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Oropouche virus cases identified in Ecuador using an optimised rRT-PCR informed by metagenomic sequencing

https://doi.org/10.1101/683953
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1016/j.meegid.2018.11.020openalex-snapshot
Oropouche orthobunyavirus: Genetic characterization of full-length genomes and development of molecular methods to discriminate natural reassortments
inferredcites →https://doi.org/10.1016/j.vaccine.2010.08.037openalex-snapshot
Hepatitis A virus seroprevalence by age and world region, 1990 and 2005
inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot
Basic Local Alignment Search Tool
inferredcites →https://doi.org/10.1038/nprot.2017.066openalex-snapshot
Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples
inferredcites →https://doi.org/10.1038/nrmicro3332openalex-snapshot
Orthobunyaviruses: recent genetic and structural insights
inferredcites →https://doi.org/10.1089/cmb.2012.0021openalex-snapshot
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/nar/gks540openalex-snapshot
RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics
inferredcites →https://doi.org/10.1101/gr.210641.116openalex-snapshot
Centrifuge: rapid and sensitive classification of metagenomic sequences
inferredcites →https://doi.org/10.1128/jcm.41.7.3299-3305.2003openalex-snapshot
Rapid Detection of Human Pathogenic Orthobunyaviruses
inferredcites →https://doi.org/10.1146/annurev.micro.51.1.151openalex-snapshot
RNA VIRUS MUTATIONS AND FITNESS FOR SURVIVAL
inferredcites →https://doi.org/10.1186/gb-2010-11-8-r86openalex-snapshot
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
inferredcites →https://doi.org/10.1186/s12862-019-1567-0openalex-snapshot
The ability of single genes vs full genomes to resolve time and space in outbreak analysis
inferredcites →https://doi.org/10.1371/journal.pntd.0001315openalex-snapshot
Iquitos Virus: A Novel Reassortant Orthobunyavirus Associated with Human Illness in Peru
inferredcites →https://doi.org/10.1371/journal.pntd.0004990openalex-snapshot
High Leptospira Diversity in Animals and Humans Complicates the Search for Common Reservoirs of Human Disease in Rural Ecuador
inferredcites →https://doi.org/10.1371/journal.pntd.0006014openalex-snapshot
Neutralizing antibodies for orthobunyaviruses in Pantanal, Brazil
inferredcites →https://doi.org/10.1371/journal.pone.0143081openalex-snapshot
Assessment of the Utility of Whole Genome Sequencing of Measles Virus in the Characterisation of Outbreaks
inferredcites →https://doi.org/10.1590/0074-02760160062openalex-snapshot
Multiplexed reverse transcription real-time polymerase chain reaction for simultaneous detection of Mayaro, Oropouche, and Oropouche-like viruses
inferredcites →https://doi.org/10.2807/1560-7917.es.2018.23.50.1800228openalex-snapshot
Assessment of metagenomic Nanopore and Illumina sequencing for recovering whole genome sequences of chikungunya and dengue viruses directly from clinical samples
inferredcites →https://doi.org/10.3201/eid1910.130137openalex-snapshot
Transition in the Cause of Fever from Malaria to Dengue, Northwestern Ecuador, 1990–2011
inferredcites →https://doi.org/10.3201/eid2405.171569openalex-snapshot
Isolation of Oropouche Virus from Febrile Patient, Ecuador
inferredcites →https://doi.org/10.3390/v10040175openalex-snapshot
Oropouche Fever: A Review
inferredcites →https://doi.org/10.4269/ajtmh.16-0323openalex-snapshot
Zika Virus and Chikungunya Virus CoInfections: A Series of Three Cases from a Single Center in Ecuador
inferredcites →https://doi.org/10.4269/ajtmh.16-0672openalex-snapshot
Oropouche Virus: Clinical, Epidemiological, and Molecular Aspects of a Neglected Orthobunyavirus
inferredcites →https://doi.org/10.4269/ajtmh.2012.11-0485openalex-snapshot
Identification of Oropouche Orthobunyavirus in the Cerebrospinal Fluid of Three Patients in the Amazonas, Brazil
inferredcites →https://doi.org/10.6084/m9.figshare.963153.v1openalex-snapshot
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1099/jgv.0.002027openalex-snapshot
Oropouche Virus: An Emerging Orthobunyavirus
inferred← citeshttps://doi.org/10.1128/jvi.01127-19openalex-snapshot
Evolutionary Dynamics of Oropouche Virus in South America
inferred← citeshttps://doi.org/10.11606/d.17.2020.tde-25082020-085916openalex-snapshot
Estudo da infecção do sistema nervoso central pelo vírus Oropouche em um modelo de fatias de cérebro humano adulto
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