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1.
Sci Rep ; 12(1): 19274, 2022 Nov 11.
Article in English | MEDLINE | ID: covidwho-2118834

ABSTRACT

Since the beginning of the SARS-CoV-2 coronavirus pandemic, genome sequencing is essential to monitor viral mutations over time and by territory. This need for complete genetic information is further reinforced by the rapid spread of variants of concern. In this paper, we assess the ability of the hybridization technique, Capture-Seq, to detect the SARS-CoV-2 genome, either partially or in its integrity on patients samples. We studied 20 patient nasal swab samples broken down into five series of four samples of equivalent viral load from CT25 to CT36+ . For this, we tested 3 multi-virus panel as well as 2 SARS-CoV-2 only panels. The panels were chosen based on their specificity, global or specific, as well as their technological difference in the composition of the probes: ssRNA, ssDNA and dsDNA. The multi-virus panels are able to capture high-abundance targets but fail to capture the lowest-abundance targets, with a high percentage of off-target reads corresponding to the abundance of the host sequences. Both SARS-CoV-2-only panels were very effective, with high percentage of reads corresponding to the target. Overall, capture followed by sequencing is very effective for the study of SARS-CoV-2 in low-abundance patient samples and is suitable for samples with CT values up to 35.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , COVID-19/diagnosis , Pandemics , COVID-19 Testing , Base Sequence , Genome, Viral
2.
Front Public Health ; 10: 1006631, 2022.
Article in English | MEDLINE | ID: covidwho-2093783

ABSTRACT

Aim: We aimed to describe the characteristics of individuals infected by BA.4 or BA.5 in France in comparison to BA.1, and analyze the factors associated with hospitalization among BA.4 and BA.5 cases. Methods: A standardized questionnaire was used to collect information on confirmed and probable Omicron cases. Hospitalization risk factors among BA.4/BA.5 cases were analyzed using Poisson regression. Variables with a p-value below 0.2 in the univariate analysis and a priori confounders were included in the multivariable regression model. Results: The median age of the 301 cases investigated was 47 years and 97% of cases were symptomatic. The most common clinical signs were asthenia/fatigue (75.7%), cough (58.3%), fever (58.3%), headache (52.1%) and rhinorrhea (50.7%). Twelve cases were hospitalized, and 27.1% reported risk factors. No admissions to intensive care and no deaths were reported. Vaccination status was available for 292 cases, 20.9% were unvaccinated, 1.4% had received one dose, 38.3% two doses and 39.4% three doses. Cases presenting at least one risk factor were almost seventeen times more likely to be hospitalized than those with no risk factors (aRR = 16.72 [95% CI2.59-326.86]). Conclusion: Despite the longer duration of and the differences in symptoms and their possible immune escape, BA.4/BA.5 Omicron sub-lineages globally showed no severe clinical presentation. The presence of at least one risk factor for severe disease significantly increased the risk of hospitalization for those infected with BA.4 or BA.5.


Subject(s)
Cough , Hospitalization , Humans , Middle Aged , Risk Factors , Surveys and Questionnaires , Time Factors
3.
Infect Genet Evol ; 105: 105370, 2022 Sep 30.
Article in English | MEDLINE | ID: covidwho-2049657

ABSTRACT

Since the first cases of SARS-CoV-2 infection in Wuhan in December 2019, this RNA virus gave rise to different viral lineages with different virological, epidemiological and immunological properties. Here we describe the dynamics of circulation of SARS-CoV-2 lineages in an Amazonian South American French overseas territory, French Guiana (FG). The data analyzed are based on the general epidemic course, and genomic surveillance data come from whole genome sequencing (WGS) as well as typing PCRs. From March 2020 to October 2021, four COVID-19 epidemic waves were observed in FG with an evolution of viral lineages influenced by virus introductions from continental France and above all by land-based introductions from neighbouring countries. The third epidemic wave from March to June 2021 was driven by a predominant Gamma introduced from Brazil and a less frequent Alpha introduced from France. This coexistence was completely substituted by Delta that initiated the fourth epidemic wave.

