universal saturation transfer analysis

Author: Sergio Daga, Alessandra Renieri, Philip N. Ward, Simone Furini, Lachlan P. Deimel, Raymond J. Owens, Alexandre M. J. J. Bonvin, Francesca Fava, Jiwei Liu, Georgios Papadakis, Kapil Gupta, Marco Gori, Quentin J. Sattentau, Margherita Baldassarri, Aziz Khan, Andrew Baldwin, Elisa Benetti, Gen-Covid Multicenter Study, Ben Gaunt, Christiane Schaffitzel, Yun Yang, Jiandong Huo, Maud Dumoux, Charles J. Buchanan, Benjamin G. Davis, Andrew M. Giltrap, Virginia Casablancas-Antras, Panagiotis I. Koukos, Peter J. Harrison, Annarita Giliberti, Abirami Lakshminarayanan, Xiaochao Xue, Nicola Picchiotti, Chiara Fallerini, Timothy D. W. Claridge, Imre Berger, Audrey Le Bas, and James H. Naismith
Subjects: chemistry.chemical_classification, Glycan, Glycosylation, biology, Computational biology, Ligand (biochemistry), Sialic acid, A-site, chemistry.chemical_compound, chemistry, biology.protein, Binding site, Glycoprotein, Function (biology)
Abstract: Many host pathogen interactions such as human viruses (including non-SARS-coronaviruses) rely on attachment to host cell-surface glycans. There are conflicting reports about whether the Spike protein of SARS-CoV-2 binds to sialic acid commonly found on host cell-surface N-linked glycans. In the absence of a biochemical assay, the ability to analyze the binding of glycans to heavily- modified proteins and resolve this issue is limited. Classical Saturation Transfer Difference (STD) NMR can be confounded by overlapping sugar resonances that compound with known experimental constraints. Here we present ‘universal saturation transfer analysis’ (uSTA), an NMR method that builds on existing approaches to provide a general and automated workflow for studying protein-ligand interactions. uSTA reveals that B-origin-lineage-SARS-CoV-2 spike trimer binds sialoside sugars in an ‘end on’ manner and modelling guided by uSTA localises binding to the spike N-terminal domain (NTD). The sialylated-polylactosamine motif is found on tetraantennary human N-linked-glycoproteins in deeper lung and may have played a role in zoonosis. Provocatively, sialic acid binding is abolished by mutations in some subsequent SARS- CoV-2 variants-of-concern. A very high resolution cryo-EM structure confirms the NTD location and ‘end on’ mode; it rationalises the effect of NTD mutations and the structure-activity relationship of sialic acid analogues. uSTA is demonstrated to be a robust, rapid and quantitative tool for analysis of binding, even in the most demanding systems.Extended AbstractThe surface proteins found on both pathogens and host cells mediate entry (and exit) and influence disease progression and transmission. Both types can bear host-generated post- translational modifications such as glycosylation that are essential for function but can confound biophysical methods used for dissecting key interactions. Several human viruses (including non- SARS-coronaviruses) attach to host cell-surfaceN-linked glycans that include forms of sialic acid (sialosides). There remains, however, conflicting evidence as to if or how SARS-associated coronaviruses might use such a mechanism. Here, we demonstrate quantitative extension of ‘saturation transfer’ protein NMR methods to a complete mathematical model of the magnetization transfer caused by interactions between protein and ligand. The method couples objective resonance-identification via a deconvolution algorithm with Bloch-McConnell analysis to enable a structural, kinetic and thermodynamic analysis of ligand binding beyond previously-perceived limits of exchange rates, concentration or system. Using an automated and openly available workflow this ‘universal saturation transfer’ analysis (uSTA) can be readily-applied in a range of even heavily-modified systems in a general manner to now obtain quantitative binding interaction parameters (KD, kEx). uSTA proved critical in mapping direct interactions between natural sialoside sugar ligands and relevant virus-surface attachment glycoproteins – SARS-CoV-2-spike and influenza-H1N1-haemagglutinin variants – by quantitating ligand signal in spectral regions otherwise occluded by resonances from mobile protein glycans (that also include sialosides). In B- origin-lineage-SARS-CoV-2 spike trimer ‘end on’-binding to sialoside sugars was revealed contrasting with ‘extended surface’-binding for heparin sugar ligands; uSTA-derived constraints used in structural modelling suggested sialoside-glycan binding sites in a beta-sheet-rich region of spike N-terminal domain (NTD). Consistent with this, uSTA-glycan binding was minimally- perturbed by antibodies that neutralize the ACE2-binding domain (RBD) but strongly disrupted in spike from the B1.1.7/alpha and B1.351/beta variants-of-concern, which possess hotspot mutations in the NTD. Sialoside binding in B-origin-lineage-NTD was unequivocally pinpointed by cryo-EM to a site that is created from residues that are notably deleted in variants (e.g. H69,V70,Y145 in alpha). An analysis of beneficial genetic variances in cohorts of patients from early 2020 suggests a model in which this site in the NTD of B-origin-lineage-SARS-CoV-2 (but not in alpha/beta-variants) may have exploited a specific sialylated-polylactosamine motif found on tetraantennary humanN-linked-glycoproteins in deeper lung. Together these confirm a novel binding mode mediated by the unusual NTD of SARS-CoV-2 and suggest how it may drive virulence and/or zoonosis via modulation of glycan attachment. Since cell-surface glycans are widely relevant to biology and pathology, uSTA can now provide ready, quantitative, widespread analysis of complex, host-derived and post-translationally modified proteins with putative ligands relevant to disease even in previously confounding complex systems.
Published: 2021
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6. Association of gut microbiota and environment in children with AD, comparison of three cohorts of children

