34 results on '"Constantinides, Bede"'
Search Results
2. A burst of genomic innovation at the origin of placental mammals mediated embryo implantation
- Author
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Taylor, Alysha S., Tinning, Haidee, Ovchinnikov, Vladimir, Edge, Jessica, Smith, William, Pullinger, Anna L., Sutton, Ruth A., Constantinides, Bede, Wang, Dapeng, Forbes, Karen, Forde, Niamh, and O’Connell, Mary J.
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- 2023
- Full Text
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3. Constructing custom-made radiotranscriptomic signatures of vascular inflammation from routine CT angiograms: a prospective outcomes validation study in COVID-19
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Ahern, David J, Ai, Zhichao, Ainsworth, Mark, Allan, Chris, Allcock, Alice, Angus, Brian, Ansari, M Azim, Arancibia-Cárcamo, Carolina, Aschenbrenner, Dominik, Attar, Moustafa, Baillie, J Kenneth, Barnes, Eleanor, Bashford-Rogers, Rachael, Bashyal, Archana, Beer, Sally, Berridge, Georgina, Beveridge, Amy, Bibi, Sagida, Bicanic, Tihana, Blackwell, Luke, Bowness, Paul, Brent, Andrew, Brown, Andrew, Broxholme, John, Buck, David, Burnham, Katie, Byrne, Helen, Camara, Susana, Ferreira, Ivan Candido, Charles, Philip, Chen, Wentao, Chen, Yi-Ling, Chong, Amanda, Clutterbuck, Elizabeth, Coles, Mark, Conlon, Christopher, Cornall, Richard, Cribbs, Adam, Curion, Fabiola, Davenport, Emma, Davidson, Neil, Davis, Simon, Dendrou, Calliope, Dequaire, Julie, Dib, Lea, Docker, James, Dold, Christina, Dong, Tao, Downes, Damien, Drakesmith, Hal, Dunachie, Susanna, Duncan, David, Eijsbouts, Chris, Esnouf, Robert, Espinosa, Alexis, Etherington, Rachel, Fairfax, Benjamin, Fairhead, Rory, Fang, Hai, Fassih, Shayan, Felle, Sally, Fernandez Mendoza, Maria, Ferreira, Ricardo, Fischer, Roman, Foord, Thomas, Forrow, Aden, Frater, John, Fries, Anastasia, Gallardo Sanchez, Veronica, Garner, Lucy, Geeves, Clementine, Georgiou, Dominique, Godfrey, Leila, Golubchik, Tanya, Gomez Vazquez, Maria, Green, Angie, Harper, Hong, Harrington, Heather, Heilig, Raphael, Hester, Svenja, Hill, Jennifer, Hinds, Charles, Hird, Clare, Ho, Ling-Pei, Hoekzema, Renee, Hollis, Benjamin, Hughes, Jim, Hutton, Paula, Jackson-Wood, Matthew, Jainarayanan, Ashwin, James-Bott, Anna, Jansen, Kathrin, Jeffery, Katie, Jones, Elizabeth, Jostins, Luke, Kerr, Georgina, Kim, David, Klenerman, Paul, Knight, Julian, Kumar, Vinod, Kumar Sharma, Piyush, Kurupati, Prathiba, Kwok, Andrew, Lee, Angela, Linder, Aline, Lockett, Teresa, Lonie, Lorne, Lopopolo, Maria, Lukoseviciute, Martyna, Luo, Jian, Marinou, Spyridoula, Marsden, Brian, Martinez, Jose, Matthews, Philippa, Mazurczyk, Michalina, McGowan, Simon, McKechnie, Stuart, Mead, Adam, Mentzer, Alexander, Mi, Yuxin, Monaco, Claudia, Montadon, Ruddy, Napolitani, Giorgio, Nassiri, Isar, Novak, Alex, O'Brien, Darragh, O'Connor, Daniel, O'Donnell, Denise, Ogg, Graham, Overend, Lauren, Park, Inhye, Pavord, Ian, Peng, Yanchun, Penkava, Frank, Pereira Pinho, Mariana, Perez, Elena, Pollard, Andrew, Powrie, Fiona, Psaila, Bethan, Quan, T Phuong, Repapi, Emmanouela, Revale, Santiago, Silva-Reyes, Laura, Richard, Jean-Baptiste, Rich-Griffin, Charlotte, Ritter, Thomas, Rollier, Christine, Rowland, Matthew, Ruehle, Fabian, Salio, Mariolina, Sansom, Stephen Nicholas, Sanches Peres, Raphael, Santos Delgado, Alberto, Sauka-Spengler, Tatjana, Schwessinger, Ron, Scozzafava, Giuseppe, Screaton, Gavin, Seigal, Anna, Semple, Malcolm, Sergeant, Martin, Simoglou Karali, Christina, Sims, David, Skelly, Donal, Slawinski, Hubert, Sobrinodiaz, Alberto, Sousos, Nikolaos, Stafford, Lizzie, Stockdale, Lisa, Strickland, Marie, Sumray, Otto, Sun, Bo, Taylor, Chelsea, Taylor, Stephen, Taylor, Adan, Thongjuea, Supat, Thraves, Hannah, Todd, John, Tomic, Adriana, Tong, Orion, Trebes, Amy, Trzupek, Dominik, Tucci, Felicia Anna, Turtle, Lance, Udalova, Irina, Uhlig, Holm, van Grinsven, Erinke, Vendrell, Iolanda, Verheul, Marije, Voda, Alexandru, Wang, Guanlin, Wang, Lihui, Wang, Dapeng, Watkinson, Peter, Watson, Robert, Weinberger, Michael, Whalley, Justin, Witty, Lorna, Wray, Katherine, Xue, Luzheng, Yuen Yeung, Hing, Yin, Zixi, Young, Rebecca, Youngs, Jonathan, Zhang, Ping, Zurke, Yasemin-Xiomara, Banning, Adrian, Antonopoulos, Alexios, Bajaj, Amrita, Kelion, Andrew, Deshpande, Aparna, Kardos, Attila, Hudson, Benjamin, Koo, Bon-Kwon, Shirodaria, Cheerag, Xie, Cheng, Kotanidis, Christos, Mahon, Ciara, Berry, Colin, Adlam, David, Newby, David, Connolly, Derek, Scaletta, Diane, Alexander, Donna, Nicol, Ed, McAlindon, Elisa, Oikonomou, Evangelos, Pugliese, Francesca, Pontone, Gianluca, Benedetti, Giulia, He, Guo-Wei, West, Henry, Kondo, Hidekazu, Benedek, Imre, Das, Intrajeet, Deanfield, John, Graby, John, Greenwood, John, Rodrigues, Jonathan, Ge, Junbo, Channon, Keith, Fabritz, Larissa, Fan, Li-Juan, Kingham, Lucy, Guglielmo, Marco, Lyasheva, Maria, Schmitt, Matthias, Beer, Meinrad, Anderson, Michelle, Desai, Milind, Marwan, Mohamed, Takahashi, Naohiko, Mehta, Nehal, Dai, Neng, Screaton, Nicholas, Sabharwal, Nikant, Maurovich-Horvat, Pál, Rao, Praveen, Kotronias, Rafail, Kharbanda, Rajesh, Preston, Rebecca, Wood, Richard, Blankstein, Ron, Rajani, Ronak, Mirsadraee, Saeed, Munir, Shahzad, Thomas, Sheena, Neubauer, Stefan, Klömpken, Steffen, Petersen, Steffen, Achenbach, Stephan, Anthony, Susan, Mak, Sze, Mittal, Tarun, Benedek, Theodora, Sharma, Vinoda, Lin, Wen-Hua, Kotanidis, Christos P, Rodrigues, Jonathan C L, O’Connor, Daniel, Siddique, Muhammad, Lockstone, Helen, Oikonomou, Evangelos K, Badi, Ileana, Lumley, Sheila F, Constantinides, Bede, Sanderson, Nicholas, Rodger, Gillian, Chau, Kevin K, Lodge, Archie, Tsakok, Maria, Gleeson, Fergus, Indrajeet, Das, Hudson, Benjamin J, Srivastava, Vivek, Farid, Shakil, Krasopoulos, George, Sayeed, Rana, Newby, David E, Channon, Keith M, and Antoniades, Charalambos
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- 2022
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4. Characterising viral populations with genome sequencing data
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Constantinides, Bede, Walton, Catherine, and Robertson, David
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572.8 - Abstract
Viral populations exhibit extensive genomic diversity that may be be profiled with contemporary nucleotide sequencing instruments, offering insight into virus transmission and the evolution of clinically relevant phenotypes within intrapatient infections. Emerging understanding of the role of the microbiome in human health and disease has pushed routine study of viruses beyond that of specific pathogen populations to include prospecting entire viral communities. In the current absence of high fidelity long read sequencing, analyses of such data must begin with reconstructing the short sequence fragments generated by sequencing instruments through either alignment to an appropriate reference sequence or de novo fragment assembly. By consequence of their error prone polymerases, RNA viruses in particular can present intrapopulation diversity to an extent that is problematic for the application of either of these approaches. In this thesis I present novel computational methodologies for robust de novo and reference-guided inference of viral consensus sequences, together with methods for characterising both interspecific and intraspecific genomic variation within viral populations. Through development and application of a wavelet-based sequence comparison approach to simulated viral populations, we demonstrate that seeding alignments using reduced dimensionality sequence representations provides accuracy broadly comparable withâand in some circumstances exceedingâthat of the most accurate available aligners. Separately, I present a methodology that identifies sample-specific preprocessing and assembly parameters for optimal reconstruction of specific viruses, together with a companion tool that enables visual exploration of metagenome assemblies with taxonomic annotations retrieved using web services. I also present Kindel, an efficient approach for inferring population consensus sequences from read alignments of arbitrary quality, that unlike existing approaches is able to reconcile both aligned insertions/deletions and leverage unaligned sequence context to locally reassemble discordant alignment regions of up 1.5x read length. I apply Kindel to the characterisation of highly diverse and difficult to assemble intrapatient hepatitis C virus populations, and propose a feature extraction and decomposition methodology for monitoring temporal shifts in the state of specific viral populations. Used in conjunction with the taxonomic annotation and filtering tool Tictax, these approaches represent efficient and composable tools for the reconstruction and exploration of viral genomic and metagenomic communities using a portable computer. In the final chapter I describe the application of these methodologies to profiling the nasopharyngeal viromes of a cohort of asthmatic children and healthy controls, identifying differences in viral composition indicative of microbial dysbiosis within the asthmatic virome.
