One health system supporting surveillance during COVID-19 epidemic in Abruzzo region, southern Italy

Alessio Di Lorenzo; Iolanda Mangone; Patrizia Colangeli; Daniela Cioci; Valentina Curini; Giacomo Vincifori; Maria Teresa Mercante; Adriano Di Pasquale; Simona Iannetti

doi:10.1016/j.onehlt.2022.100471

One health system supporting surveillance during COVID-19 epidemic in Abruzzo region, southern Italy

One Health. 2023 Jun:16:100471. doi: 10.1016/j.onehlt.2022.100471. Epub 2022 Dec 7.

Authors

Alessio Di Lorenzo¹, Iolanda Mangone¹, Patrizia Colangeli¹, Daniela Cioci¹, Valentina Curini¹, Giacomo Vincifori¹, Maria Teresa Mercante¹, Adriano Di Pasquale¹, Simona Iannetti¹

Affiliation

¹ Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", Campo Boario, 64100 Teramo, Abruzzo, Italy.

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. In particular, the IZS 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 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 for managing data of human origin, with tools for the automatic registration of information improving the quality of the data. 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 adapting and integrating both SILAB and GENPAT tools for supporting surveillance during COVID-19 epidemic in the Abruzzo region, southern Italy. The developed dashboard permits the health authorities to observe the SARS-CoV-2 spread in the region, and by combining spatio-temporal information with metagenomics provides early evidence for the identification of emerging space-time clusters of variants at the municipality level. The implementation of the One Health module was designed to be easily modelled and adapted for the management of other diseases and future hypothetical events of pandemic nature.

Keywords: Bioinformatics analysis; COVID-19 surveillance; GIS; Laboratory information system; Metagenomics; One health.