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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.
Francesco Messina; Chiara Montaldo; Isabella Abbate; Manuela Antonioli; Veronica Bordoni; Giulia Matusali; Alessandra Sacchi; Emanuela Giombini; Gian Fimia; Mauro Piacentini; Maria Capobianchi; Francesco Lauria; Giuseppe Ippolito; on behalf of COVID-19 Scoping Review Working Group. Rationale and Criteria for a COVID-19 Model Framework. Viruses 2021, 13, 1309 .
AMA StyleFrancesco Messina, Chiara Montaldo, Isabella Abbate, Manuela Antonioli, Veronica Bordoni, Giulia Matusali, Alessandra Sacchi, Emanuela Giombini, Gian Fimia, Mauro Piacentini, Maria Capobianchi, Francesco Lauria, Giuseppe Ippolito, on behalf of COVID-19 Scoping Review Working Group. Rationale and Criteria for a COVID-19 Model Framework. Viruses. 2021; 13 (7):1309.
Chicago/Turabian StyleFrancesco Messina; Chiara Montaldo; Isabella Abbate; Manuela Antonioli; Veronica Bordoni; Giulia Matusali; Alessandra Sacchi; Emanuela Giombini; Gian Fimia; Mauro Piacentini; Maria Capobianchi; Francesco Lauria; Giuseppe Ippolito; on behalf of COVID-19 Scoping Review Working Group. 2021. "Rationale and Criteria for a COVID-19 Model Framework." Viruses 13, no. 7: 1309.
Background Detailed temporal analyses of complete (full) blood count (CBC) parameters, their evolution and relationship to patient age, gender, co-morbidities and management outcomes in survivors and non-survivors with COVID-19 disease, could identify prognostic clinical biomarkers. Methods From 29 January 2020 until 28 March 2020, we performed a longitudinal cohort study of COVID-19 inpatients at the Italian National Institute for Infectious Diseases, Rome, Italy. 9 CBC parameters were studied as continuous variables [neutrophils, lymphocytes, monocytes, platelets, mean platelet volume, red blood cell count, haemoglobin concentration, mean red blood cell volume and red blood cell distribution width (RDW %)]. Model-based punctual estimates, as average of all patients’ values, and differences between survivors and non-survivors, overall, and by co-morbidities, at specific times after symptoms, with relative 95% CI and P-values, were obtained by marginal prediction and ANOVA- style joint tests. All analyses were carried out by STATA 15 statistical package. Main findings 379 COVID-19 patients [273 (72% were male; mean age was 61.67 (SD 15.60)] were enrolled and 1,805 measures per parameter were analysed. Neutrophils’ counts were on average significantly higher in non-survivors than in survivors (P60 years (OR = 4.21; 95%CI 1.82–9.77; p = 0.001). Age (OR = 2.59; 95%CI 1.04–6.45; p = 0.042), obesity (OR = 5.13; 95%CI 1.81–14.50; p = 0.002), renal chronic failure (OR = 5.20; 95%CI 1.80–14.97; p = 0.002) and cardiovascular diseases (OR 2.79; 95%CI 1.29–6.03; p = 0.009) were independently associated with poor clinical outcome at 30 days after symptoms’ onset. Interpretation Increased neutrophil counts, reduced lymphocyte counts, increased median platelet volume and anaemia with anisocytosis, are poor prognostic indicators for COVID19, after adjusting for the confounding effect of obesity, chronic renal failure, COPD, cardiovascular diseases and age >60 years.
Simone Lanini; Chiara Montaldo; Emanuele Nicastri; Francesco Vairo; Chiara Agrati; Nicola Petrosillo; Paola Scognamiglio; Andrea Antinori; Vincenzo Puro; Antonino Di Caro; Gabriella De Carli; Assunta Navarra; Alessandro Agresta; Claudia Cimaglia; Fabrizio Palmieri; Gianpiero D’Offizi; Luisa Marchioni; Gary Pignac Kobinger; Markus Maeurer; Enrico Girardi; Maria Rosaria Capobianchi; Alimuddin Zumla; Franco Locatelli; Giuseppe Ippolito. COVID-19 disease—Temporal analyses of complete blood count parameters over course of illness, and relationship to patient demographics and management outcomes in survivors and non-survivors: A longitudinal descriptive cohort study. PLoS ONE 2020, 15, e0244129 .
