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1.
Nat Rev Microbiol ; 2022 Oct 28.
Article in English | MEDLINE | ID: covidwho-2096724

ABSTRACT

Monoclonal antibodies (mAbs) offer a treatment option for individuals with severe COVID-19 and are especially important in high-risk individuals where vaccination is not an option. Given the importance of understanding the evolution of resistance to mAbs by SARS-CoV-2, we reviewed the available in vitro neutralization data for mAbs against live variants and viral constructs containing spike mutations of interest. Unfortunately, evasion of mAb-induced protection is being reported with new SARS-CoV-2 variants. The magnitude of neutralization reduction varied greatly among mAb-variant pairs. For example, sotrovimab retained its neutralization capacity against Omicron BA.1 but showed reduced efficacy against BA.2, BA.4 and BA.5, and BA.2.12.1. At present, only bebtelovimab has been reported to retain its efficacy against all SARS-CoV-2 variants considered here. Resistance to mAb neutralization was dominated by the action of epitope single amino acid substitutions in the spike protein. Although not all observed epitope mutations result in increased mAb evasion, amino acid substitutions at non-epitope positions and combinations of mutations also contribute to evasion of neutralization. This Review highlights the implications for the rational design of viral genomic surveillance and factors to consider for the development of novel mAb therapies.

3.
Elife ; 112022 09 13.
Article in English | MEDLINE | ID: covidwho-2030290

ABSTRACT

Background: Viral sequencing of SARS-CoV-2 has been used for outbreak investigation, but there is limited evidence supporting routine use for infection prevention and control (IPC) within hospital settings. Methods: We conducted a prospective non-randomised trial of sequencing at 14 acute UK hospital trusts. Sites each had a 4-week baseline data collection period, followed by intervention periods comprising 8 weeks of 'rapid' (<48 hr) and 4 weeks of 'longer-turnaround' (5-10 days) sequencing using a sequence reporting tool (SRT). Data were collected on all hospital-onset COVID-19 infections (HOCIs; detected ≥48 hr from admission). The impact of the sequencing intervention on IPC knowledge and actions, and on the incidence of probable/definite hospital-acquired infections (HAIs), was evaluated. Results: A total of 2170 HOCI cases were recorded from October 2020 to April 2021, corresponding to a period of extreme strain on the health service, with sequence reports returned for 650/1320 (49.2%) during intervention phases. We did not detect a statistically significant change in weekly incidence of HAIs in longer-turnaround (incidence rate ratio 1.60, 95% CI 0.85-3.01; p=0.14) or rapid (0.85, 0.48-1.50; p=0.54) intervention phases compared to baseline phase. However, IPC practice was changed in 7.8 and 7.4% of all HOCI cases in rapid and longer-turnaround phases, respectively, and 17.2 and 11.6% of cases where the report was returned. In a 'per-protocol' sensitivity analysis, there was an impact on IPC actions in 20.7% of HOCI cases when the SRT report was returned within 5 days. Capacity to respond effectively to insights from sequencing was breached in most sites by the volume of cases and limited resources. Conclusions: While we did not demonstrate a direct impact of sequencing on the incidence of nosocomial transmission, our results suggest that sequencing can inform IPC response to HOCIs, particularly when returned within 5 days. Funding: 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. Clinical trial number: NCT04405934.


Subject(s)
COVID-19 , Cross Infection , Humans , SARS-CoV-2/genetics , COVID-19/epidemiology , COVID-19/prevention & control , Prospective Studies , Infection Control/methods , Cross Infection/epidemiology , Cross Infection/prevention & control , Hospitals
4.
Adv Exp Med Biol ; 1388: 129-152, 2022.
Article in English | MEDLINE | ID: covidwho-2027433

ABSTRACT

Since the COVID-19 pandemic started in 2019, the virus responsible for the outbreak-SARS-CoV-2-has continued to evolve. Mutations of the virus' spike protein, the main protein driving infectivity and transmissibility, are especially concerning as they may allow the virus to improve its infectivity, transmissibility, and ability to evade the immune system. Understanding how specific molecular changes can alter the behaviour of a virus is challenging for non-experts, but this information helps us to understand the pandemic we are living through and the public health measures and interventions needed to bring it under control. In response to communication challenges arising from the COVID-19 pandemic, we recently developed an online educational application to explain the molecular biology of SARS-CoV-2 spike protein mutations to the general public. We used visualisation techniques such as 3D modelling and animation, which have been shown to be highly effective teaching tools in molecular biology, allowing the viewer to better understand protein structure, function, and dynamics. We also included interactive elements for users to learn actively by engaging with the digital content, and consequently improve information retention.This chapter presents the methodological and technological framework which we used to create this resource, the 'SARS-CoV-2 Spike Protein Mutation Explorer' (SSPME). It explains how molecular visualisation and 3D modelling software were used to develop accurate models of relevant proteins; how 3D animation software was used to accurately visualise the dynamic molecular processes of SARS-CoV-2 infection, transmission, and antibody evasion; and how game development software was used to compile the 3D models and animations into a comprehensive, informative interactive application on SARS-CoV-2 spike protein mutations. This chapter indicates how cutting-edge visualisation techniques and technologies can be used to improve science communication about complex topics in molecular biology and infection biology to the general public, something that is critical to gaining control of the continuing COVID-19 pandemic.


