Whole-genome sequencing reveals host factors underlying critical COVID-19

Kousathanas, Athanasios; Pairo‐Castineira, Erola; Rawlik, Konrad; Stuckey, A.; A. Odhams, Christopher; Walker, Susan; D Russell, Clark; Malinauskas, Tomas; Wu, Yang; Millar, Jonathan; Shen, Xia; S. Elliott, Katherine; Griffiths, Fiona; Oosthuyzen, Wilna; Morrice, Kirstie; Keating, Seán; Wang, Bo; R. Rhodes, Daniel; Klarić, Lucija; Zechner, Marie; Parkinson, Nick; Siddiq, Afshan; Goddard, Peter; Donovan, Sally; M. Maslove, David; Nichol, Alistair; G. Semple, Malcolm; Zainy, Tala; Maleady-Crowe, F.; Todd, Linda; Salehi, Shahla; C. Knight, Julian; Elgar, Greg; C. Chan, G.; Arumugam, Prabhu; Patch, Christine; Rendon, Augusto; Bentley, David; Kingsley, Clare; A. Kosmicki, Jack; Horowitz, Julie; Baras, Aris; R. Abecasis, Gonçalo; A. R. Ferreira, Manuel; E. Justice, Anne; Mirshahi, Tooraj; T. Oetjens, Matthew; J. Rader, Daniel; D. Ritchie, Marylyn; Verma, Anurag; Fowler, Tom; Shankar‐Hari, Manu; Summers, Charlotte; Hinds, Charles; Horby, Peter; Ling, Lowell; F. McAuley, Daniel; Montgomery, Hugh; Openshaw, Peter; Elliott, Paul; Walsh, Timothy; Tenesa, Albert; investigators, GenOMICC; co-investigators, GenOMICC; Kenneth Baillie, J.; B. Begg, Colin; Clohisey, Sara; Hinds, Charles; Horby, Peter; Knight, Julian; Ling, Lowell; M. Maslove, David; McAuley, Danny; Millar, Johnny; Montgomery, Hugh; Nichol, Alistair; J. M. Openshaw, Peter; C. Pereira, Alexandre; P. Ponting, Chris; Rowan, Kathy; G. Semple, Malcolm; Shankar‐Hari, Manu; Summers, Charlotte; Walsh, Timothy; Aravindan, Latha; Armstrong, Ruth; Biggs, Heather; Boz, Ceilia; Brown, Adam; Clark, Richard; Coutts, Audrey; Terrence Coyle, J.; Cullum, Louise; Das, Sukamal; Day, Nicky; Donnelly, Lorna; Duncan, Esther; Fawkes, Angie; Finernan, Paul; Head Fourman, Max; Furlong, Anita; Furniss, James; Gallagher, Bernadette; Gilchrist, Tammy; Golightly, Ailsa; Griffiths, Fiona; Hafezi, Katarzyna; Hamilton, Debbie; Hendry, Ross; Law, Andy; Law, Dawn; M. Law, R.; Law, Sarah; Lidstone-Scott, Rebecca; MacGillivray, Louise; Maclean, Alan; Mal, Hanning; McCafferty, Sarah; Mcmaster, Ellie; Meikle, Jen; C. Moore, Shona; Morrice, Kirstie; Murphy, Lee; Murphy, Sheena; Hellen, Mybaya; Oosthuyzen, Wilna; Zheng, Chenqing; Chen, Jiantao; Parkinson, Nick; Paterson, Trevor; Schon, Katherine; Stenhouse, Andrew; Das, Mihaela; Swets, Maaike; Szoor-McElhinney, Helen; Taneski, Filip; Turtle, Lance; Wackett, Tony; Ward, Mairi; Weaver, Jane; Wrobel, Nicola; Zechner, Marie; Arbane, Gill; Bociek, Aneta; Campos, Sara; Grau, Neus; Jones, Tim; Lim, Rosario; Marotti, Martina; Ostermann, Marlies; Shankar‐Hari, Manu; Chris Whitton, R.; Health NHS Trust