Oropouche virus cases identified in Ecuador using an optimised qRT-PCR informed by metagenomic sequencing
dc.contributor.author | Wise, EL | |
dc.contributor.author | Márquez, S | |
dc.contributor.author | Mellors, J | |
dc.contributor.author | Paz, V | |
dc.contributor.author | Atkinson, B | |
dc.contributor.author | Gutierrez, B | |
dc.contributor.author | Zapata, S | |
dc.contributor.author | Coloma, J | |
dc.contributor.author | Pybus, OG | |
dc.contributor.author | Jackson, SK | |
dc.contributor.author | Trueba, G | |
dc.contributor.author | Fejer, Gyorgy | |
dc.contributor.author | Logue, CH | |
dc.contributor.author | Pullan, ST | |
dc.date.accessioned | 2020-10-09T21:58:03Z | |
dc.date.issued | 2020-01-21 | |
dc.identifier.issn | 1935-2735 | |
dc.identifier.issn | 1935-2735 | |
dc.identifier.other | ARTN e0007897 | |
dc.identifier.uri | http://hdl.handle.net/10026.1/16499 | |
dc.description.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. | |
dc.format.extent | e0007897-e0007897 | |
dc.format.medium | Electronic-eCollection | |
dc.language | en | |
dc.language.iso | en | |
dc.publisher | Public Library of Science (PLoS) | |
dc.subject | Bunyaviridae Infections | |
dc.subject | Cohort Studies | |
dc.subject | Ecuador | |
dc.subject | Genome, Viral | |
dc.subject | Humans | |
dc.subject | Metagenome | |
dc.subject | Orthobunyavirus | |
dc.subject | Phylogeny | |
dc.subject | RNA, Viral | |
dc.subject | Reverse Transcriptase Polymerase Chain Reaction | |
dc.title | Oropouche virus cases identified in Ecuador using an optimised qRT-PCR informed by metagenomic sequencing | |
dc.type | journal-article | |
dc.type | Journal Article | |
dc.type | Research Support, Non-U.S. Gov't | |
dc.type | Validation Study | |
plymouth.author-url | https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000548903800017&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=11bb513d99f797142bcfeffcc58ea008 | |
plymouth.issue | 1 | |
plymouth.volume | 14 | |
plymouth.publication-status | Published online | |
plymouth.journal | PLOS Neglected Tropical Diseases | |
dc.identifier.doi | 10.1371/journal.pntd.0007897 | |
plymouth.organisational-group | /Plymouth | |
plymouth.organisational-group | /Plymouth/Faculty of Health | |
plymouth.organisational-group | /Plymouth/Faculty of Health/School of Biomedical Sciences | |
plymouth.organisational-group | /Plymouth/REF 2021 Researchers by UoA | |
plymouth.organisational-group | /Plymouth/REF 2021 Researchers by UoA/UoA01 Clinical Medicine | |
plymouth.organisational-group | /Plymouth/Research Groups | |
plymouth.organisational-group | /Plymouth/Research Groups/Institute of Translational and Stratified Medicine (ITSMED) | |
plymouth.organisational-group | /Plymouth/Research Groups/Institute of Translational and Stratified Medicine (ITSMED)/CBR | |
plymouth.organisational-group | /Plymouth/Users by role | |
plymouth.organisational-group | /Plymouth/Users by role/Academics | |
plymouth.organisational-group | /Plymouth/Users by role/Researchers in ResearchFish submission | |
dc.publisher.place | United States | |
dcterms.dateAccepted | 2019-10-31 | |
dc.rights.embargodate | 2020-10-14 | |
dc.identifier.eissn | 1935-2735 | |
dc.rights.embargoperiod | Not known | |
rioxxterms.versionofrecord | 10.1371/journal.pntd.0007897 | |
rioxxterms.licenseref.uri | http://www.rioxx.net/licenses/all-rights-reserved | |
rioxxterms.licenseref.startdate | 2020-01-21 | |
rioxxterms.type | Journal Article/Review |