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Article ; Online: Application of the ARIMA model on the COVID-2019 epidemic dataset

Domenico Benvenuto / Marta Giovanetti / Lazzaro Vassallo / Silvia Angeletti / Massimo Ciccozzi

Data in Brief, Vol 29, Iss , Pp - (2020)

2020

Abstract: Coronavirus disease 2019 (COVID-2019) has been recognized as a global threat, and several studies are being conducted using various mathematical models to predict the probable evolution of this epidemic. These mathematical models based on various factors ...

Abstract	Coronavirus disease 2019 (COVID-2019) has been recognized as a global threat, and several studies are being conducted using various mathematical models to predict the probable evolution of this epidemic. These mathematical models based on various factors and analyses are subject to potential bias. Here, we propose a simple econometric model that could be useful to predict the spread of COVID-2019. We performed Auto Regressive Integrated Moving Average (ARIMA) model prediction on the Johns Hopkins epidemiological data to predict the epidemiological trend of the prevalence and incidence of COVID-2019. For further comparison or for future perspective, case definition and data collection have to be maintained in real time. Keywords: COVID-2019 epidemic, ARIMA model, Forecast, Infection control
Keywords	Computer applications to medicine. Medical informatics ; R858-859.7 ; Science (General) ; Q1-390
Language	English
Publishing date	2020-04-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Microbiological Laboratory Diagnosis of Human Brucellosis

Giovanni Di Bonaventura / Silvia Angeletti / Andrea Ianni / Tommasangelo Petitti / Giovanni Gherardi

Pathogens, Vol 10, Iss 1623, p

An Overview

2021 Volume 1623

Abstract: Brucella spp. are Gram-negative, non-motile, non-spore-forming, slow-growing, facultative intracellular bacteria causing brucellosis. Brucellosis is an endemic of specific geographic areas and, although underreported, represents the most common zoonotic ... ...

Abstract	Brucella spp. are Gram-negative, non-motile, non-spore-forming, slow-growing, facultative intracellular bacteria causing brucellosis. Brucellosis is an endemic of specific geographic areas and, although underreported, represents the most common zoonotic infection, with an annual global incidence of 500,000 cases among humans. Humans represent an occasional host where the infection is mainly caused by B. melitensis , which is the most virulent; B. abortus B. suis and B. canis . A microbiological analysis is crucial to identifying human cases because clinical symptoms of human brucellosis are variable and aspecific. The laboratory diagnosis is based on three different microbiological approaches: (i) direct diagnosis by culture, (ii) indirect diagnosis by serological tests, and (iii) direct rapid diagnosis by molecular PCR-based methods. Despite the established experience with serological tests and highly sensitive nucleic acid amplification tests (NAATs), a culture is still considered the “gold standard” in the laboratory diagnosis of brucellosis due to its clinical and epidemiological relevance. Moreover, the automated BC systems now available have increased the sensitivity of BCs and shortened the time to detection of Brucella species. The main limitations of serological tests are the lack of common interpretative criteria, the suboptimal specificity due to interspecies cross-reactivity, and the low sensitivity during the early stage of disease. Despite that, serological tests remain the main diagnostic tool, especially in endemic areas because they are inexpensive, user friendly, and have high negative predictive value. Promising serological tests based on new synthetic antigens have been recently developed together with novel point-of-care tests without the need for dedicated equipment and expertise. NAATs are rapid tests that can help diagnose brucellosis in a few hours with high sensitivity and specificity. Nevertheless, the interpretation of NAAT-positive results requires attention because it may not ...
Keywords	brucellosis ; laboratory diagnosis ; culture method ; serological test ; nucleic acid amplification test ; Medicine ; R
Subject code	610
Language	English
Publishing date	2021-12-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Implications of Possible HBV-Driven Regulation of Gene Expression in Stem Cell-like Subpopulation of Huh-7 Hepatocellular Carcinoma Cell Line

Ayse Banu Demir / Domenico Benvenuto / Bilge Karacicek / Yasemin Erac / Silvia Spoto / Silvia Angeletti / Massimo Ciccozzi / Metiner Tosun

Journal of Personalized Medicine, Vol 12, Iss 2065, p

2022 Volume 2065

Abstract: Elevated levels of STIM1, an endoplasmic reticulum Ca 2+ sensor/buffering protein, appear to be correlated with poor cancer prognosis in which microRNAs are also known to play critical roles. The purpose of this study is to investigate possible HBV ... ...

