Search

Your search keyword '"Crown, Matthew"' showing total 22 results
Start Over Author "Crown, Matthew"
22 results on '"Crown, Matthew"'

1. Prevalence of persistent SARS-CoV-2 in a large community surveillance study

Author

Ghafari, Mahan, Hall, Matthew, Golubchik, Tanya, Ayoubkhani, Daniel, House, Thomas, MacIntyre-Cockett, George, Fryer, Helen R., Thomson, Laura, Nurtay, Anel, Kemp, Steven A., Ferretti, Luca, Buck, David, Green, Angie, Trebes, Amy, Piazza, Paolo, Lonie, Lorne J., Studley, Ruth, Rourke, Emma, Smith, Darren L., Bashton, Matthew, Nelson, Andrew, Crown, Matthew, McCann, Clare, Young, Gregory R., Santos, Rui Andre Nunes dos, Richards, Zack, Tariq, Mohammad Adnan, Cahuantzi, Roberto, Barrett, Jeff, Fraser, Christophe, Bonsall, David, Walker, Ann Sarah, and Lythgoe, Katrina

Published
2024
Full Text
View/download PDF

3. Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes

Author

Robson, Samuel C., Connor, Thomas R., Loman, Nicholas J., Golubchik, Tanya, Martinez Nunez, Rocio T., Bonsall, David, Rambaut, Andrew, Snell, Luke B., Livett, Rich, Ludden, Catherine, Corden, Sally, Nastouli, Eleni, Nebbia, Gaia, Johnston, Ian, Prieto, Jacqui A., Saeed, Kordo, Jackson, David K., Houlihan, Catherine, Frampton, Dan, Hamilton, William L., Witney, Adam A., Bucca, Giselda, Pope, Cassie F., Moore, Catherine, Thomson, Emma C., Cutino-Moguel, Teresa, Harrison, Ewan M., Smith, Colin P., Rogan, Fiona, Beckwith, Shaun M., Murray, Abigail, Singleton, Dawn, Eastick, Kirstine, Sheridan, Liz A., Randell, Paul, Jackson, Leigh M., Ariani, Cristina V., Gonçalves, Sónia, Fairley, Derek J., Loose, Matthew W., Watkins, Joanne, Moses, Samuel, Nicholls, Sam, Bull, Matthew, Amato, Roberto, Smith, Darren L., Aanensen, David M., Barrett, Jeffrey C., Kele, Beatrix, Aggarwal, Dinesh, Shepherd, James G., Curran, Martin D., Parmar, Surendra, Parker, Matthew D., Williams, Catryn, Glaysher, Sharon, Underwood, Anthony P., Bashton, Matthew, Pacchiarini, Nicole, Loveson, Katie F., Byott, Matthew, Carabelli, Alessandro M., Templeton, Kate E., Peacock, Sharon J., de Silva, Thushan I., Wang, Dennis, Langford, Cordelia F., Sillitoe, John, Gunson, Rory N., Cottrell, Simon, O’Grady, Justin, Kwiatkowski, Dominic, Lillie, Patrick J., Cortes, Nicholas, Moore, Nathan, Thomas, Claire, Burns, Phillipa J., Mahungu, Tabitha W., Liggett, Steven, Beckett, Angela H., Holden, Matthew TG., Levett, Lisa J., Osman, Husam, Hassan-Ibrahim, Mohammed O., Simpson, David A., Chand, Meera, Gupta, Ravi K., Darby, Alistair C., Paterson, Steve, Pybus, Oliver G., Volz, Erik M., de Angelis, Daniela, Robertson, David L., Page, Andrew J., Martincorena, Inigo, Aigrain, Louise, Bassett, Andrew R., Wong, Nick, Taha, Yusri, Erkiert, Michelle J., Spencer Chapman, Michael H., Dewar, Rebecca, McHugh, Martin P., Mookerjee, Siddharth, Aplin, Stephen, Harvey, Matthew, Sass, Thea, Umpleby, Helen, Wheeler, Helen, McKenna, James P., Warne, Ben, Taylor, Joshua F., Chaudhry, Yasmin, Izuagbe, Rhys, Jahun, Aminu S., Young, Gregory R., McMurray, Claire, McCann, Clare M., Nelson, Andrew, Elliott, Scott, Lowe, Hannah, Price, Anna, Crown, Matthew R., Rey, Sara, Roy, Sunando, Temperton, Ben, Shaaban, Sharif, Hesketh, Andrew R., Laing, Kenneth G., Monahan, Irene M., Heaney, Judith, Pelosi, Emanuela, Silviera, Siona, Wilson-Davies, Eleri, Fryer, Helen, Adams, Helen, du Plessis, Louis, Johnson, Rob, Harvey, William T., Hughes, Joseph, Orton, Richard J., Spurgin, Lewis G., Bourgeois, Yann, Ruis, Chris, O'Toole, Áine, Gourtovaia, Marina, Sanderson, Theo, Fraser, Christophe, Edgeworth, Jonathan, Breuer, Judith, Michell, Stephen L., Todd, John A., John, Michaela, Buck, David, Gajee, Kavitha, Kay, Gemma L., Heyburn, David, Charalampous, Themoula, Alcolea-Medina, Adela, Kitchman, Katie, McNal, Alan, Pritch, David T., Dervisevic, Samir, Muir, Peter, Robinson, Esther, Vipond, Barry B., Ramadan, Newara A., Jeanes, Christopher, Weldon, Danni, Catalan, Jana, Jones, Neil, da Silva Filipe, Ana, Williams, Chris, Fuchs, Marc, Miskelly, Julia, Jeffries, Aaron R., Oliver, Karen, Park, Naomi R., Ash, Amy, Koshy, Cherian, Barrow, Magdalena, Buchan, Sarah L., Mantzouratou, Anna, Clark, Gemma, Holmes, Christopher W., Campbell, Sharon, Davis, Thomas, Tan, Ngee Keong, Brown, Julianne R., Harris, Kathryn A., Kidd, Stephen P., Grant, Paul R., Xu-McCrae, Li, Cox, Alison, Madona, Pinglawathee, Pond, Marcus, Randell, Paul A., Withell, Karen T., Williams, Cheryl, Graham, Clive, Denton-Smith, Rebecca, Swindells, Emma, Turnbull, Robyn, Sloan, Tim J., Bosworth, Andrew, Hutchings, Stephanie, Pymont, Hannah M., Casey, Anna, Ratcliffe, Liz, Jones, Christopher R., Knight, Bridget A., Haque, Tanzina, Hart, Jennifer, Irish-Tavares, Dianne, Witele, Eric, Mower, Craig, Watson DipHE, Louisa K., Collins, Jennifer, Eltringham, Gary, Crudgington, Dorian, Macklin, Ben, Iturriza-Gomara, Miren, Lucaci, Anita O., McClure, Patrick C., Carlile, Matthew, Holmes, Nadine, Moore, Christopher, Storey, Nathaniel, Rooke, Stefan, Yebra, Gonzalo, Craine, Noel, Perry, Malorie, Alikhan, Nabil-Fareed, Bridgett, Stephen, Cook, Kate F., Fearn, Christopher, Goudarzi, Salman, Lyons, Ronan A., Williams, Thomas, Haldenby, Sam T., Durham, Jillian, Leonard, Steven, Davies, Robert M., Batra, Rahul, Blane, Beth, Spyer, Moira J., Smith, Perminder, Yavus, Mehmet, Williams, Rachel J., Mahanama, Adhyana IK., Samaraweera, Buddhini, Girgis, Sophia T., Hansford, Samantha E., Green, Angie, Beaver, Charlotte, Bellis, Katherine L., Dorman, Matthew J., Kay, Sally, Prestwood, Liam, Rajatileka, Shavanthi, Quick, Joshua, Poplawski, Radoslaw, Reynolds, Nicola, Mack, Andrew, Morriss, Arthur, Whalley, Thomas, Patel, Bindi, Georgana, Iliana, Hosmillo, Myra, Pinckert, Malte L., Stockton, Joanne, Henderson, John H., Hollis, Amy, Stanley, William, Yew, Wen C., Myers, Richard, Thornton, Alicia, Adams, Alexander, Annett, Tara, Asad, Hibo, Birchley, Alec, Coombes, Jason, Evans, Johnathan M., Fina, Laia, Gatica-Wilcox, Bree, Gilbert, Lauren, Graham, Lee, Hey, Jessica, Hilvers, Ember, Jones, Sophie, Jones, Hannah, Kumziene-Summerhayes, Sara, McKerr, Caoimhe, Powell, Jessica, Pugh, Georgia, Taylor, Sarah, Trotter, Alexander J., Williams, Charlotte A., Kermack, Leanne M., Foulkes, Benjamin H., Gallis, Marta, Hornsby, Hailey R., Louka, Stavroula F., Pohare, Manoj, Wolverson, Paige, Zhang, Peijun, MacIntyre-Cockett, George, Trebes, Amy, Moll, Robin J., Ferguson, Lynne, Goldstein, Emily J., Maclean, Alasdair, Tomb, Rachael, Starinskij, Igor, Thomson, Laura, Southgate, Joel, Kraemer, Moritz UG., Raghwani, Jayna, Zarebski, Alex E., Boyd, Olivia, Geidelberg, Lily, Illingworth, Chris J., Jackson, Chris, Pascall, David, Vattipally, Sreenu, Freeman, Timothy M., Hsu, Sharon N., Lindsey, Benjamin B., James, Keith, Lewis, Kevin, Tonkin-Hill, Gerry, Tovar-Corona, Jaime M., Cox, MacGregor, Abudahab, Khalil, Menegazzo, Mirko, Taylor, Ben EW., Yeats, Corin A., Mukaddas, Afrida, Wright, Derek W., de Oliveira Martins, Leonardo, Colquhoun, Rachel, Hill, Verity, Jackson, Ben, McCrone, J.T., Medd, Nathan, Scher, Emily, Keatley, Jon-Paul, Curran, Tanya, Morgan, Sian, Maxwell, Patrick, Smith, Ken, Eldirdiri, Sahar, Kenyon, Anita, Holmes, Alison H., Price, James R., Wyatt, Tim, Mather, Alison E., Skvortsov, Timofey, Hartley, John A., Guest, Martyn, Kitchen, Christine, Merrick, Ian, Munn, Robert, Bertolusso, Beatrice, Lynch, Jessica, Vernet, Gabrielle, Kirk, Stuart, Wastnedge, Elizabeth, Stanley, Rachael, Idle, Giles, Bradley, Declan T., Killough, Nicholas F., Poyner, Jennifer, Mori, Matilde, Jones, Owen, Wright, Victoria, Brooks, Ellena, Churcher, Carol M., Delgado Callico, Laia, Fragakis, Mireille, Galai, Katerina, Jermy, Andrew, Judges, Sarah, Markov, Anna, McManus, Georgina M., Smith, Kim S., Thomas-McEwen, Peter MD., Westwick, Elaine, Attwood, Stephen W., Bolt, Frances, Davies, Alisha, De Lacy, Elen, Downing, Fatima, Edwards, Sue, Meadows, Lizzie, Jeremiah, Sarah, Smith, Nikki, Foulser, Luke, Patel, Amita, Berry, Louise, Boswell, Tim, Fleming, Vicki M., Howson-Wells, Hannah C., Joseph, Amelia, Khakh, Manjinder, Lister, Michelle M., Bird, Paul W., Fallon, Karlie, Helmer, Thomas, McMurray, Claire L., Odedra, Mina, Shaw, Jessica, Tang, Julian W., Willford, Nicholas J., Blakey, Victoria, Raviprakash, Veena, Sheriff, Nicola, Williams, Lesley-Anne, Feltwell, Theresa, Bedford, Luke, Cargill, James S., Hughes, Warwick, Moore, Jonathan, Stonehouse, Susanne, Atkinson, Laura, Lee, Jack CD., Shah, Divya, Ohemeng-Kumi, Natasha, Ramble, John, Sehmi, Jasveen, Williams, Rebecca, Chatterton, Wendy, Pusok, Monika, Everson, William, Castigador, Anibolina, Macnaughton, Emily, El Bouzidi, Kate, Lampejo, Temi, Sudhanva, Malur, Breen, Cassie, Sluga, Graciela, Ahmad, Shazaad SY., George, Ryan P., Machin, Nicholas W., Binns, Debbie, James, Victoria, Blacow, Rachel, Coupland, Lindsay, Smith, Louise, Barton, Edward, Padgett, Debra, Scott, Garren, Cross, Aidan, Mirfenderesky, Mariyam, Greenaway, Jane, Cole, Kevin, Clarke, Phillip, Duckworth, Nichola, Walsh, Sarah, Bicknell, Kelly, Impey, Robert, Wyllie, Sarah, Hopes, Richard, Bishop, Chloe, Chalker, Vicki, Harrison, Ian, Gifford, Laura, Molnar, Zoltan, Auckland, Cressida, Evans, Cariad, Johnson, Kate, Partridge, David G., Raza, Mohammad, Baker, Paul, Bonner, Stephen, Essex, Sarah, Murray, Leanne J., Lawton, Andrew I., Burton-Fanning, Shirelle, Payne, Brendan AI., Waugh, Sheila, Gomes, Andrea N., Kimuli, Maimuna, Murray, Darren R., Ashfield, Paula, Dobie, Donald, Ashford, Fiona, Best, Angus, Crawford, Liam, Cumley, Nicola, Mayhew, Megan, Megram, Oliver, Mirza, Jeremy, Moles-Garcia, Emma, Percival, Benita, Driscoll, Megan, Ensell, Leah, Lowe, Helen L., Maftei, Laurentiu, Mondani, Matteo, Chaloner, Nicola J., Cogger, Benjamin J., Easton, Lisa J., Huckson, Hannah, Lewis, Jonathan, Lowdon, Sarah, Malone, Cassandra S., Munemo, Florence, Mutingwende, Manasa, Nicodemi, Roberto, Podplomyk FD, Olga, Somassa, Thomas, Beggs, Andrew, Richter, Alex, Cormie, Claire, Dias, Joana, Forrest, Sally, Higginson, Ellen E., Maes, Mailis, Young, Jamie, Davidson, Rose K., Jackson, Kathryn A., Keeley, Alexander J., Ball, Jonathan, Byaruhanga, Timothy, Chappell, Joseph G., Dey, Jayasree, Hill, Jack D., Park, Emily J., Fanaie, Arezou, Hilson, Rachel A., Yaze, Geraldine, Lo, Stephanie, Afifi, Safiah, Beer, Robert, Maksimovic, Joshua, McCluggage, Kathryn, Spellman, Karla, Bresner, Catherine, Fuller, William, Marchbank, Angela, Workma, Trudy, Shelest, Ekaterina, Debebe, Johnny, Sang, Fei, Francois, Sarah, Gutierrez, Bernardo, Vasylyeva, Tetyana I., Flaviani, Flavia, Ragonnet-Cronin, Manon, Smollett, Katherine L., Broos, Alice, Mair, Daniel, Nichols, Jenna, Nomikou, Kyriaki, Tong, Lily, Tsatsani, Ioulia, O'Brien, Sarah, Rushton, Steven, Sanderson, Roy, Perkins, Jon, Cotton, Seb, Gallagher, Abbie, Allara, Elias, Pearson, Clare, Bibby, David, Dabrer, Gavin, Ellaby, Nicholas, Gallagher, Eileen, Hubb, Jonathan, Lackenby, Angie, Lee, David, Manesis, Nikos, Mbisa, Tamyo, Platt, Steven, Twohig, Katherine A., Morgan, Mari, Aydin, Alp, Baker, David J., Foster-Nyarko, Ebenezer, Prosolek, Sophie J., Rudder, Steven, Baxter, Chris, Carvalho, Sílvia F., Lavin, Deborah, Mariappan, Arun, Radulescu, Clara, Singh, Aditi, Tang, Miao, Morcrette, Helen, Bayzid, Nadua, Cotic, Marius, Balcazar, Carlos E., Gallagher, Michael D., Maloney, Daniel, Stanton, Thomas D., Williamson, Kathleen A., Manley, Robin, Michelsen, Michelle L., Sambles, Christine M., Studholme, David J., Warwick-Dugdale, Joanna, Eccles, Richard, Gemmell, Matthew, Gregory, Richard, Hughes, Margaret, Nelson, Charlotte, Rainbow, Lucille, Vamos, Edith E., Webster, Hermione J., Whitehead, Mark, Wierzbicki, Claudia, Angyal, Adrienn, Green, Luke R., Whiteley, Max, Betteridge, Emma, Bronner, Iraad F., Farr, Ben W., Goodwin, Scott, Lensing, Stefanie V., McCarthy, Shane A., Quail, Michael A., Rajan, Diana, Redshaw, Nicholas M., Scott, Carol, Shirley, Lesley, Thurston, Scott AJ., Rowe, Will, Gaskin, Amy, Le-Viet, Thanh, Bonfield, James, Liddle, Jennifier, Whitwham, Andrew, Cotton, S., McHugh, M.P., Dewar, R., Haas, J.G., and Templeton, K.

