Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

@article{Alm2020GeographicalAT,
  title={Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020},
  author={Erik Alm and Eeva K Broberg and Thomas Richard Connor and Emma B. Hodcroft and Andrey B. Komissarov and Sebastian Maurer-Stroh and Angeliki Melidou and Richard A. Neher and {\'A}ine Niamh O'toole and Dmitriy Pereyaslov and Niko Beerenwinkel and Susana Posada-C{\'e}spedes and Kim Philipp Jablonski and Pedro F. Ferreira and Ivan Topolsky and Tatjana Av{\vs}i{\vc}-Županc and Mi{\vs}a Korva and Mario Poljak and Samo Zakotnik and Toma{\vz} Mark Zorec and Karoline Bragstad and Olav Hungnes and Kathrine Stene-Johansen and Chantal B.E.M. Reusken and Adam Meijer and Harry Vennema and Lidia Ruiz-Rold{\'a}n and Maria Alma Bracho and Neris Garc{\'i}a-Gonz{\'a}lez and {\'A}lvaro Chiner-Oms and Irving Cancino-Mu{\~n}oz and I{\~n}aki Comas and Galo A. Goig and Manuela Torres-Puente and Mariana G. L{\'o}pez and Ll{\'u}cia Martinez-Priego and Giuseppe D’Auria and Loreto Ferr{\'u}s-Abad and Griselda de Marco and Inmaculada Galan-Vendrell and Sandra Carb{\'o}-Ramirez and Paula Ruiz-Hueso and Mireia Coscoll{\'a} and Katerina Polackova and Lenka Kramn{\'a} and Ondřej Cinek and Jan Richter and George Krashias and Christina Tryfonos and Stavros Bashiardes and Dana Koptides and Christina G. Christodoulou and Barbara Bartolini and Cesare Em Gruber and Antonino di Caro and Concetta Castilletti and Fabrizio Stefani and Sara Giordana Rimoldi and Francesca Romeri and Franco Salerno and Stefano Polesello and Alexander Nagy and Helena Jiřincov{\'a} and Jaromira Vecerova and Ludmila Nov{\'a}kov{\'a} and Samuel Cordey and Marine Murtskhvaladze and Nato Kotaria and Tobias Sch{\"a}r and Christian Beisel and Oliver Vugrek and Filip Roki{\'c} and Lovro Trgovec-Greif and Igor Jurak and Tomislav Rukavina and Neven Su{\vc}i{\'c} and Kristian Sch{\o}nning and S{\o}ren Michael Karst and Rasmus Hansen Kirkegaard and Thomas Yssing Michaelsen and Emil Aa S{\o}rensen and Simon Knutson and Jakob Brandt and Vang Le-Quy and Trine S{\o}rensen and Celine Petersen and Martin Schou Pedersen and Sanne L{\o}kkegaard Larsen and Marianne N. Skov and Morten Rasmussen and Jannik Fonager and Anders Fomsgaard and Rinat A. Maksyutov and Elena V. Gavrilova and Oleg V. Pyankov and Sergey A. Bodnev and Tatyana V. Tregubchak and Alexander N. Shvalov and Denis V. Antonets and Paola Cristina Resende and Stephanie Goya and Amandine Perrin and Raphael Tc Lee and Shilpa Yadahalli and Alvin X. Han and Colin A. Russell and Stefan Schmutz and Maryam Zaheri and Verena Kufner and Michael Huber and Alexandra Trkola and Markus H. Antwerpen and Mathias C. Walter and Sylvie van der Werf and Fabiana G{\'a}mbaro and Sylvie Behillil and Vincent Enouf and Flora Donati and Monta Ustinova and Vita Rovite and Janis Klovins and Oksana Savicka and Anke Wienecke-Baldacchino and Catherine Ragimbeau and Guillaume Fournier and Jo{\"e}l Mossong and Stephan Walter Aberle and Mattias Haukland and Theresa Enkirch and Abdolreza Advani and Maria Lind Karlberg and Oskar Karlsson Lindsj{\"o} and Sandra Broddesson and Monika Sl{\'a}vikov{\'a} and Martina Li{\vc}kov{\'a} and Boris Klempa and Edita Staroňov{\'a} and Elena Tich{\'a} and