team, Barts; Alldis, Zoe; Astin-Chamberlain, Raine; Bibi, Fatima; Biddle, Jack; Blow, Sarah; L. Bolton, Matthew; Borra, Catherine; Bowles, Ruth; Burton, Maudrian; Choudhury, Yasmin; Collier, David; Cox, Amber; Easthope, Amy; Ebano, Patrizia; Fotiadis, Stavros; Gurasashvili, Jana; Halls, Rosslyn; Hartridge, Pippa; Kallon, Delordson; Kassam, Jamila; Lancoma-Malcolm, Ivone; Matharu, Maninderpal; May, P.; Mitchelmore, Oliver; Newman, Tabitha; Patel, Mital; Pheby, Jane; Pinzuti, Irene; Prime, Zoe; Prysyazhna, Oleksandra; Shiel, Julian; Taylor, Melanie; Tierney, Carey; M. Wood, S.; Zak, Anne; Zongo, Olivier; Bonner, Stephen; Hugill, Keith; Jones, Jessica; Liggett, Steven; Headlam, Evie; Bandla, Nageswar; Gellamucho, Minnie; Davies, Michelle; C. 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Drummond, A.; Mulcahy, Michelle; Munt, Sheila; O’Connor, Gráinne; Philbin, Jennifer; Rishton, Chloe; Tully, Redmond; Winnard, Sarah; Royal Infirmary team, Glasgow; Cathcart, Susanne; Duffy, Katharine; Puxty, Alex; Puxty, Kathryn; Turner, Lynne; Ireland, Jane; Semple, Gary; Long, Kate; Whiteley, Simon; Wilby, Elizabeth; Ogg, Bethan; Cowton, Amanda; Kay, Andrea; Kent, Melanie; Potts, Kathryn; Wilkinson, Ami; Campbell, Suzanne; Brown, Ellen; Melville, Julie; Naisbitt, Jay; Joseph, Rosane; Lazo, Maria; Walton, Olivia; Neal, Alan; Alexander, Peter; Allen, Schvearn; Bradley-Potts, Joanne; Brantwood, Craig; Egan, Jasmine; Felton, Timothy; Padden, Grace; Ward, Luke; Moss, Stuart; Glasgow, Susannah; Abel, Lynn; Brett, Michael; Digby, Brian; Gemmell, Lisa; Hornsby, James; MacGoey, Patrick; O’Neil, Pauline; Arlen Price, R.; Rodden, Natalie; Rooney, Kevin; Sundaram, Radha; Thomson, Nicola; Hopkins, Bridget; Scriven, James; Thrasyvoulou, Laura; Willis, Heather; Clark, Martyn; Coulding, M; B. 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Jenkins, Sarah; Reschreiter, Henrik; Wadams, Beverley; DeAth, Yasmin; Bastion, Victoria; Clarke, Daphene; David, Beena; Kent, Harriet; Lorusso, Rachel; Lubimbi, Gamu; Murdoch, Sophie; Penacerrada, Melchizedek; Thomas, Alastair; Valentine, Jennifer; Vochin, Ana; Wulandari, Retno; Djeugam, Brice; Bell, Gillian; English, Katy; Katary, Amro; Wilcox, Louise; Bruce, Michelle; Connolly, Karen; Duncan, Tracy; Michael, Helen; Lindergard, Gabriella; Hey, Samuel; Fox, Claire; Alfonso, Jordan; Jayne Durrans, Laura; Guerin, Jacinta; Blackledge, Bethan; Harris, Jade; Hruška, Martin; Eltayeb, Ayaa; Lamb, Thomas; Hodgkiss, Tracey; Cooper, Lisa; Rothwell, Joanne; Royal Infirmary team, Aberdeen; Allan, Angela; Anderson, Felicity; Kaye, Callum; Liew, Jade; Medhora, Jasmine; Scott, Teresa; Trumper, Erin; Botello, Adriana; Lankester, Liana; Nikitas, Nikitas; Wells, Colin; Stowe, Bethan; Spencer, Kayleigh; Royal