Journal of Microbiology

Editor’s Choice articles are curated by our senior editors, who represent each section, to highlight research published in 2025 that they consider particularly interesting to our readers and/or important within the respective research area.

editor_pick

Evolutionary Microbiology and Systematics
Microbial Ecology and Environmental Microbiology
Microbial Physiology and Biochemistry
Microbial Genetics, Genomics
and Molecular Biology (Prokaryote)
Microbial Genetics, Genomics
and Molecular Biology (Eukaryote)
Microbial Pathogenesis
and Host-Microbe Interaction
Synthetic Microbiology and Biotechnology
Virology

Virology

Journal of Microbiology is pleased to present Editor’s Choice 2025 for the Virology section, spotlighting the most highly cited and most frequently downloaded articles published in the journal this year. In alignment with the section’s scope, this curation traces the full arc of contemporary virology — from the molecular tools that allow us to build and interrogate viral genomes, to the host pathways that decide the outcome of infection, to the vaccines that translate this knowledge into public health impact.

Framed by the collection theme, “Engineering Viral Genomes, Decoding Host Defense: Enabling Technologies for Next-Generation Virology,” the selected papers reflect both the technical depth and the translational reach of current virological research. Three of the five articles are enabling methodological resources of immediate, practical value to laboratories worldwide. Two complementary studies advance reverse genetics for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): a systematic head-to-head benchmarking of bacteria-free rescue strategies — circular polymerase extension reaction (CPER), CPER with nick sealing, and infectious subgenomic amplicons — against conventional bacterial artificial chromosome technology, which establishes clear guidance on which route delivers the highest rescue efficiency and faithful replication kinetics; and an efficient, modular assembly platform that enables the rapid generation of recombinant SARS-CoV-2 for dissecting viral gene function, identifying antiviral targets, and developing live-attenuated vaccine candidates. A third contribution extends precision engineering to large double-stranded DNA viruses, combining CRISPR-Cas9 knock-in with lentiviral delivery to install auxin-inducible degron tags in the human cytomegalovirus genome, thereby providing temporal control over the function of individual viral proteins — a long-standing bottleneck in herpesvirus genetics.

Two further studies deepen the mechanistic and translational dimensions of the collection. The first defines the antiviral mode of action of Korean Red ginseng against influenza A virus, showing that it potentiates Z-DNA-binding protein 1 (ZBP1)-mediated programmed cell death to restrict viral protein expression and reduce pulmonary inflammation in vivo, and thus links a widely used natural product to a well-defined innate immune sensor. The second is a comprehensive review of dengue vaccine development that charts the field from Dengvaxia® and Qdenga® through the persistent challenges of balanced tetravalent immunity and antibody-dependent enhancement, and evaluates the next-generation candidates now entering the pipeline.

Curated by our Associate Editor-in-Chief for Virology, Jinjong Myoung, this collection showcases the methodological rigor, mechanistic insight, and translational ambition that define virology in Journal of Microbiology. All five articles are openly accessible, and we warmly invite the virology community to read, cite, and build upon them. Through this scholarly expertise and careful curation, this Editor’s Choice Collection will enhance the visibility of distinguished articles published in Journal of Microbiology and further strengthen the academic impact of the journal.

Editor’s Choice Curator

Jinjong Myoung
Jeonbuk National University

Professor Myoung is a Senior Editor, Section of Virology, of Journal of Microbiology, based at the Korea Zoonosis Research Institute. His research addresses emerging and zoonotic viruses, with a particular focus on the molecular determinants of coronavirus infectivity and immune evasion and on reverse genetics platforms for engineering recombinant viruses.

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Review

Advancements in dengue vaccines: A historical overview and pro-spects for following next-generation candidates: Kai Yan, Lingjing Mao, Jiaming Lan, Zhongdang Xiao; J. Microbiol. 2025;63(2):e2410018. Published online February 27, 2025; DOI: https://doi.org/10.71150/jm.2410018

19,558 View
594 Download
16 Web of Science
18 Crossref

Abstract PDF

Dengue, caused by four serotypes of dengue viruses (DENV-1 to DENV-4), is the most prevalent and widely mosquito-borne viral disease affecting humans. Dengue virus (DENV) infection has been reported in over 100 countries, and approximately half of the world's population is now at risk. The paucity of universally licensed DENV vaccines highlights the urgent need to address this public health concern. Action and attention to antibody-dependent enhancement increase the difficulty of vaccine development. With the worsening dengue fever epidemic, Dengvaxia^® (CYD-TDV) and Qdenga^® (TAK-003) have been approved for use in specific populations in affected areas. However, these vaccines do not provide a balanced immune response to all four DENV serotypes and the vaccination cannot cover all populations. There is still a need to develop a safe, broad-spectrum, and effective vaccine to address the increasing number of dengue cases worldwide. This review provides an overview of the existing DENV vaccines, as well as potential candidates for future studies on DENV vaccine development, and discusses the challenges and possible solutions in the field.

