SARS-CoV-2 surveillance in Italy through phylogenomic inferences based on Hamming distances derived from pan-SNPs, -MNPs and -InDels

Background Faced with the ongoing global pandemic of coronavirus disease, the ‘National Reference Centre for Whole Genome Sequencing of microbial pathogens: database and bioinformatic analysis’ (GENPAT) formally established at the ‘Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise’ (IZSAM) in Teramo (Italy) is in charge of the SARS-CoV-2 surveillance at the genomic scale. In a context of SARS-CoV-2 surveillance requiring correct and fast assessment of epidemiological clusters from substantial amount of samples, the present study proposes an analytical workflow for identifying accurately the PANGO lineages of SARS-CoV-2 samples and building of discriminant minimum spanning trees (MST) bypassing the usual time consuming phylogenomic inferences based on multiple sequence alignment (MSA) and substitution model. Results GENPAT constituted two collections of SARS-CoV-2 samples. The first collection consisted of SARS-CoV-2 positive swabs collected by IZSAM from the Abruzzo region (Italy), then sequenced by next generation sequencing (NGS) and analyzed in GENPAT (n = 1592), while the second collection included samples from several Italian provinces and retrieved from the reference Global Initiative on Sharing All Influenza Data (GISAID) (n = 17,201). The main results of the present work showed that (i) GENPAT and GISAID detected the same PANGO lineages, (ii) the PANGO lineages B.1.177 (i.e. historical in Italy) and B.1.1.7 (i.e. ‘UK variant’) are major concerns today in several Italian provinces, and the new MST-based method (iii) clusters most of the PANGO lineages together, (iv) with a higher dicriminatory power than PANGO lineages, (v) and faster that the usual phylogenomic methods based on MSA and substitution model. Conclusions The genome sequencing efforts of Italian provinces, combined with a structured national system of NGS data management, provided support for surveillance SARS-CoV-2 in Italy. We propose to build phylogenomic trees of SARS-CoV-2 variants through an accurate, discriminant and fast MST-based method avoiding the typical time consuming steps related to MSA and substitution model-based phylogenomic inference.

Spatio-Temporal Spread Pattern of COVID-19 in Italy

This paper investigates the spatio-temporal spread pattern of COVID-19 in Italy, during the first wave of infections, from February to October 2020. Disease mappings of the virus infections by using the Besag–York–Mollié model and some spatio-temporal extensions are provided. This modeling framework, which includes a temporal component, allows the studying of the time evolution of the spread pattern among the 107 Italian provinces. The focus is on the effect of citizens’ mobility patterns, represented here by the three distinct phases of the Italian virus first wave, identified by the Italian government, also characterized by the lockdown period. Results show the effectiveness of the lockdown action and an inhomogeneous spatial trend that characterizes the virus spread during the first wave. Furthermore, the results suggest that the temporal evolution of each province’s cases is independent of the temporal evolution of the other ones, meaning that the contagions and temporal trend may be caused by some province-specific aspects rather than by the subjects’ spatial movements.

Assessing the impact of long-term exposure to nine outdoor air pollutants on spatial spread of Covid-19: evidence from 107 Italian provinces

The coronavirus (COVID-19) pandemic has dramatically changed every aspect of people’s lives around the world over the past year and a half. Although the global vaccination campaign is progressing worldwide, new variants of COVID-19 have emerged, driving many countries into a fourth wave of COVID-19 contagion. This paper investigates the air quality in 107 Italian provinces in the period 2014–2019 and the association between long-term exposure to nine outdoor air pollutants and the prevalence of COVID-19 in the same areas. The methods used were negative binomial (NB) regressions, ordinary least squares (OLS) models, and spatial autoregressive models with autoregressive disturbances (SARAR). The air pollutants examined were common air pollutants (NO2, O3, PM2.5, PM10), polycyclic aromatic hydrocarbons (PAHs) (benzene and BaP), and heavy metals (As, Cd, and Ni). The results showed that i) common air pollutants were generally highly and positively correlated with density of large firms, energy and gas consumption, public transport, and the livestock sector; and ii) long-term exposure to NO2, PM2.5, PM10, benzene, BaP, and Cd was positively and significantly correlated with the spread of COVID-19, even after controlling for cofactors and spatial effects. This outcome seems of interest and relevance because PAHs and heavy metals have not been considered at all in recent literature. It also seems to suggest the need for a national strategy to drive down air pollutant concentrations in order to cope better with possible future pandemics.

