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Viruses
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Influenza and Other Respiratory Viruses: Prevention, Diagnosis, Treatment: 3rd Edition
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Influenza and Other Respiratory Viruses: Prevention, Diagnosis, Treatment: 3rd Edition

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Animal Viruses".

Deadline for manuscript submissions: 31 October 2026 | Viewed by 5968

Editor

Dr. Eric Yager

E-Mail Website
Guest Editor
Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, 106 New Scotland Avenue, Albany, NY 12208, USA
Interests: RNA viruses; influenza; vaccine development; antiviral development; viral immunology; viral pathogenesis; molecular virology; virus–host interaction
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Viral respiratory infections are the most common diseases in humans, contributing to substantial morbidity, mortality, and economic losses annually worldwide. As the world continues to deal with COVID-19, upsurges in infections caused by other respiratory viruses, such as influenza, respiratory syncytial virus, parainfluenza, metapneumovirus, bocaviruses, and non-rhinovirus enteroviruses, have burdened healthcare systems in several countries. Because of their transmissibility, advances in the diagnosis and surveillance of these respiratory viruses are critically needed to guide the use of available therapeutics, the allocation of hospital as well as community resources, and the targeting of vaccination in addition to behavioral change campaigns by public health officials to mitigate their spread. Furthermore, since many of these respiratory viruses have limited therapeutic options and lack effective vaccines, there is an urgent need for further research into the biology of these viruses to help guide the development of effective strategies for the treatment and prevention of infection.

This Special Issue of Viruses seeks to attract original research and review articles focused on (1) advances and innovations in the development of highly sensitive diagnostic tests for the early detection of human respiratory virus infections; (2) timely findings on the epidemiology and transmission of human respiratory viruses; (3) the development and clinical trials of new vaccines, antivirals, and immunotherapeutics for influenza, RSV, coronaviruses, and other clinically relevant human respiratory viruses; (4) studies detailing the effectiveness and/or immunogenicity of existing vaccines; and (5) mitigation measures or strategies to reduce viral transmission/community spread, disease incidence in at-risk populations, and cross-species transmission.

Dr. Eric Yager
Guest Editor

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-anonymized 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

  • influenza
  • adenovirus
  • coronoavirus
  • respiratory syncytial virus
  • rhinovirus
  • respiratory virus
  • antiviral strategies
  • epidemiology
  • diagnosis
  • treatment
  • vaccination
  • surveillance
  • vaccine development

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Related Special Issues

Published Papers (4 papers)