Tom{\'a}{\vs} Szeme{\vs} and Diana Rusň{\'a}kov{\'a} and Tanja Stadler and Josep Quer and Andr{\'e}s Ant{\'o}n and Cristina Andr{\'e}s and Maria Pi{\~n}ana and Damir Garcia-Cehic and Tom{\`a}s Pumarola and Jacques Izopet and G Gioula and Maria Exindari and Anna Papa and Dimitrios Chatzidimitriou and Symeon Metallidis and Stella Pappa and Milan Macek Jr and Jan Geryk and Petr Bro{\vz} and Ale{\vs} Briks{\'i} and Petr Hub{\'a}{\vc}ek and Pavel Dřev{\'i}nek and Miroslav Zajac and Petr Kvapil and Michal Holub and Kateřina Kvapilov{\'a} and Adam Novotn{\'y} and Martin Ka{\vs}n{\'y} and Petr Klempt and Olli Vapalahti and Teemu Smura and Tarja Sironen and Philippe Selhorst and Colin Anthony and Kevin K Ari{\"e}n and Etienne Simon-Lori{\`e}re and Lukasz Rabalski and Krystyna Bieńkowska-Szewczyk and V{\'i}tor Borges and Joana Isidro and Jo{\~a}o Paulo Gomes and Raquel Guiomar and Pedro Pechirra and In{\^e}s Costa and S{\'i}lvia Duarte and Lu{\'i}s Vieira and Krzysztof Pyr{\'c} and Neta S. Zuckerman and Shahlo Turdikulova and A. A. Abdullaev and Dilbar Dalimova and Abror Abdurakhimov and Adriano Tagliabracci and Federica Alessandrini and Filomena Melchionda and Valerio Onofri and Chiara Turchi and Patrizia Bagnarelli and Stefano Menzo and Sara Caucci and Laura Di Sante and Alexandra M Popa and Jakob-Wendelin Genger and Benedikt Agerer and Alexander Lercher and Lukas Endler and Mark J. Smyth and Thomas Penz and Michael Schuster and Martin Senekowitsch and Jani Laine and Christoph Bock and Andreas Bergthaler and Alexandr Shevtsov and Ruslan Kalendar and Yerlan M. Ramanculov and Alexander Graf and Maximilian Muenchhoff and Oliver T. Keppler and Stefan Krebs and Helmut Blum and Alessandro Marcello and Danilo Licastro and Pierlanfranco D’Agaro and Florian Laubscher and Dejan Vidanovi{\'c} and Bojana Te{\vs}ovi{\'c} and Jeremy D. Volkening and Nicola Clementi and Nicasio Mancini and Maja Rupnik and Aleksander Mahni{\vc} and Andreas Walker and Torsten Houwaart and Tobias Wienemann and Malte Kohns Vasconcelos and Daniel Strelow and B-E Jensen and Tina Senff and Lisanna H{\"u}lse and Ortwin Adams and Marcel Andr{\'e}e and Sandra Hauka and Torsten Feldt and Verena Keitel and Detlef Kindgen-Milles and J{\"o}rg Timm and Klaus Pfeffer and Alexander T. Dilthey and Catherine Moore and Aykut Ozdarendeli and Shaikh Terkis Islam Pavel and Hazel Yetiskin and Gunsu Aydin and Can Holyavkin and Muhammet Ali Uygut and Ceren Cevik and Alexey M. Shchetinin and Vladimir A. Gushchin and Gizem Dinler-Doganay and Levent Doğanay and Tugba Kizilboga-Akgun and Ilker Karacan and Katarzyna Wanda Pancer and Piet Maes and Joan Mart{\'i}-Carreras and Tony Wawina-Bokalanga and Bert Vanmechelen and Andrea Th{\"u}rmer and Marianne Wedde and Ralf D{\"u}rrwald and Max von Kleist and Oliver Drechsel and Thorsten Wolff and Stephan Fuchs and René Kmiecinski and Janine Michel and Andreas Nitsche and Inmaculada Casas and Mar{\'i}a Iglesias Caballero and {\'A}ngel Zaballos and Pilar Jim{\'e}nez and Mercedes Jim{\'e}nez and Sara Fern{\'a}ndez and Sarai Varona Fern{\'a}ndez and Isabel Cuesta De La Plaza and Artem Fadeev and A. A. Ivanova and Mariia Sergeeva and Paola Stefanelli and M Estee Torok and Grant Hall and Ana da Silva Filipe and Lance Turtle