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Microorganisms
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Molecular Epidemiology, Diagnostics and Management of Respiratory Virus Infections 2.0
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Molecular Epidemiology, Diagnostics and Management of Respiratory Virus Infections 2.0

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

Deadline for manuscript submissions: 31 December 2024 | Viewed by 6530

Special Issue Editors

Prof. Dr. Hirokazu Kimura

E-Mail Website
Guest Editor
Department of Health Science, Gunma Paz University, Takasaki-shi, Gunma Prefecture, Japan
Interests: epidemiology; virology; infectious diseases
Special Issues, Collections and Topics in MDPI journals
Dr. Mitsuru Sada

E-Mail Website
Guest Editor
Advanced Medical Science Research Center, Gunma Paz University, Shibukawa 377-0008, Japan
Interests: molecular pharmacology; SARS-CoV-2

Special Issue Information

Dear Colleagues,

This Special Issue is the continuation of our previous Special Issue "Molecular Epidemiology, Diagnostics and Management of Respiratory Virus Infections", which was published in 2020.

Although many types of viruses affect acute respiratory infection in humans, most of them are not well-controlled/prevented at present. To better understand this type of infection, it may be important to elucidate their molecular epidemiology. Moreover, to treat respiratory infections, the accurate diagnosis and management of the diseases are essential. From these circumstances, we will focus on molecular epidemiology based on advanced bioinformatics technologies and recent advances in the diagnosis and management of various viral respiratory infections.

Manuscripts that deal with systemic reviews will only be acceptable in rare cases.

Prof. Dr. Hirokazu Kimura
Dr. Mitsuru Sada
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.

Keywords

  • viral respiratory infections
  • molecular epidemiology
  • diagnostics
  • management

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Published Papers (5 papers)