Author: Carol Hlela, Alan L. Landay, Phillip A. Engen, Kylie N. Jungles, Erica Sodergren, Maresa Botha, Alexandra Watkins, Wisdom Basera, Heidi E. Facey‐Thomas, George M. Weinstock, Michael Levin, Avumile Mankahla, Victoria Teixeira-Reis, Claudia L. Gray, Heather E. Rasmussen, Thi Dong Binh Tran, Mahboobeh Mahdavinia, Lelani Hobane, Ali Keshavarzian, Nonhlanhla Lunjani, and Ben Gaunt
Subjects: Skin barrier, medicine.medical_specialty, biology, business.industry, Immunology, Infant, Atopic dermatitis, Gut flora, medicine.disease, biology.organism_classification, Gut microbiome, Dermatitis, Atopic, Gastrointestinal Microbiome, body regions, Lifestyle factors, Food allergy, Epidemiology, medicine, Immunology and Allergy, Humans, business, Child, Food Hypersensitivity, Asthma
Abstract: Atopic dermatitis (AD) is one of the most common diseases in pediatric patients, with over 12.5% of US children diagnosed with the condition.1 Previous studies have shown that the impaired skin barrier caused by AD leads to the development of other atopic conditions later in life.2 The rate of AD among black children in Africa is similar to reported rates among African Americans (AA), while the rate of other atopic diseases such as asthma and food allergy (FA) in black children living in African countries are lower compared to most western populations. 3 The lower rate of asthma and FA, despite similar AD rates among rural African children, calls into question the critical role environment plays in protection against the progression of the atopic march. Previous evidence suggests gut microbiota differences are linked to the initiation and progression of atopic diseases.4 It is possible that changes in the environment including diet, exposure to microbes, and lifestyle factors result in alteration in the gut microbiome and contribute to the risk of atopic diseases. In certain African countries, many individuals still live in completely natural settings. Studying these populations provides the opportunity to evaluate the protective role of environment and lifestyle on gut microbiota and atopic diseases.
Published: 2021

