ABSTRACT
Pathogen genomics is a critical tool for public health surveillance, infection control, outbreak investigations as well as research. In order to make use of pathogen genomics data, they must be interpreted using contextual data (metadata). Contextual data include sample metadata, laboratory methods, patient demographics, clinical outcomes and epidemiological information. However, the variability in how contextual information is captured by different authorities and how it is encoded in different databases poses challenges for data interpretation, integration and their use/re-use. The DataHarmonizer is a template-driven spreadsheet application for harmonizing, validating and transforming genomics contextual data into submission-ready formats for public or private repositories. The tool's web browser-based JavaScript environment enables validation and its offline functionality and local installation increases data security. The DataHarmonizer was developed to address the data sharing needs that arose during the COVID-19 pandemic, and was used by members of the Canadian COVID Genomics Network (CanCOGeN) to harmonize SARS-CoV-2 contextual data for national surveillance and for public repository submission. In order to support coordination of international surveillance efforts, we have partnered with the Public Health Alliance for Genomic Epidemiology to also provide a template conforming to its SARS-CoV-2 contextual data specification for use worldwide. Templates are also being developed for One Health and foodborne pathogens. Overall, the DataHarmonizer tool improves the effectiveness and fidelity of contextual data capture as well as its subsequent usability. Harmonization of contextual information across authorities, platforms and systems globally improves interoperability and reusability of data for concerted public health and research initiatives to fight the current pandemic and future public health emergencies. While initially developed for the COVID-19 pandemic, its expansion to other data management applications and pathogens is already underway.
Subject(s)
COVID-19 , Humans , COVID-19/epidemiology , Pandemics , SARS-CoV-2/genetics , Canada , Genomics/methodsABSTRACT
PURPOSE: This retrospective analysis aims to examine the effectiveness of the current chest imaging guidelines regarding COVID-19 positive pediatric patients on our study group of patients aged 0 to 18. MATERIALS AND METHODS: We examined clinical and imaging data of 178 pediatric COVID-19 positive patients confirmed by PCR admitted to the Children's Hospital of Los Angeles between March 6, 2020 and June 23, 2020. RESULTS: Of 178 patients, only 46 (27%) patients underwent any form of chest imaging. Thirteen (28%) of 46 imaged patients had positive chest X-rays (CXR) or computed tomography (CT) chest findings, with 8 (62%) of the 13 patients suggesting pneumonia or multifocal pneumonia, 3 (23%) patients having acute respiratory distress syndrome, and 2 (15%) patients demonstrating left sided pleural effusions thought to be the result of ruptured appendicitis unrelated to their COVID-19 diagnosis. All but one patient had significant prior medical histories with an associated comorbid medical condition. Of the 46 imaged patients, 17 (37%) patients had a negative chest X-ray, and 15 (33%) patients had suggestive findings of viral etiology. 132 patients were not imaged. CONCLUSION: Our study population corroborated current chest imaging guidelines in pediatric patients. Chest imaging modalities such as CXR and CT should be reserved for patients who are severely symptomatic and/or possess prior comorbidities such as immunosuppression, diabetes, asthma, obesity, or where other differential etiologies must be entertained.
Subject(s)
COVID-19 , COVID-19 Testing , Child , Humans , Lung , Radiography, Thoracic , Retrospective Studies , SARS-CoV-2ABSTRACT
Background: The first case of coronavirus disease 2019 (COVID-19) in Alberta, Canada, was confirmed on March 5, 2020. Because the virus testing criteria had changed significantly over this time period, we wanted to ascertain whether previous cases of COVID-19 had been missed in the province. Methods: Our aim was to retrospectively evaluate specimens submitted for respiratory virus testing from December 1, 2019, through March 7, 2020, for undetected severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections before the first confirmed case. Results: Testing of 23,517 samples (representing 23,394 patients) identified 1 patient positive for SARS-CoV-2. This specimen was collected on February 24, 2020, from a patient with symptoms consistent with COVID-19 who had recently returned from the western United States. Phylogenetic analysis confirmed this viral isolate belonged to lineage B.1. The epidemiology of this case is consistent with those of other early cases before sustained community transmission, which included a travel history outside of Canada. Conclusion: This exercise provides support that local public health pandemic planning was satisfactory and timely.
Historique: Le premier cas de maladie à coronavirus 2019 (COVID-19) en Alberta, au Canada, a été confirmé le 15 mars 2020. Puisque les critères de dépistage ont beaucoup évolué pendant cette période, les chercheurs voulaient vérifier si des cas antérieurs de COVID-19 avaient été omis dans la province. Méthodologie: Les chercheurs ont procédé à l'évaluation rétrospective d'échantillons soumis en vue du dépistage d'un virus respiratoire entre le 1er décembre 2019 et le 7 mars 2020, afin de retracer les infections par le coronavirus 2 du syndrome respiratoire aigu sévère (SARS-CoV-2) non décelées avant le premier cas confirmé. Résultats: Le dépistage de 23 517 échantillons (représentant 23 394 patients) a fait ressortir un patient positif au SARS-CoV-2. Le prélèvement avait été effectué le 24 février 2020 chez un patient éprouvant des symptômes correspondant à la COVID-19 revenu récemment de l'ouest des États-Unis. L'analyse phylogénétique a confirmé que l'isolat viral appartenait à la lignée B.1. L'épidémiologie de ce cas est compatible avec celle des autres premiers cas précédant une transmission communautaire soutenue, qui incluait un voyage à l'extérieur du Canada. Conclusion: Cet exercice appuie la pertinence et la rapidité de la planification sanitaire locale de la pandémie.