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Research

11 pages, 1327 KiB  
Article
Antigenic Divergence from the Seasonal Vaccine of the Influenza Virus Strains Circulating in Romania During Three Successive Seasons (2021–2024)
by Ovidiu Vlaicu, Leontina Banica, Robert Hohan, Marius Surleac, Dragoş Florea, Victor Daniel Miron, Andreea Tudor, Oana Săndulescu, Anca Cristina Drăgănescu, Dan Oțelea and Simona Paraschiv
Microorganisms 2024, 12(11), 2363; https://doi.org/10.3390/microorganisms12112363 - 19 Nov 2024
Viewed by 441
Abstract
Influenza viruses continue to be an important public health threat. Vaccination is the most effective measure to control the influenza virus circulation. However, these viruses are continuously evolving through antigenic drift/shift, and thus the vaccine efficiency is affected. The aim of this study [...] Read more.
Influenza viruses continue to be an important public health threat. Vaccination is the most effective measure to control the influenza virus circulation. However, these viruses are continuously evolving through antigenic drift/shift, and thus the vaccine efficiency is affected. The aim of this study was to characterize the viral strains circulating in Romania, in a population with declining vaccination coverage, during the last three cold seasons by evaluating the hemagglutinin antigenic relatedness to the vaccine strains. All the available sequences collected between August 2021 and June 2024 were analyzed by using phylogenetic analysis and the Pepitope model to predict vaccine efficacy. The results showed that the 2021/2022 influenza season was dominated by the circulation of highly diverse clades of A(H3N2) viruses with high mutational divergence as compared to the vaccine strain, which might contribute to the reduction in vaccine efficacy. During the 2022/2023 influenza season, both influenza A and B viruses were reported, with few antigenic site mutations. The 2023/2024 influenza season was dominated by the circulation of influenza A viruses: A/H1N1pdm09 clade 6B.1A.5a.2a and A/H3N2 clade 2a.3a.1. The clade 2a.3a.1 also showed high variability when compared to the vaccine strain, presumably leading to reduced vaccine efficacy. This study illustrates the high diversity of influenza viruses circulating in a population with low vaccination coverage during the previous cold seasons. The viral diversity impacted vaccine efficacy, hence the need for public health programs to increase vaccine uptake and improve vaccine formulation in order to limit viral transmission. Full article
(This article belongs to the Special Issue Molecular Epidemiology, Diagnostics and Management of Respiratory Virus Infections 2.0)
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13 pages, 2441 KiB  
Article
Molecular Evolutionary Analyses of the Fusion Genes in Human Parainfluenza Virus Type 4
by Fuminori Mizukoshi, Hirokazu Kimura, Satoko Sugimoto, Ryusuke Kimura, Norika Nagasawa, Yuriko Hayashi, Koichi Hashimoto, Mitsuaki Hosoya, Kazuya Shirato and Akihide Ryo
Microorganisms 2024, 12(8), 1633; https://doi.org/10.3390/microorganisms12081633 - 9 Aug 2024
Viewed by 845
Abstract
The human parainfluenza virus type 4 (HPIV4) can be classified into two distinct subtypes, 4a and 4b. The full lengths of the fusion gene (F gene) of 48 HPIV4 strains collected during the period of 1966–2022 were analyzed. Based on these gene [...] Read more.
The human parainfluenza virus type 4 (HPIV4) can be classified into two distinct subtypes, 4a and 4b. The full lengths of the fusion gene (F gene) of 48 HPIV4 strains collected during the period of 1966–2022 were analyzed. Based on these gene sequences, the time-scaled evolutionary tree was constructed using Bayesian Markov chain Monte Carlo methods. A phylogenetic tree showed that the first division of the two subtypes occurred around 1823, and the most recent common ancestors of each type, 4a and 4b, existed until about 1940 and 1939, respectively. Although the mean genetic distances of all strains were relatively wide, the distances in each subtype were not wide, indicating that this gene was conserved in each subtype. The evolutionary rates of the genes were relatively low (4.41 × 10−4 substitutions/site/year). Moreover, conformational B-cell epitopes were predicted in the apex of the trimer fusion protein. These results suggest that HPIV4 subtypes diverged 200 years ago and the progenies further diverged and evolved. Full article
(This article belongs to the Special Issue Molecular Epidemiology, Diagnostics and Management of Respiratory Virus Infections 2.0)
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16 pages, 4479 KiB  
Article
Seasonality and Genotype Diversity of Human Rhinoviruses during an Eight-Year Period in Slovenia
by Nataša Berginc, Maja Sočan, Katarina Prosenc Trilar and Miroslav Petrovec
Microorganisms 2024, 12(2), 341; https://doi.org/10.3390/microorganisms12020341 - 6 Feb 2024
Cited by 1 | Viewed by 1392
Abstract
Due to the high socioeconomic burden of rhinoviruses, the development of prevention and treatment strategies is of high importance. Understanding the epidemiological and clinical features of rhinoviruses is essential in order to address these issues. Our study aimed to define the seasonality and [...] Read more.
Due to the high socioeconomic burden of rhinoviruses, the development of prevention and treatment strategies is of high importance. Understanding the epidemiological and clinical features of rhinoviruses is essential in order to address these issues. Our study aimed to define the seasonality and molecular epidemiology of rhinoviruses in Slovenia. Over a period of eight years, a total of 20,425 patients from sentinel primary healthcare settings and sentinel hospitals were examined for a panel of respiratory viruses in the national programme for the surveillance of influenza-like illnesses and acute respiratory infections. The patients were from all age groups and had respiratory infections of various severity. Infection with a rhinovirus was confirmed using an RT-rPCR in 1834 patients, and 1480 rhinoviruses were genotyped. The molecular analysis was linked to demographical and meteorological data. We confirmed the year-round circulation of rhinoviruses with clear seasonal cycles, resulting in two seasonal waves with peaks in spring and autumn. High levels of genotype variability and co-circulation were confirmed between and within seasons and were analysed in terms of patient age, the patient source reflecting disease severity, and meteorological factors. Our study provides missing scientific information on the genotype diversity of rhinoviruses in Slovenia. As most previous investigations focused on exclusive segments of the population, such as children or hospitalised patients, and for shorter study periods, our study, with its design, size and length, contributes complementary aspects and new evidence-based knowledge to the regional and global understanding of rhinovirus seasonality and molecular epidemiology. Full article