7. House dust microbiota and atopic dermatitis; effect of urbanization

Author: Avumile Mankahla, Ali Keshavarzian, Nonhlanhla Lunjani, Michael Levin, Alexandra Watkins, Alan L. Landay, Phillip A. Engen, Carol Hlela, Ben Gaunt, Lelani Hobane, Claudia L. Gray, Maresa Botha, Heidi E. Facey‐Thomas, Mahboobeh Mahdavinia, Wisdom Basera, Donyea Moore, and Leah R. Greenfield
Subjects: Immunology, Dermatitis, Atopic, Atopy, 03 medical and health sciences, 0302 clinical medicine, Environmental health, Urbanization, medicine, Immunology and Allergy, Humans, 030212 general & internal medicine, Microbiome, Risk factor, Child, Home environment, business.industry, Microbiota, Lachnospiraceae, Infant, Dust, Atopic dermatitis, medicine.disease, body regions, 030228 respiratory system, Case-Control Studies, Child, Preschool, Pediatrics, Perinatology and Child Health, business, Ruminococcaceae
Abstract: Background Previous studies have shown that a child's risk of developing atopic disease is impacted by both genetic and environmental factors. Because small children spend the majority of their time in their homes, exposure to microbial factors in their home environment may be protective or risk factors for development of atopic diseases, such as atopic dermatitis. Methods Dust samples from the homes of 86 Black South African children 12 to 36 months old were collected for analysis of the bacterial microbiome. This case-control study design included children with and without atopic dermatitis from rural and urban environments. Results Significant differences in bacterial composition and diversity were found when comparing children with and without atopic dermatitis. Furthermore, house dust microbiota was significantly different in rural and urban areas. Differences were best accounted for by higher relative abundance of Ruminococcaceae, Lachnospiraceae, and Bacteroidaceae families in rural compared with urban houses. Levels of Ruminococcaceae were also found to be significantly depleted in the house dust of rural children with atopic dermatitis as compared to control children. Conclusions House dust composition may be an important risk factor for the development of atopic disease, and this association may be driven in part by the gut microbiome. Low levels of the Ruminococcaceae family from Clostridia class in particular may explain the association between urban living and atopy. However, further research is needed to elucidate these links.
Published: 2021

8. Associations between Environmental dust composition and Atopic Dermatitis in urban and rural settings

Author: Maresa Botha, Nonhlanhla Lunjani, Carol Hlela, Jordache Ramjith, Wisdom Basera, Avumile Mankahla, Ben Gaunt, Jon Genuneit, Thulja Trikamjee, Frank Kirstein, Heidi E. Facey‐Thomas, Sabelo Hadebe, Claudia L. Gray, and Michael Levin
Subjects: Rural Population, Immunology, Eczema, medicine.disease_cause, Dermatitis, Atopic, 03 medical and health sciences, Mice, 0302 clinical medicine, Allergen, Dogs, Urbanization, Environmental health, medicine, Immunology and Allergy, Animals, Humans, 030212 general & internal medicine, Antigens, Dermatophagoides, House dust mite, biology, business.industry, House dust mite allergen, Aeroallergen, Dust, Atopic dermatitis, Environmental Exposure, Allergens, medicine.disease, biology.organism_classification, Women's cancers Radboud Institute for Health Sciences [Radboudumc 17], respiratory tract diseases, Pet ownership, 030228 respiratory system, Pediatrics, Perinatology and Child Health, Cats, ALLERGEN EXPOSURE, business
Abstract: Item does not contain fulltext BACKGROUND: Environmental exposures are involved in the pathogenesis of the allergic phenotype and in determining which individual triggers a person becomes sensitized to. Atopic dermatitis (AD) may modulate these effects through increased penetration through the skin modifying the immune system and AD may be triggered or intensified by environmental exposures. These exposures and immune-modulating factors may differ in urban and rural environments. OBJECTIVES: To compare house dust composition in urban and rural settings and correlate them with AD outcomes. METHODS: Dust samples were collected from the beds of 156 children aged 6 months to 3 years. 42% of participants had atopic dermatitis. Samples were analyzed for bacterial endotoxin, fungal (β-1,3-glucan) levels, and house dust mite, cockroach, dog, cat, mouse, and peanut allergen. Exposures were compared in urban and rural environments and in participants with and without AD. RESULTS: Endotoxin but not fungal β-glucan exposure is higher in the environment of healthy controls than children with AD in both urban and rural settings. House dust mite allergen exposure is high in urban and rural settings with Dermatophagoides detected in 100% of samples. Cat and dog allergen exposure mirrors pet ownership patterns which differ slightly between groups and environments. Mouse allergen exposure is higher in urban homes. CONCLUSION: Environmental endotoxin may be protective against AD in both urban and rural settings. There are marked differences in allergen exposure in urban and rural settings, but these are unlikely to be important protective or risk factors.
Published: 2021
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9. Author response for 'Molecular IgE‐sensitisation profiles of urban and rural children in South Africa'

