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174 results on '"Smit, Erasmus"'

3. Global phylogeny of Treponema pallidum lineages reveals recent expansion and spread of contemporary syphilis

Author

Beale, Mathew A., Marks, Michael, Cole, Michelle J., Lee, Min-Kuang, Pitt, Rachel, Ruis, Christopher, Balla, Eszter, Crucitti, Tania, Ewens, Michael, Fernández-Naval, Candela, Grankvist, Anna, Guiver, Malcolm, Kenyon, Chris R., Khairullin, Rafil, Kularatne, Ranmini, Arando, Maider, Molini, Barbara J., Obukhov, Andrey, Page, Emma E., Petrovay, Fruzsina, Rietmeijer, Cornelis, Rowley, Dominic, Shokoples, Sandy, Smit, Erasmus, Sweeney, Emma L., Taiaroa, George, Vera, Jaime H., Wennerås, Christine, Whiley, David M., Williamson, Deborah A., Hughes, Gwenda, Naidu, Prenilla, Unemo, Magnus, Krajden, Mel, Lukehart, Sheila A., Morshed, Muhammad G., Fifer, Helen, and Thomson, Nicholas R.

Published
2021
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5. Genomic Evidence of In-Flight Transmission of SARS-CoV-2 Despite Predeparture Testing

Author

Swadi, Tara, Geoghegan, Jemma L., Devine, Tom, McElnay, Caroline, Sherwood, Jillian, Shoemack, Phil, Ren, Xiaoyun, Storey, Matt, Jefferies, Sarah, Smit, Erasmus, Hadfield, James, Kenny, Aoife, Jelley, Lauren, Sporle, Andrew, McNeill, Andrea, Reynolds, G. Edwin, Mouldey, Kip, Lowe, Lindsay, Sonder, Gerard, Drummond, Alexei J., Huang, Sue, Welch, David, Holmes, Edward C., French, Nigel, Simpson, Colin R., and de Ligt, Joep

Subjects
Epidemics -- Distribution -- New Zealand, Airline passengers -- Health aspects, Disease transmission -- Demographic aspects -- Causes of, Company distribution practices, Health
Abstract

In response to the growing international risks associated with importation of coronavirus disease (COVID-19), on March 20, 2020, New Zealand closed its borders to all but New Zealand citizens, permanent [...]

Published
2021
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6. Associations between baseline characteristics, CD4 cell count response and virological failure on first-line efavirenz + tenofovir + emtricitabine for HIV

Author

Stirrup, Oliver T., Sabin, Caroline A., Phillips, Andrew N., Williams, Ian, Churchill, Duncan, Tostevin, Anna, Hill, Teresa, Dunn, David T., Asboe, David, Pozniak, Anton, Cane, Patricia, Chadwick, David, Clark, Duncan, Collins, Simon, Delpech, Valerie, Douthwaite, Samuel, Dunn, David, Fearnhill, Esther, Porter, Kholoud, Stirrup, Oliver, Fraser, Christophe, Geretti, Anna Maria, Gunson, Rory, Hale, Antony, Hué, Stéphane, Lazarus, Linda, Leigh-Brown, Andrew, Mbisa, Tamyo, Mackie, Nicola, Orkin, Chloe, Nastouli, Eleni, Pillay, Deenan, Phillips, Andrew, Sabin, Caroline, Smit, Erasmus, Templeton, Kate, Tilston, Peter, Volz, Erik, Zhang, Hongyi, Fairbrother, Keith, Dawkins, Justine, O’Shea, Siobhan, Mullen, Jane, Cox, Alison, Tandy, Richard, Fawcett, Tracy, Hopkins, Mark, Booth, Clare, Renwick, Lynne, Schmid, Matthias L., Payne, Brendan, Hubb, Jonathan, Dustan, Simon, Kirk, Stuart, Bradley-Stewart, Amanda, Jose, Sophie, Thornton, Alicia, Huntington, Susie, Glabay, Adam, Shidfar, Shaadi, Lynch, Janet, Hand, James, de Souza, Carl, Perry, Nicky, Tilbury, Stuart, Youssef, Elaney, Gazzard, Brian, Nelson, Mark, Mabika, Tracey, Mandalia, Sundhiya, Anderson, Jane, Munshi, Sajid, Post, Frank, Adefisan, Ade, Taylor, Chris, Gleisner, Zachary, Ibrahim, Fowzia, Campbell, Lucy, Baillie, Kirsty, Gilson, Richard, Brima, Nataliya, Ainsworth, Jonathan, Schwenk, Achim, Miller, Sheila, Wood, Chris, Johnson, Margaret, Youle, Mike, Lampe, Fiona, Smith, Colette, Tsintas, Rob, Chaloner, Clinton, Hutchinson, Samantha, Walsh, John, Mackie, Nicky, Winston, Alan, Weber, Jonathan, Ramzan, Farhan, Carder, Mark, Leen, Clifford, Wilson, Alan, Morris, Sheila, Gompels, Mark, Allan, Sue, Palfreeman, Adrian, Lewszuk, Adam, Kegg, Stephen, Faleye, Akin, Ogunbiyi, Victoria, Mitchell, Sue, Hay, Phillip, Kemble, Christian, Martin, Fabiola, Russell-Sharpe, Sarah, Gravely, Janet, Allan, Sris, Harte, Andrew, Tariq, Anjum, Spencer, Hazel, Jones, Ron, Pritchard, Jillian, Cumming, Shirley, Atkinson, Claire, Mital, Dushyant, Edgell, Veronica, Allen, Juli, Ustianowski, Andy, Murphy, Cynthia, Gunder, Ilise, Trevelion, Roy, and Babiker, Abdel

Published
2019
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8. Low frequency of genotypic resistance in HIV-1-infected patients failing an atazanavir-containing regimen: a clinical cohort study

