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Viruses
Special Issues
Respiratory Viral Pathogenesis and Host-Microbe Crosstalk: From Bench to Bedside
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Respiratory Viral Pathogenesis and Host-Microbe Crosstalk: From Bench to Bedside

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Human Virology and Viral Diseases".

Deadline for manuscript submissions: 1 December 2026 | Viewed by 3706

Special Issue Editors

Prof. Dr. Shenghai Huang

E-Mail Website
Guest Editor
Department of Microbiology, The Institute of Clinical Virology, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
Interests: respiratory syncytial virus; pathogenesis; host-microbe crosstalk; viral RNA detection; prevention and treatment
Dr. Theo J. Moraes

E-Mail Website
Guest Editor
Division of Respiratory Medicine, SickKids, University of Toronto, Toronto, ON, Canada
Interests: respiratory epithelial cell biology; pediatric lung disease; respiratory viral infections; respiratory syncytial virus; asthma; cystic fibrosis; in vitro models; vaping

Special Issue Information

Dear Colleagues,

Respiratory viruses pose a significant global health threat, with clinical outcomes ranging from mild symptoms to severe pneumonia. Their clinical variability is driven by interactions among viruses, host immunity, and the respiratory microbiota. This special issue highlights recent advances in respiratory viral infections, focusing on the following key topics:

  • Epidemiology and Transmission：Exploring the transmission dynamics of SARS-CoV-2, influenza, and RSV, etc., with a focus on how virus–host interactions shape their spread.
  • Molecular and Cellular Biology：Insights into viral entry, replication, host–virus interactions, pathogenesis mechanisms, and mechanisms of immune evasion and cellular damage.
  • Immunology：Characterizing innate and adaptive immune responses, inflammatory regulation, and immunopathology such as cytokine storms.
  • Microbiota-Virus Interactions：Exploring how respiratory microbiota modulate immunity and influence disease severity in bacterial-viral co-infections.
  • Clinical Research：Translating fundamental discoveries into clinical applications through biomarkers, etiological diagnostics, and therapies, as well as disease management and the monitoring of progression.
  • Therapeutics and Vaccines：Advances in antivirals, immunotherapies, and vaccines to enhance prevention and the treatment of respiratory viruses.
  • Public Health and Policy：Developing evidence-based policies for epidemic preparedness, infection control, and improved respiratory disease management.

Prof. Dr. Shenghai Huang
Dr. Theo J. Moraes
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 250 words) can be sent to the Editorial Office for assessment.

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. Viruses 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 2600 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

  • respiratory viruses
  • pathogenesis
  • host–microbe crosstalk
  • etiological diagnosis
  • prevention and treatment
  • RSV
  • influenza
  • coronavirus

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Published Papers (4 papers)

