RSV whole genome sequencing using ONT v1

Respiratory Syncytial Virus (RSV) is a leading cause of hospitalization due to acute lower respiratory infection in infants and young children. Monoclonal antibodies palivizumab is available option for treating RSV limited to select populations in high-resource settings. There is no vaccine to prevent RSV to the moment. Fortunately, several vaccine candidates are now in the human testing phase targeting young children, older adults and pregnant women, and an effective safe vaccine is likely to be available in the near future. For vaccine and therapy development RSV surveillance is essential. Using whole-genome sequencing data helps ensure the vaccine has the most up-to-date coverage and more-effective global reach. Through genomic surveillance we can track the spread of variants, monitor changes to the genetic code of the virus. Finally, this data is used to better understand how virus might impact public health. Here we provide the protocol for genome sequencing of RSV A using Oxford Nanopore Technology platform. The four overlapping genome fragments together comprise of the full RSV genome encompassing all viral genes, yet lacking the far 3′ and 5′ genome termini.