Author

Dolling, David I, Dunn, David T, Sutherland, Katherine A, Pillay, Deenan, Mbisa, Jean L, Parry, Chris M, Post, Frank A, Sabin, Caroline A, Cane, Patricia A, Aitken, Celia, Asboe, David, Webster, Daniel, Cane, Patricia, Castro, Hannah, Dunn, David, Dolling, David, Chadwick, David, Churchill, Duncan, Clark, Duncan, Collins, Simon, Delpech, Valerie, Geretti, Anna Maria, Goldberg, David, Hale, Antony, Hué, Stéphane, Kaye, Steve, Kellam, Paul, Lazarus, Linda, Leigh-Brown, Andrew, Mackie, Nicola, Orkin, Chloe, Rice, Philip, Phillips, Andrew, Sabin, Caroline, Smit, Erasmus, Templeton, Kate, Tilston, Peter, Tong, William, Williams, Ian, Zhang, Hongyi, Zuckerman, Mark, Greatorex, Jane, Wildfire, Adrian, O'Shea, Siobhan, Mullen, Jane, Mbisa, Tamyo, Cox, Alison, Tandy, Richard, Hale, Tony, Fawcett, Tracy, Hopkins, Mark, Ashton, Lynn, Booth, Claire, Garcia-Diaz, Ana, Shepherd, Jill, Schmid, Matthias L, Payne, Brendan, Hay, Phillip, Rice, Phillip, Paynter, Mary, Bibby, David, Kirk, Stuart, MacLean, Alasdair, Gunson, Rory, Coughlin, Kate, Fearnhill, Esther, Fradette, Lorraine, Porter, Kholoud, Ainsworth, Jonathan, Anderson, Jane, Babiker, Abdel, Fisher, Martin, Gazzard, Brian, Gilson, Richard, Gompels, Mark, Hill, Teresa, Johnson, Margaret, Kegg, Stephen, Leen, Clifford, Nelson, Mark, Palfreeman, Adrian, Post, Frank, Sachikonye, Memory, Schwenk, Achim, Walsh, John, Huntington, Susie, Jose, Sophie, Thornton, Alicia, Glabay, Adam, Orkin, C, Garrett, N, Lynch, J, Hand, J, de Souza, C, Fisher, M, Perry, N, Tilbury, S, Gazzard, B, and Nelson, M

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Clinical Sciences, Clinical Trials and Supportive Activities, Infectious Diseases, Antimicrobial Resistance, Clinical Research, Infection, Adult, Anti-HIV Agents, Atazanavir Sulfate, Cohort Studies, Drug Resistance, Viral, Female, HIV Infections, HIV Protease, HIV-1, Humans, Male, Medication Adherence, Middle Aged, Mutation Rate, Mutation, Missense, Oligopeptides, Pyridines, Treatment Failure, United States, UK HIV Drug Resistance Database, UK Collaborative HIV Cohort Study, HIV, drug resistance mutations, naive patients, protease inhibitors, virological failure, Microbiology, Pharmacology and Pharmaceutical Sciences, Clinical sciences, Pharmacology and pharmaceutical sciences
Abstract

ObjectivesTo determine protease mutations that develop at viral failure for protease inhibitor (PI)-naive patients on a regimen containing the PI atazanavir.MethodsResistance tests on patients failing atazanavir, conducted as part of routine clinical care in a multicentre observational study, were randomly matched by subtype to resistance tests from PI-naive controls to account for natural polymorphisms. Mutations from the consensus B sequence across the protease region were analysed for association and defined using the IAS-USA 2011 classification list.ResultsFour hundred and five of 2528 (16%) patients failed therapy containing atazanavir as a first PI over a median (IQR) follow-up of 1.76 (0.84-3.15) years and 322 resistance tests were available for analysis. Recognized major atazanavir mutations were found in six atazanavir-experienced patients (P < 0.001), including I50L and N88S. The minor mutations most strongly associated with atazanavir experience were M36I, M46I, F53L, A71V, V82T and I85V (P < 0.05). Multiple novel mutations, I15S, L19T, K43T, L63P/V, K70Q, V77I and L89I/T/V, were also associated with atazanavir experience.ConclusionsViral failure on atazanavir-containing regimens was not common and major resistance mutations were rare, suggesting that adherence may be a major contributor to viral failure. Novel mutations were described that have not been previously documented.

Published
2013

10. Global epidemiology of drug resistance after failure of WHO recommended first-line regimens for adult HIV-1 infection: a multicentre retrospective cohort study

Author

Gregson, John, Tang, Michele, Ndembi, Nicaise, Hamers, Raph L, Rhee, Soo-Yon, Marconi, Vincent C, Diero, Lameck, Brooks, Katherine A, Theys, Kristof, Rinke de Wit, Tobias, Arruda, Monica, Garcia, Frederico, Monge, Susana, Günthard, Huldrych F, Hoffmann, Christopher J, Kanki, Phyllis J, Kumarasamy, Nagalingeshwaran, Kerschberger, Bernard, Mor, Orna, Charpentier, Charlotte, Todesco, Eva, Rokx, Casper, Gras, Luuk, Helvas, Elias K, Sunpath, Henry, Di Carlo, Domenico, Antinori, Antonio, Andreoni, Massimo, Latini, Alessandra, Mussini, Cristina, Aghokeng, Avelin, Sonnerborg, Anders, Neogi, Ujjwal, Fessel, William J, Agolory, Simon, Yang, Chunfu, Blanco, Jose L, Juma, James M, Smit, Erasmus, Schmidt, Daniel, Watera, Christine, Asio, Juliet, Kurungi, Wilford, Tostevin, Anna, El-Hay, Tal, Clumeck, Nathan, Goedhals, Dominique, Van Vuuren, Cloete, Bester, Philip A, Sabin, Caroline, Mukui, Irene, Santoro, MARIA M, Perno, Carlo F, Hunt, Gillian, Morris, Lynn, Camacho, Ricardo, De Oliveira, Tulio, Pillay, Deenan, Schulter, Eugene, Murakami-Ogasawara, Akio, Reyes-Terán, Gustavo, Romero, Karla, Avila-Rios, Santiago, Sirivichayakul, Sunee, Ruxrungtham, Kiat, Mekprasan, Suwanna, Dunn, David, Kaleebu, Pontiano, Raizes, Elliot, Kantor, Rami, Shafer, Robert W, and Gupta, Ravindra K

Published
2016
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13. Using whole-genome sequencing in the rapid response to SARS-CoV-2 in Aotearoa New Zealand