4.
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases ; 105:105370-105370, 2022.
Article in English | EuropePMC | ID: covidwho-2046203

ABSTRACT

Since the first cases of SARS-CoV-2 infection in Wuhan in December 2019, this RNA virus gave rise to different viral lineages with different virological, epidemiological and immunological properties. Here we describe the dynamics of circulation of SARS-CoV-2 lineages in an Amazonian South American French overseas territory, French Guiana (FG). The data analyzed are based on the general epidemic course, and genomic surveillance data come from whole genome sequencing (WGS) as well as typing PCRs. From March 2020 to October 2021, four COVID-19 epidemic waves were observed in FG with an evolution of viral lineages influenced by virus introductions from continental France and above all by land-based introductions from neighbouring countries. The third epidemic wave from March to June 2021 was driven by a predominant Gamma introduced from Brazil and a less frequent Alpha introduced from France. This coexistence was completely substituted by Delta that initiated the fourth epidemic wave.

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.
Infect Dis Now ; 52(6): 374-378, 2022 Sep.
Article in English | MEDLINE | ID: covidwho-1907105

ABSTRACT

OBJECTIVES: We described bronchiolitis epidemics during the 2020-2021 and 2021-2022 seasons in France and their interaction with the COVID outbreak. PATIENTS AND METHODS: Data on family physician (FP) visits, emergency department (ED) visits, hospitalizations for bronchiolitis for children˂2 years, and hospital virological data were analyzed and compared with previous seasons (2015-2020). RESULTS: The 2020-2021 epidemic arrived very late, and its impact was lower than in previous seasons (2015-2020) (FP visits: -23%, ED visits: -38%, and hospitalizations: -30%). The 2021-2022 epidemic started early (week 40) and lasted for a relatively long time (13 weeks). The impact was higher than in 2015-2020 (FP visits: +13%, ED visits: +34%, hospitalizations: +28%). CONCLUSION: Findings from the 2020-2021 epidemic may be linked to the implementation of non-pharmaceutical COVID-19 prevention measures. For 2021-2022, findings may be linked to an "immunity debt" resulting from the lower impact of the previous season.


Subject(s)
Bronchiolitis , COVID-19 , Bronchiolitis/epidemiology , COVID-19/epidemiology , Humans , Pandemics , SARS-CoV-2 , Seasons
7.
J Clin Virol Plus ; 1(4): 100041, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1734699

ABSTRACT

Background: The systemic antibody responses to SARS-CoV-2 in COVID-19 patients has been extensively studied. However, less is known about the mucosal responses in the upper airways, the site of initial SARS-CoV-2 replication. Methods: The IgG and IgA antibody responses were analysed in plasma and nasopharyngeal swabs from the first four confirmed COVID-19 patients in France. Two were pauci-symptomatic while two developed severe disease. We characterized their antibody profiles by using an in-house ELISA to detect antibodies directed against SARS-CoV-2 Nucleoprotein and Spike. Results: Anti-N IgG and IgA antibodies were detected in the NPS of severe patients only. The levels of antibodies in the plasma markedly differed amongst the patients. The most distinctive features are a strong anti-N IgG response in the severe patient who recovered, and a high anti-N IgA response specifically detected in the fatal case of COVID-19. Conclusions: Anti-N IgG and IgA antibodies are detected in NPS only for severe patients, with levels related to serological antibodies. The severe patients showed different antibody profiles in the plasma, notably regarding the IgA and IgG response to the N antigen, that may reflect different disease outcome. By contrast, pauci-symptomatic patients did not exhibit any mucosal antibodies in NSP, which is associated with a low or absent serological response against both N and S.

8.
Nat Commun ; 13(1): 1152, 2022 03 03.
Article in English | MEDLINE | ID: covidwho-1730284

ABSTRACT

In spring 2021, an increasing number of infections was observed caused by the hitherto rarely described SARS-CoV-2 variant A.27 in south-west Germany. From December 2020 to June 2021 this lineage has been detected in 31 countries. Phylogeographic analyses of A.27 sequences obtained from national and international databases reveal a global spread of this lineage through multiple introductions from its inferred origin in Western Africa. Variant A.27 is characterized by a mutational pattern in the spike gene that includes the L18F, L452R and N501Y spike amino acid substitutions found in various variants of concern but lacks the globally dominant D614G. Neutralization assays demonstrate an escape of A.27 from convalescent and vaccine-elicited antibody-mediated immunity. Moreover, the therapeutic monoclonal antibody Bamlanivimab and partially the REGN-COV2 cocktail fail to block infection by A.27. Our data emphasize the need for continued global monitoring of novel lineages because of the independent evolution of new escape mutations.