Author: Avumile Mankahla, Michael Levin, Claudia L. Gray, Maresa Botha, Heidi E. Facey‐Thomas, Jordache Ramjith, Wisdom Basera, Carol Hlela, Pia Gattinger, Sheron Dzoro, Ben Gaunt, Sabine Flicker, Nonhlanhla Lunjani, Rudolf Valenta, Jon Genuneit, and Irene Mittermann
Subjects: Geography, biology, Environmental health, biology.protein, Immunoglobulin E
Published: 2020
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10. Association of HIV infection and antiretroviral therapy with the occurrence of an unfavorable TB treatment outcome in a rural district hospital in Eastern Cape, South Africa: A retrospective cohort study

Author: Brittney J. van de Water, Isabel Fulcher, Suretha Cilliers, Nadishani Meyer, Michael Wilson, Catherine Young, Ben Gaunt, and Karl le Roux
Subjects: Adult, South Africa, Treatment Outcome, Multidisciplinary, HIV-2, Antitubercular Agents, Humans, Tuberculosis, HIV Infections, Hospitals, District, Retrospective Studies
Abstract: Background Our objective was to assess differences in TB treatment outcomes between individuals who were HIV negative, HIV positive on anti-retroviral treatment (ART) and HIV positive not on ART, at TB treatment initiation at a rural district hospital in Eastern Cape, South Africa. Methods This was a retrospective cohort study of individuals diagnosed with TB between January 2017 and April 2020 at a district hospital. Adults 15 years and over with reported HIV status and treatment outcome were included (N = 711). A categorical outcome with three levels was considered: unfavorable, down referral, and success. We report descriptive statistics for the association between HIV and ART status and treatment outcome using Chi-square and Fisher’s exact tests. A multinomial baseline logit model was used to estimate odds ratios for treatment outcomes. Results Overall, 59% of included patients were HIV positive with 75% on ART. Eighty-eight patients 12% had an unfavorable outcome. Half of all patients were down referred with an additional 37% having a successful outcome. Individuals without HIV were more likely to be down referred (versus unfavorable) compared to individuals with untreated HIV (2.90 OR, 1.36, 6.17 95% CI). There was a greater likelihood for individuals without HIV having a successful TB treatment outcome compared to individuals with untreated HIV (4.98 OR, 2.07, 11.25 95% CI). Conclusion The majority of individuals had positive TB treatment outcomes (down referred or success). However, people without HIV had nearly five times greater odds of having successful outcomes than those with untreated HIV.
Published: 2022
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11. Nutrition and allergic diseases in urban and rural communities from the South African Food Allergy cohort

