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Viruses
Volume 17
Issue 6
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Viruses, Volume 17, Issue 6 (June 2025) – 131 articles

Cover Story (view full-size image): In this study, we conducted a comprehensive analysis of the interactions between the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein and four neutralizing antibodies—S309, S304, CYFN1006, and VIR-7229. Using integrative computational modeling that combined all-atom molecular dynamics (MD) simulations, mutational scanning, and MM-GBSA binding free energy calculations, we elucidated the structural, energetic, and dynamic determinants of antibody binding. Our findings reveal distinct dynamic binding mechanisms and evolutionary adaptation driving the broad neutralization effect of these antibodies. View this paper
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32 pages, 1658 KiB  
Review
Advances in Viroporin Function and Structure: A Comparative Analysis of Alphavirus 6K with Well-Characterized Viroporins
by Vashi Negi, Andrew S. Miller and Richard J. Kuhn
Viruses 2025, 17(6), 868; https://doi.org/10.3390/v17060868 - 19 Jun 2025
Viewed by 704
Abstract
Viruses encode ion channel proteins called viroporins to assist in infection and immune evasion. The alphavirus 6K protein is classified as a member of the viroporin family of proteins. Several studies have characterized the role of 6K in alphavirus budding and infection since [...] Read more.
Viruses encode ion channel proteins called viroporins to assist in infection and immune evasion. The alphavirus 6K protein is classified as a member of the viroporin family of proteins. Several studies have characterized the role of 6K in alphavirus budding and infection since its discovery in the late 1970s. In this review, we summarize 6K research and discuss some unanswered questions regarding 6K biology. We highlight the similarities and differences between 6K and viroporins of clinically relevant viruses—influenza A virus, HIV-1, hepatitis C virus, and SARS-CoV-2—and address their importance as therapeutic targets. The sensitivity of these viroporins to common inhibitors and their ability to functionally complement each other underscore their potential as targets for broad-spectrum antiviral therapies. Full article
(This article belongs to the Section Viral Immunology, Vaccines, and Antivirals)
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9 pages, 1391 KiB  
Brief Report
Discovery of a Novel Parahenipavirus, Parahenipavirus_GH, in Shrews in South Korea, 2022
by Gyuri Sim, Chi-Hwan Choi, Minji Lee, Hak Seon Lee, Seong Yoon Kim, Seung Hun Lee, Hee Il Lee and Yoon-Seok Chung
Viruses 2025, 17(6), 867; https://doi.org/10.3390/v17060867 - 19 Jun 2025
Viewed by 551
Abstract
Highly pathogenic henipaviruses (Nipah and Hendra viruses) and parahenipaviruses (Langya virus) have demonstrated significant zoonotic potential. We aimed to identify Henipavirus or Parahenipavirus species in rodents and shrews in South Korea to underline the potential zoonotic transmission risk. Kidney and lung tissues from [...] Read more.
Highly pathogenic henipaviruses (Nipah and Hendra viruses) and parahenipaviruses (Langya virus) have demonstrated significant zoonotic potential. We aimed to identify Henipavirus or Parahenipavirus species in rodents and shrews in South Korea to underline the potential zoonotic transmission risk. Kidney and lung tissues from 285 rodents and shrews were screened for Henipavirus and Parahenipavirus using quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) targeting the Gamak virus and Daeryong virus (DARV) sequences. Based on the qRT-PCR results, 75 out of the 285 individuals tested positive, with the highest viral loads in the kidneys of Apodemus agrarius, Crocidura lasiura, and Crocidura shantungensis. A kidney sample from C. shantungensis that exhibited the lowest Ct value was further analyzed using PCR, Sanger sequencing, and metagenomic analysis, yielding a near-complete genome of a novel Parahenipavirus, designated Parahenipavirus_GH (PHNV-GH), which is phylogenetically related to DARV and Jingmen virus but exhibits distinct genomic features. Ixodes granulatus ticks were also identified on the host shrew. The identification of PHNV-GH in southern South Korea expands the known geographical distribution range of parahenipaviruses and highlights the ongoing risk of zoonotic transmission. Given the uncertain transmission dynamics and pathogenic potential of parahenipaviruses, comprehensive environmental surveillance and characterization of emerging parahenipaviruses are essential for preventing future outbreaks. Full article
(This article belongs to the Special Issue Emerging Zoonotic Paramyxoviruses)
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17 pages, 5218 KiB  
Review
Trafficking and Activation of Henipavirus, Parahenipavirus, and Henipa-like Virus Fusion Proteins
by Chanakha K. Navaratnarajah and Roberto Cattaneo
Viruses 2025, 17(6), 866; https://doi.org/10.3390/v17060866 - 19 Jun 2025
Viewed by 393
Abstract
Henipaviruses are emerging zoonotic viruses that have caused deadly outbreaks in humans and livestock across several regions of the world. The fusion (F) protein of henipaviruses plays a critical role in viral entry into host cells and represents a key determinant of viral [...] Read more.
Henipaviruses are emerging zoonotic viruses that have caused deadly outbreaks in humans and livestock across several regions of the world. The fusion (F) protein of henipaviruses plays a critical role in viral entry into host cells and represents a key determinant of viral pathogenicity. This review provides a comprehensive analysis of current knowledge regarding trafficking, activation, as well as the role in particle assembly, of henipavirus F proteins. We discuss the unique characteristics of henipavirus F proteins compared to other paramyxovirus fusion proteins, with particular emphasis on their distinctive trafficking and activation mechanisms. Attention is also given to novel henipaviruses that have been detected in hosts other than bats, namely rodents and shrews. These viruses are sufficiently different that the International Committee on Taxonomy of Viruses has proposed a new genus for them, the Parahenipaviruses. We discuss how variations in F protein characteristics between Henipaviruses, Parahenipaviruses, and yet-unclassified henipa-like viruses might influence their trafficking and activation. Understanding these molecular mechanisms is crucial for developing effective therapeutic strategies against henipavirus infections and for predicting the emergence of novel henipavirus strains with pandemic potential. Full article
(This article belongs to the Special Issue 15-Year Anniversary of Viruses)
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17 pages, 1812 KiB  
Review
The Multigene Family Genes-Encoded Proteins of African Swine Fever Virus: Roles in Evolution, Cell Tropism, Immune Evasion, and Pathogenesis
by Ruojia Huang, Rui Luo, Jing Lan, Zhanhao Lu, Hua-Ji Qiu, Tao Wang and Yuan Sun
Viruses 2025, 17(6), 865; https://doi.org/10.3390/v17060865 - 19 Jun 2025
Viewed by 376
Abstract
African swine fever virus (ASFV), the causative agent of African swine fever (ASF), poses a catastrophic threat to global swine industries through its capacity for immune subversion and rapid evolution. Multigene family genes (MGFs)-encoded proteins serve as molecular hubs governing viral evolution, immune [...] Read more.
African swine fever virus (ASFV), the causative agent of African swine fever (ASF), poses a catastrophic threat to global swine industries through its capacity for immune subversion and rapid evolution. Multigene family genes (MGFs)-encoded proteins serve as molecular hubs governing viral evolution, immune evasion, cell tropism, and disease pathogenesis. This review synthesizes structural and functional evidence demonstrating that MGFs-encoded proteins suppress both interferon signaling and inflammasome activation, while their genomic plasticity in variable terminal regions drives strain diversification and adaptation. Translationally, targeted deletion of immunomodulatory MGFs enables the rational design of live attenuated vaccines that improve protective efficacy while minimizing residual virulence. Moreover, hypervariable MGFs provide strain-specific signatures for PCR-based diagnostics and phylogeographic tracking, directly addressing outbreak surveillance challenges. By unifying virology with translational innovation, this review establishes MGFs as priority targets for next-generation ASF countermeasures. Full article
(This article belongs to the Collection African Swine Fever Virus (ASFV))
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6 pages, 180 KiB  
Case Report
Brainstem Encephalitis: An Atypical Manifestation of Zika Virus Infection in Brazil
by Mateus Santana do Rosário, Pedro Antonio Pereira de Jesus, Italo Andrade Barbosa Lima, Marcos Vinicius Oliveira Francisco, Cleiton Silva Santos, Lorena Cunha Martins, Luiza Vieira Luedy Trindade, Ricardo Khouri and Isadora Cristina de Siqueira
Viruses 2025, 17(6), 864; https://doi.org/10.3390/v17060864 - 18 Jun 2025
Viewed by 328
Abstract
Zika virus (ZIKV), once considered a relatively benign pathogen, has emerged as a cause of severe neurological complications, including Guillain-Barrè Syndrome and encephalitis. This report presents the case of a 21-year-old Brazilian woman who initially presented with fever, rash, and arthralgia. Seven days [...] Read more.
