Genomics and Epidemiology of Emerging Viruses

A special issue of Pathogens (ISSN 2076-0817). This special issue belongs to the section "Emerging Pathogens".

Deadline for manuscript submissions: 30 June 2026 | Viewed by 1980

Special Issue Editor


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Guest Editor
Division of High-Risk Pathogens, Bureau of Infectious Disease Diagnosis Control, Korea Diseases Control and Prevention Agency, Cheongju 28159, Republic of Korea
Interests: viral infection; molecular detection; pathogenesis; phylogenetic analysis
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Special Issue Information

Dear Colleagues,

Emerging viruses continue to pose major threats to global health, driven by rapid genomic evolution, cross-species transmission, and changing ecological and social dynamics. Advances in next-generation sequencing and molecular diagnostics have greatly improved our ability to detect, characterize, and monitor these pathogens. This Special Issue, entitled “Genomics and Epidemiology of Emerging Viruses”, will highlight recent progress in understanding the genetic diversity, evolution, and epidemiology of emerging viral pathogens across human, animal, and environmental interfaces.

We invite original research and reviews focusing on full-genome analyses, hypervariable genomic regions, and comparative studies of vaccine strains. Submissions addressing the development of sensitive and specific diagnostic methods, as well as investigations linking genomic data to outbreak dynamics, transmission routes, and public-health interventions, are particularly encouraged. Studies integrating molecular, epidemiological, and bioinformatic approaches to elucidate viral emergence, adaptation, and spread are also welcome.

Through this Special Issue, we will provide a comprehensive platform for sharing insights that advance surveillance, preparedness, and response to future viral threats.

Dr. Yoon-Seok Chung
Guest Editor

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Keywords

  • emerging viruses
  • genomic surveillance
  • molecular epidemiology
  • vaccine strain comparison
  • diagnostic assay development

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Published Papers (2 papers)

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Research

11 pages, 1397 KB  
Article
Detection of Enteroviruses on Environmental Surfaces in Daycare Centers Using Droplet Digital PCR (ddPCR) and Its Public Health Implications
by Kyung-Seon Kim, Hye-Jin Jang, Seo-Youn Koo, Jeong-Hyun Lee, In-Hae Choi, Chae-Hyeon Sim, Ni-Na Yoo, Jin-Gyun Eom, Kyoung-Yong Jung, Eun-Ok Bang and Yoon-Seok Chung
Pathogens 2026, 15(2), 161; https://doi.org/10.3390/pathogens15020161 - 2 Feb 2026
Viewed by 785
Abstract
Enteroviruses (EVs) are major pathogens transmitted via direct and indirect contact, with children being particularly susceptible. As EVs persist on surfaces, environmental hygiene is critical in communal environments. We investigated EVs presence on environmental surfaces in daycare centers from April to July 2024. [...] Read more.
Enteroviruses (EVs) are major pathogens transmitted via direct and indirect contact, with children being particularly susceptible. As EVs persist on surfaces, environmental hygiene is critical in communal environments. We investigated EVs presence on environmental surfaces in daycare centers from April to July 2024. Environmental samples (300) were collected from floors, toys, and desks. Viral RNA was extracted and analyzed using real-time reverse transcription polymerase chain reaction (real-time RT-PCR) and ddPCR to detect pan-Enterovirus (pan-EVs) and Enterovirus D68 (EV-D68). EVs were detected in 45.3% of the samples. The detection rate refers to the combined results, including both ddPCR and real-time PCR. Specifically, pan-EVs were found in 88 samples (1.12–505 copies/20 μL) and EV-D68 in 104 samples (1.12–309 copies/20 μL). Floors (31%) were the most contaminated surfaces. Monthly analysis showed a gradual decrease in detection rates from 88.6% in April to 18.5% in July, appearing to align with the implementation of enhanced hygiene measures. However, this trend may also reflect multifaceted factors, including natural viral reduction, exclusion of symptomatic children, and increased hygiene awareness. Notably ddPCR (83.0%) exhibited nearly twice the detection rate of real-time RT-PCR (42.5%), identifying low-level viral persistence. These findings suggest that environmental surfaces serve as reservoirs for transmission, and integrating sensitive detection like ddPCR with proactive hygiene management may help mitigate EVs spread. Full article
(This article belongs to the Special Issue Genomics and Epidemiology of Emerging Viruses)
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10 pages, 1016 KB  
Article
First Molecular Detection of Orthohantaviruses (Orthohantavirus hantanense and O. jejuense) in Trombiculid Mites from Wild Rodents in the Republic of Korea
by Seong Yoon Kim, Hak Seon Lee, Hyunyoung Yoon and Hee Il Lee
Pathogens 2025, 14(12), 1260; https://doi.org/10.3390/pathogens14121260 - 9 Dec 2025
Viewed by 635
Abstract
Orthohantaviruses are zoonotic pathogens that cause severe diseases in humans primarily through inhalation of aerosols from rodent excreta. Recent studies suggest that ectoparasites may be potential vectors for Orthohantaviruses. This study aimed to obtain molecular evidence of Orthohantavirus in trombiculid mites collected from [...] Read more.
Orthohantaviruses are zoonotic pathogens that cause severe diseases in humans primarily through inhalation of aerosols from rodent excreta. Recent studies suggest that ectoparasites may be potential vectors for Orthohantaviruses. This study aimed to obtain molecular evidence of Orthohantavirus in trombiculid mites collected from wild rodents. In April 2025, 4963 trombiculid mites were collected from 128 wild rodents captured in 17 regions of the Republic of Korea (ROK). Among them, 1660 mites were grouped into 204 pools by collection sites and tested for the Orthohantavirus RNA using quantitative real-time polymerase chain reaction (PCR) and reverse transcription-nested PCR. OrthoHantavirus RNA was detected in seven trombiculid mite pools, with a minimum infection rate of 0.4/100 mites. Orthohantavirus hantanense was identified in trombiculid mites from Cheongju, Gimcheon, and Yeongdeok, while O. jejuense was identified in trombiculid mites from Boryeong and Jeongeup. Notably, Orthohantaviruses were not detected in the host rodents of the Orthohantavirus-positive trombiculid mites from Cheongju, Jeongeup, and Gimcheon, indicating host-independent infection. This study is the first to report detection of Orthohantaviruses, O. hantanense and O. jejuense, from trombiculid mites in the ROK. The host-independent infection suggests that these mites could serve as independent vectors/reservoirs for Orthohantaviruses, distinct from previously known transmission routes. Full article
(This article belongs to the Special Issue Genomics and Epidemiology of Emerging Viruses)
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