Tracking the re-emergence and spread of measles virus in Brazil: a pilot study using nanopore whole genome sequencing

Paola Cristina Resende, from the Oswaldo Cruz Institute, FIOCRUZ, Brazil discusses how she conducted genomic surveillance using nanopore sequencing to investigate the spatial and temporal viral spread of measles (MeV) in brazil. Previous genotyping methods relied on a 450-nucleotide region responsible for the MeV nucleoprotein, which did identify three different genotypes recovered, however, provided ‘no phylogenetic signal to define lineages.

To increase linage resolution an RT-PCR amplicon workflow was developed to obtain the whole MeV genome and identified 22 different MeV genomes. Nanopore sequencing with epidemiological data detected the MeV responsible for the outbreak in 2018 had originated from neighbouring Venezuela and was able to track the spread of other genotypes through Brazil.

Paola: ‘In comparison to Sanger and other NGS strategies MeV nanopore genomic sequencing showed:
•Good performance
•Low cost
• Fast library prep'