2 research outputs found
Quantitative proteomic dataset from oro- and naso-pharyngeal swabs used for COVID-19 diagnosis: detection of viral proteins and host's biological processes altered by the infection
Since January 2020, the world is facing the COVID-19 pandemic caused by SARS-CoV-2. In a big effort to cope with this outbreak, two Uruguayan institutions, Institut Pasteur de Montevideo and Universidad de la RepĂșblica, have developed and implemented a diagnosis pipeline based on qRT-PCR using entirely local resources. In this context, we performed comparative quantitative proteomic analysis from oro- and naso-pharyngeal swabs used for diagnosis. Tryptic peptides obtained from five positive and five negative samples were analysed by nano-LC-MS/MS using a Q-Exactive Plus mass spectrometer. Data analysis was performed using PatternLab for Proteomics software. From all SARS-CoV-2 positive swabs we were able to detect peptides of the SARS-CoV-2 nucleoprotein that encapsulates and protect the RNA genome. Additionally, we detected an average of 1100 human proteins from each sample. The most abundant proteins exclusively detected in positive swabs were âGuanylate-binding protein 1â, âTapasinâ and âHLA class II histocompatibility antigen DR beta chainâ. The biological processes overrepresented in infected host cells were âSRP-dependent cotranslational protein targeting to membraneâ, ânuclear-transcribed mRNA catabolic process, nonsense-mediated decayâ, âviral transcriptionâ and âtranslational initiationâ. Data is available via ProteomeXchange with identifier PXD020394. We expect that this data can contribute to the future development of mass spectrometry based approaches for COVID-19 diagnosis. Also, we share this preliminary proteomic characterization concerning the host response to infection for its reuse in basic investigation
Real-Time genomic surveillance for SARS-CoV-2 variants of concern, Uruguay
We developed a genomic surveillance program for realtime monitoring of severe acute respiratory syndrome
coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) in Uruguay. We report on a PCR method for SARSCoV-
2 VOCs, the surveillance workflow, and multiple independent introductions and community transmission of
the SARS-CoV-2 P.1 VOC in Uruguay