Francesco Nicola Lauria

Complex systems are inherently multilevel and multiscale systems. The infectious disease system is considered a complex system resulting from the interaction between three sub-systems (host, pathogen, and environment) organized into a hierarchical structure, ranging from the cellular to the macro-ecosystem level, with multiscales. Therefore, to describe infectious disease phenomena that change through time and space and at different scales, we built a model framework where infectious disease must be considered the set of biological responses of human hosts to pathogens, with biological pathways shared with other pathologies in an ecological interaction context. In this paper, we aimed to design a framework for building a disease model for COVID-19 based on current literature evidence. The model was set up by identifying the molecular pathophysiology related to the COVID-19 phenotypes, collecting the mechanistic knowledge scattered across scientific literature and bioinformatic databases, and integrating it using a logical/conceptual model systems biology. The model framework building process began from the results of a domain-based literature review regarding a multiomics approach to COVID-19. This evidence allowed us to define a framework of COVID-19 conceptual model and to report all concepts in a multilevel and multiscale structure. The same interdisciplinary working groups that carried out the scoping review were involved. The conclusive result is a conceptual method to design multiscale models of infectious diseases. The methodology, applied in this paper, is a set of partially ordered research and development activities that result in a COVID-19 multiscale model.

Background: Epidemiological, virological and pathogenetic characteristics of SARS-CoV-2 infection are under evaluation. A better understanding of the pathophysiology associated with COVID-19 is crucial to improve treatment modalities and to develop effective prevention strategies. Transcriptomic and proteomic data on the host response against SARS-CoV-2 still have anecdotic character; currently available data from other coronavirus infections are therefore a key source of information. Methods: We investigated selected molecular aspects of three human coronavirus (HCoV) infections, namely SARS-CoV, MERS-CoV and HCoV-229E, through a network based-approach. A functional analysis of HCoV-host interactome was carried out in order to provide a theoretic host-pathogen interaction model for HCoV infections and in order to translate the results in prediction for SARS-CoV-2 pathogenesis. The 3D model of S-glycoprotein of SARS-CoV-2 was compared to the structure of the corresponding SARS-CoV, HCoV-229E and MERS-CoV S-glycoprotein. SARS-CoV, MERS-CoV, HCoV-229E and the host interactome were inferred through published protein-protein interactions (PPI) as well as gene co-expression, triggered by HCoV S-glycoprotein in host cells. Results: Although the amino acid sequences of the S-glycoprotein were found to be different between the various HCoV, the structures showed high similarity, but the best 3D structural overlap shared by SARS-CoV and SARS-CoV-2, consistent with the shared ACE2 predicted receptor. The host interactome, linked to the S-glycoprotein of SARS-CoV and MERS-CoV, mainly highlighted innate immunity pathway components, such as Toll Like receptors, cytokines and chemokines. Conclusions: In this paper, we developed a network-based model with the aim to define molecular aspects of pathogenic phenotypes in HCoV infections. The resulting pattern may facilitate the process of structure-guided pharmaceutical and diagnostic research with the prospect to identify potential new biological targets.

Zika virus (ZIKV) is mainly transmitted by mosquitoes bites. However, transmission by sexual contacts has been reported in 11 non endemic countries. The rapid spread of ZIKV in Latin American and Caribbean Countries (LCR), person-to-person transmission and perceived risk on people's well being can affect the emerging economies of LCR which historically dependent on truism. Here we present an analysis on economic outputs for assessing the current impact of ZIKV on markets. Our analysis show an unexpected resilience of LCR markets to international alerts. This positive response represents an opportunity to scale-up interventions for preventing the further spreading of the ZIKV epidemic.

In the current Ebola epidemic in Western Africa, many healthcare workers have become infected. Some of these have been medically evacuated to hospitals in Europe and the USA. These clinical experiences provide unique insights into the course of Ebola virus disease under optimized condition within high level isolation units. A 50-year-old Caucasian male physician contracted Ebola virus diseases in Sierra Leone and was medically evacuated to Italy. Few days after the admission the course of the illness was characterized by severe gastro-intestinal symptoms followed by respiratory failure, accompanied by pulmonary infiltration and high Ebola viral load in the bronchial aspirate and Plasmodium vivax co-infection. The patient received experimental antiviral therapy with favipiravir, convalescent plasma and ZMAb. Ebola viral load started to steadily decrease in the blood after ZMAb administration and became undetectable by day 19 after admission, while it persisted longer in urine samples. No temporal association was observed between viral load decay in plasma and administration of favipiravir. The patient completely recovered and was discharged 39 days after admission. This is the first case of Ebola-related interstitial pneumonia documented by molecular testing of lung fluid specimens. This reports underlines the pivotal role of fluid replacement and advanced life support with mechanical ventilation in the management of patients with Ebola virus diseases respiratory failure. Beside our finding indicates a close temporal association between administration of cZMAb and Ebola virus clearance from blood.