Infirmary team, Manchester; Brandwood, Craig; Smith, Lara; Clark, Richard; Birchall, Katie; Kolakaluri, Laurel; L. Baines, Deborah; Sukumaran, Anila; Apetri, Elena; Basikolo, Cathrine; Blackledge, Bethan; Catlow, Laura; Charles, Bethan; Dark, Paul; Doonan, Reece; Harris, Jade; Harvey, Alice; Horner, Daniel; Knowles, Karen; J. Lee, Stephanie; Lomas, Diane; Lyons, Chloe; Marsden, Tracy; McLaughlan, Danielle; McMorrow, Liam; Pendlebury, Jessica; Perez, Jane; Poulaka, Maria; Proudfoot, Nicola; Slaughter, Melanie; Slevin, Kathryn; Taylor, Melanie; Thomas, Vicky; Walker, Danielle; Michael, Angiy; Collis, Matthew; Cosier, Tracey; Millen, Gemma; Richardson, Neil; Schumacher, Natasha; Weston, Heather; Rand, James; Baxter, Nicola; Henderson, Steven; Kennedy-Hay, Sophie; McParland, Christopher; Rooney, Laura; Sim, Malcolm; McCreath, Gordan; Royal Infirmary team, Bradford; Akeroyd, Louise; Bano, Shereen; Bromley, Matt; Gurr, Lucy; Lawton, Tom; P. Morgan, James; Sellick, Kirsten; Warren, Deborah; J. Wilkinson, Brian; McGowan, Janet; Ledgard, Camilla; Stacey, Amelia; Pye, Kate; Bellwood, Ruth; J. Bentley, Michael; Royal Infirmary team, Bristol; Bewley, Jeremy; Garland, Zoe; Grimmer, Lisa; Gumbrill, Bethany; Johnson, Rebekah; Sweet, Katie; Webster, Denise; Efford, Georgia; Convery, Karen; Fottrell-Gould, Deirdre; Hudig, Lisa; Keshet-Price, Jocelyn; Randell, Georgina; Stammers, Katie; Bokhari, Maria; Linnett, Vanessa; Lucas, Rachael; McCormick, W; Ritzema, Jenny; Sanderson, Amanda; Wild, Helen; Rostron, Anthony; Roy, Alistair; Woods, Lindsey; Cornell, Sarah; Wakinshaw, Fiona; Rogerson, Kimberley; Jarmain, Jordan; S. Parker, Robert; Reddy, Amie; Turner-Bone, Ian; Wilding, Laura; Harding, Peter; Royal Infirmary team, Hull; R. Abernathy, C.; Foster, Louise; Gratrix, Andrew; Martinson, Vicky; Parkinson, Priyai; Stones, Elizabeth; Carbral-Ortega, Llucia; Bercades, Georgia; Brealey, David; Hass, Ingrid; MacCallum, Niall; Martir, Gladys; Raith, Eamon; Reyes, Anna; Smyth, Deborah; Zitter, Letizia; Benyon, Sarah; Marriott, Suzie; Park, Linda; Keenan, Samantha; Gordón, Elizabeth; R. Quinn, Helen; Baines, Kizzy; Cagova, Lenka; Fofano, Adama; Garner, Lucie; Holcombe, Helen; Mepham, Sue; Michael Mitchell, Alice; Mwaura, Lucy; Praman, Krithivasan; Vuylsteke, Alain; Zamikula, Julie; Purewal, Bally; Rivers, Vanessa; Bell, Stephanie; Blakemore, Hayley; Borislavova, Borislava; Faulkner, Beverley; Gendall, Emma; Goff, Elizabeth; Hayes, Kati; Thomas, Matt; Worner, Ruth; Smith, Kerry; Stephens, Deanna; Mew, Louise; Mwaura, Esther; Stewart, Richard; Williams, Felicity; Wren, Lynn; Sutherland, Sara-Beth; Bevan, Emily; Martin, Jane; Trodd, Dawn; Watson, Geoff; Wrey