SARS-CoV-2 whole-genome sequencing was performed by using QIAseq DIRECT SARS-CoV-2 Kit (QIAGEN). The quality of paired-end reads obtained from MiSeq sequencing was analyzed by using Qiagen CLC Genomics Workbench 22.0.1 and the Identify ARTIC V3 SARS-CoV-2 Low Frequency and Shared Variants (Illumina) workflow was used in genetic variant analyses. Nucleotide sequences were aligned using MAFFT v7.471, and the mutations were analyzed using nextclade (https://clades.nextstrain.org ). Pan-viral target hybridization enrichment sequencing was performed by using RNA Prep with Enrichment (L) Tagmentation Kit (Illumina) and Comprehensive Viral Research Panel (Twist Biosciences).
Comprehensive viral research panel
Manufactured by Twist Bioscience
Sourced in United States
The Comprehensive Viral Research Panel is a laboratory equipment designed to detect and analyze a wide range of viruses. It provides a comprehensive screening tool for researchers studying viral infections and diseases.
Automatically generated - may contain errors
2 protocols using comprehensive viral research panel
1
SARS-CoV-2 Whole Genome Sequencing
2
Whole Genome Sequencing of Orthonairovirus
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For whole genome sequencing of the novel Orthonairovirus, we selected the tick and 27 shrew kidney samples from different sampling occasions and/or sites and with the highest viral RNA copy number. An enriched NGS library was prepared using the Comprehensive Viral Research Panel (Twist Bioscience, San Francisco, USA) coupled with a custom probe set, including oligos designed using the novel Orthonairovirus genome from the metagenomic dataset. The Twist EF library prep kit (Twist Bioscience, San Francisco, USA) was used to prepare an Illumina compatible NGS library (see Supplementary methods) that was sequenced as above with 150 bp paired-end reads. De novo assembly was conducted using SPAdes v3 [27 (link)], and the resulting contigs were classified by DIAMOND and MEGAN6 as described above.
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