AMA StyleSimone Lanini, Chiara Montaldo, Emanuele Nicastri, Francesco Vairo, Chiara Agrati, Nicola Petrosillo, Paola Scognamiglio, Andrea Antinori, Vincenzo Puro, Antonino Di Caro, Gabriella De Carli, Assunta Navarra, Alessandro Agresta, Claudia Cimaglia, Fabrizio Palmieri, Gianpiero D’Offizi, Luisa Marchioni, Gary Pignac Kobinger, Markus Maeurer, Enrico Girardi, Maria Rosaria Capobianchi, Alimuddin Zumla, Franco Locatelli, Giuseppe Ippolito. COVID-19 disease—Temporal analyses of complete blood count parameters over course of illness, and relationship to patient demographics and management outcomes in survivors and non-survivors: A longitudinal descriptive cohort study. PLoS ONE. 2020; 15 (12):e0244129.
Chicago/Turabian StyleSimone Lanini; Chiara Montaldo; Emanuele Nicastri; Francesco Vairo; Chiara Agrati; Nicola Petrosillo; Paola Scognamiglio; Andrea Antinori; Vincenzo Puro; Antonino Di Caro; Gabriella De Carli; Assunta Navarra; Alessandro Agresta; Claudia Cimaglia; Fabrizio Palmieri; Gianpiero D’Offizi; Luisa Marchioni; Gary Pignac Kobinger; Markus Maeurer; Enrico Girardi; Maria Rosaria Capobianchi; Alimuddin Zumla; Franco Locatelli; Giuseppe Ippolito. 2020. "COVID-19 disease—Temporal analyses of complete blood count parameters over course of illness, and relationship to patient demographics and management outcomes in survivors and non-survivors: A longitudinal descriptive cohort study." PLoS ONE 15, no. 12: e0244129.
Giuseppe Ippolito; Francesco Nicola Lauria; Franco Locatelli; Nicola Magrini; Chiara Montaldo; Raffaella Sadun; Markus Maeurer; Gino Strada; Francesco Vairo; Salvatore Curiale; Antoine Lafont; Antonino di Caro; Maria Rosaria Capobianchi; Rainer Meilicke; Eskild Petersen; Alimuddin Zumla; Michel Pletschette. Lessons from the COVID-19 Pandemic—Unique Opportunities for Unifying, Revamping and Reshaping Epidemic Preparedness of Europe’s Public Health Systems. International Journal of Infectious Diseases 2020, 101, 361 -366.
AMA StyleGiuseppe Ippolito, Francesco Nicola Lauria, Franco Locatelli, Nicola Magrini, Chiara Montaldo, Raffaella Sadun, Markus Maeurer, Gino Strada, Francesco Vairo, Salvatore Curiale, Antoine Lafont, Antonino di Caro, Maria Rosaria Capobianchi, Rainer Meilicke, Eskild Petersen, Alimuddin Zumla, Michel Pletschette. Lessons from the COVID-19 Pandemic—Unique Opportunities for Unifying, Revamping and Reshaping Epidemic Preparedness of Europe’s Public Health Systems. International Journal of Infectious Diseases. 2020; 101 ():361-366.
Chicago/Turabian StyleGiuseppe Ippolito; Francesco Nicola Lauria; Franco Locatelli; Nicola Magrini; Chiara Montaldo; Raffaella Sadun; Markus Maeurer; Gino Strada; Francesco Vairo; Salvatore Curiale; Antoine Lafont; Antonino di Caro; Maria Rosaria Capobianchi; Rainer Meilicke; Eskild Petersen; Alimuddin Zumla; Michel Pletschette. 2020. "Lessons from the COVID-19 Pandemic—Unique Opportunities for Unifying, Revamping and Reshaping Epidemic Preparedness of Europe’s Public Health Systems." International Journal of Infectious Diseases 101, no. : 361-366.
The Republic of Congo (RoC) declared a chikungunya (CHIK) outbreak on 9 February 2019. We conducted a ONE-Human-Animal HEALTH epidemiological, virological and entomological investigation. Methods: We collected national surveillance and epidemiological data. CHIK diagnosis was based on RT-PCR and CHIKV-specific antibodies. Full CHIKV genome sequences were obtained by Sanger and MinION approaches and Bayesian tree phylogenetic analysis was performed. Mosquito larvae and 215 adult mosquitoes were collected in different villages of Kouilou and Pointe-Noire districts and estimates of Aedes (Ae.) mosquitos’ CHIKV-infectious bites obtained. We found two new CHIKV sequences of the East/Central/South African (ECSA) lineage, clustering with the recent enzootic sub-clade 2, showing the A226V mutation. The RoC 2019 CHIKV strain has two novel mutations, E2-T126M and E2-H351N. Phylogenetic suggests a common origin from 2016 Angola strain, from which it diverged around 1989 (95% HPD 1985–1994). The infectious bite pattern was similar for 2017, 2018 and early 2019. One Ae. albopictus pool was RT-PCR positive. The 2019 RoC CHIKV strain seems to be recently introduced or be endemic in sylvatic cycle. Distinct from the contemporary Indian CHIKV isolates and in contrast to the original Central-African strains (transmitted by Ae. aegypti), it carries the A226V mutation, indicating an independent adaptive mutation in response to vector replacement (Ae. albopictus vs Ae. aegypti).
