SARS-CoV-2 Genome Sequencing Protocol

Based on the Ct values of the NP-OP samples, the total RNA was extracted using the MagMAX™ Viral/Pathogen II (MVP II) Nucleic Acid Isolation Kit (Catalog number: A48383) (Applied Biosystems) and carried out according to the instructions of the manufacturer. The target whole viral genome library preparation was constructed using the QIAseq^TM SARS-CoV-2 Primer Panel (Catalog number: 333896; Qiagen, Hilden, Germany). Sequencing was done at the Core Facility to Support Research—University of São Paulo (CEFAP-USP/GENIAL) using the Illumina MiSeq platform. Each sample was barcoded individually, which allowed the separation of reads for each one of them. Short unpaired reads and low-quality bases and reads were removed using Trimmomatic version 0.39 (LEADING:20 TRAILING:20 SLIDINGWINDOW:4:25 MINLEN:36) (23 (link)). Consensus genomes were assembled with paired end reads using Bowtie2 version 2.0.6 using default parameters (24 (link)). All the datasets analyzed during the current study are available from the corresponding author on reasonable request. The new sequence here characterized was deposited in GenBank under the accession number MW495017.