Subject(s)
COVID-19 , Spike Glycoprotein, Coronavirus , COVID-19/epidemiology , COVID-19/genetics , Humans , Molecular Biology , Mutation , Pandemics , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/metabolism
5.
Baruch, Joaquin, Rojek, Amanda, Kartsonaki, Christiana, Vijayaraghavan, Bharath K. T.; Gonçalves, Bronner P.; Pritchard, Mark G.; Merson, Laura, Dunning, Jake, Hall, Matthew, Sigfrid, Louise, Citarella, Barbara W.; Murthy, Srinivas, Yeabah, Trokon O.; Olliaro, Piero, Abbas, Ali, Abdukahil, Sheryl Ann, Abdulkadir, Nurul Najmee, Abe, Ryuzo, Abel, Laurent, Absil, Lara, Acharya, Subhash, Acker, Andrew, Adam, Elisabeth, Adrião, Diana, Al Ageel, Saleh, Ahmed, Shakeel, Ainscough, Kate, Airlangga, Eka, Aisa, Tharwat, Hssain, Ali Ait, Tamlihat, Younes Ait, Akimoto, Takako, Akmal, Ernita, Al Qasim, Eman, Alalqam, Razi, Alberti, Angela, Al‐dabbous, Tala, Alegesan, Senthilkumar, Alegre, Cynthia, Alessi, Marta, Alex, Beatrice, Alexandre, Kévin, Al‐Fares, Abdulrahman, Alfoudri, Huda, Ali, Imran, Ali, Adam, Shah, Naseem Ali, Alidjnou, Kazali Enagnon, Aliudin, Jeffrey, Alkhafajee, Qabas, Allavena, Clotilde, Allou, Nathalie, Altaf, Aneela, Alves, João, Alves, Rita, Alves, João Melo, Amaral, Maria, Amira, Nur, Ampaw, Phoebe, Andini, Roberto, Andréjak, Claire, Angheben, Andrea, Angoulvant, François, Ansart, Séverine, Anthonidass, Sivanesen, Antonelli, Massimo, de Brito, Carlos Alexandre Antunes, Apriyana, Ardiyan, Arabi, Yaseen, Aragao, Irene, Araujo, Carolline, Arcadipane, Antonio, Archambault, Patrick, Arenz, Lukas, Arlet, Jean‐Benoît, Arora, Lovkesh, Arora, Rakesh, Artaud‐Macari, Elise, Aryal, Diptesh, Asensio, Angel, Ashraf, Muhammad, Asif, Namra, Asim, Mohammad, Assie, Jean Baptiste, Asyraf, Amirul, Atique, Anika, Attanyake, A. M. Udara Lakshan, Auchabie, Johann, Aumaitre, Hugues, Auvet, Adrien, Axelsen, Eyvind W.; Azemar, Laurène, Azoulay, Cecile, Bach, Benjamin, Bachelet, Delphine, Badr, Claudine, Bævre‐Jensen, Roar, Baig, Nadia, Baillie, J. Kenneth, Baird, J. Kevin, Bak, Erica, Bakakos, Agamemnon, Bakar, Nazreen Abu, Bal, Andriy, Balakrishnan, Mohanaprasanth, Balan, Valeria, Bani‐Sadr, Firouzé, Barbalho, Renata, Barbosa, Nicholas Yuri, Barclay, Wendy S.; Barnett, Saef Umar, Barnikel, Michaela, Barrasa, Helena, Barrelet, Audrey, Barrigoto, Cleide, Bartoli, Marie, Baruch, Joaquín, Bashir, Mustehan, Basmaci, Romain, Basri, Muhammad Fadhli Hassin, Battaglini, Denise, Bauer, Jules, Rincon, Diego Fernando Bautista, Dow, Denisse Bazan, Beane, Abigail, Bedossa, Alexandra, Bee, Ker Hong, Begum, Husna, Behilill, Sylvie, Beishuizen, Albertus, Beljantsev, Aleksandr, Bellemare, David, Beltrame, Anna, Beltrão, Beatriz Amorim, Beluze, Marine, Benech, Nicolas, Benjiman, Lionel Eric, Benkerrou, Dehbia, Bennett, Suzanne, Bento, Luís, Berdal, Jan‐Erik, Bergeaud, Delphine, Bergin, Hazel, Sobrino, José Luis Bernal, Bertoli, Giulia, Bertolino, Lorenzo, Bessis, Simon, Bevilcaqua, Sybille, Bezulier, Karine, Bhatt, Amar, Bhavsar, Krishna, Bianco, Claudia, Bidin, Farah Nadiah, Singh, Moirangthem Bikram, Humaid, Felwa Bin, Kamarudin, Mohd Nazlin Bin, Bissuel, François, Bitker, Laurent, Bitton, Jonathan, Blanco‐Schweizer, Pablo, Blier, Catherine, Bloos, Frank, Blot, Mathieu, Boccia, Filomena, Bodenes, Laetitia, Bogaarts, Alice, Bogaert, Debby, Boivin, Anne‐Hélène, Bolze, Pierre‐Adrien, Bompart, François, Bonfasius, Aurelius, Borges, Diogo, Borie, Raphaël, Bosse, Hans Martin, Botelho‐Nevers, Elisabeth, Bouadma, Lila, Bouchaud, Olivier, Bouchez, Sabelline, Bouhmani, Dounia, Bouhour, Damien, Bouiller, Kévin, Bouillet, Laurence, Bouisse, Camile, Boureau, Anne‐Sophie, Bourke, John, Bouscambert, Maude, Bousquet, Aurore, Bouziotis, Jason, Boxma, Bianca, Boyer‐Besseyre, Marielle, Boylan, Maria, Bozza, Fernando Augusto, Braconnier, Axelle, Braga, Cynthia, Brandenburger, Timo, Monteiro, Filipa Brás, Brazzi, Luca, Breen, Patrick, Breen, Dorothy, Breen, Patrick, Brickell, Kathy, Browne, Shaunagh, Browne, Alex, Brozzi, Nicolas, Brunvoll, Sonja Hjellegjerde, Brusse‐Keizer, Marjolein, Buchtele, Nina, Buesaquillo, Christian, Bugaeva, Polina, Buisson, Marielle, Buonsenso, Danilo, Burhan, Erlina, Burrell, Aidan, Bustos, Ingrid G.; Butnaru, Denis, Cabie, André, Cabral, Susana, Caceres, Eder, Cadoz, Cyril, Calligy, Kate, Calvache, Jose Andres, Camões, João, Campana, Valentine, Campbell, Paul, Campisi, Josie, Canepa, Cecilia, Cantero, Mireia, Caraux‐Paz, Pauline, Cárcel, Sheila, Cardellino, Chiara Simona, Cardoso, Sofia, Cardoso, Filipe, Cardoso, Filipa, Cardoso, Nelson, Carelli, Simone, Carlier, Nicolas, Carmoi, Thierry, Carney, Gayle, Carqueja, Inês, Carret, Marie‐Christine, Carrier, François Martin, Carroll, Ida, Carson, Gail, Casanova, Maire‐Laure, Cascão, Mariana, Casey, Siobhan, Casimiro, José, Cassandra, Bailey, Castañeda, Silvia, Castanheira, Nidyanara, Castor‐Alexandre, Guylaine, Castrillón, Henry, Castro, Ivo, Catarino, Ana, Catherine, François‐Xavier, Cattaneo, Paolo, Cavalin, Roberta, Cavalli, Giulio Giovanni, Cavayas, Alexandros, Ceccato, Adrian, Cervantes‐Gonzalez, Minerva, Chair, Anissa, Chakveatze, Catherine, Chan, Adrienne, Chand, Meera, Auger, Christelle Chantalat, Chapplain, Jean‐Marc, Chas, Julie, Chatterjee, Allegra, Chaudry, Mobin, Iñiguez, Jonathan Samuel Chávez, Chen, Anjellica, Chen, Yih‐Sharng, Cheng, Matthew Pellan, Cheret, Antoine, Chiarabini, Thibault, Chica, Julian, Chidambaram, Suresh Kumar, Tho, Leong Chin, Chirouze, Catherine, Chiumello, Davide, Cho, Sung‐Min, Cholley, Bernard, Chopin, Marie‐Charlotte, Chow, Ting Soo, Chow, Yock Ping, Chua, Jonathan, Chua, Hiu Jian, Cidade, Jose Pedro, Herreros, José Miguel Cisneros, Citarella, Barbara Wanjiru, Ciullo, Anna, Clarke, Jennifer, Clarke, Emma, Granado, Rolando Claure‐Del, Clohisey, Sara, Cobb, Perren J.; Codan, Cassidy, Cody, Caitriona, Coelho, Alexandra, Coles, Megan, Colin, Gwenhaël, Collins, Michael, Colombo, Sebastiano Maria, Combs, Pamela, Connor, Marie, Conrad, Anne, Contreras, Sofía, Conway, Elaine, Cooke, Graham S.; Copland, Mary, Cordel, Hugues, Corley, Amanda, Cornelis, Sabine, Cornet, Alexander Daniel, Corpuz, Arianne Joy, Cortegiani, Andrea, Corvaisier, Grégory, Costigan, Emma, Couffignal, Camille, Couffin‐Cadiergues, Sandrine, Courtois, Roxane, Cousse, Stéphanie, Cregan, Rachel, Croonen, Sabine, Crowl, Gloria, Crump, Jonathan, Cruz, Claudina, Bermúdez, Juan Luis Cruz, Rojo, Jaime Cruz, Csete, Marc, Cullen, Ailbhe, Cummings, Matthew, Curley, Gerard, Curlier, Elodie, Curran, Colleen, Custodio, Paula, da Silva Filipe, Ana, Da Silveira, Charlene, Dabaliz, Al‐Awwab, Dagens, Andrew, Dahl, John Arne, Dahly, Darren, Dalton, Heidi, Dalton, Jo, Daly, Seamus, Daneman, Nick, Daniel, Corinne, Dankwa, Emmanuelle A.; Dantas, Jorge, D'Aragon, Frédérick, de Loughry, Gillian, de Mendoza, Diego, De Montmollin, Etienne, de Oliveira França, Rafael Freitas, de Pinho Oliveira, Ana Isabel, De Rosa, Rosanna, De Rose, Cristina, de Silva, Thushan, de Vries, Peter, Deacon, Jillian, Dean, David, Debard, Alexa, Debray, Marie‐Pierre, DeCastro, Nathalie, Dechert, William, Deconninck, Lauren, Decours, Romain, Defous, Eve, Delacroix, Isabelle, Delaveuve, Eric, Delavigne, Karen, Delfos, Nathalie