Zika virus (ZIKV), once considered a relatively benign pathogen, has emerged as a cause of severe neurological complications, including Guillain-Barrè Syndrome and encephalitis. This report presents the case of a 21-year-old Brazilian woman who initially presented with fever, rash, and arthralgia. Seven days later, she developed confusion, speech impairment, and gait disturbance. Following a tonic-clonic seizure, neurological examination revealed dysphonia, dysarthria and facial palsy, suggestive of brainstem involvement. ZIKV infection was detected by positive IgM serology and a plaque reduction neutralization test. The patient was treated with corticosteroids and antiepileptic drugs, leading to substantial clinical improvement, and discharge after 25 days of hospitalization. This case underscores the neuroinvasive potential of ZIKV and highlights the importance of early recognition and management of atypical neurological manifestations. It also reinforces the need to consider ZIKV in the differential diagnosis of encephalitis, particularly in endemic regions, and contributes to the growing understanding of ZIKV neurotropism and possible therapeutic approaches for severe presentations. Full article
(This article belongs to the Special Issue Mosquito-Borne Encephalitis Viruses)
10 pages, 1350 KiB  
Brief Report
Complete Genome and Recombination Analysis of a Novel Porcine Reproductive and Respiratory Syndrome Virus 2 (Variant 1H.18) Identified in the Midwestern USA
by Joao P. Herrera da Silva, Stephanie Rossow, Igor A. D. Paploski, Mariana Kikuti, Cesar A. Corzo and Kimberly VanderWaal
Viruses 2025, 17(6), 863; https://doi.org/10.3390/v17060863 - 18 Jun 2025
Viewed by 398
Abstract
Porcine Reproductive and Respiratory Syndrome Virus 2 (PRRSV-2) represents one of the greatest threats to global pork production. Increased incidence of a genetic variant of Porcine Reproductive and Respiratory Syndrome Virus (variant 1H.18) was recently reported in the Midwestern USA Sequence comparisons in [...] Read more.
Porcine Reproductive and Respiratory Syndrome Virus 2 (PRRSV-2) represents one of the greatest threats to global pork production. Increased incidence of a genetic variant of Porcine Reproductive and Respiratory Syndrome Virus (variant 1H.18) was recently reported in the Midwestern USA Sequence comparisons in the ORF5 region indicate that 1H.18 was closely related to both sub-lineages L1H and L1C. To expand our understanding and attempt to elucidate the origin of the 1H.18, we sequenced a near-complete genome, covering all coding regions, and investigated the occurrence of recombination events that may have contributed to the emergence of the new variant. At least six distinct recombination events were identified across the coding portion of the genome. Evidence of recombination in the ORF5 region between variants 1H.31 and 1C.3 was detected. Our results suggest a likely origin of 1H.18 driven by recombination. Full article
(This article belongs to the Special Issue Research Progress on Porcine Reproductive and Respiratory Syndrome Virus)
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10 pages, 576 KiB  
Brief Report
First Molecular Evidence of Equine Herpesvirus Type 1 (EHV-1) in Ocular Swabs of Clinically Affected Horses
by Beatriz Musoles-Cuenca, Miguel Padilla-Blanco, Valentina Vitale, Teresa Lorenzo-Bermejo, María de la Cuesta-Torrado, Beatriz Ballester, Elisa Maiques, Consuelo Rubio-Guerri and Ana Velloso Alvarez
Viruses 2025, 17(6), 862; https://doi.org/10.3390/v17060862 - 18 Jun 2025
Viewed by 329
Abstract
Equine Herpesvirus Type 1 (EHV-1) is a significant pathogen within the Alphaherpesvirinae subfamily, causing respiratory disease, abortions, and, in severe cases, equine herpesvirus myeloencephalopathy (EHM). While nasal swabs and blood samples are commonly used for real-time polymerase chain reaction (RT-PCR) diagnosis, variability in [...] Read more.
Equine Herpesvirus Type 1 (EHV-1) is a significant pathogen within the Alphaherpesvirinae subfamily, causing respiratory disease, abortions, and, in severe cases, equine herpesvirus myeloencephalopathy (EHM). While nasal swabs and blood samples are commonly used for real-time polymerase chain reaction (RT-PCR) diagnosis, variability in viral shedding necessitates exploring additional sample types. This study reports the first molecular detection of EHV-1 in ocular swabs from naturally infected horses during an outbreak in the Valencian Community in 2023. Nasal and ocular swabs were collected from ten symptomatic horses and analyzed via RT-PCR. EHV-1 was detected in all cases, with higher viral loads in nasal samples. Although nasal swabs remain the most reliable sample for EHV-1 detection, the presence of viral DNA in tear fluid suggests a previously unrecognized route of viral shedding. These findings support further investigation into the role of ocular secretions in the pathogenesis and epidemiology of EHV-1. Additional studies are needed to determine the clinical relevance and potential utility of ocular swabs in specific outbreak scenarios. Full article
(This article belongs to the Special Issue Advances in Endemic and Emerging Viral Diseases in Livestock)
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13 pages, 239 KiB  
Review
A Comparison of Vaccination Policies and Immunity Assessment for Measles Control: Insights from the United States and Japan
by Naruhito Otani, Toshiomi Okuno, Toshie Tsuchida, Kaori Ishikawa, Kaoru Ichiki, Takashi Ueda, Satoshi Higasa and Kazuhiko Nakajima
Viruses 2025, 17(6), 861; https://doi.org/10.3390/v17060861 - 17 Jun 2025
Viewed by 424
Abstract
Measles is a highly contagious viral disease and remains a global health challenge despite the availability of effective vaccines. Although many regions have successfully eliminated measles, outbreaks continue to occur owing to vaccine hesitancy, inadequate coverage, and imported cases. Differences in epidemiology, vaccination [...] Read more.
Measles is a highly contagious viral disease and remains a global health challenge despite the availability of effective vaccines. Although many regions have successfully eliminated measles, outbreaks continue to occur owing to vaccine hesitancy, inadequate coverage, and imported cases. Differences in epidemiology, vaccination policies, and immunity assessment influence measles control across countries. This paper compares measles epidemiology, vaccination policies, and immunity assessment approaches in the United States and Japan. Data were obtained from surveillance reports, national immunization programs, and peer-reviewed literature. The introduction of the measles vaccine led to substantial reductions in incidence. The United States eliminated measles in 2000 but continues to experience outbreaks due to vaccine hesitancy and imported cases. Japan implemented a two-dose policy in 2006, reducing case numbers; however, sporadic outbreaks among adults persist. In the United States, immunity is primarily assessed using documented vaccination history, whereas in Japan, enzyme immunoassay is commonly used to evaluate immunity status. Despite progress in measles elimination, achieving high vaccination coverage and addressing vaccine hesitancy remain critical challenges. Variations in immunity assessment methods impact surveillance accuracy and outbreak control. Strengthening international collaboration, standardizing assessment protocols, and enhancing public health education are crucial for sustained measles elimination. Full article
(This article belongs to the Special Issue Measles, Mumps, and Rubella)
16 pages, 1128 KiB  
Article
Surveillance of Respiratory Pathogens Among Rapid Diagnostic Test-Negative Acute Respiratory Infection Patients in Myanmar in 2023, with a Focus on Rhinovirus and Enterovirus Genotyping
by Yuyang Sun, Tsutomu Tamura, Yadanar Kyaw, Swe Setk, Moe Myat Aye, Htay Htay Tin, Su Mon Kyaw Win, Jiaming Li, Tri Bayu Purnama, Irina Chon, Keita Wagatsuma, Hisami Watanabe and Reiko Saito
Viruses 2025, 17(6), 860; https://doi.org/10.3390/v17060860 - 17 Jun 2025
Viewed by 476
Abstract
This study explored the distribution and genetic characteristics of respiratory pathogens in outpatients with acute respiratory infections (ARIs) in Yangon, Myanmar, during the 2023 rainy season. Among 267 patients who tested negative for influenza, RSV, and SARS-CoV-2 using rapid diagnostic tests, 84.6% were [...] Read more.
