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Article: Genomic epidemiology and phylogenetics applied to the study of SARS-CoV-2 pandemic.

Lai, Alessia / Bergna, Annalisa / Della Ventura, Carla / Zehender, Gianguglielmo

2023 Volume 46, Issue 1, Page(s) 1–8

Abstract: The study of characteristics, prevalence and patterns of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is significant to monitor and define the status of the pandemic, helping to design and evaluate control strategies. In this ... ...

Abstract	The study of characteristics, prevalence and patterns of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is significant to monitor and define the status of the pandemic, helping to design and evaluate control strategies. In this setting, the continuous emergence of new variants and their dynamic of replacement underline the importance of implementing genomic epidemiology and phylogenetic methods for the molecular monitoring and surveillance of this new virus. The current profile of the pandemic can change rapidly when new variants emerge and spread, impacting epidemiology and public health in terms of prevention and treatment and making it necessary to develop new molecules and formulate vaccines. In this paper, we reviewed and synthesized the main studies on molecular genomics and phylogeny of SARS-CoV-2 during the pandemic, and highlighted their contributions to our understanding of this new emergent pathogen.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; Phylogeny ; Pandemics ; COVID-19/epidemiology ; Genomics
Language	English
Publishing date	2023-01-09
Publishing country	Italy
Document type	Review ; Journal Article
ZDB-ID	756168-4
ISSN	1121-7138 ; 0391-5352
ISSN	1121-7138 ; 0391-5352
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Zs.B 2267: Show issues

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Article: Epidemiology and molecular analyses of respiratory syncytial virus in the 2021-2022 season in northern Italy.

Lai, Alessia / Bergna, Annalisa / Fabiano, Valentina / Ventura, Carla Della / Fumagalli, Giulia / Mari, Alessandra / Loiodice, Martina / Zuccotti, Gian Vincenzo / Zehender, Gianguglielmo

Frontiers in microbiology

2024 Volume 14, Page(s) 1327239

Abstract: Background: Human respiratory syncytial virus (RSV) is the leading cause of acute lower respiratory tract infection among infants and young children worldwide, with seasonal peaks in January and February. This study aimed to characterize the RSV samples ...

Abstract	Background: Human respiratory syncytial virus (RSV) is the leading cause of acute lower respiratory tract infection among infants and young children worldwide, with seasonal peaks in January and February. This study aimed to characterize the RSV samples from a pediatric cohort in the 2021-2022 season in Italy. Methods: In total, 104 samples were collected from pediatric patients attending the "Vittore Buzzi" Children's Hospital in Milan, Italy in the 2021-2022 season. RT-PCR and next-generation sequencing were used to discriminate subgroups and obtain whole genomes. Maximum likelihood and Bayesian phylogenetic methods were used to analyze Italian sequences in the European contest and date Italian clusters. Results: The median age was 78 days, and 76.9% of subjects required hospitalization, with a higher proportion of patients under 3 months of age. An equal proportion of subgroups A (GA2.3.5) and B (GB5.0.5a) was found, with significant differences in length of hospitalization, days of supplemental oxygen treatment, and intravenous hydration duration. Phylogeny highlighted 26 and 37 clusters containing quite the total of Italian sequences for RSV-A and -B, respectively. Clusters presented a tMRCA between December 2011-February 2017 and May 2014-December 2016 for A and B subgroups, respectively. Compared to European sequences, specific mutations were observed in Italian strains. Conclusion: These data confirmed a more severe clinical course of RSV-A, particularly in young children. This study permitted the characterization of recent Italian RSV whole genomes, highlighting the peculiar pattern of mutations that needs to be investigated further and monitored.
Language	English
Publishing date	2024-01-04
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2023.1327239
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Article ; Online: Fetal Myocarditis Associated With Maternal SARS-CoV-2 Infection.

Mannarino, Savina / Lanna, Mariano / Calcaterra, Valeria / Carzaniga, Thomas / Casiraghi, Luca / Lai, Alessia / Gabrieli, Arianna / Bergna, Annalisa / Fini, Giulia / Bianchi, Silvia / De Amici, Mara / Zehender, Gianguglielmo / Bellini, Tommaso / Buscaglia, Marco / Zuccotti, Gianvincenzo

The Pediatric infectious disease journal

2024 Volume 43, Issue 5, Page(s) 454–456

Abstract: We report the first case of significant fetal myocardial involvement associated with maternal SARS-CoV-2 infection, in which restoration of cardiac function at birth was noted. The demonstration of previous infection was supported by the quantification ... ...