Abstract	Elevated levels of STIM1, an endoplasmic reticulum Ca 2+ sensor/buffering protein, appear to be correlated with poor cancer prognosis in which microRNAs are also known to play critical roles. The purpose of this study is to investigate possible HBV origins of specific microRNAs we identified in a stem cell-like subpopulation of Huh-7 hepatocellular carcinoma (HCC) cell lines with enhanced STIM1 and/or Orai1 expression that mimicked poor cancer prognosis. Computational strategies including phylogenetic analyses were performed on miRNome data we obtained from an EpCAM- and CD133-expressing Huh-7 HCC stem cell-like subpopulation with enhanced STIM1 and/or Orai1 expression originally cultured in the present work. Results revealed two putative regions in the HBV genome based on the apparent clustering pattern of stem loop sequences of microRNAs, including miR3653. Reciprocal analysis of these regions identified critical human genes, of which their transcripts are among the predicted targets of miR3653, which was increased significantly by STIM1 or Orai1 enhancement. Briefly, this study provides phylogenetic evidence for a possible HBV-driven epigenetic remodeling that alters the expression pattern of Ca 2+ homeostasis-associated genes in STIM1 - or Orai1 overexpressing liver cancer stem-like cells for a possible mutual survival outcome. A novel region on HBV-X protein may affect liver carcinogenesis in a genotype-dependent manner. Therefore, detection of the viral genotype would have a clinical impact on prognosis of HBV-induced liver cancers.
Keywords	hepatocellular carcinoma ; HBx ; miR3653 ; epithelial–mesenchymal transition (EMT) ; molecular evolution ; Medicine ; R
Subject code	570
Language	English
Publishing date	2022-12-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Sars-CoV-2 Envelope and Membrane Proteins

Martina Bianchi / Domenico Benvenuto / Marta Giovanetti / Silvia Angeletti / Massimo Ciccozzi / Stefano Pascarella

BioMed Research International, Vol

Structural Differences Linked to Virus Characteristics?

2020 Volume 2020

Abstract: The Coronavirus Disease 2019 (COVID-19) is a new viral infection caused by the severe acute respiratory coronavirus 2 (SARS-CoV-2). Genomic analyses have revealed that SARS-CoV-2 is related to Pangolin and Bat coronaviruses. In this report, a structural ... ...

Abstract	The Coronavirus Disease 2019 (COVID-19) is a new viral infection caused by the severe acute respiratory coronavirus 2 (SARS-CoV-2). Genomic analyses have revealed that SARS-CoV-2 is related to Pangolin and Bat coronaviruses. In this report, a structural comparison between the Sars-CoV-2 Envelope and Membrane proteins from different human isolates with homologous proteins from closely related viruses is described. The analyses here reported show the high structural similarity of Envelope and Membrane proteins to the counterparts from Pangolin and Bat coronavirus isolates. However, the comparisons have also highlighted structural differences specific of Sars-CoV-2 proteins which may be correlated to the cross-species transmission and/or to the properties of the virus. Structural modelling has been applied to map the variant sites onto the predicted three-dimensional structure of the Envelope and Membrane proteins.
Keywords	Medicine ; R ; covid19
Subject code	572
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	Hindawi Limited
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: An algorithm of good clinical practice to reduce intra-hospital 90-day mortality and need for Intensive Care Unit transfer

Silvia Spoto / Sebastiano Costantino / Marta Fogolari / Emanuele Valeriani / Massimo Ciccozzi / Silvia Angeletti

Italian Journal of Medicine, Vol 14, Iss

a new approach for septic patient management

2020 Volume 1

Abstract: Sepsis accounts for 50% of intra-hospital mortality. Septic shock is diagnosed in 2% of patients with half of these needing for Intensive Care Unit (ICU) transfer. An algorithm was applied for mortality, need for intensive care transfer and length of ... ...