Published
2023
Full Text
View/download PDF

4. The impact of viral mutations on recognition by SARS-CoV-2 specific T cells

Author

Aanensen, David M., Abudahab, Khalil, Adams, Helen, Adams, Alexander, Afifi, Safiah, Aggarwal, Dinesh, Ahmad, Shazaad S.Y., Aigrain, Louise, Alcolea-Medina, Adela, Alikhan, Nabil-Fareed, Allara, Elias, Amato, Roberto, Annett, Tara, Aplin, Stephen, Ariani, Cristina V., Asad, Hibo, Ash, Amy, Ashfield, Paula, Ashford, Fiona, Atkinson, Laura, Attwood, Stephen W., Auckland, Cressida, Aydin, Alp, Baker, David J., Baker, Paul, Balcazar, Carlos E., Ball, Jonathan, Barrett, Jeffrey C., Barrow, Magdalena, Barton, Edward, Bashton, Matthew, Bassett, Andrew R., Batra, Rahul, Baxter, Chris, Bayzid, Nadua, Beaver, Charlotte, Beckett, Angela H., Beckwith, Shaun M., Bedford, Luke, Beer, Robert, Beggs, Andrew, Bellis, Katherine L., Berry, Louise, Bertolusso, Beatrice, Best, Angus, Betteridge, Emma, Bibby, David, Bicknell, Kelly, Binns, Debbie, Birchley, Alec, Bird, Paul W., Bishop, Chloe, Blacow, Rachel, Blakey, Victoria, Blane, Beth, Bolt, Frances, Bonfield, James, Bonner, Stephen, Bonsall, David, Boswell, Tim, Bosworth, Andrew, Bourgeois, Yann, Boyd, Olivia, Bradley, Declan T., Breen, Cassie, Bresner, Catherine, Breuer, Judith, Bridgett, Stephen, Bronner, Iraad F., Brooks, Ellena, Broos, Alice, Brown, Julianne R., Bucca, Giselda, Buchan, Sarah L., Buck, David, Bull, Matthew, Burns, Phillipa J., Burton-Fanning, Shirelle, Byaruhanga, Timothy, Byott, Matthew, Campbell, Sharon, Carabelli, Alessandro M., Cargill, James S., Carlile, Matthew, Carvalho, Silvia F., Casey, Anna, Castigador, Anibolina, Catalan, Jana, Chalker, Vicki, Chaloner, Nicola J., Chand, Meera, Chappell, Joseph G., Charalampous, Themoula, Chatterton, Wendy, Chaudhry, Yasmin, Churcher, Carol M., Clark, Gemma, Clarke, Phillip, Cogger, Benjamin J., Cole, Kevin, Collins, Jennifer, Colquhoun, Rachel, Connor, Thomas R., Cook, Kate F., Coombes, Jason, Corden, Sally, Cormie, Claire, Cortes, Nicholas, Cotic, Marius, Cotton, Seb, Cottrell, Simon, Coupland, Lindsay, Cox, MacGregor, Cox, Alison, Craine, Noel, Crawford, Liam, Cross, Aidan, Crown, Matthew R., Crudgington, Dorian, Cumley, Nicola, Curran, Tanya, Curran, Martin D., da Silva Filipe, Ana, Dabrera, Gavin, Darby, Alistair C., Davidson, Rose K., Davies, Alisha, Davies, Robert M., Davis, Thomas, de Angelis, Daniela, De Lacy, Elen, de Oliveira Martins, Leonardo, Debebe, Johnny, Denton-Smith, Rebecca, Dervisevic, Samir, Dewar, Rebecca, Dey, Jayasree, Dias, Joana, Dobie, Donald, Dorman, Matthew J., Downing, Fatima, Driscoll, Megan, du Plessis, Louis, Duckworth, Nichola, Durham, Jillian, Eastick, Kirstine, Easton, Lisa J., Eccles, Richard, Edgeworth, Jonathan, Edwards, Sue, El Bouzidi, Kate, Eldirdiri, Sahar, Ellaby, Nicholas, Elliott, Scott, Eltringham, Gary, Ensell, Leah, Erkiert, Michelle J., Zamudio, Marina Escalera, Essex, Sarah, Evans, Johnathan M., Evans, Cariad, Everson, William, Fairley, Derek J., Fallon, Karlie, Fanaie, Arezou, Farr, Ben W., Fearn, Christopher, Feltwell, Theresa, Ferguson, Lynne, Fina, Laia, Flaviani, Flavia, Fleming, Vicki M., Forrest, Sally, Foster-Nyarko, Ebenezer, Foulkes, Benjamin H., Foulser, Luke, Fragakis, Mireille, Frampton, Dan, Francois, Sarah, Fraser, Christophe, Freeman, Timothy M., Fryer, Helen, Fuchs, Marc, Fuller, William, Gajee, Kavitha, Galai, Katerina, Gallagher, Abbie, Gallagher, Eileen, Gallagher, Michael D., Gallis, Marta, Gaskin, Amy, Gatica-Wilcox, Bree, Geidelberg, Lily, Gemmell, Matthew, Georgana, Iliana, George, Ryan P., Gifford, Laura, Gilbert, Lauren, Girgis, Sophia T., Glaysher, Sharon, Goldstein, Emily J., Golubchik, Tanya, Gomes, Andrea N., Gonçalves, Sónia, Goodfellow, Ian G., Goodwin, Scott, Goudarzi, Salman, Gourtovaia, Marina, Graham, Clive, Graham, Lee, Grant, Paul R., Green, Luke R., Green, Angie, Greenaway, Jane, Gregory, Richard, Guest, Martyn, Gunson, Rory N., Gupta, Ravi K., Gutierrez, Bernardo, Haldenby, Sam T., Hamilton, William L., Hansford, Samantha E., Haque, Tanzina, Harris, Kathryn A., Harrison, Ian, Harrison, Ewan M., Hart, Jennifer, Hartley, John A., Harvey, William T., Harvey, Matthew, Hassan-Ibrahim, Mohammed O., Heaney, Judith, Helmer, Thomas, Henderson, John H., Hesketh, Andrew R., Hey, Jessica, Heyburn, David, Higginson, Ellen E., Hill, Verity, Hill, Jack D., Hilson, Rachel A., Hilvers, Ember, Holden, Matthew T.G., Hollis, Amy, Holmes, Christopher W., Holmes, Nadine, Holmes, Alison H., Hopes, Richard, Hornsby, Hailey R., Hosmillo, Myra, Houlihan, Catherine, Howson-Wells, Hannah C., Hubb, Jonathan, Huckson, Hannah, Hughes, Warwick, Hughes, Joseph, Hughes, Margaret, Hutchings, Stephanie, Idle, Giles, Illingworth, Chris J., Impey, Robert, Irish-Tavares, Dianne, Iturriza-Gomara, Miren, Izuagbe, Rhys, Jackson, Chris, Jackson, Ben, Jackson, Leigh M., Jackson, Kathryn A., Jackson, David K., Jahun, Aminu S., James, Victoria, James, Keith, Jeanes, Christopher, Jeffries, Aaron R., Jeremiah, Sarah, Jermy, Andrew, John, Michaela, Johnson, Rob, Johnson, Kate, Johnston, Ian, Jones, Owen, Jones, Sophie, Jones, Hannah, Jones, Christopher R., Jones, Neil, Joseph, Amelia, Judges, Sarah, Kay, Gemma L., Kay, Sally, Keatley, Jon-Paul, Keeley, Alexander J., Kenyon, Anita, Kermack, Leanne M., Khakh, Manjinder, Kidd, Stephen P., Kimuli, Maimuna, Kirk, Stuart, Kitchen, Christine, Kitchman, Katie, Knight, Bridget A., Koshy, Cherian, Kraemer, Moritz U.G., Kumziene-Summerhayes, Sara, Kwiatkowski, Dominic, Lackenby, Angie, Laing, Kenneth G., Lampejo, Temi, Langford, Cordelia F., Lavin, Deborah, Lawton, Andrew I., Lee, Jack, Lee, David, Lensing, Stefanie V., Leonard, Steven, Levett, Lisa J., Le-Viet, Thanh, Lewis, Jonathan, Lewis, Kevin, Liddle, Jennifier, Liggett, Steven, Lillie, Patrick J., Lister, Michelle M., Livett, Rich, Lo, Stephanie, Loman, Nicholas J., Loose, Matthew W., Louka, Stavroula F., Loveson, Katie F., Lowdon, Sarah, Lowe, Hannah, Lowe, Helen L., Lucaci, Anita O., Ludden, Catherine, Lynch, Jessica, Lyons, Ronan A., Lythgoe, Katrina, Machin, Nicholas W., MacIntyre-Cockett, George, Mack, Andrew, Macklin, Ben, Maclean, Alasdair, Macnaughton, Emily, Madona, Pinglawathee, Maes, Mailis, Maftei, Laurentiu, Mahanama, Adhyana I.K., Mahungu, Tabitha W., Mair, Daniel, Maksimovic, Joshua, Malone, Cassandra S., Maloney, Daniel, Manesis, Nikos, Manley, Robin, Mantzouratou, Anna, Marchbank, Angela, Mariappan, Arun, Martincorena, Inigo, Martinez Nunez, Rocio T., Mather, Alison E., Maxwell, Patrick, Mayhew, Megan, Mbisa, Tamyo, McCann, Clare M., McCarthy, Shane A., McCluggage, Kathryn, McClure, Patrick C., McCrone, J.T., McHugh, Martin P., McKenna, James P., McKerr, Caoimhe, McManus, Georgina M., McMurray, Claire L., McMurray, Claire, McNally, Alan, Meadows, Lizzie, Medd, Nathan, Megram, Oliver, Menegazzo, Mirko, Merrick, Ian, Michell, Stephen L., Michelsen, Michelle L., Mirfenderesky, Mariyam, Mirza, Jeremy, Miskelly, Julia, Moles-Garcia, Emma, Moll, Robin J., Molnar, Zoltan, Monahan, Irene M., Mondani, Matteo, Mookerjee, Siddharth, Moore, Christopher, Moore, Jonathan, Moore, Nathan, Moore, Catherine, Morcrette, Helen, Morgan, Sian, Morgan, Mari, Mori, Matilde, Morriss, Arthur, Moses, Samuel, Mower, Craig, Muir, Peter, Mukaddas, Afrida, Munemo, Florence, Munn, Robert, Murray, Abigail, Murray, Leanne J., Murray, Darren R., Mutingwende, Manasa, Myers, Richard, Nastouli, Eleni, Nebbia, Gaia, Nelson, Andrew, Nelson, Charlotte, Nicholls, Sam, Nichols, Jenna, Nicodemi, Roberto, Nomikou, Kyriaki, O’Grady, Justin, O'Brien, Sarah, Odedra, Mina, Ohemeng-Kumi, Natasha, Oliver, Karen, Orton, Richard J., Osman, Husam, xeine O'Toole, Pacchiarini, Nicole, Padgett, Debra, Page, Andrew J., Park, Emily J., Park, Naomi R., Parmar, Surendra, Partridge, David G., Pascall, David, Patel, Amita, Patel, Bindi, Paterson, Steve, Payne, Brendan A.I., Peacock, Sharon J., Pearson, Clare, Pelosi, Emanuela, Percival, Benita, Perkins, Jon, Perry, Malorie, Pinckert, Malte L., Platt, Steven, Podplomyk, Olga, Pohare, Manoj, Pond, Marcus, Pope, Cassie F., Poplawski, Radoslaw, Powell, Jessica, Poyner, Jennifer, Prestwood, Liam, Price, Anna, Price, James R., Prieto, Jacqui A., Pritchard, David T., Prosolek, Sophie J., Pugh, Georgia, Pusok, Monika, Pybus, Oliver G., Pymont, Hannah M., Quail, Michael A., Quick, Joshua, Radulescu, Clara, Raghwani, Jayna, Ragonnet-Cronin, Manon, Rainbow, Lucille, Rajan, Diana, Rajatileka, Shavanthi, Ramadan, Newara A., Rambaut, Andrew, Ramble, John, Randell, Paul A., Randell, Paul, Ratcliffe, Liz, Raviprakash, Veena, Raza, Mohammad, Redshaw, Nicholas M., Rey, Sara, Reynolds, Nicola, Richter, Alex, Robertson, David L., Robinson, Esther, Robson, Samuel C., Rogan, Fiona, Rooke, Stefan, Rowe, Will, Roy, Sunando, Rudder, Steven, Ruis, Chris, Rushton, Steven, Ryan, Felicity, Saeed, Kordo, Samaraweera, Buddhini, Sambles, Christine M., Sanderson, Roy, Sanderson, Theo, Sang, Fei, Sass, Thea, Scher, Emily, Scott, Garren, Scott, Carol, Sehmi, Jasveen, Shaaban, Sharif, Shah, Divya, Shaw, Jessica, Shelest, Ekaterina, Shepherd, James G., Sheridan, Liz A., Sheriff, Nicola, Shirley, Lesley, Sillitoe, John, Silviera, Siona, Simpson, David A., Singh, Aditi, Singleton, Dawn, Skvortsov, Timofey, Sloan, Tim J., Sluga, Graciela, Smith, Ken, Smith, Kim S., Smith, Perminder, Smith, Darren L., Smith, Louise, Smith, Colin P., Smith, Nikki, Smollett, Katherine L., Snell, Luke B., Somassa, Thomas, Southgate, Joel, Spellman, Karla, Spencer Chapman, Michael H., Spurgin, Lewis G., Spyer, Moira J., Stanley, Rachael, Stanley, William, Stanton, Thomas D., Starinskij, Igor, Stockton, Joanne, Stonehouse, Susanne, Storey, Nathaniel, Studholme, David J., Sudhanva, Malur, Swindells, Emma, Taha, Yusri, Tan, Ngee Keong, Tang, Julian W., Tang, Miao, Taylor, Ben E.W., Taylor, Joshua F., Taylor, Sarah, Temperton, Ben, Templeton, Kate E., Thomas, Claire, Thomson, Laura, Thomson, Emma C., Thornton, Alicia, Thurston, Scott A.J., Todd, John A., Tomb, Rachael, Tong, Lily, Tonkin-Hill, Gerry, Torok, M. Estee, Tovar-Corona, Jaime M., Trebes, Amy, Trotter, Alexander J., Tsatsani, Ioulia, Turnbull, Robyn, Twohig, Katherine A., Umpleby, Helen, Underwood, Anthony P., Vamos, Edith E., Vasylyeva, Tetyana I., Vattipally, Sreenu, Vernet, Gabrielle, Vipond, Barry B., Volz, Erik M., Walsh, Sarah, Wang, Dennis, Warne, Ben, Warwick-Dugdale, Joanna, Wastnedge, Elizabeth, Watkins, Joanne, Watson, Louisa K., Waugh, Sheila, Webster, Hermione J., Weldon, Danni, Westwick, Elaine, Whalley, Thomas, Wheeler, Helen, Whitehead, Mark, Whiteley, Max, Whitwham, Andrew, Wierzbicki, Claudia, Willford, Nicholas J., Williams, Lesley-Anne, Williams, Rebecca, Williams, Cheryl, Williams, Chris, Williams, Charlotte A., Williams, Rachel J., Williams, Thomas, Williams, Catryn, Williamson, Kathleen A., Wilson-Davies, Eleri, Witele, Eric, Withell, Karen T., Witney, Adam A., Wolverson, Paige, Wong, Nick, Workman, Trudy, Wright, Victoria, Wright, Derek W., Wyatt, Tim, Wyllie, Sarah, Xu-McCrae, Li, Yavus, Mehmet, Yaze, Geraldine, Yeats, Corin A., Yebra, Gonzalo, Yew, Wen C., Young, Gregory R., Young, Jamie, Zarebski, Alex E., Zhang, Peijun, Baillie, J. Kenneth, Semple, Malcolm G., Openshaw, Peter J.M., Carson, Gail, Alex, Beatrice, Andrikopoulos, Petros, Bach, Benjamin, Barclay, Wendy S., Bogaert, Debby, Chechi, Kanta, Cooke, Graham S., Docherty, Annemarie B., Correia, Gonçalo dos Santos, Dumas, Marc-Emmanuel, Dunning, Jake, Fletcher, Tom, Green, Christopher A., Greenhalf, William, Griffin, Julian L., Gupta, Rishi K., Harrison, Ewen M., Hiscox, Julian A., Wai Ho, Antonia Ying, Horby, Peter W., Ijaz, Samreen, Khoo, Saye, Klenerman, Paul, Law, Andrew, Lewis, Matthew R., Liggi, Sonia, Lim, Wei Shen, Maslen, Lynn, Mentzer, Alexander J., Merson, Laura, Meynert, Alison M., Noursadeghi, Mahdad, Olanipekun, Michael, Osagie, Anthonia, Palmarini, Massimo, Palmieri, Carlo, Paxton, William A., Pollakis, Georgios, Price, Nicholas, Russell, Clark D., Sancho-Shimizu, Vanessa, Sands, Caroline J., Scott, Janet T., Sigfrid, Louise, Solomon, Tom, Sriskandan, Shiranee, Stuart, David, Summers, Charlotte, Swann, Olivia V., Takats, Zoltan, Takis, Panteleimon, Tedder, Richard S., Thompson, A.A. Roger, Thwaites, Ryan S., Zambon, Maria, Hardwick, Hayley, Donohue, Chloe, Griffiths, Fiona, Oosthuyzen, Wilna, Donegan, Cara, Spencer, Rebecca G., Dalton, Jo, Girvan, Michelle, Saviciute, Egle, Roberts, Stephanie, Harrison, Janet, Marsh, Laura, Connor, Marie, Halpin, Sophie, Jackson, Clare, Gamble, Carrol, Plotkin, Daniel, Lee, James, Leeming, Gary, Wham, Murray, Clohisey, Sara, Hendry, Ross, Scott-Brown, James, Shaw, Victoria, McDonald, Sarah E., Keating, Seán, Ahmed, Katie A., Armstrong, Jane A., Ashworth, Milton, Asiimwe, Innocent G., Bakshi, Siddharth, Barlow, Samantha L., Booth, Laura, Brennan, Benjamin, Bullock, Katie, Catterall, Benjamin W.A., Clark, Jordan J., Clarke, Emily A., Cole, Sarah, Cooper, Louise, Cox, Helen, Davis, Christopher, Dincarslan, Oslem, Dunn, Chris, Dyer, Philip, Elliott, Angela, Evans, Anthony, Finch, Lorna, Fisher, Lewis W.S., Foster, Terry, Garcia-Dorival, Isabel, Gunning, Philip, Hartley, Catherine, Jensen, Rebecca L., Jones, Christopher B., Jones, Trevor R., Khandaker, Shadia, King, Katharine, Kiy, Robyn T., Koukorava, Chrysa, Lake, Annette, Lant, Suzannah, Latawiec, Diane, Lavelle-Langham, Lara, Lefteri, Daniella, Lett, Lauren, Livoti, Lucia A., Mancini, Maria, McDonald, Sarah, McEvoy, Laurence, McLauchlan, John, Metelmann, Soeren, Miah, Nahida S., Middleton, Joanna, Mitchell, Joyce, Moore, Shona C., Murphy, Ellen G., Penrice-Randal, Rebekah, Pilgrim, Jack, Prince, Tessa, Reynolds, Will, Ridley, P. Matthew, Sales, Debby, Shaw, Victoria E., Shears, Rebecca K., Small, Benjamin, Subramaniam, Krishanthi S., Szemiel, Agnieska, Taggart, Aislynn, Tanianis-Hughes, Jolanta, Thomas, Jordan, Trochu, Erwan, van Tonder, Libby, Wilcock, Eve, Zhang, J. Eunice, Flaherty, Lisa, Maziere, Nicole, Cass, Emily, Carracedo, Alejandra Doce, Carlucci, Nicola, Holmes, Anthony, Massey, Hannah, Murphy, Lee, Wrobel, Nicola, McCafferty, Sarah, Morrice, Kirstie, MacLean, Alan, Adeniji, Kayode, Agranoff, Daniel, Agwuh, Ken, Ail, Dhiraj, Aldera, Erin L., Alegria, Ana, Allen, Sam, Angus, Brian, Ashish, Abdul, Atkinson, Dougal, Bari, Shahedal, Barlow, Gavin, Barnass, Stella, Barrett, Nicholas, Bassford, Christopher, Basude, Sneha, Baxter, David, Beadsworth, Michael, Bernatoniene, Jolanta, Berridge, John, Berry, Colin, Best, Nicola, Bothma, Pieter, Chadwick, David, Brittain-Long, Robin, Bulteel, Naomi, Burden, Tom, Burtenshaw, Andrew, Caruth, Vikki, Chambler, Duncan, Chee, Nigel, Child, Jenny, Chukkambotla, Srikanth, Clark, Tom, Collini, Paul, Cosgrove, Catherine, Cupitt, Jason, Cutino-Moguel, Maria-Teresa, Dark, Paul, Dawson, Chris, Donnison, Phil, Douthwaite, Sam, Drummond, Andrew, DuRand, Ingrid, Dushianthan, Ahilanadan, Dyer, Tristan, Eziefula, Chi, Fegan, Chrisopher, Finn, Adam, Fullerton, Duncan, Garg, Sanjeev, Garg, Atul, Gkrania-Klotsas, Effrossyni, Godden, Jo, Goldsmith, Arthur, Hardy, Elaine, Hartshorn, Stuart, Harvey, Daniel, Havalda, Peter, Hawcutt, Daniel B., Hobrok, Maria, Hodgson, Luke, Hormis, Anil, Jacobs, Michael, Jain, Susan, Jennings, Paul, Kaliappan, Agilan, Kasipandian, Vidya, Kegg, Stephen, Kelsey, Michael, Kendall, Jason, Kerrison, Caroline, Kerslake, Ian, Koch, Oliver, Koduri, Gouri, Koshy, George, Laha, Shondipon, Laird, Steven, Larkin, Susan, Leiner, Tamas, Lillie, Patrick, Limb, James, Linnett, Vanessa, Little, Jeff, Lyttle, Mark, MacMahon, Michael, MacNaughton, Emily, Mankregod, Ravish, Masson, Huw, Matovu, Elijah, McCullough, Katherine, McEwen, Ruth, Meda, Manjula, Mills, Gary, Minton, Jane, Mohandas, Kavya, Mok, Quen, Moon, James, Moore, Elinoor, Morgan, Patrick, Morris, Craig, Mortimore, Katherine, Mpenge, Mbiye, Mulla, Rohinton, Murphy, Michael, Nagel, Megan, Nagarajan, Thapas, Nelson, Mark, Norris, Lillian, O'Shea, Matthew K., Otahal, Igor, Ostermann, Marlies, Pais, Mark, Panchatsharam, Selva, Papakonstantinou, Danai, Paraiso, Hassan, Patel, Brij, Pattison, Natalie, Pepperell, Justin, Peters, Mark, Phull, Mandeep, Pintus, Stefania, Pooni, Jagtur Singh, Planche, Tim, Post, Frank, Price, David, Prout, Rachel, Rae, Nikolas, Reschreiter, Henrik, Reynolds, Tim, Richardson, Neil, Roberts, Mark, Roberts, Devender, Rose, Alistair, Rousseau, Guy, Ruge, Bobby, Ryan, Brendan, Saluja, Taranprit, Schmid, Matthias L., Shah, Aarti, Shanmuga, Prad, Sharma, Anil, Shawcross, Anna, Sizer, Jeremy, Shankar-Hari, Manu, Smith, Richard, Snelson, Catherine, Spittle, Nick, Staines, Nikki, Stambach, Tom, Stewart, Richard, Subudhi, Pradeep, Szakmany, Tamas, Tatham, Kate, Thomas, Jo, Thompson, Chris, Thompson, Robert, Tridente, Ascanio, Tupper-Carey, Darell, Twagira, Mary, Vallotton, Nick, Vancheeswaran, Rama, Vincent-Smith, Lisa, Visuvanathan, Shico, Vuylsteke, Alan, Waddy, Sam, Wake, Rachel, Walden, Andrew, Welters, Ingeborg, Whitehouse, Tony, Whittaker, Paul, Whittington, Ashley, Papineni, Padmasayee, Wijesinghe, Meme, Williams, Martin, Wilson, Lawrence, Winchester, Stephen, Wiselka, Martin, Wolverson, Adam, Wootton, Daniel G., Workman, Andrew, Yates, Bryan, Young, Peter, de Silva, Thushan I., Liu, Guihai, Lindsey, Benjamin B., Dong, Danning, Hsu, Nienyun Sharon, Shah, Dhruv, Wellington, Dannielle, Angyal, Adrienn, Brown, Rebecca, Parker, Matthew D., Ying, Zixi, Yao, Xuan, Turtle, Lance, Dunachie, Susanna, Maini, Mala K., Ogg, Graham, Knight, Julian C., Peng, Yanchun, Rowland-Jones, Sarah L., and Dong, Tao

