Direct sequencing of measles virus complete genomes in the midst of a large-scale outbreak

Efrat Bucris, Victoria Indenbaum, Roberto Azar, Oran Erster, Eric Haas, Ella Mendelson, Neta S. Zuckerman

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Measles outbreaks escalated globally despite worldwide elimination efforts. Molecular epidemiological investigations utilizing partial measles virus (MeV) genomes are challenged by reduction in global genotypes and low evolutionary rates. Greater resolution was reached using MeV complete genomes, however time and costs limit the application to numerous samples. We developed an approach to unbiasedly sequence complete MeV genomes directly from patient urine samples. Samples were enriched for MeV using filtration or nucleases and the minimal number of sequence reads to allocate per sample based on its MeV content was assessed using in-silico reduction of sequencing depth. Application of limited-resource sequencing to treated MeV-positive samples demonstrated that 1–5 million sequences for samples with high/medium MeV quantities and 10–15 million sequences for samples with lower MeV quantities are sufficient to obtain >98% MeV genome coverage and over X50 average depth. This approach enables real-time high-resolution molecular epidemiological investigations of large-scale MeV outbreaks.

Original languageEnglish
Article numbere0255663
JournalPLoS ONE
Issue number9 September
StatePublished - Sep 2021
Externally publishedYes

Bibliographical note

Publisher Copyright:
Copyright: © 2021 Bucris et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


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