Author

White, Rhys T, Jelley, Lauren, Douglas, Jordan, Xiaoyun Ren, Winter, David, Genomics Team, Covid-19 Wgs, Bunce, Michael, Carr, Sam, Mcneill, Andrea, Q Sue Huang, Swadi, Tara, Devine, Tom, Mcelnay, Caroline, Sherwood, Jillian, Shoemack, Phil, Fox-Lewis, Andrew, Williamson, Felicity, Harrower, Jay, Storey, Matt, Jefferies, Sarah, Smit, Erasmus, Hadfield, James, Kenny, Aoife, Sporle, Andrew, G Edwin Reynolds, Mouldey, Kip, Lowe, Lindsay, Sonder, Gerard, Drummond, Alexei J, Welch, David, Holmes, Edward C, French, Nigel, Simpson, Colin R, De Ligt, Joep, and Geoghegan, Jemma

Published
2023
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14. Investigating the role of whole genome sequencing in syphilis epidemiology: an English case study

Author

Beale, Mathew A., primary, Thorn, Louise, additional, Cole, Michelle J., additional, Pitt, Rachel, additional, Charles, Hannah, additional, Ewens, Michael, additional, French, Patrick, additional, Guiver, Malcolm, additional, Page, Emma E., additional, Smit, Erasmus, additional, Vera, Jaime H., additional, Sinka, Katy, additional, Hughes, Gwenda, additional, Marks, Michael, additional, Fifer, Helen, additional, and Thomson, Nicholas R., additional

Published
2022
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18. A comparison of the performance of saliva and nasopharyngeal nucleic acid amplification testing for the detection of SARS-CoV-2 in New Zealand

Author

Ussher, James, primary, McAuliffe, Gary, additional, Blackmore, Timothy, additional, Elvy, Juliet, additional, Fox-Lewis, Shivani, additional, Gilpin, Brent, additional, Grant, Jenny, additional, Nagappan, Radhika, additional, Smit, Erasmus, additional, Tan, Chor, additional, and Tiongko, Fernalynn, additional

Published
2022
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19. Real-time, portable genome sequencing for Ebola surveillance

Author

Quick, Joshua, Loman, Nicholas J., Duraffour, Sophie, Simpson, Jared T., Severi, Ettore, Cowley, Lauren, Bore, Joseph Akoi, Koundouno, Raymond, Dudas, Gytis, Mikhail, Amy, Ouédraogo, Nobila, Afrough, Babak, Bah, Amadou, Baum, Jonathan H. J., Becker-Ziaja, Beate, Boettcher, Jan Peter, Cabeza-Cabrerizo, Mar, Camino-Sánchez, Álvaro, Carter, Lisa L., Doerrbecker, Juliane, Enkirch, Theresa, Dorival, Isabel García-, Hetzelt, Nicole, Hinzmann, Julia, Holm, Tobias, Kafetzopoulou, Liana Eleni, Koropogui, Michel, Kosgey, Abigael, Kuisma, Eeva, Logue, Christopher H., Mazzarelli, Antonio, Meisel, Sarah, Mertens, Marc, Michel, Janine, Ngabo, Didier, Nitzsche, Katja, Pallasch, Elisa, Patrono, Livia Victoria, Portmann, Jasmine, Repits, Johanna Gabriella, Rickett, Natasha Y., Sachse, Andreas, Singethan, Katrin, Vitoriano, Inês, Yemanaberhan, Rahel L., Zekeng, Elsa G., Racine, Trina, Bello, Alexander, Sall, Amadou Alpha, Faye, Ousmane, Faye, Oumar, Magassouba, NʼFaly, Williams, Cecelia V., Amburgey, Victoria, Winona, Linda, Davis, Emily, Gerlach, Jon, Washington, Frank, Monteil, Vanessa, Jourdain, Marine, Bererd, Marion, Camara, Alimou, Somlare, Hermann, Camara, Abdoulaye, Gerard, Marianne, Bado, Guillaume, Baillet, Bernard, Delaune, Déborah, Nebie, Koumpingnin Yacouba, Diarra, Abdoulaye, Savane, Yacouba, Pallawo, Raymond Bernard, Gutierrez, Giovanna Jaramillo, Milhano, Natacha, Roger, Isabelle, Williams, Christopher J., Yattara, Facinet, Lewandowski, Kuiama, Taylor, James, Rachwal, Phillip, Turner, Daniel J., Pollakis, Georgios, Hiscox, Julian A., Matthews, David A., Shea, Matthew K. Oʼ, Johnston, Andrew McD., Wilson, Duncan, Hutley, Emma, Smit, Erasmus, Di Caro, Antonino, Wölfel, Roman, Stoecker, Kilian, Fleischmann, Erna, Gabriel, Martin, Weller, Simon A., Koivogui, Lamine, Diallo, Boubacar, Keïta, Sakoba, Rambaut, Andrew, Formenty, Pierre, Günther, Stephan, and Carroll, Miles W.

Published
2016
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21. Detection of drug resistance mutations at low plasma HIV-1 RNA load in a European multicentre cohort study