Subject(s)
COVID-19/immunology , COVID-19/virology , Pandemics , SARS-CoV-2/immunology , Africa, Western/epidemiology , Amino Acid Substitution , Antibodies, Monoclonal, Humanized/pharmacology , Antibodies, Neutralizing/immunology , Antibodies, Neutralizing/pharmacology , Antibodies, Viral/immunology , Antiviral Agents/pharmacology , COVID-19/transmission , Drug Combinations , Germany/epidemiology , Global Health , Humans , Immune Evasion/genetics , Mutation , Phylogeography , SARS-CoV-2/drug effects , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/immunology
9.
J Clin Virol ; 145: 105021, 2021 12.
Article in English | MEDLINE | ID: covidwho-1487825

ABSTRACT

BACKGROUND: Rapid testing for COVID-19 has been clearly identified as an essential component of the strategy to control the SARS-CoV-2 epidemic, worldwide. The ID NOW COVID-19 assay is a simple, user-friendly, rapid molecular biology test based on nicking and extension amplification reaction (NEAR). OBJECTIVES: The aim of this study was to evaluate the ID NOW COVID-19 assay when used as a point-of-care test (POCT) in our Emergency Department (ED). TYPE OF STUDY: This prospective study enrolled 395 consecutive patients; paired nasopharyngeal swabs were collected from each study participant. The first swab was tested with the ID NOW COVID-19 assay at the point-of-care by ED nurses. The second swab was diluted in viral transport medium (VTM) and sent to the clinical microbiology department for analysis by both the RT-PCR Simplexa test COVID-19 Direct assay as the study reference method, and the ID NOW COVID-19 assay performed in the laboratory. RESULTS: Nasopharyngeal swabs directly tested with the ID NOW COVID-19 assay yielded a sensitivity, specificity, PPV and NPV of 98.0%, 97.5%, 96.2% and 98.7%, respectively, in comparison with the RT-PCR study reference assay. When the ID NOW COVID-19 assay was performed in the laboratory using the VTM samples, the sensitivity decreased to 62.5% and the NPV to 79.7%. Three false negative test results were reported with the ID NOW COVID-19 assay when performed using undiluted swabs directly in the ED; these results were obtained from patients with elevated CT values (> 30). CONCLUSION: We demonstrated that the ID NOW COVID-19 assay, performed as a point of care test in the ED using dry swabs, provides a rapid and reliable alternative to laboratory-based RT-PCR methods.


Subject(s)
COVID-19 , COVID-19 Testing , Emergency Service, Hospital , Humans , Nasopharynx , Point-of-Care Testing , Prospective Studies , SARS-CoV-2 , Sensitivity and Specificity
10.
Clin Microbiol Infect ; 28(2): 298.e9-298.e15, 2022 Feb.
Article in English | MEDLINE | ID: covidwho-1458608

ABSTRACT

OBJECTIVES: In early January 2021 an outbreak of nosocomial cases of coronavirus disease 2019 (COVID-19) emerged in Western France; RT-PCR tests were repeatedly negative on nasopharyngeal samples but positive on lower respiratory tract samples. Whole-genome sequencing (WGS) revealed a new variant, currently defining a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage B.1.616. In March, the WHO classified this as a 'variant under investigation' (VUI). We analysed the characteristics and outcomes of COVID-19 cases related to this new variant. METHODS: Clinical, virological, and radiological data were retrospectively collected from medical charts in the two hospitals involved. We enrolled those inpatients with: (a) positive SARS-CoV-2 RT-PCR on a respiratory sample, (b) seroconversion with anti-SARS-CoV-2 IgG/IgM, or (c) suggestive symptoms and typical features of COVID-19 on a chest CT scan. Cases were categorized as B.1.616, a variant of concern (VOC), or unknown. RESULTS: From 1st January to 24th March 2021, 114 patients fulfilled the inclusion criteria: B.1.616 (n = 39), VOC (n = 32), and unknown (n = 43). B.1.616-related cases were older than VOC-related cases (81 years, interquartile range (IQR) 73-88 versus 73 years, IQR 67-82, p < 0.05) and their first RT-PCR tests were rarely positive (6/39, 15% versus 31/32, 97%, p < 0.05). The B.1.616 variant was independently associated with severe disease (multivariable Cox model HR 4.0, 95%CI 1.5-10.9) and increased lethality (28-day mortality 18/39 (46%) for B.1.616 versus 5/32 (16%) for VOC, p = 0.006). CONCLUSION: We report a nosocomial outbreak of COVID-19 cases related to a new variant, B.1.616, which is poorly detected by RT-PCR on nasopharyngeal samples and is associated with high lethality.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/epidemiology , COVID-19/virology , France/epidemiology , Humans , Retrospective Studies , Reverse Transcriptase Polymerase Chain Reaction
11.
Lancet Reg Health Eur ; 8: 100171, 2021 Sep.
Article in English | MEDLINE | ID: covidwho-1397543

