Optimisation of methodology for whole genome sequencing of Measles Virus directly from patient specimens

•Here we describe a probe enrichment method that allows whole viral genome sequences of measles to be performed directly on clinical samples, without the use of laborious methods.•This method was tested on a set of over 200 samples and was shown to have approximately 70-75% success rate, where succe...

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Veröffentlicht in:Journal of virological methods 2022-01, Vol.299, p.114348-114348, Article 114348
Hauptverfasser: Schulz, Helene, Hiebert, Joanne, Frost, Jasmine, McLachlan, Elizabeth, Severini, Alberto
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Sprache:eng
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Zusammenfassung:•Here we describe a probe enrichment method that allows whole viral genome sequences of measles to be performed directly on clinical samples, without the use of laborious methods.•This method was tested on a set of over 200 samples and was shown to have approximately 70-75% success rate, where successful samples were defined at those with full genomes with at least 10x coverage.•This method will be an asset in the molecular epidemiology of measles outbreaks in near elimination settings. In an era of decreasing genetic diversity of Measles Virus (MeV), effective surveillance requires a higher-resolution genotyping method or whole genome sequencing (WGS) to document elimination. Through optimization of MeV WGS protocol, we developed a MeV-specific probe enrichment method that allows next generation sequencing from clinical specimens. With the probe enrichment method, 70% of specimens can be sequenced at a read depth of greater than 10 reads with minimal off-target sequences.
ISSN:0166-0934
1879-0984
DOI:10.1016/j.jviromet.2021.114348