M.; Deligiannis, Ionna, Dell'Amore, Andrea, Delmas, Christelle, Delobel, Pierre, Delsing, Corine, Demonchy, Elisa, Denis, Emmanuelle, Deplanque, Dominique, Depuydt, Pieter, Desai, Mehul, Descamps, Diane, Desvallées, Mathilde, Dewayanti, Santi, Dhanger, Pathik, Diallo, Alpha, Diamantis, Sylvain, Dias, André, Diaz, Juan Jose, Diaz, Priscila, Diaz, Rodrigo, Didier, Kévin, Diehl, Jean‐Luc, Dieperink, Wim, Dimet, Jérôme, Dinot, Vincent, Diop, Fara, Diouf, Alphonsine, Dishon, Yael, Djossou, Félix, Docherty, Annemarie B.; Doherty, Helen, Dondorp, Arjen M.; Donnelly, Maria, Donnelly, Christl A.; Donohue, Sean, Donohue, Yoann, Donohue, Chloe, Doran, Peter, Dorival, Céline, D'Ortenzio, Eric, Douglas, James Joshua, Douma, Renee, Dournon, Nathalie, Downer, Triona, Downey, Joanne, Downing, Mark, Drake, Tom, Driscoll, Aoife, Dryden, Murray, Fonseca, Claudio Duarte, Dubee, Vincent, Dubos, François, Ducancelle, Alexandre, Duculan, Toni, Dudman, Susanne, Duggal, Abhijit, Dunand, Paul, Dunning, Jake, Duplaix, Mathilde, Durante‐Mangoni, Emanuele, Durham, Lucian, Dussol, Bertrand, Duthoit, Juliette, Duval, Xavier, Dyrhol‐Riise, Anne Margarita, Ean, Sim Choon, Echeverria‐Villalobos, Marco, Egan, Siobhan, Eggesbø, Linn Margrete, Eira, Carla, El Sanharawi, Mohammed, Elapavaluru, Subbarao, Elharrar, Brigitte, Ellerbroek, Jacobien, Ellingjord‐Dale, Merete, Eloy, Philippine, Elshazly, Tarek, Elyazar, Iqbal, Enderle, Isabelle, Endo, Tomoyuki, Eng, Chan Chee, Engelmann, Ilka, Enouf, Vincent, Epaulard, Olivier, Escher, Martina, Esperatti, Mariano, Esperou, Hélène, Esposito‐Farese, Marina, Estevão, João, Etienne, Manuel, Ettalhaoui, Nadia, Everding, Anna Greti, Evers, Mirjam, Fabre, Marc, Fabre, Isabelle, Faheem, Amna, Fahy, Arabella, Fairfield, Cameron J.; Fakar, Zul, Fareed, Komal, Faria, Pedro, Farooq, Ahmed, Fateena, Hanan, Fatoni, Arie Zainul, Faure, Karine, Favory, Raphaël, Fayed, Mohamed, Feely, Niamh, Feeney, Laura, Fernandes, Jorge, Fernandes, Marília Andreia, Fernandes, Susana, Ferrand, François‐Xavier, Devouge, Eglantine Ferrand, Ferrão, Joana, Ferraz, Mário, Ferreira, Sílvia, Ferreira, Isabel, Ferreira, Benigno, Ferrer‐Roca, Ricard, Ferriere, Nicolas, Ficko, Céline, Figueiredo‐Mello, Claudia, Finlayson, William, Fiorda, Juan, Flament, Thomas, Flateau, Clara, Fletcher, Tom, Florio, Letizia Lucia, Flynn, Deirdre, Foley, Claire, Foley, Jean, Fomin, Victor, Fonseca, Tatiana, Fontela, Patricia, Forsyth, Simon, Foster, Denise, Foti, Giuseppe, Fourn, Erwan, Fowler, Robert A.; Fraher, Marianne, Franch‐Llasat, Diego, Fraser, John F.; Fraser, Christophe, Freire, Marcela Vieira, Ribeiro, Ana Freitas, Friedrich, Caren, Fry, Stéphanie, Fuentes, Nora, Fukuda, Masahiro, Argin, G.; Gaborieau, Valérie, Gaci, Rostane, Gagliardi, Massimo, Gagnard, Jean‐Charles, Gagneux‐Brunon, Amandine, Gaião, Sérgio, Skeie, Linda Gail, Gallagher, Phil, Gamble, Carrol, Gani, Yasmin, Garan, Arthur, Garcia, Rebekha, Barrio, Noelia García, Garcia‐Diaz, Julia, Garcia‐Gallo, Esteban, Garimella, Navya, Garot, Denis, Garrait, Valérie, Gauli, Basanta, Gault, Nathalie, Gavin, Aisling, Gavrylov, Anatoliy, Gaymard, Alexandre, Gebauer, Johannes, Geraud, Eva, Morlaes, Louis Gerbaud, Germano, Nuno, Ghisulal, Praveen Kumar, Ghosn, Jade, Giani, Marco, Gibson, Jess, Gigante, Tristan, Gilg, Morgane, Gilroy, Elaine, Giordano, Guillermo, Girvan, Michelle, Gissot, Valérie, Glikman, Daniel, Glybochko, Petr, Gnall, Eric, Goco, Geraldine, Goehringer, François, Goepel, Siri, Goffard, Jean‐Christophe, Goh, Jin Yi, Golob, Jonathan, Gomez, Kyle, Gómez‐Junyent, Joan, Gominet, Marie, Gonçalves, Bronner P.; Gonzalez, Alicia, Gordon, Patricia, Gorenne, Isabelle, Goubert, Laure, Goujard, Cécile, Goulenok, Tiphaine, Grable, Margarite, Graf, Jeronimo, Grandin, Edward Wilson, Granier, Pascal, Grasselli, Giacomo, Green, Christopher A.; Greene, Courtney, Greenhalf, William, Greffe, Segolène, Grieco, Domenico Luca, Griffee, Matthew, Griffiths, Fiona, Grigoras, Ioana, Groenendijk, Albert, Lordemann, Anja Grosse, Gruner, Heidi, Gu, Yusing, Guedj, Jérémie, Guego, Martin, Guellec, Dewi, Guerguerian, Anne‐Marie, Guerreiro, Daniela, Guery, Romain, Guillaumot, Anne, Guilleminault, Laurent, Guimarães de Castro, Maisa, Guimard, Thomas, Haalboom, Marieke, Haber, Daniel, Habraken, Hannah, Hachemi, Ali, Hackmann, Amy, Hadri, Nadir, Haidri, Fakhir, Hakak, Sheeba, Hall, Adam, Hall, Matthew, Halpin, Sophie, Hameed, Jawad, Hamer, Ansley, Hamers, Raph L.; Hamidfar, Rebecca, Hammarström, Bato, Hammond, Terese, Han, Lim Yuen, Haniffa, Rashan, Hao, Kok Wei, Hardwick, Hayley, Harrison, Ewen M.; Harrison, Janet, Harrison, Samuel Bernard Ekow, Hartman, Alan, Hasan, Mohd Shahnaz, Hashmi, Junaid, Hayat, Muhammad, Hayes, Ailbhe, Hays, Leanne, Heerman, Jan, Heggelund, Lars, Hendry, Ross, Hennessy, Martina, Henriquez‐Trujillo, Aquiles, Hentzien, Maxime, Hernandez‐Montfort, Jaime, Hershey, Andrew, Hesstvedt, Liv, Hidayah, Astarini, Higgins, Eibhilin, Higgins, Dawn, Higgins, Rupert, Hinchion, Rita, Hinton, Samuel, Hiraiwa, Hiroaki, Hirkani, Haider, Hitoto, Hikombo, Ho, Yi Bin, Ho, Antonia, Hoctin, Alexandre, Hoffmann, Isabelle, Hoh, Wei Han, Hoiting, Oscar, Holt, Rebecca, Holter, Jan Cato, Horby, Peter, Horcajada, Juan Pablo, Hoshino, Koji, Houas, Ikram, Hough, Catherine L.; Houltham, Stuart, Hsu, Jimmy Ming‐Yang, Hulot, Jean‐Sébastien, Huo, Stella, Hurd, Abby, Hussain, Iqbal, Ijaz, Samreen, Illes, Hajnal‐Gabriela, Imbert, Patrick, Imran, Mohammad, Sikander, Rana Imran, Imtiaz, Aftab, Inácio, Hugo, Dominguez, Carmen Infante, Ing, Yun Sii, Iosifidis, Elias, Ippolito, Mariachiara, Isgett, Sarah, Isidoro, Tiago, Ismail, Nadiah, Isnard, Margaux, Istre, Mette Stausland, Itai, Junji, Ivulich, Daniel, Jaafar, Danielle, Jaafoura, Salma, Jabot, Julien, Jackson, Clare, Jamieson, Nina, Jaquet, Pierre, Jaud‐Fischer, Coline, Jaureguiberry, Stéphane, Jaworsky, Denise, Jego, Florence, Jelani, Anilawati Mat, Jenum, Synne, Jimbo‐Sotomayor, Ruth, Joe, Ong Yiaw, Jorge García, Ruth N.; Jørgensen, Silje Bakken, Joseph, Cédric, Joseph, Mark, Joshi, Swosti, Jourdain, Mercé, Jouvet, Philippe, Jung, Hanna, Jung, Anna, Juzar, Dafsah, Kafif, Ouifiya, Kaguelidou, Florentia, Kaisbain, Neerusha, Kaleesvran, Thavamany, Kali, Sabina, Kalicinska, Alina, Kalleberg, Karl Trygve, Kalomoiri, Smaragdi, Kamaluddin, Muhammad Aisar Ayadi, Kamaruddin, Zul Amali Che, Kamarudin, Nadiah, Kamineni, Kavita, Kandamby, Darshana Hewa, Kandel, Chris, Kang, Kong Yeow, Kanwal, Darakhshan, Karpayah, Pratap, Kartsonaki, Christiana, Kasugai, Daisuke, Kataria, Anant, Katz, Kevin, Kaur, Aasmine, Kay, Christy, Keane, Hannah, Keating, Seán, Kedia, Pulak, Kelly, Claire, Kelly, Yvelynne, Kelly, Andrea, Kelly, Niamh, Kelly, Aoife, Kelly, Sadie, Kelsey, Maeve, Kennedy, Ryan, Kennon, Kalynn, Kernan, Maeve, Kerroumi, Younes, Keshav, Sharma, Khalid, Imrana, Khalid, Osama, Khalil, Antoine, Khan, Coralie, Khan, Irfan, Khan, Quratul Ain, Khanal, Sushil, Khatak, Abid, Khawaja, Amin, Kherajani, Krish, Kho, Michelle E.; Khoo, Ryan, Khoo, Denisa, Khoo, Saye, Khoso, Nasir, Kiat, Khor How, Kida, Yuri, Kiiza, Peter, Granerud, Beathe Kiland, Kildal, Anders Benjamin, Kim, Jae Burm, Kimmoun, Antoine, Kindgen‐Milles, Detlef, King, Alexander, Kitamura, Nobuya, Kjetland, Eyrun