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- 2018
5. PubTree: A Hierarchical Search Tool for the MEDLINE Database
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Rowe, William, Dobson, Paul D., Constantinides, Bede, and Platt, Mark
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Computer Science - Information Retrieval ,Computer Science - Digital Libraries - Abstract
Keeping track of the ever-increasing body of scientific literature is an escalating challenge. We present PubTree a hierarchical search tool that efficiently searches the PubMed/MEDLINE dataset based upon a decision tree constructed using >26 million abstracts. The tool is implemented as a webpage, where users are asked a series of eighteen questions to locate pertinent articles. The implementation of this hierarchical search tool highlights issues endemic with document retrieval. However, the construction of this tree indicates that with future developments hierarchical search could become an effective tool (or adjunct) in the mining of biological literature., Comment: 7 pages, 2 figures
- Published
- 2017
6. Detecting macroecological patterns in bacterial communities across independent studies of global soils.
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Ramirez, Kelly S, Knight, Christopher G, de Hollander, Mattias, Brearley, Francis Q, Constantinides, Bede, Cotton, Anne, Creer, Si, Crowther, Thomas W, Davison, John, Delgado-Baquerizo, Manuel, Dorrepaal, Ellen, Elliott, David R, Fox, Graeme, Griffiths, Robert I, Hale, Chris, Hartman, Kyle, Houlden, Ashley, Jones, David L, Krab, Eveline J, Maestre, Fernando T, McGuire, Krista L, Monteux, Sylvain, Orr, Caroline H, van der Putten, Wim H, Roberts, Ian S, Robinson, David A, Rocca, Jennifer D, Rowntree, Jennifer, Schlaeppi, Klaus, Shepherd, Matthew, Singh, Brajesh K, Straathof, Angela L, Bhatnagar, Jennifer M, Thion, Cécile, van der Heijden, Marcel GA, and de Vries, Franciska T
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Bacteria ,DNA ,Bacterial ,RNA ,Ribosomal ,16S ,Soil ,Ecology ,Soil Microbiology ,Ecosystem ,Biodiversity ,Phylogeny ,Bacterial Physiological Phenomena ,Microbial Interactions ,High-Throughput Nucleotide Sequencing ,Microbiota ,Machine Learning - Abstract
The emergence of high-throughput DNA sequencing methods provides unprecedented opportunities to further unravel bacterial biodiversity and its worldwide role from human health to ecosystem functioning. However, despite the abundance of sequencing studies, combining data from multiple individual studies to address macroecological questions of bacterial diversity remains methodically challenging and plagued with biases. Here, using a machine-learning approach that accounts for differences among studies and complex interactions among taxa, we merge 30 independent bacterial data sets comprising 1,998 soil samples from 21 countries. Whereas previous meta-analysis efforts have focused on bacterial diversity measures or abundances of major taxa, we show that disparate amplicon sequence data can be combined at the taxonomy-based level to assess bacterial community structure. We find that rarer taxa are more important for structuring soil communities than abundant taxa, and that these rarer taxa are better predictors of community structure than environmental factors, which are often confounded across studies. We conclude that combining data from independent studies can be used to explore bacterial community dynamics, identify potential 'indicator' taxa with an important role in structuring communities, and propose hypotheses on the factors that shape bacterial biogeography that have been overlooked in the past.
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- 2018
7. The khmer software package: enabling efficient nucleotide sequence analysis
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Crusoe, Michael R, Alameldin, Hussien F, Awad, Sherine, Boucher, Elmar, Caldwell, Adam, Cartwright, Reed, Charbonneau, Amanda, Constantinides, Bede, Edvenson, Greg, Fay, Scott, Fenton, Jacob, Fenzl, Thomas, Fish, Jordan, Garcia-Gutierrez, Leonor, Garland, Phillip, Gluck, Jonathan, González, Iván, Guermond, Sarah, Guo, Jiarong, Gupta, Aditi, Herr, Joshua R, Howe, Adina, Hyer, Alex, Härpfer, Andreas, Irber, Luiz, Kidd, Rhys, Lin, David, Lippi, Justin, Mansour, Tamer, McA'Nulty, Pamela, McDonald, Eric, Mizzi, Jessica, Murray, Kevin D, Nahum, Joshua R, Nanlohy, Kaben, Nederbragt, Alexander Johan, Ortiz-Zuazaga, Humberto, Ory, Jeramia, Pell, Jason, Pepe-Ranney, Charles, Russ, Zachary N, Schwarz, Erich, Scott, Camille, Seaman, Josiah, Sievert, Scott, Simpson, Jared, Skennerton, Connor T, Spencer, James, Srinivasan, Ramakrishnan, Standage, Daniel, Stapleton, James A, Steinman, Susan R, Stein, Joe, Taylor, Benjamin, Trimble, Will, Wiencko, Heather L, Wright, Michael, Wyss, Brian, Zhang, Qingpeng, zyme, en, and Brown, C. Titus
- Abstract
The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at https://github.com/dib-lab/khmer/.
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- 2015
8. Hostile: accurate host decontamination of microbial sequences
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Constantinides, Bede, primary, Hunt, Martin, additional, and Crook, Derrick W, additional
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- 2023
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9. Hostile: accurate decontamination of microbial host sequences.
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Constantinides, Bede, Hunt, Martin, and Crook, Derrick W
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DECONTAMINATION of food , *MORAL reasoning , *LEGAL reasoning - Abstract
Motivation Microbial sequences generated from clinical samples are often contaminated with human host sequences that must be removed for ethical and legal reasons. Care must be taken to excise host sequences without inadvertently removing target microbial sequences to the detriment of downstream analyses such as variant calling and de novo assembly. Results To facilitate accurate host decontamination of both short and long sequencing reads, we developed Hostile, a tool capable of accurate host read removal using a laptop. We demonstrate that our approach removes at least 99.6% of real human reads and retains at least 99.989% of simulated bacterial reads. Using Hostile with a masked reference genome further increases bacterial read retention ( ≥ 99.997%) with negligible ( ≤ 0.001%) reduction in human read removal performance. Compared with an existing tool, Hostile removes 21%–23% more human short reads and 21–43 times fewer bacterial reads, typically in less time. Availability and implementation Hostile is implemented as an MIT-licensed Python package available from https://github.com/bede/hostile together with supplementary material. [ABSTRACT FROM AUTHOR]
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- 2023
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10. Respiratory virome profiles reflect antiviral immune responses
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Rovira Rubió, Judit, primary, Megremis, Spyridon, additional, Pasioti, Maria, additional, Lakoumentas, John, additional, Constantinides, Bede, additional, Xepapadaki, Paraskevi, additional, Bachert, Claus, additional, Finotto, Susetta, additional, Jartti, Tuomas, additional, Andreakos, Evangelos, additional, Stanic, Barbara, additional, Akdis, Cezmi A., additional, Akdis, Mübeccel, additional, and Papadopoulos, Nikolaos G., additional
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- 2023
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11. Constructing custom-made radiotranscriptomic signatures of vascular inflammation from routine CT angiograms: a prospective outcomes validation study in COVID-19