Citations

Citations to this article as recorded by

E protein inhibitors and host-directed therapies in dengue virus infection: perspectives on combination and complementary antiviral strategies
Ricardo Jiménez-Camacho, Carlos Noe Farfan-Morales, José De Jesús Bravo-Silva, Magda Lizbeth Benítez-Vega, Marcos Pérez-García, Jonathan Hernández-Castillo, Carlos Daniel Cordero-Rivera, Rosa María Del Ángel
Expert Opinion on Drug Discovery.2026; 21(1): 101. CrossRef
Dengue Fever Vaccines: Progress and Challenges
Alan L. Rothman, Heather Friberg
Annual Review of Pharmacology and Toxicology .2026; 66(1): 129. CrossRef
A Capabilities, Opportunities, and Motivations behavioral analysis of healthcare professionals concerning dengue vaccination in selected countries from Latin America and Asia Pacific
Andrew Green, Alberta Di Pasquale, Eduardo Lopez-Medina
Human Vaccines & Immunotherapeutics.2026;[Epub] CrossRef
A Multivalent Dengue Fusion Protein ΔcNS1–cEDIII–ΔnNS3 Confers Cross‐Serotype Protection and Durable Immunity in Mice
Mu‐Fan Pi, Wei‐Chiao Liao, Xin‐Yan Li, Miao‐Huei Cheng, Chu‐En Tsai, Yen‐Chung Lai, Hsing‐Han Lin, Yung‐Chun Chuang, Chin‐Kai Tseng, Yee‐Shin Lin, Chih‐Peng Chang, Tzong‐Shiann Ho, Guan‐Da Syu, Trai‐Ming Yeh, Jen‑Ren Wang, Justin Jang Hann Chu, Chia‐Yi Yu
Journal of Medical Virology.2026;[Epub] CrossRef
Pharmaceutical design of mRNA vaccines for endemic infectious diseases: integrating antigen discovery with platform engineering
Shuaibu Abdullahi Hudu, Abdulgafar Olayiwola Jimoh
Clinical and Experimental Vaccine Research.2026; 15(2): 101. CrossRef
Association of Viraemic Phase Viral Load, Antibody Responses, and Immune Biomarkers With Severe Dengue
Kalichamy Alagarasu, Yogesh K. Gurav, Anisha Pulinchani, Rupali Bachal, Pradnya Bhadale, Aishwarya Telmore, Mahadeo Kakade, Susmit Sambhare, Pratiksha Sonare, Vasant Nagvekar, R. T. Borse, Ameet Dravid, Palkar Sonali, Supriya Barsode, Soni Pravin, Ambike
Journal of Medical Virology.2026;[Epub] CrossRef
Achievements and Challenges in Therapy and Vaccines Development of Viral Hemorrhagic Fevers: An Up-to-Date Review
Dan Lupascu, Andreea-Teodora Iacob, Maria Apotrosoaei, Ioana-Mirela Vasincu, Florentina-Geanina Lupascu, Oana-Maria Chirliu, Bianca-Stefania Profire, Roxana-Georgiana Tauser, Lenuta Profire
Pharmaceutics.2026; 18(4): 426. CrossRef
LRP‐1 as Target of Broad‐Specific Antivirals: Benefits, Risks and Challenges
Daniela Isabel Maldonado‐Bauzá, Luis Gabriel González‐Lodeiro, Li Wen, Vivian Huerta Galindo
Reviews in Medical Virology.2026;[Epub] CrossRef
Nanoparticle vaccine formulations for dengue virus
Connor T. Murphy, Kristy M. Ainslie
RSC Pharmaceutics.2026; 3(4): 935. CrossRef
Targeting dengue through mucosal vaccination: the potential of NS1 and bacterial spore-based delivery platforms
Nurfatihah Zulkifli, Ok Sarah Shin, Sazaly AbuBakar
Frontiers in Immunology.2026;[Epub] CrossRef
Experimental cloning, recombinant expression, and computational characterization of the PSDV-2 dengue vaccine candidate
Hikmat Ullah, Saima Saman, Shaukat Ullah, Sultan Muhammad
In Silico Research in Biomedicine.2026; 2: 100567. CrossRef
Role of c-ABL in DENV-2 Infection and Actin Remodeling in Vero Cells
Grace Paola Carreño-Flórez, Alexandra Milena Cuartas-López, Ryan L. Boudreau, Miguel Vicente-Manzanares, Juan Carlos Gallego-Gómez
International Journal of Molecular Sciences.2025; 26(9): 4206. CrossRef
Crystallographic Fragment Screening of the Dengue Virus Polymerase Reveals Multiple Binding Sites for the Development of Non-nucleoside Antiflavivirals
Manisha Saini, Jasmin C. Aschenbrenner, Francesc Xavier Ruiz, Ashima Chopra, Anu V. Chandran, Peter G. Marples, Blake H. Balcomb, Daren Fearon, Frank von Delft, Eddy Arnold
Journal of Medicinal Chemistry.2025; 68(17): 18356. CrossRef
Understanding the Diversity of Dengue Serotypes: Impacts on Public Health and Disease Control
Gopinath Ramalingam, Madhumitha Patchaiyappan, M. Arundadhi, Krishnapriya Subramani, A. Dhanasezhian, Sucila Thangam Ganesan
The Journal of Medical Research.2025; 11(4): 69. CrossRef
Dengue Fever Resurgence in Iran: An Integrative Review of Causative Factors and Control Strategies
Seyed Hassan Nikookar, Saeedeh Hoseini, Omid Dehghan, Mahmoud Fazelidinan, Ahmadali Enayati
Tropical Medicine and Infectious Disease.2025; 10(11): 309. CrossRef
Enhancement of viral infection by antibodies and consequences
Corentin Morvan, Magloire Pandoua Nekoua, Cyril Debuysschere, Enagnon Kazali Alidjinou, Didier Hober, Sebla Bulent Kutluay
Microbiology and Molecular Biology Reviews.2025;[Epub] CrossRef
Microbial Volatiles from Human Skin and Floral Nectar: Insufficiently Understood Adult Feeding Cues To Improve Odor-Based Traps for Aedes Vector Control
Simon Malassigné, Claire Valiente Moro, Patricia Luis
Journal of Chemical Ecology.2025;[Epub] CrossRef
An interpretable machine learning model for dengue detection with clinical hematological data
Izaz Ahmmed Tuhin, A.K.M.Fazlul Kobir Siam, Md Mahfuzur Rahman Shanto, Md Rajib Mia, Imran Mahmud, Apurba Ghosh
Healthcare Analytics.2025; 8: 100430. CrossRef