Floerecke Kjetland, Klenerman, Paul, Klont, Rob, Bekken, Gry Kloumann, Knight, Stephen R.; Kobbe, Robin, Kodippily, Chamira, Vasconcelos, Malte Kohns, Koirala, Sabin, Komatsu, Mamoru, Kosgei, Caroline, Kpangon, Arsène, Krawczyk, Karolina, Krishnan, Vinothini, Krishnan, Sudhir, Kruglova, Oksana, Kumar, Ganesh, Kumar, Deepali, Kumar, Mukesh, Vecham, Pavan Kumar, Kuriakose, Dinesh, Kurtzman, Ethan, Kutsogiannis, Demetrios, Kutsyna, Galyna, Kyriakoulis, Konstantinos, Lachatre, Marie, Lacoste, Marie, Laffey, John G.; Lagrange, Marie, Laine, Fabrice, Lairez, Olivier, Lakhey, Sanjay, Lalueza, Antonio, Lambert, Marc, Lamontagne, François, Langelot‐Richard, Marie, Langlois, Vincent, Lantang, Eka Yudha, Lanza, Marina, Laouénan, Cédric, Laribi, Samira, Lariviere, Delphine, Lasry, Stéphane, Lath, Sakshi, Latif, Naveed, Launay, Odile, Laureillard, Didier, Lavie‐Badie, Yoan, Law, Andy, Lawrence, Teresa, Lawrence, Cassie, Le, Minh, Le Bihan, Clément, Le Bris, Cyril, Le Falher, Georges, Le Fevre, Lucie, Le Hingrat, Quentin, Le Maréchal, Marion, Le Mestre, Soizic, Le Moal, Gwenaël, Le Moing, Vincent, Le Nagard, Hervé, Le Turnier, Paul, Leal, Ema, Santos, Marta Leal, Lee, Heng Gee, Lee, Biing Horng, Lee, Yi Lin, Lee, Todd C.; Lee, James, Lee, Jennifer, Lee, Su Hwan, Leeming, Gary, Lefebvre, Laurent, Lefebvre, Bénédicte, Lefèvre, Benjamin, LeGac, Sylvie, Lelievre, Jean‐Daniel, Lellouche, François, Lemaignen, Adrien, Lemee, Véronique, Lemeur, Anthony, Lemmink, Gretchen, Lene, Ha Sha, Lennon, Jenny, León, Rafael, Leone, Marc, Leone, Michela, Lepiller, Quentin, Lescure, François‐Xavier, Lesens, Olivier, Lesouhaitier, Mathieu, Lester‐Grant, Amy, Levy, Yves, Levy, Bruno, Levy‐Marchal, Claire, Lewandowska, Katarzyna, L'Her, Erwan, Bassi, Gianluigi Li, Liang, Janet, Liaquat, Ali, Liegeon, Geoffrey, Lim, Kah Chuan, Lim, Wei Shen, Lima, Chantre, Lina, Lim, Lina, Bruno, Lind, Andreas, Lingad, Maja Katherine, Lingas, Guillaume, Lion‐Daolio, Sylvie, Lissauer, Samantha, Liu, Keibun, Livrozet, Marine, Lizotte, Patricia, Loforte, Antonio, Lolong, Navy, Loon, Leong Chee, Lopes, Diogo, Lopez‐Colon, Dalia, Lopez‐Revilla, Jose W.; Loschner, Anthony L.; Loubet, Paul, Loufti, Bouchra, Louis, Guillame, Lourenco, Silvia, Lovelace‐Macon, Lara, Low, Lee Lee, Lowik, Marije, Loy, Jia Shyi, Lucet, Jean Christophe, Bermejo, Carlos Lumbreras, Luna, Carlos M.; Lungu, Olguta, Luong, Liem, Luque, Nestor, Luton, Dominique, Lwin, Nilar, Lyons, Ruth, Maasikas, Olavi, Mabiala, Oryane, Machado, Moïse, Macheda, Gabriel, Madiha, Hashmi, Maestro de la Calle, Guillermo, Mahieu, Rafael, Mahy, Sophie, Maia, Ana Raquel, Maier, Lars S.; Maillet, Mylène, Maitre, Thomas, Malfertheiner, Maximilian, Malik, Nadia, Mallon, Paddy, Maltez, Fernando, Malvy, Denis, Manda, Victoria, Mandelbrot, Laurent, Manetta, Frank, Mankikian, Julie, Manning, Edmund, Manuel, Aldric, Sant'Ana Malaque, Ceila Maria, Marino, Flávio, Marino, Daniel, Markowicz, Samuel, Maroun Eid, Charbel, Marques, Ana, Marquis, Catherine, Marsh, Brian, Marsh, Laura, Marshal, Megan, Marshall, John, Martelli, Celina Turchi, Martin, Dori‐Ann, Martin, Emily, Martin‐Blondel, Guillaume, Martin‐Loeches, Ignacio, Martinot, Martin, Martin‐Quiros, Alejandro, Martins, João, Martins, Ana, Martins, Nuno, Rego, Caroline Martins, Martucci, Gennaro, Martynenko, Olga, Marwali, Eva Miranda, Marzukie, Marsilla, Maslove, David, Mason, Sabina, Masood, Sobia, Nor, Basri Mat, Matan, Moshe, Mathew, Meghena, Mathieu, Daniel, Mattei, Mathieu, Matulevics, Romans, Maulin, Laurence, Maxwell, Michael, Maynar, Javier, Mazzoni, Thierry, Evoy, Natalie Mc, Sweeney, Lisa Mc, McArthur, Colin, McArthur, Colin, McCarthy, Anne, McCarthy, Aine, McCloskey, Colin, McConnochie, Rachael, McDermott, Sherry, McDonald, Sarah E.; McElroy, Aine, McElwee, Samuel, McEneany, Victoria, McGeer, Allison, McKay, Chris, McKeown, Johnny, McLean, Kenneth A.; McNally, Paul, McNicholas, Bairbre, McPartlan, Elaine, Meaney, Edel, Mear‐Passard, Cécile, Mechlin, Maggie, Meher, Maqsood, Mehkri, Omar, Mele, Ferruccio, Melo, Luis, Memon, Kashif, Mendes, Joao Joao, Menkiti, Ogechukwu, Menon, Kusum, Mentré, France, Mentzer, Alexander J.; Mercier, Noémie, Mercier, Emmanuelle, Merckx, Antoine, Mergeay‐Fabre, Mayka, Mergler, Blake, Merson, Laura, Mesquita, António, Meta, Roberta, Metwally, Osama, Meybeck, Agnès, Meyer, Dan, Meynert, Alison M.; Meysonnier, Vanina, Meziane, Amina, Mezidi, Mehdi, Michelanglei, Céline, Michelet, Isabelle, Mihelis, Efstathia, Mihnovit, Vladislav, Miranda‐Maldonado, Hugo, Misnan, Nor Arisah, Mohamed, Tahira Jamal, Mohamed, Nik Nur Eliza, Moin, Asma, Molina, David, Molinos, Elena, Molloy, Brenda, Mone, Mary, Monteiro, Agostinho, Montes, Claudia, Montrucchio, Giorgia, Moore, Shona C.; Moore, Sarah, Cely, Lina Morales, Moro, Lucia, Morton, Ben, Motherway, Catherine, Motos, Ana, Mouquet, Hugo, Perrot, Clara Mouton, Moyet, Julien, Mudara, Caroline, Mufti, Aisha Kalsoom, Muh, Ng Yong, Muhamad, Dzawani, Mullaert, Jimmy, Müller, Fredrik, Müller, Karl Erik, Munblit, Daniel, Muneeb, Syed, Munir, Nadeem, Munshi, Laveena, Murphy, Aisling, Murphy, Lorna, Murphy, Aisling, Murris, Marlène, Murthy, Srinivas, Musaab, Himed, Muvindi, Himasha, Muyandy, Gugapriyaa, Myrodia, Dimitra Melia, Mohd‐Hanafiah, Farah Nadia, Nagpal, Dave, Nagrebetsky, Alex, Narasimhan, Mangala, Narayanan, Nageswaran, Khan, Rashid Nasim, Nazerali‐Maitland, Alasdair, Neant, Nadège, Neb, Holger, Nekliudov, Nikita, Nelwan, Erni, Neto, Raul, Neumann, Emily, Ng, Pauline Yeung, Ng, Wing Yiu, Nghi, Anthony, Nguyen, Duc, Choileain, Orna Ni, Leathlobhair, Niamh Ni, Nichol, Alistair, Nitayavardhana, Prompak, Nonas, Stephanie, Noordin, Nurul Amani Mohd, Noret, Marion, Norharizam, Nurul Faten Izzati, Norman, Lisa, Notari, Alessandra, Noursadeghi, Mahdad, Nowicka, Karolina, Nowinski, Adam, Nseir, Saad, Nunez, Jose I.; Nurnaningsih, Nurnaningsih, Nusantara, Dwi Utomo, Nyamankolly, Elsa, Nygaard, Anders Benteson, Brien, Fionnuala O.; Callaghan, Annmarie O.; O'Callaghan, Annmarie, Occhipinti, Giovanna, Oconnor, Derbrenn, O'Donnell, Max, Ogston, Tawnya, Ogura, Takayuki, Oh, Tak‐Hyuk, O'Halloran, Sophie, O'Hearn, Katie, Ohshimo, Shinichiro, Oldakowska, Agnieszka, Oliveira, João, Oliveira, Larissa, Olliaro, Piero L.; Ong, Jee Yan, Ong, David S. Y.; Oosthuyzen, Wilna, Opavsky, Anne, Openshaw, Peter, Orakzai, Saijad, Orozco‐Chamorro, Claudia Milena, Ortoleva, Jamel, Osatnik, Javier, O'Shea, Linda, O'Sullivan, Miriam, Othman, Siti Zubaidah, Ouamara, Nadia, Ouissa, Rachida, Oziol, Eric, Pagadoy, Maïder, Pages, Justine, Palacios, Mario, Palacios, Amanda, Palmarini, Massimo, Panarello, Giovanna, Panda, Prasan Kumar, Paneru, Hem, Pang, Lai Hui, Panigada, Mauro, Pansu, Nathalie, Papadopoulos, Aurélie, Parke, Rachael, Parker, Melissa, Parra, Briseida, Pasha, Taha, Pasquier, Jérémie, Pastene, Bruno, Patauner, Fabian, Patel, Drashti, Pathmanathan, Mohan Dass, Patrão, Luís, Patricio, Patricia, Patrier, Juliette, Patterson, Lisa, Pattnaik, Rajyabardhan, Paul, Mical, Paul, Christelle, Paulos, Jorge, Paxton, William A.; Payen, Jean‐François, Peariasamy, Kalaiarasu, Jiménez, Miguel Pedrera, Peek, Giles