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

• Published in: Euro surveillance : bulletin européen sur les maladies transmissibles Vol. 25; no. 32; p. 1
• Main Authors: Alm, Erik, Broberg, Eeva K, Connor, Thomas, Hodcroft, Emma B, Komissarov, Andrey B, Maurer-Stroh, Sebastian, Melidou, Angeliki, Neher, Richard A, O’Toole, Áine, Pereyaslov, Dmitriy
• Format: Journal Article
• Language: English
• Published: Sweden Centre Europeen pour la Surveillance Epidemiologique du SIDA (European Centre for the Epidemiological Monitoring of AIDS) 13.08.2020; European Centre for Disease Prevention and Control; European Centre for Disease Prevention and Control (ECDC)
• Subjects: Base Sequence; Betacoronavirus; Betacoronavirus - genetics; Betacoronavirus - pathogenicity; Coronavirus; Coronavirus - genetics; Coronavirus - isolation & purification; Coronavirus Infections; Coronavirus Infections - epidemiology; Coronavirus Infections - virology; COVID-19; Epidemiology; Europe; Europe - epidemiology; Genome, Viral; Genome, Viral - genetics; Genomics; Global health; Health surveillance; Humans; Life Sciences; Pandemics; Phylogeography; Pneumonia, Viral; Pneumonia, Viral - epidemiology; Pneumonia, Viral - virology; Rapid Communication; RNA, Viral; RNA, Viral - analysis; RNA, Viral - genetics; RNA-Dependent RNA Polymerase; RNA-Dependent RNA Polymerase - genetics; SARS-CoV-2; Severe Acute Respiratory Syndrome; Severe acute respiratory syndrome coronavirus 2; Spatio-Temporal Analysis; World Health Organization; Europe; COVID-19; nomenclature; SARS-CoV-2; WGS; Europe; NGS; sequencing
• ISSN: 1560-7917; 1025-496X; 1560-7917; 1025-496X
• DOI: 10.2807/1560-7917.ES.2020.25.32.2001410

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 European genomic surveillance of SARS-CoV-2.