Brown, Caroline; Akinkugbe, Olugbenga; Bamford, Alasdair; Beech, Emily; Belfield, Holly; J. Bell, M.; Davies, Charlene; A. Jones, Gareth; McHugh, Tara; Meghari, Hamza; O’Neill, Lauran; Peters, Mark; Ray, Samiran; Luisa Tomas, Ana; Burn, Iona; Hambrook, Geraldine; Manso, Katarina; Penn, Ruth; Shanmugasundaram, Pradeep; Tebbutt, Julie; Thornton, Danielle; Cole, Jade; Davies, Michelle; Davies, Rhys; Duffin, Donna; Hill, Helen; Player, Ben; Thomas, Emma; Williams, Angharad; Griffin, Denise; Muchenje, Nycola; Mupudzi, McDonald; Partridge, Richard; Conyngham, Jo-Anna; Thomas, Rachel; Wright, Mary; Alvarez Corral, Maria; Jacob, Reni; Jones, Cathy; Denmade, Craig; Beavis, Sarah; Dale, Katie; Gascoyne, Rachel; Hawes, Joanne; Pritchard, Kelly; Stevenson, Lesley; Whileman, Amanda; Doble, Patricia; Hutter, Joanne; Pawley, Corinne; Shovelton, Charmaine; Vaida, Marius; Butcher, Deborah; O’Sullivan, Susie; Butterworth‐Cowin, Nicola; Ahmad, Norfaizan; Barker, Joann; Bauchmüller, Kris; Bird, Sarah; Cawthron, Kay; Harrington, Kate; Jackson, Yvonne; Kibutu, Faith; Lenagh, Becky; Masuko, Shamiso; Mills, Gary; Raithatha, Ajay; D. Wiles, M.; Willson, Jayne; Newell, Helen; Lye, Alison; Nwafor, Lorenza; Jarman, Claire; Rowland‐Jones, Sarah; Foote, David; Cole, Joby; Thompson, Roger; Watson, James; Hesseldon, Lisa; Macharia, Irene; Chetam, Luke; Smith, Jacqui; Ford, Amber; Anderson, Samantha; Birchall, Kathryn; Housley, Kay; E. Walker, Sara; Milner, L; Hanratty, Helena; Trower, Helen; Phillips, Patrick; Oxspring, Simon; Donne, B.; and Galloway Royal Infirmary team, Dumfries; Jardine, Catherine; Williams, Dewi; Hay, Alasdair; C. Flanagan, Rebecca; Hughes, Gareth; Latham, Scott; McKenna, Emma; Anderson, Jennifer; Hull, Robert; Rhead, Kat; Cruz, Carina; Pattison, Natalie; Charnock, Rob; McFarland, Denise; Cosgrove, Denise; Ahmed, Ashar; Morris, Anna; Jakkula, Srinivas; Nune, Arvind; Ali, Asifa; Brady, Megan; Dale, Sam; Dance, Annalisa; Gledhill, Lisa; Greig, Jill; Hanson, Kathryn; Holdroyd, Kelly; Home, Marie; Kelly, Diane; Kitson, Ross; Matapure, Lear; Salas y Mélia, D.; Mellor, Samantha; Nortcliffe, Tonicha; Pinnell, Jez; K. Robinson, Matthew; Shaw, Lisa; Shaw, Ryan; Thomis, Lesley; Wilson, Alison; Wood, Tracy; Bayo, Lee-Ann; Merwaha, Ekta; Ishaq, Tahira; Hanley, Sarah; Deacon, Bethan; Hibbert, Meg; Pothecary, Carla; Tetla, Dariusz; Woodford, Christopher; Durga, Latha; Kennard-Holden, Gareth; Branney, Debbie; Frankham, Jordan; Pitts, Sally; White, Nigel; Laha, Shondipon; Verlander, Mark; Williams, Alexandra; Altabaibeh, Abdelhakim; Alvaro, Ana; Gilbert, Kayleigh; Ma, Louise; Mostoles, Loreta; Parmar, Chetan; Simpson, Kathryn; Jetha, Champa; Booker, Lauren; Pratley, Anezka; Adams, Colene; Agasou, Anita; Arden, Tracie; Bowes, Amy; Boyle, Pauline; Beekes, Mandy; Button, Heather; Capps, Nigel; Carnahan, Mandy; Carter, Anne; Childs, Danielle; Donaldson, Denise; Hard, Kelly; Hurford, F; Hussain, Yasmin; Javaid, Ayesha; Jones, James; Jose, Sanal; Leigh, Michael; Martin, Terry; Millward, Helen; Motherwell, Nichola; Rikunenko, Rachel; Stickley, Jo; Summers, Julie; Ting, Louise; Tivenan, Helen; Tonks, Louise; Wilcox, Rebecca; Skinner, Denise; Gaylard, Jane; Mullan, Dee; Newman, Julie; Holland, Maureen; Keenan, Natalie; Lyons, Marc; Wassall, Helen; Marsh, Chris; Mahenthran, Mervin; Carter, Emma; Kong, Thomas; Blackman, Helen; Creagh‐Brown, Ben; Donlon, Sinead; Michalak-Glinska, Natalia; Mtuwa, Sheila; Pristopan, Veronika; Salberg, Armorel; Smith, Eleanor; Stone, Sarah; Piercy, Charles; Verula, Jerik; Burda, D; Montaser, Rugia; Harden, Lesley; Mayangao, Irving; Marriott, Cheryl; Bradley, Paul; B. Harris, Celia; M. Anderson, Susan; Andrews, Eleanor; Birch, Janine; Collins, Emma; Hammerton, Kate; O’Leary, Ryan; Clark, Michele; Purvis, Sarah; Barber, Russell; Hewitt, Claire; Hilldrith, Annette; Jackson-Lawrence, Karen; Shepardson, Sarah; Wills, Maryanne; Butler, Susan; Tavares, Silvia; Cunningham, Amy; Hindale, Julia; Arif, Sarwat; Bean, Sarah; Burt, Karen; Z. Spivey, Michael; Demetriou, Carrie; Eckbad, Charlotte; Hierons, Sarah; Howie, Lucy; Mitchard, Sarah; Ramos, Lidia; Serrano-Ruiz, Alfredo; White, Katie; M. Kelly, F.; Cristiano, Daniele; Dormand, Natalie; Farzad, Zohreh; Gummadi, Mahitha; Liyanage, Kamal; Patel, Brijesh; Salmi, Sara; Sloane, Geraldine; Thwaites, Vicky; Varghese, Mathew; Catelan Zborowski, Anelise; Allan, John; Geary, Tim; Graeme Houston, J.; Meikle, A.W.; C. O’Brien, Peter; Forsey, Miranda; Kaliappan, Agilan; Nicholson, Anne; Riches, Joanne; Vertue, Mark; Allan, Elizabeth; Darlington, Kate; Davies, Ffyon; Easton, Jack; Kumar, Sumit; Lean, Richard; Menzies, Daniel; Pugh, Richard; Qiu, Xinyi; Davies, Llinos; Williams, Hannah; Scanlon, Jeremy; Davies, Gwyneth; Mackay, Callum; Lewis, Joanne; Rees, Stephanie; Oblak, Metod; Popescu, Monica; Thankachen, Mini; Lancaster Infirmary team, Royal; Higham, Andrew; Simpson, Kerry; Craig, Jayne; Baruah, Rosie; Morris, Sheila; Ferguson, Susie; Shepherd, Amy; Moore, Luke; P. Vizcaychipi, Marcela; Gomes de Almeida Martins, Laura; Carungcong, Jaime; Ali Mohamed Ali, Inthakab; Beaumont, Karen; Blunt, Mark; Coton, Zoe; Curgenven, Hollie; Elsaadany, Mohamed; Fernandes, Kay; Mohamed