Article

Efficient and modular reverse genetics system for rapid generation of recombinant severe acute respiratory syndrome coronavirus 2: Sojung Bae, Jinjong Myoung; J. Microbiol. 2025;63(7):e2504015. Published online July 21, 2025; DOI: https://doi.org/10.71150/jm.2504015

7,161 View
430 Download
2 Web of Science
2 Crossref

Abstract PDF

The global spread of COVID-19 has underscored the urgent need for advanced tools to study emerging coronaviruses. Reverse genetics systems have become indispensable for dissecting viral gene functions, developing live-attenuated vaccine candidates, and identifying antiviral targets. In this study, we describe a robust and efficient reverse genetics platform for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The system is based on the assembly of a full-length infectious cDNA clone from seven overlapping fragments, each flanked by homologous sequences to facilitate seamless assembly using the Gibson assembly method. Individual cloning of each fragment into plasmids enables modular manipulation of the viral genome, allowing rapid site-directed mutagenesis by fragment exchange. Infectious recombinant virus was successfully recovered from the assembled cDNA, exhibiting uniform plaque morphology and genetic homogeneity compared to clinical isolates. Additionally, fluorescent reporter viruses were generated to enable real-time visualization of infection, and the effects of different mammalian promoters on viral rescue were evaluated. This reverse genetics platform enables efficient generation and manipulation of recombinant SARS-CoV-2, providing a valuable resource for virological research and the development of preventive and therapeutic antiviral measures.