and Safiah Afifi and Kathryn Mccluggage and Robert Beer and Juan Ledesma and Joshua Maksimovic and Karla Spellman and William L. Hamilton and Angela M Marchbank and Joel Southgate and Anthony Underwood and Ben Taylor and Corin A. Yeats and Khalil AbuDahab and Matthew R. Gemmell and Richard J. Eccles and Anita O. Lucaci and Charlotte Nelson and Lucille Rainbow and Mark A Whitehead and Richard Gregory and Sam T. Haldenby and Steve Paterson and Margaret A. Hughes and Martin D. Curran and Dave J. Baker and Rachel M. Tucker and Luke R. Green and Theresa Feltwell and Fenella D Halstead and Matthew D. Wyles and Aminu S. Jahun and Shazaad Ahmad and Iliana Georgana and Ian G. Goodfellow and Anna Yakovleva and Luke W. Meredith and Artemis Gavriil and Ali R. Awan and Chloe Fisher and Jonathan D. Edgeworth and Jessica Lynch and Nathan Moore and Rebecca Williams and Stephen P. Kidd and Nicholas J. Cortes and Kirstyn Brunker and John T. McCrone and Joshua Quick and Nichola Duckworth and Sarah Walsh and Tim J. Sloan and Catherine Ludden and Ryan P. George and Gary J A Eltringham and Julianne R. Brown and Elihu Aranday-Cortes and James G. Shepherd and Joseph Hughes and Kathy K Li and Thomas C Williams and Natasha Johnson and Natasha Jesudason and Daniel Mair and Emma C. Thomson and Rajiv Shah and Yasmin A Parr and Stephen Carmichael and David L. Robertson and Kyriaki Nomikou and Alice Broos and Marc Niebel and Katherine Smollett and Lily Tong and Shahjahan Miah and Anita Wittner and Nicole Phillips and Brendan A.I. Payne and Rebecca Dewar and Alison H. Holmes and Frances Bolt and James R. Price and Siddharth Mookerjee and Dheeraj K. Sethi and Will Potter and Rachael Stanley and Reenesh Prakash and Samir Dervisevic and John C. Graham and Andrew Nelson and Darren L. Smith and Gregory R. Young and Wen Chyin Yew and John A. Todd and Amy Trebes and Monique I. Andersson and Matthew J. Bull and Joanne Watkins and Alec Birchley and Bree Gatica-Wilcox and Lauren Gilbert and Sara Kum{\vz}iene-Summerhayes and Sara M. Rey and Anoop J. Chauhan and Ethan Butcher and Kelly Bicknell and Scott Elliott and Sharon Glaysher and Angie Lackenby and David F Bibby and Steven Platt and Hodan Mohamed and Nicholas W. Machin and Jean L Mbisa and Jonathan Evans and Malorie Perry and Nicole Pacchiarini and Sally Corden and Alexander Adams and Amy Gaskin and Jason Coombs and Lee Graham and Simon Cottrell and Mari Morgan and Laura Gifford and Anastasia Kolyva and Steven J. Rudder and Alexander J. Trotter and Alison E. Mather and Alp Aydin and Andrew J. Page and Gemma L. Kay and Leonardo de Oliveira Martins and Muhammad Yasir and Nabil-Fareed Alikhan and Nicholas M. Thomson and Rachel Gilroy and Robert A. Kingsley and Justin O’Grady and Ana Victoria Guti{\'e}rrez and Marilyn Diaz and Thanh Le Viet and Ana P. Tedim and Evelien M. Adriaenssens and C. Patrick McClure and Christopher Moore and Fei Sang and Gemma Clark and Hannah C. Howson-Wells and Johnny Debebe and Jonathan K. Ball and Joseph G. Chappell and Manjinder Khakh and Matthew Carlile and Matthew W. Loose and Michelle M. Lister and Nadine Holmes and Theocharis Tsoleridis and Vicki M. Fleming and Victoria Wright and Wendy J.M. Smith and Michael D Gallagher and Matthew D. Parker and David