J.; Peelman, Florent, Peiffer‐Smadja, Nathan, Peigne, Vincent, Pejkovska, Mare, Pelosi, Paolo, Peltan, Ithan D.; Pereira, Rui, Perez, Daniel, Periel, Luis, Perpoint, Thomas, Pesenti, Antonio, Pestre, Vincent, Petrou, Lenka, Petrovic, Michele, Petrov‐Sanchez, Ventzislava, Pettersen, Frank Olav, Peytavin, Gilles, Pharand, Scott, Picard, Walter, Picone, Olivier, de Piero, Maria, Pierobon, Carola, Piersma, Djura, Pimentel, Carlos, Pinto, Raquel, Pires, Catarina, Pironneau, Isabelle, Piroth, Lionel, Pitaloka, Ayodhia, Pius, Riinu, Plantier, Laurent, Png, Hon Shen, Poissy, Julien, Pokeerbux, Ryadh, Pokorska‐Spiewak, Maria, Poli, Sergio, Pollakis, Georgios, Ponscarme, Diane, Popielska, Jolanta, Porto, Diego Bastos, Post, Andra‐Maris, Postma, Douwe F.; Povoa, Pedro, Póvoas, Diana, Powis, Jeff, Prapa, Sofia, Preau, Sébastien, Prebensen, Christian, Preiser, Jean‐Charles, Prinssen, Anton, Pritchard, Mark G.; Priyadarshani, Gamage Dona Dilanthi, Proença, Lucia, Pudota, Sravya, Puéchal, Oriane, Semedi, Bambang Pujo, Pulicken, Mathew, Purcell, Gregory, Quesada, Luisa, Quinones‐Cardona, Vilmaris, González, Víctor Quirós, Quist‐Paulsen, Else, Quraishi, Mohammed, Rabaa, Maia, Rabaud, Christian, Rabindrarajan, Ebenezer, Rafael, Aldo, Rafiq, Marie, Rahardjani, Mutia, Rahman, Rozanah Abd, Rahman, Ahmad Kashfi Haji Ab, Rahutullah, Arsalan, Rainieri, Fernando, Rajahram, Giri Shan, Ramachandran, Pratheema, Ramakrishnan, Nagarajan, Ramli, Ahmad Afiq, Rammaert, Blandine, Ramos, Grazielle Viana, Rana, Asim, Rangappa, Rajavardhan, Ranjan, Ritika, Rapp, Christophe, Rashan, Aasiyah, Rashan, Thalha, Rasheed, Ghulam, Rasmin, Menaldi, Rätsep, Indrek, Rau, Cornelius, Ravi, Tharmini, Raza, Ali, Real, Andre, Rebaudet, Stanislas, Redl, Sarah, Reeve, Brenda, Rehman, Attaur, Reid, Liadain, Reikvam, Dag Henrik, Reis, Renato, Rello, Jordi, Remppis, Jonathan, Remy, Martine, Ren, Hongru, Renk, Hanna, Resseguier, Anne‐Sophie, Revest, Matthieu, Rewa, Oleksa, Reyes, Luis Felipe, Reyes, Tiago, Ribeiro, Maria Ines, Ricchiuto, Antonia, Richardson, David, Richardson, Denise, Richier, Laurent, Ridzuan, Siti Nurul Atikah Ahmad, Riera, Jordi, Rios, Ana L.; Rishu, Asgar, Rispal, Patrick, Risso, Karine, Nuñez, Maria Angelica Rivera, Rizer, Nicholas, Robba, Chiara, Roberto, André, Roberts, Stephanie, Robertson, David L.; Robineau, Olivier, Roche‐Campo, Ferran, Rodari, Paola, Rodeia, Simão, Abreu, Julia Rodriguez, Roessler, Bernhard, Roger, Pierre‐Marie, Roger, Claire, Roilides, Emmanuel, Rojek, Amanda, Romaru, Juliette, Roncon‐Albuquerque, Roberto, Roriz, Mélanie, Rosa‐Calatrava, Manuel, Rose, Michael, Rosenberger, Dorothea, Roslan, Nurul Hidayah Mohammad, Rossanese, Andrea, Rossetti, Matteo, Rossignol, Bénédicte, Rossignol, Patrick, Rousset, Stella, Roy, Carine, Roze, Benoît, Rusmawatiningtyas, Desy, Russell, Clark D.; Ryan, Maria, Ryan, Maeve, Ryckaert, Steffi, Holten, Aleksander Rygh, Saba, Isabela, Sadaf, Sairah, Sadat, Musharaf, Sahraei, Valla, Saint‐Gilles, Maximilien, Sakiyalak, Pranya, Salahuddin, Nawal, Salazar, Leonardo, Saleem, Jodat, Sales, Gabriele, Sallaberry, Stéphane, Salmon Gandonniere, Charlotte, Salvator, Hélène, Sanchez, Olivier, Sanchez‐Miralles, Angel, Sancho‐Shimizu, Vanessa, Sandhu, Gyan, Sandhu, Zulfiqar, Sandrine, Pierre‐François, Sandulescu, Oana, Santos, Marlene, Sarfo‐Mensah, Shirley, Banheiro, Bruno Sarmento, Sarmiento, Iam Claire E.; Sarton, Benjamine, Satya, Ankana, Satyapriya, Sree, Satyawati, Rumaisah, Saviciute, Egle, Savvidou, Parthena, Saw, Yen Tsen, Schaffer, Justin, Schermer, Tjard, Scherpereel, Arnaud, Schneider, Marion, Schroll, Stephan, Schwameis, Michael, Schwartz, Gary, Scott, Janet T.; Scott‐Brown, James, Sedillot, Nicholas, Seitz, Tamara, Selvanayagam, Jaganathan, Selvarajoo, Mageswari, Semaille, Caroline, Semple, Malcolm G.; Senian, Rasidah Bt, Senneville, Eric, Sequeira, Filipa, Sequeira, Tânia, Neto, Ary Serpa, Balazote, Pablo Serrano, Shadowitz, Ellen, Shahidan, Syamin Asyraf, Shamsah, Mohammad, Shankar, Anuraj, Sharjeel, Shaikh, Sharma, Pratima, Shaw, Catherine A.; Shaw, Victoria, Sheharyar, Ashraf, Shetty, Rohan, Shetty, Rajesh Mohan, Shi, Haixia, Shiekh, Mohiuddin, Shime, Nobuaki, Shimizu, Keiki, Shrapnel, Sally, Shrestha, Pramesh Sundar, Shrestha, Shubha Kalyan, Shum, Hoi Ping, Mohammed, Nassima Si, Siang, Ng Yong, Sibiude, Jeanne, Siddiqui, Atif, Sigfrid, Louise, Sillaots, Piret, Silva, Catarina, Silva, Rogério, Silva, Maria Joao, Heng, Benedict Sim Lim, Sin, Wai Ching, Sinatti, Dario, Singh, Punam, Singh, Budha Charan, Sitompul, Pompini Agustina, Sivam, Karisha, Skogen, Vegard, Smith, Sue, Smood, Benjamin, Smyth, Coilin, Smyth, Michelle, Snacken, Morgane, So, Dominic, Soh, Tze Vee, Solberg, Lene Bergendal, Solomon, Joshua, Solomon, Tom, Somers, Emily, Sommet, Agnès, Song, Rima, Song, Myung Jin, Song, Tae, Chia, Jack Song, Sonntagbauer, Michael, Soom, Azlan Mat, Søraas, Arne, Søraas, Camilla Lund, Sotto, Alberto, Soum, Edouard, Sousa, Marta, Sousa, Ana Chora, Uva, Maria Sousa, Souza‐Dantas, Vicente, Sperry, Alexandra, Spinuzza, Elisabetta, Darshana, B. P. Sanka Ruwan Sri, Sriskandan, Shiranee, Stabler, Sarah, Staudinger, Thomas, Stecher, Stephanie‐Susanne, Steinsvik, Trude, Stienstra, Ymkje, Stiksrud, Birgitte, Stolz, Eva, Stone, Amy, Streinu‐Cercel, Adrian, Streinu‐Cercel, Anca, Stuart, David, Stuart, Ami, Subekti, Decy, Suen, Gabriel, Suen, Jacky Y.; Sultana, Asfia, Summers, Charlotte, Supic, Dubravka, Suppiah, Deepashankari, Surovcová, Magdalena, Suwarti, Suwarti, Svistunov, Andrey, Syahrin, Sarah, Syrigos, Konstantinos, Sztajnbok, Jaques, Szuldrzynski, Konstanty, Tabrizi, Shirin, Taccone, Fabio S.; Tagherset, Lysa, Taib, Shahdattul Mawarni, Talarek, Ewa, Taleb, Sara, Talsma, Jelmer, Tamisier, Renaud, Tampubolon, Maria Lawrensia, Tan, Kim Keat, Tan, Yan Chyi, Tanaka, Taku, Tanaka, Hiroyuki, Taniguchi, Hayato, Taqdees, Huda, Taqi, Arshad, Tardivon, Coralie, Tattevin, Pierre, Taufik, M. Azhari, Tawfik, Hassan, Tedder, Richard S.; Tee, Tze Yuan, Teixeira, João, Tejada, Sofia, Tellier, Marie‐Capucine, Teoh, Sze Kye, Teotonio, Vanessa, Téoulé, François, Terpstra, Pleun, Terrier, Olivier, Terzi, Nicolas, Tessier‐Grenier, Hubert, Tey, Adrian, Thabit, Alif Adlan Mohd, Thakur, Anand, Tham, Zhang Duan, Thangavelu, Suvintheran, Thibault, Vincent, Thiberville, Simon‐Djamel, Thill, Benoît, Thirumanickam, Jananee, Thompson, Shaun, Thomson, Emma C.; Thurai, Surain Raaj Thanga, Thwaites, Ryan S.; Tierney, Paul, Tieroshyn, Vadim, Timashev, Peter S.; Timsit, Jean‐François, Vijayaraghavan, Bharath Kumar Tirupakuzhi, Tissot, Noémie, Toh, Jordan Zhien Yang, Toki, Maria, Tonby, Kristian, Tonnii, Sia Loong, Torres, Margarida, Torres, Antoni, Santos‐Olmo, Rosario Maria Torres, Torres‐Zevallos, Hernando, Towers, Michael, Trapani, Tony, Treoux, Théo, Tromeur, Cécile, Trontzas, Ioannis, Trouillon, Tiffany, Truong, Jeanne, Tual, Christelle, Tubiana, Sarah, Tuite, Helen, Turmel, Jean‐Marie, Turtle, Lance C. W.; Tveita, Anders, Twardowski, Pawel, Uchiyama, Makoto, Udayanga, P. G. Ishara, Udy, Andrew, Ullrich, Roman, Uribe, Alberto, Usman, Asad.
Influenza and Other Respiratory Viruses ; 2022.
Article in English | Web of Science | ID: covidwho-2019369