Abstract	Sepsis accounts for 50% of intra-hospital mortality. Septic shock is diagnosed in 2% of patients with half of these needing for Intensive Care Unit (ICU) transfer. An algorithm was applied for mortality, need for intensive care transfer and length of stay decrease. The observational study was performed on 231 consecutive enrolled patients with sepsis or septic shock admitted to the University Campus Bio-Medico of Rome. The algorithm was based on good clinical practice application of antimicrobial stewardship. Data were compared with data from comparable population of National and European surveys. In the study group, the global mortality rate was 26.8% (3.9% was intra-hospital and 23% 90-d mortality), need of ICU transfer was registered in 21.6%, and the median length of stay was 15 days. Globally, intra-hospital and 90-day mortality, were significantly lower than at national level (26.8% vs 63.6%, P<0.0001; 3.9% vs 25%, P<0.0001 and 23% vs 37.5%, P=0.0092). Need for ICU transfer in patients with septic shock was significantly lower than in the English survey (31.9% by vs 80.8% P<0.0001). A significant decrease of intra-hospital, 90-d mortality and need of ICU transfer was achieved.
Keywords	Sepsis ; mortality ; Intensive Care Unit transfer ; algorithm ; antimicrobial stewardship ; Medicine ; R
Subject code	310
Language	English
Publishing date	2020-03-01T00:00:00Z
Publisher	PAGEPress Publications
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Human Immunodeficiency Virus Type 2

Giancarlo Ceccarelli / Marta Giovanetti / Caterina Sagnelli / Alessandra Ciccozzi / Gabriella d’Ettorre / Silvia Angeletti / Alessandra Borsetti / Massimo Ciccozzi

Pathogens, Vol 10, Iss 1377, p

The Neglected Threat

2021 Volume 1377

Abstract: West Africa has the highest prevalence of human immunodeficiency virus (HIV)-2 infection in the world, but a high number of cases has been recognized in Europe, India, and the United States. The virus is less transmissible than HIV-1, with sexual ... ...

Abstract	West Africa has the highest prevalence of human immunodeficiency virus (HIV)-2 infection in the world, but a high number of cases has been recognized in Europe, India, and the United States. The virus is less transmissible than HIV-1, with sexual contacts being the most frequent route of acquisition. In the absence of specific antiretroviral therapy, most HIV-2 carriers will develop AIDS. Although, it requires more time than HIV-1 infection, CD4+ T cell decline occurs more slowly in HIV-2 than in HIV-1 patients. HIV-2 is resistant to non-nucleoside reverse transcriptase inhibitors (NNRTIs) and some protease inhibitors. Misdiagnosis of HIV-2 in patients mistakenly considered HIV-1-positive or in those with dual infections can cause treatment failures with undetectable HIV-1 RNA. In this era of global integration, clinicians must be aware of when to consider the diagnosis of HIV-2 infection and how to test for this virus. Although there is debate regarding when therapy should be initiated and which regimen should be chosen, recent trials have provided important information on treatment options for HIV-2 infection. In this review, we focus mainly on data available and on the insight they offer about molecular epidemiology, clinical presentation, antiretroviral therapy, and diagnostic tests of HIV-2 infection.
Keywords	HIV-2 ; epidemiology ; AIDS ; Medicine ; R
Subject code	310
Language	English
Publishing date	2021-10-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Phylogeny of Culex theileri virus flavivirus in Spain, Myanmar, Portugal and Turkey

Eleonora Cella / Domenico Benvenuto / Daniele Donati / Francesco Garilli / Silvia Angeletti / Stefano Pascarella / Massimo Ciccozzi

Asian Pacific Journal of Tropical Medicine, Vol 12, Iss 5, Pp 216-

2019 Volume 223

Abstract: Objective: To study the genetic diversity of Culex theileri flavivirus and the spread of this virus among Spain, Portugal and Turkey. Methods: A database consisting of 55 sequences of the NS5/3’UTR region of Culex theileri flavivirus group downloaded ... ...