Author

Prosperi, Mattia C. F., Mackie, Nicola, Di Giambenedetto, Simona, Zazzi, Maurizio, Camacho, Ricardo, Fanti, Iuri, Torti, Carlo, Sönnerborg, Anders, Kaiser, Rolf, Codoñer, Francisco M., Van Laethem, Kristel, Bansi, Loveleen, van de Vijver, David A. M. C., Geretti, Anna Maria, De Luca, Andrea, Giacometti, Andrea, Butini, Luca, del Gobbo, Romana, Menzo, Stefano, Tacconi, Danilo, Corbelli, Giovanni, Zanussi, Stefania, Monno, Laura, Punzi, Grazia, Maggiolo, Franco, Callegaro, Annapaola, Calza, Leonardo, Carla Re, Maria, Pristerà, Raffaele, Turconi, Paola, Mandas, Antonella, Tini, Sauro, Zoncada, Alessia, Paolini, Elisabetta, Amadio, Giorgio, Sighinolfi, Laura, Zuccati, Giuliano, Morfini, Massimo, Manetti, Roberto, Corsi, Paola, Galli, Luisa, Di Pietro, Massimo, Bartalesi, Filippo, Colao, Grazia, Tosti, Andrea, Di Biagio, Antonio, Setti, Maurizio, Bruzzone, Bianca, Penco, Giovanni, Trezzi, Michele, Orani, Anna, Pardelli, Riccardo, De Gennaro, Michele, Chiodera, Alessandro, Scalzini, Alfredo, Palvarini, Loredana, Almi, Paolo, Todaro, Giovanni, dʼArminio Monforte, Antonella, Cicconi, Paola, Rusconi, Stefano, Gismondo, Maria Rita, Gismondo, Maria Rita, Micheli, Valeria, Biondi, Maria Luisa, Gianotti, Nicola, Capetti, Amedeo, Meraviglia, Paola, Boeri, Enzo, Mussini, Cristina, Pecorari, Monica, Soria, Alessandro, Vecchi, Laura, Santirocchi, Maurizio, Brustia, Diego, Ravanini, Paolo, Bello, Federico Dal, Romano, Nino, Mancuso, Salvatrice, Calzetti, Carlo, Maserati, Renato, Filice, Gaetano, Baldanti, Fausto, Francisci, Daniela, Parruti, Giustino, Polilli, Ennio, Sacchini, Daria, Martinelli, Chiara, Consolini, Rita, Vatteroni, Linda, Vivarelli, Angela, Dionisio, Daniele, Nerli, Alessandro, Lenzi, Lucia, Magnani, Giacomo, Ortolani, Patrizia, Andreoni, Massimo, Palamara, Guido, Fimiani, Caterina, Palmisano, Lucia, De Luca, Andrea, Fadda, Giovanni, Vullo, Vincenzo, Turriziani, Ombretta, Montano, Marco, Cenderello, Giovanni, Gonnelli, Angela, Zazzi, Maurizio, Palumbo, Michele, Ghisetti, Valeria, Bonora, Stefano, Foglie, Palma Delle, Rossi, Cristina, Grossi, Paolo, Seminari, Elena, Poletti, Federica, Mondino, Vincenzo, Malena, Marina, Lattuada, Emanuela, Lengauer, Thomas, Däumer, Martin, Hoffmann, Daniel, Kaiser, Rolf, Schülter, Eugen, Müller, Claudia, Oette, Mark, Reuter, Stefan, Esser, Stefan, Fätkenheuer, Gerd, Rockstroh, Jürgen, van de Vijver, David AMC, Incardona, Francesca, Rosen-Zvi, Michal, Lengauer, Thomas, Camacho, Ricardo, Clotet, Bonaventura, Thalme, Anders, Svedhem, Veronica, Bratt, Göran, Gargiulo, Franco, Lapadula, Giuseppe, Manca, Nino, Paraninfo, Giuseppe, Quiros-Roldan, Eugenia, Carosi, Giampiero, Castelnuovo, Filippo, Vandamme, Anne-Mieke, Van Laethem, Kristel, Van Wijngaerden, Eric, Ainsworth, Jonathan, Anderson, Jane, Babiker, Abdel, Dunn, David, Easterbrook, Philippa, Fisher, Martin, Gazzard, Brian, Garrett, Nigel, Gilson, Richard, Gompels, Mark, Hill, Teresa, Johnson, Margaret, Leen, Clifford, Orkin, Chloe, Phillips, Andrew, Pillay, Deenan, Porter, Kholoud, Post, Frank, Sabin, Caroline, Sadiq, Tariq, Schwenk, Achim, Walsh, John, Delpech, Valerie, Palfreeman, Adrian, Dunn, David, Glabay, Adam, Porter, Kholoud, Bansi, Loveleen, Hill, Teresa, Phillips, Andrew, Sabin, Caroline, Orkin, Chloe, Garrett, Nigel, Lynch, Janet, Hand, James, de Souza, Carl, Fisher, Martin, Perry, Nicky, Tilbury, Stuart, Churchill, Duncan, Gazzard, Brian, Nelson, Mark, Waxman, Matthew, Mandalia, Sundhiya, Delpech, Valerie, Anderson, Jane, Kall, Meaghan, Post, Frank, Korat, Hardik, Taylor, Chris, Ibrahim, Fowzia, Campbell, Lucy, Easterbrook, Philippa, Babiker, Abdel, Dunn, David, Glabay, Adam, Porter, Kholoud, Gilson, Richard, James, Laura, Brima, Nataliya, Williams, Ian, Schwenk, Achim, Johnson, Margaret, Youle, Mike, Lampe, Fiona, Smith, Colette, Grabowska, Helen, Chaloner, Clinton, Puradiredja, Dewi Ismajani, Bansi, Loveleen, Hill, Teresa, Phillips, Andrew, Sabin, Caroline, Walsh, John, Weber, Jonathan, Ramzan, Farhan, Carder, Mark, Leen, Clifford, Wilson, Alan, Gompels, Mark, Dooley, Debbie, Palfreeman, Adrian, Anderson, Jane, Asboe, David, Pozniak, Anton, Cameron, Sheila, Cane, Patricia, Chadwick, David, Churchill, Duncan, Clark, Duncan, Collins, Simon, Delpech, Valerie, Pillay, Deenan, Lazarus, Linda, Dunn, David, Dolling, David, Fearnhill, Esther, Castro, Hannah, Porter, Kholoud, Coughlin, Kate, Dolling, David, Zuckerman, Mark, Anna Maria, Geretti, Booth, Clare, Goldberg, David, Gompels, Mark, Hale, Antony, Kaye, Steve, Kellam, Paul, Leigh-Brown, Andrew, Mackie, Nicola, Orkin, Chloe, Pillay, Deenan, Phillips, Andrew, Sabin, Caroline, Smit, Erasmus, Templeton, Kate, Tilston, Peter, Tong, William, Williams, Ian, Zhang, Hongyi, Zhang, Hongyi, Clark, Duncan, Ushiro-Lumb, Ines, Oliver, Tony, Bibby, David, Mitchell, Suzanne, Smit, Erasmus, Mbisa, Tamyo, Wildfire, Adrian, Tandy, Richard, Shepherd, Jill, Chadwick, David, MacLean, Alasdair, Tong, William, Bennett, Diane, Hopkins, Mark, Tilston, Peter, Booth, Clare, Garcia-Diaz, Ana, Kaye, Steve, and Kirk, Stuart

Published
2011
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23. A case study of extended in-flight transmission of SARS-CoV-2 en route to Aotearoa New Zealand

Author

Swadi, Tara, L. Geoghegan, Jemma, Devine, Tom, McElnay, Caroline, Shoemack, Phil, Ren, Xiaoyun, Storey, Matt, Jefferies, Sarah, Sherwood, Jillian, Smit, Erasmus, Hadfield, James, Kenny, Aoife, Jelley, Lauren, Sporle, Andrew, McNeill, Andrea, Reynolds, G. Edwin, Mouldey, Kip, Lowe, Lindsay, Sonder, Gerard, J. Drummond, Alexei, Huang, Qiu Sue, Welch, David, C. Holmes, Edward, French, Nigel, Simpson, Colin R., and Ligt, Joep de