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Research

18 pages, 1372 KB  
Article
Changes in Seasonal Patterns of Pediatric Respiratory Viral Infections Before, During, and After the COVID-19 Pandemic: A Seventeen-Year Surveillance Study in the Republic of Korea
by Mi-Ru Oh, Jeong Su Han, Jae-Sik Jeon and Jae Kyung Kim
Viruses 2026, 18(4), 420; https://doi.org/10.3390/v18040420 - 29 Mar 2026
Viewed by 553
Abstract
The coronavirus disease 19 pandemic disrupted pediatric respiratory infections through non-pharmaceutical interventions and altered contact patterns. Long-term comparisons across the pandemic timeline in children remain limited. In this study, we analyzed 15,657 respiratory specimens from patients ≤ 18 years at Dankook University Hospital [...] Read more.
The coronavirus disease 19 pandemic disrupted pediatric respiratory infections through non-pharmaceutical interventions and altered contact patterns. Long-term comparisons across the pandemic timeline in children remain limited. In this study, we analyzed 15,657 respiratory specimens from patients ≤ 18 years at Dankook University Hospital (2007–2023) using multiplex polymerase chain reaction assays targeting 15 viruses. Age-stratified positivity rates were compared across pandemic phases. Children ≤ 6 years comprised 88.61% of the study population. Human rhinovirus showed the highest detection rate (24.06%), followed by adenovirus (12.33%), respiratory syncytial virus-subtypes A and B (RSV-A: 11.13%; RSV-B: 8.65%), human parainfluenza virus-type 3 (HPIV-3; 6.21%), human metapneumovirus (HMPV; 5.33%), and enterovirus (2018–2023; EV; 10.96%). Monthly distributions differed (p < 0.001). RSV peaked in late autumn and winter; influenza and seasonal coronaviruses in winter and spring; HMPV, HPIV-3, EV, and human bocavirus in summer and fall. Positivity declined during the pandemic, rebounding in 2023, most prominently among children aged 1–6 years (84.91%). HPIV-3 and EV increased (p < 0.001). RSV-A predominated pre-pandemic, whereas RSV-B showed a non-significant relative increase post-pandemic; no subtype differences occurred during the pandemic. Findings demonstrate pathogen-specific shifts in predominance and seasonality and support ongoing surveillance and pediatric care planning. Full article
(This article belongs to the Special Issue Respiratory Viral Pathogenesis and Host-Microbe Crosstalk: From Bench to Bedside)
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15 pages, 2655 KB  
Article
Post-Mortem Detection and Visualization of Mimivirus Reactivation in Fatal Viral Pneumonia
by Parandzem Khachatryan, Naira Karalyan, Anna Semerjyan, Marina Tatoyan, Hakob Davtyan, Arsham Yeremyan, Sona Hakobyan, Hranush Avagyan, Lina Hakobyan, Liana Abroyan, Aida Avetisyan, Elena Karalova, Nane Bayramyan, Tigranuhi Vardanyan, Vahagn Gevorgyan, Elina Arakelova, Alexandr Karalyan and Zaven Karalyan
Viruses 2026, 18(3), 379; https://doi.org/10.3390/v18030379 - 18 Mar 2026
Viewed by 684
Abstract
Mimivirus, a giant double-stranded DNA virus ($1.2$ Mbp), possesses unique bacteria-like features, including a Gram-positive staining reaction due to peptidoglycan-containing surface fibers. While detected in the respiratory secretions of pneumonia patients since 2005, its clinical role remains controversial due to high genetic variability [...] Read more.
Mimivirus, a giant double-stranded DNA virus ($1.2$ Mbp), possesses unique bacteria-like features, including a Gram-positive staining reaction due to peptidoglycan-containing surface fibers. While detected in the respiratory secretions of pneumonia patients since 2005, its clinical role remains controversial due to high genetic variability and detection challenges. This study aims to clarify the pathological significance of Mimivirus by investigating its presence and replication potential in human lung tissue, specifically exploring its association with fatal respiratory outcomes. A comparative post-mortem analysis was conducted on lung tissue samples from two cohorts: patients who succumbed to lethal viral pneumonia and a control group with no history of pulmonary pathology. Mimivirus is known to productively infect alveolar macrophages, suggesting they may serve as a reservoir for lung inflammation and tissue damage. Current evidence suggests it may act as an opportunistic or commensal agent, particularly in immunocompromised or critically ill patients. By systematically screening autopsy samples, this research seeks to establish whether Mimivirus is a primary causative agent of fatal pneumonia or an incidental inhabitant of the human respiratory tract. Full article
(This article belongs to the Special Issue Respiratory Viral Pathogenesis and Host-Microbe Crosstalk: From Bench to Bedside)
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17 pages, 2330 KB  
Article
Monopoly of Minor Group Rhinovirus Infections in Hospitalised Children in Hong Kong During the SARS-CoV-2 Pandemic
