Tiled-ClickSeq for targeted sequencing of complete coronavirus genomes with simultaneous capture of RNA recombination and minority variants

Author(s):Show less -

Jaworski, Elizabeth ^{[1, 2]} ; Langsjoen, Rose M. ^[1] ; Mitchell, Brooke ^{[3, 4]} ; Judy, Barbara ^[5] ; Newman, Patrick ^[5] ; Plante, Jessica A. ^{[6, 7, 4]} ; Plante, Kenneth S. ^{[6, 7, 4]} ; Miller, Aaron L. ^[5] ; Zhou, Yiyang ^[1] ; Swetnam, Daniele ^[1] ; Sotcheff, Stephanea ^[1] ; Morris, Victoria ^[1] ; Saada, Nehad ^{[3, 4]} ; Machado, Rafael R. G. ^{[3, 4]} ; McConnell, Allan ^{[3, 4]} ; Widen, Steven G. ^{[1, 8]} ; Thompson, Jill ^[8] ; Dong, Jianli ^{[7, 5]} ; Ren, Ping ^[3] ; Pyles, Rick B. ^[5] ; Ksiazek, Thomas G. ^{[6, 4]} ; Menachery, Vineet D. ^{[7, 3, 4]} ; Weaver, Scott C. ^{[7, 3, 4]} ; Routh, Andrew L. ^{[7, 1, 9]}

Affiliation

^[1] Univ Texas Med Branch, Dept Biochem & Mol Biol, Galveston, TX 77555 - USA

^[2] ClickSeq Technol LLC, Galveston, TX - USA

^[3] Univ Texas Med Branch, Dept Microbiol & Immunol, Galveston, TX 77555 - USA

^[4] Univ Texas Med Branch, World Reference Ctr Emerging Viruses & Arboviruse, Galveston, TX 77555 - USA

^[5] Univ Texas Med Branch, Dept Pediat, Galveston, TX 77555 - USA

^[6] Univ Texas Med Branch, Dept Pathol, Galveston, TX 77555 - USA

^[7] Univ Texas Med Branch, Inst Human Infect & Immun, Galveston, TX 77555 - USA

^[8] Univ Texas Med Branch, Next Generat Sequencing Core, Galveston, TX 77555 - USA

^[9] Univ Texas Med Branch, Sealy Ctr Struct Biol & Mol Biophys, Galveston, TX 77555 - USA

• Document type: Journal article
• Source: eLIFE; v. 10, SEP 28 2021.
• Web of Science Citations: 2

Abstract

High-throughput genomics of SARS-CoV-2 is essential to characterize virus evolution and to identify adaptations that affect pathogenicity or transmission. While single-nucleotide variations (SNVs) are commonly considered as driving virus adaption, RNA recombination events that delete or insert nucleic acid sequences are also critical. Whole genome targeting sequencing of SARS-CoV-2 is typically achieved using pairs of primers to generate cDNA amplicons suitable for next-generation sequencing (NGS). However, paired-primer approaches impose constraints on where primers can be designed, how many amplicons are synthesized and requires multiple PCR reactions with non-overlapping primer pools. This imparts sensitivity to underlying SNVs and fails to resolve RNA recombination junctions that are not flanked by primer pairs. To address these limitations, we have designed an approach called `Tiled-ClickSeq', which uses hundreds of tiled-primers spaced evenly along the virus genome in a single reverse-transcription reaction. The other end of the cDNA amplicon is generated by azido-nucleotides that stochastically terminate cDNA synthesis, removing the need for a paired-primer. A sequencing adaptor containing a Unique Molecular Identifier (UMI) is appended to the cDNA fragment using click-chemistry and a PCR reaction generates a final NGS library. Tiled-ClickSeq provides complete genome coverage, including the 5'UTR, at high depth and specificity to the virus on both Illumina and Nanopore NGS platforms. Here, we analyze multiple SARS-CoV-2 isolates and clinical samples to simultaneously characterize minority variants, sub-genomic mRNAs (sgmRNAs), structural variants (SVs) and D-RNAs. Tiled-ClickSeq therefore provides a convenient and robust platform for SARS-CoV-2 genomics that captures the full range of RNA species in a single, simple assay. (AU)

• FAPESP's process: 19/27803-2 - Immune-mediated mayaro virus protection from wild-type chikungunya virus infection
• Grantee: Rafael Rahal Guaragna Machado
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate (Direct)