Published
2021
Full Text
View/download PDF

7. Environmental microbiome in the home and daycare settings during the COVID‐19 pandemic, and potential risk of non‐communicable disease in children.

Author

McKay, Jill A., Crown, Matthew, Bashton, Matthew, Pearce, David, Entwistle, Jane A., and Sangal, Vartul

Subjects
*COVID-19 pandemic, *NON-communicable diseases, *ECOLOGICAL houses, *COMMUNICABLE diseases, *MICROORGANISM populations, *MICROBIAL diversity
Abstract

An exposure to diverse microbial population early in life is important for the development of immunity against various non‐communicable diseases including asthma, childhood leukaemia and other cancers. Social mixing in daycare settings helps with exposure to a variety of microbes. However, social isolation and a high emphasis on workplace hygiene during the COVID pandemic may have affected children's exposure to diverse microbiota. The structure of microbial communities and their role in developing immunity to various diseases are not well understood. In this study, we investigated the structure of microbial communities in daycare and home settings during the pandemic. Interestingly, microbial diversity was relatively higher in dust samples collected from homes, with human‐associated taxa being more prevalent compared to those from daycare settings. Environmental microbes were more abundant in dust samples from daycare providers. These results potentially suggest that cleaning practices during the pandemic may have influenced the diversity and microbial abundance of the daycare samples. Several bacterial taxa detected in both the environments are known to induce anti‐inflammatory and immunomodulatory responses, conferring protection from various diseases. Therefore, exposure to diverse microbial population in early childhood may play an important role in developing immunity against various non‐communicable and infectious diseases. [ABSTRACT FROM AUTHOR]