This study explored the distribution and genetic characteristics of respiratory pathogens in outpatients with acute respiratory infections (ARIs) in Yangon, Myanmar, during the 2023 rainy season. Among 267 patients who tested negative for influenza, RSV, and SARS-CoV-2 using rapid diagnostic tests, 84.6% were positive for at least one pathogen according to a multiplex polymerase chain reaction (PCR) assay, the BioFire® FilmArray® Respiratory Panel 2.1. The most common viruses detected were rhinovirus/enterovirus (RV/EV) at 37.8%, respiratory syncytial virus (RSV) at 22.4%, and human metapneumovirus (hMPV) at 10.0%. These pathogens co-circulated mainly from July to September, with RV/EV consistently predominant. Symptom comparison among RV/EV-, RSV-, and hMPV-infected patients showed similar clinical features, though fever was more common in hMPV cases. Among RV/EV-positive patients, 59.3% had single infections, while 40.7% experienced co-infections, especially with RSV and adenovirus. Genotyping identified 28 types from five species, primarily RV-A and RV-C, which were genetically diverse. One EV-D68 case was also found, emphasizing its potential risk. This study underscores the genetic diversity and clinical impact of RV/EV and stresses the importance of ongoing molecular surveillance in Myanmar’s post-COVID-19 context to inform effective public health responses. Full article
(This article belongs to the Special Issue Influenza and Other Respiratory Viruses: Prevention, Diagnosis, Treatment: 2nd Edition)
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13 pages, 2750 KiB  
Article
Dengue Infections Among Household Contacts of Symptomatic Index Cases: Implications for Community-Based Intervention Studies
by Erik Koehne, Liesbeth Van Wesenbeeck, Martin L. Hibberd, Annemie Buelens, Michiko Toizumi, Kim De Clerck, Leen Vijgen, Ole Lagatie, Lucy Masdin, Hien Anh Thi Nguyen, Hoang Huy Le, Duc Anh Dang, Mai Kim Huynh, Lien Thuy Le, Trieu Bao Nguyên, Stephane Hue, Hung Thai Do, Guillermo Herrera-Taracena, Freya Rasschaert and Lay-Myint Yoshida
Viruses 2025, 17(6), 859; https://doi.org/10.3390/v17060859 - 17 Jun 2025
Viewed by 389
Abstract
Background: Dengue is a global health concern, with half of the world’s population at risk and no antiviral treatment available. This Phase 0 study investigated dengue infections among household contacts (HHCs) of dengue index cases (ICs) and assessed the feasibility of conducting a [...] Read more.
Background: Dengue is a global health concern, with half of the world’s population at risk and no antiviral treatment available. This Phase 0 study investigated dengue infections among household contacts (HHCs) of dengue index cases (ICs) and assessed the feasibility of conducting a Phase 2 trial for a novel antiviral. Methods: Participants were enrolled in Nha Trang, Vietnam, from April 2022 to February 2023. Dengue ICs were identified within 72 h of fever onset, and their healthy adult HHCs enrolled within 48 h. Blood samples and questionnaires were collected bi-weekly for four weeks, with a follow-up visit on day 40. DENV RT-qPCR, NS1, and anti-DENV IgM/IgG ELISAs were performed. Results: Overall, 130 dengue ICs and 301 HHCs were enrolled, with 91.7% (276/301) completing all follow-up visits. Baseline anti-DENV IgG showed prior dengue infections in 262/301 HHCs (87.0%). Fifty HHCs were excluded from the HHC infection analysis based on evidence of a DENV infection (viral load [VL], NS1, IgM, and IgG results) at enrollment. During follow-up, 2.0% of HHCs (5/251) had DENV infections based on virological parameters (DENV RNA and/or NS1 positivity), and anti-DENV IgG/IgM seroconversion was detected in 7.2% (18/251). Conclusions: This study demonstrated the operational feasibility of a dengue IC-HHC design for a Phase 2 trial. Full article
(This article belongs to the Section Viral Immunology, Vaccines, and Antivirals)
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19 pages, 1819 KiB  
Article
Rotavirus alphagastroenteritidis: Circulating Strains After the Introduction of the Rotavirus Vaccine (Rotarix®) in Luanda Province of Angola
by Dikudila G. Vita, Cristina Santiso-Bellón, Manuel Lemos, Zoraima Neto, Elsa Fortes-Gabriel, Miguel Brito, Cruz S. Sebastião, Jesus Rodriguez-Diaz, Celso Cunha and Claudia Istrate
Viruses 2025, 17(6), 858; https://doi.org/10.3390/v17060858 - 17 Jun 2025
Viewed by 614
Abstract
Rotavirus alphagastroenteritidis (R. alphagastroenteritidis) remains the leading cause of pediatric diarrhea. Although Angola introduced Rotarix®, the human monovalent R. alphagastroenteritidis vaccine since 2014 as part of its routine childhood immunization program, no follow-up study has been conducted. [...] Read more.
Rotavirus alphagastroenteritidis (R. alphagastroenteritidis) remains the leading cause of pediatric diarrhea. Although Angola introduced Rotarix®, the human monovalent R. alphagastroenteritidis vaccine since 2014 as part of its routine childhood immunization program, no follow-up study has been conducted. The aim of this study was to evaluate the distribution of R. alphagastroenteritidis genotypes among children under five years of age, hospitalized with acute gastroenteritis (AGE), after the introduction of the rotavirus vaccine. To achieve this goal, stool samples collected between 2021 and 2022 from children under 5 years of age diagnosed with AGE at six hospitals in Luanda Province were analyzed. The R. alphagastroenteritidis-antigen immunochromatographic test (SD Bioline™, Abbott, Chicago, IL, USA) was performed, and 121 positive samples were genotyped. Ten samples were randomly selected for further Sanger sequencing. The results showed that the G9P[6] was the most prevalent genotype (17.3%), followed by G9P[8] (16.5%), G2P[4] (14.9%), G3P[6] (13.2%), G8P[6] (11.5%), and less frequently G12P[8] (9.1%), G1P[6] (4.1%), and G1P[8] (2.5%). The genotype combinations G3P[6], G8P[6], and G12P[8] were detected for the first time in Luanda Province. In conclusion, the emergence of new genotype combinations supports the need for continuous surveillance to identify the trend in R. alphagastroenteritidis infection and the emergence of new strains circulating in Luanda Province in the post-vaccination period. Full article
(This article belongs to the Special Issue Viruses Associated with Gastroenteritis)
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24 pages, 488 KiB  
Systematic Review
Transmission Pathways of Zoonotic Influenza Viruses and Influencing Factors: A Systematic Review of Recent Findings
by Rebecca Badra, Wenqing Zhang, John S. L. Tam, Richard Webby, Sylvie van der Werf, Sergejs Nikisins, Ann Cullinane, Saad Gharaibeh, Richard Njouom, Malik Peiris, Ghazi Kayali and Jean-Michel Heraud
Viruses 2025, 17(6), 857; https://doi.org/10.3390/v17060857 - 17 Jun 2025
Viewed by 567
Abstract
Recent outbreaks of zoonotic influenza viruses underscored the need for a deeper understanding of transmission pathways and factors influencing spillover events. Understanding the combined effects of environmental conditions, host interactions, and viral adaptations is essential for effective preparedness and response. The WHO public [...] Read more.
Recent outbreaks of zoonotic influenza viruses underscored the need for a deeper understanding of transmission pathways and factors influencing spillover events. Understanding the combined effects of environmental conditions, host interactions, and viral adaptations is essential for effective preparedness and response. The WHO public health research agenda for influenza, revised in 2017, recommended research to further define the host-to-host transmission pathways of influenza type A viruses. Since 2017, important research has been conducted, and the global health landscape has changed. Therefore, there is a need to review the transmission pathway studies conducted during the last eight years. We conducted a systematic analysis following the PRISMA guidelines on 7490 PubMed records from 2017 to 2024, of which 219 records were retained. This review evaluates research on zoonotic influenza virus transmission among wild and domestic animals and cross-species transmission to humans. By examining pathways, host, environmental, and viral factors, this review identified key findings and research gaps. Research remains limited in critical areas including transmission pathways among diverse animals, role of environmental factors, and zoonotic potential across regions. Addressing these gaps is essential for improving public health strategies. This review highlights the necessity of integrating a One Health approach in addressing zoonotic influenza risks. Full article
(This article belongs to the Section Human Virology and Viral Diseases)
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15 pages, 1340 KiB  
Article
Intersegment Recombination During Influenza A Virus Replication Gives Rise to a Novel Class of Defective Viral Genomes
by Soraya Anisi, George Noble, Rory Williams, Jack Hales, Hannah E. Bridgewater, Andrew Easton, William Collier and Phillip Gould
Viruses 2025, 17(6), 856; https://doi.org/10.3390/v17060856 - 16 Jun 2025
Viewed by 461
Abstract
Influenza A virus (IAV) is a highly diverse pathogen with genetic variability primarily driven by mutation and reassortment. Using next-generation sequencing (NGS), we characterised defective viral genomes (DVGs) generated during the serial passaging of influenza A/Puerto Rico/8/1934 (H1N1) virus in embryonated chicken eggs. [...] Read more.