Author: Heidi E. Facey‐Thomas, Maresa Botha, Wisdom Basera, Claudia L. Gray, Wanjiku Kiragu, Alexandra Watkins, Ben Gaunt, Jon Genuneit, Jordache Ramjith, and Michael Levin
Subjects: Male, Rural Population, Allergy, Urban Population, Immunology, Nutritional Status, medicine.disease_cause, Cohort Studies, Atopy, South Africa, 03 medical and health sciences, 0302 clinical medicine, Food allergy, Environmental health, medicine, Humans, Immunology and Allergy, Obesity, 030212 general & internal medicine, Skin Tests, business.industry, Infant, Aeroallergen, Atopic dermatitis, Allergens, medicine.disease, Asthma, Women's cancers Radboud Institute for Health Sciences [Radboudumc 17], Breast Feeding, 030228 respiratory system, Child, Preschool, Pediatrics, Perinatology and Child Health, Cohort, Female, Immunization, Rural area, business, Food Hypersensitivity, Cohort study
Abstract: Contains fulltext : 208818.pdf (Publisher’s version ) (Closed access) This study describes and compares allergic diseases and sensitization in urban and rural children in the SAFFA study cohort as well as infant feeding patterns and nutritional status. We assessed the relationship between nutritional status, breastfeeding, complementary feeding patterns, and atopic diseases including aeroallergen and food allergen sensitization, self-reported atopic dermatitis, allergic rhinitis, asthma, and challenge-proven food allergy (FA). METHODOLOGY: A total of 1185 urban and 398 rural toddlers aged 12-36 months were screened for food sensitization (FS) and FA using skin prick testing and oral food challenges. Of these, 535 and 347, respectively, were additionally screened for aeroallergen sensitization. Information was collected on infant feeding practices, and anthropometric measurements and clinical signs for atopy were documented. RESULTS: Markedly higher rates of allergy (asthma 9.0% vs 1.0%, eczema 25.6% vs 2.0%, rhinitis 25.3% vs 3.3%, and FA 2.5% vs 0.5%) exist in urban vs rural children. 13.1% unselected urban South African children were sensitized to aeroallergens compared to 3.8% of their rural counterparts and 9.0% to any food compared to 0.5%. Exclusive breastfeeding duration was longer, and there was a later introduction of allergenic foods in rural communities. Obesity rates were similar between the two groups, but rural children were more likely to be stunted. Being overweight was associated with asthma in urban but not rural settings. In the urban cohort, children with FS and allergy were thinner than their peers. CONCLUSION: Allergy and sensitization rates are significantly higher in unselected urban South African toddlers than their rural counterparts. Risk and protective factors for allergy and atopy may differ between urban and rural settings.
Published: 2019
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12. Environmental factors associated with allergy in urban and rural children from the South African Food Allergy (SAFFA) cohort

Author: Alexandra Watkins, Ben Gaunt, Heidi E. Facey‐Thomas, Wisdom Basera, Michael Levin, Jon Genuneit, Maresa Botha, Claudia L. Gray, Jordache Ramjith, and Wanjiku Kiragu
Subjects: Male, Rural Population, Allergy, Urban Population, Immunology, Protective factor, medicine.disease_cause, Dermatitis, Atopic, South Africa, All institutes and research themes of the Radboud University Medical Center, Food allergy, Environmental health, Immunology and Allergy, Medicine, Humans, Asthma, Oral food challenge, business.industry, Infant, Aeroallergen, Atopic dermatitis, Environmental Exposure, Delivery mode, medicine.disease, Women's cancers Radboud Institute for Health Sciences [Radboudumc 17], Child, Preschool, Female, business, Food Hypersensitivity
Abstract: Background The prevalence of allergic diseases differs in urban and rural populations. Objective We sought to assess associations between environmental and dietary factors with allergic diseases in urban and rural South African children. Methods Toddlers aged 12 to 36 months were assessed for food allergen and aeroallergen sensitization, atopic dermatitis, allergic rhinitis, asthma, and challenge-proved food allergy. Information was collected on family history of allergic diseases, household size, socioeconomic status, delivery mode, antibiotic and probiotic use, exposure to fermented and unpasteurized milk, antihelminth treatment, sunlight exposure, pet and farm animal exposure, cigarette smoke, and household cooking and heating fuels. Antenatal exposures to pets, livestock, and cigarette smoke were assessed. A subsection completed questions on consumption of fruits and vegetables, fast foods, soft drinks/fruit juices, and fried/microwaved meat. Results Risk and protective factors differed between urban and rural settings. Exposure to farm animals in infants and their mothers during pregnancy was protective against allergic outcomes in the rural population. Consumption of unpasteurized milk is uncommon in this group of rural children and is unlikely to be an important factor in rural protection. In urban children birth by cesarean section is associated with food allergy, and consumption of fermented milk products is associated with reduced asthma and atopic dermatitis. In both cohorts antenatal maternal smoking and environmental smoking exposure were predominantly associated with asthma, and consumption of fast foods and fried meats were associated with allergy. Conclusion In this rural environment exposure to livestock is the strongest protective factor. In urban communities, where animal contact is rare, risk factors include cesarian section, and protective factors include consumption of fermented milk products. Modifiable risk factors urgently require interventions to prevent increasing allergy rates in countries undergoing rapid urbanization.
Published: 2019