Published
2024
Full Text
View/download PDF

8. Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes

Author

Cotton, S., primary, McHugh, M.P., additional, Dewar, R., additional, Haas, J.G., additional, Templeton, K., additional, Robson, Samuel C., additional, Connor, Thomas R., additional, Loman, Nicholas J., additional, Golubchik, Tanya, additional, Martinez Nunez, Rocio T., additional, Bonsall, David, additional, Rambaut, Andrew, additional, Snell, Luke B., additional, Livett, Rich, additional, Ludden, Catherine, additional, Corden, Sally, additional, Nastouli, Eleni, additional, Nebbia, Gaia, additional, Johnston, Ian, additional, Prieto, Jacqui A., additional, Saeed, Kordo, additional, Jackson, David K., additional, Houlihan, Catherine, additional, Frampton, Dan, additional, Hamilton, William L., additional, Witney, Adam A., additional, Bucca, Giselda, additional, Pope, Cassie F., additional, Moore, Catherine, additional, Thomson, Emma C., additional, Cutino-Moguel, Teresa, additional, Harrison, Ewan M., additional, Smith, Colin P., additional, Rogan, Fiona, additional, Beckwith, Shaun M., additional, Murray, Abigail, additional, Singleton, Dawn, additional, Eastick, Kirstine, additional, Sheridan, Liz A., additional, Randell, Paul, additional, Jackson, Leigh M., additional, Ariani, Cristina V., additional, Gonçalves, Sónia, additional, Fairley, Derek J., additional, Loose, Matthew W., additional, Watkins, Joanne, additional, Moses, Samuel, additional, Nicholls, Sam, additional, Bull, Matthew, additional, Amato, Roberto, additional, Smith, Darren L., additional, Aanensen, David M., additional, Barrett, Jeffrey C., additional, Kele, Beatrix, additional, Aggarwal, Dinesh, additional, Shepherd, James G., additional, Curran, Martin D., additional, Parmar, Surendra, additional, Parker, Matthew D., additional, Williams, Catryn, additional, Glaysher, Sharon, additional, Underwood, Anthony P., additional, Bashton, Matthew, additional, Pacchiarini, Nicole, additional, Loveson, Katie F., additional, Byott, Matthew, additional, Carabelli, Alessandro M., additional, Templeton, Kate E., additional, Peacock, Sharon J., additional, de Silva, Thushan I., additional, Wang, Dennis, additional, Langford, Cordelia F., additional, Sillitoe, John, additional, Gunson, Rory N., additional, Cottrell, Simon, additional, O’Grady, Justin, additional, Kwiatkowski, Dominic, additional, Lillie, Patrick J., additional, Cortes, Nicholas, additional, Moore, Nathan, additional, Thomas, Claire, additional, Burns, Phillipa J., additional, Mahungu, Tabitha W., additional, Liggett, Steven, additional, Beckett, Angela H., additional, Holden, Matthew TG., additional, Levett, Lisa J., additional, Osman, Husam, additional, Hassan-Ibrahim, Mohammed O., additional, Simpson, David A., additional, Chand, Meera, additional, Gupta, Ravi K., additional, Darby, Alistair C., additional, Paterson, Steve, additional, Pybus, Oliver G., additional, Volz, Erik M., additional, de Angelis, Daniela, additional, Robertson, David L., additional, Page, Andrew J., additional, Martincorena, Inigo, additional, Aigrain, Louise, additional, Bassett, Andrew R., additional, Wong, Nick, additional, Taha, Yusri, additional, Erkiert, Michelle J., additional, Spencer Chapman, Michael H., additional, Dewar, Rebecca, additional, McHugh, Martin P., additional, Mookerjee, Siddharth, additional, Aplin, Stephen, additional, Harvey, Matthew, additional, Sass, Thea, additional, Umpleby, Helen, additional, Wheeler, Helen, additional, McKenna, James P., additional, Warne, Ben, additional, Taylor, Joshua F., additional, Chaudhry, Yasmin, additional, Izuagbe, Rhys, additional, Jahun, Aminu S., additional, Young, Gregory R., additional, McMurray, Claire, additional, McCann, Clare M., additional, Nelson, Andrew, additional, Elliott, Scott, additional, Lowe, Hannah, additional, Price, Anna, additional, Crown, Matthew R., additional, Rey, Sara, additional, Roy, Sunando, additional, Temperton, Ben, additional, Shaaban, Sharif, additional, Hesketh, Andrew R., additional, Laing, Kenneth G., additional, Monahan, Irene M., additional, Heaney, Judith, additional, Pelosi, Emanuela, additional, Silviera, Siona, additional, Wilson-Davies, Eleri, additional, Fryer, Helen, additional, Adams, Helen, additional, du Plessis, Louis, additional, Johnson, Rob, additional, Harvey, William T., additional, Hughes, Joseph, additional, Orton, Richard J., additional, Spurgin, Lewis G., additional, Bourgeois, Yann, additional, Ruis, Chris, additional, O'Toole, Áine, additional, Gourtovaia, Marina, additional, Sanderson, Theo, additional, Fraser, Christophe, additional, Edgeworth, Jonathan, additional, Breuer, Judith, additional, Michell, Stephen L., additional, Todd, John A., additional, John, Michaela, additional, Buck, David, additional, Gajee, Kavitha, additional, Kay, Gemma L., additional, Heyburn, David, additional, Charalampous, Themoula, additional, Alcolea-Medina, Adela, additional, Kitchman, Katie, additional, McNal, Alan, additional, Pritch, David T., additional, Dervisevic, Samir, additional, Muir, Peter, additional, Robinson, Esther, additional, Vipond, Barry B., additional, Ramadan, Newara A., additional, Jeanes, Christopher, additional, Weldon, Danni, additional, Catalan, Jana, additional, Jones, Neil, additional, da Silva Filipe, Ana, additional, Williams, Chris, additional, Fuchs, Marc, additional, Miskelly, Julia, additional, Jeffries, Aaron R., additional, Oliver, Karen, additional, Park, Naomi R., additional, Ash, Amy, additional, Koshy, Cherian, additional, Barrow, Magdalena, additional, Buchan, Sarah L., additional, Mantzouratou, Anna, additional, Clark, Gemma, additional, Holmes, Christopher W., additional, Campbell, Sharon, additional, Davis, Thomas, additional, Tan, Ngee Keong, additional, Brown, Julianne R., additional, Harris, Kathryn A., additional, Kidd, Stephen P., additional, Grant, Paul R., additional, Xu-McCrae, Li, additional, Cox, Alison, additional, Madona, Pinglawathee, additional, Pond, Marcus, additional, Randell, Paul A., additional, Withell, Karen T., additional, Williams, Cheryl, additional, Graham, Clive, additional, Denton-Smith, Rebecca, additional, Swindells, Emma, additional, Turnbull, Robyn, additional, Sloan, Tim J., additional, Bosworth, Andrew, additional, Hutchings, Stephanie, additional, Pymont, Hannah M., additional, Casey, Anna, additional, Ratcliffe, Liz, additional, Jones, Christopher R., additional, Knight, Bridget A., additional, Haque, Tanzina, additional, Hart, Jennifer, additional, Irish-Tavares, Dianne, additional, Witele, Eric, additional, Mower, Craig, additional, Watson DipHE, Louisa K., additional, Collins, Jennifer, additional, Eltringham, Gary, additional, Crudgington, Dorian, additional, Macklin, Ben, additional, Iturriza-Gomara, Miren, additional, Lucaci, Anita O., additional, McClure, Patrick C., additional, Carlile, Matthew, additional, Holmes, Nadine, additional, Moore, Christopher, additional, Storey, Nathaniel, additional, Rooke, Stefan, additional, Yebra, Gonzalo, additional, Craine, Noel, additional, Perry, Malorie, additional, Alikhan, Nabil-Fareed, additional, Bridgett, Stephen, additional, Cook, Kate F., additional, Fearn, Christopher, additional, Goudarzi, Salman, additional, Lyons, Ronan A., additional, Williams, Thomas, additional, Haldenby, Sam T., additional, Durham, Jillian, additional, Leonard, Steven, additional, Davies, Robert M., additional, Batra, Rahul, additional, Blane, Beth, additional, Spyer, Moira J., additional, Smith, Perminder, additional, Yavus, Mehmet, additional, Williams, Rachel J., additional, Mahanama, Adhyana IK., additional, Samaraweera, Buddhini, additional, Girgis, Sophia T., additional, Hansford, Samantha E., additional, Green, Angie, additional, Beaver, Charlotte, additional, Bellis, Katherine L., additional, Dorman, Matthew J., additional, Kay, Sally, additional, Prestwood, Liam, additional, Rajatileka, Shavanthi, additional, Quick, Joshua, additional, Poplawski, Radoslaw, additional, Reynolds, Nicola, additional, Mack, Andrew, additional, Morriss, Arthur, additional, Whalley, Thomas, additional, Patel, Bindi, additional, Georgana, Iliana, additional, Hosmillo, Myra, additional, Pinckert, Malte L., additional, Stockton, Joanne, additional, Henderson, John H., additional, Hollis, Amy, additional, Stanley, William, additional, Yew, Wen C., additional, Myers, Richard, additional, Thornton, Alicia, additional, Adams, Alexander, additional, Annett, Tara, additional, Asad, Hibo, additional, Birchley, Alec, additional, Coombes, Jason, additional, Evans, Johnathan M., additional, Fina, Laia, additional, Gatica-Wilcox, Bree, additional, Gilbert, Lauren, additional, Graham, Lee, additional, Hey, Jessica, additional, Hilvers, Ember, additional, Jones, Sophie, additional, Jones, Hannah, additional, Kumziene-Summerhayes, Sara, additional, McKerr, Caoimhe, additional, Powell, Jessica, additional, Pugh, Georgia, additional, Taylor, Sarah, additional, Trotter, Alexander J., additional, Williams, Charlotte A., additional, Kermack, Leanne M., additional, Foulkes, Benjamin H., additional, Gallis, Marta, additional, Hornsby, Hailey R., additional, Louka, Stavroula F., additional, Pohare, Manoj, additional, Wolverson, Paige, additional, Zhang, Peijun, additional, MacIntyre-Cockett, George, additional, Trebes, Amy, additional, Moll, Robin J., additional, Ferguson, Lynne, additional, Goldstein, Emily J., additional, Maclean, Alasdair, additional, Tomb, Rachael, additional, Starinskij, Igor, additional, Thomson, Laura, additional, Southgate, Joel, additional, Kraemer, Moritz UG., additional, Raghwani, Jayna, additional, Zarebski, Alex E., additional, Boyd, Olivia, additional, Geidelberg, Lily, additional, Illingworth, Chris J., additional, Jackson, Chris, additional, Pascall, David, additional, Vattipally, Sreenu, additional, Freeman, Timothy M., additional, Hsu, Sharon N., additional, Lindsey, Benjamin B., additional, James, Keith, additional, Lewis, Kevin, additional, Tonkin-Hill, Gerry, additional, Tovar-Corona, Jaime M., additional, Cox, MacGregor, additional, Abudahab, Khalil, additional, Menegazzo, Mirko, additional, Taylor, Ben EW., additional, Yeats, Corin A., additional, Mukaddas, Afrida, additional, Wright, Derek W., additional, de Oliveira Martins, Leonardo, additional, Colquhoun, Rachel, additional, Hill, Verity, additional, Jackson, Ben, additional, McCrone, J.T., additional, Medd, Nathan, additional, Scher, Emily, additional, Keatley, Jon-Paul, additional, Curran, Tanya, additional, Morgan, Sian, additional, Maxwell, Patrick, additional, Smith, Ken, additional, Eldirdiri, Sahar, additional, Kenyon, Anita, additional, Holmes, Alison H., additional, Price, James R., additional, Wyatt, Tim, additional, Mather, Alison E., additional, Skvortsov, Timofey, additional, Hartley, John A., additional, Guest, Martyn, additional, Kitchen, Christine, additional, Merrick, Ian, additional, Munn, Robert, additional, Bertolusso, Beatrice, additional, Lynch, Jessica, additional, Vernet, Gabrielle, additional, Kirk, Stuart, additional, Wastnedge, Elizabeth, additional, Stanley, Rachael, additional, Idle, Giles, additional, Bradley, Declan T., additional, Killough, Nicholas F., additional, Poyner, Jennifer, additional, Mori, Matilde, additional, Jones, Owen, additional, Wright, Victoria, additional, Brooks, Ellena, additional, Churcher, Carol M., additional, Delgado Callico, Laia, additional, Fragakis, Mireille, additional, Galai, Katerina, additional, Jermy, Andrew, additional, Judges, Sarah, additional, Markov, Anna, additional, McManus, Georgina M., additional, Smith, Kim S., additional, Thomas-McEwen, Peter MD., additional, Westwick, Elaine, additional, Attwood, Stephen W., additional, Bolt, Frances, additional, Davies, Alisha, additional, De Lacy, Elen, additional, Downing, Fatima, additional, Edwards, Sue, additional, Meadows, Lizzie, additional, Jeremiah, Sarah, additional, Smith, Nikki, additional, Foulser, Luke, additional, Patel, Amita, additional, Berry, Louise, additional, Boswell, Tim, additional, Fleming, Vicki M., additional, Howson-Wells, Hannah C., additional, Joseph, Amelia, additional, Khakh, Manjinder, additional, Lister, Michelle M., additional, Bird, Paul W., additional, Fallon, Karlie, additional, Helmer, Thomas, additional, McMurray, Claire L., additional, Odedra, Mina, additional, Shaw, Jessica, additional, Tang, Julian W., additional, Willford, Nicholas J., additional, Blakey, Victoria, additional, Raviprakash, Veena, additional, Sheriff, Nicola, additional, Williams, Lesley-Anne, additional, Feltwell, Theresa, additional, Bedford, Luke, additional, Cargill, James S., additional, Hughes, Warwick, additional, Moore, Jonathan, additional, Stonehouse, Susanne, additional, Atkinson, Laura, additional, Lee, Jack CD., additional, Shah, Divya, additional, Ohemeng-Kumi, Natasha, additional, Ramble, John, additional, Sehmi, Jasveen, additional, Williams, Rebecca, additional, Chatterton, Wendy, additional, Pusok, Monika, additional, Everson, William, additional, Castigador, Anibolina, additional, Macnaughton, Emily, additional, El Bouzidi, Kate, additional, Lampejo, Temi, additional, Sudhanva, Malur, additional, Breen, Cassie, additional, Sluga, Graciela, additional, Ahmad, Shazaad SY., additional, George, Ryan P., additional, Machin, Nicholas W., additional, Binns, Debbie, additional, James, Victoria, additional, Blacow, Rachel, additional, Coupland, Lindsay, additional, Smith, Louise, additional, Barton, Edward, additional, Padgett, Debra, additional, Scott, Garren, additional, Cross, Aidan, additional, Mirfenderesky, Mariyam, additional, Greenaway, Jane, additional, Cole, Kevin, additional, Clarke, Phillip, additional, Duckworth, Nichola, additional, Walsh, Sarah, additional, Bicknell, Kelly, additional, Impey, Robert, additional, Wyllie, Sarah, additional, Hopes, Richard, additional, Bishop, Chloe, additional, Chalker, Vicki, additional, Harrison, Ian, additional, Gifford, Laura, additional, Molnar, Zoltan, additional, Auckland, Cressida, additional, Evans, Cariad, additional, Johnson, Kate, additional, Partridge, David G., additional, Raza, Mohammad, additional, Baker, Paul, additional, Bonner, Stephen, additional, Essex, Sarah, additional, Murray, Leanne J., additional, Lawton, Andrew I., additional, Burton-Fanning, Shirelle, additional, Payne, Brendan AI., additional, Waugh, Sheila, additional, Gomes, Andrea N., additional, Kimuli, Maimuna, additional, Murray, Darren R., additional, Ashfield, Paula, additional, Dobie, Donald, additional, Ashford, Fiona, additional, Best, Angus, additional, Crawford, Liam, additional, Cumley, Nicola, additional, Mayhew, Megan, additional, Megram, Oliver, additional, Mirza, Jeremy, additional, Moles-Garcia, Emma, additional, Percival, Benita, additional, Driscoll, Megan, additional, Ensell, Leah, additional, Lowe, Helen L., additional, Maftei, Laurentiu, additional, Mondani, Matteo, additional, Chaloner, Nicola J., additional, Cogger, Benjamin J., additional, Easton, Lisa J., additional, Huckson, Hannah, additional, Lewis, Jonathan, additional, Lowdon, Sarah, additional, Malone, Cassandra S., additional, Munemo, Florence, additional, Mutingwende, Manasa, additional, Nicodemi, Roberto, additional, Podplomyk FD, Olga, additional, Somassa, Thomas, additional, Beggs, Andrew, additional, Richter, Alex, additional, Cormie, Claire, additional, Dias, Joana, additional, Forrest, Sally, additional, Higginson, Ellen E., additional, Maes, Mailis, additional, Young, Jamie, additional, Davidson, Rose K., additional, Jackson, Kathryn A., additional, Keeley, Alexander J., additional, Ball, Jonathan, additional, Byaruhanga, Timothy, additional, Chappell, Joseph G., additional, Dey, Jayasree, additional, Hill, Jack D., additional, Park, Emily J., additional, Fanaie, Arezou, additional, Hilson, Rachel A., additional, Yaze, Geraldine, additional, Lo, Stephanie, additional, Afifi, Safiah, additional, Beer, Robert, additional, Maksimovic, Joshua, additional, McCluggage, Kathryn, additional, Spellman, Karla, additional, Bresner, Catherine, additional, Fuller, William, additional, Marchbank, Angela, additional, Workma, Trudy, additional, Shelest, Ekaterina, additional, Debebe, Johnny, additional, Sang, Fei, additional, Francois, Sarah, additional, Gutierrez, Bernardo, additional, Vasylyeva, Tetyana I., additional, Flaviani, Flavia, additional, Ragonnet-Cronin, Manon, additional, Smollett, Katherine L., additional, Broos, Alice, additional, Mair, Daniel, additional, Nichols, Jenna, additional, Nomikou, Kyriaki, additional, Tong, Lily, additional, Tsatsani, Ioulia, additional, O'Brien, Sarah, additional, Rushton, Steven, additional, Sanderson, Roy, additional, Perkins, Jon, additional, Cotton, Seb, additional, Gallagher, Abbie, additional, Allara, Elias, additional, Pearson, Clare, additional, Bibby, David, additional, Dabrer, Gavin, additional, Ellaby, Nicholas, additional, Gallagher, Eileen, additional, Hubb, Jonathan, additional, Lackenby, Angie, additional, Lee, David, additional, Manesis, Nikos, additional, Mbisa, Tamyo, additional, Platt, Steven, additional, Twohig, Katherine A., additional, Morgan, Mari, additional, Aydin, Alp, additional, Baker, David J., additional, Foster-Nyarko, Ebenezer, additional, Prosolek, Sophie J., additional, Rudder, Steven, additional, Baxter, Chris, additional, Carvalho, Sílvia F., additional, Lavin, Deborah, additional, Mariappan, Arun, additional, Radulescu, Clara, additional, Singh, Aditi, additional, Tang, Miao, additional, Morcrette, Helen, additional, Bayzid, Nadua, additional, Cotic, Marius, additional, Balcazar, Carlos E., additional, Gallagher, Michael D., additional, Maloney, Daniel, additional, Stanton, Thomas D., additional, Williamson, Kathleen A., additional, Manley, Robin, additional, Michelsen, Michelle L., additional, Sambles, Christine M., additional, Studholme, David J., additional, Warwick-Dugdale, Joanna, additional, Eccles, Richard, additional, Gemmell, Matthew, additional, Gregory, Richard, additional, Hughes, Margaret, additional, Nelson, Charlotte, additional, Rainbow, Lucille, additional, Vamos, Edith E., additional, Webster, Hermione J., additional, Whitehead, Mark, additional, Wierzbicki, Claudia, additional, Angyal, Adrienn, additional, Green, Luke R., additional, Whiteley, Max, additional, Betteridge, Emma, additional, Bronner, Iraad F., additional, Farr, Ben W., additional, Goodwin, Scott, additional, Lensing, Stefanie V., additional, McCarthy, Shane A., additional, Quail, Michael A., additional, Rajan, Diana, additional, Redshaw, Nicholas M., additional, Scott, Carol, additional, Shirley, Lesley, additional, Thurston, Scott AJ., additional, Rowe, Will, additional, Gaskin, Amy, additional, Le-Viet, Thanh, additional, Bonfield, James, additional, Liddle, Jennifier, additional, and Whitwham, Andrew, additional