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Kotanidis, Christos P, primary, Xie, Cheng, additional, Alexander, Donna, additional, Rodrigues, Jonathan C L, additional, Burnham, Katie, additional, Mentzer, Alexander, additional, O’Connor, Daniel, additional, Knight, Julian, additional, Siddique, Muhammad, additional, Lockstone, Helen, additional, Thomas, Sheena, additional, Kotronias, Rafail, additional, Oikonomou, Evangelos K, additional, Badi, Ileana, additional, Lyasheva, Maria, additional, Shirodaria, Cheerag, additional, Lumley, Sheila F, additional, Constantinides, Bede, additional, Sanderson, Nicholas, additional, Rodger, Gillian, additional, Chau, Kevin K, additional, Lodge, Archie, additional, Tsakok, Maria, additional, Gleeson, Fergus, additional, Adlam, David, additional, Rao, Praveen, additional, Indrajeet, Das, additional, Deshpande, Aparna, additional, Bajaj, Amrita, additional, Hudson, Benjamin J, additional, Srivastava, Vivek, additional, Farid, Shakil, additional, Krasopoulos, George, additional, Sayeed, Rana, additional, Ho, Ling-Pei, additional, Neubauer, Stefan, additional, Newby, David E, additional, Channon, Keith M, additional, Deanfield, John, additional, Antoniades, Charalambos, additional, Ahern, David J, additional, Ai, Zhichao, additional, Ainsworth, Mark, additional, Allan, Chris, additional, Allcock, Alice, additional, Angus, Brian, additional, Ansari, M Azim, additional, Arancibia-Cárcamo, Carolina, additional, Aschenbrenner, Dominik, additional, Attar, Moustafa, additional, Baillie, J Kenneth, additional, Barnes, Eleanor, additional, Bashford-Rogers, Rachael, additional, Bashyal, Archana, additional, Beer, Sally, additional, Berridge, Georgina, additional, Beveridge, Amy, additional, Bibi, Sagida, additional, Bicanic, Tihana, additional, Blackwell, Luke, additional, Bowness, Paul, additional, Brent, Andrew, additional, Brown, Andrew, additional, Broxholme, John, additional, Buck, David, additional, Byrne, Helen, additional, Camara, Susana, additional, Ferreira, Ivan Candido, additional, Charles, Philip, additional, Chen, Wentao, additional, Chen, Yi-Ling, additional, Chong, Amanda, additional, Clutterbuck, Elizabeth, additional, Coles, Mark, additional, Conlon, Christopher, additional, Cornall, Richard, additional, Cribbs, Adam, additional, Curion, Fabiola, additional, Davenport, Emma, additional, Davidson, Neil, additional, Davis, Simon, additional, Dendrou, Calliope, additional, Dequaire, Julie, additional, Dib, Lea, additional, Docker, James, additional, Dold, Christina, additional, Dong, Tao, additional, Downes, Damien, additional, Drakesmith, Hal, additional, Dunachie, Susanna, additional, Duncan, David, additional, Eijsbouts, Chris, additional, Esnouf, Robert, additional, Espinosa, Alexis, additional, Etherington, Rachel, additional, Fairfax, Benjamin, additional, Fairhead, Rory, additional, Fang, Hai, additional, Fassih, Shayan, additional, Felle, Sally, additional, Fernandez Mendoza, Maria, additional, Ferreira, Ricardo, additional, Fischer, Roman, additional, Foord, Thomas, additional, Forrow, Aden, additional, Frater, John, additional, Fries, Anastasia, additional, Gallardo Sanchez, Veronica, additional, Garner, Lucy, additional, Geeves, Clementine, additional, Georgiou, Dominique, additional, Godfrey, Leila, additional, Golubchik, Tanya, additional, Gomez Vazquez, Maria, additional, Green, Angie, additional, Harper, Hong, additional, Harrington, Heather, additional, Heilig, Raphael, additional, Hester, Svenja, additional, Hill, Jennifer, additional, Hinds, Charles, additional, Hird, Clare, additional, Hoekzema, Renee, additional, Hollis, Benjamin, additional, Hughes, Jim, additional, Hutton, Paula, additional, Jackson-Wood, Matthew, additional, Jainarayanan, Ashwin, additional, James-Bott, Anna, additional, Jansen, Kathrin, additional, Jeffery, Katie, additional, Jones, Elizabeth, additional, Jostins, Luke, additional, Kerr, Georgina, additional, Kim, David, additional, Klenerman, Paul, additional, Kumar, Vinod, additional, Kumar Sharma, Piyush, additional, Kurupati, Prathiba, additional, Kwok, Andrew, additional, Lee, Angela, additional, Linder, Aline, additional, Lockett, Teresa, additional, Lonie, Lorne, additional, Lopopolo, Maria, additional, Lukoseviciute, Martyna, additional, Luo, Jian, additional, Marinou, Spyridoula, additional, Marsden, Brian, additional, Martinez, Jose, additional, Matthews, Philippa, additional, Mazurczyk, Michalina, additional, McGowan, Simon, additional, McKechnie, Stuart, additional, Mead, Adam, additional, Mi, Yuxin, additional, Monaco, Claudia, additional, Montadon, Ruddy, additional, Napolitani, Giorgio, additional, Nassiri, Isar, additional, Novak, Alex, additional, O'Brien, Darragh, additional, O'Connor, Daniel, additional, O'Donnell, Denise, additional, Ogg, Graham, additional, Overend, Lauren, additional, Park, Inhye, additional, Pavord, Ian, additional, Peng, Yanchun, additional, Penkava, Frank, additional, Pereira Pinho, Mariana, additional, Perez, Elena, additional, Pollard, Andrew, additional, Powrie, Fiona, additional, Psaila, Bethan, additional, Quan, T Phuong, additional, Repapi, Emmanouela, additional, Revale, Santiago, additional, Silva-Reyes, Laura, additional, Richard, Jean-Baptiste, additional, Rich-Griffin, Charlotte, additional, Ritter, Thomas, additional, Rollier, Christine, additional, Rowland, Matthew, additional, Ruehle, Fabian, additional, Salio, Mariolina, additional, Sansom, Stephen Nicholas, additional, Sanches Peres, Raphael, additional, Santos Delgado, Alberto, additional, Sauka-Spengler, Tatjana, additional, Schwessinger, Ron, additional, Scozzafava, Giuseppe, additional, Screaton, Gavin, additional, Seigal, Anna, additional, Semple, Malcolm, additional, Sergeant, Martin, additional, Simoglou Karali, Christina, additional, Sims, David, additional, Skelly, Donal, additional, Slawinski, Hubert, additional, Sobrinodiaz, Alberto, additional, Sousos, Nikolaos, additional, Stafford, Lizzie, additional, Stockdale, Lisa, additional, Strickland, Marie, additional, Sumray, Otto, additional, Sun, Bo, additional, Taylor, Chelsea, additional, Taylor, Stephen, additional, Taylor, Adan, additional, Thongjuea, Supat, additional, Thraves, Hannah, additional, Todd, John, additional, Tomic, Adriana, additional, Tong, Orion, additional, Trebes, Amy, additional, Trzupek, Dominik, additional, Tucci, Felicia Anna, additional, Turtle, Lance, additional, Udalova, Irina, additional, Uhlig, Holm, additional, van Grinsven, Erinke, additional, Vendrell, Iolanda, additional, Verheul, Marije, additional, Voda, Alexandru, additional, Wang, Guanlin, additional, Wang, Lihui, additional, Wang, Dapeng, additional, Watkinson, Peter, additional, Watson, Robert, additional, Weinberger, Michael, additional, Whalley, Justin, additional, Witty, Lorna, additional, Wray, Katherine, additional, Xue, Luzheng, additional, Yuen Yeung, Hing, additional, Yin, Zixi, additional, Young, Rebecca, additional, Youngs, Jonathan, additional, Zhang, Ping, additional, Zurke, Yasemin-Xiomara, additional, Banning, Adrian, additional, Antonopoulos, Alexios, additional, Kelion, Andrew, additional, Kardos, Attila, additional, Hudson, Benjamin, additional, Koo, Bon-Kwon, additional, Kotanidis, Christos, additional, Mahon, Ciara, additional, Berry, Colin, additional, Newby, David, additional, Connolly, Derek, additional, Scaletta, Diane, additional, Nicol, Ed, additional, McAlindon, Elisa, additional, Oikonomou, Evangelos, additional, Pugliese, Francesca, additional, Pontone, Gianluca, additional, Benedetti, Giulia, additional, He, Guo-Wei, additional, West, Henry, additional, Kondo, Hidekazu, additional, Benedek, Imre, additional, Das, Intrajeet, additional, Graby, John, additional, Greenwood, John, additional, Rodrigues, Jonathan, additional, Ge, Junbo, additional, Channon, Keith, additional, Fabritz, Larissa, additional, Fan, Li-Juan, additional, Kingham, Lucy, additional, Guglielmo, Marco, additional, Schmitt, Matthias, additional, Beer, Meinrad, additional, Anderson, Michelle, additional, Desai, Milind, additional, Marwan, Mohamed, additional, Takahashi, Naohiko, additional, Mehta, Nehal, additional, Dai, Neng, additional, Screaton, Nicholas, additional, Sabharwal, Nikant, additional, Maurovich-Horvat, Pál, additional, Kharbanda, Rajesh, additional, Preston, Rebecca, additional, Wood, Richard, additional, Blankstein, Ron, additional, Rajani, Ronak, additional, Mirsadraee, Saeed, additional, Munir, Shahzad, additional, Klömpken, Steffen, additional, Petersen, Steffen, additional, Achenbach, Stephan, additional, Anthony, Susan, additional, Mak, Sze, additional, Mittal, Tarun, additional, Benedek, Theodora, additional, Sharma, Vinoda, additional, and Lin, Wen-Hua, additional
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- 2022
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12. Respiratory virome profiles reflect antiviral immune responses
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Rubió, Judit Rovira, primary, Megremis, Spyridon, additional, Passioti, Maria, additional, Lakoumentas, John, additional, Constantinides, Bede, additional, XEPAPADAKI, PARASKEVI, additional, Bachert, Claus, additional, Finotto, Susetta, additional, Jartti, Tuomas, additional, Andreakos, Evangelos, additional, Stanic, Barbara, additional, Akdis, Cezmi, additional, Akdis, Mubeccel, additional, and Papadopoulos, Nikolaos, additional
- Published
- 2022
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13. Antibody escape of SARS-CoV-2 Omicron BA.4 and BA.5 from vaccine and BA.1 serum