Abstract	We report the first case of significant fetal myocardial involvement associated with maternal SARS-CoV-2 infection, in which restoration of cardiac function at birth was noted. The demonstration of previous infection was supported by the quantification of humoral response in child and mother, in particular the presence of anti-N antibodies and through the detection of specific antibodies against the BA.4/5 variant.
MeSH term(s)	Child ; Female ; Humans ; Myocarditis/etiology ; COVID-19/complications ; SARS-CoV-2 ; Antibodies ; Mothers ; Antibodies, Viral
Chemical Substances	Antibodies ; Antibodies, Viral
Language	English
Publishing date	2024-01-04
Publishing country	United States
Document type	Case Reports ; Journal Article
ZDB-ID	392481-6
ISSN	1532-0987 ; 0891-3668
ISSN (online)	1532-0987
ISSN	0891-3668
DOI	10.1097/INF.0000000000004245
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Article ; Online: Phylogeographical and evolutionary history of

Bergna, Annalisa / Ventura, Carla Della / Marzo, Rossella / Ciccozzi, Massimo / Galli, Massimo / Zehender, Gianguglielmo / Lai, Alessia

Le infezioni in medicina

2022 Volume 30, Issue 1, Page(s) 109–118

Abstract: Aim of this study was to reconstruct the phylogeography ... ...

Abstract	Aim of this study was to reconstruct the phylogeography of
Language	English
Publishing date	2022-03-01
Publishing country	Italy
Document type	Journal Article
ZDB-ID	2041081-5
ISSN	2532-8689 ; 1124-9390
ISSN (online)	2532-8689
ISSN	1124-9390
DOI	10.53854/liim-3001-13
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Zs.A 5576: Show issues

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Article ; Online: Serum antibody fingerprinting of SARS-CoV-2 variants in infected and vaccinated subjects by label-free microarray biosensor.

Carzaniga, Thomas / Casiraghi, Luca / Nava, Giovanni / Zanchetta, Giuliano / Inzani, Tommaso / Chiari, Marcella / Bollati, Valentina / Epis, Sara / Bandi, Claudio / Lai, Alessia / Zehender, Gianguglielmo / Bellini, Tommaso / Buscaglia, Marco

Frontiers in immunology

2024 Volume 15, Page(s) 1323406

Abstract: Both viral infection and vaccination affect the antibody repertoire of a person. Here, we demonstrate that the analysis of serum antibodies generates information not only on the virus type that caused the infection but also on the specific virus variant. ...

Abstract	Both viral infection and vaccination affect the antibody repertoire of a person. Here, we demonstrate that the analysis of serum antibodies generates information not only on the virus type that caused the infection but also on the specific virus variant. We developed a rapid multiplex assay providing a fingerprint of serum antibodies against five different SARS-CoV-2 variants based on a microarray of virus antigens immobilized on the surface of a label-free reflectometric biosensor. We analyzed serum from the plasma of convalescent subjects and vaccinated volunteers and extracted individual antibody profiles of both total immunoglobulin Ig and IgA fractions. We found that Ig level profiles were strongly correlated with the specific variant of infection or vaccination and that vaccinated subjects displayed a larger quantity of total Ig and a lower fraction of IgA relative to the population of convalescent unvaccinated subjects.
MeSH term(s)	Humans ; SARS-CoV-2 ; COVID-19 ; Immunoglobulins ; Immunoglobulin A
Chemical Substances	Immunoglobulins ; Immunoglobulin A
Language	English
Publishing date	2024-02-27
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2024.1323406
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Article ; Online: Long-term effects of SARS-CoV-2 infection in hospitalized children: findings from an Italian single-center study.

Calcaterra, Valeria / Tagi, Veronica Maria / D'Auria, Enza / Lai, Alessia / Zanelli, Sara / Montanari, Chiara / Biganzoli, Elia Maria / Marano, Giuseppe / Borghi, Elisa / Massa, Valentina / Riva, Agostino / Zuccotti, Gianvincenzo

Italian journal of pediatrics

2024 Volume 50, Issue 1, Page(s) 27

Abstract: Background: Limited evidence exists regarding the association between COVID-19 and Long COVID manifestations in children, particularly concerning variants of concern (VOCs). We aimed to characterize a cohort of pediatric patients hospitalized with ... ...