Influenza A virus (IAV) is a highly diverse pathogen with genetic variability primarily driven by mutation and reassortment. Using next-generation sequencing (NGS), we characterised defective viral genomes (DVGs) generated during the serial passaging of influenza A/Puerto Rico/8/1934 (H1N1) virus in embryonated chicken eggs. Deletions were the most abundant DVG type, predominantly accumulating in the polymerase-encoding segments. Notably, we identified and validated a novel class of multisegment DVGs arising from intersegment recombination events, providing evidence that the IAV RNA polymerase can detach from one genomic template and resume synthesis on another. Multisegment recombination primarily involved segments 1–3 but also occurred between other segment pairings. In specific lineages, certain multisegment DVGs reached high frequencies and persisted through multiple passages, suggesting they are not transient by-products of recombination but may possess features that support stable maintenance. Furthermore, multisegment DVGs were shown to be encapsidated within virions, similar to deletion DVGs. The observation of recombination between segments with limited sequence homology underscores the potential for complex recombination to expand IAV genetic diversity. These findings suggest recombination-driven DVGs represent a previously underappreciated mechanism in influenza virus evolution. Full article
(This article belongs to the Section Human Virology and Viral Diseases)
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12 pages, 570 KiB  
Article
The Seroprevalence of Influenza A Virus Infections in Polish Cats During a Feline H5N1 Influenza Outbreak in 2023
by Anna Golke, Tomasz Dzieciątkowski, Olga Szaluś-Jordanow, Michał Czopowicz, Lucjan Witkowski, Monika Żychska, Ewa Domańska, Dawid Jańczak, Tomasz Nalbert, Stephanie Lesceu, Marzena Paszkowska, Justyna Giergielewicz and Tadeusz Frymus
Viruses 2025, 17(6), 855; https://doi.org/10.3390/v17060855 - 16 Jun 2025
Viewed by 843
Abstract
Recently, cats have emerged as potential incidental hosts for avian and human influenza A viruses (IAVs), including the highly pathogenic avian influenza (HPAI) H5N1 virus. Following an unprecedented outbreak of H5N1 HPAI in cats in Poland in June 2023, we conducted a cross-sectional [...] Read more.
Recently, cats have emerged as potential incidental hosts for avian and human influenza A viruses (IAVs), including the highly pathogenic avian influenza (HPAI) H5N1 virus. Following an unprecedented outbreak of H5N1 HPAI in cats in Poland in June 2023, we conducted a cross-sectional epidemiological study to assess the seroprevalence of IAV, especially H5Nx, infections in domestic cats. Eight hundred thirty-five serum samples collected in June 2023 were tested using a competitive ELISA for antibodies to IAV nucleoprotein. Positive or doubtful samples were further screened for H5-specific antibodies. The overall seropositivity for IAV was 8.5% (CI 95%: 6.8%, 10.6%; 71/835 cats), and 23/68 IAV-seropositive cats (33.8%) were also seropositive for H5 antigen. Multivariable analysis identified young age (≤8 years) and male sex as significant risk factors for H5 seropositivity, while non-H5-IAV seropositivity was more common in cats aged ≥12 years. These findings suggest different exposure pathways and host risk profiles for H5 and non-H5 IAVs and underscore the importance of enhanced surveillance in cats, particularly in regions affected by HPAI outbreaks. Given the susceptibility of cats to both avian and human IAVs, including subclinical infections, there is a theoretical risk for viral reassortment. Preventive measures, including vaccinating humans and restricting outdoor access for cats, should be considered in endemic areas. Full article
(This article belongs to the Special Issue H5N1 Influenza Viruses)
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13 pages, 2605 KiB  
Article
Identification of Endemic Region for Severe Fever with Thrombocytopenia Syndrome in an Alluvial Plain of Hebei Province, China
by Yanan Cai, Yamei Wei, Luling Li, Minghao Geng, Yan Zheng, Xinyang Zhang, Zhanying Han, Yanbo Zhang, Yonggang Xu, Xu Han and Qi Li
Viruses 2025, 17(6), 854; https://doi.org/10.3390/v17060854 - 16 Jun 2025
Viewed by 310
Abstract
Severe fever with thrombocytopenia syndrome (SFTS), an emerging infectious tick-borne viral disease, is increasingly affecting human beings worldwide. SFTS monitoring has been carried out since 2010 in mainland China. Since 2022, an increase in local cases has been noted in the central coastal [...] Read more.
Severe fever with thrombocytopenia syndrome (SFTS), an emerging infectious tick-borne viral disease, is increasingly affecting human beings worldwide. SFTS monitoring has been carried out since 2010 in mainland China. Since 2022, an increase in local cases has been noted in the central coastal plain region of Hebei Province. This study aimed to identify the endemic region in the central coastal plain region by epidemiological characteristics, antibody surveillance and molecular characterization. Case data were obtained from the Chinese Disease Control and Prevention Information System. Serum samples from suspected or clinically diagnosed cases, the indigenous healthy population and native domesticated animals were collected for laboratory tests, along with ticks in the central coastal plain region of Hebei Province, China. The local cases were mainly distributed in Cangzhou City, located at the central coastal plain region of Hebei Province. The 0.68% of IgM antibody detection rate and 1.71% of IgG antibody detection rate in this study showed the potential existence of subclinical or mild infections in Cangzhou. Phylogenetic analysis indicated that all sequences from patients, ticks and sheep clustered within the F subtype, exhibiting a close evolutionary relationship and the possible circulation of SFTSV having established among animal hosts and ticks in Cangzhou. These findings first identify the natural focus of SFTSV in the central plain region of Hebei Province, highlighting enhanced surveillance measures for preventing and controlling SFTSV. Full article
(This article belongs to the Section Animal Viruses)
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16 pages, 6985 KiB  
Article
Development of a Quadruplex RT-qPCR Assay for Rapid Detection and Differentiation of PRRSV-2 and Its Predominant Genetic Sublineages in China
by Guishan Ye, Siyu Xiong, Zhipeng Su, Guosheng Chen, Siyuan Liu, Zixuan Wang, Huanchun Chen and Anding Zhang
Viruses 2025, 17(6), 853; https://doi.org/10.3390/v17060853 - 16 Jun 2025
Viewed by 350
Abstract
Background: Porcine Reproductive and Respiratory Syndrome (PRRS) is a highly contagious disease characterized by reproductive failure in sows and severe respiratory disorders across all swine ages, causing significant economic losses. In China, the PRRSV epidemiological landscape is complex, with the coexistence of multiple [...] Read more.
