Emergence and Spread of SARS-CoV-2 Lineages B.1.1.7 and P.1 in Italy.

作者: Francesca Di Giallonardo , Joanna C A Cobbin , Iolanda Mangone , Edward C Holmes , Cesare Cammà

DOI: 10.3390/V13050794

关键词:

摘要: Italy's second wave of SARS-CoV-2 has hit hard, with more than three million cases and over 100,000 deaths, representing an almost ten-fold increase in the numbers reported by August 2020. Herein, we present analysis 6515 sequences sampled Italy between 29 January 2020 1 March 2021 show how different lineages emerged multiple times independently despite lockdown restrictions. Virus lineage B.1.177 became dominant variant November 2020, when peaked at 40,000 a day, but since this is being replaced B.1.1.7 'variant concern'. In addition, report sudden another documented concern-lineage P.1-from December onwards, most likely caused single introduction into Italy. We again highlight international importations drive emergence new that genome sequencing should remain top priority for ongoing surveillance

参考文章(20)
Shigehiro Kuraku, Christian M. Zmasek, Osamu Nishimura, Kazutaka Katoh, aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity. Nucleic Acids Research. ,vol. 41, pp. 22- 28 ,(2013) , 10.1093/NAR/GKT389
Lam-Tung Nguyen, Heiko A. Schmidt, Arndt von Haeseler, Bui Quang Minh, IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies Molecular Biology and Evolution. ,vol. 32, pp. 268- 274 ,(2015) , 10.1093/MOLBEV/MSU300
Jana Trifinopoulos, Lam-Tung Nguyen, Arndt von Haeseler, Bui Quang Minh, W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Research. ,vol. 44, ,(2016) , 10.1093/NAR/GKW256
Andrew Rambaut, Edward C. Holmes, Áine O’Toole, Verity Hill, John T. McCrone, Christopher Ruis, Louis du Plessis, Oliver G. Pybus, A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature microbiology. ,vol. 5, pp. 1403- 1407 ,(2020) , 10.1038/S41564-020-0770-5
Frank Schlosser, Benjamin F. Maier, Olivia Jack, David Hinrichs, Adrian Zachariae, Dirk Brockmann, COVID-19 lockdown induces disease-mitigating structural changes in mobility networks. Proceedings of the National Academy of Sciences of the United States of America. ,vol. 117, pp. 32883- 32890 ,(2020) , 10.1073/PNAS.2012326117
Francesca Di Giallonardo, Sebastian Duchene, Ilaria Puglia, Valentina Curini, Francesca Profeta, Cesare Cammà, Maurilia Marcacci, Paolo Calistri, Edward C. Holmes, Alessio Lorusso, Genomic Epidemiology of the First Wave of SARS-CoV-2 in Italy. Viruses. ,vol. 12, pp. 1438- ,(2020) , 10.3390/V12121438
Lewis F Buss, Carlos A Prete Jr, Claudia MM Abrahim, Alfredo Mendrone Jr, Tassila Salomon, Cesar de Almeida-Neto, Rafael FO França, Maria C Belotti, Maria PSS Carvalho, Allyson G Costa, Myuki AE Crispim, Suzete C Ferreira, Nelson A Fraiji, Susie Gurzenda, Charles Whittaker, Leonardo T Kamaura, Pedro L Takecian, Pedro da Silva Peixoto, Marcio K Oikawa, Anna S Nishiya, Vanderson Rocha, Nanci A Salles, Andreza Aruska de Souza Santos, Martirene A da Silva, Brian Custer, Kris V Parag, Manoel Barral-Netto, Moritz UG Kraemer, Rafael HM Pereira, Oliver G Pybus, Michael P Busch, Márcia C Castro, Christopher Dye, Vítor H Nascimento, Nuno R Faria, Ester C Sabino, None, Three-quarters attack rate of SARS-CoV-2 in the Brazilian Amazon during a largely unmitigated epidemic. Science. ,vol. 371, pp. 288- 292 ,(2021) , 10.1126/SCIENCE.ABE9728
Houriiyah Tegally, Eduan Wilkinson, Marta Giovanetti, Arash Iranzadeh, Vagner Fonseca, Jennifer Giandhari, Deelan Doolabh, Sureshnee Pillay, Emmanuel James San, Nokukhanya Msomi, Koleka Mlisana, Anne von Gottberg, Sibongile Walaza, Mushal Allam, Arshad Ismail, Thabo Mohale, Allison J Glass, Susan Engelbrecht, Gert Van Zyl, Wolfgang Preiser, Francesco Petruccione, Alex Sigal, Diana Hardie, Gert Marais, Marvin Hsiao, Stephen Korsman, Mary-Ann Davies, Lynn Tyers, Innocent Mudau, Denis York, Caroline Maslo, Dominique Goedhals, Shareef Abrahams, Oluwakemi Laguda-Akingba, Arghavan Alisoltani-Dehkordi, Adam Godzik, Constantinos Kurt Wibmer, Bryan Trevor Sewell, José Lourenço, Luiz Carlos Junior Alcantara, Sergei L Kosakovsky Pond, Steven Weaver, Darren Martin, Richard J Lessells, Jinal N Bhiman, Carolyn Williamson, Tulio de Oliveira, None, Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa medRxiv. ,(2020) , 10.1101/2020.12.21.20248640
Tara Swadi, Jemma L. Geoghegan, Tom Devine, Caroline McElnay, Jillian Sherwood, Phil Shoemack, Xiaoyun Ren, Matt Storey, Sarah Jefferies, Erasmus Smit, James Hadfield, Aoife Kenny, Lauren Jelley, Andrew Sporle, Andrea McNeill, G. Edwin Reynolds, Kip Mouldey, Lindsay Lowe, Gerard Sonder, Alexei J. Drummond, Sue Huang, David Welch, Edward C. Holmes, Nigel French, Colin R. Simpson, Joep de Ligt, Genomic Evidence of In-Flight Transmission of SARS-CoV-2 Despite Predeparture Testing. Emerging Infectious Diseases. ,vol. 27, pp. 687- 693 ,(2021) , 10.3201/EID2703.204714
Ester C Sabino, Lewis F Buss, Maria PS Carvalho, Carlos A Prete, Myuki AE Crispim, Nelson A Fraiji, Rafael HM Pereira, Kris V Parag, Pedro da Silva Peixoto, Moritz UG Kraemer, Marcio K Oikawa, Tassila Salomon, Zulma M Cucunuba, Márcia C Castro, Andreza Aruska de Souza Santos, Vítor H Nascimento, Henrique S Pereira, Neil M Ferguson, Oliver G Pybus, Adam Kucharski, Michael P Busch, Christopher Dye, Nuno R Faria, None, Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence. The Lancet. ,vol. 397, pp. 452- 455 ,(2021) , 10.1016/S0140-6736(21)00183-5