Whole genome sequencing of in vitro propagated SARS-CoV-2 at the Karolinska Institutet BSL-3 Core Facility

SARS-CoV-2 RNA var. UK B117 210201 #1 Information

This dataset contains raw and processed sequencing data for SARS-CoV-2 strains obtained from the Public Health Agency of Sweden (Folkhälsomyndigheten). These include a UK reference sample (B.1.1.7: “SARS-CoV-2 RNA var. UK B117 210201”) and a Wuhan variant (B) that was sampled in Sweden during spring 2020 and in vitro propagated at the Karolinska Institutet BSL-3 core facility (see (1) for more details).

Methods

Libraries were constructed using EasySeq™ RC-PCR SARS CoV-2 Whole Genome Sequencing kit (Nimagen, SKU: RC-COV096) and sequenced on an Illumina NextSeq550. Raw data was extracted, and adapter trimmed using bcl2fastq v2.20.0.442 [--no-lane-splitting] then quality trimmed using fastp (2) v0.20.0 [default settings] and aligned against the SARS-CoV-2 Wuhan-Hu-1 reference sequence [ASM985889v3/GCA_009858895.3/MN908947.3] using bowtie2 (3) v2.4.1 [--very-sensitive -N 1]. Genotype likelihoods were calculated using bcftools (4) v1.10.2 [mpileup  -C 50 -d 1000 -E] and variants were called using bcftools (4) v1.10.2 [call -mv --ploidy 1]. Resulting SNPs were filtered based on quality and excluded if they were within 5 bp from indels using bcftools v1.10.2 [filter -g 5 -I ‘QUAL>30 %% TYPE=”snp”’]. Variant effects were predicted using the Ensembl VEP tool (5) v102.0 [--offline –symbol –hgvs –distance 0 -custom {blacklist},,vcf,exact,0,] and marked for problematic sites [{blacklist} = https://raw.githubusercontent.com/W-L/ProblematicSites_SARS-CoV2/master/problematic_sites_sarsCov2.vcf, (for more details, see: https://virological.org/t/issues-with-sars-cov-2-sequencing-data/473)]. Next, problematic sites were excluded, and consensus genome sequences were constructed per sample by inserting variants into the reference genome [bcftools consensus]. SARS-CoV-2 lineage was confirmed using Pangolin (6) v2.2.1 [lineages version 2021-02-06].

References

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