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A year living with SARS-CoV-2: an epidemiological overview of viral lineage circulation by whole-genome sequencing in Barcelona city (Catalonia, Spain) Piñana Moro, Maria González Sánchez, Alejandra Garcia Cehic, Damir Esperalba Esquerra, Juliana Zules Oña, Ricardo Gabriel Campos Martinez, Carolina Codina Grau, Gema Blanco Grau, Albert Colomer Castell, Sergi Martin Perez, Maria Carmen Castillo Oliveda, Carla García-Comuñas, Karen Vásquez-Mercado, Rodrigo Martins-Martins, Reginald Saubí Roca, Narcís Pumarola Suñé, Tomàs Quer Sivila, Josep Campins Martí, Magda Rando Segura, Ariadna Borras Bermejo, Blanca Antón Pagarolas, Andrés Andrés Vergés, Cristina Institut Català de la Salut [Andrés C, Piñana M, González-Sánchez A, Esperalba J, Rando A, Codina MG, Martín MC, Castillo C, García-Comuñas K, Vásquez-Mercado R, Martins-Martins R, Pumarola T, Antón A, Saubi N] Unitat de Virus Respiratoris, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain. Servei de Microbiologia, Vall d’Hebron Hospital Universitari, Barcelona, Spain. [Borràs-Bermejo B, Zules-Oña RG, Campins-Martí M] Servei de Medicina Preventiva i Epidemiologia, Vall d’Hebron Hospital Universitari, Barcelona, Spain. Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain. [García-Cehic D, Quer J] Grup de Recerca de les Malalties Hepàtiques, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain. Unitat Hepàtica, Vall d’Hebron Hospital Universitari, Barcelona, Spain. Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain [Campos C, Colomer-Castell S] Grup de Recerca de les Malalties Hepàtiques, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain. Unitat Hepàtica, Vall d’Hebron Hospital Universitari, Barcelona, Spain. [Blanco-Grau A] Servei de Laboratoris Clínics, Vall d’Hebron Barcelona Hospital Universitari, Barcelona, Spain Vall d'Hebron Barcelona Hospital Campus COVID-19 (Malaltia) - Epidemiologia Seqüència de nucleòtids Genomes ANALYTICAL, DIAGNOSTIC AND THERAPEUTIC TECHNIQUES, AND EQUIPMENT::Investigative Techniques::Genetic Techniques::Sequence Analysis::Sequence Analysis, DNA::Whole Genome Sequencing DISEASES::Virus Diseases::RNA Virus Infections::Nidovirales Infections::Coronaviridae Infections::Coronavirus Infections Other subheadings::Other subheadings::Other subheadings::/epidemiology TÉCNICAS Y EQUIPOS ANALÍTICOS, DIAGNÓSTICOS Y TERAPÉUTICOS::técnicas de investigación::técnicas genéticas::análisis de secuencias::análisis de secuencias de ADN::secuenciación del genoma completo ENFERMEDADES::virosis::infecciones por virus ARN::infecciones por Nidovirales::infecciones por Coronaviridae::infecciones por Coronavirus Otros calificadores::Otros calificadores::Otros calificadores::/epidemiología Catalonia; SARS-CoV-2; Molecular epidemiology Cataluña; SARS-CoV-2; Epidemiología molecular Catalunya; SARS-CoV-2; Epidemiologia molecular Herein, we describe the genetic diversity of circulating SARS-CoV-2 viruses by whole-genome sequencing (WGS) in Barcelona city (Catalonia, Spain) throughout the first four pandemic waves. From weeks 11/2020–24/2021, SARS-CoV-2-positive respiratory samples were randomly selected per clinical setting (80% from primary care or 20% from the hospital), age group, and week. WGS was performed following the ARTICv3 protocol on MiSeq or NextSeq2000 Illumina platforms. Nearly complete consensus sequences were used for genetic characterization based on GISAID and PANGOLIN nomenclatures. From 2475 samples, 2166 (87%) were fully sequenced (78% from primary care and 22% from hospital settings). Multiple genetic lineages were co-circulating, but four were predominant at different periods. While B.1.5 (50.68%) and B.1.1 (32.88%) were the major lineages during the first pandemic wave, B.1.177 (66.85%) and B.1.1.7 (83.80%) were predominant during the second, third, and fourth waves, respectively. Almost all (96.4%) were carrying D614G mutation in the S protein, with additional mutations that define lineages or variants. But some mutations of concern, such as E484K from B.1.351 and P.1 lineages are currently under monitoring, together with those observed in the receptor-binding domain or N-terminal domain, such as L452R and T478K from B.1.617.2 lineage. The fact that a predominant lineage was observed in each pandemic wave suggests advantageous properties over other contemporary co-circulating variants. This genetic variability should be monitored, especially when a massive vaccination campaign is ongoing because the potential selection and emergence of novel antigenic SARS-CoV-2 strains related to immunological escapement events. This work was supported by Spanish Network for the Research in Infectious Diseases: [Grant Number REIPI RD16/0016/0003]; Centro para el Desarrollo Tecnológico Industrial (CDTI) from the Spanish Ministry of Economy and Business [Grant Number IDI-20200297]; Direcció General de Recerca i Innovació en Salut (DGRIS); European Development Regional Fund (ERDF) “A way to achieve Europe” by Spanish Network for Research in Infectious Diseases [REIPI RD16/0016/0003]. 2023-01-30T13:24:33Z 2023-01-30T13:24:33Z 2022-12 info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion Andrés C, Piñana M, Borràs-Bermejo B, González-Sánchez A, García-Cehic D, Esperalba J, et al. A year living with SARS-CoV-2: an epidemiological overview of viral lineage circulation by whole-genome sequencing in Barcelona city (Catalonia, Spain). Emerg Microbes Infect. 2022 Dec;11(1):172–81. 2222-1751 https://hdl.handle.net/11351/8934 10.1080/22221751.2021.2011617 34842496 000738781300001 eng Emerging Microbes & Infections;11(1) https://doi.org/10.1080/22221751.2021.2011617 info:eu-repo/grantAgreement/ES/PE2013-2016/RD16%2F0016%2F0003 Attribution 4.0 International http://creativecommons.org/licenses/by/4.0/ info:eu-repo/semantics/openAccess application/pdf Taylor & Francis Scientia