Background: Porcine Reproductive and Respiratory Syndrome (PRRS) is a highly contagious disease characterized by reproductive failure in sows and severe respiratory disorders across all swine ages, causing significant economic losses. In China, the PRRSV epidemiological landscape is complex, with the coexistence of multiple lineages and frequent recombination. The major circulating strains include sublineages 1.8 (NADC30-like PRRSV) and 1.5 (NADC34-like PRRSV), along with lineages 8 (HP-like PRRSV) and 5 (VR2332-like PRRSV), highlighting the urgent need for rapid detection and lineage differentiation. Methods: A quadruplex RT-qPCR assay was developed targeting lineage-specific deletions in the NSP2 gene to simultaneously detect PRRSV-2 and differentiate NADC30-like PRRSV, HP-like PRRSV, and NADC34-like PRRSV strains. The assay was optimized with respect to reaction conditions, including annealing temperature, primers, and probe concentrations. The method’s performance was evaluated in terms of specificity, sensitivity, repeatability, stability, limit of detection (LOD), and consistency with sequencing results. Results: The assay demonstrated high sensitivity (LOD of 3 copies/μL), high specificity, and good repeatability (coefficient of variation < 1.5%). Field application using 938 samples from Guangxi A and B farms revealed NADC30-like PRRSV wild-type strains at positivity rates of 13.44% and 3.53%, respectively. Positive samples selected for sequencing were further confirmed using ORF5-based phylogenetic analysis and NSP2 deletion pattern comparison, which aligned with RT-qPCR detection results. Field application primarily detected NADC30-like PRRSV, while further validation is still needed for HP-like and NADC34-like strains. The developed quadruplex RT-qPCR assay enables rapid and simultaneous detection of PRRSV-2 and differentiation of three major lineages, providing a sensitive, specific, and reliable tool for distinguishing vaccine-derived from circulating strains and supporting targeted disease surveillance and control in swine farms. Full article
(This article belongs to the Section Animal Viruses)
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12 pages, 1358 KiB  
Article
Persistence and Active Replication Status of Oropouche Virus in Different Body Sites: Longitudinal Analysis of a Traveler Infected with a Strain Spreading in Latin America
by Andrea Matucci, Elena Pomari, Antonio Mori, Silvia Accordini, Natasha Gianesini, Rebeca Passarelli Mantovani, Federico Giovanni Gobbi, Concetta Castilletti and Maria Rosaria Capobianchi
Viruses 2025, 17(6), 852; https://doi.org/10.3390/v17060852 - 16 Jun 2025
Viewed by 431
Abstract
An unprecedented outbreak of Oropouche virus (OROV) is occurring in the Americas, characterized by thousands of confirmed cases and a wide geographical spread, including areas outside the Amazon Basin. Little is known about this neglected arbovirus regarding its pathophysiological aspects and potentially different [...] Read more.
An unprecedented outbreak of Oropouche virus (OROV) is occurring in the Americas, characterized by thousands of confirmed cases and a wide geographical spread, including areas outside the Amazon Basin. Little is known about this neglected arbovirus regarding its pathophysiological aspects and potentially different transmission modes. This study describes the clinical course of a man who returned from a trip to Cuba and presented to our hospital 4 days after the onset of febrile symptoms. The patient was diagnosed with Oropouche fever and was followed for 177 days after the onset of symptoms. We performed a longitudinal investigation of the samples collected from several body sites (whole blood, serum, urine, and semen) with the aim of providing further insights into OROV infection dynamics, using the detection of antigenomic RNA as a marker of active viral replication. Clinical samples that were longitudinally collected over the course of OROV infection showed consistently higher amounts of antigenomic RNA compared to genomic RNA, even after viral clearance from serum. Moreover, our case study showed the persistence of OROV RNA in serum of less than 15 days from the onset of symptoms, as compared to up to one month in urine, three months in semen, and four months in whole blood. Our study suggests that Oropouche virus may persist in an actively replicating state in different body sites for long periods of time, with important implications for transmission dynamics. Furthermore, our results provide a diagnostic indication, suggesting that serum is inferior to both urine and whole blood as preferred diagnostic samples. Further studies are needed to determine the pathogenetic implications of these findings, as they have been derived from a single case and must be confirmed using a larger number of cases. Full article
(This article belongs to the Special Issue Bunyaviruses 2025)
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15 pages, 707 KiB  
Systematic Review
The Effect on Mortality of Bacterial Co-Infections on Critically Ill Patients with Community-Acquired COVID-19 and Influenza Pneumonia: A Systematic Review
by Apostolos A. Menis, Efrosyni Gerovasileiou, Konstantinos Mantzarlis, Efstratios Manoulakas, Konstantina Deskata, Vasileios Vazgiourakis, Demosthenes Makris and George Dimopoulos
Viruses 2025, 17(6), 851; https://doi.org/10.3390/v17060851 - 16 Jun 2025
Viewed by 358
Abstract
Background: Bacterial co-infections in patients with viral pneumonia might increase mortality. In this study we aimed to evaluate their effect on the mortality of critically ill patients with viral pneumonia. Methods: A systematic search was conducted in PubMed, Web of Science, Scopus and [...] Read more.
Background: Bacterial co-infections in patients with viral pneumonia might increase mortality. In this study we aimed to evaluate their effect on the mortality of critically ill patients with viral pneumonia. Methods: A systematic search was conducted in PubMed, Web of Science, Scopus and Cochrane from inception until 30 March 2025. We included studies comparing the effect on mortality of bacterial co-infections in critically ill patients with viral pneumonia. The risk of bias was assessed by the Newcastle–Ottawa Scale. Results: From 3643 studies, 10 were included in our study with a total of 2862 COVID-19 patients and 4573 influenza patients. Seven studies were retrospective and three prospective. In total, 359/2862 of the COVID-19 and 904/4573 of the influenza patients were co-infected. Co-infections increased mortality in five out of the six studies evaluating COVID-19 patients and in two out of the eight studies evaluating influenza patients. Conclusions: The majority of the included studies were retrospective, which may limit the accuracy of these results. The exclusion of non-English literature may have led to the omission of relevant data. Based on our results, the impact of bacterial co-infection may be more pronounced in patients with COVID-19 pneumonia admitted to the ICU than in patients with influenza pneumonia. Full article
(This article belongs to the Section Human Virology and Viral Diseases)
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18 pages, 2588 KiB  
Review
Integrative Computational Approaches for Understanding Drug Resistance in HIV-1 Protease Subtype C
by Sankaran Venkatachalam, Nisha Muralidharan, Ramesh Pandian, Yasien Sayed and M. Michael Gromiha
Viruses 2025, 17(6), 850; https://doi.org/10.3390/v17060850 - 16 Jun 2025
Viewed by 415
Abstract
Acquired immunodeficiency syndrome (AIDS) is a chronic disease condition caused by the human immunodeficiency virus (HIV). The widespread availability of highly active antiretroviral therapies has helped to control HIV. There are ten FDA-approved protease inhibitors (PIs) that are used as part of antiretroviral [...] Read more.
Acquired immunodeficiency syndrome (AIDS) is a chronic disease condition caused by the human immunodeficiency virus (HIV). The widespread availability of highly active antiretroviral therapies has helped to control HIV. There are ten FDA-approved protease inhibitors (PIs) that are used as part of antiretroviral therapies in HIV treatment. Importantly, all these drugs are designed and developed against the protease (PR) from HIV subtype B. On the other hand, HIV-1 PR subtype C, which is the most dominant strain in countries including South Africa and India, has shown resistance to PIs due to its genetic diversity and varied mutations. The emergence of resistance is concerning because the virus continues to replicate despite treatment; hence, it is necessary to develop drugs specifically against subtype C. This review focuses on the origin, genetic diversity, and mutations associated with HIV-1 PR subtype C. Furthermore, computational studies performed on HIV-1 PR subtype C and mutations associated with its resistance to PIs are highlighted. Moreover, potential research gaps and future directions in the study of HIV-1 PR subtype C are discussed. Full article
(This article belongs to the Special Issue HIV Protease)
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14 pages, 1556 KiB  
Article
Impact of Delayed Early Antiretroviral Therapy Initiation on Treatment Outcomes in Infant Macaques Exposed to SHIVAD8
by Li Ma, Yoshiaki Nishimura, Xueling Wu, Olivia Donau, Eunice Vincent, Hong Lu, Robert V. Blair, Lara A. Doyle-Meyers, Malcolm Martin, Ronald S. Veazey, Huanbin Xu and Xiaolei Wang
Viruses 2025, 17(6), 849; https://doi.org/10.3390/v17060849 - 14 Jun 2025
Viewed by 446
Abstract
Infants born to HIV-positive mothers remain at significant risk of HIV acquisition despite maternal adherence to antiretroviral therapy, cesarean delivery, and formula feeding. Our previous study reported that initiating early antiretroviral treatment at three days post-SIV infection resulted in approximately eighty percent of [...] Read more.
