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Respiratory Syncytial Virus (RSV) Sequencing

RSV is a leading cause of significant respiratory infections that disproportionately impact infants, young children, and the elderly. Recently, the development of vaccines to protect against RSV infections has changed the landscape of seasonal respiratory disease risk and response. Sequencing of the RSV A and/or RSV B genomes can support public health monitoring of disease spread, the development of treatments, or molecular diagnostic tools. The NEBNext RSV Primer Module (NEB #E9642) has been demonstrated to effectively detect strain-specific sequence information from clinical samples (i.e., nasopharyngeal swab) in collaboration with an academic laboratory.

Figure 1: NEBNext® RSV Primer Module generates high RSV genome coverage from clinical samples

The NEBNext® RSV Primer Module and LunaScript® Multiplex One-Step RT-PCR Kit (NEB #E1555) were used to generate amplicons from IRBapproved clinical (nasopharyngeal swab) samples. Amplicon sequencing libraries were made for the Oxford Nanopore Technologies® platform (MinION® Flow Cell R10.4.1; high-accuracy basecalling). Each sample initially tested positive for RSV via the BioFire® assay; Ct values shown are from subsequent qRT-PCR assays. The qRT-PCR, targeted whole-genome RT-PCR, library prep, and sequencing of an equal volume library pool of these clinical samples was performed by collaborators at the Applied Physics Laboratory at Johns Hopkins University. Sequencing reads were aligned to a composite reference containing Human (T2T), RSV A (ATCC® VR-1540, and RSV B (ATCC VR-1580) genomes, with MiniMap2. A. Percent of reads that aligned to the human, RSV A, or RSV B reference for each sample; all samples were identified as RSV A. B. Integrative Genome Viewer plot of RSV A genome coverage (0–1,000 log scale) for each sample.

NEB’s Primer Monitor Tool gathers RSV sequence data from publicly available databases for easy access to updated variant burden in primer regions. The tool is regularly updated to support the infectious disease community. The tool also aggregates data on SARS-CoV-2 variants.

For more information on how NEBNext supports Infectious Disease research and development, visit Infectious Diseases & ARTIC Sequencing.

 

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NEBNext® RSV Primer Module

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