Does Long-Read Sequencing Technology Produce Superior Viral Genome Assemblies?

ATCC provides a growing portfolio of clinically relevant viral strains that are used in a variety of research areas like drug discovery and therapeutic development. While the genomes for many of these viruses are available in public databases, we have shown that the referenced genomes published by third parties are often error prone, incomplete, or generated using a variety of methods, which makes the downstream use of the data challenging. To address this problem, we developed reproducible next-generation sequencing and genome assembly workflows to produce viral assemblies for over three hundred viruses within our diverse collection. Until recently, we produced viral genome assemblies using only short-read sequencing technology. Here, we set out to determine if we could produce higher quality assemblies using long-read sequencing technology. To identify the optimal platform required for producing complete and accurate viral genome assemblies, we used a standardized workflow to extract nucleic acids from twenty-seven unique viruses from the Papillomaviridae, Polyomaviridae, Orthoherpesviridae, Adenoviridae, and Poxviridae families. We then sequenced the material on both the Oxford Nanopore Technologies^® (ONT) and Illumina^® platforms. Next, we produced individual de novo assemblies from the ONT^® and Illumina^® instruments as well as hybrid de novo assemblies using data from both platforms. All three assembly approaches were compared for completeness, depth, and accuracy to determine if one platform, the other, or both produced the optimal viral genome. Moving forward, ATCC will produce and publish genomes for the viruses maintained in our collection. Only the genomes that pass all quality control standards are published to the ATCC Genome Portal (https://genomes.atcc.org). This platform allows users to interactively browse and search through indexed genomic data and metadata for a growing collection of over 4,000 ATCC microbial reference materials including viruses, bacteria, protists, and fungi.