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Tuekprakhon, Aekkachai, primary, Nutalai, Rungtiwa, additional, Dijokaite-Guraliuc, Aiste, additional, Zhou, Daming, additional, Ginn, Helen M., additional, Selvaraj, Muneeswaran, additional, Liu, Chang, additional, Mentzer, Alexander J., additional, Supasa, Piyada, additional, Duyvesteyn, Helen M.E., additional, Das, Raksha, additional, Skelly, Donal, additional, Ritter, Thomas G., additional, Amini, Ali, additional, Bibi, Sagida, additional, Adele, Sandra, additional, Johnson, Sile Ann, additional, Constantinides, Bede, additional, Webster, Hermione, additional, Temperton, Nigel, additional, Klenerman, Paul, additional, Barnes, Eleanor, additional, Dunachie, Susanna J., additional, Crook, Derrick, additional, Pollard, Andrew J., additional, Lambe, Teresa, additional, Goulder, Philip, additional, Paterson, Neil G., additional, Williams, Mark A., additional, Hall, David R., additional, Fry, Elizabeth E., additional, Huo, Jiandong, additional, Mongkolsapaya, Juthathip, additional, Ren, Jingshan, additional, Stuart, David I., additional, Screaton, Gavin R., additional, Conlon, Christopher, additional, Deeks, Alexandra, additional, Frater, John, additional, Frending, Lisa, additional, Gardiner, Siobhan, additional, Jämsén, Anni, additional, Jeffery, Katie, additional, Malone, Tom, additional, Phillips, Eloise, additional, Rothwell, Lucy, additional, and Stafford, Lizzie, additional
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- 2022
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14. Potent cross-reactive antibodies following Omicron breakthrough in vaccinees
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Nutalai, Rungtiwa, primary, Zhou, Daming, additional, Tuekprakhon, Aekkachai, additional, Ginn, Helen M., additional, Supasa, Piyada, additional, Liu, Chang, additional, Huo, Jiandong, additional, Mentzer, Alexander J., additional, Duyvesteyn, Helen M.E., additional, Dijokaite-Guraliuc, Aiste, additional, Skelly, Donal, additional, Ritter, Thomas G., additional, Amini, Ali, additional, Bibi, Sagida, additional, Adele, Sandra, additional, Johnson, Sile Ann, additional, Constantinides, Bede, additional, Webster, Hermione, additional, Temperton, Nigel, additional, Klenerman, Paul, additional, Barnes, Eleanor, additional, Dunachie, Susanna J., additional, Crook, Derrick, additional, Pollard, Andrew J., additional, Lambe, Teresa, additional, Goulder, Philip, additional, Paterson, Neil G., additional, Williams, Mark A., additional, Hall, David R., additional, Mongkolsapaya, Juthathip, additional, Fry, Elizabeth E., additional, Dejnirattisai, Wanwisa, additional, Ren, Jingshan, additional, Stuart, David I., additional, and Screaton, Gavin R., additional
- Published
- 2022
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15. ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads
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Hunt, Martin, primary, Swann, Jeremy, additional, Constantinides, Bede, additional, Fowler, Philip W, additional, and Iqbal, Zamin, additional
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- 2022
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16. SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses
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Dejnirattisai, Wanwisa, primary, Huo, Jiandong, additional, Zhou, Daming, additional, Zahradník, Jiří, additional, Supasa, Piyada, additional, Liu, Chang, additional, Duyvesteyn, Helen M.E., additional, Ginn, Helen M., additional, Mentzer, Alexander J., additional, Tuekprakhon, Aekkachai, additional, Nutalai, Rungtiwa, additional, Wang, Beibei, additional, Dijokaite, Aiste, additional, Khan, Suman, additional, Avinoam, Ori, additional, Bahar, Mohammad, additional, Skelly, Donal, additional, Adele, Sandra, additional, Johnson, Sile Ann, additional, Amini, Ali, additional, Ritter, Thomas G., additional, Mason, Chris, additional, Dold, Christina, additional, Pan, Daniel, additional, Assadi, Sara, additional, Bellass, Adam, additional, Omo-Dare, Nicola, additional, Koeckerling, David, additional, Flaxman, Amy, additional, Jenkin, Daniel, additional, Aley, Parvinder K., additional, Voysey, Merryn, additional, Costa Clemens, Sue Ann, additional, Naveca, Felipe Gomes, additional, Nascimento, Valdinete, additional, Nascimento, Fernanda, additional, Fernandes da Costa, Cristiano, additional, Resende, Paola Cristina, additional, Pauvolid-Correa, Alex, additional, Siqueira, Marilda M., additional, Baillie, Vicky, additional, Serafin, Natali, additional, Kwatra, Gaurav, additional, Da Silva, Kelly, additional, Madhi, Shabir A., additional, Nunes, Marta C., additional, Malik, Tariq, additional, Openshaw, Peter J.M., additional, Baillie, J. Kenneth, additional, Semple, Malcolm G., additional, Townsend, Alain R., additional, Huang, Kuan-Ying A., additional, Tan, Tiong Kit, additional, Carroll, Miles W., additional, Klenerman, Paul, additional, Barnes, Eleanor, additional, Dunachie, Susanna J., additional, Constantinides, Bede, additional, Webster, Hermione, additional, Crook, Derrick, additional, Pollard, Andrew J., additional, Lambe, Teresa, additional, Paterson, Neil G., additional, Williams, Mark A., additional, Hall, David R., additional, Fry, Elizabeth E., additional, Mongkolsapaya, Juthathip, additional, Ren, Jingshan, additional, Schreiber, Gideon, additional, Stuart, David I., additional, Screaton, Gavin R., additional, Conlon, Christopher, additional, Deeks, Alexandra S., additional, Frater, John, additional, Frending, Lisa, additional, Gardiner, Siobhan, additional, Jämsén, Anni, additional, Jeffery, Katie, additional, Malone, Tom, additional, Phillips, Eloise, additional, Rothwell, Lucy, additional, Stafford, Lizzie, additional, Baillie, J Kenneth, additional, Openshaw, Peter JM., additional, Carson, Gail, additional, Alex, Beatrice, additional, Andrikopoulos, Petros, additional, Bach, Benjamin, additional, Barclay, Wendy S., additional, Bogaert, Debby, additional, Chand, Meera, additional, Chechi, Kanta, additional, Cooke, Graham S., additional, da Silva Filipe, Ana, additional, de Silva, Thushan, additional, Docherty, Annemarie B., additional, dos Santos Correia, Gonçalo, additional, Dumas, Marc-Emmanuel, additional, Dunning, Jake, additional, Fletcher, Tom, additional, Green, Christoper A., additional, Greenhalf, William, additional, Griffin, Julian L., additional, Gupta, Rishi K., additional, Harrison, Ewen M., additional, Hiscox, Julian A., additional, Wai Ho, Antonia Ying, additional, Horby, Peter W., additional, Ijaz, Samreen, additional, Khoo, Saye, additional, Law, Andrew, additional, Lewis, Matthew R., additional, Liggi, Sonia, additional, Lim, Wei Shen, additional, Maslen, Lynn, additional, Merson, Laura, additional, Meynert, Alison M., additional, Moore, Shona C., additional, Noursadeghi, Mahdad, additional, Olanipekun, Michael, additional, Osagie, Anthonia, additional, Palmarini, Massimo, additional, Palmieri, Carlo, additional, Paxton, William A., additional, Pollakis, Georgios, additional, Price, Nicholas, additional, Rambaut, Andrew, additional, Robertson, David L., additional, Russell, Clark D., additional, Sancho-Shimizu, Vanessa, additional, Sands, Caroline J., additional, Scott, Janet T., additional, Sigfrid, Louise, additional, Solomon, Tom, additional, Sriskandan, Shiranee, additional, Stuart, David, additional, Summers, Charlotte, additional, Swann, Olivia V., additional, Takats, Zoltan, additional, Takis, Panteleimon, additional, Tedder, Richard S., additional, Thompson, AA Roger, additional, Thomson, Emma C., additional, Thwaites, Ryan S., additional, Turtle, Lance CW., additional, Zambon, Maria, additional, Hardwick, Hayley, additional, Donohue, Chloe, additional, Griffiths, Fiona, additional, Oosthuyzen, Wilna, additional, Donegan, Cara, additional, Spencer, Rebecca G., additional, Norman, Lisa, additional, Pius, Riinu, additional, Drake, Thomas M., additional, Fairfield, Cameron J., additional, Knight, Stephen R., additional, Mclean, Kenneth A., additional, Murphy, Derek, additional, Shaw, Catherine A., additional, Dalton, Jo, additional, Girvan, Michelle, additional, Saviciute, Egle, additional, Roberts, Stephanie, additional, Harrison, Janet, additional, Marsh, Laura, additional, Connor, Marie, additional, Halpin, Sophie, additional, Jackson, Clare, additional, Gamble, Carrol, additional, Plotkin, Daniel, additional, Lee, James, additional, Leeming, Gary, additional, Wham, Murray, additional, Clohisey, Sara, additional, Hendry, Ross, additional, Scott-Brown, James, additional, Shaw, Victoria, additional, McDonald, Sarah E., additional, Keating, Seán, additional, Ahmed, Katie