Published
2023
Full Text
View/download PDF

9. Outcomes of SARS-CoV-2 omicron infection in residents of long-term care facilities in England (VIVALDI): a prospective, cohort study

Author

Krutikov, Maria, Stirrup, Oliver, Nacer-Laidi, Hadjer, Azmi, Borscha, Fuller, Chris, Tut, Gokhan, Palmer, Tom, Shrotri, Madhumita, Irwin-Singer, Aidan, Baynton, Verity, Hayward, Andrew, Moss, Paul, Copas, Andrew, Shallcross, Laura, The COVID-19 Genomics UK (COG-UK) Consortium, Smith, Darren, Bashton, Matthew, McCann, Clare, Young, Greg, Nelson, Andrew, Crown, Matthew, Henderson, John, Hollis, Amy, Stanley, William, and Yew, Wen Chyin

Subjects
Aged, 80 and over, Male, Health (social science), SARS-CoV-2, COVID-19, B100, C500, Long-Term Care, State Medicine, Cohort Studies, Psychiatry and Mental health, Humans, Female, Prospective Studies, Geriatrics and Gerontology, Family Practice
Abstract

Background: The SARS-CoV-2 omicron variant (B.1.1.529) is highly transmissible, but disease severity appears to be reduced compared with previous variants such as alpha and delta. We investigated the risk of severe outcomes following infection in residents of long-term care facilities. Methods: We did a prospective cohort study in residents of long-term care facilities in England who were tested regularly for SARS-CoV-2 between Sept 1, 2021, and Feb 1, 2022, and who were participants of the VIVALDI study. Residents were eligible for inclusion if they had a positive PCR or lateral flow device test during the study period, which could be linked to a National Health Service (NHS) number, enabling linkage to hospital admissions and mortality datasets. PCR or lateral flow device test results were linked to national hospital admission and mortality records using the NHS-number-based pseudo-identifier. We compared the risk of hospital admission (within 14 days following a positive SARS-CoV-2 test) or death (within 28 days) in residents who had tested positive for SARS-CoV-2 in the period shortly before omicron emerged (delta-dominant) and in the omicron-dominant period, adjusting for age, sex, primary vaccine course, past infection, and booster vaccination. Variants were confirmed by sequencing or spike-gene status in a subset of samples. Results: 795 233 tests were done in 333 long-term care facilities, of which 159 084 (20·0%) could not be linked to a pseudo-identifier and 138 012 (17·4%) were done in residents. Eight residents had two episodes of infection (>28 days apart) and in these cases the second episode was excluded from the analysis. 2264 residents in 259 long-term care facilities (median age 84·5 years, IQR 77·9–90·0) were diagnosed with SARS-CoV-2, of whom 253 (11·2%) had a previous infection and 1468 (64·8%) had received a booster vaccination. About a third of participants were male. Risk of hospital admissions was markedly lower in the 1864 residents infected in the omicron-period (4·51%, 95% CI 3·65–5·55) than in the 400 residents infected in the pre-omicron period (10·50%, 7·87–13·94), as was risk of death (5·48% [4·52–6·64] vs 10·75% [8·09–14·22]). Adjusted hazard ratios (aHR) also indicated a reduction in hospital admissions (0·64, 95% CI 0·41–1·00; p=0·051) and mortality (aHR 0·68, 0·44–1·04; p=0·076) in the omicron versus the pre-omicron period. Findings were similar in residents with a confirmed variant. Interpretation: Observed reduced severity of the omicron variant compared with previous variants suggests that the wave of omicron infections is unlikely to lead to a major surge in severe disease in long-term care facility populations with high levels of vaccine coverage or natural immunity. Continued surveillance in this vulnerable population is important to protect residents from infection and monitor the public health effect of emerging variants. Funding: UK Department of Health and Social Care.

Published
2022
Full Text
View/download PDF

10. Viral burden is associated with age, vaccination, and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection-related sampling bias.

Author

Fryer, Helen R., Golubchik, Tanya, Hall, Matthew, Fraser, Christophe, Hinch, Robert, Ferretti, Luca, Thomson, Laura, Nurtay, Anel, Pellis, Lorenzo, House, Thomas, MacIntyre-Cockett, George, Trebes, Amy, Buck, David, Piazza, Paolo, Green, Angie, Lonie, Lorne J, Smith, Darren, Bashton, Matthew, Crown, Matthew, and Nelson, Andrew

Subjects
PARTIAL least squares regression, SARS-CoV-2 Delta variant, VACCINATION status, SARS-CoV-2, VACCINATION
Abstract

In this study, we evaluated the impact of viral variant, in addition to other variables, on within-host viral burden, by analysing cycle threshold (Ct) values derived from nose and throat swabs, collected as part of the UK COVID-19 Infection Survey. Because viral burden distributions determined from community survey data can be biased due to the impact of variant epidemiology on the time-since-infection of samples, we developed a method to explicitly adjust observed Ct value distributions to account for the expected bias. By analysing the adjusted Ct values using partial least squares regression, we found that among unvaccinated individuals with no known prior exposure, viral burden was 44% lower among Alpha variant infections, compared to those with the predecessor strain, B.1.177. Vaccination reduced viral burden by 67%, and among vaccinated individuals, viral burden was 286% higher among Delta variant, compared to Alpha variant, infections. In addition, viral burden increased by 17% for every 10-year age increment of the infected individual. In summary, within-host viral burden increases with age, is reduced by vaccination, and is influenced by the interplay of vaccination status and viral variant. Author summary: The SARS-CoV-2 epidemic in the United Kingdom (UK) has been characterized by the successive transmission of distinct viral variants. Viral variation can impact viral properties, including infectiousness and pathogenicity. These properties may be linked to the amount of virus present in an infected individual. In this study, we examined the association between intra-patient viral burden and a range of factors, including viral variant, using a large, population-representative SARS-CoV-2 survey conducted in the UK. As part of our investigation, we developed a novel method to account for bias in sampled viral burden resulting from the study's sampling methodology. Our findings indicate that viral burden within the host increases with age, is reduced by vaccination, and is influenced by the interplay between vaccination status and viral variant. [ABSTRACT FROM AUTHOR]

