key: cord-0928425-cu606oti authors: Delli Compagni, Emiliano; Mangone, Iolanda; Bonfini, Barbara; Di Gennaro, Annapia; Teodori, Liana; Leone, Alessandra; Casaccia, Claudia; Portanti, Ottavio; Averaimo, Daniela; Zilli, Katiuscia; Malatesta, Daniela; Ancora, Massimo; Scialabba, Silvia; Di Domenico, Marco; Lorusso, Alessio title: Whole-Genome Sequences of SARS-CoV-2 Lineage B.1.525 Strains (Variant η) Detected from Patients in the Abruzzo Region (Central Italy) during Spring 2021 date: 2021-08-05 journal: Microbiology resource announcements DOI: 10.1128/mra.00618-21 sha: a95479cf6c96bfcd5dabb61f81eb1fc505a4f324 doc_id: 928425 cord_uid: cu606oti Novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are emerging worldwide. Here, we report the complete genome sequences of 13 severe acute SARS-CoV-2 strains belonging to lineage B.1.525 (variant η). is designed to target three different regions in the viral genome (ORF1ab, S and N proteinencoding genes). All samples tested positive with threshold cycle (C T ) values of ,20 for all targets. Next generation sequencing was carried out using the Illumina COVIDSeq Test (San Diego, CA, USA). Deep sequencing was performed on the NextSeq 500 platform (Illumina, Inc.) using the NextSeq 500/550 high-output reagent cartridge v2, with 75 cycles and 36-bp paired-end format (13) . Quality control of the reads was performed using FastQC v0.11.9 quality control software. The reads obtained were trimmed using Trimmomatic (14) . The SARS-CoV-2 reads were mapped to the Wuhan-Hu-1 reference sequence (GenBank accession number NC_045512) using Snippy v4.5.1 (https://github.com/tseemann/snippy). Consensus sequences were obtained using iVar v1.3 (15) . All tools were run with default parameters. Details about the obtained reads are listed in Table 1 . Multiple sequence alignment of the 13 consensus sequences, using MegAlign PRO (Lasergene; DNASTAR, Madison, WI, USA), showed differences in the nucleotide sequences resulting in missense mutations and therefore in modifications in the amino acid composition. Before submission to the GISAID and NCBI databases, the sequences were uploaded to the Pangolin COVID-19 lineage assigner (https://cov-lineages.org) and assigned to the B.1.525 lineage. These strains share the same set of mutations with regard to the proteins E, M, N, and NSP6, whereas some mutations are unique to some strains. Interestingly, strain TE274189/ 2021 is the only one that displays the mutation L513F in the S protein; this mutation is located within the S1 protein but does not belong to the receptor-binding domain (16) . The sequences were released promptly after the sample collection. Here, we want to highlight that the punctual tracking of variants and discovery of novel and relevant mutations are essential strategies for better understanding the virus evolution and transmission and for developing effective countermeasures. Therefore, a global sequencing effort is needed to tackle the COVID-19 pandemic. This work was supported by funding from the European Union's Horizon 2020 Research and Innovation program, One Health European Joint Programme under grant agreement number 773830, and by funding from the Ministry of Health (Ricerca Corrente 2020, PanCO "Epidemiologia e Patogenesi dei coronavirus umani ed animali" to Alessio Lorusso and Ricerca Strategica 2020, "Suscettibilità dei mammiferi a SARS-COV-2: rischi di zoonosi inversa e possibilità in medicina traslazionale"). We declare no conflicts of interest. 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