Abstract	Objective: To study the genetic diversity of Culex theileri flavivirus and the spread of this virus among Spain, Portugal and Turkey. Methods: A database consisting of 55 sequences of the NS5/3’UTR region of Culex theileri flavivirus group downloaded from GenBank were aligned and manual edited with Bioedit. ModelTest v. 3.7 was used to select the simplest evolutionary model that adequately fitted the sequence data. Maximum likelihood analysis was performed using MEGA7. The phylogenetic signal of the dataset was investigated by the likelihood mapping analysis. Results: The phylogenetic tree showed three clusters. Myanmar sequences clusterd together with Turkish sequences, Spain and Portugal strains grouped together and two Turkish sequences grouped separately. Selective pressure analysis showed a moderate percentage of sites (22.5%) under pervasive negative selection and only 1% under pervasive positive selection. The sites subject to selective pressure in CTFV RdRp NS5 fragments have been located onto the predicted three-dimensional structure. Conclusions: Phylogenetic and evolutionary analysis can be an important tool for understanding the evolutionary impact of the probable contemporary existence between non-pathogenic and pathogenic flaviviruses among these vectors.
Keywords	culex virus ; flaviviridae ; phylogenetic analysis ; evolution ; Arctic medicine. Tropical medicine ; RC955-962
Subject code	572
Language	English
Publishing date	2019-01-01T00:00:00Z
Publisher	Wolters Kluwer Medknow Publications
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Neutralizing Antibodies against SARS-CoV-2 Beta and Omicron Variants Inhibition Comparison after BNT162b2 mRNA Booster Doses with a New PETIA sVNT Assay

Marta Fogolari / Bruno Daniele Leoni / Marina De Cesaris / Rita Italiano / Flavio Davini / Ginevra Azzurra Miccoli / Daniele Donati / Luigi Clerico / Andrea Stanziale / Giovanni Savini / Nicola Petrosillo / Massimo Ciccozzi / Lorenzo Sommella / Elisabetta Riva / Paolo Fazii / Silvia Angeletti

Diagnostics, Vol 13, Iss 889, p

2023 Volume 889

Abstract: Background: Monitoring antibody response following SARS-CoV-2 vaccination is strategic, and neutralizing antibodies represent the gold standard. The neutralizing response to Beta and Omicron VOCs was evaluated versus the gold standard by a new commercial ...

Abstract	Background: Monitoring antibody response following SARS-CoV-2 vaccination is strategic, and neutralizing antibodies represent the gold standard. The neutralizing response to Beta and Omicron VOCs was evaluated versus the gold standard by a new commercial automated assay. Methods: Serum samples from 100 healthcare workers from the Fondazione Policlinico Universitario Campus Biomedico and the Pescara Hospital were collected. IgG levels were determined by chemiluminescent immunoassay (Abbott Laboratories, Wiesbaden, Germany) and serum neutralization assay as the gold standard. Moreover, a new commercial immunoassay, the PETIA test Nab (SGM, Rome, Italy), was used for neutralization evaluation. Statistical analysis was performed with R software, version 3.6.0. Results: Anti-SARS-CoV-2 IgG titers decayed during the first ninety days after the vaccine second dose. The following booster dose significantly ( p < 0.001) increased IgG levels. A correlation between IgG expression and neutralizing activity modulation was found with a significant increase after the second and the third booster dose ( p < 0.05. Compared to the Beta variant of the virus, the Omicron VOC was associated with a significantly larger quantity of IgG antibodies needed to achieve the same degree of neutralization. The best Nab test cutoff for high neutralization titer (≥1:80) was set for both Beta and Omicron variants. Conclusion: This study correlates vaccine-induced IgG expression and neutralizing activity using a new PETIA assay, suggesting its usefulness for SARS-CoV2 infection management.
Keywords	SARS-CoV-2 ; VOCs ; serum antibodies ; vaccine ; neutralization assay ; PETIA assay ; Medicine (General) ; R5-920
Subject code	630
Language	English
Publishing date	2023-02-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Mid-Regional Pro-Adrenomedullin Can Predict Organ Failure and Prognosis in Sepsis?

Silvia Spoto / Stefania Basili / Roberto Cangemi / Giorgio D’Avanzo / Domenica Marika Lupoi / Giulio Francesco Romiti / Josepmaria Argemi / José Ramón Yuste / Felipe Lucena / Luciana Locorriere / Francesco Masini / Giulia Testorio / Rodolfo Calarco / Marta Fogolari / Maria Francesconi / Giulia Battifoglia / Sebastiano Costantino / Silvia Angeletti

International Journal of Molecular Sciences, Vol 24, Iss 24, p

2023 Volume 17429

Abstract: Sepsis causes immune dysregulation and endotheliitis, with an increase in mid-regional pro-adrenomedullin (MR-proADM). The aim of the study is to determine an MR-proADM value that, in addition to clinical diagnosis, can identify patients with localized ... ...