Infants born to HIV-positive mothers remain at significant risk of HIV acquisition despite maternal adherence to antiretroviral therapy, cesarean delivery, and formula feeding. Our previous study reported that initiating early antiretroviral treatment at three days post-SIV infection resulted in approximately eighty percent of pediatric virologic remission. In this study, we investigated treatment outcomes in postnatally SHIV-exposed infant macaques when early intervention was delayed by two days, as well as the mechanisms underlying virologic control. The results showed that, although initiating treatment at five days post-exposure effectively suppressed viral replication, only one of the three infant macaques achieved a sustained state of virologic remission following analytical treatment interruption. Notably, this virus-controlled infant lacked detectable virus-specific immunity, including neutralizing antibodies, cytotoxic T cell responses, and antibody-dependent cellular cytotoxicity. These findings highlight the critical importance of early treatment initiation as a key determinant of virologic control in HIV-exposed, infected infants. This study provides valuable insights for guiding early pediatric HIV intervention strategies in clinical settings. Full article
(This article belongs to the Special Issue The Challenge of HIV Diversity)
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26 pages, 2617 KiB  
Article
Humoral and Cellular Immune Responses to SARS-CoV-2 in Participants with Head and Neck Cancer
by Luminita Mărutescu, Alexandru Enea, Nefeli-Maria Antoniadis, Marian Neculae, Diana Antonia Costea, Marcela Popa, Elena Dragu, Elena Codrici, Violeta Ristoiu, Bianca Galateanu, Ariana Hudita, Gratiela Gradisteanu Pircalabioru, Abdelali Filali-Mouhim, Serban Vifor Gabriel Bertesteanu, Veronica Lazăr, Carmen Chifiriuc, Raluca Grigore and Petronela Ancuta
Viruses 2025, 17(6), 848; https://doi.org/10.3390/v17060848 - 13 Jun 2025
Viewed by 554
Abstract
Background: SARS-CoV-2 immunity is understudied in cancer patients. Here, we monitored natural/vaccine-induced SARS-CoV-2 immunity in patients with head and neck cancer (HNC) stratified as vaccinated (mRNA/adenovirus-based vaccines), convalescent, and hybrid immunity. Methods: Plasma/PBMC samples were collected from 49 patients with HNC and 14 [...] Read more.
Background: SARS-CoV-2 immunity is understudied in cancer patients. Here, we monitored natural/vaccine-induced SARS-CoV-2 immunity in patients with head and neck cancer (HNC) stratified as vaccinated (mRNA/adenovirus-based vaccines), convalescent, and hybrid immunity. Methods: Plasma/PBMC samples were collected from 49 patients with HNC and 14 non-oncologic controls recruited between August 2021 and March 2022. Longitudinal follow-up was performed on 25 HNC patients. Plasma antibodies (Abs) against Spike (S1/S2), receptor-binding domain (RBD), and nucleocapsid (NC) of IgG/IgA isotypes and 25 cytokines/chemokines were quantified using MILLIPLEX® technology. The frequency, phenotype, and isotype of circulating SARS-CoV-2-specific B-cells were studied by flow cytometry using RBD tetramers (Tet++). The proliferation of B-cells and CD4+ and CD8+ T-cells in response to Spike/NC peptides was monitored by a carboxyfluorescein succinimidyl ester (CFSE) assay. Results: Plasma SARS-CoV-2 S1/S2/RBD IgG/IgA Abs were detected in all HNC participants at enrollment median time since immunization (TSI) 117 days at levels similar to controls and were significantly higher in convalescent/hybrid versus vaccinated. NC IgG/IgA Abs were only detected after infection. The frequency of Tet++ B-cells, enriched in the CD27+ memory phenotype and IgG/IgA isotype, positively correlated with plasma levels of RBD IgG/IgA Abs and Spike-specific CD4+ T-cell proliferation, regardless of the immunization status and TSI. Spike/NC-specific B-cell proliferation reached the highest levels in convalescent HNC and was positively correlated with NC IgG Abs, but not with the frequency of Tet++ B-cells. Finally, Tet++ B-cell frequencies remained stable between the two subsequent visits (median TSI: 117 versus 341 days), indicating their ability to persist for a relatively long time. Conclusions: This study monitored SARS-CoV-2 humoral/cellular immunity in an HNC cohort relative to non-oncologic participants and demonstrates that SARS-CoV-2-specific B-cells persist beyond 11 months post-immunization. These findings have implications for the management of HNC in the context of SARS-CoV-2 infection and other viral infections. Full article
(This article belongs to the Section Coronaviruses)
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22 pages, 1363 KiB  
Review
Live-Cell Imaging of Flaviviridae Family Virus Infections: Progress and Challenges
by Siena M. Centofanti and Nicholas S. Eyre
Viruses 2025, 17(6), 847; https://doi.org/10.3390/v17060847 - 13 Jun 2025
Viewed by 370
Abstract
The ability of a virus to be propagated within a host cell is dependent on a multitude of dynamic virus–host interactions. Live-cell imaging is an invaluable approach in the study of virus replication cycles and virus–host interactions as it can allow for the [...] Read more.
The ability of a virus to be propagated within a host cell is dependent on a multitude of dynamic virus–host interactions. Live-cell imaging is an invaluable approach in the study of virus replication cycles and virus–host interactions as it can allow for the direct visualisation of key events and interactions in real time. These details can provide unique insights into many aspects of viral infections including the cellular pathways that are exploited by viruses, the evasion of host immune defences, and viral pathogenesis. This review summarises the live-cell fluorescence imaging approaches that have been developed and applied to study Flaviviridae virus family members that are responsible for significant public health burdens and outbreaks which, in many instances, are increasing in frequency and severity. We discuss how these approaches have expanded our understanding of fundamental stages of viral replication cycles by enabling the direct visualisation of the localisation, trafficking, and interactions of virus particles, proteins, and genomes at distinct stages. The strategies that can be employed to enhance the biological relevance of live-cell fluorescence imaging acquisitions are discussed, along with how live-cell imaging approaches can be further developed to increase resolution, enable multi-colour imaging, and support the long-term visualisation of multiple stages of a viral replication cycle. Full article
(This article belongs to the Section Human Virology and Viral Diseases)
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19 pages, 4197 KiB  
Article
Re-Emergence of Usutu Virus and Spreading of West Nile Virus Neuroinvasive Infections During the 2024 Transmission Season in Croatia
by Tatjana Vilibić-Čavlek, Ljubo Barbić, Ana Klobučar, Marko Vucelja, Maja Bogdanić, Dario Sabadi, Marko Kutleša, Branimir Gjurašin, Vladimir Stevanović, Marcela Curman Posavec, Linda Bjedov, Marko Boljfetić, Tonka Jozić-Novinc, Robert Škara, Morana Tomljenović, Željka Hruškar, Mahmoud Al-Mufleh, Tanja Potočnik-Hunjadi, Ivana Rončević and Vladimir Savić
Viruses 2025, 17(6), 846; https://doi.org/10.3390/v17060846 - 13 Jun 2025
Viewed by 866
Abstract
Neuroinvasive arboviruses such as tick-borne encephalitis virus (TBEV), West Nile virus (WNV), Usutu virus (USUV), and Toscana virus (TOSV) have (re-)emerged with increasing incidence and geographic range. We analyzed the epidemiology of arboviral infections in Croatia during the 2024 transmission season. A total [...] Read more.
Neuroinvasive arboviruses such as tick-borne encephalitis virus (TBEV), West Nile virus (WNV), Usutu virus (USUV), and Toscana virus (TOSV) have (re-)emerged with increasing incidence and geographic range. We analyzed the epidemiology of arboviral infections in Croatia during the 2024 transmission season. A total of 154 patients with neuroinvasive diseases (NID), 1596 horses, 69 dead birds, and 7726 mosquitoes were tested. Viral RNA was detected using RT-qPCR. IgM/IgG-specific antibodies were detected using commercial ELISA or IFA, with confirmation of cross-reactive samples by virus neutralization test. RT-qPCR-positive samples were Sanger sequenced. Arboviral etiology was confirmed in 33/21.42% of patients with NID. WNV was most frequently detected (17/11.03%), followed by TBEV (10/6.49%), USUV (5/3.24%), and TOSV (1/0.64%). WNV infections were reported in regions previously known as endemic, while in one continental county, WNV was recorded for the first time. USUV infections re-emerged after a six-year absence. In addition to human cases, acute WNV infections were recorded in 11/395 (2.78%) of horses and two dead crows. WNV IgG seropositivity was detected in 276/1168 (23.63%) and TBEV IgG seropositivity in 68/428 (15.88%) horses. None of the tested mosquito pools were positive for WNV and USUV RNA. Phylogenetic analysis showed the circulation of WNV lineage 2 and Usutu Europe 2 lineage. Climate conditions in 2024 in Croatia were classified as extremely warm, which could, at least in part, impact the quite intense arboviral season. The spreading of flaviviruses in Croatia highlights the need for continuous surveillance in humans, animals, and vectors (“One Health”). Full article
(This article belongs to the Special Issue Arboviral Lifecycle 2025)
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21 pages, 574 KiB  
Review
A Scoping Review of Preclinical Research on Monoclonal Antibody Development for Prophylaxis and Treatment of West Nile Virus Infections
by Amanda E. Calvert, Kerri L. Miazgowicz, Bailey Atkinson, Audrey H. Long, Elisa Thrasher, Aaron C. Brault and Randall J. Nett
Viruses 2025, 17(6), 845; https://doi.org/10.3390/v17060845 - 12 Jun 2025
Viewed by 584
Abstract
West Nile virus (WNV) causes thousands of arboviral infections in the United States each year. Patients with immune-compromising conditions and elderly people are at higher risk of severe WNV neuroinvasive disease (WNND). Despite its broad endemicity nationwide, no U.S. Food and Drug Administration-approved [...] Read more.
