SARS-CoV-2 Genomic Surveillance via Automated Extraction

Automated nucleic acid extraction was performed as described previously (20 (link), 21 (link)) using the chemagic 360 (PerkinElmer) following the manufacturer’s protocol. Whole genome sequencing and analysis were performed as previously described (23 (link)).
For a subset of samples, 25 ng of RNA, previously extracted using QIAGEN’s Viral RNA mini kit, was processed following the Illumina RNA Prep with Enrichment (L) Tagmentation protocol with Illumina Respiratory Virus Oligo Panel for single-plex enrichment. Libraries were sequenced on the Illumina MiSeq (2 × 76 bp) or iSeq (2 × 151 bp) platform. FASTQ files were analyzed in Illumina’s BaseSpace using the DRAGEN Pathogen Detection application to generate consensus files. The pangolin web-based application, Phylogenetic Assignment of named Global Outbreak LINeages (PANGOLIN) (https://pangolin.cog-uk.io/) was used to identify the SARS-CoV2 lineages from these consensus sequences. Nextclade (https://clades.nextstrain.org/) was used for clade assignment, sequence quality check, and phylogenetic tree construction.

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Park H.S., Shapiro J.R., Sitaras I., Woldemeskel B.A., Garliss C.C., Dziedzic A., Sachithanandham J., Jedlicka A.E., Caputo C.A., Rousseau K.E., Thakar M., Suwanmanee S., Hauk P., Aliyu L., Majewska N.I., Koley S., Patel B., Broderick P., Mosnaim G., Heath S.L., Spivak E.S., Shenoy A., Bloch E.M., Gniadek T.J., Shoham S., Casadevall A., Hanley D., Cox A.L., Laeyendecker O., Betenbaugh M.J., Cramer S.M., Mostafa H.H., Pekosz A., Blankson J.N., Klein S.L., Tobian A.A., Sullivan D, & Gebo K.A. (2022). Adaptive immune responses in vaccinated patients with symptomatic SARS-CoV-2 Alpha infection. JCI Insight, 7(5), e155944.

Publication 2022

chemagic 360 Respiratory Virus Oligo Panel

Consensus sequences Nucleic acid Oligo Pangolin Pathogen Respiratory Sars Viral rna Virus

Corresponding Organization :

Other organizations : Johns Hopkins University, Johns Hopkins Medicine, Rensselaer Polytechnic Institute, The University of Texas Health Science Center at Houston, Danbury Hospital, NorthShore University HealthSystem, University of Alabama at Birmingham, University of Utah, MedStar Washington Hospital Center, National Institute of Allergy and Infectious Diseases

Top 5 similar protocols

Variable analysis

independent variables

Automated nucleic acid extraction protocol
Whole genome sequencing and analysis

dependent variables

SARS-CoV-2 lineages
SARS-CoV-2 clades

control variables

Manufacturer's protocol for chemagic 360 (PerkinElmer)
Previously described protocols for whole genome sequencing and analysis (23)

controls

Positive control: Not explicitly mentioned
Negative control: Not explicitly mentioned

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