A., additional, Armstrong, Jane A., additional, Ashworth, Milton, additional, Asiimwe, Innocent G., additional, Bakshi, Siddharth, additional, Barlow, Samantha L., additional, Booth, Laura, additional, Brennan, Benjamin, additional, Bullock, Katie, additional, Catterall, Benjamin WA., additional, Clark, Jordan J., additional, Clarke, Emily A., additional, Cole, Sarah, additional, Cooper, Louise, additional, Cox, Helen, additional, Davis, Christopher, additional, Dincarslan, Oslem, additional, Dunn, Chris, additional, Dyer, Philip, additional, Elliott, Angela, additional, Evans, Anthony, additional, Finch, Lorna, additional, Fisher, Lewis WS., additional, Foster, Terry, additional, Garcia-Dorival, Isabel, additional, Gunning, Philip, additional, Hartley, Catherine, additional, Jensen, Rebecca L., additional, Jones, Christopher B., additional, Jones, Trevor R., additional, Khandaker, Shadia, additional, King, Katharine, additional, Kiy, Robyn T., additional, Koukorava, Chrysa, additional, Lake, Annette, additional, Lant, Suzannah, additional, Latawiec, Diane, additional, Lavelle-Langham, Lara, additional, Lefteri, Daniella, additional, Lett, Lauren, additional, Livoti, Lucia A., additional, Mancini, Maria, additional, McDonald, Sarah, additional, McEvoy, Laurence, additional, McLauchlan, John, additional, Metelmann, Soeren, additional, Miah, Nahida S., additional, Middleton, Joanna, additional, Mitchell, Joyce, additional, Murphy, Ellen G., additional, Penrice-Randal, Rebekah, additional, Pilgrim, Jack, additional, Prince, Tessa, additional, Reynolds, Will, additional, Ridley, P. Matthew, additional, Sales, Debby, additional, Shaw, Victoria E., additional, Shears, Rebecca K., additional, Small, Benjamin, additional, Subramaniam, Krishanthi S., additional, Szemiel, Agnieska, additional, Taggart, Aislynn, additional, Tanianis-Hughes, Jolanta, additional, Thomas, Jordan, additional, Trochu, Erwan, additional, van Tonder, Libby, additional, Wilcock, Eve, additional, Zhang, J. Eunice, additional, Flaherty, Lisa, additional, Maziere, Nicole, additional, Cass, Emily, additional, Carracedo, Alejandra Doce, additional, Carlucci, Nicola, additional, Holmes, Anthony, additional, Massey, Hannah, additional, Murphy, Lee, additional, McCafferty, Sarah, additional, Clark, Richard, additional, Fawkes, Angie, additional, Morrice, Kirstie, additional, Maclean, Alan, additional, Wrobel, Nicola, additional, Donnelly, Lorna, additional, Coutts, Audrey, additional, Hafezi, Katarzyna, additional, MacGillivray, Louise, additional, Gilchrist, Tammy, additional, Adeniji, Kayode, additional, Agranoff, Daniel, additional, Agwuh, Ken, additional, Ail, Dhiraj, additional, Aldera, Erin L., additional, Alegria, Ana, additional, Allen, Sam, additional, Angus, Brian, additional, Ashish, Abdul, additional, Atkinson, Dougal, additional, Bari, Shahedal, additional, Barlow, Gavin, additional, Barnass, Stella, additional, Barrett, Nicholas, additional, Bassford, Christopher, additional, Basude, Sneha, additional, Baxter, David, additional, Beadsworth, Michael, additional, Bernatoniene, Jolanta, additional, Berridge, John, additional, Berry, Colin, additional, Best, Nicola, additional, Bothma, Pieter, additional, Chadwick, David, additional, Brittain-Long, Robin, additional, Bulteel, Naomi, additional, Burden, Tom, additional, Burtenshaw, Andrew, additional, Caruth, Vikki, additional, Chambler, Duncan, additional, Chee, Nigel, additional, Child, Jenny, additional, Chukkambotla, Srikanth, additional, Clark, Tom, additional, Collini, Paul, additional, Cosgrove, Catherine, additional, Cupitt, Jason, additional, Cutino-Moguel, Maria-Teresa, additional, Dark, Paul, additional, Dawson, Chris, additional, Dervisevic, Samir, additional, Donnison, Phil, additional, Douthwaite, Sam, additional, Drummond, Andrew, additional, DuRand, Ingrid, additional, Dushianthan, Ahilanadan, additional, Dyer, Tristan, additional, Evans, Cariad, additional, Eziefula, Chi, additional, Fegan, Chrisopher, additional, Finn, Adam, additional, Fullerton, Duncan, additional, Garg, Sanjeev, additional, Garg, Atul, additional, Gkrania-Klotsas, Effrossyni, additional, Godden, Jo, additional, Goldsmith, Arthur, additional, Graham, Clive, additional, Hardy, Elaine, additional, Hartshorn, Stuart, additional, Harvey, Daniel, additional, Havalda, Peter, additional, Hawcutt, Daniel B., additional, Hobrok, Maria, additional, Hodgson, Luke, additional, Hormis, Anil, additional, Jacobs, Michael, additional, Jain, Susan, additional, Jennings, Paul, additional, Kaliappan, Agilan, additional, Kasipandian, Vidya, additional, Kegg, Stephen, additional, Kelsey, Michael, additional, Kendall, Jason, additional, Kerrison, Caroline, additional, Kerslake, Ian, additional, Koch, Oliver, additional, Koduri, Gouri, additional, Koshy, George, additional, Laha, Shondipon, additional, Laird, Steven, additional, Larkin, Susan, additional, Leiner, Tamas, additional, Lillie, Patrick, additional, Limb, James, additional, Linnett, Vanessa, additional, Little, Jeff, additional, Lyttle, Mark, additional, MacMahon, Michael, additional, MacNaughton, Emily, additional, Mankregod, Ravish, additional, Masson, Huw, additional, Matovu, Elijah, additional, McCullough, Katherine, additional, McEwen, Ruth, additional, Meda, Manjula, additional, Mills, Gary, additional, Minton, Jane, additional, Mirfenderesky, Mariyam, additional, Mohandas, Kavya, additional, Mok, Quen, additional, Moon, James, additional, Moore, Elinoor, additional, Morgan, Patrick, additional, Morris, Craig, additional, Mortimore, Katherine, additional, Moses, Samuel, additional, Mpenge, Mbiye, additional, Mulla, Rohinton, additional, Murphy, Michael, additional, Nagel, Megan, additional, Nagarajan, Thapas, additional, Nelson, Mark, additional, Norris, Lillian, additional, O’Shea, Matthew K., additional, Otahal, Igor, additional, Ostermann, Marlies, additional, Pais, Mark, additional, Panchatsharam, Selva, additional, Papakonstantinou, Danai, additional, Paraiso, Hassan, additional, Patel, Brij, additional, Pattison, Natalie, additional, Pepperell, Justin, additional, Peters, Mark, additional, Phull, Mandeep, additional, Pintus, Stefania, additional, Pooni, Jagtur Singh, additional, Planche, Tim, additional, Post, Frank, additional, Price, David, additional, Prout, Rachel, additional, Rae, Nikolas, additional, Reschreiter, Henrik, additional, Reynolds, Tim, additional, Richardson, Neil, additional, Roberts, Mark, additional, Roberts, Devender, additional, Rose, Alistair, additional, Rousseau, Guy, additional, Ruge, Bobby, additional, Ryan, Brendan, additional, Saluja, Taranprit, additional, Schmid, Matthias L., additional, Shah, Aarti, additional, Shanmuga, Prad, additional, Sharma, Anil, additional, Shawcross, Anna, additional, Sizer, Jeremy, additional, Shankar-Hari, Manu, additional, Smith, Richard, additional, Snelson, Catherine, additional, Spittle, Nick, additional, Staines, Nikki, additional, Stambach, Tom, additional, Stewart, Richard, additional, Subudhi, Pradeep, additional, Szakmany, Tamas, additional, Tatham, Kate, additional, Thomas, Jo, additional, Thompson, Chris, additional, Thompson, Robert, additional, Tridente, Ascanio, additional, Tupper-Carey, Darell, additional, Twagira, Mary, additional, Vallotton, Nick, additional, Vancheeswaran, Rama, additional, Vincent-Smith, Lisa, additional, Visuvanathan, Shico, additional, Vuylsteke, Alan, additional, Waddy, Sam, additional, Wake, Rachel, additional, Walden, Andrew, additional, Welters, Ingeborg, additional, Whitehouse, Tony, additional, Whittaker, Paul, additional, Whittington, Ashley, additional, Papineni, Padmasayee, additional, Wijesinghe, Meme, additional, Williams, Martin, additional, Wilson, Lawrence, additional, Winchester, Stephen, additional, Wiselka, Martin, additional, Wolverson, Adam, additional, Wootton, Daniel G., additional, Workman, Andrew, additional, Yates, Bryan, additional, and Young, Peter, additional
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- 2022
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17. Rapid turnaround multiplex sequencing of SARS-CoV-2: comparing tiling amplicon protocol performance
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Constantinides, Bede, primary, Webster, Hermione, additional, Gentry, Jessica, additional, Bastable, Jasmine, additional, Dunn, Laura, additional, Oakley, Sarah, additional, Swann, Jeremy, additional, Sanderson, Nicholas D, additional, Fowler, Philip W, additional, Ma, Geoffrey, additional, Rodger, Gillian, additional, Barrett, Lucinda, additional, Jeffery, Katie JM, additional, Peto, Timothy EA JM, additional, Stoesser, Nicole, additional, Street, Teresa L, additional, and Crook, Derrick W, additional