ABSTRACT

BACKGROUND: We aimed to assess the effectiveness of two doses of mRNA COVID-19 vaccines against COVID-19 with the original virus and other lineages circulating in France. METHODS: In this nationwide case-control study, cases were SARS-CoV-2 infected adults with onset of symptoms between 14 February and 3 May 2021. Controls were non-infected adults from a national representative panel matched to cases by age, sex, region, population density and calendar week. Participants completed an online questionnaire on recent activity-related exposures and vaccination history. Information about the infecting virus was based on a screening RT-PCR for either B.1.1.7 or B.1.351/P.1 variants. FINDINGS: Included in our analysis were 7 288 adults infected with the original SARS-CoV-2 virus, 31 313 with the B.1.1.7 lineage, 2 550 with B.1.351/P1 lineages, and 3 644 controls. In multivariable analysis, the vaccine effectiveness (95% confidence interval) seven days after the second dose of mRNA vaccine was estimated at 88% (81-92), 86% (81-90) and 77% (63-86) against COVID-19 with the original virus, the B.1.1.7 lineage, and the B.1.351/P.1 lineages, respectively. Recent (2 to 6 months) history of virologically confirmed SARS-CoV-2 infection was found to be 83% (76-88), 88% (85-91) and 83% (71-90) protective against COVID-19 with the original virus, the B.1.1.7 lineage, and the B.1.351/P.1 lineages, respectively; and more distant (> 6 months) infections were 76% (54-87), 84% (75-90), and 74% (41-89) protective against COVID-19 with the original virus, the B.1.1.7 lineage, and the B.1.351/P.1 lineages, respectively. INTERPRETATION: In real-life settings, two doses of mRNA vaccines proved to be effective against COVID-19 with the original virus, B.1.1.7 lineage and B.1.351/P.1 lineages. FUNDING: Institut Pasteur, Research & Action Emerging Infectious Diseases (REACTing), Fondation de France (Alliance "Tous unis contre le virus").

12.
BMC Infect Dis ; 21(1): 457, 2021 May 19.
Article in English | MEDLINE | ID: covidwho-1236545

ABSTRACT

BACKGROUND: This study presents the methods and results of the investigation into a SARS-CoV-2 outbreak in a professional community. Due to the limited testing capacity available in France at the time, we elaborated a testing strategy according to pre-test probability. METHODS: The investigation design combined active case finding and contact tracing around each confirmed case with testing of at-risk contact persons who had any evocative symptoms (n = 88). One month later, we performed serology testing to test and screen symptomatic and asymptomatic cases again (n = 79). RESULTS: Twenty-four patients were confirmed (14 with RT-PCR and 10 with serology). The attack rate was 29% (24/83). Median age was 40 (24 to 59), and the sex ratio was 15/12. Only three cases were asymptomatic (= no symptoms at all, 13%, 95% CI, 3-32). Nineteen symptomatic cases (79%, 95% CI, 63-95) presented a respiratory infection, two of which were severe. All the RT-PCR confirmed cases acquired protective antibodies. Median incubation was 4 days (from 1 to 13 days), and the median serial interval was 3 days (0 to 15). We identified pre-symptomatic transmission in 40% of this cluster, but no transmission from asymptomatic to symptomatic cases. CONCLUSION: We report the effective use of targeted testing according to pre-test probability, specifically prioritizing symptomatic COVID-19 diagnosis and contact tracing. The asymptomatic rate raises questions about the real role of asymptomatic infected people in transmission. Conversely, pre-symptomatic contamination occurred frequently in this cluster, highlighting the need to identify, test, and quarantine asymptomatic at-risk contact persons (= contact tracing). The local lockdown imposed helped reduce transmission during the investigation period.