West Nile virus (WNV) causes thousands of arboviral infections in the United States each year. Patients with immune-compromising conditions and elderly people are at higher risk of severe WNV neuroinvasive disease (WNND). Despite its broad endemicity nationwide, no U.S. Food and Drug Administration-approved vaccine or therapeutic treatments exist. We summarized existing peer-reviewed literature on the preclinical development of monoclonal antibody (MAb) prophylaxis and therapeutics for the prevention and treatment of WNND. Five bibliographical databases (CINAHL, Cochrane Library, Embase, MEDLINE, and Scopus) were searched for applicable research studies performed from 1 January 1998 to 1 May 2025. In total, 2347 titles and abstracts were screened, 263 full-text publications reviewed, and 25 studies included. Studies included detailed preclinical development and evaluations of MAbs targeting the envelope (E) protein (n = 13), other viral proteins (n = 3), flaviviral cross-protective monoclonal antibodies (n = 4), and novel antibody configurations or delivery methods (n = 5). The most well-studied MAb, E16, targeting E- Domain III (E-DIII), was effective at inhibiting and treating WNND in experimental animal models. No work investigated ways to traffic therapeutic antibodies across the blood–brain barrier. This review summarizes the current research in the development of monoclonal antibody therapeutics for WNV and addresses gaps in the knowledge for future consideration. Full article
(This article belongs to the Special Issue Development of Diagnostics and Therapeutic Interventions for Viral Infections of the Central Nervous System)
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16 pages, 3629 KiB  
Article
Ten Previously Unassigned Human Cosavirus Genotypes Detected in Feces of Children with Non-Polio Acute Flaccid Paralysis in Nigeria in 2020
by Toluwani Goodnews Ajileye, Toluwanimi Emmanuel Akinleye, Temitope O. C. Faleye, Lander De Coninck, Uwem Etop George, Anyebe Bernard Onoja, Sheriff Tunde Agbaje, Ijeoma Maryjoy Ifeorah, Oluseyi Adebowale Olayinka, Elijah Igbekele Oni, Arthur Obinna Oragwa, Bolutife Olubukola Popoola, Olaitan Titilola Olayinka, Oluwadamilola Gideon Osasona, Oluwadamilola Adefunke George, Philip G. Ajayi, Adedolapo A. Suleiman, Ahmed Iluoreh Muhammad, Isaac Komolafe, Adekunle Johnson Adeniji, Jelle Matthijnssens and Moses Olubusuyi Adewumiadd Show full author list remove Hide full author list
Viruses 2025, 17(6), 844; https://doi.org/10.3390/v17060844 - 12 Jun 2025
Viewed by 520
Abstract
Since its discovery via metagenomics in 2008, human cosavirus (HCoSV) has been detected in the cerebrospinal fluid (CSF) and feces of humans with meningitis, acute flaccid paralysis (AFP), and acute gastroenteritis. To date, 34 HCoSV genotypes have been documented by the Picornaviridae study [...] Read more.
Since its discovery via metagenomics in 2008, human cosavirus (HCoSV) has been detected in the cerebrospinal fluid (CSF) and feces of humans with meningitis, acute flaccid paralysis (AFP), and acute gastroenteritis. To date, 34 HCoSV genotypes have been documented by the Picornaviridae study group. However, the documented genetic diversity of HCoSV in Nigeria is limited. Here we describe the genetic diversity of HCoSV in Nigeria using a metagenomics approach. Archived and anonymized fecal specimens from children (under 15 years old) diagnosed with non-polio AFP from five states in Nigeria were analyzed. Virus-like particles were purified from 55 pools (made from 254 samples) using the NetoVIR protocol. Pools were subjected to nucleic acid extraction and metagenomic sequencing. Reads were trimmed and assembled, and contigs classified as HCoSV were subjected to phylogenetic, pairwise identity, recombination analysis, and, when necessary, immuno-informatics and capsid structure prediction. Fifteen pools yielded 23 genomes of HCoSV. Phylogenetic and pairwise identity analysis showed that all belonged to four species (eleven, three, three, and six members of Cosavirus asiani, Cosavirus bepakis, Cosavirus depakis, and Cosavirus eaustrali, respectively) and seventeen genotypes. Ten genomes belong to seven (HCoSV-A3/A10, A15, A17, A19, A24, D3, and E1) previously assigned genotypes, while the remaining thirteen genomes belonged to ten newly proposed genotypes across the four HCoSV species, based on the near-complete VP1 region (VP1*) of the cosavirus genome. Our analysis suggests the existence of at least seven and eight Cosavirus bepakis and Cosavirus eaustrali genotypes, respectively (including those described here). We report the first near-complete genomes of Cosavirus bepakis and Cosavirus depakis from Nigeria, which contributes to the increasing knowledge of the diversity of HCoSV, raising the number of tentative genotypes from 34 to over 40. Our findings suggest that the genetic diversity of HCoSV might be broader than is currently documented, highlighting the need for enhanced surveillance. Full article
(This article belongs to the Section Human Virology and Viral Diseases)
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11 pages, 520 KiB  
Article
Prevalence of Hepatitis C in the Emilia-Romagna Region of Italy: Population-Wide Screening
by Gianmarco Imperiali, Matteo Fiore, Alessandro Bianconi, Giovanna Mattei, Giulio Matteo, Giuseppe Diegoli, Esther Rita De Gioia, Cecilia Acuti Martellucci, Maria Elena Flacco, Lamberto Manzoli and Regional HCV Working Group
Viruses 2025, 17(6), 843; https://doi.org/10.3390/v17060843 - 12 Jun 2025
Viewed by 434
Abstract
In agreement with WHO recommendations, the Emilia-Romagna Region, Italy, implemented a population-wide HCV screening program for the treatment of the large asymptomatic infected population. From January 2022, the free-of-charge screening targeted all residents born between 1969 and 1989, prison inmates, and injection drug [...] Read more.
In agreement with WHO recommendations, the Emilia-Romagna Region, Italy, implemented a population-wide HCV screening program for the treatment of the large asymptomatic infected population. From January 2022, the free-of-charge screening targeted all residents born between 1969 and 1989, prison inmates, and injection drug users. Participants were recruited using phone messages, electronic health record notifications, public advertisement, and direct contact with general practitioners. A single blood sample was collected for anti-HCV IgG testing and, if positive, for reflex HCV–RNA testing. Infected subjects were offered an evidence-based therapeutic pathway. By June 2024, 72.8% of high-risk subjects (n = 19,732), and 36.9% of the general population (n = 488,065) had been screened. A total of 1032 individuals were positive based on the HCV–RNA test, and the detection rate widely differed between the high-risk and the general population (23.8‰ vs. 1.2‰, respectively). Of the infected individuals, 88.1% were seen by a specialist physician, and 74.3% (n = 767) started antiviral therapy. Thanks to multiple recruitment approaches, over one third of the general population participated in HCV screening. The program performance was substantially greater among high-risk individuals compared to the general population. To achieve WHO targets, policymakers might consider expanding the screening to other high-risk subgroups and/or adapting birth cohorts. Full article
(This article belongs to the Section Human Virology and Viral Diseases)
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18 pages, 2111 KiB  
Article
Consensus Sequences for Gag and Pol Introduced into HIV-1 Clade B Laboratory Strains Differentially Influence the Impact of Point Mutations Associated with Immune Escape and with Drug Resistance on Viral Replicative Capacity
by Sven Breitschwerdt, Benedikt Grandel, Benedikt Asbach, Franziska Winter, Todd Allen, Ralf Wagner, Bernd Salzberger and Arne Schneidewind
Viruses 2025, 17(6), 842; https://doi.org/10.3390/v17060842 - 12 Jun 2025
Viewed by 505
Abstract
Viral evasion from effective human immunodeficiency virus type 1 (HIV-1)-specific CD8+ T-cell responses and from antiretroviral therapy through viral sequence variation is frequently accompanied by a loss in viral fitness. The impact of sequence variations on replication capacity in vitro was mostly studied [...] Read more.
