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Microorganisms
Special Issues
Surveillance of Viral Epidemics
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Surveillance of Viral Epidemics

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Medical Microbiology".

Deadline for manuscript submissions: closed (15 November 2023) | Viewed by 4591

Special Issue Editors

Dr. Mirko Buttrini

E-Mail Website
Guest Editor
Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
Interests: bacteria; anaerobe; virology; molecular diagnosis; MALDI-ToF mass spectrometry
Dr. Sara Montecchini

E-Mail Website
Guest Editor
Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
Interests: virology; parasitology; molecular diagnosis
Prof. Dr. Adriana Calderaro

E-Mail Website
Guest Editor
Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
Interests: virology; parasitology; bacteria; molecular diagnosisl MALDI-ToF mass spectrometry
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

As these last few years have unfortunately taught us, viruses can cause serious illnesses, sometimes resulting in epidemics and pandemics associated with significant morbidity and mortality worldwide. Hence, continuous surveillance of the behavior and distribution of existing viruses and the emergence of new ones is necessary to help us make effective and appropriate decisions regarding their control.

This Special Issue, entitled "Surveillance of viral epidemics", aims to present recent research on any aspect of the distribution of different viruses, their association with possible seasonal activities, and their changing epidemiological profiles, focusing on their introduction in different countries and most prevalent sub-lineages.

Some of the focal points include, but are not limited to, the following:

  • epidemiological data;
  • genotypic characterization;
  • new tools, approaches, and assays for the diagnosis of viral infectious diseases;
  • virus–host interactions.

Reviews, original research, and communications are all welcome.

Dr. Mirko Buttrini
Dr. Sara Montecchini
Prof. Dr. Adriana Calderaro
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Published Papers (3 papers)