Subject(s)
COVID-19/prevention & control , Contact Tracing , Adult , COVID-19/diagnosis , COVID-19/epidemiology , COVID-19/virology , COVID-19 Testing , Disease Outbreaks , France/epidemiology , Humans , Male , Middle Aged , RNA, Viral/analysis , RNA, Viral/metabolism , Reverse Transcriptase Polymerase Chain Reaction , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Young Adult
13.
PLoS Comput Biol ; 17(3): e1008785, 2021 03.
Article in English | MEDLINE | ID: covidwho-1181165

ABSTRACT

Non-human primates infected with SARS-CoV-2 exhibit mild clinical signs. Here we used a mathematical model to characterize in detail the viral dynamics in 31 cynomolgus macaques for which nasopharyngeal and tracheal viral load were frequently assessed. We identified that infected cells had a large burst size (>104 virus) and a within-host reproductive basic number of approximately 6 and 4 in nasopharyngeal and tracheal compartment, respectively. After peak viral load, infected cells were rapidly lost with a half-life of 9 hours, with no significant association between cytokine elevation and clearance, leading to a median time to viral clearance of 10 days, consistent with observations in mild human infections. Given these parameter estimates, we predict that a prophylactic treatment blocking 90% of viral production or viral infection could prevent viral growth. In conclusion, our results provide estimates of SARS-CoV-2 viral kinetic parameters in an experimental model of mild infection and they provide means to assess the efficacy of future antiviral treatments.


Subject(s)
COVID-19/virology , Macaca fascicularis/virology , SARS-CoV-2/physiology , Animals , Antiviral Agents/pharmacology , Basic Reproduction Number , COVID-19/blood , COVID-19/prevention & control , Cytokines/blood , Disease Models, Animal , Nasopharynx/virology , SARS-CoV-2/drug effects , Trachea/virology , Viral Load , Virus Replication/drug effects
14.
Euro Surveill ; 26(13)2021 04.
Article in English | MEDLINE | ID: covidwho-1167263

ABSTRACT

BackgroundChildren have a low rate of COVID-19 and secondary severe multisystem inflammatory syndrome (MIS) but present a high prevalence of symptomatic seasonal coronavirus infections.AimWe tested if prior infections by seasonal coronaviruses (HCoV) NL63, HKU1, 229E or OC43 as assessed by serology, provide cross-protective immunity against SARS-CoV-2 infection.MethodsWe set a cross-sectional observational multicentric study in pauci- or asymptomatic children hospitalised in Paris during the first wave for reasons other than COVID (hospitalised children (HOS), n = 739) plus children presenting with MIS (n = 36). SARS-CoV-2 antibodies directed against the nucleoprotein (N) and S1 and S2 domains of the spike (S) proteins were monitored by an in-house luciferase immunoprecipitation system assay. We randomly selected 69 SARS-CoV-2-seropositive patients (including 15 with MIS) and 115 matched SARS-CoV-2-seronegative patients (controls (CTL)). We measured antibodies against SARS-CoV-2 and HCoV as evidence for prior corresponding infections and assessed if SARS-CoV-2 prevalence of infection and levels of antibody responses were shaped by prior seasonal coronavirus infections.ResultsPrevalence of HCoV infections were similar in HOS, MIS and CTL groups. Antibody levels against HCoV were not significantly different in the three groups and were not related to the level of SARS-CoV-2 antibodies in the HOS and MIS groups. SARS-CoV-2 antibody profiles were different between HOS and MIS children.ConclusionPrior infection by seasonal coronaviruses, as assessed by serology, does not interfere with SARS-CoV-2 infection and related MIS in children.