Background: In Italy the proportion of cases of tuberculosis in persons originating from high-prevalence countries has been increasing in the last decade. We designed a study to assess adherence to and yield of a tuberculosis screening programme based on symptom screening conducted at primary care centres for regular and irregular immigrants and refugees/asylum seekers. Methods: Presence of symptoms suggestive of active tuberculosis was investigated by verbal screening in migrants presenting for any medical condition to 3 free primary care centres in the province of Rome. Individuals reporting at least one symptom were referred to a tuberculosis clinic for diagnostic workup. Results: Among 2142 migrants enrolled, 254 (11.9%) reported at least one symptom suggestive of active tuberculosis and 176 were referred to the tuberculosis clinic. Of them, 80 (45.4%) did not present for diagnostic evaluation. Tuberculosis was diagnosed in 7 individuals representing 0.33% of those screened and 7.3% of those evaluated for tuberculosis. Conclusion: The overall yield of this intervention was in the range reported for other tuberculosis screening programmes for migrants, although we recorded an unsatisfactory adherence to diagnostic workup. Possible advantages of this intervention include low cost and reduced burden of medical procedures for the screened population. Further evaluation of this approach appears to be warranted.

Background: Computer Tomography (CT) is considered the gold standard for assessing the morphological changes of lung parenchyma. Although novel CT techniques have substantially decreased the radiation dose, radiation exposure is still high. Magnetic Resonance Imaging (MRI) has been established as a radiation- free alternative to CT for several lung diseases, but its role in infectious diseases still needs to be explored further. Therefore, the purpose of our study was to compare MRI with high resolution CT (HRCT) for assessing pulmonary tuberculosis. Methods: 50 patients with culture-proven pulmonary tuberculosis underwent chest HRCT as the standard of reference and were evaluated by MRI within 24 h after HRCT. Altogether we performed 60 CT and MRI examinations, because 10 patients were also examined by CT and MRI at follow- up. Pulmonary abnormalities, their characteristics, location and distribution were analyzed by two readers who were blinded to the HRCT results. Results: Artifacts did not interfere with the diagnostic value of MRI. Both HRCT and MRI correctly diagnosed pulmonary tuberculosis and identified pulmonary abnormalities in all patients. There were no significant differences between the two techniques in terms of identifying the location and distribution of the lung lesions, though the higher resolution of MRI did allow for better identification of parenchymal dishomogeneity, caseosis, and pleural or nodal involvement. Conclusion: Technical developments and the refinement of pulse sequences have improved the quality and speed of MRI. Our data indicate that in terms of identifying lung lesions in non-AIDS patients with non- miliary pulmonary tuberculosis, MRI achieves diagnostic performances comparable to those obtained by HRCT but with better and more rapid identification of pulmonary tissue abnormalities due to the excellent contrast resolution.

Background: The first influenza pandemic of the 21th century was ignited by a new strain of influenza A virus (A/H1N1pdm). Specific patient groups, including those with comorbidities, pregnant women, young children, older and immunocompromised patients, are at increased risk for serious influenza-related disease. This study was aimed at investigating the influence of clinical presentation, antiviral treatment and possible drug resistance-associated mutations, on the extent and duration of viral shedding in patients infected with A/H1N1pdm. Methods: An observational study was performed, based on retrospective review of clinical and laboratory records of patients who were hospitalized for A/H1N1pdm infection at the National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy, between April 24 and December 31, 2009. Among 119 hospitalized patients, 39 were selected for a post hoc analysis, based on the availability of serial nasopharyngeal swabs samples and related information. Results: Eleven out of the 39 study patients (28.2%) presented with pneumonia; 29 (74.4%) received antiviral treatment. Patients with pneumonia were significantly older than patients without pneumonia. The mean values of viral RNA concentration were not significantly increased in patients with pneumonia, but a significant increase in the duration of viral shedding was observed as compared to patients without pneumonia. In patients receiving antivirals, the viral RNA concentration was significantly reduced in comparison to untreated patients at days 4-5 after symptom onset, while the overall duration of viral shedding was only marginally affected. A significant correlation between duration of viral shedding and time elapsed between symptom onset and therapy start was observed, with a significant reduction of days of viral shedding when therapy was initiated within 2 days of symptoms appearance. No known drug resistance mutations were detected in patients with prolonged viral shedding. Conclusions: Our results show that severe respiratory illness is associated with delayed virus clearance in patients with A/H1N1pdm infection. Antivirals caused an early reduction of viral load, but only marginally affected the overall duration of shedding. Prolonged shedding was not associated with the emergence of strains carrying known drug-resistance mutations.

The influenza virus infection may be severe in non-immune people. Common complications of influenza virus include upper and lower respiratory tract infections, otitis media, myocarditis, acute respiratory distress syndrome and multi-organ failure. There have been cases of vasculitis following influenza vaccination, and rash and acute purpura may occur in certain viral infections. To the best of our knowledge, there are no reports concerning cases of systemic vasculitis associated with pandemic 2009 (H1N1) infection.