Abstract	Sepsis causes immune dysregulation and endotheliitis, with an increase in mid-regional pro-adrenomedullin (MR-proADM). The aim of the study is to determine an MR-proADM value that, in addition to clinical diagnosis, can identify patients with localized infection or those with sepsis/septic shock, with specific organ damage or with the need for intensive care unit (ICU) transfer and prognosis. The secondary aim is to correlate the MR-proADM value with the length of stay (LOS). In total, 301 subjects with sepsis (124/301 with septic shock) and 126 with localized infection were retrospectively included. In sepsis, MR-proADM ≥ 3.39 ng/mL identified acute kidney injury (AKI); ≥2.99 ng/mL acute respiratory distress syndrome (ARDS); ≥2.28 ng/mL acute heart failure (AHF); ≥2.55 ng/mL Glascow Coma Scale (GCS) < 15; ≥3.38 multi-organ involvement; ≥3.33 need for ICU transfer; ≥2.0 Sequential Organ Failure Assessment (SOFA) score ≥ 2; and ≥3.15 ng/mL non-survivors. The multivariate analysis showed that MR-proADM ≥ 2 ng/mL correlates with AKI, anemia and SOFA score ≥ 2, and MR-proADM ≥ 3 ng/mL correlates with AKI, GCS < 15 and SOFA score ≥ 2. A correlation between mortality and AKI, GCS < 15, ICU transfer and cathecolamine administration was found. In localized infection, MR-proADM at admission ≥ 1.44 ng/mL identified patients with AKI; ≥1.0 ng/mL with AHF; and ≥1.44 ng/mL with anemia and SOFA score ≥ 2. In the multivariate analysis, MR-proADM ≥ 1.44 ng/mL correlated with AKI, anemia, SOFA score ≥ 2 and AHF. MR-proADM is a marker of oxidative stress due to an infection, reflecting severity proportionally to organ damage.
Keywords	sepsis ; septic shock ; organ failure ; mid-regional pro-adrenomedullin (MR-proADM) ; acute kidney injury (AKI) ; acute respiratory distress syndrome (ARDS) ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	610
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Genetic Variability of the Monkeypox Virus Clade IIb B.1

Fabio Scarpa / Daria Sanna / Ilenia Azzena / Piero Cossu / Chiara Locci / Silvia Angeletti / Antonello Maruotti / Giancarlo Ceccarelli / Marco Casu / Pier Luigi Fiori / Nicola Petrosillo / Massimo Ciccozzi

Journal of Clinical Medicine, Vol 11, Iss 6388, p

2022 Volume 6388

Abstract: Monkeypox is caused by a sylvatic, double-stranded DNA zoonotic virus. Since 1 January 2022, monkeypox cases have been reported to WHO from 106 Member States across six WHO regions, and as of 2 October 2022, a total of 68,900 confirmed cases, including ... ...

Abstract	Monkeypox is caused by a sylvatic, double-stranded DNA zoonotic virus. Since 1 January 2022, monkeypox cases have been reported to WHO from 106 Member States across six WHO regions, and as of 2 October 2022, a total of 68,900 confirmed cases, including 25 deaths, occurred. Here, by using a whole genome approach, we perform a genetic and phylodynamic survey of the monkeypox virus Clade IIb B.1, which is the lineage causing the current multi-country outbreak. Results suggest that outbreaks seem to be isolated and localized in several epidemic clusters with geographic consistency. Currently, monkeypox appears to be a virus with a flattened genetic variability in terms of evolutionary path, with a very slow rate of growth in the population size. This scenario confirms that the monkeypox virus lacks the evolutionary advantage, given by the high level of mutation rate, which is very strong in RNA viruses. Of course, constant genome-based monitoring must be performed over time in order to detect the change in its genetic composition, if any.
Keywords	genetic diversity ; monkeypox ; lineage B.1 ; epidemiology ; orthopoxviruses ; Medicine ; R
Language	English
Publishing date	2022-10-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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