Subject(s)
Antibodies, Viral/immunology , COVID-19/immunology , Coronavirus OC43, Human , SARS-CoV-2/immunology , Systemic Inflammatory Response Syndrome , Adolescent , Antibodies, Viral/blood , COVID-19/blood , COVID-19/diagnosis , Child , Child, Preschool , Cross-Sectional Studies , Female , France/epidemiology , Humans , Infant , Infant, Newborn , Male , Paris , Seasons , Serologic Tests/methods , Spike Glycoprotein, Coronavirus
15.
Nat Med ; 27(5): 917-924, 2021 05.
Article in English | MEDLINE | ID: covidwho-1152868

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.7 and B.1.351 variants were first identified in the United Kingdom and South Africa, respectively, and have since spread to many countries. These variants harboring diverse mutations in the gene encoding the spike protein raise important concerns about their immune evasion potential. Here, we isolated infectious B.1.1.7 and B.1.351 strains from acutely infected individuals. We examined sensitivity of the two variants to SARS-CoV-2 antibodies present in sera and nasal swabs from individuals infected with previously circulating strains or who were recently vaccinated, in comparison with a D614G reference virus. We utilized a new rapid neutralization assay, based on reporter cells that become positive for GFP after overnight infection. Sera from 58 convalescent individuals collected up to 9 months after symptoms, similarly neutralized B.1.1.7 and D614G. In contrast, after 9 months, convalescent sera had a mean sixfold reduction in neutralizing titers, and 40% of the samples lacked any activity against B.1.351. Sera from 19 individuals vaccinated twice with Pfizer Cominarty, longitudinally tested up to 6 weeks after vaccination, were similarly potent against B.1.1.7 but less efficacious against B.1.351, when compared to D614G. Neutralizing titers increased after the second vaccine dose, but remained 14-fold lower against B.1.351. In contrast, sera from convalescent or vaccinated individuals similarly bound the three spike proteins in a flow cytometry-based serological assay. Neutralizing antibodies were rarely detected in nasal swabs from vaccinees. Thus, faster-spreading SARS-CoV-2 variants acquired a partial resistance to neutralizing antibodies generated by natural infection or vaccination, which was most frequently detected in individuals with low antibody levels. Our results indicate that B1.351, but not B.1.1.7, may increase the risk of infection in immunized individuals.


Subject(s)
Antibodies, Neutralizing/immunology , Antibodies, Viral/immunology , COVID-19/immunology , SARS-CoV-2/immunology , COVID-19 Vaccines/immunology , Convalescence , Cross Reactions , Humans , Neutralization Tests , Sensitivity and Specificity , Vaccination
16.
Euro Surveill ; 26(9)2021 03.
Article in English | MEDLINE | ID: covidwho-1154191

ABSTRACT

The emergence of SARS-CoV-2 variant 20I/501Y.V1 (VOC-202012/1 or GR/501Y.V1) is concerning given its increased transmissibility. We reanalysed 11,916 PCR-positive tests (41% of all positive tests) performed on 7-8 January 2021 in France. The prevalence of 20I/501Y.V1 was 3.3% among positive tests nationwide and 6.9% in the Paris region. Analysing the recent rise in the prevalence of 20I/501Y.V1, we estimate that, in the French context, 20I/501Y.V1 is 52-69% more transmissible than the previously circulating lineages, depending on modelling assumptions.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/epidemiology , France/epidemiology , Humans , Paris
17.
Influenza Other Respir Viruses ; 15(4): 429-438, 2021 07.
Article in English | MEDLINE | ID: covidwho-1042709

ABSTRACT

BACKGROUND: Claims of influenza vaccination increasing COVID-19 risk are circulating. Within the I-MOVE-COVID-19 primary care multicentre study, we measured the association between 2019-20 influenza vaccination and COVID-19. METHODS: We conducted a multicentre test-negative case-control study at primary care level, in study sites in five European countries, from March to August 2020. Patients presenting with acute respiratory infection were swabbed, with demographic, 2019-20 influenza vaccination and clinical information documented. Using logistic regression, we measured the adjusted odds ratio (aOR), adjusting for study site and age, sex, calendar time, presence of chronic conditions. The main analysis included patients swabbed ≤7 days after onset from the three countries with <15% of missing influenza vaccination. In secondary analyses, we included five countries, using multiple imputation with chained equations to account for missing data. RESULTS: We included 257 COVID-19 cases and 1631 controls in the main analysis (three countries). The overall aOR between influenza vaccination and COVID-19 was 0.93 (95% CI: 0.66-1.32). The aOR was 0.92 (95% CI: 0.58-1.46) and 0.92 (95% CI: 0.51-1.67) among those aged 20-59 and ≥60 years, respectively. In secondary analyses, we included 6457 cases and 69 272 controls. The imputed aOR was 0.87 (95% CI: 0.79-0.95) among all ages and any delay between swab and symptom onset. CONCLUSIONS: There was no evidence that COVID-19 cases were more likely to be vaccinated against influenza than controls. Influenza vaccination should be encouraged among target groups for vaccination. I-MOVE-COVID-19 will continue documenting influenza vaccination status in 2020-21, in order to learn about effects of recent influenza vaccination.


