Next - generation sequencing whole genome respiratory syncytial virus in North Viet Nam, 2017 – 2020

Abstract

Human Respiratory Syncytial Virus (RSV) infections pose a significant risk to both children and adults worldwide. 95% of children have been affected by RSV at least one time before 2 years old. This study aims to develop and apply a high-throughput sequencing strategy to sequence Vietnamese RSV whole genomes directly from clinical specimens in North Vietnam, 2017 - 2020. 38 clinical RSV-A  and 43 clinical RSV-B samples were used to extract RNA,  then converted to cDNA and PCR with specific primer sets. Next-generation sequencer with Illumina platform and analysis data by CLC Genomics Workbench. In silico analysis and laboratory testing revealed that the primer sets worked well and successfully amplified the whole genome of RSV. The nucleotide positions of gene start and gene end, as well as the substitutions in amino acid in each gene were determined. This protocol is simple to set up, easily scalable in sample preparation, and suitable for analysis. This reseach is the first public method of whole genome RSV sequencing and the most updated data of molecular RSV genome after 2015 in Viet Nam.