Subjects
Epidemiology not elsewhere classified, Genomics, Health surveillance
Abstract

Background: Since the first wave of COVID-19 in March 2020, people returning to New Zealand have been required to undergo managed isolation and quarantine (MIQ) for 14 days with mandatory testing for SARS-CoV-2. As of 20 October, testing in MIQ had identified 215 cases of SARS-CoV-2 from a total of 62,698 arrivals. While the majority of infections were likely obtained in the country of origin prior to departure, there have been possible reports of in-flight transmission. Methods: Seven people who arrived in New Zealand on the same flight on 29 September tested positive during their stay in MIQ (out of 86 passengers). The seven passengers originated from five different countries before travelling on the same flight from Dubai, United Arab Emirates (UAE) to Auckland, New Zealand. Information about their journeys, disease progression and virus genomic data was used to assess possible points of infection. Findings: All seven SARS-CoV-2 genomes were genetically identical, with the exception of a single mutation in one case, and all genomes had five signature mutations seen in only six other genomes from the >155,000 genomes sequenced globally. Four of these six related genome sequences were from Switzerland, the country of origin of the suspected index case. Interpretation: By combining information on disease progression, travel dynamics and genomic analysis, we conclude that at least four in-flight transmission events of SARS-CoV-2 likely took place.

Published
2020
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24. Contemporary syphilis is characterised by rapid global spread of pandemic Treponema pallidum lineages

Author

Beale, Mathew A., primary, Marks, Michael, additional, Cole, Michelle J., additional, Lee, Min-Kuang, additional, Pitt, Rachel, additional, Ruis, Christopher, additional, Balla, Eszter, additional, Crucitti, Tania, additional, Ewens, Michael, additional, Fernández-Naval, Candela, additional, Grankvist, Anna, additional, Guiver, Malcolm, additional, Kenyon, Chris R., additional, Khairulin, Rafil, additional, Kularatne, Ranmini, additional, Arando, Maider, additional, Molini, Barbara J., additional, Obukhov, Andrey, additional, Page, Emma E., additional, Petrovay, Fruzsina, additional, Rietmeijer, Cornelis, additional, Rowley, Dominic, additional, Shokoples, Sandy, additional, Smit, Erasmus, additional, Sweeney, Emma L., additional, Taiaroa, George, additional, Vera, Jaime H., additional, Wennerås, Christine, additional, Whiley, David M., additional, Williamson, Deborah A., additional, Hughes, Gwenda, additional, Naidu, Prenilla, additional, Unemo, Magnus, additional, Krajden, Mel, additional, Lukehart, Sheila A., additional, Morshed, Muhammad G., additional, Fifer, Helen, additional, and Thomson, Nicholas R., additional

Published
2021
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28. SARS-CoV-2 antibodies in the Southern Region of New Zealand, 2020

Author

Craigie, Alyson, primary, McGregor, Reuben, additional, Whitcombe, Alana, additional, Carlton, Lauren, additional, Harte, David, additional, Sutherland, Michelle, additional, Parry, Matthew, additional, Smit, Erasmus, additional, McAuliffe, Gary, additional, Ussher, James, additional, Moreland, Nicole, additional, Jack, Susan, additional, and Upton, Arlo, additional

Published
2020
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38. Virological failure and development of new resistance mutations according to CD4 count at combination antiretroviral therapy initiation

Author

Jose, S., Quinn, K., Dunn, D., Cox, A., Sabin, C., Fidler, S., Fisher, Martin, Gazzard, Brian, Gilson, Richard, Gompels, Mark, Hay, Phillip, Johnson, Margaret, Kegg, Stephen, Leen, C., Martin, Fabiola, Nelson, Mark, Palfreeman, Adrian, Post, F., Pritchard, Jillian, Sachikonye, Memory, Schwenk, Achim, Tariq, Anjum, Walsh, John, Hill, Teresa, Jose, Sophie, Phillips, Andrew, Sabin, Caroline, Thornton, Alicia, Dunn, David, Glabay, Adam, Fisher, M., Perry, N., Tilbury, S., Youssef, E., Churchill, D., Gazzard, B., Nelson, M., Everett, R., Asboe, D., Mandalia, S., Korat, H., Taylor, C., Gleisner, Z., Ibrahim, F., Campbell, L., Gilson, R., Brima, N., Williams, I., Johnson, M., Youle, M., Lampe, F., Smith, C., Tsintas, R., Chaloner, C., Hutchinson, S., Phillips, A., Hill, T., Thornton, A., Huntington, S., Walsh, J., Mackie, N., Winston, A., Weber, J., Ramzan, F., Carder, M., Orkin, C., Lynch, J., Hand, J., de Souza, C., Anderson, J., Munshi, S., Ainsworth, J., Schwenk, A., Miller, S., Wood, C., Wilson, A., Morris, S., Gompels, M., Allan, S., Palfreeman, A., Memon, K., Lewszuk, A., Chadwick, D., Cope, E., Gibson, J., Kegg, S., Main, P., Mitchell, Hunter, Hay, P., Dhillon, M., Martin, F., Russell-Sharpe, S., Harte, A., Clay, S., Tariq, A., Spencer, H., Jones, R., Pritchard, J., Cumming, S., Atkinson, C., Delpech, Valerie, Sachikony, M., Aitken, Celia, Asboe, David, Pozniak, Anton, Cane, Patricia, Chadwick, David, Churchill, Duncan, Clark, Duncan, Collins, Simon, Douthwaite, Samuel, Fearnhill, Esther, Porter, Kholoud, Tostevin, Anna, White, Ellen, Fraser, Christophe, Geretti, Anna Maria, Hale, Antony, Hué, Stéphane, Kaye, Steve, Kellam, Paul, Lazarus, Linda, Leigh-Brown, Andrew, Mbisa, Tamyo, Mackie, Nicola, Moses, Samuel, Orkin, Chloe, Nastouli, Eleni, Pillay, Deenan, Smit, Erasmus, Templeton, Kate, Tilston, Peter, Webster, Daniel, Williams, Ian, Zhang, Hongyi, Greatorex, Jane, O'Shea, Siobhan, Mullen, Jane, Cox, Alison, Tandy, Richard, Fawcett, Tracy, Hopkins, Mark, Ashton, Lynn, Booth, Claire, Garcia-Diaz, Ana, Shepherd, Jill, Schmid, Matthias L., Payne, Brendan, Pereira, Spiro, Hubb, Jonathan, Kirk, Stuart, Gunson, Rory, Bradley-Stewart, Amanda, and Medical Research Council (MRC)