Francesco Vairo; Martin Aimè Coussoud-Mavoungou; Francine Ntoumi; Concetta Castilletti; Lambert Kitembo; Najmul Haider; Fabrizio Carletti; Francesca Colavita; Cesare Gruber; Marco Iannetta; Francesco Messina; Simone Lanini; Biez Ulrich Judicaël; Emanuela Giombini; Chiara Montaldo; Chantal Portella; Steve Diafouka-Diatela; Martina Rueca; Richard Kock; Barbara Bartolini; Leonard Mboera; Vincent Munster; Robert Fischer; Stephanie Seifert; César Muñoz-Fontela; Beatriz Escudero-Pérez; Sergio Gomez-Medina; Emily Nelson; Patrick Kjia Tungu; Emanuele Nicastri; Vincenzo Puro; Antonino Di Caro; Maria Capobianchi; Jacqueline Mikolo; Alimuddin Zumla; Giuseppe Ippolito; on behalf of the Pandora-ID-NET Consortium Chikungunya Outbreak Group Taskforce. Chikungunya Outbreak in the Republic of the Congo, 2019—Epidemiological, Virological and Entomological Findings of a South-North Multidisciplinary Taskforce Investigation. Viruses 2020, 12, 1020 .
AMA StyleFrancesco Vairo, Martin Aimè Coussoud-Mavoungou, Francine Ntoumi, Concetta Castilletti, Lambert Kitembo, Najmul Haider, Fabrizio Carletti, Francesca Colavita, Cesare Gruber, Marco Iannetta, Francesco Messina, Simone Lanini, Biez Ulrich Judicaël, Emanuela Giombini, Chiara Montaldo, Chantal Portella, Steve Diafouka-Diatela, Martina Rueca, Richard Kock, Barbara Bartolini, Leonard Mboera, Vincent Munster, Robert Fischer, Stephanie Seifert, César Muñoz-Fontela, Beatriz Escudero-Pérez, Sergio Gomez-Medina, Emily Nelson, Patrick Kjia Tungu, Emanuele Nicastri, Vincenzo Puro, Antonino Di Caro, Maria Capobianchi, Jacqueline Mikolo, Alimuddin Zumla, Giuseppe Ippolito, on behalf of the Pandora-ID-NET Consortium Chikungunya Outbreak Group Taskforce. Chikungunya Outbreak in the Republic of the Congo, 2019—Epidemiological, Virological and Entomological Findings of a South-North Multidisciplinary Taskforce Investigation. Viruses. 2020; 12 (9):1020.
Chicago/Turabian StyleFrancesco Vairo; Martin Aimè Coussoud-Mavoungou; Francine Ntoumi; Concetta Castilletti; Lambert Kitembo; Najmul Haider; Fabrizio Carletti; Francesca Colavita; Cesare Gruber; Marco Iannetta; Francesco Messina; Simone Lanini; Biez Ulrich Judicaël; Emanuela Giombini; Chiara Montaldo; Chantal Portella; Steve Diafouka-Diatela; Martina Rueca; Richard Kock; Barbara Bartolini; Leonard Mboera; Vincent Munster; Robert Fischer; Stephanie Seifert; César Muñoz-Fontela; Beatriz Escudero-Pérez; Sergio Gomez-Medina; Emily Nelson; Patrick Kjia Tungu; Emanuele Nicastri; Vincenzo Puro; Antonino Di Caro; Maria Capobianchi; Jacqueline Mikolo; Alimuddin Zumla; Giuseppe Ippolito; on behalf of the Pandora-ID-NET Consortium Chikungunya Outbreak Group Taskforce. 2020. "Chikungunya Outbreak in the Republic of the Congo, 2019—Epidemiological, Virological and Entomological Findings of a South-North Multidisciplinary Taskforce Investigation." Viruses 12, no. 9: 1020.