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- 2022
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18. Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses
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Dejnirattisai, Wanwisa, Huo, Jiandong, Zhou, Daming, Zahradník, Jiří, Supasa, Piyada, Liu, Chang, Duyvesteyn, Helen M.E., Ginn, Helen M., Mentzer, Alexander J., Tuekprakhon, Aekkachai, Nutalai, Rungtiwa, Wang, Beibei, Dijokaite, Aiste, Khan, Suman, Avinoam, Ori, Bahar, Mohammad, Skelly, Donal, Adele, Sandra, Johnson, Sile Ann, Amini, Ali, Ritter, Thomas, Mason, Chris, Dold, Christina, Pan, Daniel, Assadi, Sara, Bellass, Adam, Omo-Dare, Nikki, Koeckerling, David, Flaxman, Amy, Jenkin, Daniel, Aley, Parvinder K, Voysey, Merryn, Clemens, Sue Ann Costa, Naveca, Felipe Gomes, Nascimento, Valdinete, Nascimento, Fernanda, Fernandes da Costa, Cristiano, Resende, Paola Cristina, Pauvolid-Correa, Alex, Siqueira, Marilda M., Baillie, Vicky, Serafin, Natali, Ditse, Zanele, Da Silva, Kelly, Madhi, Shabir, Nunes, Marta C, Malik, Tariq, Openshaw, Peter JM, Baillie, J Kenneth, Semple, Malcolm G, Townsend, Alain R, Huang, Kuan-Ying A., Tan, Tiong Kit, Carroll, Miles W., Klenerman, Paul, Barnes, Eleanor, Dunachie, Susanna J., Constantinides, Bede, Webster, Hermione, Crook, Derrick, Pollard, Andrew J, Lambe, Teresa, Paterson, Neil G., Williams, Mark A., Hall, David R., Fry, Elizabeth E., Mongkolsapaya, Juthathip, Ren, Jingshan, Schreiber, Gideon, Stuart, David I., and Screaton, Gavin R
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Article - Abstract
SummaryOn the 24th November 2021 the sequence of a new SARS CoV-2 viral isolate spreading rapidly in Southern Africa was announced, containing far more mutations in Spike (S) than previously reported variants. Neutralization titres of Omicron by sera from vaccinees and convalescent subjects infected with early pandemic as well as Alpha, Beta, Gamma, Delta are substantially reduced or fail to neutralize. Titres against Omicron are boosted by third vaccine doses and are high in cases both vaccinated and infected by Delta. Mutations in Omicron knock out or substantially reduce neutralization by most of a large panel of potent monoclonal antibodies and antibodies under commercial development. Omicron S has structural changes from earlier viruses, combining mutations conferring tight binding to ACE2 to unleash evolution driven by immune escape, leading to a large number of mutations in the ACE2 binding site which rebalance receptor affinity to that of early pandemic viruses.
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- 2021
19. Epidemiological data and genome sequencing reveals that nosocomial transmission of SARS-CoV-2 is underestimated and mostly mediated by a small number of highly infectious individuals
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Lumley, Sheila F, primary, Constantinides, Bede, additional, Sanderson, Nicholas, additional, Rodger, Gillian, additional, Street, Teresa L, additional, Swann, Jeremy, additional, Chau, Kevin K, additional, O'Donnell, Denise, additional, Warren, Fiona, additional, Hoosdally, Sarah, additional, O'Donnell, Anne-Marie, additional, Walker, Timothy M, additional, Stoesser, Nicole E, additional, Butcher, Lisa, additional, Peto, Tim EA, additional, Crook, Derrick W, additional, Jeffery, Katie, additional, Matthews, Philippa C, additional, and Eyre, David W, additional
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- 2021
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20. Flanker: a tool for comparative genomics of gene flanking regions
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Matlock, William, primary, Lipworth, Samuel, additional, Constantinides, Bede, additional, Peto, Timothy E. A., additional, Walker, A. Sarah, additional, Crook, Derrick, additional, Hopkins, Susan, additional, Shaw, Liam P., additional, and Stoesser, Nicole, additional
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- 2021
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21. A burst of regulatory and protein innovation at the origin of placental mammals drove the emergence of placenta and underpins divergent early pregnancy strategies in modern mammals
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Taylor, Alysha S., primary, Tinning, Haidee, additional, Ovchinnikov, Vladimir, additional, Smith, William, additional, Pullinger, Anna L., additional, Sutton, Ruth A., additional, Constantinides, Bede, additional, Wang, Dapeng, additional, Forde, Niamh, additional, and O’Connell, Mary J, additional
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- 2021
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22. Observational Cohort Study on the Incidence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection and B.1.1.7 Variant Infection in Healthcare Workers by Antibody and Vaccination Status.
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Lumley, Sheila F, Rodger, Gillian, Constantinides, Bede, Sanderson, Nicholas, Chau, Kevin K, Street, Teresa L, O'Donnell, Denise, Howarth, Alison, Hatch, Stephanie B, Marsden, Brian D, Cox, Stuart, James, Tim, Warren, Fiona, Peck, Liam J, Ritter, Thomas G, Toledo, Zoe de, Warren, Laura, Axten, David, Cornall, Richard J, and Jones, E Yvonne
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NATURAL immunity ,COVID-19 ,IMMUNOGLOBULINS ,SCIENTIFIC observation ,SEQUENCE analysis ,CONFIDENCE intervals ,COVID-19 vaccines ,GENETIC variation ,DISEASE incidence ,ANTIBODY formation ,DESCRIPTIVE statistics ,POLYMERASE chain reaction ,LONGITUDINAL method ,POISSON distribution - Abstract
Background Natural and vaccine-induced immunity will play a key role in controlling the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. SARS-CoV-2 variants have the potential to evade natural and vaccine-induced immunity. Methods In a longitudinal cohort study of healthcare workers (HCWs) in Oxfordshire, United Kingdom, we investigated the protection from symptomatic and asymptomatic polymerase chain reaction (PCR)-confirmed SARS-CoV-2 infection conferred by vaccination (Pfizer-BioNTech BNT162b2, Oxford-AstraZeneca ChAdOx1 nCOV-19) and prior infection (determined using anti-spike antibody status), using Poisson regression adjusted for age, sex, temporal changes in incidence and role. We estimated protection conferred after 1 versus 2 vaccinations and from infections with the B.1.1.7 variant identified using whole genome sequencing. Results In total, 13 109 HCWs participated; 8285 received the Pfizer-BioNTech vaccine (1407 two doses), and 2738 the Oxford-AstraZeneca vaccine (49 two doses). Compared to unvaccinated seronegative HCWs, natural immunity and 2 vaccination doses provided similar protection against symptomatic infection: no HCW vaccinated twice had symptomatic infection, and incidence was 98% lower in seropositive HCWs (adjusted incidence rate ratio 0.02 [95% confidence interval {CI} < .01–.18]). Two vaccine doses or seropositivity reduced the incidence of any PCR-positive result with or without symptoms by 90% (0.10 [95% CI.02–.38]) and 85% (0.15 [95% CI.08–.26]), respectively. Single-dose vaccination reduced the incidence of symptomatic infection by 67% (0.33 [95% CI.21–.52]) and any PCR-positive result by 64% (0.36 [95% CI.26–.50]). There was no evidence of differences in immunity induced by natural infection and vaccination for infections with S-gene target failure and B.1.1.7. Conclusions Natural infection resulting in detectable anti-spike antibodies and 2 vaccine doses both provide robust protection against SARS-CoV-2 infection, including against the B.1.1.7 variant. [ABSTRACT FROM AUTHOR]
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- 2022
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23. Bacteriophage deficiency characterizes respiratory virome dysbiosis in childhood asthma
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Megremis, Spyridon, primary, Constantinides, Bede, additional, Xepapadaki, Paraskevi, additional, Bachert, Claus, additional, Neurath-Finotto, Susetta, additional, Jartti, Tuomas, additional, Kowalski, Marek L, additional, Sotiropoulos, Alexandros Georgios, additional, Tapinos, Avraam, additional, Vuorinen, Tytti, additional, Andreakos, Evangelos, additional, Robertson, David, additional, and Papadopoulos, Nikolaos, additional
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- 2020
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24. The role of CAPG in molecular communication between the embryo and the uterine endometrium: Is its function conserved in species with different implantation strategies?