Subjects
0301 basic medicine, Male, HAART, HIV Infections, Treatment failure, law.invention, 0302 clinical medicine, Randomized controlled trial, law, Antiretroviral Therapy, Highly Active, Pharmacology (medical), 030212 general & internal medicine, Treatment Failure, virological failure, Health Policy, UK CHIC and UK HDRD Steering Committees, Virological failure, 3. Good health, Antiretroviral therapy, Patient benefit, Infectious Diseases, Female, medicine.symptom, Life Sciences & Biomedicine, Viral load, Cart, medicine.medical_specialty, Anti-HIV Agents, Short Communication, antiretroviral therapy, CD4 count, Asymptomatic, 03 medical and health sciences, HIV-INFECTION, Virology, Internal medicine, Drug Resistance, Viral, medicine, Humans, Science & Technology, business.industry, HIV resistance, 1103 Clinical Sciences, 030112 virology, CD4 Lymphocyte Count, Immunology, Mutation, business
Abstract

Objectives No randomized controlled trials have yet reported an individual patient benefit of initiating combination antiretroviral therapy (cART) at CD4 counts > 350 cells/μL. It is hypothesized that earlier initiation of cART in asymptomatic and otherwise healthy individuals may lead to poorer adherence and subsequently higher rates of resistance development. Methods In a large cohort of HIV-positive individuals, we investigated the emergence of new resistance mutations upon virological treatment failure according to the CD4 count at the initiation of cART. Results Of 7918 included individuals, 6514 (82.3%), 996 (12.6%) and 408 (5.2%) started cART with a CD4 count ≤ 350, 351–499 and ≥ 500 cells/μL, respectively. Virological rebound occurred while on cART in 488 (7.5%), 46 (4.6%) and 30 (7.4%) with a baseline CD4 count ≤ 350, 351–499 and ≥ 500 cells/μL, respectively. Only four (13.0%) individuals with a baseline CD4 count > 350 cells/μL in receipt of a resistance test at viral load rebound were found to have developed new resistance mutations. This compared to 107 (41.2%) of those with virological failure who had initiated cART with a CD4 count

Published
2015
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41. Phylogeographical footprint of colonial history in the global dispersal of human immunodeficiency virus type 2 group A

Author

Sabelle Jallow, Ana Treviño, Maria de Fátima Gonçalves, Smit Erasmus, Stefania Paolucci, Li Xu, Jean Ruelle, Philippe Lemey, Joao Sousa, Berta Rodés, Vincent Soriano, Ioannis Hodges-Mameletzis, Nuno Taveira, Patrick Goubau, Ricardo Jorge Camacho, Danuta Pieniazek, Joana Cavaco Silva, Nuno R. Faria, Anne-Mieke Vandamme, Marc A. Suchard, UCL - SSS/IREC/MBLG - Pôle de Microbiologie médicale, and UCL - (SLuc) Service de microbiologie

Subjects
Genes, Viral, Molecular Sequence Data, HIV Infections, Genome, Viral, Colonialism, Biology, Cape verde, 03 medical and health sciences, Bayes' theorem, 0302 clinical medicine, Virology, Cabo Verde, Humans, Guinea-Bissau, 030212 general & internal medicine, 030304 developmental biology, Sampling bias, Estimation, Cape Verde, 0303 health sciences, Phylogenetic tree, Animal, Ecology, Sampling (statistics), Bayes Theorem, History, 20th Century, Senegal, 3. Good health, Africa, Western, Phylogeography, Cote d'Ivoire, Cote d, HIV-2, Biological dispersal
Abstract

Human immunodeficiency virus type 2 (HIV-2) emerged in West Africa and has spread further to countries that share socio-historical ties with this region. However, viral origins and dispersal patterns at a global scale remain poorly understood. Here, we adopt a Bayesian phylogeographic approach to investigate the spatial dynamics of HIV-2 group A (HIV-2A) using a collection of 320 partial pol and 248 partial env sequences sampled throughout 19 countries worldwide. We extend phylogenetic diffusion models that simultaneously draw information from multiple loci to estimate location states throughout distinct phylogenies and explicitly attempt to incorporate human migratory fluxes. Our study highlights that Guinea-Bissau, together with Côte d’Ivoire and Senegal, have acted as the main viral sources in the early stages of the epidemic. We show that convenience sampling can obfuscate the estimation of the spatial root of HIV-2A. We explicitly attempt to circumvent this by incorporating rate priors that reflect the ratio of human flow from and to West Africa. We recover four main routes of HIV-2A dispersal that are laid out along colonial ties: Guinea-Bissau and Cape Verde to Portugal, Côte d’Ivoire and Senegal to France. Within Europe, we find strong support for epidemiological linkage from Portugal to Luxembourg and to the UK. We demonstrate that probabilistic models can uncover global patterns of HIV-2A dispersal providing sampling bias is taken into account and we provide a scenario for the international spread of this virus.

Published
2012
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43. Integrase inhibitor (INI) genotypic resistance in treatment-naive and raltegravir-experienced patients infected with diverse HIV-1 clades

Author

Doyle, Tomas, Dunn, David T., Ceccherini-Silberstein, Francesca, De Mendoza, Carmen, Garcia, Frederico, Smit, Erasmus, Fearnhill, Esther, Marcelin, Anne-Genevieve, Martinez-Picado, Javier, Kaiser, Rolf, Geretti, Anna Maria, CORONET Study Group, [Doyle,T] Department of Infectious Diseases, King's College London, London, UK. [Dunn,DT, Fearnhill,E] MRC Clinical Trial Unit at UCL, London, UK. [Ceccherini-Silberstein,F] Faculty of Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy. [De Mendoza,C] Research Institute and Hospital Puerta de Hierro, Madrid, Spain. [Garcia,F] HU San Cecilio, Granada, Spain. [Smit,E] Heart of England NHS Foundation Trust, Birmingham, UK. [Marcelin,AG] AP-HP, Hôpital Pitié-Salpêtrière, INSERM-Sorbonne Universités, Paris, France. [Martinez-Picado,J] IrsiCaixa, ICREA and UVic-UCC, Barcelona, Spain. [Kaiser,R] Institute of Virology, University of Cologne, Cologne, Germany. [Geretti,AM] Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK., and The study was supported by a research award made by Merck to the Royal Free Charitable Trust.