Citations

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Research Progress of Coronavirus Reverse Genetics Technology
Ziqi Han, Jiaxu Han, Yan Zhao, Chao Xu, Xue Leng, Boyin Jia, Naichao Diao, Fei Liu, Chunmei Cui, Jian Liang, Yuhang Jiang, Rui Du
Journal of Medical Virology.2026;[Epub] CrossRef
Development, applications, and future prospects of RNA virus reverse genetics technology
Yu Guo, Ting Xue, Jianhua Wang, Xueqiao Xie, Furui Cao, Yijun Zhang, Huiting Wang, Bingqing Lu
Frontiers in Virology.2026;[Epub] CrossRef

Article

Efficient CRISPR-based genome editing for inducible degron systems to enable temporal control of protein function in large double-stranded DNA virus genomes: Kihye Shin, Eui Tae Kim; J. Microbiol. 2025;63(9):e2504008. Published online August 29, 2025; DOI: https://doi.org/10.71150/jm.2504008

3,621 View
125 Download
1 Web of Science
1 Crossref

Abstract PDF

CRISPR-Cas9-based gene editing enables precise genetic modifications. However, its application to human cytomegalovirus (HCMV) remains challenging due to the large size of the viral genome and the essential roles of key regulatory genes. Here, we establish an optimized CRISPR-Cas9 system for precise labeling and functional analysis of HCMV immediate early (IE) genes. By integrating a multifunctional cassette encoding an auxin-inducible degron (AID), a self-cleaving peptide (P2A), and GFP into the viral genome via homology-directed repair (HDR), we achieved efficient knock-ins without reliance on bacterial artificial chromosome (BAC) cloning, a labor-intensive and time-consuming approach. We optimized delivery strategies, donor template designs, and component ratios to enhance HDR efficiency, significantly improving knock-in success rates. This system enables real-time fluorescent tracking and inducible protein degradation, allowing temporal control of essential viral proteins through auxin-mediated depletion. Our approach provides a powerful tool for dissecting the dynamic roles of viral proteins throughout the HCMV life cycle, facilitating a deeper understanding of viral pathogenesis and potential therapeutic targets.

Citations

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Viral genome editing methods and applications in the CRISPR era
Kihye Shin, Eui Tae Kim, Herman W. Favoreel
Journal of Virology.2026;[Epub] CrossRef

Article

Korean Red ginseng enhances ZBP1-mediated cell death to suppress viral protein expression in host defense against Influenza A virus: Jueun Oh, Hayeon Kim, Jihye Lee, Suhyun Kim, Seyun Shin, Young-Eui Kim, Sehee Park, SangJoon Lee; J. Microbiol. 2025;63(1):e.2409007. Published online January 24, 2025; DOI: https://doi.org/10.71150/jm.2409007

3,756 View
141 Download
8 Web of Science
9 Crossref

Abstract PDF Supplementary Material

Korean Red ginseng has emerged as a potent candidate in the fight against various viral infections, demonstrating significant efficacy both in vitro and in vivo, particularly against influenza A viruses. Despite substantial evidence of its antiviral properties, the detailed molecular mechanisms through which it reduces viral lethality remain insufficiently understood. Our investigations have highlighted the superior effectiveness of Korean Red ginseng against influenza viruses, outperforming its effects on numerous other viral strains. We aim to uncover the specific mechanisms by which Korean Red ginseng exerts its antiviral effects, focusing on influenza A viruses. Our prior studies have identified the role of Z-DNA-binding protein 1 (ZBP1), a signaling complex involved in inducing programmed cell death in response to influenza virus infection. Given the critical role of ZBP1 as a sensor for viral nucleic acid, we hypothesize that Korean Red ginseng may modulate the ZBP1-derived cell death pathway. This interaction is anticipated to enhance cell death while concurrently suppressing viral protein expression, offering novel insights into the antiviral mechanism of Korean Red ginseng against influenza A viruses.