ABSTRACT

Introduction: Case definitions are used to guide clinical practice, surveillance and research protocols. However, how they identify COVID-19-hospitalised patients is not fully understood. We analysed the proportion of hospitalised patients with laboratory-confirmed COVID-19, in the ISARIC prospective cohort study database, meeting widely used case definitions. Methods: Patients were assessed using the Centers for Disease Control (CDC), European Centre for Disease Prevention and Control (ECDC), World Health Organization (WHO) and UK Health Security Agency (UKHSA) case definitions by age, region and time. Case fatality ratios (CFRs) and symptoms of those who did and who did not meet the case definitions were evaluated. Patients with incomplete data and non-laboratory-confirmed test result were excluded. Results: A total of 263,218 of the patients (42%) in the ISARIC database were included. Most patients (90.4%) were from Europe arid Central Asia. The proportions of patients meeting the case definitions were 56.8% (WHO), 74.4% (UKHSA), 81.6% (ECDC) and 82.3% (CDC). For each case definition, patients at the extremes of age distribution met the criteria less frequently than those aged 30 to 70 years;geographical and time variations were also observed. Estimated CFRs were similar for the patients who met the case definitions. However, when more patients did riot meet the case definition, the CFR increased. Conclusions: The performance of case definitions might be different in different regions and may change over time. Similarly concerning is the fact that older patients often did not meet case definitions, risking delayed medical care. While epidemiologists must balance their analytics with field applicability, ongoing revision of case definitions is necessary to improve patient care through early diagnosis and limit potential nosocomial spread.

6.
EMBO Rep ; 23(10): e54322, 2022 10 06.
Article in English | MEDLINE | ID: covidwho-2002704

ABSTRACT

The emergence of SARS-CoV-2 variants has exacerbated the COVID-19 global health crisis. Thus far, all variants carry mutations in the spike glycoprotein, which is a critical determinant of viral transmission being responsible for attachment, receptor engagement and membrane fusion, and an important target of immunity. Variants frequently bear truncations of flexible loops in the N-terminal domain (NTD) of spike; the functional importance of these modifications has remained poorly characterised. We demonstrate that NTD deletions are important for efficient entry by the Alpha and Omicron variants and that this correlates with spike stability. Phylogenetic analysis reveals extensive NTD loop length polymorphisms across the sarbecoviruses, setting an evolutionary precedent for loop remodelling. Guided by these analyses, we demonstrate that variations in NTD loop length, alone, are sufficient to modulate virus entry. We propose that variations in NTD loop length act to fine-tune spike; this may provide a mechanism for SARS-CoV-2 to navigate a complex selection landscape encompassing optimisation of essential functionality, immune-driven antigenic variation and ongoing adaptation to a new host.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/genetics , Humans , Phylogeny , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics
7.
Science ; 377(6609): 951-959, 2022 08 26.
Article in English | MEDLINE | ID: covidwho-1962061

ABSTRACT

Understanding how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in 2019 is critical to preventing future zoonotic outbreaks before they become the next pandemic. The Huanan Seafood Wholesale Market in Wuhan, China, was identified as a likely source of cases in early reports, but later this conclusion became controversial. We show here that the earliest known COVID-19 cases from December 2019, including those without reported direct links, were geographically centered on this market. We report that live SARS-CoV-2-susceptible mammals were sold at the market in late 2019 and that within the market, SARS-CoV-2-positive environmental samples were spatially associated with vendors selling live mammals. Although there is insufficient evidence to define upstream events, and exact circumstances remain obscure, our analyses indicate that the emergence of SARS-CoV-2 occurred through the live wildlife trade in China and show that the Huanan market was the epicenter of the COVID-19 pandemic.


Subject(s)
COVID-19 , Pandemics , SARS-CoV-2 , Seafood , Viral Zoonoses , Animals , COVID-19/epidemiology , COVID-19/transmission , COVID-19/virology , China/epidemiology , Humans , SARS-CoV-2/isolation & purification , Seafood/virology , Viral Zoonoses/epidemiology , Viral Zoonoses/transmission , Viral Zoonoses/virology
8.
Sci Rep ; 12(1): 11735, 2022 07 19.
Article in English | MEDLINE | ID: covidwho-1947493

ABSTRACT

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.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/epidemiology , Disease Outbreaks , Genomics , Health Planning , Humans , SARS-CoV-2/genetics , United States , Universities
9.
Virus Evol ; 8(2): veac054, 2022.
Article in English | MEDLINE | ID: covidwho-1931907

ABSTRACT

Recombination contributes to the genetic diversity found in coronaviruses and is known to be a prominent mechanism whereby they evolve. It is apparent, both from controlled experiments and in genome sequences sampled from nature, that patterns of recombination in coronaviruses are non-random and that this is likely attributable to a combination of sequence features that favour the occurrence of recombination break points at specific genomic sites, and selection disfavouring the survival of recombinants within which favourable intra-genome interactions have been disrupted. Here we leverage available whole-genome sequence data for six coronavirus subgenera to identify specific patterns of recombination that are conserved between multiple subgenera and then identify the likely factors that underlie these conserved patterns. Specifically, we confirm the non-randomness of recombination break points across all six tested coronavirus subgenera, locate conserved recombination hot- and cold-spots, and determine that the locations of transcriptional regulatory sequences are likely major determinants of conserved recombination break-point hotspot locations. We find that while the locations of recombination break points are not uniformly associated with degrees of nucleotide sequence conservation, they display significant tendencies in multiple coronavirus subgenera to occur in low guanine-cytosine content genome regions, in non-coding regions, at the edges of genes, and at sites within the Spike gene that are predicted to be minimally disruptive of Spike protein folding. While it is apparent that sequence features such as transcriptional regulatory sequences are likely major determinants of where the template-switching events that yield recombination break points most commonly occur, it is evident that selection against misfolded recombinant proteins also strongly impacts observable recombination break-point distributions in coronavirus genomes sampled from nature.