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Tinning, Haidee, primary, Taylor, Alysha, additional, Wang, Dapeng, additional, Constantinides, Bede, additional, Sutton, Ruth, additional, Oikonomou, Georgios, additional, Velazquez, Miguel A., additional, Thompson, Paul, additional, Treumann, Achim, additional, O'Connell, Mary J., additional, and Forde, Niamh, additional
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- 2020
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25. Genomic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients
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Constantinides, Bede, primary, Chau, Kevin K., additional, Quan, T. Phuong, additional, Rodger, Gillian, additional, Andersson, Monique I., additional, Jeffery, Katie, additional, Lipworth, Sam, additional, Gweon, Hyun S., additional, Peniket, Andy, additional, Pike, Graham, additional, Millo, Julian, additional, Byukusenge, Mary, additional, Holdaway, Matt, additional, Gibbons, Cat, additional, Mathers, Amy J., additional, Crook, Derrick W., additional, Peto, Timothy E.A., additional, Walker, A. Sarah, additional, and Stoesser, Nicole, additional
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- 2020
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26. The Utility of Data Transformation for Alignment, De Novo Assembly and Classification of Short Read Virus Sequences
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Tapinos, Avraam, primary, Constantinides, Bede, additional, Phan, My V. T., additional, Kouchaki, Samaneh, additional, Cotten, Matthew, additional, and Robertson, David L., additional
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- 2019
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27. Detecting macroecological patterns in bacterial communities across independent studies of global soils
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Ramirez, Kelly S., primary, Knight, Christopher G., additional, de Hollander, Mattias, additional, Brearley, Francis Q., additional, Constantinides, Bede, additional, Cotton, Anne, additional, Creer, Si, additional, Crowther, Thomas W., additional, Davison, John, additional, Delgado-Baquerizo, Manuel, additional, Dorrepaal, Ellen, additional, Elliott, David R., additional, Fox, Graeme, additional, Griffiths, Robert I., additional, Hale, Chris, additional, Hartman, Kyle, additional, Houlden, Ashley, additional, Jones, David L., additional, Krab, Eveline J., additional, Maestre, Fernando T., additional, McGuire, Krista L., additional, Monteux, Sylvain, additional, Orr, Caroline H., additional, van der Putten, Wim H., additional, Roberts, Ian S., additional, Robinson, David A., additional, Rocca, Jennifer D., additional, Rowntree, Jennifer, additional, Schlaeppi, Klaus, additional, Shepherd, Matthew, additional, Singh, Brajesh K., additional, Straathof, Angela L., additional, Bhatnagar, Jennifer M., additional, Thion, Cécile, additional, van der Heijden, Marcel G. A., additional, and de Vries, Franciska T., additional
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- 2017
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28. Kindel: indel-aware consensus for nucleotide sequence alignments
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Constantinides, Bede, primary and L. Robertson, David, additional
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- 2017
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29. Abstracts from the 3rd International Severe Asthma Forum (ISAF)
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Ketelaar, M. E., primary, Van De Kant, K., additional, Dijk, F. N., additional, Klaassen, E. M. M., additional, Grotenboer, N., additional, Nawijn, M. C., additional, Dompeling, E., additional, Koppelman, G. H., additional, Murray, Clare, additional, Foden, Philip, additional, Lowe, Lesley, additional, Durrington, Hannah, additional, Custovic, Adnan, additional, Simpson, Angela, additional, Simpson, Andrew J., additional, Shaw, Dominick E., additional, Sousa, Ana R., additional, Fleming, Louise J., additional, Roberts, Graham, additional, Pandis, Ioannis, additional, Bansal, Aruna T., additional, Corfield, Julie, additional, Wagers, Scott, additional, Djukanovic, Ratko, additional, Chung, Kian Fan, additional, Sterk, Peter J., additional, Vestbo, Jorgen, additional, Fowler, Stephen J., additional, Tebbutt, S. J., additional, Singh, A., additional, Shannon, C. P., additional, Kim, Y. W., additional, Yang, C. X., additional, Gauvreau, G. M., additional, Fitzgerald, J. M., additional, Boulet, L. P., additional, O’Byrne, P. M., additional, Begley, N., additional, Loudon, A., additional, Ray, D. W., additional, Baos, Selene, additional, Cremades, Lucía, additional, Calzada, David, additional, Lahoz, Carlos, additional, Cárdaba, Blanca, additional, Asosingh, Kewal, additional, Lauruschkat, Chris, additional, Queisser, Kimberly, additional, Wanner, Nicholas, additional, Weiss, Kelly, additional, Xu, Weiling, additional, Erzurum, Serpil, additional, Sokolowska, Milena, additional, Chen, Li-Yuan, additional, Liu, Yueqin, additional, Martinez-Anton, Asuncion, additional, Logun, Carolea, additional, Alsaaty, Sara, additional, Cuento, Rosemarie, additional, Cai, Rongman, additional, Sun, Junfeng, additional, Quehenberger, Oswald, additional, Armando, Aaron, additional, Dennis, Edward, additional, Levine, Stewart, additional, Shelhamer, James, additional, Choi, Kilyong, additional, Lazova, Snezhina, additional, Perenovska, Penka, additional, Miteva, Dimitrinka, additional, Priftis, Stamatios, additional, Petrova, Guergana, additional, Yablanski, Vassil, additional, Vlaev, Evgeni, additional, Rafailova, Hristina, additional, Kumae, Takashi, additional, Holmes, L. J., additional, Yorke, J., additional, Ryan, D. M., additional, Chinratanapisit, Sasawan, additional, Matchimmadamrong, Khlongtip, additional, Deerojanawong, Jitladda, additional, Karoonboonyanan, Wissaroot, additional, Sritipsukho, Paskorn, additional, Youroukova, Vania, additional, Dimitrova, Denitsa, additional, Slavova, Yanina, additional, Lesichkova, Spaska, additional, Tzocheva, Iren, additional, Parina, Snezhana, additional, Angelova, Svetla, additional, Korsun, Neli, additional, Craiu, Mihai, additional, Stan, Iustina Violeta, additional, Deliu, Matea, additional, Yavuz, Tolga, additional, Sperrin, Matthew, additional, Sahiner, Umit M., additional, Belgrave, Danielle, additional, Sackesen, Cansin Sackesen, additional, Kalayci, Ömer, additional, Velikov, Petar, additional, Velikova, Tsvetelina, additional, Ivanova-Todorova, Ekaterina, additional, Tumangelova-Yuzeir, Kalina, additional, Kyurkchiev, Dobroslav, additional, Megremis, Spyridon, additional, Constantinides, Bede, additional, Sotiropoulos, Alexandros Georgios, additional, Xepapadaki, Paraskevi, additional, Robertson, David, additional, Papadopoulos, Nikolaos, additional, Wilkinson, Maxim, additional, Portsmouth, Craig, additional, Ray, David, additional, Goodacre, Royston, additional, Valerieva, Anna, additional, Bobolea, Irina, additional, Vera, Daiana Guillén, additional, Gonzalez-Salazar, Gabriel, additional, Moreno, Carlos Melero, additional, Rodriguez, Consuelo Fernandez, additional, De Las Cuevas Moreno, Natividad, additional, Wang, R., additional, Satia, I., additional, Niven, R., additional, Smith, J. A., additional, Southworth, T., additional, Plumb, J., additional, Gupta, V., additional, Pearson, J., additional, Ramis, I., additional, Lehner, M. D., additional, Miralpeix, M., additional, Singh, D., additional, Satia, Imran, additional, Woodhead, Mark, additional, O’Byrne, Paul, additional, Smith, Jaclyn Ann, additional, Forss, Cecilia, additional, Cook, Peter, additional, Brown, Sheila, additional, Svedberg, Freya, additional, Stephenson, Katherine, additional, Bertuzzi, Margherita, additional, Bignell, Elaine, additional, Enerbäck, Malin, additional, Cunoosamy, Danen, additional, Macdonald, Andrew, additional, Liu, Caini, additional, Zhu, Liang, additional, Fukuda, Kiochi, additional, Zhang, Cunjin, additional, Ouyang, Suidong, additional, Chen, Xing, additional, Qin, Luke, additional, Rachakonda, Suguna, additional, Aronica, Mark, additional, Qin, Jun, additional, Li, Xiaoxia, additional, Larose, Marie-Chantal, additional, Archambault, Anne-Sophie, additional, Provost, Véronique, additional, Chakir, Jamila, additional, Laviolette, Michel, additional, Flamand, Nicolas, additional, Logan, Nicola, additional, Ruckerl, Dominik, additional, Allen, Judith E., additional, Sutherland, Tara E., additional, Hamelmann, E., additional, Vogelberg, C., additional, Goldstein, S., additional, Azzi, G. E., additional, Engel, M., additional, Sigmund, R., additional, Szefler, S. J., additional, Mesquita, Raquel, additional, Coentrão, Luis, additional, Veiga, Rui, additional, Paiva, José-Artur, additional, Roncon-Albuquerque, Roberto, additional, Porras, Wendy Vargas, additional, Moreno, Ana González, additional, Iglesias, Jesus Macías, additional, Ramos, Gustavo Córdova, additional, Acevedo, Yesenia Peña, additional, Alonso, Miguel Angel Tejedor, additional, Del Mar Moro Moro, Maria, additional, Krcmova, Irena, additional, Novosad, Jakub, additional, Hanania, Nicola Alexander, additional, Massanari, Marc, additional, Hecker, Heike, additional, Kassel, Eric, additional, Laforce, Craig, additional, Rickard, Kathy, additional, Snelder, Sanne, additional, Braunstahl, Gert-Jan, additional, Jones, T. L., additional, Neville, D., additional, Heiden, E. R., additional, Lanning, E., additional, Brown, T., additional, Rupani, H., additional, Babu, K. S., additional, Chauhan, A. J., additional, Eldegeir, M. Y., additional, Chapman, A. A., additional, Ferwana, M., additional, and Caldron, M., additional
- Published
- 2017
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30. Challenges in the analysis of viral metagenomes
- Author
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Rose, Rebecca, primary, Constantinides, Bede, additional, Tapinos, Avraam, additional, Robertson, David L, additional, and Prosperi, Mattia, additional
- Published
- 2016
- Full Text
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31. Alignment by numbers: sequence assembly using compressed numerical representations
- Author
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Tapinos, Avraam, primary, Constantinides, Bede, additional, Kell, Douglas B, additional, and Robertson, David L, additional
- Published
- 2014
- Full Text
- View/download PDF
32. Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.