Abstract	Background: Limited evidence exists regarding the association between COVID-19 and Long COVID manifestations in children, particularly concerning variants of concern (VOCs). We aimed to characterize a cohort of pediatric patients hospitalized with confirmed acute SARS-CoV-2 and monitor them for Long COVID symptoms. Additionally, it seeks to explore any potential correlations between VOCs and clinical symptoms. Methods: We conducted a prospective study involving children hospitalized from November 2021 to March 2023, with confirmed acute SARS-CoV-2 infection. A telephone survey was conducted at 3-6-12 months after discharge. Results: We included 167 patients (77 F/90 M). Upon hospital admission, 95.5% of patients presented as symptomatic. Regarding patients for whom it was feasible to determine the SARS-CoV-2 variant (n = 51), the Delta variant was identified in 11 children (21.6%) and Omicron variant in the remaining 40 patients (78.4%: 27.5% BA.1 variant; 15% BA.2 variant; 57.5% BA.5 variant). 19 patients (16.5%) reported experiencing at least one symptom indicative of Long COVID (weight loss 31.6%, inappetence 26.3%, chronic cough 21.1%, fatigue 21.1%, and sleep disturbances, wheezing, abdominal pain and mood disorders 15.8%). In only 4 patients with Long COVID we could identified a specific SARS-CoV-2 variant (3 Omicron: 2 BA.1 and 1 BA.2; 1 Delta). Conclusions: this study underscores that long COVID is a significant concern in the pediatric population. Our data reinforce the importance of continuously monitoring the impact of long-COVID in infants, children, and adolescents. A follow-up following SARS-CoV-2 infection is therefore advisable, with symptom investigation tailored to the patient's age.
MeSH term(s)	Adolescent ; Infant ; Humans ; Child ; Child, Hospitalized ; SARS-CoV-2 ; COVID-19/epidemiology ; Post-Acute COVID-19 Syndrome ; Prospective Studies ; Italy/epidemiology
Language	English
Publishing date	2024-02-14
Publishing country	England
Document type	Journal Article
ZDB-ID	2088556-8
ISSN	1824-7288 ; 1720-8424
ISSN (online)	1824-7288
ISSN	1720-8424
DOI	10.1186/s13052-024-01596-y
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Article ; Online: Neutralizing antibodies response to novel SARS-CoV-2 omicron sublineages in long-term care facility residents after the fourth dose of monovalent BNT162b2 COVID-19 vaccination.

Varasi, Ilenia / Lai, Alessia / Fiaschi, Lia / Bergna, Annalisa / Gatti, Antonella / Caimi, Barbara / Biba, Camilla / Della Ventura, Carla / Balotta, Claudia / Riva, Agostino / Zehender, Gianguglielmo / Zazzi, Maurizio / Vicenti, Ilaria

The Journal of infection

2023 Volume 87, Issue 3, Page(s) 270–272

MeSH term(s)	Humans ; BNT162 Vaccine ; COVID-19/prevention & control ; COVID-19 Vaccines ; Long-Term Care ; SARS-CoV-2 ; Antibodies, Viral ; Vaccination
Chemical Substances	BNT162 Vaccine ; COVID-19 Vaccines ; Antibodies, Viral
Language	English
Publishing date	2023-06-30
Publishing country	England
Document type	Letter ; Research Support, Non-U.S. Gov't
ZDB-ID	424417-5
ISSN	1532-2742 ; 0163-4453
ISSN (online)	1532-2742
ISSN	0163-4453
DOI	10.1016/j.jinf.2023.06.019
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Article: Pandemic experiences and psychopathological aspects in individuals with mood disorders and other mental disorders.

Del Casale, Antonio / Lai, Carlo / Iannuccelli, Alessia / Ciacchella, Chiara / Veneziani, Giorgio / Ali, Mohamed / Zocchi, Clarissa / Bilotta, Irene / Pompili, Maurizio

Frontiers in psychiatry

2022 Volume 13, Page(s) 1039072

Abstract: Individuals with different personality traits, temperaments, and psychological symptoms have different attitudes toward the pandemic experiences and restrictive measures. The aim of the present study was to evaluate the associations between the ... ...