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Research

10 pages, 2169 KB  
Communication
Genotype Diversity of Highly Pathogenic Avian Influenza H5N1 Clade 2.3.4.4b in Pennsylvania Poultry During Disease Outbreak from April 2022 to March 2023
by Deepanker Tewari, Manoj K. Sekhwal, Chrislyn Nicholson, Mary L. Killian, Corey Zellers, Julia Livengood, Kristina Lantz, Mia Torchetti and Alex Hamberg
Viruses 2026, 18(5), 502; https://doi.org/10.3390/v18050502 - 28 Apr 2026
Viewed by 1193
Abstract
The 2022 highly pathogenic avian influenza (HPAI) outbreak of H5N1 clade 2.3.4.4b was one of the major avian influenza outbreaks, leading to multiple spillover events infecting domestic and wild bird flocks, as well as mammals. The sustained spread was a result of viral [...] Read more.
The 2022 highly pathogenic avian influenza (HPAI) outbreak of H5N1 clade 2.3.4.4b was one of the major avian influenza outbreaks, leading to multiple spillover events infecting domestic and wild bird flocks, as well as mammals. The sustained spread was a result of viral circulation in wild birds across migratory flyways in North America. Pennsylvania has a significant poultry population that supports both retail and live bird markets. The state also features migratory bird stopovers on the Atlantic flyway, increasing exposure to HPAI infections. This study investigates clinical presentation and sequence data from H5N1 clade 2.3.4.4b viruses during the 2022 outbreak in Pennsylvania. Eight different H5N1 clade 2.3.4.4b genotypes were detected (A1, B1.1, B1.2, B1.3, B2.2, B3.3, B3.5, and one minor genotype) during the first year. The earliest detection was genotype A1, a fully Eurasian virus, in commercial poultry in April 2022. All other genotypes identified were reassortants of A1 with North American avian influenza gene segments (denoted with “B”). Genotype B3.3 was a rare genotype prior to the initial spillover into the live bird market system, but remained predominant among backyard flocks in Pennsylvania and surrounding states until September 2023. Genotype B3.3 has not been detected in migratory waterfowl since, suggesting the genotype has waned and is no longer in circulation. This study sheds light on the genotype diversity of H5N1 during the 2022 outbreak in Pennsylvania poultry, contributing to the understanding of virus evolution and its potential impacts. Full article
(This article belongs to the Special Issue Influenza and Other Respiratory Viruses: Prevention, Diagnosis, Treatment: 3rd Edition)
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23 pages, 4838 KB  
Article
Nationwide Genomic Surveillance of Human Respiratory Adenoviruses in 2023–2024: Evidence of Extensive Diversity and Recombination in Russia
by Nikita D. Yolshin, Anna A. Ivanova, Alexander A. Perederiy, Irina V. Amosova, Tatyana A. Timoshicheva, Kirill A. Stolyarov, Daria M. Danilenko, Dmitry A. Lioznov and Andrey B. Komissarov
Viruses 2026, 18(1), 136; https://doi.org/10.3390/v18010136 - 21 Jan 2026
Cited by 2 | Viewed by 1332
Abstract
Human adenoviruses (HAdVs) are globally distributed pathogens capable of causing a wide range of clinical manifestations, particularly acute respiratory infections. However, their genomic diversity remains insufficiently characterized, with substantial geographic gaps in available sequence data, including for Russia, where only a few complete [...] Read more.
Human adenoviruses (HAdVs) are globally distributed pathogens capable of causing a wide range of clinical manifestations, particularly acute respiratory infections. However, their genomic diversity remains insufficiently characterized, with substantial geographic gaps in available sequence data, including for Russia, where only a few complete genomes have been deposited prior to this work. In this study, we analyzed more than 1200 PCR-positive respiratory specimens collected from hospitalized patients within routine surveillance projects and the Global Influenza Hospital Surveillance Network (GIHSN) across plenty of Russian regions during 2023–2024. Virus isolation followed by next-generation sequencing yielded 128 complete HAdV genomes representing species B, C, and D. The dataset included 27 B3, 9 B7, 44 B55, 12 C1, 16 C2, 4 C5, 7 C89, 5 C108, and one D109 genome, as well as three unassigned recombinant viruses with p89h5f5, p5h6f6 and p5h57f6 genomic structures (p, penton base; h, hexon; f, fiber). Phylogenetic analyses of whole genomes and capsid genes revealed extensive variability in immunogenic regions, particularly in species C, and identified clusters within B3 viruses. Notably, HAdV-D109 was identified in Russia, marking only the second reported detection of this genotype worldwide. Together, these findings substantially expand the currently available genomic landscape of HAdVs, highlighting the circulation of diverse and recombinant strains in Russia. Full article
(This article belongs to the Special Issue Influenza and Other Respiratory Viruses: Prevention, Diagnosis, Treatment: 3rd Edition)
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16 pages, 3513 KB  
Communication
Cnidium monnieri Polysaccharides Exhibit Inhibitory Effect on Airborne Transmission of Influenza A Virus
by Heng Wang, Yifei Jin, Yanrui Li, Yan Wang, Yixin Zhao, Shuang Cheng, Zhenyue Li, Mengxi Yan, Zitong Yang, Xiaolong Chen, Yan Zhang, Zhixin Yang, Zhongyi Wang, Kun Liu and Ligong Chen
Viruses 2026, 18(1), 86; https://doi.org/10.3390/v18010086 - 8 Jan 2026
Viewed by 1021
Abstract
Influenza A virus (IAV) continues to present a threat to public health, highlighting the need for safe and multi-target antivirals. In this study, anti-influenza activity, airborne transmission blocking capacity, and immunomodulatory effects of Cnidium monnieri polysaccharides (CMP) were evaluated. Cytotoxicity in A549 cells [...] Read more.