- Author
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Hunt M, Hinrichs AS, Anderson D, Karim L, Dearlove BL, Knaggs J, Constantinides B, Fowler PW, Rodger G, Street T, Lumley S, Webster H, Sanderson T, Ruis C, de Maio N, Amenga-Etego LN, Amuzu DSY, Avaro M, Awandare GA, Ayivor-Djanie R, Bashton M, Batty EM, Bediako Y, De Belder D, Benedetti E, Bergthaler A, Boers SA, Campos J, Carr RAA, Cuba F, Dattero ME, Dejnirattisai W, Dilthey A, Duedu KO, Endler L, Engelmann I, Francisco NM, Fuchs J, Gnimpieba EZ, Groc S, Gyamfi J, Heemskerk D, Houwaart T, Hsiao NY, Huska M, Hölzer M, Iranzadeh A, Jarva H, Jeewandara C, Jolly B, Joseph R, Kant R, Ki KKK, Kurkela S, Lappalainen M, Lataretu M, Liu C, Malavige GN, Mashe T, Mongkolsapaya J, Montes B, Molina Mora JA, Morang'a CM, Mvula B, Nagarajan N, Nelson A, Ngoi JM, da Paixão JP, Panning M, Poklepovich T, Quashie PK, Ranasinghe D, Russo M, San JE, Sanderson ND, Scaria V, Screaton G, Sironen T, Sisay A, Smith D, Smura T, Supasa P, Suphavilai C, Swann J, Tegally H, Tegomoh B, Vapalahti O, Walker A, Wilkinson RJ, Williamson C, de Oliveira T, Peto TE, Crook D, Corbett-Detig R, and Iqbal Z
- Abstract
The SARS-CoV-2 genome occupies a unique place in infection biology - it is the most highly sequenced genome on earth (making up over 20% of public sequencing datasets) with fine scale information on sampling date and geography, and has been subject to unprecedented intense analysis. As a result, these phylogenetic data are an incredibly valuable resource for science and public health. However, the vast majority of the data was sequenced by tiling amplicons across the full genome, with amplicon schemes that changed over the pandemic as mutations in the viral genome interacted with primer binding sites. In combination with the disparate set of genome assembly workflows and lack of consistent quality control (QC) processes, the current genomes have many systematic errors that have evolved with the virus and amplicon schemes. These errors have significant impacts on the phylogeny, and therefore over the last few years, many thousands of hours of researchers time has been spent in "eyeballing" trees, looking for artefacts, and then patching the tree. Given the huge value of this dataset, we therefore set out to reprocess the complete set of public raw sequence data in a rigorous amplicon-aware manner, and build a cleaner phylogeny. Here we provide a global tree of 3,960,704 samples, built from a consistently assembled set of high quality consensus sequences from all available public data as of March 2023, viewable at https://viridian.taxonium.org. Each genome was constructed using a novel assembly tool called Viridian (https://github.com/iqbal-lab-org/viridian), developed specifically to process amplicon sequence data, eliminating artefactual errors and mask the genome at low quality positions. We provide simulation and empirical validation of the methodology, and quantify the improvement in the phylogeny. Phase 2 of our project will address the fact that the data in the public archives is heavily geographically biased towards the Global North. We therefore have contributed new raw data to ENA/SRA from many countries including Ghana, Thailand, Laos, Sri Lanka, India, Argentina and Singapore. We will incorporate these, along with all public raw data submitted between March 2023 and the current day, into an updated set of assemblies, and phylogeny. We hope the tree, consensus sequences and Viridian will be a valuable resource for researchers., Competing Interests: Conflict of Interest Gavin Screaton sits on the GSK Vaccines Scientific Advisory Board, consults for AstraZeneca, and is a founding member of RQ Biotechnology.
- Published
- 2024
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33. An Observational Cohort Study on the Incidence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection and B.1.1.7 Variant Infection in Healthcare Workers by Antibody and Vaccination Status.
- Author
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Lumley SF, Rodger G, Constantinides B, Sanderson N, Chau KK, Street TL, O'Donnell D, Howarth A, Hatch SB, Marsden BD, Cox S, James T, Warren F, Peck LJ, Ritter TG, de Toledo Z, Warren L, Axten D, Cornall RJ, Jones EY, Stuart DI, Screaton G, Ebner D, Hoosdally S, Chand M, Crook DW, O'Donnell AM, Conlon CP, Pouwels KB, Walker AS, Peto TEA, Hopkins S, Walker TM, Stoesser NE, Matthews PC, Jeffery K, and Eyre DW
- Subjects
- BNT162 Vaccine, COVID-19 Vaccines, ChAdOx1 nCoV-19, Cohort Studies, Health Personnel, Humans, Immunoglobulins, Incidence, Longitudinal Studies, Vaccination, COVID-19 epidemiology, COVID-19 prevention & control, SARS-CoV-2
- Abstract
Background: Natural and vaccine-induced immunity will play a key role in controlling the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. SARS-CoV-2 variants have the potential to evade natural and vaccine-induced immunity., Methods: In a longitudinal cohort study of healthcare workers (HCWs) in Oxfordshire, United Kingdom, we investigated the protection from symptomatic and asymptomatic polymerase chain reaction (PCR)-confirmed SARS-CoV-2 infection conferred by vaccination (Pfizer-BioNTech BNT162b2, Oxford-AstraZeneca ChAdOx1 nCOV-19) and prior infection (determined using anti-spike antibody status), using Poisson regression adjusted for age, sex, temporal changes in incidence and role. We estimated protection conferred after 1 versus 2 vaccinations and from infections with the B.1.1.7 variant identified using whole genome sequencing., Results: In total, 13 109 HCWs participated; 8285 received the Pfizer-BioNTech vaccine (1407 two doses), and 2738 the Oxford-AstraZeneca vaccine (49 two doses). Compared to unvaccinated seronegative HCWs, natural immunity and 2 vaccination doses provided similar protection against symptomatic infection: no HCW vaccinated twice had symptomatic infection, and incidence was 98% lower in seropositive HCWs (adjusted incidence rate ratio 0.02 [95% confidence interval {CI} < .01-.18]). Two vaccine doses or seropositivity reduced the incidence of any PCR-positive result with or without symptoms by 90% (0.10 [95% CI .02-.38]) and 85% (0.15 [95% CI .08-.26]), respectively. Single-dose vaccination reduced the incidence of symptomatic infection by 67% (0.33 [95% CI .21-.52]) and any PCR-positive result by 64% (0.36 [95% CI .26-.50]). There was no evidence of differences in immunity induced by natural infection and vaccination for infections with S-gene target failure and B.1.1.7., Conclusions: Natural infection resulting in detectable anti-spike antibodies and 2 vaccine doses both provide robust protection against SARS-CoV-2 infection, including against the B.1.1.7 variant., (© The Author(s) 2021. Published by Oxford University Press for the Infectious Diseases Society of America.)
- Published
- 2022
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34. Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses.
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Dejnirattisai W, Huo J, Zhou D, Zahradník J, Supasa P, Liu C, Duyvesteyn HME, Ginn HM, Mentzer AJ, Tuekprakhon A, Nutalai R, Wang B, Dijokaite A, Khan S, Avinoam O, Bahar M, Skelly D, Adele S, Johnson SA, Amini A, Ritter T, Mason C, Dold C, Pan D, Assadi S, Bellass A, Omo-Dare N, Koeckerling D, Flaxman A, Jenkin D, Aley PK, Voysey M, Clemens SAC, Naveca FG, Nascimento V, Nascimento F, Fernandes da Costa C, Resende PC, Pauvolid-Correa A, Siqueira MM, Baillie V, Serafin N, Ditse Z, Da Silva K, Madhi S, Nunes MC, Malik T, Openshaw PJ, Baillie JK, Semple MG, Townsend AR, Huang KA, Tan TK, Carroll MW, Klenerman P, Barnes E, Dunachie SJ, Constantinides B, Webster H, Crook D, Pollard AJ, Lambe T, Paterson NG, Williams MA, Hall DR, Fry EE, Mongkolsapaya J, Ren J, Schreiber G, Stuart DI, and Screaton GR
- Abstract
On the 24
th November 2021 the sequence of a new SARS CoV-2 viral isolate spreading rapidly in Southern Africa was announced, containing far more mutations in Spike (S) than previously reported variants. Neutralization titres of Omicron by sera from vaccinees and convalescent subjects infected with early pandemic as well as Alpha, Beta, Gamma, Delta are substantially reduced or fail to neutralize. Titres against Omicron are boosted by third vaccine doses and are high in cases both vaccinated and infected by Delta. Mutations in Omicron knock out or substantially reduce neutralization by most of a large panel of potent monoclonal antibodies and antibodies under commercial development. Omicron S has structural changes from earlier viruses, combining mutations conferring tight binding to ACE2 to unleash evolution driven by immune escape, leading to a large number of mutations in the ACE2 binding site which rebalance receptor affinity to that of early pandemic viruses.- Published
- 2021
- Full Text
- View/download PDF
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