Oropouche virus cases identified in Ecuador using an optimised qrt-pcr informed by metagenomic sequencing

Emma L. Wise; Sully Márquez; Jack Mellors; Verónica Paz; Barry Atkinson; Bernardo Gutierrez; Sonia Zapata; Josefina Coloma; Oliver G. Pybus; Simon K. Jackson; Gabriel Trueba; Gyorgy Fejer; Christopher H. Logue; Steven Pullan

doi:10.1371/journal.pntd.0007897

Oropouche virus cases identified in Ecuador using an optimised qrt-pcr informed by metagenomic sequencing

Emma L. Wise, Sully Márquez, Jack Mellors, Verónica Paz, Barry Atkinson, Bernardo Gutierrez, Sonia Zapata, Josefina Coloma, Oliver G. Pybus, Simon K. Jackson, Gabriel Trueba, Gyorgy Fejer, Christopher H. Logue^*, Steven Pullan

^*Corresponding author for this work

Research & Technical Staff

Research output: Contribution to journal › Article › peer-review

13 Citations (Scopus)

22 Downloads (Pure)

Abstract

Oropouche virus (OROV) is responsible for outbreaks of Oropouche fever in parts of South America. We recently identified and isolated OROV from a febrile Ecuadorian patient, however, a previously published qRT-PCR assay did not detect OROV in the patient sample. A primer mismatch to the Ecuadorian OROV lineage was identified from metagenomic sequencing data. We report the optimisation of an qRT-PCR assay for the Ecuadorian OROV lineage, which subsequently identified a further five cases in a cohort of 196 febrile patients. We isolated OROV via cell culture and developed an algorithmically-designed primer set for whole-genome amplification of the virus. Metagenomic sequencing of the patient samples provided OROV genome coverage ranging from 68–99%. The additional cases formed a single phylogenetic cluster together with the initial case. OROV should be considered as a differential diagnosis for Ecuadorian patients with febrile illness to avoid mis-diagnosis with other circulating pathogens.

Original language	English
Article number	e0007897
Pages (from-to)	1-15
Number of pages	15
Journal	PLoS Neglected Tropical Diseases
Volume	14
Issue number	1
DOIs	https://doi.org/10.1371/journal.pntd.0007897
Publication status	Published - 21 Jan 2020

Bibliographical note

Funding Information: This work was funded by Public Health England as part of a PHE-funded PhD studentship awarded to ELW, SKJ, GF, CHL, and STP. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Open Access: 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.

Publisher Copyright: © 2020 Wise et al.

Citation: Wise EL, Ma´rquez S, Mellors J, Paz V, Atkinson B, Gutierrez B, et al. (2020) Oropouche virus cases identified in Ecuador using an optimised qRT-PCR informed by metagenomic sequencing. PLoS Negl Trop Dis 14(1): e0007897.

DOI: https://doi.org/10.1371/journal.pntd.0007897

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1371/journal.pntd.0007897Licence: CC BY

Wise2020OropoucheVirusCasesIdentifiedInEcuadorPLoSNeglTropDisFinal published version, 1.35 MBLicence: CC BY

Cite this

Wise, E. L., Márquez, S., Mellors, J., Paz, V., Atkinson, B., Gutierrez, B., Zapata, S., Coloma, J., Pybus, O. G., Jackson, S. K., Trueba, G., Fejer, G., Logue, C. H., & Pullan, S. (2020). Oropouche virus cases identified in Ecuador using an optimised qrt-pcr informed by metagenomic sequencing. PLoS Neglected Tropical Diseases, 14(1), 1-15. Article e0007897. https://doi.org/10.1371/journal.pntd.0007897

@article{4d45deb5f34f4f8daec813d374c5459e,

title = "Oropouche virus cases identified in Ecuador using an optimised qrt-pcr informed by metagenomic sequencing",

abstract = "Oropouche virus (OROV) is responsible for outbreaks of Oropouche fever in parts of South America. We recently identified and isolated OROV from a febrile Ecuadorian patient, however, a previously published qRT-PCR assay did not detect OROV in the patient sample. A primer mismatch to the Ecuadorian OROV lineage was identified from metagenomic sequencing data. We report the optimisation of an qRT-PCR assay for the Ecuadorian OROV lineage, which subsequently identified a further five cases in a cohort of 196 febrile patients. We isolated OROV via cell culture and developed an algorithmically-designed primer set for whole-genome amplification of the virus. Metagenomic sequencing of the patient samples provided OROV genome coverage ranging from 68–99%. The additional cases formed a single phylogenetic cluster together with the initial case. OROV should be considered as a differential diagnosis for Ecuadorian patients with febrile illness to avoid mis-diagnosis with other circulating pathogens.",

author = "Wise, {Emma L.} and Sully M{\'a}rquez and Jack Mellors and Ver{\'o}nica Paz and Barry Atkinson and Bernardo Gutierrez and Sonia Zapata and Josefina Coloma and Pybus, {Oliver G.} and Jackson, {Simon K.} and Gabriel Trueba and Gyorgy Fejer and Logue, {Christopher H.} and Steven Pullan",