Subjects
Genotype, Anti-HIV Agents, Chemicals and Drugs::Chemical Actions and Uses::Pharmacologic Actions::Molecular Mechanisms of Pharmacological Action::Enzyme Inhibitors::Integrase Inhibitors [Medical Subject Headings], Estudios de cohortes, Mutation, Missense, HIV Infections, Integrase Inhibitors, Diseases::Virus Diseases::RNA Virus Infections::Retroviridae Infections::Lentivirus Infections::HIV Infections [Medical Subject Headings], Organisms::Viruses::RNA Viruses::Retroviridae::Lentivirus::Lentiviruses, Primate::HIV [Medical Subject Headings], Europa (continente), Cohort Studies, Mutación Missense, Raltegravir Potassium, Inhibidores de integrasa, Drug Resistance, Viral, Humans, Original Research, Farmacorresistencia viral, Geographicals::Geographic Locations::Europe [Medical Subject Headings], Infecciones por VIH, Europe, Phenomena and Processes::Genetic Phenomena::Genetic Variation::Mutation::Mutation, Missense [Medical Subject Headings], Chemicals and Drugs::Chemical Actions and Uses::Pharmacologic Actions::Therapeutic Uses::Anti-Infective Agents::Antiviral Agents::Anti-Retroviral Agents::Anti-HIV Agents [Medical Subject Headings], Fármacos anti-VIH, Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Epidemiologic Methods::Epidemiologic Study Characteristics as Topic::Epidemiologic Studies::Cohort Studies [Medical Subject Headings], HIV-1, VIH-1, Phenomena and Processes::Microbiological Phenomena::Drug Resistance, Microbial::Drug Resistance, Viral [Medical Subject Headings]
Abstract

Journal Article; Research Support, Non-U.S. Gov't; OBJECTIVES The aim of this study was to characterize the prevalence and patterns of genotypic integrase inhibitor (INI) resistance in relation to HIV-1 clade. METHODS The cohort comprised 533 INI-naive subjects and 255 raltegravir recipients with viraemia who underwent integrase sequencing in routine care across Europe, including 134/533 (25.1%) and 46/255 (18.0%), respectively, with non-B clades (A, C, D, F, G, CRF01, CRF02, other CRFs, complex). RESULTS No major INI resistance-associated mutations (RAMs) occurred in INI-naive subjects. Among raltegravir recipients with viraemia (median 3523 HIV-1 RNA copies/mL), 113/255 (44.3%) had one or more major INI RAMs, most commonly N155H (45/255, 17.6%), Q148H/R/K + G140S/A (35/255, 13.7%) and Y143R/C/H (12/255, 4.7%). In addition, four (1.6%) raltegravir recipients showed novel mutations at recognized resistance sites (E92A, S147I, N155D, N155Q) and novel mutations at other integrase positions that were statistically associated with raltegravir exposure (K159Q/R, I161L/M/T/V, E170A/G). Comparing subtype B with non-B clades, Q148H/R/K occurred in 42/209 (20.1%) versus 2/46 (4.3%) subjects (P = 0.009) and G140S/A occurred in 36/209 (17.2%) versus 1/46 (2.2%) subjects (P = 0.005). Intermediate- to high-level cross-resistance to twice-daily dolutegravir was predicted in 40/255 (15.7%) subjects, more commonly in subtype B versus non-B clades (39/209, 18.7% versus 1/46, 2.2%; P = 0.003). A glycine (G) to serine (S) substitution at integrase position 140 required one nucleotide change in subtype B and two nucleotide changes in all non-B clades. CONCLUSIONS No major INI resistance mutations occurred in INI-naive subjects. Reduced occurrence of Q148H/R/K + G140S/A was seen in non-B clades versus subtype B, and was explained by the higher genetic barrier to the G140S mutation observed in all non-B clades analysed. Yes

Published
2015

45. Tjaart van der Walt: slaaf van Christus – δοῦλος Χριστοῦ

Author

Smit, Erasmus Johannes and Janse van Rensburg, Johan Jacob (Fika)

Abstract

Tjaart van der Walt: slave of Christ – δοῦλος Χριστοῦ Tjaart van der Walt has carried an array of titles: from Boy, to Young Man, to Mister, to Reverend, to Doctorandus, to Doctor, to Professor, to Rector, to Vice-Chancellor, to CEO, to Ambassador! But the one title he gladly accepts, is “slave of Christ” – or in the Greek he loves so much: δοῦλος Χριστοῦ (doulos Christou)! This has become typical of him and his life: a slave taking his instructions from Jesus Christ as his Owner, his Κύριος (Kurios), being willing to – in each situation and in relationship with any person or organisation – put on his slave clothing, roll up his sleeves, and serve! In this narrative of the life of Tjaart van der Walt we do not want to share lists of successes and failures, but rather we survey the serving life of this “slave of Christ”, as if from an Archimedes vantage point. The present, November 2011, is this Archimedes vantage point. Tjaart van der Walt: slaaf van Christus – δοῦλος Χριστοῦ Tjaart van der Walt het in sy lewe baie titels gedra: van Boetman, tot Jongman, tot Meneer, tot Dominee, tot Doctorandus, tot Doktor, tot Professor, tot Rektor, tot Visekansellier, tot Hoof Uitvoerende Beampte, tot Ambassadeur! Maar die één titel wat hy met graagte dra, is “slaaf van Christus” – of in sy geliefde Grieks: δοῦλος Χριστοῦ (doulos Christou)! Dít is wat sy lewe kenmerk: ’n slaaf wat onder opdrag van die Here Jesus Christus as sy Eienaar, sy Κύριος (Kurios), bereid is om in elke situasie en in verhouding met watter mens of organisasie ook al, die slaafklere aan te trek, die moue op te rol, en te díén! In hierdie narratief van die lewe van Tjaart van der Walt wil ons nie lysies maak van prestasies en mislukkings, van hoogte- en laagtepunte nie, maar eerder die dienpad van hierdie “slaaf van Christus” in oënskou neem, asof van ’n archimedespunt af. Die hede, November 2011, is hierdie archimedespunt. http://dx.doi.org/10.4102/ids.v45i2&3.13