Ally, Sameena; Rangarajan, Harini; Sarathy, Varun; Selvanayagam, Sivarupan; Vedage, Dave; White, Matthew; Gill, Mandy; Paul, Paul; Ratnam, Valli; Shelton, Sarah; Wynter, Inez; Carmody, Siobhain; Page, Valérie; Beith, Claire; Black, Karen; Clements, Suzanne; Morrison, Alan; Strachan, Dominic; Taylor, Margaret; Clarkson, Michelle; D’Sylva, Stuart; Norman, K.; C. Auld, F.; Donnachie, Joanne; Edmond, Ian; Prentice, Lynn; Runciman, Nikole; Salutous, Dario; Symon, Lesley; Todd, Anne; Turner, Patricia; Short, Abigail; Sweeney, Laura; Murdoch, Euan; Senaratne, Dhaneesha; Hill, Michaela; Kannan, Thogulava; Wild, Laura; Crawley, Rikki; Crew, Abigail; Cunningham, Mishell; Daniels, Allison; Harrison, Laura; Hope, Susan; Inweregbu, Ken; Jones, Siân; Lancaster, Nicola; Matthews, Jamie; Nicholson, Alice; Wray, Gemma; Langton, Helen; Prout, Rachel; Watters, Malcolm; Novis, Catherine; Barron, Anthony; Collins, Ciara; Kaul, Sundeep; Passmore, Heather; Prendergast, Claire; Reed, Anna; Rogers, Paula; Shokkar, Rajvinder; Woodruff, Meriel; Middleton, Hayley; Polgar, Oliver; M. Nolan, Claire; Thwaites, Vicky; Mahay, Kanta; Collier, Dawn; Hormis, Anil; Maynard, Victoria; Graham, Cheryl; Walker, Rachel; Gwynedd team, Ysbyty; Knights, Ellen; Price, Alicia; Thomas, Alice; Thorpe, Chris; Behan, Teresa; Burnett, Caroline; Hatton, Jonathan; Heeney, Elaine; Mitra, Atideb; Newton, Maria; E. Pollard, Rachel; Stead, Rachael; Amin, Vishal; Anastasescu, Elena; Anumakonda, Vikram; Karthik, Komala; Kausar, Rizwana; Reid, Karen; Smith, Jacqueline; Imeson-Wood, Janet; Brown, Alison; Crickmore, Vikki; Debreceni, Gabor; Wilkins, Joy; Nicol, Liz; Khaliq, Waqas; Reece-Anthony, Rosie; Birt, Mark; Ghosh, Alison; Williams, Emma; Allen, Louise; Beranová, Eva; Crisp, Nikki; Deery, Joanne; Hazelton, Tracy; Knight, Alicia; Price, Carly; Tilbey, Sorrell; Turki, Salah; Turney, Sharon; Albert Edward Infirmary team, Royal; Cooper, Joshua; Finch, Cheryl; Liderth, Sarah; Quinn, Alison; Waddington, Natalia; Coventry, Tina; A. Fowler, Susan; MacMahon, Michael; McGregor, Amanda; Cowley, Anne; Highgate, Judith; Infirmary team, Cumberland; Brown, Alison; Gregory, Jane; O’Çonnell, Susan; F. Smith, Timothy; Barberis, Luigi; Gopal, Shameer; Harris, Nichola; Lake, Victoria; Metherell, Stella; J. 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doi:10.1038/s41586-022-04576-6

Public

Whole-genome sequencing reveals host factors underlying critical COVID-19

Published in Nature • Mar 7, 2022

Authors:

Athanasios Kousathanas

Erola Pairo‐Castineira

Konrad Rawlik

Abstract

after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill ...

Subject

Biology

Population

Disease

Research Assistant

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