10.
Nat Microbiol ; 7(8): 1161-1179, 2022 08.
Article in English | MEDLINE | ID: covidwho-1921616

ABSTRACT

Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response to COVID-19. The emergence of hypermutated, increasingly transmissible variants of concern (VOCs) threaten this strategy. Omicron (B.1.1.529), the fifth VOC to be described, harbours multiple amino acid mutations in spike, half of which lie within the receptor-binding domain. Here we demonstrate substantial evasion of neutralization by Omicron BA.1 and BA.2 variants in vitro using sera from individuals vaccinated with ChAdOx1, BNT162b2 and mRNA-1273. These data were mirrored by a substantial reduction in real-world vaccine effectiveness that was partially restored by booster vaccination. The Omicron variants BA.1 and BA.2 did not induce cell syncytia in vitro and favoured a TMPRSS2-independent endosomal entry pathway, these phenotypes mapping to distinct regions of the spike protein. Impaired cell fusion was determined by the receptor-binding domain, while endosomal entry mapped to the S2 domain. Such marked changes in antigenicity and replicative biology may underlie the rapid global spread and altered pathogenicity of the Omicron variant.


Subject(s)
COVID-19 , Spike Glycoprotein, Coronavirus , Antibodies, Viral , BNT162 Vaccine , Humans , Membrane Glycoproteins/metabolism , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics , Viral Envelope Proteins/metabolism , Virus Internalization
11.
Cold Spring Harb Perspect Med ; 12(5)2022 05 27.
Article in English | MEDLINE | ID: covidwho-1806779

ABSTRACT

Our understanding of the still unfolding severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic would have been extremely limited without the study of the genetics and evolution of this new human coronavirus. Large-scale genome-sequencing efforts have provided close to real-time tracking of the global spread and diversification of SARS-CoV-2 since its entry into the human population in late 2019. These data have underpinned analysis of its origins, epidemiology, and adaptations to the human population: principally immune evasion and increasing transmissibility. SARS-CoV-2, despite being a new human pathogen, was highly capable of human-to-human transmission. During its rapid spread in humans, SARS-CoV-2 has evolved independent new forms, the so-called "variants of concern," that are better optimized for human-to-human transmission. The most important adaptation of the bat coronavirus progenitor of both SARS-CoV-1 and SARS-CoV-2 for human infection (and other mammals) is the use of the angiotensin-converting enzyme 2 (ACE2) receptor. Relaxed structural constraints provide plasticity to SARS-related coronavirus spike protein permitting it to accommodate significant amino acid replacements of antigenic consequence without compromising the ability to bind to ACE2. Although the bulk of research has justifiably concentrated on the viral spike protein as the main determinant of antigenic evolution and changes in transmissibility, there is accumulating evidence for the contribution of other regions of the viral proteome to virus-host interaction. Whereas levels of community transmission of recombinants compromising genetically distinct variants are at present low, when divergent variants cocirculate, recombination between SARS-CoV-2 clades is being detected, increasing the risk that viruses with new properties emerge. Applying computational and machine learning methods to genome sequence data sets to generate experimentally verifiable predictions will serve as an early warning system for novel variant surveillance and will be important in future vaccine planning. Omicron, the latest SARS-CoV-2 variant of concern, has focused attention on step change antigenic events, "shift," as opposed to incremental "drift" changes in antigenicity. Both an increase in transmissibility and antigenic shift in Omicron led to it readily causing infections in the fully vaccinated and/or previously infected. Omicron's virulence, while reduced relative to the variant of concern it replaced, Delta, is very much premised on the past immune exposure of individuals with a clear signal that boosted vaccination protects from severe disease. Currently, SARS-CoV-2 has proven itself to be a dangerous new human respiratory pathogen with an unpredictable evolutionary capacity, leading to a risk of future variants too great not to ensure all regions of the world are screened by viral genome sequencing, protected through available and affordable vaccines, and have non-punitive strategies in place for detecting and responding to novel variants of concern.


Subject(s)
COVID-19 , Evolution, Molecular , SARS-CoV-2 , Angiotensin-Converting Enzyme 2 , Animals , Humans , Mammals/metabolism , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/metabolism
12.
Virus Evol ; 8(1): veac023, 2022.
Article in English | MEDLINE | ID: covidwho-1795112

ABSTRACT

COG-UK Mutation Explorer (COG-UK-ME, https://sars2.cvr.gla.ac.uk/cog-uk/-last accessed date 16 March 2022) is a web resource that displays knowledge and analyses on SARS-CoV-2 virus genome mutations and variants circulating in the UK, with a focus on the observed amino acid replacements that have an antigenic role in the context of the human humoral and cellular immune response. This analysis is based on more than 2 million genome sequences (as of March 2022) for UK SARS-CoV-2 data held in the CLIMB-COVID centralised data environment. COG-UK-ME curates these data and displays analyses that are cross-referenced to experimental data collated from the primary literature. The aim is to track mutations of immunological importance that are accumulating in current variants of concern and variants of interest that could alter the neutralising activity of monoclonal antibodies (mAbs), convalescent sera, and vaccines. Changes in epitopes recognised by T cells, including those where reduced T cell binding has been demonstrated, are reported. Mutations that have been shown to confer SARS-CoV-2 resistance to antiviral drugs are also included. Using visualisation tools, COG-UK-ME also allows users to identify the emergence of variants carrying mutations that could decrease the neutralising activity of both mAbs present in therapeutic cocktails, e.g. Ronapreve. COG-UK-ME tracks changes in the frequency of combinations of mutations and brings together the curated literature on the impact of those mutations on various functional aspects of the virus and therapeutics. Given the unpredictable nature of SARS-CoV-2 as exemplified by yet another variant of concern, Omicron, continued surveillance of SARS-CoV-2 remains imperative to monitor virus evolution linked to the efficacy of therapeutics.

13.
EuropePMC; 2022.
Preprint in English | EuropePMC | ID: ppcovidwho-331670

ABSTRACT

Objective To determine how the severity of successively dominant SARS-CoV-2 variants has changed over the course of the COVID-19 pandemic. Design Prospective cohort analysis. Setting Community- and hospital- sequenced COVID-19 cases in the NHS Greater Glasgow and Clyde (NHS GG&C) Health Board (1.2 million people). Participants All sequenced non-nosocomial adult COVID-19 cases in NHS GG&C identified to be infected with the relevant SARS-CoV-2 lineage during the following analysis periods. B.1.177/Alpha analysis: 1st November 2020 - 30th January 2021 (n = 1640). Alpha/Delta analysis: 1st April - 30th June 2021 (n = 5552). AY.4.2 Delta/non-AY.4.2 Delta analysis: 1st July – 31st October 2021 (n = 9613). Non-AY.4.2 Delta/Omicron analysis: 1st – 31st December 2021 (n = 3858). Main outcome measures Admission to hospital, admission to ICU, or death within 28 days of first positive COVID-19 test Results In the B.1.177/Alpha analysis, 300 of 807 (37.2%) B.1.177 cases were recorded as hospitalised or having a more severe outcome, compared to 232 of 833 (27.9%) Alpha cases. After adjusting for the following covariates: age, sex, time of positive test, comorbidities and partial postcode, the cumulative odds ratio was 1.51 (95% central credible interval 1.08-2.11) for Alpha versus B.1.177. In the Alpha/Delta analysis, 113 of 2104 (5.4%) Alpha cases were recorded as hospitalised or having a more severe outcome, compared to 230 of 3448 (6.7%) Delta cases. After adjusting for the above covariates plus number of vaccine doses and reinfection, the cumulative odds ratio was 2.09 (95% central credible interval 1.42-3.08) for Delta versus Alpha. In the non-AY.4.2 Delta/AY.4.2 Delta analysis, 845 of 8644 (9.8%) non-AY.4.2 Delta cases were recorded as hospitalised or having a more severe outcome, compared to 101 of 969 (10.4%) AY.4.2 Delta cases. After adjusting for the previously stated covariates, the cumulative odds ratio was 0.99 (95% central credible interval 0.76-1.27) for AY.4.2 Delta versus non-AY.4.2 Delta. In the non-AY.4.2 Delta/Omicron analysis, 30 of 1164 (2.6%) non-AY.4.2 Delta cases were recorded as hospitalised or having a more severe outcome, compared to 26 of 2694 (1.0%) Omicron cases. After adjusting for the previously listed covariates, the median cumulative odds ratio was 0.49 (95% central credible interval 0.22-1.06) for Omicron versus non-AY.4.2 Delta. Conclusions The direction of change in disease severity between successively emerging SARS-CoV-2 variants of concern was inconsistent. This heterogeneity in virulence between variants, coupled with independent evolutionary emergence, demonstrates that severity associated with future SARS-CoV-2 variants is inherently unpredictable.