Published
2011

47. Integrase inhibitor (INI) genotypic resistance in treatment-naive and raltegravir-experienced patients infected with diverse HIV-1 clades

Author

Doyle, Tomas, primary, Dunn, David T., additional, Ceccherini-Silberstein, Francesca, additional, De Mendoza, Carmen, additional, Garcia, Frederico, additional, Smit, Erasmus, additional, Fearnhill, Esther, additional, Marcelin, Anne-Genevieve, additional, Martinez-Picado, Javier, additional, Kaiser, Rolf, additional, and Geretti, Anna Maria, additional

Published
2015
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49. Die bydrae van die gereformeerde kerklied tot versoening en eenheid in 'n multikulturele Suid-Afrika

Author

Smit, Erasmus Johannes

Subjects
Apartheid (Separateness), Multi-culturality, Unity, Conflict, Alienation, Reformed worship, Culture, Western culture, Reformed liturgical song, Reconciliation, South Africa, Truth and Reconciliation Commission (TRC), Poetry, African culture, Music
Abstract

Thesis (Ph.D. (Liturgics))--North-West University, Potchefstroom Campus, 2007 The two most prominent cultures that continue to have a defining influence on the socio-political developments in a multi-cutural South African society, are the Western and African cultures. Because of the differences between these two cultures and the respective roles members of each culture have played in the socio-political history of South Africa (especially with regard to the rise and fall of apartheid), conflict and alienation in most cases define the relationship between members of these cultures. Not only does it negatively impact on the multi-cultural society of South Africa as such, it also has far-reaching Implications for the continent as a whole, seeing that South Africa Is regarded as the economical and political powerhouse of Africa upon which are pinned the hopes of millions for a better life. As a result, the importance of reconciliation and unity in the multi-cultural South African society cannot be overemphasized. It is a Biblical imperative that all members of society should live together in peace and harmony. To this end, the church is commanded to serve the reconciliation of Christ to the world (2 Corinthians 5:11-21). One of the instruments to the dlsposal of the reformed churches in South Africa for the completion of this mission, is the liturgical song. The reformed liturgical song consists of poetry (text) and music (melody) which are woven together in such a way that the text of the song is carried directly into the heart of the singer or listener. The combined power of poetry and music provides the church with a powerful therapeutic and communicative instrument by which the truth of the gospel of Christ can effectively be proclaimed to the world. A closer look at the current situation in the multi-cultural South African society reveals that the reformed churches in South Africa (of both Western and African backgrounds) haven't as yet properly played their part in the attaining of reconciliation and unity in society. The central question for research in this study, therefore, is the following: In what way can the reformed liturgical song contribute to the attainment of the ideal of reconciliation and unity in the multi-cultural South African society? The research in this study is structured according to the model for Practical Theology that was developed by Zerfass (1974:164-177). This model entails that specific base theoretical principles are compared with meta-theoretical perspectives to eventually arrive at a theory of practice from which is derived a new set of practical guidelines. In Part 1 of this study, research centres around the base-theoretical principles with regard to culture, multi-culturality, reconciliation, unity, reformed worship and liturgical song, In Part 2 meta-theoretical perspectives are given with regard to culture and multi-culturality in South Africa, reconciliation and unity in the South African context, as well as reformed worship and the use of liturgical song in the multi-cultural South African society. In Part 3 a theory of practice is articulated in which a new set of practical guidelines for the use of the reformed liturgical song towards the attaining of reconciliation and unity in the multi-cultural South African society is given. Finally it is concluded that, with certain adjustments, the reformed liturgical song can effectively be used as an instrument for attaining reconciliation and unity in the multicultural South African society. Doctoral

Published
2007

50. An association between K65R and HIV-1 subtype C viruses in patients treated with multiple NRTIs.

Author

Smit, Erasmus, White, Ellen, Clark, Duncan, Churchill, Duncan, Hongyi Zhang, Collins, Simon, Pillay, Deenan, Sabin, Caroline, Nelson, Mark, Winston, Alan, Jose, Sophie, Tostevin, Anna, Dunn, David T., Zhang, Hongyi, and UK HIV Drug Resistance Database and the UK Collaborative HIV Cohort

Subjects
*HIV-positive persons, *HIV, *TENOFOVIR, *MEDICAL care, *HIV infections, *THERAPEUTICS, *ANTI-HIV agents, *REVERSE transcriptase inhibitors, *DRUG resistance in microorganisms, *GENETIC techniques, *MULTIVARIATE analysis, *GENETIC mutation, *RESEARCH funding, *HIGHLY active antiretroviral therapy, *DIDANOSINE (Drug), *STAVUDINE, *DEOXYRIBONUCLEOSIDES, *SEQUENCE analysis, *GENOTYPES
Abstract

Objectives: HIV-1 subtype C might have a greater propensity to develop K65R mutations in patients with virological failure compared with other subtypes. However, the strong association between viral subtype and confounding factors such as exposure groups and ethnicity affects the calculation of this propensity. We exploited the diversity of viral subtypes within the UK to undertake a direct comparative analysis.Patients and methods: We analysed only sequences with major IAS-defined mutations from patients with virological failure. Prevalence of K65R was related to subtype and exposure to the NRTIs that primarily select for this mutation (tenofovir, abacavir, didanosine and stavudine). A multivariate logistic regression model quantified the effect of subtype on the prevalence of K65R, adjusting for previous and current exposure to all four specified drugs.Results: Subtype B patients ( n  =   3410) were mostly MSM (78%) and those with subtype C ( n  =   810) were mostly heterosexual (82%). K65R was detected in 7.8% of subtype B patients compared with 14.2% of subtype C patients. The subtype difference in K65R prevalence was observed irrespective of NRTI exposure and K65R was frequently selected by abacavir, didanosine and stavudine in patients with no previous exposure to tenofovir. Multivariate logistic regression confirmed that K65R was significantly more common in subtype C viruses (adjusted OR = 2.02, 95% CI = 1.55-2.62, P  <   0.001).Conclusions: Patients with subtype C HIV-1 have approximately double the frequency of K65R in our database compared with other subtypes. The exact clinical implications of this finding need to be further elucidated. [ABSTRACT FROM AUTHOR]

Published
2017
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