Subject(s)
COVID-19/epidemiology , Influenza Vaccines/administration & dosage , Influenza, Human/prevention & control , Orthomyxoviridae/immunology , Vaccination/statistics & numerical data , COVID-19/diagnosis , Case-Control Studies , Europe/epidemiology , Female , Humans , Influenza, Human/diagnosis , Influenza, Human/epidemiology , Logistic Models , Male , Odds Ratio , Primary Health Care/organization & administration , Primary Health Care/statistics & numerical data , Respiratory Tract Infections/diagnosis , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/prevention & control , SARS-CoV-2
18.
PLoS One ; 16(1): e0243712, 2021.
Article in English | MEDLINE | ID: covidwho-1024413

ABSTRACT

To respond to the urgent need for COVID-19 testing, countries perform nucleic acid amplification tests (NAAT) for the detection of SARS-CoV-2 in centralized laboratories. Real-time RT-PCR (Reverse transcription-Polymerase Chain Reaction), used to amplify and detect the viral RNA., is considered, as the current gold standard for diagnostics. It is an efficient process, but the complex engineering required for automated RNA extraction and temperature cycling makes it incompatible for use in point of care settings [1]. In the present work, by harnessing progress made in the past two decades in isothermal amplification and paper microfluidics, we created a portable test, in which SARS-CoV-2 RNA is extracted, amplified isothermally by RT-LAMP (Loop-mediated Isothermal Amplification), and detected using intercalating dyes or fluorescent probes. Depending on the viral load in the tested samples, the detection takes between twenty minutes and one hour. Using a set of 16 pools of naso-pharyngal swab eluates, we estimated a limit of detection comparable to real-time RT-PCR (i.e. 1 genome copies per microliter of clinical sample) and no cross-reaction with eight major respiratory viruses currently circulating in Europe. We designed and fabricated an easy-to-use portable device called "COVIDISC" to carry out the test at the point of care. The low cost of the materials along with the absence of complex equipment will expedite the widespread dissemination of this device. What is proposed here is a new efficient tool to help managing the pandemics.


Subject(s)
COVID-19 Testing/instrumentation , COVID-19/diagnosis , Molecular Diagnostic Techniques/instrumentation , Nucleic Acid Amplification Techniques/instrumentation , Point-of-Care Testing , RNA, Viral/genetics , SARS-CoV-2/genetics , COVID-19 Testing/economics , Equipment Design , Humans , Limit of Detection , Molecular Diagnostic Techniques/economics , Nucleic Acid Amplification Techniques/economics , Point-of-Care Testing/economics , RNA, Viral/isolation & purification , SARS-CoV-2/isolation & purification , Time Factors
20.
One Health ; 10: 100164, 2020 Dec.
Article in English | MEDLINE | ID: covidwho-733676

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which originated in Wuhan, China, in 2019, is responsible for the COVID-19 pandemic. It is now accepted that the wild fauna, probably bats, constitute the initial reservoir of the virus, but little is known about the role pets can play in the spread of the disease in human communities, knowing the ability of SARS-CoV-2 to infect some domestic animals. In this cross-sectional study, we tested the antibody response in a cluster of 21 domestic pets (9 cats and 12 dogs) living in close contact with their owners (belonging to a veterinary community of 20 students) in which two students tested positive for COVID-19 and several others (n = 11/18) consecutively showed clinical signs (fever, cough, anosmia, etc.) compatible with COVID-19 infection. Although a few pets presented many clinical signs indicative for a coronavirus infection, no antibodies against SARS-CoV-2 were detectable in their blood one month after the index case was reported, using an immunoprecipitation assay. These original data can serve a better evaluation of the host range of SARS-CoV-2 in natural environment exposure conditions.

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