(This article belongs to the Special Issue Molecular Epidemiology, Diagnostics and Management of Respiratory Virus Infections 2.0)
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15 pages, 2158 KiB  
Article
Molecular Evolutionary Analyses of the Spike Protein Gene and Spike Protein in the SARS-CoV-2 Omicron Subvariants
by Norika Nagasawa, Ryusuke Kimura, Mao Akagawa, Tatsuya Shirai, Mitsuru Sada, Kaori Okayama, Yuka Sato-Fujimoto, Makoto Saito, Mayumi Kondo, Kazuhiko Katayama, Akihide Ryo, Makoto Kuroda and Hirokazu Kimura
Microorganisms 2023, 11(9), 2336; https://doi.org/10.3390/microorganisms11092336 - 18 Sep 2023
Viewed by 1472
Abstract
To better understand the evolution of the SARS-CoV-2 Omicron subvariants, we performed molecular evolutionary analyses of the spike (S) protein gene/S protein using advanced bioinformatics technologies. First, time-scaled phylogenetic analysis estimated that a common ancestor of the Wuhan, Alpha, Beta, Delta [...] Read more.
To better understand the evolution of the SARS-CoV-2 Omicron subvariants, we performed molecular evolutionary analyses of the spike (S) protein gene/S protein using advanced bioinformatics technologies. First, time-scaled phylogenetic analysis estimated that a common ancestor of the Wuhan, Alpha, Beta, Delta variants, and Omicron variants/subvariants diverged in May 2020. After that, a common ancestor of the Omicron variant generated various Omicron subvariants over one year. Furthermore, a chimeric virus between the BM.1.1.1 and BJ.1 subvariants, known as XBB, diverged in July 2021, leading to the emergence of the prevalent subvariants XBB.1.5 and XBB.1.16. Next, similarity plot (SimPlot) data estimated that the recombination point (breakpoint) corresponded to nucleotide position 1373. As a result, XBB.1.5 subvariants had the 5′ nucleotide side from the breakpoint as a strain with a BJ.1 sequence and the 3′ nucleotide side as a strain with a BM.1.1.1 sequence. Genome network data showed that Omicron subvariants were genetically linked with the common ancestors of the Wuhan and Delta variants, resulting in many amino acid mutations. Selective pressure analysis estimated that the prevalent subvariants, XBB.1.5 and XBB.1.16, had specific amino acid mutations, such as V445P, G446S, N460K, and F486P, located in the RBD when compared with the BA.4 and BA.5 subvariants. Moreover, some representative immunogenicity-associated amino acid mutations, including L452R, F486V, R493Q, and V490S, were also found in these subvariants. These substitutions were involved in the conformational epitopes, implying that these mutations affect immunogenicity and vaccine evasion. Furthermore, these mutations were identified as positive selection sites. These results suggest that the S gene/S protein Omicron subvariants rapidly evolved, and mutations observed in the conformational epitopes may reduce the effectiveness of the current vaccine, including bivalent vaccines such as mRNA vaccines containing the BA.4/BA.5 subvariants. Full article
(This article belongs to the Special Issue Molecular Epidemiology, Diagnostics and Management of Respiratory Virus Infections 2.0)
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12 pages, 272 KiB  
Article
Pathogen Profiles in Outpatients with Non-COVID-19 during the 7th Prevalent Period of COVID-19 in Gunma, Japan
by Hirokazu Kimura, Yuriko Hayashi, Masanari Kitagawa, Miwa Yoshizaki, Kensuke Saito, Kazuhiko Harada, Kaori Okayama, Yusuke Miura, Ryusuke Kimura, Tatsuya Shirai, Kiyotaka Fujita, Suguru Machida, Kazuto Ito and Isao Kurosawa
Microorganisms 2023, 11(9), 2142; https://doi.org/10.3390/microorganisms11092142 - 24 Aug 2023
Cited by 1 | Viewed by 1608
Abstract
The identification of pathogens associated with respiratory symptoms other than the novel coronavirus disease 2019 (COVID-19) can be challenging. However, the diagnosis of pathogens is crucial for assessing the clinical outcome of patients. We comprehensively profiled pathogens causing non-COVID-19 respiratory symptoms during the [...] Read more.
The identification of pathogens associated with respiratory symptoms other than the novel coronavirus disease 2019 (COVID-19) can be challenging. However, the diagnosis of pathogens is crucial for assessing the clinical outcome of patients. We comprehensively profiled pathogens causing non-COVID-19 respiratory symptoms during the 7th prevalent period in Gunma, Japan, using deep sequencing combined with a next-generation sequencer (NGS) and advanced bioinformatics technologies. The study included nasopharyngeal swabs from 40 patients who tested negative for severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) using immuno-chromatography and/or quantitative reverse transcription polymerase chain reaction (qRT-PCR) methods. Comprehensive pathogen sequencing was conducted through deep sequencing using NGS. Additionally, short reads obtained from NGS were analyzed for comprehensive pathogen estimation using MePIC (Metagenomic Pathogen Identification Pipeline for Clinical Specimens) and/or VirusTap. The results revealed the presence of various pathogens, including respiratory viruses and bacteria, in the present subjects. Notably, human adenovirus (HAdV) was the most frequently detected virus in 16 of the 40 cases (40.0%), followed by coryneforms, which were the most frequently detected bacteria in 21 of the 40 cases (52.5%). Seasonal human coronaviruses (NL63 type, 229E type, HKU1 type, and OC43 type), human bocaviruses, and human herpesviruses (human herpesvirus types 1–7) were not detected. Moreover, multiple pathogens were detected in 50% of the subjects. These results suggest that various respiratory pathogens may be associated with non-COVID-19 patients during the 7th prevalent period in Gunma Prefecture, Japan. Consequently, for an accurate diagnosis of pathogens causing respiratory infections, detailed pathogen analyses may be necessary. Furthermore, it is possible that various pathogens, excluding SARS-CoV-2, may be linked to fever and/or respiratory infections even during the COVID-19 pandemic. Full article
(This article belongs to the Special Issue Molecular Epidemiology, Diagnostics and Management of Respiratory Virus Infections 2.0)
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