Published
2023
Full Text
View/download PDF

11. Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning

Author

Nickbakhsh, Sema, Hughes, Joseph, Christofidis, Nicolaos, Griffiths, Emily, Shaaban, Sharif, Enright, Jessica, Smollett, Katherine, Nomikou, Kyriaki, Palmalux, Natasha, Tong, Lily, Carmichael, Stephen, Sreenu, Vattipally B., Orton, Richard, Goldstein, Emily J., Tomb, Rachael M., Robson, Samuel C., Connor, Thomas R., Loman, Nicholas J., Golubchik, Tanya, Nunez, Rocio T. Martinez, Bonsall, David, Rambaut, Andrew, Snell, Luke B., Livett, Rich, Ludden, Catherine, Corden, Sally, Nastouli, Eleni, Nebbia, Gaia, Johnston, Ian, Lythgoe, Katrina, Torok, M. Estee, Goodfellow, Ian G., Prieto, Jacqui A., Saeed, Kordo, Jackson, David K., Houlihan, Catherine, Frampton, Dan, Hamilton, William L., Witney, Adam A., Bucca, Giselda, Pope, Cassie F., Moore, Catherine, Thomson, Emma C., Harrison, Ewan M., Smith, Colin P., Rogan, Fiona, Beckwith, Shaun M., Murray, Abigail, Singleton, Dawn, Eastick, Kirstine, Sheridan, Liz A., Randell, Paul, Jackson, Leigh M., Ariani, Cristina V., Gonçalves, Sónia, Fairley, Derek J., Loose, Matthew W., Watkins, Joanne, Moses, Samuel, Nicholls, Sam, Bull, Matthew, Amato, Roberto, Smith, Darren L., Aanensen, David M., Barrett, Jeffrey C., Aggarwal, Dinesh, Shepherd, James G., Curran, Martin D., Parmar, Surendra, Parker, Matthew D., Williams, Catryn, Glaysher, Sharon, Underwood, Anthony P., Bashton, Matthew, Pacchiarini, Nicole, Loveson, Katie F., Byott, Matthew, Carabelli, Alessandro M., Templeton, Kate E., de Silva, Thushan I., Wang, Dennis, Langford, Cordelia F., Sillitoe, John, Gunson, Rory N., Cottrell, Simon, O?Grady, Justin, Kwiatkowski, Dominic, Lillie, Patrick J., Cortes, Nicholas, Moore, Nathan, Thomas, Claire, Burns, Phillipa J., Mahungu, Tabitha W., Liggett, Steven, Beckett, Angela H., Holden, Matthew T. G., Levett, Lisa J., Osman, Husam, Hassan-Ibrahim, Mohammed O., Simpson, David A., Chand, Mrera, Gupta, Ravi K., Darby, Alistair C., Paterson, Steve, Pybus, Oliver G., Volz, Erik M., de Angelis, Daniela, Robertson, David L., Page, Andrew J., Martincorena, Inigo, Aigrain, Louise, Bassett, Andrew R., Wong, Nick, Taha, Yusri, Erkiert, Michelle J., Chapman, Michael H. Spencer, Dewar, Rebecca, McHugh, Martin P., Mookerjee, Siddharth, Aplin, Stephen, Harvey, Matthew, Sass, Thea, Umpleby, Helen, Wheeler, Helen, McKenna, James P., Warne, Ben, Taylor, Joshua F., Chaudhry, Yasmin, Izuagbe, Rhys, Jahun, Aminu S., Young, Gregory R., McMurray, Claire, McCann, Clare M., Nelson, Andrew, Elliott, Scott, Lowe, Hannah, Price, Anna, Crown, Matthew R., Rey, Sara, Roy, Sunando, Temperton, Ben, Hesketh, Andrew R., Laing, Kenneth G., Monahan, Irene M., Heaney, Judith, Pelosi, Emanuela, Silviera, Siona, Wilson-Davies, Eleri, Fryer, Helen, Adams, Helen, du Plessis, Louis, Johnson, Rob, Harvey, William T., Orton, Richard J., Spurgin, Lewis G., Bourgeois, Yann, Ruis, Chris, O?Toole, Áine, Gourtovaia, Marina, Sanderson, Theo, Fraser, Christophe, Edgeworth, Jonathan, Breuer, Judith, Michell, Stephen L., Todd, John A., John, Michaela, Buck, David, Gajee, Kavitha, Kay, Gemma L., Peacock, Sharon J., Heyburn, David, Kitchman, Katie, McNally, Alan, Pritchard, David T., Dervisevic, Samir, Muir, Peter, Robinson, Esther, Vipond, Barry B., Ramadan, Newara A., Jeanes, Christopher, Weldon, Danni, Catalan, Jana, Jones, Neil, da Silva Filipe, Ana, Williams, Chris, Fuchs, Marc, Miskelly, Julia, Jeffries, Aaron R., Oliver, Karen, Park, Naomi R., Ash, Amy, Koshy, Cherian, Barrow, Magdalena, Buchan, Sarah L., Mantzouratou, Anna, Clark, Gemma, Holmes, Christopher W., Campbell, Sharon, Davis, Thomas, Tan, Ngee Keong, Brown, Julianne R., Harris, Kathryn A., Kidd, Stephen P., Grant, Paul R., Xu-McCrae, Li, Cox, Alison, Madona, Pinglawathee, Pond, Marcus, Randell, Paul A., Withell, Karen T., Williams, Cheryl, Graham, Clive, Denton-Smith, Rebecca, Swindells, Emma, Turnbull, Robyn, Sloan, Tim J., Bosworth, Andrew, Hutchings, Stephanie, Pymont, Hannah M., Casey, Anna, Ratcliffe, Liz, Jones, Christopher R., Knight, Bridget A., Haque, Tanzina, Hart, Jennifer, Irish-Tavares, Dianne, Witele, Eric, Mower, Craig, Watson, Louisa K., Collins, Jennifer, Eltringham, Gary, Crudgington, Dorian, Macklin, Ben, Iturriza-Gomara, Miren, Lucaci, Anita O., McClure, Patrick C., Carlile, Matthew, Holmes, Nadine, Moore, Christopher, Storey, Nathaniel, Rooke, Stefan, Yebra, Gonzalo, Craine, Noel, Perry, Malorie, Alikhan, Nabil-Fareed, Bridgett, Stephen, Cook, Kate F., Fearn, Christopher, Goudarzi, Salman, Lyons, Ronan A., Williams, Thomas, Haldenby, Sam T., Durham, Jillian, Leonard, Steven, Davies, Robert M., Batra, Rahul, Blane, Beth, Spyer, Moira J., Smith, Perminder, Yavus, Mehmet, Williams, Rachel J., Mahanama, Adhyana I. K., Samaraweera, Buddhini, Girgis, Sophia T., Hansford, Samantha E., Green, Angie, Beaver, Charlotte, Bellis, Katherine L., Dorman, Matthew J., Kay, Sally, Prestwood, Liam, Rajatileka, Shavanthi, Quick, Joshua, Poplawski, Radoslaw, Reynolds, Nicola, Mack, Andrew, Morriss, Arthur, Whalley, Thomas, Patel, Bindi, Georgana, Iliana, Hosmillo, Myra, Pinckert, Malte L., Stockton, Joanne, Henderson, John H., Hollis, Amy, Stanley, William, Yew, Wen C., Myers, Richard, Thornton, Alicia, Adams, Alexander, Annett, Tara, Asad, Hibo, Birchley, Alec, Coombes, Jason, Evans, Johnathan M., Fina, Laia, Gatica-Wilcox, Bree, Gilbert, Lauren, Graham, Lee, Hey, Jessica, Hilvers, Ember, Jones, Sophie, Jones, Hannah, Kumziene-Summerhayes, Sara, McKerr, Caoimhe, Powell, Jessica, Pugh, Georgia, Taylor, Sarah, Trotter, Alexander J., Williams, Charlotte A., Kermack, Leanne M., Foulkes, Benjamin H., Gallis, Marta, Hornsby, Hailey R., Louka, Stavroula F., Pohare, Manoj, Wolverson, Paige, Zhang, Peijun, MacIntyre-Cockett, George, Trebes, Amy, Moll, Robin J., Ferguson, Lynne, Maclean, Alasdair, Tomb, Rachael, Starinskij, Igor, Thomson, Laura, Southgate, Joel, Kraemer, Moritz U. G., Raghwani, Jayna, Zarebski, Alex E., Boyd, Olivia, Geidelberg, Lily, Illingworth, Chris J., Jackson, Chris, Pascall, David, Vattipally, Sreenu, Freeman, Timothy M., Hsu, Sharon N., Lindsey, Benjamin B., James, Keith, Lewis, Kevin, Tonkin-Hill, Gerry, Tovar-Corona, Jaime M., Cox, MacGregor, Abudahab, Khalil, Menegazzo, Mirko, Taylor, Ben E. W., Yeats, Corin A., Mukaddas, Afrida, Wright, Derek W., de Oliveira Martins, Leonardo, Colquhoun, Rachel, Hill, Verity, Jackson, Ben, McCrone, J. T., Medd, Nathan, Scher, Emily, Keatley, Jon-Paul, Curran, Tanya, Morgan, Sian, Maxwell, Patrick, Smith, Ken, Eldirdiri, Sahar, Kenyon, Anita, Holmes, Alison H., Price, James R., Wyatt, Tim, Mather, Alison E., SkvortsovHartley, Timofey John A., Guest, Martyn, Kitchen, Christine, Merrick, Ian, Munn, Robert, Bertolusso, Beatrice, Lynch, Jessica, Vernet, Gabrielle, Kirk, Stuart, Wastnedge, Elizabeth, Stanley, Rachael, Idle, Giles, Bradley, Declan T., Poyner, Jennifer, Mori, Matilde, Jones, Owen, Wright, Victoria, Brooks, Ellena, Churcher, Carol M., Fragakis, Mireille, Galai, Katerina, Jermy, Andrew, Judges, Sarah, McManus, Georgina M., Smith, Kim S., Westwick, Elaine, Attwood, Stephen W., Bolt, Frances, Davies, Alisha, De Lacy, Elen, Downing, Fatima, Edwards, Sue, Meadows, Lizzie, Jeremiah, Sarah, Smith, Nikki, Foulser, Luke, Charalampous, Themoula, Patel, Amita, Berry, Louise, Boswell, Tim, Fleming, Vicki M., Howson-Wells, Hannah C., Joseph, Amelia, Khakh, Manjinder, Lister, Michelle M., Bird, Paul W., Fallon, Karlie, Helmer, Thomas, McMurray, Claire L., Odedra, Mina, Shaw, Jessica, Tang, Julian W., Willford, Nicholas J., Blakey, Victoria, Raviprakash, Veena, Sheriff, Nicola, Williams, Lesley-Anne, Feltwell, Theresa, Bedford, Luke, Cargill, James S., Hughes, Warwick, Moore, Jonathan, Stonehouse, Susanne, Atkinson, Laura, Lee, Jack C. D., Shah, Divya, Alcolea-Medina, Adela, Ohemeng-Kumi, Natasha, Ramble, John, Sehmi, Jasveen, Williams, Rebecca, Chatterton, Wendy, Pusok, Monika, Everson, William, Castigador, Anibolina, Macnaughton, Emily, El Bouzidi, Kate, Lampejo, Temi, Sudhanva, Malur, Breen, Cassie, Sluga, Graciela, Ahmad, Shazaad S. Y., George, Ryan P., Machin, Nicholas W., Binns, Debbie, James, Victoria, Blacow, Rachel, Coupland, Lindsay, Smith, Louise, Barton, Edward, Padgett, Debra, Scott, Garren, Cross, Aidan, Mirfenderesky, Mariyam, Greenaway, Jane, Cole, Kevin, Clarke, Phillip, Duckworth, Nichola, Walsh, Sarah, Bicknell, Kelly, Impey, Robert, Wyllie, Sarah, Hopes, Richard, Bishop, Chloe, Chalker, Vicki, Harrison, Ian, Gifford, Laura, Molnar, Zoltan, Auckland, Cressida, Evans, Cariad, Johnson, Kate, Partridge, David G., Raza, Mohammad, Baker, Paul, Bonner, Stephen, Essex, Sarah, Murray, Leanne J., Lawton, Andrew I., Burton-Fanning, Shirelle, Payne, Brendan A. I., Waugh, Sheila, Gomes, Andrea N., Kimuli, Maimuna, Murray, Darren R., Ashfield, Paula, Dobie, Donald, Ashford, Fiona, Best, Angus, Crawford, Liam, Cumley, Nicola, Mayhew, Megan, Megram, Oliver, Mirza, Jeremy, Moles-Garcia, Emma, Percival, Benita, Driscoll, Megan, Ensell, Leah, Lowe, Helen L., Maftei, Laurentiu, Mondani, Matteo, Chaloner, Nicola J., Cogger, Benjamin J., Easton, Lisa J., Huckson, Hannah, Lewis, Jonathan, Lowdon, Sarah, Malone, Cassandra S., Munemo, Florence, Mutingwende, Manasa, Nicodemi, Roberto, Podplomyk, Olga, Somassa, Thomas, Beggs, Andrew, Richter, Alex, Cormie, Claire, Dias, Joana, Forrest, Sally, Higginson, Ellen E., Maes, Mailis, Young, Jamie, Davidson, Rose K., Jackson, Kathryn A., Turtle, Lance, Keeley, Alexander J., Ball, Jonathan, Byaruhanga, Timothy, Chappell, Joseph G., Dey, Jayasree, Hill, Jack D., Park, Emily J., Fanaie, Arezou, Hilson, Rachel A., Yaze, Geraldine, Lo, Stephanie, Afifi, Safiah, Beer, Robert, Maksimovic, Joshua, McCluggage, Kathryn, Spellman, Karla, Bresner, Catherine, Fuller, William, Marchbank, Angela, Workman, Trudy, Shelest, Ekaterina, Debebe, Johnny, Sang, Fei, Zamudio, Marina Escalera, Francois, Sarah, Gutierrez, Bernardo, Vasylyeva, Tetyana I., Flaviani, Flavia, Ragonnet-Cronin, Manon, Smollett, Katherine L., Broos, Alice, Mair, Daniel, Nichols, Jenna, Tsatsani, Ioulia, O?Brien, Sarah, Rushton, Steven, Sanderson, Roy, Perkins, Jon, Cotton, Seb, Gallagher, Abbie, Allara, Elias, Pearson, Clare, Bibby, David, Dabrera, Gavin, Ellaby, Nicholas, Gallagher, Eileen, Hubb, Jonathan, Lackenby, Angie, Lee, David, Manesis, Nikos, Mbisa, Tamyo, Platt, Steven, Twohig, Katherine A., Morgan, Mari, Aydin, Alp, Baker, David J., Foster-Nyarko, Ebenezer, Prosolek, Sophie J., Rudder, Steven, Baxter, Chris, Carvalho, Sílvia F., Lavin, Deborah, Mariappan, Arun, Radulescu, Clara, Singh, Aditi, Tang, Miao, Morcrette, Helen, Bayzid, Nadua, Cotic, Marius, Balcazar, Carlos E., Gallagher, Michael D., Maloney, Daniel, Stanton, Thomas D., Williamson, Kathleen A., Manley, Robin, Michelsen, Michelle L., Sambles, Christine M., Studholme, David J., Warwick-Dugdale, Joanna, Eccles, Richard, Gemmell, Matthew, Gregory, Richard, Hughes, Margaret, Nelson, Charlotte, Rainbow, Lucille, Vamos, Edith E., Webster, Hermione J., Whitehead, Mark, Wierzbicki, Claudia, Angyal, Adrienn, Green, Luke R., Whiteley, Max, Betteridge, Emma, Bronner, Iraad F., Farr, Ben W., Goodwin, Scott, Lensing, Stefanie V., McCarthy, Shane A., Quail, Michael A., Rajan, Diana, Redshaw, Nicholas M., Scott, Carol, Shirley, Lesley, Thurston, Scott A. J., Rowe, Will, Gaskin, Amy, Le-Viet, Thanh, Bonfield, James, Liddle, Jennifier, Whitwham, Andrew, Templeton, Kate, Milosevic, Catriona, Thomson, Emma, Illingworth, Christopher J. R., Smith-Palmer, Alison, Nickbakhsh, Sema [0000-0001-9543-7536], Sreenu, Vattipally B [0000-0001-6673-4697], Orton, Richard [0000-0002-3389-4325], Thomson, Emma [0000-0003-1482-0889], Robertson, David L [0000-0001-6338-0221], Apollo - University of Cambridge Repository, University of St Andrews. St Andrews Bioinformatics Unit, University of St Andrews. Infection and Global Health Division, University of St Andrews. Biomedical Sciences Research Complex, and University of St Andrews. School of Medicine

Subjects
631/114/739, Multidisciplinary, Universities, SARS-CoV-2, article, COVID-19, QH426 Genetics, 3rd-DAS, Genomics, C400, 692/700/478/174, United States, Disease Outbreaks, B900, Health Planning, SDG 3 - Good Health and Well-being, 692/699/255/2514, 631/114/2397, RA0421, RA0421 Public health. Hygiene. Preventive Medicine, Humans, 631/181/457, QH426
Abstract

Funding: The CVR authors are supported by the Medical Research Council [MC_UU_12014/12 and MC_UU_12018/12]. COG-UK is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) [Grant code: MC_PC_19027], and Genome Research Limited, operating as the Wellcome Sanger Institute. Whole genome sequencing of SARS-CoV-2 has occurred at an unprecedented scale, and can be exploited for characterising outbreak risks at the fine-scale needed to inform control strategies. One setting at continued risk of COVID-19 outbreaks are higher education institutions, associated with student movements at the start of term, close living conditions within residential halls, and high social contact rates. Here we analysed SARS-CoV-2 whole genome sequences in combination with epidemiological data to investigate a large cluster of student cases associated with University of Glasgow accommodation in autumn 2020, Scotland. We identified 519 student cases of SARS-CoV-2 infection associated with this large cluster through contact tracing data, with 30% sequencing coverage for further analysis. We estimated at least 11 independent introductions of SARS-CoV-2 into the student population, with four comprising the majority of detected cases and consistent with separate outbreaks. These four outbreaks were curtailed within a week following implementation of control measures. The impact of student infections on the local community was short-term despite an underlying increase in community infections. Our study highlights the need for context-specific information in the formation of public health policy for higher educational settings. Publisher PDF

Published
2022

12. COVID-19 due to the B.1.617.2 (Delta) variant compared to B.1.1.7 (Alpha) variant of SARS-CoV-2: a prospective observational cohort study