by Jason Chun Sang Pun, Kin Pong Tao, Shaojun Liu, Ben Kam San Wong, Tony Chun Hei Lei, Lucky Lu Yi Tsoi, Joseph Gar Shun Tsun, Agnes Sze Yin Leung, Paul Kay Sheung Chan and Renee Wan Yi Chan
Viruses 2025, 17(10), 1316; https://doi.org/10.3390/v17101316 - 28 Sep 2025
Viewed by 1088
Abstract
Background: While rhinoviruses (RVs) typically cause mild respiratory infections, their persistence during the SARS-CoV-2 pandemic, particularly in Hong Kong’s strict zero-coronavirus disease 2019 policy, revealed unexpected epidemiological patterns. Two distinct RV surges emerged despite stringent public health measures, suggesting unique transmission advantages among [...] Read more.
Background: While rhinoviruses (RVs) typically cause mild respiratory infections, their persistence during the SARS-CoV-2 pandemic, particularly in Hong Kong’s strict zero-coronavirus disease 2019 policy, revealed unexpected epidemiological patterns. Two distinct RV surges emerged despite stringent public health measures, suggesting unique transmission advantages among circulating strains. We hypothesised that RV persistence during pandemic restrictions reflected strain-specific adaptations in respiratory tract replication efficiency and/or immune evasion. Methods: We analysed RV genotypes and conducted blinded clinical severity assessment for 96 paediatric hospitalisations during 2020–2021 outbreaks, compared with 180 age- and sex-matched control subjects from the corresponding weeks in pre-pandemic years (2018–2019). RV isolates from 2020 to 2021 outbreaks were characterised for their replication competence and transcriptomic responses in primary human nasal epithelial cell (HNEC) and environmental stability assays, using RV-A16 and RV-A1B as controls. Result: Minor group genotypes RV-A47 and RV-A49 were overrepresented during these two outbreaks. RV-A49 exhibited comparable replication efficiency to RV-A16 but induced significantly stronger transcriptomic responses, notably enhanced TNF and IL-1 signalling, in HNECs, alongside robust replication competence. Our data also suggests the association of RV-A49 with tachypnoea in 2021, particularly in younger males, though limited by a small sample size and single-centre design. Conclusion: The predominance of RV-A49 in hospitalised children during the SARS-CoV-2 pandemic potentially driven by its replication competence in HNECs and its capacity to enhanced inflammatory responses. The result is hypothesis-generating, warranting further studies with historical strains and broader populations to confirm strain-specific severity. Full article
(This article belongs to the Special Issue Respiratory Viral Pathogenesis and Host-Microbe Crosstalk: From Bench to Bedside)
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13 pages, 709 KB  
Article
Co-Detection of ADV, Influenza B, and HPIV: Independent Risk Factors for SMPP with Changes in NPIs
by Linlin Huang and Ting Shi
Viruses 2025, 17(9), 1266; https://doi.org/10.3390/v17091266 - 19 Sep 2025
Cited by 1 | Viewed by 890
Abstract
Background: This study investigated the epidemiology of Mycoplasma pneumoniae (MP) in children with acute respiratory tract infections (ARTIs) and explored the risk factors for severe mycoplasma pneumoniae pneumonia (SMPP) in children. Methods: A retrospective analysis was conducted on 36,380 children with acute respiratory [...] Read more.
Background: This study investigated the epidemiology of Mycoplasma pneumoniae (MP) in children with acute respiratory tract infections (ARTIs) and explored the risk factors for severe mycoplasma pneumoniae pneumonia (SMPP) in children. Methods: A retrospective analysis was conducted on 36,380 children with acute respiratory infections who underwent multiplex real-time polymerase chain reaction (RT-PCR) assays for nine respiratory pathogens from September 2021 to November 2024. Results: A total of 36,380 children with ARTIs were enrolled in this study. The co-detection rate of MP with other pathogens was significantly higher in the post-NPIs period than in the NPIs period (36.5% vs. 25.7%, p < 0.01). Multivariate regression identified the detection of influenza A virus (InfA), InfB, human parainfluenza virus (HPIV), human bocaparvovirus (HBoV), human rhinovirus (HRV), adenovirus (ADV), human respiratory syncytial virus (HRSV), and human metapneumovirus (HMPV) as protective factors against MP epidemics (p < 0.01); meanwhile, older age, the cancellation of NPIs, and summer–autumn seasons were found to be risk factors. After adjusting for sex, age, period, season, and pathogens, InfB (OR: 3.009, 95%CI: 1.041–8.697, p = 0.042), HPIV (OR: 2.226, 95%CI: 1.170–4.235, p = 0.015), and ADV (OR: 2.035, 95%CI: 1.105–3.750, p = 0.023) were identified as independent risk factors for SMPP. Conclusions: These findings highlight post-NPI shifts in MP epidemiology and identify ADV, InfB, and HPIV as early warning markers for SMPP. Full article
(This article belongs to the Special Issue Respiratory Viral Pathogenesis and Host-Microbe Crosstalk: From Bench to Bedside)
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