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

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, ho...

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Autores principales:	Efrat Bucris, Victoria Indenbaum, Roberto Azar, Oran Erster, Eric Haas, Ella Mendelson, Neta S Zuckerman
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/b2c04f661e8f4840a4c7d0b09193074d
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spelling	oai:doaj.org-article:b2c04f661e8f4840a4c7d0b09193074d2021-12-02T20:08:21ZDirect sequencing of measles virus complete genomes in the midst of a large-scale outbreak.1932-620310.1371/journal.pone.0255663https://doaj.org/article/b2c04f661e8f4840a4c7d0b09193074d2021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0255663https://doaj.org/toc/1932-6203Measles 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.Efrat BucrisVictoria IndenbaumRoberto AzarOran ErsterEric HaasElla MendelsonNeta S ZuckermanPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 9, p e0255663 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Efrat Bucris Victoria Indenbaum Roberto Azar Oran Erster Eric Haas Ella Mendelson Neta S Zuckerman Direct sequencing of measles virus complete genomes in the midst of a large-scale outbreak.
description	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.
format	article
author	Efrat Bucris Victoria Indenbaum Roberto Azar Oran Erster Eric Haas Ella Mendelson Neta S Zuckerman
author_facet	Efrat Bucris Victoria Indenbaum Roberto Azar Oran Erster Eric Haas Ella Mendelson Neta S Zuckerman
author_sort	Efrat Bucris
title	Direct sequencing of measles virus complete genomes in the midst of a large-scale outbreak.
title_short	Direct sequencing of measles virus complete genomes in the midst of a large-scale outbreak.
title_full	Direct sequencing of measles virus complete genomes in the midst of a large-scale outbreak.
title_fullStr	Direct sequencing of measles virus complete genomes in the midst of a large-scale outbreak.
title_full_unstemmed	Direct sequencing of measles virus complete genomes in the midst of a large-scale outbreak.
title_sort	direct sequencing of measles virus complete genomes in the midst of a large-scale outbreak.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/b2c04f661e8f4840a4c7d0b09193074d
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Direct sequencing of measles virus complete genomes in the midst of a large-scale outbreak.

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