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Research

10 pages, 621 KiB  
Article
Exploring Clinical Predictors of Severe Human Metapneumovirus Respiratory Tract Infections in Children: Insights from a Recent Outbreak
by Airin Veronese, Tina Uršič, Simona Bizjak Vojinovič and Jasna Rodman Berlot
Microorganisms 2024, 12(4), 641; https://doi.org/10.3390/microorganisms12040641 - 23 Mar 2024
Viewed by 601
Abstract
Human metapneumovirus (hMPV) is an important pathogen that causes both upper (URTIs) and lower respiratory tract infections (LRTIs) in children. The virus can be implicated in severe bronchiolitis and pneumonia, necessitating hospitalization, with certain cases requiring intensive care unit intervention. As part of [...] Read more.
Human metapneumovirus (hMPV) is an important pathogen that causes both upper (URTIs) and lower respiratory tract infections (LRTIs) in children. The virus can be implicated in severe bronchiolitis and pneumonia, necessitating hospitalization, with certain cases requiring intensive care unit intervention. As part of a retrospective observational study, we aimed to identify indicators of severe hMPV respiratory tract infections in children referred to the University Children’s Hospital Ljubljana and the Department of Infectious Diseases Ljubljana, Slovenia, during a recent outbreak. We analyzed clinical data from November 2022 to January 2023 and compared the characteristics of children presenting with URTIs and LRTIs. We also examined the characteristics of children with hMPV LRTIs, distinguishing between children with and without LRTI-associated hypoxemia. Of 78 hMPV-PCR-positive pediatric patients (mean age 3.1 years; 60.3% boys), 36% had a URTI, and 64% had an LRTI. Hospitalization was required in 64% (50/78), with 42% (21/50) requiring oxygen therapy. LRTI-associated hypoxemia was more common in patients with atopy who showed dyspnea, tachypnea, crackles, and wheezing on lung auscultation. In a multivariable logistic regression analysis, wheezing detected on lung auscultation was a significant predictive factor for hypoxemic hMPV-LRTI. Specifically, children presenting with wheezing were found to be ten times more likely to experience hypoxemia. Prematurity and chronic conditions did not influence the presentation or severity of hMPV infection. This study highlights wheezing and atopy as crucial indicators of severe hMPV LRTI in children, emphasizing the importance of early recognition and intervention. Full article
(This article belongs to the Special Issue Surveillance of Viral Epidemics)
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12 pages, 606 KiB  
Article
Development of a Droplet Digital PCR to Monitor SARS-CoV-2 Omicron Variant BA.2 in Wastewater Samples
by Laura A. E. Van Poelvoorde, Corinne Picalausa, Andrea Gobbo, Bavo Verhaegen, Marie Lesenfants, Philippe Herman, Koenraad Van Hoorde and Nancy H. C. Roosens
Microorganisms 2023, 11(3), 729; https://doi.org/10.3390/microorganisms11030729 - 12 Mar 2023
Cited by 2 | Viewed by 1764
Abstract
Wastewater-based surveillance can be used as a complementary method to other SARS-CoV-2 surveillance systems. It allows the emergence and spread of infections and SARS-CoV-2 variants to be monitored in time and place. This study presents an RT-ddPCR method that targets the T19I amino [...] Read more.
Wastewater-based surveillance can be used as a complementary method to other SARS-CoV-2 surveillance systems. It allows the emergence and spread of infections and SARS-CoV-2 variants to be monitored in time and place. This study presents an RT-ddPCR method that targets the T19I amino acid mutation in the spike protein of the SARS-CoV-2 genomes, which is specific to the BA.2 variant (omicron). The T19I assay was evaluated both in silico and in vitro for its inclusivity, sensitivity, and specificity. Moreover, wastewater samples were used as a proof of concept to monitor and quantify the emergence of the BA.2 variant from January until May 2022 in the Brussels-Capital Region which covers a population of more than 1.2 million inhabitants. The in silico analysis showed that more than 99% of the BA.2 genomes could be characterized using the T19I assay. Subsequently, the sensitivity and specificity of the T19I assay were successfully experimentally evaluated. Thanks to our specific method design, the positive signal from the mutant probe and wild-type probe of the T19I assay was measured and the proportion of genomes with the T19I mutation, characteristic of the BA.2 mutant, compared to the entire SARS-CoV-2 population was calculated. The applicability of the proposed RT-ddPCR method was evaluated to monitor and quantify the emergence of the BA.2 variant over time. To validate this assay as a proof of concept, the measurement of the proportion of a specific circulating variant with genomes containing the T19I mutation in comparison to the total viral population was carried out in wastewater samples from wastewater treatment plants in the Brussels-Capital Region in the winter and spring of 2022. This emergence and proportional increase in BA.2 genomes correspond to what was observed in the surveillance using respiratory samples; however, the emergence was observed slightly earlier, which suggests that wastewater sampling could be an early warning system and could be an interesting alternative to extensive human testing. Full article
(This article belongs to the Special Issue Surveillance of Viral Epidemics)
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12 pages, 3713 KiB  
Article
Association of Dengue Virus Serotypes 1&2 with Severe Dengue Having Deletions in Their 3′Untranslated Regions (3′UTRs)
by Deepti Maisnam, Arcy Billoria, V. S. V Prasad and Musturi Venkataramana
Microorganisms 2023, 11(3), 666; https://doi.org/10.3390/microorganisms11030666 - 06 Mar 2023
Viewed by 1557
Abstract
Dengue virus infections are recorded as hyper-endemic in many countries, including India. Research pertaining to the reasons for frequent outbreaks and severe dengue is ongoing. Hyderabad city, India, has been recorded as a ‘hotspot’ for dengue virus infections. Dengue virus strains circulating over [...] Read more.
Dengue virus infections are recorded as hyper-endemic in many countries, including India. Research pertaining to the reasons for frequent outbreaks and severe dengue is ongoing. Hyderabad city, India, has been recorded as a ‘hotspot’ for dengue virus infections. Dengue virus strains circulating over the past few years in Hyderabad city have been characterized at the molecular level to analyze the serotype/genotypes; 3′UTRs were further amplified and sequenced. The disease severity in patients infected with dengue virus strains with complete and 3′UTR deletion mutants was analyzed. Genotype I of the serotype 1 replaced genotype III, which has been circulating over the past few years in this region. Coincidentally, the number of dengue virus infections significantly increased in this region during the study period. Nucleotide sequence analysis suggested twenty-two and eight nucleotide deletions in the 3′UTR of DENV-1. The eight nucleotide deletions observed in the case of DENV-1 3′UTR were the first reported in this instance. A 50 nucleotide deletion was identified in the case of the serotype DENV-2. Importantly, these deletion mutants were found to cause severe dengue, even though they were found to be replication incompetent. This study emphasized the role of dengue virus 3′UTRs on severe dengue and emerging outbreaks. Full article
(This article belongs to the Special Issue Surveillance of Viral Epidemics)
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