note = "Funding Information: This work was funded by Public Health England as part of a PHE-funded PhD studentship awarded to ELW, SKJ, GF, CHL, and STP. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Open Access: 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. Publisher Copyright: {\textcopyright} 2020 Wise et al. Citation: Wise EL, Ma´rquez S, Mellors J, Paz V, Atkinson B, Gutierrez B, et al. (2020) Oropouche virus cases identified in Ecuador using an optimised qRT-PCR informed by metagenomic sequencing. PLoS Negl Trop Dis 14(1): e0007897. DOI: https://doi.org/10.1371/journal.pntd.0007897",

year = "2020",

month = jan,

day = "21",

doi = "10.1371/journal.pntd.0007897",

language = "English",

volume = "14",

pages = "1--15",

journal = "PLoS Neglected Tropical Diseases",

issn = "1935-2727",

publisher = "Public Library of Science",

number = "1",

}

Wise, EL, Márquez, S, Mellors, J, Paz, V, Atkinson, B, Gutierrez, B, Zapata, S, Coloma, J, Pybus, OG, Jackson, SK, Trueba, G, Fejer, G, Logue, CH & Pullan, S 2020, 'Oropouche virus cases identified in Ecuador using an optimised qrt-pcr informed by metagenomic sequencing', PLoS Neglected Tropical Diseases, vol. 14, no. 1, e0007897, pp. 1-15. https://doi.org/10.1371/journal.pntd.0007897

TY - JOUR

T1 - Oropouche virus cases identified in Ecuador using an optimised qrt-pcr informed by metagenomic sequencing

AU - Wise, Emma L.

AU - Márquez, Sully

AU - Mellors, Jack

AU - Paz, Verónica

AU - Atkinson, Barry

AU - Gutierrez, Bernardo

AU - Zapata, Sonia

AU - Coloma, Josefina

AU - Pybus, Oliver G.

AU - Jackson, Simon K.

AU - Trueba, Gabriel

AU - Fejer, Gyorgy

AU - Logue, Christopher H.

AU - Pullan, Steven

N1 - Funding Information: This work was funded by Public Health England as part of a PHE-funded PhD studentship awarded to ELW, SKJ, GF, CHL, and STP. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Open Access: 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. Publisher Copyright: © 2020 Wise et al. Citation: Wise EL, Ma´rquez S, Mellors J, Paz V, Atkinson B, Gutierrez B, et al. (2020) Oropouche virus cases identified in Ecuador using an optimised qRT-PCR informed by metagenomic sequencing. PLoS Negl Trop Dis 14(1): e0007897. DOI: https://doi.org/10.1371/journal.pntd.0007897

PY - 2020/1/21

Y1 - 2020/1/21

N2 - Oropouche virus (OROV) is responsible for outbreaks of Oropouche fever in parts of South America. We recently identified and isolated OROV from a febrile Ecuadorian patient, however, a previously published qRT-PCR assay did not detect OROV in the patient sample. A primer mismatch to the Ecuadorian OROV lineage was identified from metagenomic sequencing data. We report the optimisation of an qRT-PCR assay for the Ecuadorian OROV lineage, which subsequently identified a further five cases in a cohort of 196 febrile patients. We isolated OROV via cell culture and developed an algorithmically-designed primer set for whole-genome amplification of the virus. Metagenomic sequencing of the patient samples provided OROV genome coverage ranging from 68–99%. The additional cases formed a single phylogenetic cluster together with the initial case. OROV should be considered as a differential diagnosis for Ecuadorian patients with febrile illness to avoid mis-diagnosis with other circulating pathogens.

AB - Oropouche virus (OROV) is responsible for outbreaks of Oropouche fever in parts of South America. We recently identified and isolated OROV from a febrile Ecuadorian patient, however, a previously published qRT-PCR assay did not detect OROV in the patient sample. A primer mismatch to the Ecuadorian OROV lineage was identified from metagenomic sequencing data. We report the optimisation of an qRT-PCR assay for the Ecuadorian OROV lineage, which subsequently identified a further five cases in a cohort of 196 febrile patients. We isolated OROV via cell culture and developed an algorithmically-designed primer set for whole-genome amplification of the virus. Metagenomic sequencing of the patient samples provided OROV genome coverage ranging from 68–99%. The additional cases formed a single phylogenetic cluster together with the initial case. OROV should be considered as a differential diagnosis for Ecuadorian patients with febrile illness to avoid mis-diagnosis with other circulating pathogens.

UR - http://www.scopus.com/inward/record.url?scp=85078867391&partnerID=8YFLogxK

U2 - 10.1371/journal.pntd.0007897

DO - 10.1371/journal.pntd.0007897

M3 - Article

C2 - 31961856

AN - SCOPUS:85078867391

SN - 1935-2727

VL - 14

SP - 1

EP - 15

JO - PLoS Neglected Tropical Diseases

JF - PLoS Neglected Tropical Diseases

IS - 1

M1 - e0007897

ER -

Oropouche virus cases identified in Ecuador using an optimised qrt-pcr informed by metagenomic sequencing

Abstract

Bibliographical note

UN SDGs

Access to Document

Other files and links

Fingerprint

Cite this