One Health System Supporting Surveillance During COVID-19 Epidemic in Abruzzo Region, Southern Italy
13 Pages Posted: 5 Oct 2022
Abstract
The Istituti Zooprofilattici Sperimentali (IZSs) are public health institutes dealing with the aetiology and pathogenesis of infectious diseases of domestic and wild animals. During Coronavirus Disease 2019 epidemic, the Italian Ministry of Health appointed the IZSs to carry out diagnostic tests for the detection of SARS-CoV-2 in human samples, with the aim of supporting the National Health Care System by increasing the total capacity of the analysis laboratories. In particular, the Istituto Zooprofilattico Sperimentale of Abruzzo and Molise (IZS-Teramo) was involved in the diagnosis of SARS-CoV-2 through testing nasopharyngeal swabs by Real Time RT-PCR. Activities and infrastructures were reorganised and adapted to the new priorities, in a "One Health" framework, based on interdisciplinary, laboratory promptness, accreditation of the test for the detection of the RNA of SARS-CoV-2 in human samples, and management of confidentiality of sensitive data. The laboratory information system – SILAB – was implemented with a One Health module appropriate for managing of data of human origin, with tools for the automatic registration of information which allowed avoiding errors and improving the quality of the data. Over 590.000 human samples were tested during the 2020 and 2021 epidemic, and up to 4000 samples were daily tested. Over 88.0% of the test results were reported within 24 hours from the delivery and registration of the samples in SILAB. Moreover, the “National Reference Centre for Whole Genome Sequencing of microbial pathogens - database and bioinformatics analysis” – GENPAT – formally established at the IZS-Teramo, developed bioinformatics workflows and IT dashboard with ad hoc surveillance tools to support the metagenomics-based SARS-CoV-2 surveillance, providing molecular sequencing analysis to quickly intercept the variants circulating in the area. This manuscript describes the One Health system developed by the IZS-Teramo, by adapting and integrating both SILAB and GENPAT tools for supporting surveillance during COVID-19 epidemic in Abruzzo region, southern Italy.
Note:
Funding Information: This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.
Declaration of Interests: None.
Keywords: Bioinformatics analysis, COVID-19 surveillance, laboratory information system, metagenomics, One Health
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