Viral evasion from effective human immunodeficiency virus type 1 (HIV-1)-specific CD8+ T-cell responses and from antiretroviral therapy through viral sequence variation is frequently accompanied by a loss in viral fitness. The impact of sequence variations on replication capacity in vitro was mostly studied by introducing single mutations into a specific clonal strain such as NL4-3. How the specific viral backbone itself impacts replicative fitness remains elusive. To test for a potential effect of the viral backbone, we constructed HIV-1 clade B clones with consensus sequences for gag and/or pol and evaluated the infectivity of viral variants harboring well-defined cytotoxic T-lymphocyte (CTL) escape mutations or drug resistance mutations within this backbone or the clonal NL4-3 strain. Viral variants with consensus sequences were replication-competent in vitro, although at lower rates than the NL4-3 virus. Introduction of the dominant CTL escape mutation R264K into the newly constructed viruses or into NL4-3 led to a dramatic reduction in infection rates. In contrast to the NL4-3 backbone, the combination of R264K with its compensatory mutation S173A on the consensus backbone led to higher infection rates as compared to the same virus in the absence of R264K and S173A. Furthermore, 2 out of 10 drug resistance mutations in pol led to opposing effects, with an increase in infection rates on the consensus gag/pol backbone and a reduction on NL4-3. Therefore, the effect of the respective viral backbone on infectivity observed in vitro might constitute an additional factor to explain differential kinetics of mutational evasion from immune and pharmaceutical pressure. Full article
(This article belongs to the Section Viral Immunology, Vaccines, and Antivirals)
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13 pages, 2677 KiB  
Article
A Single-Tube Two-Step MIRA-CRISPR/Cas12b Assay for the Rapid Detection of Mpox Virus
by Ge Hu, Zhijie Wei, Jinlei Guo, Kangchen Zhao, Qiao Qiao, Xiaojuan Zhu, Tao Wu, Heng Rong, Shuo Ning, Ziyang Hao, Ying Chi, Lunbiao Cui and Yiyue Ge
Viruses 2025, 17(6), 841; https://doi.org/10.3390/v17060841 - 12 Jun 2025
Viewed by 440
Abstract
Mpox is a zoonotic disease caused by the Mpox virus (MPXV). The rapid and accurate diagnosis of MPXV is essential for the timely and effective prevention, control, and treatment of the disease. In this study, we combined Multienzyme Isothermal Rapid Amplification (MIRA) (at [...] Read more.
Mpox is a zoonotic disease caused by the Mpox virus (MPXV). The rapid and accurate diagnosis of MPXV is essential for the timely and effective prevention, control, and treatment of the disease. In this study, we combined Multienzyme Isothermal Rapid Amplification (MIRA) (at 42 °C) and Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 12b(CRISPR/Cas12b) (at 60 °C) to develop a single-tube two-step assay for rapid MPXV detection, leveraging the distinct physical states of tricosane at these temperatures. MIRA amplification primers and CRISPR/cas12b SgRNA were designed based on the MPXV F3L gene. After screening the primers and sgRNAs, the reaction conditions were optimized, and the performances of the assay were evaluated. The detection limit (LOD) of this single-tube two-step MIRA-CRISPR/Cas12b assay for MPXV is four copies of DNA molecules. No cross-reactivity with other pathogens (herpes simplex virus (HSV), Epstein–Barr virus (EBV), Coxsackievirus A16 (CVA16), Enterovirus A71 (EV-A71), and measles virus (MeV)) was found. The assay also showed good consistency with quantitative real-time PCR (qPCR) (Kappa = 0.9547, p < 0.05, n = 100) in the detection of clinical samples, with a sensitivity of 98.5% and a specificity of 97.0%. The single-tube two-step MIRA-CRISPR/Cas12b assay permits the rapid (within 45 min), sensitive, and specific detection of MPXV. The lack of need for opening the reaction tube eliminates the risk of product contamination. Full article
(This article belongs to the Section General Virology)
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16 pages, 2095 KiB  
Article
Identification of Clinical and Genomic Features Associated with SARS-CoV-2 Reinfections
by Francisco Muñoz-López, Antoni E. Bordoy, Francesc Català-Moll, Verónica Saludes, David Panisello Yagüe, Mariona Parera, Ignacio Blanco, Pere-Joan Cardona, Cristina Casañ, Ana Blanco-Suárez, Sandra Franco, Álvaro F. García-Jiménez, Roger Paredes, Bonaventura Clotet, Lourdes Mateu, Marc Noguera-Julian, Elisa Martró, José Ramón Santos and Marta Massanella
Viruses 2025, 17(6), 840; https://doi.org/10.3390/v17060840 - 11 Jun 2025
Viewed by 914
Abstract
Although SARS-CoV-2 reinfections remain a concern for healthcare systems worldwide, the factors driving them are still not fully understood. In this study, we examined data for 3303 individuals who experienced two SARS-CoV-2 infections between March 2020 and May 2022 from both clinical and [...] Read more.
Although SARS-CoV-2 reinfections remain a concern for healthcare systems worldwide, the factors driving them are still not fully understood. In this study, we examined data for 3303 individuals who experienced two SARS-CoV-2 infections between March 2020 and May 2022 from both clinical and viral genomics perspectives. Our findings indicate that viral evolution was the primary driver of reinfection. However, chronic conditions were common among reinfected individuals, including those under 26 years old, suggesting that the presence of underlying and/or chronic conditions increases susceptibility to reinfection. The median time elapsed between infections was one year, often coinciding with the emergence of new variants. While vaccination showed only a limited protective effect against reinfection, it drastically decreased the hospitalization rate, underscoring its role in mitigating disease severity. Our findings point to the need for more flexible vaccination strategies, especially for individuals with chronic conditions. Understanding the interactions between host factors and viral evolution is critical to strengthening prevention strategies and reducing the burden of reinfections and their possible long-term complications. Full article
(This article belongs to the Special Issue Emerging Variants of SARS-CoV-2)
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Review
HIV, Inflammation, and Immunometabolism: A Model of the Inflammatory Theory of Disease
by Eman Teer, Nyasha C. Mukonowenzou and M. Faadiel Essop
Viruses 2025, 17(6), 839; https://doi.org/10.3390/v17060839 - 11 Jun 2025
Viewed by 1052
Abstract
Inflammation is a crucial component of the immune response essential for host defense and tissue repair. However, when the immune response becomes dysregulated, it can contribute to the pathogenesis of chronic diseases. While acute inflammation is a short-lived, protective response, chronic inflammation is [...] Read more.
Inflammation is a crucial component of the immune response essential for host defense and tissue repair. However, when the immune response becomes dysregulated, it can contribute to the pathogenesis of chronic diseases. While acute inflammation is a short-lived, protective response, chronic inflammation is sustained over time and can lead to immune dysfunction, tissue damage, and disease progression. The chronic inflammation theory of disease suggests that persistent immune activation/inflammation underlies both infectious and non-infectious conditions and serves as a unifying mechanism across distinct pathological states. In this review article, we argue that human immunodeficiency virus (HIV) infection represents a prime model for studying chronic inflammation, and that despite effective viral suppression with antiretroviral therapy (ART), people living with HIV (PLWH) exhibit persistent immune activation, systemic inflammation, and an increased risk of cardiovascular, metabolic, and neurodegenerative diseases. Here, the interplay between microbial translocation, immune dysregulation, and metabolic reprogramming fuels a state of chronic inflammation that accelerates disease progression beyond HIV itself. Key factors such as T-cell exhaustion, persistent monocyte/macrophage activation, and immunometabolic dysfunction contribute to such a sustained inflammatory state. This review explores the molecular and cellular mechanisms driving chronic inflammation in HIV infection with a focus on immunometabolism and its implications for broader inflammatory diseases. By understanding such pathways, we can identify novel therapeutic targets to mitigate inflammation-driven disease progression not only in HIV but across a spectrum of chronic inflammatory conditions. Full article
(This article belongs to the Special Issue Viral Infections and Immune Dysregulation 2024–2025)
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