13. Atopic Dermatitis severity in patients from African ancestry; results of two cohorts

Author: Kylie N. Jungles, Michael Levin, Maresa Botha, Aame B. Andy-Nweye, Sukruthi Jois, Claudia Gray, Carol Hlela, Avumile Mankahla, Ben Gaunt, Karl le Roux, Nonhlanhla Lunjani, Mary Tobin, and Mahboobeh Mahdavinia
Subjects: Pediatrics, Perinatology and Child Health
Published: 2020
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14. Rural and urban food allergy prevalence from the South African Food Allergy (SAFFA) study

Author: Claudia L. Gray, Ben Gaunt, Alexandra Watkins, Jordache Ramjith, Heidi E. Facey‐Thomas, Michael Levin, Maresa Botha, and Wisdom Basera
Subjects: Male, Rural Population, Allergy, Urban Population, Immunology, Black People, Cohort Studies, 03 medical and health sciences, South Africa, 0302 clinical medicine, All institutes and research themes of the Radboud University Medical Center, Food allergy, Risk Factors, Environmental health, Surveys and Questionnaires, medicine, Prevalence, Immunology and Allergy, Humans, 030212 general & internal medicine, Sensitization, Skin Tests, Oral food challenge, business.industry, Infant, Allergens, Immunoglobulin E, medicine.disease, Women's cancers Radboud Institute for Health Sciences [Radboudumc 17], medicine.anatomical_structure, Cross-Sectional Studies, 030228 respiratory system, Child, Preschool, Cohort, Female, Rural area, business, Food Hypersensitivity, Egg white, Food sensitization
Abstract: Food sensitization and challenge-proved food allergy (FA) have not been compared in urban and rural settings.We sought to determine and compare the prevalence of food sensitization and challenge-proved IgE-mediated FA in urban and rural South African toddlers aged 12 to 36 months.This cross-sectional study of unselected children included 1185 participants in urban Cape Town and 398 in the rural Eastern Cape. All participants completed a questionnaire and underwent skin prick tests (SPTs) to egg, peanut, cow's milk, fish, soya, wheat, and hazelnut. Participants with SPT responses of 1 mm or greater to 1 or more foods and not tolerant on history underwent an open oral food challenge.The prevalence of FA was 2.5% (95% CI, 1.6% to 3.3%) in urban children, most commonly to raw egg white (1.9%), followed by cooked egg (0.8%), peanut (0.8%), cow's milk (0.1%), and fish (0.1%). Urban sensitization (SPT response ≥1 mm) to any food was 11.4% (95% CI, 9.6% to 13.3%) and 9.0% (95% CI, 7.5% to 10.8%) at an SPT response of 3 mm or greater. Sensitization in rural cohorts was significantly lower than in the urban cohort (1-mm SPT response, 4.5% [95% CI, 2.5% to 6.6%]; 3-mm SPT response, 2.8% [95% CI, 1.4% to 4.9%]; P .01). In the rural black African cohort 0.5% (95% CI, 0.1% to 1.8%) of children had food allergy, all to egg. This is significantly lower than the prevalence of the urban cohort overall (2.5%) and urban black African participants (2.9%; 95% CI, 1.5% to 4.3%; P = .006).FA prevalence in Cape Town is comparable with rates in industrialized middle-income countries and is significantly greater than in rural areas. Further analysis will describe and compare environmental exposures and other risk factors in this cohort.
Published: 2018