Influenza A virus (IAV) continues to present a threat to public health, highlighting the need for safe and multi-target antivirals. In this study, anti-influenza activity, airborne transmission blocking capacity, and immunomodulatory effects of Cnidium monnieri polysaccharides (CMP) were evaluated. Cytotoxicity in A549 cells was assessed by CCK-8 (CC50 = 8.49 mg/mL), antiviral efficacy against A/California/04/2009 (CA04) by dose–response (EC50 = 1.63 mg/mL), and the stage of action by time-of-addition assays (pre-, co-, post-treatment). A guinea pig model infected with CA04 was used for testing the effect of pre-exposure CMP on transmission, with readouts including nasal-wash titers, seroconversion, lung index, and tissue titers (EID50). RT-qPCR was employed to quantify the mRNA expression levels of proinflammatory cytokines, including TNF-α, IL-1β, and IL-6, in lung tissue, while Western blot analysis was performed to assess the expression and phosphorylation status of key proteins involved in the NF-κB signaling pathway. CMP suppressed viral replication in vitro within non-cytotoxic ranges, and pre-treatment—rather than co- or post-treatment—significantly reduced titers and cytopathic effect, consistent with effects at pre-entry steps and/or host priming. In vivo, pre-exposure CMP lowered nasal shedding, reduced aerosol transmission (3/6 seroconverted vs. 6/6 controls), decreased lung indices, and diminished tissue viral loads; IAV was undetectable in trachea at 7 days post-infection in pre-exposed animals, and nasal-turbinate titers declined relative to infection controls. Moreover, during in vivo treatment in mice, CMP significantly suppressed the levels of inflammatory cytokines (TNF-α, IL-1β, and IL-6) in lung tissue. This effect was mechanistically associated with CMP-mediated regulation of the NF-κB signaling pathway, leading to attenuation of inflammatory responses. These data indicate that CMP combines a favorable in vitro safety and efficacy profile with inhibition of airborne spread in vivo, supporting further mechanistic, pharmacokinetic, and fractionation studies toward translational development. Full article
(This article belongs to the Special Issue Influenza and Other Respiratory Viruses: Prevention, Diagnosis, Treatment: 3rd Edition)
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19 pages, 7447 KB  
Article
Influenza PA Substitutions and Genetic Diversity of A(H1N1)pdm09, A(H3N2), and B/Victoria Viruses in Japan During the 2023–2024 Season
by Nanjun Lee, Julian W. Tang, Irina Chon, Fujio Kakuya, Ryuta Terao, Takashi Kawashima, Isamu Sato, Naoki Kodo, Eitaro Suzuki, Hironori Masaki, Norichika Asoh, Yutaka Shirahige, Hirotsune Hamabata, Tsutomu Tamura, Keita Wagatsuma, Yuyang Sun, Jiaming Li, Tri Bayu Purnama, Yusuke Ichikawa, Hisami Watanabe and Reiko Saitoadd Show full author list remove Hide full author list
Viruses 2026, 18(1), 13; https://doi.org/10.3390/v18010013 - 21 Dec 2025
Cited by 1 | Viewed by 1789
Abstract
We characterized influenza A(H1N1)pdm09, A(H3N2), and B/Victoria viruses circulating in Japan during 2023–2024, focusing on lineage placement relative to WHO-recommended vaccine strains and on baloxavir resistance (PA/I38T substitutions). We enrolled 210 outpatients with influenza-like illness across eight clinics in six prefectures (October 2023–September [...] Read more.
We characterized influenza A(H1N1)pdm09, A(H3N2), and B/Victoria viruses circulating in Japan during 2023–2024, focusing on lineage placement relative to WHO-recommended vaccine strains and on baloxavir resistance (PA/I38T substitutions). We enrolled 210 outpatients with influenza-like illness across eight clinics in six prefectures (October 2023–September 2024). Of these, 209 had an analyzable pre-treatment respiratory specimen for RT-PCR; hemagglutinin (HA) and neuraminidase (NA) genes were sequenced by next-generation sequencing (NGS). PA/I38T substitutions that confer baloxavir resistance were assessed by cycling-probe RT-PCR, Sanger sequencing, and NGS. HA phylogenies were constructed with global datasets and WHO vaccine reference strains. Of 209 pre-treatment specimens, 181 were influenza-positive (A(H1N1)pdm09 44.2%, A(H3N2) 37.6%, B/Victoria 18.2%); 51 follow-up specimens were collected ≈4–5 days after baloxavir or neuraminidase inhibitor therapy. HA phylogeny placed A(H1N1)pdm09 in clades 5a.2a/5a.2a.1 with predominance of subclade D.2. A(H3N2) clustered exclusively in clade 2a.3a.1 (J lineage, mostly J.1), indicating a mismatch with the season’s A/Darwin/9/2021 vaccine component and supporting the subsequent J-lineage update. All B/Victoria genomes fell within V1A.3a.2 on a C.5 backbone (C.5.1 and C.5.7). No PA/I38T variant was detected in any pre-treatment specimen. Post-baloxavir, PA/I38T emerged in one A(H3N2) case (confirmed by all three methods) and in one B/Victoria case detected by NGS only (minority variant in a low-load sample). NA genes showed no substitutions associated with reduced susceptibility to laninamivir (e.g., E119A, G147E). During 2023–2024, A(H1N1)pdm09 and B/Victoria remained genetically aligned with their vaccine components, whereas A(H3N2) shifted to the J lineage, consistent with the 2024–2025 vaccine update. Although pre-treatment PA/I38T was absent, low-frequency on-therapy selection was observed, including a rare PA/I38T in influenza B/Victoria detected by NGS, suggesting the value of deep sequencing when viral loads are low. These integrated genomic–clinical data support vaccine strain realignment for H3N2 and continued monitoring of baloxavir resistance in outpatient care. Full article
(This article belongs to the Special Issue Influenza and Other Respiratory Viruses: Prevention, Diagnosis, Treatment: 3rd Edition)
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