Citations

Citations to this article as recorded by

Formation and biological implications of Z-DNA
Yonghang Run, Mahmoud Tavakoli, Yuxuan Zhang, Karen M. Vasquez, Wenli Zhang
Trends in Genetics.2026; 42(2): 163. CrossRef
Herpes simplex virus 1 harboring poly(T) DNA sequences as a key ligand for AIM2 inflammasome activation and host defense
SuHyeon Oh, Jueun Oh, Kyeongchan Im, Tae Hyoung Kim, Jihye Lee, Kihye Shin, Nabukenya Mariam, Cheong Seok, Jaewoo Park, GyeongJu Yu, Hayeon Kim, Suhyun Kim, Seyun Shin, Jinwoo Gil, Sehee Park, Yoon-Seok Chung, Daesik Kim, Young Ki Choi, Eui Tae Kim, Joo S
Nature Communications.2026;[Epub] CrossRef
Mechanistic insights and regulatory strategies of ZBP1 in tumorigenesis, progression, and cancer therapy
Baochao Wei, Rong Xiao, Jinming Yu, Meng Wu, Dawei Chen
Critical Reviews in Oncology/Hematology.2026; 224: 105379. CrossRef
The bidirectional inflammasome–lymphocyte axis in immune regulation
Yoonyoung Kwon, Seon Ah Lim, SangJoon Lee
Trends Open.2026; 1(2): 131. CrossRef
Recent advances in Mpox across innate immunity, evasion, and clinical outcomes
Jueun Oh, Yoon-Seok Chung, SangJoon Lee
Communications Biology.2026;[Epub] CrossRef
Pattern recognition receptors and inflammasome: Now and beyond
SuHyeon Oh, Young Ki Choi, SangJoon Lee
Molecules and Cells.2025; 48(8): 100239. CrossRef
Targeting innate immune sensors for therapeutic strategies in infectious diseases
Seyun Shin, Young Ki Choi, SangJoon Lee
Journal of Microbiology.2025; 63(6): e2503009. CrossRef
mGem: Noncanonical nucleic acid structures—powerful but neglected antiviral targets
Václav Brázda, Richard P. Bowater, Petr Pečinka, Martin Bartas, Vinayaka R. Prasad
mBio.2025;[Epub] CrossRef
AIM2 drives inflammatory cell death and monkeypox pathogenesis
Jueun Oh, Yun-Ho Hwang, Jihye Lee, Cheong Seok, SuHyeon Oh, Hye Yoon Kim, Nabukenya Mariam, Jaeyoung Ahn, GyeongJu Yu, Jaewoo Park, Hayeon Kim, Suhyun Kim, Seyun Shin, Min-Chul Jung, Jinwoo Gil, Joo Sang Lee, Young Ki Choi, Dokeun Kim, Daesik Kim, You-Jin
Cellular & Molecular Immunology.2025; 22(12): 1615. CrossRef

Article

Efficiency of reverse genetics methods for rescuing severe acute respiratory syndrome coronavirus 2: Chang-Joo Park, Taehun Kim, Seung-Min Yoo, Myung-Shin Lee, Nam-Hyuk Cho, Changhoon Park; J. Microbiol. 2025;63(2):e2411023. Published online February 27, 2025; DOI: https://doi.org/10.71150/jm.2411023

7,239 View
157 Download
3 Web of Science
2 Crossref

Abstract PDF

Bacteria-free reverse genetics techniques are crucial for the efficient generation of recombinant viruses, bypassing the need for labor-intensive bacterial cloning. These methods are particularly relevant for studying the pathogenesis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19. This study compared the efficiency of three bacteria-free approaches—circular polymerase extension reaction (CPER) with and without nick sealing and infectious sub-genomic amplicons (ISA)—to bacterial artificial chromosome (BAC)-based technology for rescuing SARS-CoV-2. Significant differences in viral titers following transfection were observed between methods. CPER with nick sealing generated virus titers comparable to those of the BAC-based method and 10 times higher than those of the standard CPER. In contrast, ISA demonstrated extremely low efficiency, as cytopathic effects were detected only after two passages. All rescued viruses exhibited replication kinetics consistent with those of the original strain, with no significant deviation in replication capacity. Furthermore, the utility of CPER and ISA in genetically modifying SARS-CoV-2 was demonstrated by successfully inserting the gene encoding green fluorescent protein into the genome. Overall, this study underscores the potential of bacteria-free methods, such as CPER and ISA, in advancing SARS-CoV-2 research while highlighting their significant differences in efficiency.

Citations

Citations to this article as recorded by

Research Progress of Coronavirus Reverse Genetics Technology
Ziqi Han, Jiaxu Han, Yan Zhao, Chao Xu, Xue Leng, Boyin Jia, Naichao Diao, Fei Liu, Chunmei Cui, Jian Liang, Yuhang Jiang, Rui Du
Journal of Medical Virology.2026;[Epub] CrossRef
Reverse genetics strategies for coronaviruses: platform construction and applications in vaccine development
Yuhang Jia, Xinyu Han, Yuchen Ma, Xinjuan Wang, Yunzhu Yang, Aohan Zhang, Ke Ding, Songbiao Chen
Virus Genes.2026; 62(4): 428. CrossRef

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Editor's Choice 2025

Editor’s Choice Curator