15. Atopic dermatitis phenotypes in African American and Black South African children

Author: Claudia L. Gray, Ben Gaunt, Mary C. Tobin, Carl le Roux, Kylie N. Jungles, Nonhlanhla Lunjani, Betty Andy-Nweye, Michael Levin, Maresa Botha, Sukruthi Jois, Carol Hlela, Mahboobeh Mahdavinia, and Avumile Mankahla
Subjects: African american, medicine.medical_specialty, business.industry, Immunology, medicine, Immunology and Allergy, Atopic dermatitis, medicine.disease, business, Dermatology
Published: 2018
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16. A rural perspective: four stories

Author: Steve Reid, Jennifer Nash, Ben Gaunt, and Alwyn Rapatsa
Subjects: Male, Career Choice, Primary Health Care, business.industry, Narrative style, General Medicine, Chose, South Africa, Rural management, Nursing, Pedagogy, Medicine, Humans, Female, Rural practice, Rural Health Services, Rural area, business, Competence (human resources), Clinical skills, Career choice
Abstract: These brief reflections from 4 University of Cape Town (UCT) medical graduates who chose to make their careers in rural practice are written in narrative style to try to capture something of the lived experience of working in rural areas. Although still the career choice of a minority of UCT graduates, those who have chosen to practise in rural areas have found a solid base of competence and confidence in their clinical skills, that has enabled them to tackle challenges in areas beyond anything that they or their teachers might have anticipated.
Published: 2012

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16 results on '"Ben Gaunt"'

1. Healthcare worker knowledge, attitudes, and beliefs regarding tuberculosis preventive therapy in rural South Africa: A content analysis using the consolidated framework for implementation research

2. Difference in mortality among individuals admitted to hospital with COVID-19 during the first and second waves in South Africa: a cohort study

3. Risk factors for COVID-19-related in-hospital mortality in a high HIV and tuberculosis prevalence setting in South Africa: a cohort study

4. Molecular IgE sensitization profiles of urban and rural children in South Africa

5. Cryptic pathogen-sugar interactions revealed by universal saturation transfer analysis

6. Association of gut microbiota and environment in children with AD, comparison of three cohorts of children

7. House dust microbiota and atopic dermatitis; effect of urbanization

8. Associations between Environmental dust composition and Atopic Dermatitis in urban and rural settings

9. Author response for 'Molecular IgE‐sensitisation profiles of urban and rural children in South Africa'

10. Association of HIV infection and antiretroviral therapy with the occurrence of an unfavorable TB treatment outcome in a rural district hospital in Eastern Cape, South Africa: A retrospective cohort study

11. Nutrition and allergic diseases in urban and rural communities from the South African Food Allergy cohort

12. Environmental factors associated with allergy in urban and rural children from the South African Food Allergy (SAFFA) cohort

13. Atopic Dermatitis severity in patients from African ancestry; results of two cohorts

14. Rural and urban food allergy prevalence from the South African Food Allergy (SAFFA) study

15. Atopic dermatitis phenotypes in African American and Black South African children

16. A rural perspective: four stories

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16 results on '"Ben Gaunt"'

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