Money laundering, food activities and mafia: evidences from the Italian provinces

Purpose According to the INTERPOL definition, money laundering is: “any act or attempted act to conceal or disguise the identity of illegally obtained proceeds so that they appear to have originated from legitimate sources”. Along this line, the purpose of this paper is to investigate the link amongst money laundering, mafia and food activities, in the Italian provinces. Design/methodology/approach By using annual data over the period 2010 to 2018, the author estimates balanced panel data using the instrumental variables approach. The analysis includes both fixed and random effects, as well as robustness checks. Findings The main findings of this paper reveal that, in most Italian provinces, money launderers are deterred by the probability of being identified. In particular, the deterrent action of police and investigative forces seems to be very effective. Moreover, the results of the empirical analysis show that mafia-type organisations and food activities are positively correlated with money laundering. Originality/value This paper aims to provide a specific study on the link between apparently legal activities (food and beverage) and money laundering; a link that has so far been analysed mainly on a theoretical level. Moreover, it provides several insights in terms of policy implications.

Conclusion

The ivory diptych of Rufius Probianus (Berlin, Staatsbibliothek, Ms. theol. lat. fol. 323) celebrates his installation as vicarius urbis Romae, the position of chief administrator of the southern Italian provinces. It can be dated to around AD 400 (with scholarly suggestions ranging from 396 to 416),...

Sexual violence: 10 years of case studies in a hospital in Northern Italy

Background: In the past twenty years, the fight against sexual violence has become a common goal of the entire European Union, due to a greater socio-cultural awareness of the population and the need to create guidelines for common action. Italian Law no. 66 of February 15, 1996 regarding the “Rules against sexual violence” which, with the appropriate amendments, is still in force today, defines 3 types of sexual offenses through the articles 609 of the Penal Code. Design and Methods: This study analyzes the cases relating to one of the hospitals in Northern Italy, during the decade January 2010 - December 2019, relating to suspected/reported cases of sexual violence, group sexual violence and sexual acts with minors. This study was carried out by acquiring information relating to subjects who had been victims of a sexual crime through the analysis of the consultations drawn up by specialist medical staff in the submentioned hospital. These consultations are defined by specific medical protocols that must be activated every time a victim of a suspected sexual offense comes into the Emergency Room (ER). The data were processed with descriptive analyzes, the qualitative variables were synthesized with absolute and percentage frequencies, while the quantitative variables with mean and interpolation of the data, to identify a trend line. In order to hypothesize the possible future trend of the phenomenon, data were collected relating to the type of crime according to the Penal Code, gender and age of the victim. This article also outlines future directions for improving research. Results: Our data show that females, of any age, are the most affected in all sexual crimes, often share home with their aggressor, usually a man, and in most cases, they come to the medical observation without any lesion on their body. Conclusions: In order to provide a global vision of the situation and of the diffusion throughout the territory, studies like this one could be carried out in various Italian provinces. Besides, we hope that the high degree of commitment on the part of society and institutions in combating sexual violence, through information campaigns and incitements to report, will lead in a few years to a reduction in the number of victims of repeated violence (especially in family contexts) and, consequently, also in the total number of acts of violence that comes to the attention of the healthcare facilities. Finally, primary prevention of sexual violence must begin early because a substantial portion is experienced at a young age. It will be necessary to prevent these forms of violence with strategies that address known risk factors for perpetration (e.g., low family support, high poverty, low parental education, absent or single parenting, parental substance abuse, domestic violence, low caregiver warmth), by changing social norms and behaviors and by identifying protective factors that could be strengthened.