Author

Kläser, Kerstin, Molteni, Erika, Graham, Mark, Canas, Liane S., Österdahl, Marc F., Antonelli, Michela, Chen, Liyuan, Deng, Jie, Murray, Benjamin, Kerfoot, Eric, Wolf, Jonathan, May, Anna, Fox, Ben, Capdevila, Joan, Aanensen, David M., Abudahab, Khalil, Adams, Helen, Adams, Alexander, Afifi, Safiah, Aggarwal, Dinesh, Ahmad, Shazaad S. Y., Aigrain, Louise, Alcolea-Medina, Adela, Alikhan, Nabil-Fareed, Allara, Elias, Amato, Roberto, Angyal, Adrienn, Annett, Tara, Aplin, Stephen, Ariani, Cristina V., Asad, Hibo, Ash, Amy, Ashfield, Paula, Ashford, Fiona, Atkinson, Laura, Attwood, Stephen W., Auckland, Cressida, Aydin, Alp, Baker, David J., Baker, Paul, Balcazar, Carlos E., Ball, Jonathan, Barrett, Jeffrey C., Barrow, Magdalena, Barton, Edward, Bashton, Matthew, Bassett, Andrew R., Batra, Rahul, Baxter, Chris, Bayzid, Nadua, Beaver, Charlotte, Beckett, Angela H., Beckwith, Shaun M., Bedford, Luke, Beer, Robert, Beggs, Andrew, Bellis, Katherine L., Berry, Louise, Bertolusso, Beatrice, Best, Angus, Betteridge, Emma, Bibby, David, Bicknell, Kelly, Binns, Debbie, Birchley, Alec, Bird, Paul W., Bishop, Chloe, Blacow, Rachel, Blakey, Victoria, Blane, Beth, Bolt, Frances, Bonfield, James, Bonner, Stephen, Bonsall, David, Boswell, Tim, Bosworth, Andrew, Bourgeois, Yann, Boyd, Olivia, Bradley, Declan T., Breen, Cassie, Bresner, Catherine, Breuer, Judith, Bridgett, Stephen, Bronner, Iraad F., Brooks, Ellena, Broos, Alice, Brown, Julianne R., Bucca, Giselda, Buchan, Sarah L., Buck, David, Bull, Matthew, Burns, Phillipa J., Burton-Fanning, Shirelle, Byaruhanga, Timothy, Byott, Matthew, Campbell, Sharon, Carabelli, Alessandro M., Cargill, James S., Carlile, Matthew, Carvalho, Sílvia F., Casey, Anna, Castigador, Anibolina, Catalan, Jana, Chalker, Vicki, Chaloner, Nicola J., Chand, Meera, Chappell, Joseph G., Charalampous, Themoula, Chatterton, Wendy, Chaudhry, Yasmin, Churcher, Carol M., Clark, Gemma, Clarke, Phillip, Cogger, Benjamin J., Cole, Kevin, Collins, Jennifer, Colquhoun, Rachel, Connor, Thomas R., Cook, Kate F., Coombes, Jason, Corden, Sally, Cormie, Claire, Cortes, Nicholas, Cotic, Marius, Cotton, Seb, Cottrell, Simon, Coupland, Lindsay, Cox, MacGregor, Cox, Alison, Craine, Noel, Crawford, Liam, Cross, Aidan, Crown, Matthew, Crudgington, Dorian, Cumley, Nicola, Curran, Tanya, Curran, Martin D., da Silva Filipe, Ana, Dabrera, Gavin, Darby, Alistair C., Davidson, Rose K., Davies, Alisha, Davies, Robert M., Davis, Thomas, de Angelis, Daniela, De Lacy, Elen, de Oliveira Martins, Leonardo, de Silva, Thushan I., Debebe, Johnny, Denton-Smith, Rebecca, Dervisevic, Samir, Dewar, Rebecca, Dey, Jayasree, Dias, Joana, Dobie, Donald, Dorman, Matthew J., Downing, Fatima, Driscoll, Megan, du Plessis, Louis, Duckworth, Nichola, Durham, Jillian, Eastick, Kirstine, Easton, Lisa J., Eccles, Richard, Edgeworth, Jonathan, Edwards, Sue, Bouzidi, Kate El, Eldirdiri, Sahar, Ellaby, Nicholas, Elliott, Scott, Eltringham, Gary, Ensell, Leah, Erkiert, Michelle J., Zamudio, Marina Escalera, Essex, Sarah, Evans, Johnathan M., Evans, Cariad, Everson, William, Fairley, Derek J., Fallon, Karlie, Fanaie, Arezou, Farr, Ben W., Fearn, Christopher, Feltwell, Theresa, Ferguson, Lynne, Fina, Laia, Flaviani, Flavia, Fleming, Vicki M., Forrest, Sally, Foster-Nyarko, Ebenezer, Foulkes, Benjamin H., Foulser, Luke, Fragakis, Mireille, Frampton, Dan, Francois, Sarah, Fraser, Christophe, Freeman, Timothy M., Fryer, Helen, Fuchs, Marc, Fuller, William, Gajee, Kavitha, Galai, Katerina, Gallagher, Abbie, Gallagher, Eileen, Gallagher, Michael D., Gallis, Marta, Gaskin, Amy, Gatica-Wilcox, Bree, Geidelberg, Lily, Gemmell, Matthew, Georgana, Iliana, George, Ryan P., Gifford, Laura, Gilbert, Lauren, Girgis, Sophia T., Glaysher, Sharon, Goldstein, Emily J., Golubchik, Tanya, Gomes, Andrea N., Gonçalves, Sónia, Goodfellow, Ian G., Goodwin, Scott, Goudarzi, Salman, Gourtovaia, Marina, Graham, Clive, Graham, Lee, Grant, Paul R., Green, Luke R., Green, Angie, Greenaway, Jane, Gregory, Richard, Guest, Martyn, Gunson, Rory N., Gupta, Ravi K., Gutierrez, Bernardo, Haldenby, Sam T., Hamilton, William L., Hansford, Samantha E., Haque, Tanzina, Harris, Kathryn A., Harrison, Ian, Harrison, Ewan M., Hart, Jennifer, Hartley, John A., Harvey, William T., Harvey, Matthew, Hassan-Ibrahim, Mohammed O., Heaney, Judith, Helmer, Thomas, Henderson, John, Hesketh, Andrew R., Hey, Jessica, Heyburn, David, Higginson, Ellen E., Hill, Verity, Hill, Jack D., Hilson, Rachel A., Hilvers, Ember, Holden, Matthew T. G., Hollis, Amy, Holmes, Christopher W., Holmes, Nadine, Holmes, Alison H., Hopes, Richard, Hornsby, Hailey R., Hosmillo, Myra, Houlihan, Catherine, Howson-Wells, Hannah C., Hsu, Sharon N., Hubb, Jonathan, Huckson, Hannah, Hughes, Warwick, Hughes, Joseph, Hughes, Margaret, Hutchings, Stephanie, Idle, Giles, Illingworth, Chris J., Impey, Robert, Irish-Tavares, Dianne, Iturriza-Gomara, Miren, Izuagbe, Rhys, Jackson, Chris, Jackson, Ben, Jackson, Leigh M., Jackson, Kathryn A., Jackson, David K., Jahun, Aminu S., James, Victoria, James, Keith, Jeanes, Christopher, Jeffries, Aaron R., Jeremiah, Sarah, Jermy, Andrew, John, Michaela, Johnson, Rob, Johnson, Kate, Johnston, Ian, Jones, Owen, Jones, Sophie, Jones, Hannah, Jones, Christopher R., Jones, Neil, Joseph, Amelia, Judges, Sarah, Kay, Gemma L., Kay, Sally, Keatley, Jon-Paul, Keeley, Alexander J., Kenyon, Anita, Kermack, Leanne M., Khakh, Manjinder, Kidd, Stephen P., Kimuli, Maimuna, Kirk, Stuart, Kitchen, Christine, Kitchman, Katie, Knight, Bridget A., Koshy, Cherian, Kraemer, Moritz U. G., Kumziene-Summerhayes, Sara, Kwiatkowski, Dominic, Lackenby, Angie, Laing, Kenneth G., Lampejo, Temi, Langford, Cordelia F., Lavin, Deborah, Lawton, Andrew I., Lee, Jack C. D., Lee, David, Lensing, Stefanie V., Leonard, Steven, Levett, Lisa J., Le-Viet, Thanh, Lewis, Jonathan, Lewis, Kevin, Liddle, Jennifier, Liggett, Steven, Lillie, Patrick J., Lindsey, Benjamin B., Lister, Michelle M., Livett, Rich, Lo, Stephanie, Loman, Nicholas J., Loose, Matthew W., Louka, Stavroula F., Loveson, Katie F., Lowdon, Sarah, Lowe, Hannah, Lowe, Helen L., Lucaci, Anita O., Ludden, Catherine, Lynch, Jessica, Lyons, Ronan A., Lythgoe, Katrina, Machin, Nicholas W., MacIntyre-Cockett, George, Mack, Andrew, Macklin, Ben, Maclean, Alasdair, Macnaughton, Emily, Madona, Pinglawathee, Maes, Mailis, Maftei, Laurentiu, Mahanama, Adhyana I. K., Mahungu, Tabitha W., Mair, Daniel, Maksimovic, Joshua, Malone, Cassandra S., Maloney, Daniel, Manesis, Nikos, Manley, Robin, Mantzouratou, Anna, Marchbank, Angela, Mariappan, Arun, Martincorena, Inigo, Nunez, Rocio T. Martinez, Mather, Alison E., Maxwell, Patrick, Mayhew, Megan, Mbisa, Tamyo, McCann, Clare, McCarthy, Shane A., McCluggage, Kathryn, McClure, Patrick C., McCrone, J. T., McHugh, Martin P., McKenna, James P., McKerr, Caoimhe, McManus, Georgina M., McMurray, Claire L., McMurray, Claire, McNally, Alan, Meadows, Lizzie, Medd, Nathan, Megram, Oliver, Menegazzo, Mirko, Merrick, Ian, Michell, Stephen L., Michelsen, Michelle L., Mirfenderesky, Mariyam, Mirza, Jeremy, Miskelly, Julia, Moles-Garcia, Emma, Moll, Robin J., Molnar, Zoltan, Monahan, Irene M., Mondani, Matteo, Mookerjee, Siddharth, Moore, Christopher, Moore, Jonathan, Moore, Nathan, Moore, Catherine, Morcrette, Helen, Morgan, Sian, Morgan, Mari, Mori, Matilde, Morriss, Arthur, Moses, Samuel, Mower, Craig, Muir, Peter, Mukaddas, Afrida, Munemo, Florence, Munn, Robert, Murray, Abigail, Murray, Leanne J., Murray, Darren R., Mutingwende, Manasa, Myers, Richard, Nastouli, Eleni, Nebbia, Gaia, Nelson, Andrew, Nelson, Charlotte, Nicholls, Sam, Nichols, Jenna, Nicodemi, Roberto, Nomikou, Kyriaki, O’Grady, Justin, O’Brien, Sarah, Odedra, Mina, Ohemeng-Kumi, Natasha, Oliver, Karen, Orton, Richard J., Osman, Husam, O’Toole, Áine, Pacchiarini, Nicole, Padgett, Debra, Page, Andrew J., Park, Emily J., Park, Naomi R., Parker, Matthew D., Parmar, Surendra, Partridge, David G., Pascall, David, Patel, Amita, Patel, Bindi, Paterson, Steve, Payne, Brendan A. I., Peacock, Sharon J., Pearson, Clare, Pelosi, Emanuela, Percival, Benita, Perkins, Jon, Perry, Malorie, Pinckert, Malte L., Platt, Steven, Podplomyk, Olga, Pohare, Manoj, Pond, Marcus, Pope, Cassie F., Poplawski, Radoslaw, Powell, Jessica, Poyner, Jennifer, Prestwood, Liam, Price, Anna, Price, James R., Prieto, Jacqui A., Pritchard, David T., Prosolek, Sophie J., Pugh, Georgia, Pusok, Monika, Pybus, Oliver G., Pymont, Hannah M., Quail, Michael A., Quick, Joshua, Radulescu, Clara, Raghwani, Jayna, Ragonnet-Cronin, Manon, Rainbow, Lucille, Rajan, Diana, Rajatileka, Shavanthi, Ramadan, Newara A., Rambaut, Andrew, Ramble, John, Randell, Paul A., Randell, Paul, Ratcliffe, Liz, Raviprakash, Veena, Raza, Mohammad, Redshaw, Nicholas M., Rey, Sara, Reynolds, Nicola, Richter, Alex, Robertson, David L., Robinson, Esther, Robson, Samuel C., Rogan, Fiona, Rooke, Stefan, Rowe, Will, Roy, Sunando, Rudder, Steven, Ruis, Chris, Rushton, Steven, Ryan, Felicity, Saeed, Kordo, Samaraweera, Buddhini, Sambles, Christine M., Sanderson, Roy, Sanderson, Theo, Sang, Fei, Sass, Thea, Scher, Emily, Scott, Garren, Scott, Carol, Sehmi, Jasveen, Shaaban, Sharif, Shah, Divya, Shaw, Jessica, Shelest, Ekaterina, Shepherd, James G., Sheridan, Liz A., Sheriff, Nicola, Shirley, Lesley, Sillitoe, John, Silviera, Siona, Simpson, David A., Singh, Aditi, Singleton, Dawn, Skvortsov, Timofey, Sloan, Tim J., Sluga, Graciela, Smith, Ken, Smith, Kim S., Smith, Perminder, Smith, Darren, Smith, Louise, Smith, Colin P., Smith, Nikki, Smollett, Katherine L., Snell, Luke B., Somassa, Thomas, Southgate, Joel, Spellman, Karla, Chapman, Michael H. Spencer, Spurgin, Lewis G., Spyer, Moira J., Stanley, Rachael, Stanley, William, Stanton, Thomas D., Starinskij, Igor, Stockton, Joanne, Stonehouse, Susanne, Storey, Nathaniel, Studholme, David J., Sudhanva, Malur, Swindells, Emma, Taha, Yusri, Tan, Ngee Keong, Tang, Julian W., Tang, Miao, Taylor, Ben E. W., Taylor, Joshua F., Taylor, Sarah, Temperton, Ben, Templeton, Kate E., Thomas, Claire, Thomson, Laura, Thomson, Emma C., Thornton, Alicia, Thurston, Scott A. J., Todd, John A., Tomb, Rachael, Tong, Lily, Tonkin-Hill, Gerry, Torok, M. Estee, Tovar-Corona, Jaime M., Trebes, Amy, Trotter, Alexander J., Tsatsani, Ioulia, Turnbull, Robyn, Turtle, Lance, Twohig, Katherine A., Umpleby, Helen, Underwood, Anthony P., Vamos, Edith E., Vasylyeva, Tetyana I., Vattipally, Sreenu, Vernet, Gabrielle, Vipond, Barry B., Volz, Erik M., Walsh, Sarah, Wang, Dennis, Warne, Ben, Warwick-Dugdale, Joanna, Wastnedge, Elizabeth, Watkins, Joanne, Watson, Louisa K., Waugh, Sheila, Webster, Hermione J., Weldon, Danni, Westwick, Elaine, Whalley, Thomas, Wheeler, Helen, Whitehead, Mark, Whiteley, Max, Whitwham, Andrew, Wierzbicki, Claudia, Willford, Nicholas J., Williams, Lesley-Anne, Williams, Rebecca, Williams, Cheryl, Williams, Chris, Williams, Charlotte A., Williams, Rachel J., Williams, Thomas, Williams, Catryn, Williamson, Kathleen A., Wilson-Davies, Eleri, Witele, Eric, Withell, Karen T., Witney, Adam A., Wolverson, Paige, Wong, Nick, Workman, Trudy, Wright, Victoria, Wright, Derek W., Wyatt, Tim, Wyllie, Sarah, Xu-McCrae, Li, Yavus, Mehmet, Yaze, Geraldine, Yeats, Corin A., Yebra, Gonzalo, Yew, Wen Chyin, Young, Greg, Young, Jamie, Zarebski, Alex E., Zhang, Peijun, Modat, Marc, Hammers, Alexander, Spector, Tim D., Steves, Claire J., Sudre, Carole H., Ourselin, Sebastien, Duncan, Emma L., Radiology and nuclear medicine, Peacock, Sharon [0000-0002-1718-2782], and Apollo - University of Cambridge Repository

