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Simoes, Margarida Pires; Hodcroft, Emma B; Simmonds, Peter; Albert, Jan; Alidjinou, Enagon K; Ambert-Balay, Katia; Andrés, Cristina; Antón, Andrés; Auvray, Christelle; Bailly, Jean-Luc; Baldanti, Fausto; Bastings, Capser; Beard, Stuart; Pereira, Carla Berengua; Berginc, Natasa; Bloemen, Mandy; Blomqvist, Soile; Bosma, Froukje; Böttcher, Sindy; Bubba, Laura; ... (2024). Epidemiological and clinical insights into the enterovirus D68 upsurge in Europe 2021/22 and the emergence of novel B3-derived lineages, ENPEN multicentre study. (In Press). Journal of infectious diseases Oxford University Press 10.1093/infdis/jiae154
Reichmuth, Martina L; Hodcroft, Emma B; Althaus, Christian L (2023). Importation of Alpha and Delta variants during the SARS-CoV-2 epidemic in Switzerland: Phylogenetic analysis and intervention scenarios. PLoS pathogens, 19(8), e1011553. Public Library of Science 10.1371/journal.ppat.1011553
Humbert, Marion; Olofsson, Anna; Wullimann, David; Niessl, Julia; Hodcroft, Emma B; Cai, Curtis; Gao, Yu; Sohlberg, Ebba; Dyrdak, Robert; Mikaeloff, Flora; Neogi, Ujjwal; Albert, Jan; Malmberg, Karl-Johan; Lund-Johansen, Fridtjof; Aleman, Soo; Björkhem-Bergman, Linda; Jenmalm, Maria C; Ljunggren, Hans-Gustaf; Buggert, Marcus and Karlsson, Annika C (2023). Functional SARS-CoV-2 cross-reactive CD4+ T cells established in early childhood decline with age. Proceedings of the National Academy of Sciences of the United States of America - PNAS, 120(12), e2220320120. National Academy of Sciences NAS 10.1073/pnas.2220320120
Nadeau, Sarah A; Vaughan, Timothy G; Beckmann, Christiane; Topolsky, Ivan; Chen, Chaoran; Hodcroft, Emma; Schär, Tobias; Nissen, Ina; Santacroce, Natascha; Burcklen, Elodie; Ferreira, Pedro; Jablonski, Kim Philipp; Posada-Céspedes, Susana; Capece, Vincenzo; Seidel, Sophie; Santamaria de Souza, Noemi; Martinez-Gomez, Julia M; Cheng, Phil; Bosshard, Philipp P; Levesque, Mitchell P; ... (2023). Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data. Science translational medicine, 15(680), eabn7979. American Association for the Advancement of Science 10.1126/scitranslmed.abn7979
Reichmuth, Martina L; Hodcroft, Emma B; Riou, Julien; Neher, Richard A; Hens, Niel; Althaus, Christian L (2022). Impact of cross-border-associated cases on the SARS-CoV-2 epidemic in Switzerland during summer 2020 and 2021. Epidemics, 41, p. 100654. Elsevier 10.1016/j.epidem.2022.100654
Happi, Christian; Adetifa, Ifedayo; Mbala, Placide; Njouom, Richard; Nakoune, Emmanuel; Happi, Anise; Ndodo, Nnaemeka; Ayansola, Oyeronke; Mboowa, Gerald; Bedford, Trevor; Neher, Richard A; Roemer, Cornelius; Hodcroft, Emma; Tegally, Houriiyah; O'Toole, Áine; Rambaut, Andrew; Pybus, Oliver; Kraemer, Moritz U G; Wilkinson, Eduan; Isidro, Joana; ... (2022). Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus [perspective]. PLoS biology, 20(8), e3001769. Public Library of Science 10.1371/journal.pbio.3001769
Hodcroft, Emma B; Dyrdak, Robert; Andrés, Cristina; Egli, Adrian; Reist, Josiane; García Martínez de Artola, Diego; Alcoba-Flórez, Julia; Niesters, Hubert G M; Antón, Andrés; Poelman, Randy; Reynders, Marijke; Wollants, Elke; Neher, Richard A; Albert, Jan (2022). Evolution, geographic spreading, and demographic distribution of Enterovirus D68. PLoS pathogens, 18(5), e1010515. Public Library of Science 10.1371/journal.ppat.1010515
Telenti, Amalio; Hodcroft, Emma B; Robertson, David L (2022). The Evolution and Biology of SARS-CoV-2 Variants. Cold Spring Harbor perspectives in medicine, 12(5), a041390. Cold Spring Harbor Laboratory Press 10.1101/cshperspect.a041390
Hufsky, Franziska; Beslic, Denis; Boeckaerts, Dimitri; Duchene, Sebastian; González-Tortuero, Enrique; Gruber, Andreas J; Guo, Jiarong; Jansen, Daan; Juma, John; Kongkitimanon, Kunaphas; Luque, Antoni; Ritsch, Muriel; Lencioni Lovate, Gabriel; Nishimura, Luca; Pas, Célia; Domingo, Esteban; Hodcroft, Emma; Lemey, Philippe; Sullivan, Matthew B; Weber, Friedemann; ... (2022). The International Virus Bioinformatics Meeting 2022. Viruses, 14(5), p. 973. MDPI 10.3390/v14050973