G Partridge and Cariad M. Evans and Paul Baker and Sarah J. Essex and Steven Liggett and Alexander J Keeley and Matthew Bashton and Stefan Rooke and Emma J. Meader and Carlos Balcazar Lopez and Adrienn Angyal and Mark Kristiansen and Helena J. Tutill and Jacqueline Findlay and Lamia Mestek-Boukhibar and Leysa Forrest and Patricia L. Dyal and Rachel J. Williams and Yasmin Panchbhaya and Charlotte Williams and Sunando Roy and Sarojini Pandey and Joanne D Stockton and Nicholas James Loman and Radoslaw Poplawski and Samuel M. Nicholls and Will P. M. Rowe and Fahad A Khokhar and Malte L. Pinckert and Myra Hosmillo and Yasmin Chaudhry and Laura Grace Caller and Rose K. Davidson and Luke Griffith and Andrew Rambaut and Ben Jackson and Rachel M. Colquhoun and Verity Hill and Jenna Nichols and Patawee Asamaphan and Alistair C. Darby and Kathryn Alto Jackson and Miren Iturriza-G{\'o}mara and Ecaterina Edith Vamos and Angie Green and David M. Aanensen and David Bonsall and David Buck and George Macintyre-Cockett and Mariateresa de Cesare and Oliver G. Pybus and Tanya Golubchik and Garry Scarlett and Katie F. Loveson and Samuel C. Robson and Angela H. Beckett and Benjamin B. Lindsey and Danielle C. Groves and Paul J. Parsons and Martin P. McHugh and James D. Barnes and Carmen F Manso and Dimitris K. Grammatopoulos and Katja E. Menger and Ewan M. Harrison and R Gunson and Sharon J. Peacock and Gabriel Gonz{\'a}lez and Michael Carr and Lazar Cristina Mihaela and Odette Popovici and Maria Brytting and Catherine Bresner and William Fuller and T. Race Workman and Andreas F. Mentis and Athanasios Kossyvakis and Timokratis Karamitros and Vasiliki Pogka and Antonios Kalliaropoulos and Elina Horefti and Aspasia Kontou and Beatriz Martinez-Gonzalez and Voula Labropoulou and Androniki Voulgari-kokota and Maria Evangelidou and Panagiota Bizta and Maria Belimezi and Laurens Lambrechts and Mehmet Ziya Doymaz and Merve Kalkan Yazici and Nesibe Selma Çetin and Elif Karaaslan and Hannimari Kallio-kokko and Jenni Virtanen and Maija T. Suvanto and Phuoc Thien Truong Nguyen and Pekka Ellonen and Sari Hannula and Harri Kangas and Vattipally B. Sreenu and Katalin Buri{\'a}n and Gabriella Terhes and Katalin Gombos and Attila Gyenesei and P{\'e}ter Urb{\'a}n and R{\'o}bert Herczeg and Ferenc Jakab and G{\'a}bor Kemenesi and G{\'a}bor Endre T{\'o}th and Bal{\'a}zs A. Somogyi and Brigitta Zana and Safia Zeghbib and Anett Kuczmog and Fanni F{\"o}ldes and Zs{\'o}fia Lanszki and M{\'o}nika Madai and Henrietta Papp and {\'A}gnes Nagy and Csaba Istv{\'a}n Pereszl{\'e}nyi and Gergely Csaba Babinszky and G{\'a}bor Dud{\'a}s and Eszter Csoma and Ahmad N. Abou Tayoun and Alawi A. Alsheikh-Ali and Tom Loney and Norbert Nowotny and Osama Mohammed Saed Abdul-Wahab and Fernando Gonz{\'a}lez-Candelas and Martin H Andersen and Sarah Taylor},
  journal={Eurosurveillance},
  year={2020},
  volume={25}
}
We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three genomic nomenclature systems to all sequence data from the World Health Organization European Region available until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation, compare the nomenclatures and lay a foundation for future… 

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