Abstract	Individuals with different personality traits, temperaments, and psychological symptoms have different attitudes toward the pandemic experiences and restrictive measures. The aim of the present study was to evaluate the associations between the psychological factors and the attitudes toward COVID-19, experienced during the third pandemic wave in Italy, in a sample of individuals with psychiatric disorders. Between March and September 2021, 53 patients with mood disorders and other mental disorders completed a survey composed of self-report questionnaires that assessed sleep quality, depressive and hypomanic symptoms, and temperament and personality traits. Positive and negative attitudes toward the pandemic experience were assessed using an
Language	English
Publishing date	2022-10-14
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2564218-2
ISSN	1664-0640
ISSN	1664-0640
DOI	10.3389/fpsyt.2022.1039072
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Article ; Online: Early phylogenetic estimate of the effective reproduction number of SARS-CoV-2.

Lai, Alessia / Bergna, Annalisa / Acciarri, Carla / Galli, Massimo / Zehender, Gianguglielmo

Journal of medical virology

2020 Volume 92, Issue 6, Page(s) 675–679

Abstract: To reconstruct the evolutionary dynamics of the 2019 novel-coronavirus recently causing an outbreak in Wuhan, China, 52 SARS-CoV-2 genomes available on 4 February 2020 at Global Initiative on Sharing All Influenza Data were analyzed. The two models used ... ...

Abstract	To reconstruct the evolutionary dynamics of the 2019 novel-coronavirus recently causing an outbreak in Wuhan, China, 52 SARS-CoV-2 genomes available on 4 February 2020 at Global Initiative on Sharing All Influenza Data were analyzed. The two models used to estimate the reproduction number (coalescent-based exponential growth and a birth-death skyline method) indicated an estimated mean evolutionary rate of 7.8 × 10
MeSH term(s)	Base Sequence ; Bayes Theorem ; Betacoronavirus/classification ; Betacoronavirus/genetics ; Betacoronavirus/isolation & purification ; Betacoronavirus/pathogenicity ; COVID-19 ; Coronavirus Infections/diagnosis ; Coronavirus Infections/epidemiology ; Coronavirus Infections/transmission ; Coronavirus Infections/virology ; Epidemiological Monitoring ; Evolution, Molecular ; Genome, Viral ; Humans ; Information Dissemination ; Models, Statistical ; Open Reading Frames ; Pandemics ; Phylogeny ; Pneumonia, Viral/diagnosis ; Pneumonia, Viral/epidemiology ; Pneumonia, Viral/transmission ; Pneumonia, Viral/virology ; RNA, Viral/genetics ; SARS-CoV-2 ; Sequence Alignment ; Sequence Homology, Nucleic Acid
Chemical Substances	RNA, Viral
Keywords	covid19
Language	English
Publishing date	2020-03-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.25723
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Article: Human-to-Cat SARS-CoV-2 Transmission: Case Report and Full-Genome Sequencing from an Infected Pet and Its Owner in Northern Italy.

Pagani, Gabriele / Lai, Alessia / Bergna, Annalisa / Rizzo, Alberto / Stranieri, Angelica / Giordano, Alessia / Paltrinieri, Saverio / Lelli, Davide / Decaro, Nicola / Rusconi, Stefano / Gismondo, Maria Rita / Antinori, Spinello / Lauzi, Stefania / Galli, Massimo / Zehender, Gianguglielmo

Pathogens (Basel, Switzerland)

2021 Volume 10, Issue 2

Abstract: There have been previous reports of the human-to-cat transmission of SARS-CoV-2, but there are only a few molecular studies that have compared the whole genome of the virus in cats and their owners. We here describe a case of domestic SARS-CoV-2 ... ...

Abstract	There have been previous reports of the human-to-cat transmission of SARS-CoV-2, but there are only a few molecular studies that have compared the whole genome of the virus in cats and their owners. We here describe a case of domestic SARS-CoV-2 transmission from a healthcare worker to his cat for which nasopharyngeal swabs of both the cat and its owner were used for full-genome analysis. The results indicate that quarantine measures should be extended to pets living in SARS-CoV-2-infected households.
Language	English
Publishing date	2021-02-23
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2695572-6
ISSN	2076-0817
ISSN	2076-0817
DOI	10.3390/pathogens10020252
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