Subjects
B900, Adult, Multidisciplinary, SARS-CoV-2, SARS-CoV-2/genetics, Reinfection, B100, COVID-19, Humans, C500, Prospective Studies, Hepatitis D, COVID-19/epidemiology
Abstract

The Delta (B.1.617.2) variant was the predominant UK circulating SARS-CoV-2 strain between May and December 2021. How Delta infection compares with previous variants is unknown. This prospective observational cohort study assessed symptomatic adults participating in the app-based COVID Symptom Study who tested positive for SARS-CoV-2 from May 26 to July 1, 2021 (Delta overwhelmingly the predominant circulating UK variant), compared (1:1, age- and sex-matched) with individuals presenting from December 28, 2020 to May 6, 2021 (Alpha (B.1.1.7) the predominant variant). We assessed illness (symptoms, duration, presentation to hospital) during Alpha- and Delta-predominant timeframes; and transmission, reinfection, and vaccine effectiveness during the Delta-predominant period. 3581 individuals (aged 18 to 100 years) from each timeframe were assessed. The seven most frequent symptoms were common to both variants. Within the first 28 days of illness, some symptoms were more common with Delta versus Alpha infection (including fever, sore throat, and headache) and some vice versa (dyspnoea). Symptom burden in the first week was higher with Delta versus Alpha infection; however, the odds of any given symptom lasting ≥ 7 days was either lower or unchanged. Illness duration ≥ 28 days was lower with Delta versus Alpha infection, though unchanged in unvaccinated individuals. Hospitalisation for COVID-19 was unchanged. The Delta variant appeared more (1.49) transmissible than Alpha. Re-infections were low in all UK regions. Vaccination markedly reduced the risk of Delta infection (by 69-84%). We conclude that COVID-19 from Delta or Alpha infections is similar. The Delta variant is more transmissible than Alpha; however, current vaccines showed good efficacy against disease. This research framework can be useful for future comparisons with new emerging variants.

Published
2022
Full Text
View/download PDF

15. Bacterial Diversity in House Dust: Characterization of a Core Indoor Microbiome

Author

Thompson, Jonathan R., primary, Argyraki, Ariadne, additional, Bashton, Matthew, additional, Bramwell, Lindsay, additional, Crown, Matthew, additional, Hursthouse, Andrew S., additional, Jabeen, Khadija, additional, Marinho Reis, Paula, additional, Namdeo, Anil, additional, Nelson, Andrew, additional, Pearce, David A., additional, Potgieter-Vermaak, Sanja, additional, Rasmussen, Pat E., additional, Wragg, Joanna, additional, and Entwistle, Jane A., additional

Published
2021
Full Text
View/download PDF

16. Bacterial Diversity in House Dust: Characterization of a Core Indoor Microbiome

Author

Thompson, Jonathan R. Argyraki, Ariadne Bashton, Matthew and Bramwell, Lindsay Crown, Matthew Hursthouse, Andrew S. and Jabeen, Khadija Marinho Reis, Paula Namdeo, Anil Nelson, Andrew Pearce, David A. Potgieter-Vermaak, Sanja Rasmussen, Pat E. Wragg, Joanna Entwistle, Jane A.

Subjects
complex mixtures
Abstract

Our indoor microbiome consists of a wide range of microbial taxa. Whilst many of these microbes are benign, some are beneficial, some harmful, yet our knowledge of the spatial heterogeneity of bacterial assemblages in our residential environment remains limited. To investigate the existence of a common core house dust bacterial microbiome we selected household vacuum dusts, collected through a citizen science approach, from homes across two bioclimatic regions (UK, Oceanic/Maritime and Greece, Mediterranean). Following the extraction of DNA from each dust sample, we targeted the bacterial 16S rRNA gene using Illumina NextSeq sequencing. PERMANOVA analysis of the microbial communities at family level grouped samples within their distinct bioclimatic region and SIMPER analysis at genus level identified the statistically significant taxa responsible for driving diversity between these groups. A “common to all” core house dust microbiome consisted of Acinetobacter, Massalia, Rubellimicrobium, Sphingomonas and Staphylococcus; genera typically associated with human occupancy and common environmental sources. Additionally, a “unique location specific” microbiome was identified, reflective of the bioclimatic region. The Greek dusts indicated a lower average diversity than the UK house dusts, with a high abundance of Rhizobiaceae in the Greek samples. Our study highlights citizen science as a powerful approach to access the indoor residential environment, at scale, and establishes the existence of a “core” house dust microbiome independent of bioclimatic region.

Published
2021

17. Bacterial diversity in house dust: characterization of a core indoor microbiome

Author

Thompson, Jonathan R., Argyraki, Ariadne, Bashton, Matthew, Bramwell, Lindsay, Crown, Matthew, Hursthouse, Andrew S., Jabeen, Khadija, Marinho Reis, Paula, Namdeo, Anil, Nelson, Andrew, Pearce, David A., Potgieter-Vermaak, Sanja, Rasmussen, Pat E., Wragg, Joanna, Entwisle, Jane A., Thompson, Jonathan R., Argyraki, Ariadne, Bashton, Matthew, Bramwell, Lindsay, Crown, Matthew, Hursthouse, Andrew S., Jabeen, Khadija, Marinho Reis, Paula, Namdeo, Anil, Nelson, Andrew, Pearce, David A., Potgieter-Vermaak, Sanja, Rasmussen, Pat E., Wragg, Joanna, and Entwisle, Jane A.

Abstract

Our indoor microbiome consists of a wide range of microbial taxa. Whilst many of these microbes are benign, some are beneficial, some harmful, yet our knowledge of the spatial heterogeneity of bacterial assemblages in our residential environment remains limited. To investigate the existence of a common core house dust bacterial microbiome we selected household vacuum dusts, collected through a citizen science approach, from homes across two bioclimatic regions (UK, Oceanic/Maritime and Greece, Mediterranean). Following the extraction of DNA from each dust sample, we targeted the bacterial 16S rRNA gene using Illumina NextSeq sequencing. PERMANOVA analysis of the microbial communities at family level grouped samples within their distinct bioclimatic region and SIMPER analysis at genus level identified the statistically significant taxa responsible for driving diversity between these groups. A “common to all” core house dust microbiome consisted of Acinetobacter, Massalia, Rubellimicrobium, Sphingomonas and Staphylococcus; genera typically associated with human occupancy and common environmental sources. Additionally, a “unique location specific” microbiome was identified, reflective of the bioclimatic region. The Greek dusts indicated a lower average diversity than the UK house dusts, with a high abundance of Rhizobiaceae in the Greek samples. Our study highlights citizen science as a powerful approach to access the indoor residential environment, at scale, and establishes the existence of a “core” house dust microbiome independent of bioclimatic region.

Published
2021

18. Correction: Viral burden is associated with age, vaccination, and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection-related sampling bias.

Author

Fryer, Helen R., Golubchik, Tanya, Hall, Matthew, Fraser, Christophe, Hinch, Robert, Ferretti, Luca, Thomson, Laura, Nurtay, Anel, Pellis, Lorenzo, House, Thomas, MacIntyre-Cockett, George, Trebes, Amy, Buck, David, Piazza, Paolo, Green, Angie, Lonie, Lorne J, Smith, Darren, Bashton, Matthew, Crown, Matthew, and Nelson, Andrew

Subjects
SARS-CoV-2, VACCINATION, AGE
Abstract

The correct expressions are: Graph HT aijmax=4(tijk-t˜ij)andaijmin=4(tijk-tij,k-1) ht There are a number of errors in the caption for Fig 4, "Adjusted Ct values plotted against different factors". [Extracted from the article]

Published
2023
Full Text
View/download PDF

19. ProCogGraph: a graph-based mapping of cognate ligand domain interactions.

Author

Crown M and Bashton M

Abstract

Motivation: Mappings of domain-cognate ligand interactions can enhance our understanding of the core concepts of evolution and be used to aid docking and protein design. Since the last available cognate-ligand domain database was released, the PDB has grown significantly and new tools are available for measuring similarity and determining contacts., Results: We present ProCogGraph, a graph database of cognate-ligand domain mappings in PDB structures. Building upon the work of the predecessor database, PROCOGNATE, we use data-driven approaches to develop thresholds and interaction modes. We explore new aspects of domain-cognate ligand interactions, including the chemical similarity of bound cognate ligands and how domain combinations influence cognate ligand binding. Finally, we use the graph to add specificity to partial EC IDs, showing that ProCogGraph can complete partial annotations systematically through assigned cognate ligands., Availability and Implementation: The ProCogGraph pipeline, database and flat files are available at https://github.com/bashton-lab/ProCogGraph and https://doi.org/10.5281/zenodo.13165851., Competing Interests: None declared., (© The Author(s) 2024. Published by Oxford University Press.)

Published
2024
Full Text
View/download PDF

20. TRIM7 ubiquitinates SARS-CoV-2 membrane protein to limit apoptosis and viral replication.

Author

Gonzalez-Orozco M, Tseng HC, Hage A, Xia H, Behera P, Afreen K, Peñaflor-Tellez Y, Giraldo MI, Huante M, Puebla-Clark L, van Tol S, Odle A, Crown M, Teruel N, Shelite TR, Menachery V, Endsley M, Endsley JJ, Najmanovich RJ, Bashton M, Stephens R, Shi PY, Xie X, Freiberg AN, and Rajsbaum R

Abstract

SARS-CoV-2 is a highly transmissible virus that causes COVID-19 disease. Mechanisms of viral pathogenesis include excessive inflammation and viral-induced cell death, resulting in tissue damage. We identified the host E3-ubiquitin ligase TRIM7 as an inhibitor of apoptosis and SARS-CoV-2 replication via ubiquitination of the viral membrane (M) protein. Trim7 -/- mice exhibited increased pathology and virus titers associated with epithelial apoptosis and dysregulated immune responses. Mechanistically, TRIM7 ubiquitinates M on K14, which protects cells from cell death. Longitudinal SARS-CoV-2 sequence analysis from infected patients revealed that mutations on M-K14 appeared in circulating variants during the pandemic. The relevance of these mutations was tested in a mouse model. A recombinant M-K14/K15R virus showed reduced viral replication, consistent with the role of K15 in virus assembly, and increased levels of apoptosis associated with the loss of ubiquitination on K14. TRIM7 antiviral activity requires caspase-6 inhibition, linking apoptosis with viral replication and pathology., Competing Interests: Declaration of interest The authors declare no competing interests.

Published
2024
Full Text
View/download PDF

21. OMEinfo: global geographic metadata for -omics experiments.

Author

Crown M and Bashton M

Abstract

Summary: Microbiome studies increasingly associate geographical features like rurality and climate with microbiomes. It is essential to correctly integrate rich geographical metadata; and inconsistent definitions of rurality, can hinder cross-study comparisons. We address this with OMEinfo, a tool for automated retrieval of consistent geographical metadata from user-provided location data. OMEinfo leverages open data sources such as the Global Human Settlement Layer, and Open-Data Inventory for Anthropogenic Carbon dioxide. OMEinfo's web-app enables users to visualize and investigate the spatial distribution of metadata features. OMEinfo promotes reproducibility and consistency in microbiome metadata through a standardized metadata retrieval approach. To demonstrate utility, OMEinfo is used to replicate the results of a previous study linking population density to bacterial diversity. As the field explores relationships between microbiomes and geographical features, tools like OMEinfo will prove vital in developing a robust, accurate, and interconnected understanding of these interactions, whilst having applicability beyond this field to any studies utilizing location-based metadata. Finally, we release the OMEinfo annotation dataset of 5.3 million OMEinfo annotated samples from the ENA, for use in retrospective analyses of sequencing samples, and suggest several ways researchers and sequencing read repositories can improve the quality of underlying metadata submitted to these public stores., Availability and Implementation: OMEinfo is freely available and released under an MIT licence. OMEinfo source code is available at https://github.com/m-crown/OMEinfo/ and https://doi.org/10.5281/zenodo.10518763., Competing Interests: None declared., (© The Author(s) 2024. Published by Oxford University Press.)

Published
2024
Full Text
View/download PDF

22. Lineage replacement and evolution captured by 3 years of the United Kingdom Coronavirus (COVID-19) Infection Survey.

Author

Lythgoe KA, Golubchik T, Hall M, House T, Cahuantzi R, MacIntyre-Cockett G, Fryer H, Thomson L, Nurtay A, Ghafani M, Buck D, Green A, Trebes A, Piazza P, Lonie LJ, Studley R, Rourke E, Smith D, Bashton M, Nelson A, Crown M, McCann C, Young GR, Andre Nunes Dos Santos R, Richards Z, Tariq A, Fraser C, Diamond I, Barrett J, Walker AS, and Bonsall D

Subjects
Humans, SARS-CoV-2, United Kingdom epidemiology, Surveys and Questionnaires, COVID-19 epidemiology, Epidemics
Abstract

The Office for National Statistics Coronavirus (COVID-19) Infection Survey (ONS-CIS) is the largest surveillance study of SARS-CoV-2 positivity in the community, and collected data on the United Kingdom (UK) epidemic from April 2020 until March 2023 before being paused. Here, we report on the epidemiological and evolutionary dynamics of SARS-CoV-2 determined by analysing the sequenced samples collected by the ONS-CIS during this period. We observed a series of sweeps or partial sweeps, with each sweeping lineage having a distinct growth advantage compared to their predecessors, although this was also accompanied by a gradual fall in average viral burdens from June 2021 to March 2023. The sweeps also generated an alternating pattern in which most samples had either S-gene target failure (SGTF) or non-SGTF over time. Evolution was characterized by steadily increasing divergence and diversity within lineages, but with step increases in divergence associated with each sweeping major lineage. This led to a faster overall rate of evolution when measured at the between-lineage level compared to within lineages, and fluctuating levels of diversity. These observations highlight the value of viral sequencing integrated into community surveillance studies to monitor the viral epidemiology and evolution of SARS-CoV-2, and potentially other pathogens.

Published
2023
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results