Niessl, Julia; Sekine, Takuya; Lange, Joshua; Konya, Viktoria; Forkel, Marianne; Maric, Jovana; Rao, Anna; Mazzurana, Luca; Kokkinou, Efthymia; Weigel, Whitney; Llewellyn-Lacey, Sian; Hodcroft, Emma B.; Karlsson, Annika C; Fehrm, Johan; Sundman, Joar; Price, David A; Mjösberg, Jenny; Friberg, Danielle; Buggert, Marcus (2021). Identification of resident memory CD8+ T cells with functional specificity for SARS-CoV-2 in unexposed oropharyngeal lymphoid tissue. Science immunology, 6(64), eabk0894. American Association for the Advancement of Science 10.1126/sciimmunol.abk0894
Kucharski, Adam J; Hodcroft, Emma B; Kraemer, Moritz U G (2021). Sharing, synthesis and sustainability of data analysis for epidemic preparedness in Europe. The Lancet regional health. Europe, 9, p. 100215. Elsevier 10.1016/j.lanepe.2021.100215
Hodcroft, Emma B; Zuber, Moira; Nadeau, Sarah; Vaughan, Timothy G; Crawford, Katharine H D; Althaus, Christian L; Reichmuth, Martina L; Bowen, John E; Walls, Alexandra C; Corti, Davide; Bloom, Jesse D; Veesler, David; Mateo, David; Hernando, Alberto; Comas, Iñaki; Candelas, Fernando González; Stadler, Tanja; Neher, Richard A (2021). Spread of a SARS-CoV-2 variant through Europe in the summer of 2020. Nature, 595(7869), pp. 707-712. Springer Nature 10.1038/s41586-021-03677-y
Konings, Frank; Perkins, Mark D; Kuhn, Jens H; Pallen, Mark J; Alm, Erik J; Archer, Brett N; Barakat, Amal; Bedford, Trevor; Bhiman, Jinal N; Caly, Leon; Carter, Lisa L; Cullinane, Anne; de Oliveira, Tulio; Druce, Julian; El Masry, Ihab; Evans, Roger; Gao, George F; Gorbalenya, Alexander E; Hamblion, Esther; Herring, Belinda L; ... (2021). SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse [comment]. Nature microbiology, 6(7), pp. 821-823. Springer Nature 10.1038/s41564-021-00932-w
Huddleston, John; Hadfield, James; Sibley, Thomas R; Lee, Jover; Fay, Kairsten; Ilcisin, Misja; Harkins, Elias; Bedford, Trevor; Neher, Richard A; Hodcroft, Emma B. (2021). Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens. Journal of Open Source Software, 6(57), p. 2906. Open Journals 10.21105/joss.02906
Vogels, Chantal B F; Breban, Mallery I; Ott, Isabel M; Alpert, Tara; Petrone, Mary E; Watkins, Anne E; Kalinich, Chaney C; Earnest, Rebecca; Rothman, Jessica E; Goes de Jesus, Jaqueline; Morales Claro, Ingra; Magalhães Ferreira, Giulia; Crispim, Myuki A E; Singh, Lavanya; Tegally, Houriiyah; Anyaneji, Ugochukwu J; Hodcroft, Emma B.; Mason, Christopher E; Khullar, Gaurav; Metti, Jessica; ... (2021). Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2. PLoS biology, 19(5), e3001236. Public Library of Science 10.1371/journal.pbio.3001236
Goncalves Cabecinhas, Ana Rita; Roloff, Tim; Stange, Madlen; Bertelli, Claire; Huber, Michael; Ramette, Alban; Chen, Chaoran; Nadeau, Sarah; Gerth, Yannick; Yerly, Sabine; Opota, Onya; Pillonel, Trestan; Schuster, Tobias; Metzger, Cesar M J A; Sieber, Jonas; Bel, Michael; Wohlwend, Nadia; Baumann, Christian; Koch, Michel C.; Bittel, Pascal; ... (2021). SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. Microorganisms, 9(4), p. 677. MDPI 10.3390/microorganisms9040677
Grubaugh, Nathan D; Hodcroft, Emma B.; Fauver, Joseph R; Phelan, Alexandra L; Cevik, Muge (2021). Public health actions to control new SARS-CoV-2 variants [commentary]. Cell, 184(5), pp. 1127-1132. Cell Press 10.1016/j.cell.2021.01.044
Braun, Katarina M; Moreno, Gage K; Halfmann, Peter J; Hodcroft, Emma B.; Baker, David A; Boehm, Emma C; Weiler, Andrea M; Haj, Amelia K; Hatta, Masato; Chiba, Shiho; Maemura, Tadashi; Kawaoka, Yoshihiro; Koelle, Katia; O'Connor, David H; Friedrich, Thomas C (2021). Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. PLoS pathogens, 17(2), e1009373. Public Library of Science 10.1371/journal.ppat.1009373
Lauring, Adam S; Hodcroft, Emma B. (2021). Genetic Variants of SARS-CoV-2-What Do They Mean? [viewpoint]. JAMA - the journal of the American Medical Association, 325(6), pp. 529-531. American Medical Association 10.1001/jama.2020.27124