14.
BMJ ; 376: o170, 2022 01 25.
Article in English | MEDLINE | ID: covidwho-1765103

Subject(s)
Pandemics , Humans
15.
Mol Biol Evol ; 39(4)2022 04 11.
Article in English | MEDLINE | ID: covidwho-1758789

ABSTRACT

Among the 30 nonsynonymous nucleotide substitutions in the Omicron S-gene are 13 that have only rarely been seen in other SARS-CoV-2 sequences. These mutations cluster within three functionally important regions of the S-gene at sites that will likely impact (1) interactions between subunits of the Spike trimer and the predisposition of subunits to shift from down to up configurations, (2) interactions of Spike with ACE2 receptors, and (3) the priming of Spike for membrane fusion. We show here that, based on both the rarity of these 13 mutations in intrapatient sequencing reads and patterns of selection at the codon sites where the mutations occur in SARS-CoV-2 and related sarbecoviruses, prior to the emergence of Omicron the mutations would have been predicted to decrease the fitness of any virus within which they occurred. We further propose that the mutations in each of the three clusters therefore cooperatively interact to both mitigate their individual fitness costs, and, in combination with other mutations, adaptively alter the function of Spike. Given the evident epidemic growth advantages of Omicron overall previously known SARS-CoV-2 lineages, it is crucial to determine both how such complex and highly adaptive mutation constellations were assembled within the Omicron S-gene, and why, despite unprecedented global genomic surveillance efforts, the early stages of this assembly process went completely undetected.


Subject(s)
COVID-19 , Spike Glycoprotein, Coronavirus , COVID-19/genetics , Humans , Mutation , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics
16.
EuropePMC; 2022.
Preprint in English | EuropePMC | ID: ppcovidwho-329658

ABSTRACT

The first SARS-CoV-2 variant of concern (VOC) to be designated was lineage B.1.1.7, later labelled by the World Health Organisation (WHO) as Alpha. Originating in early Autumn but discovered in December 2020, it spread rapidly and caused large waves of infections worldwide. The Alpha variant is notable for being defined by a long ancestral phylogenetic branch with an increased evolutionary rate, along which only two sequences have been sampled. Alpha genomes comprise a well-supported monophyletic clade within which the evolutionary rate is more typical of SARS-CoV-2. The Alpha epidemic continued to grow despite the continued restrictions on social mixing across the UK, and the imposition of new restrictions, in particular the English national lockdown in November 2020. While these interventions succeeded in reducing the absolute number of cases, the impact of these non-pharmaceutical interventions was predominantly to drive the decline of the SARS-CoV-2 lineages which preceded Alpha. We investigate the only two sampled sequences that fall on the branch ancestral to Alpha. We find that one is likely to be a true intermediate sequence, providing information about the order of mutational events that led to Alpha. We explore alternate hypotheses that can explain how Alpha acquired a large number of mutations yet remained largely unobserved in a region of high genomic surveillance: an under-sampled geographical location, a non-human animal population, or a chronically-infected individual. We conclude that the last hypothesis provides the best explanation of the observed behaviour and dynamics of the variant, although we find that the individual need not be immunocompromised, as persistently-infected immunocompetent hosts also display a higher within-host rate of evolution. Finally, we compare the ancestral branches and mutation profiles of other VOCs to each other, and identify that Delta appears to be an outlier both in terms of the genomic locations of its defining mutations, and its lack of rapid evolutionary rate on the ancestral branch. As new variants, such as Omicron, continue to evolve (potentially through similar mechanisms) it remains important to investigate the origins of other variants to identify ways to potentially disrupt their evolution and emergence.

17.
EuropePMC;
Preprint in English | EuropePMC | ID: ppcovidwho-327612

ABSTRACT

Introduction: Viral sequencing of SARS-CoV-2 has been used for outbreak investigation, but there is limited evidence supporting routine use for infection prevention and control (IPC) within hospital settings. Methods We conducted a prospective non-randomised trial of sequencing at 14 acute UK hospital trusts. Sites each had a 4-week baseline data-collection period, followed by intervention periods comprising 8 weeks of 'rapid' (<48h) and 4 weeks of 'longer-turnaround' (5-10 day) sequencing using a sequence reporting tool (SRT). Data were collected on all hospital onset COVID-19 infections (HOCIs;detected ≥48h from admission). The impact of the sequencing intervention on IPC knowledge and actions, and on incidence of probable/definite hospital-acquired infections (HAIs) was evaluated. Results A total of 2170 HOCI cases were recorded from October 2020-April 2021, with sequence reports returned for 650/1320 (49.2%) during intervention phases. We did not detect a statistically significant change in weekly incidence of HAIs in longer-turnaround (IRR 1.60, 95%CI 0.85-3.01;P=0.14) or rapid (0.85, 0.48-1.50;P=0.54) intervention phases compared to baseline phase. However, IPC practice was changed in 7.8% and 7.4% of all HOCI cases in rapid and longer-turnaround phases, respectively, and 17.2% and 11.6% of cases where the report was returned. In a per-protocol sensitivity analysis there was an impact on IPC actions in 20.7% of HOCI cases when the SRT report was returned within 5 days. Conclusion While we did not demonstrate a direct impact of sequencing on the incidence of nosocomial transmission, our results suggest that sequencing can inform IPC response to HOCIs, particularly when returned within 5 days.

18.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-324214

ABSTRACT

The spillover of a virus from one host species to another requires both molecular and ecological risk factors to align. While extensive research both before and after the emergence of SARS-CoV-2 in 2019 implicates horseshoe bat as the significant reservoir genus for the new coronavirus, it remains unclear why it emerged at this time. One massive disruption to human-animal contact in 2019 is linked to the on-going African swine fever virus (ASFV) pandemic. This began in Georgia in 2007 and was introduced to China in 2018. Pork is the major meat source in the Chinese diet. Severe fluctuations in the pork market prior to December 2019, may have increased the transmission of zoonotic pathogens, including severe acute respiratory syndrome–related coronaviruses, from wildlife to humans, wildlife to livestock and non-local animals to local animals. The major production and consumption regions for pork are geographically separated in China. The dramatic shortage of pork following restrictions of pig movement and culling resulted in price increases, leading to alternative meat consumption and unusual animal and meat movements nationwide such as wildlife and thus greatly increased opportunities for human-sarbecovirus contacts. Pork prices were particularly high in southern provinces (Guangdong, Guangxi, Fujian, Jiangxi, Hunan, and Hubei), where wildlife is farmed on different scales and more frequently consumed. Shandong experienced the biggest losses in pork production (~2 million metric tons), which is also the largest mink farming province. Hence, exposure of SARS-CoV-2 from wildlife or infected animals to humans by contact and consumption are more likely to have taken place in 2019, a year when China was experiencing the worst effects of the ASFV pandemic.

19.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-312777

ABSTRACT

SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causes the infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformatics tools designed explicitly for SARS-CoV-2 have only recently been developed as a rapid reaction to the need for fast detection, understanding, and treatment of COVID-19. To control the ongoing COVID-19 pandemic, it is of utmost importance to get insight into the evolution and pathogenesis of the virus. In this review, we cover bioinformatics workflows and tools for the routine detection of SARS-CoV-2 infection, the reliable analysis of sequencing data, the tracking of the COVID-19 pandemic and evaluation of containment measures, the study of coronavirus evolution, the discovery of potential drug targets and development of therapeutic strategies. For each tool, we briefly describe its use case and how it advances research specifically for SARS-CoV-2. All tools are freely available online, either through web applications or public code repositories.

20.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-311753

ABSTRACT

SARS-CoV-2 Spike amino acid replacements in the receptor binding domain (RBD) occur relatively frequently and some have a consequence for immune recognition. Here we report recurrent emergence and significant onward transmission of a six-nucleotide deletion in the S gene, which results in loss of two amino acids: H69 and V70. Of particular note this deletion, ?H69/V70, often co-occurs with the receptor binding motif amino acid replacements N501Y, N439K and Y453F. One of the ?H69/V70+ N501Y lineages, B.1.1.7, is comprised of over 4000 SARS-CoV-2 genome sequences from the UK and includes eight other S gene mutations: RBD (N501Y and A570D), S1 (?H69/V70 and ?144/145) and S2 (P681H, T716I, S982A and D1118H). Some of these mutations have presumably arisen as a result of the virus evolving from immune selection pressure in infected individuals and at least one, lineage B.1.1.7, potentially from a chronic infection. Given our recent evidence that ?H69/V70 enhances viral infectivity (Kemp et al. 2020), its effect on virus fitness appears to be independent to the RBD changes. Enhanced surveillance for the ?H69/V70 deletion with and without RBD mutations should be considered as a priority. Permissive mutations such as ?H69/V70 have the potential to enhance the ability of SARS-CoV-2 to generate new variants, including vaccine escape variants, that would have otherwise significantly reduced viral fitness.

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