RNA was extracted from patient’s blood using a Maxwell RSC simply RNA Blood purification kit according to the manufacturer’s instructions (Promega, USA). Library preparation and sequencing was performed as described26 (link). In short, cDNA was obtained by using reverse transcriptase with random priming. Following cDNA synthesis, primers based on sequences from the ARTICnetwork were used to generate 400 bp amplicons in two different PCR pools. After merging of pools and amplification, libraries were constructed using QIASeq FX DNA Library UDI Kit following the manufacturer’s instructions (Qiagen GmbH, North Rhine-Westphalia, Germany).
Sequencing was done with Illumina NextSeq® 500/550 using 149-bp paired-end reads with 10-bp indices (Illumina, California, USA). Obtained viral sequences were assembled using CLC Genomics Workbench v20.0.3 (Qiagen GmbH, North Rhine-Westphalia, Germany). SARS-CoV-2 isolate Wuhan-Hu-1 served as the reference genome (Accession NC_045512.2). SARS-CoV-2 variants were identified by uploading FASTA-files on freely accessible databases (http://cov-lineages.org/ ).
Sequencing was done with Illumina NextSeq® 500/550 using 149-bp paired-end reads with 10-bp indices (Illumina, California, USA). Obtained viral sequences were assembled using CLC Genomics Workbench v20.0.3 (Qiagen GmbH, North Rhine-Westphalia, Germany). SARS-CoV-2 isolate Wuhan-Hu-1 served as the reference genome (Accession NC_045512.2). SARS-CoV-2 variants were identified by uploading FASTA-files on freely accessible databases (
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