Journal of Microbiology

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Exploration of genes and identification of evolutionary evidence in adeno-associated viruses: Chanhee Lee, Jihong Min, Somin Lim, Anyeseu Park, Seokjin Kwak, Soyeon Hwang, Sooyeon Park, Yong-Suk Jang, Se-Yeoun Cha, Sung-Gook Cho, Jeong Yoon Lee; J. Microbiol. 2026;64(2):e2511016. Published online February 28, 2026; DOI: https://doi.org/10.71150/jm.2511016

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Abstract PDF Supplementary Material: Adeno-associated virus (AAV) commonly infects humans and non-human primates, generally inducing mild or even asymptomatic outcomes. AAVs have been shaped and diversified by evolutionary pressures, resulting in the identification of 13 serotypes thus far. Each serotype of AAV exhibits distinct tissue tropisms, targeting various organs, including the lung, central nervous system (CNS), liver, and skeletal muscle, thereby establishing AAVs as widely utilized vectors for therapeutic gene delivery. Bioinformatics analysis of specific viruses enables the inference of evolutionary patterns and offers valuable insights for predicting the emergence of novel viruses. While DNA sequence-based analysis has effectively facilitated the observation of mutation patterns accumulating within specific genes, it often provides limited insight into the actual impact of these mutations on proteins, the fundamental functional units. Utilizing proteotyping, an amino acid sequence-based comparative analysis, we identified hypervariable regions (HVR) within the AAV Cap gene and revealed concentrated evolutionary pressures in serotypes 4, 5, 11, and 12. Furthermore, we found that AAV-5 proteins exhibited considerable amino acid sequence divergence compared to those of other serotypes. Despite divergence, all AAV-5 proteins maintained a noticeable structural similarity to their counterparts in other serotypes. Our findings provide sequence-based insights into the evolutionary processes of AAV, facilitating the efficient identification of novel viruses.

Journal Article

In Silico Intensive Analysis for the E4 Gene Evolution of Human Adenovirus Species D: Chanhee Lee, Anyeseu Park, Jeong Yoon Lee; J. Microbiol. 2024;62(5):409-418. Published online April 30, 2024; DOI: https://doi.org/10.1007/s12275-024-00132-1

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Abstract PDF: Adenovirus (Ad) is a ubiquitous pathogen capable of infecting a wide range of animals and humans. Human Adenovirus (HAdV) can cause severe infection, particularly in individuals with compromised immune systems. To date, over 110 types of HAdV have been classified into seven species from A to G, with the majority belonging to the human adenovirus species D (HAdV-D). In the HAdV-D, the most significant factor for the creation of new adenovirus types is homologous recombination between viral genes involved in determining the virus tropism or evading immune system of host cells. The E4 gene, consisting of seven Open Reading Frames (ORFs), plays a role in both the regulation of host cell metabolism and the replication of viral genes. Despite long-term studies, the function of each ORF remains unclear. Based on our updated information, ORF2, ORF3, and ORF4 have been identified as regions with relatively high mutations compared to other ORFs in the E4 gene, through the use of in silico comparative analysis. Additionally, we managed to visualize high mutation sections, previously undetectable at the DNA level, through a powerful amino acid sequence analysis tool known as proteotyping. Our research has revealed the involvement of the E4 gene in the evolution of human adenovirus, and has established accurate sequence information of the E4 gene, laying the groundwork for further research.

Review

Genomic Evolution and Recombination Dynamics of Human Adenovirus D Species: Insights from Comprehensive Bioinformatic Analysis: Anyeseu Park, Chanhee Lee, Jeong Yoon Lee; J. Microbiol. 2024;62(5):393-407. Published online March 7, 2024; DOI: https://doi.org/10.1007/s12275-024-00112-5

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Abstract PDF

Human adenoviruses (HAdVs) can infect various epithelial mucosal cells, ultimately causing different symptoms in infected organ systems. With more than 110 types classified into seven species (A-G), HAdV-D species possess the highest number of viruses and are the fastest proliferating. The emergence of new adenovirus types and increased diversity are driven by homologous recombination (HR) between viral genes, primarily in structural elements such as the penton base, hexon and fiber proteins, and the E1 and E3 regions. A comprehensive analysis of the HAdV genome provides valuable insights into the evolution of human adenoviruses and identifies genes that display high variation across the entire genome to determine recombination patterns. Hypervariable regions within genetic sequences correlate with functional characteristics, thus allowing for adaptation to new environments and hosts. Proteotyping of newly emerging and already established adenoviruses allows for prediction of the characteristics of novel viruses. HAdV-D species evolved in a direction that increased diversity through gene recombination. Bioinformatics analysis across the genome, particularly in highly variable regions, allows for the verification or re-evaluation of recombination patterns in both newly introduced and pre-existing viruses, ultimately aiding in tracing various biological traits such as virus tropism and pathogenesis. Our research does not only assist in predicting the emergence of new adenoviruses but also offers critical guidance in regard to identifying potential regulatory factors of homologous recombination hotspots.

Citations

Citations to this article as recorded by

Relationship between adenovirus infection and intussusception via pathological evidence confirms
Lung-Huang Lin, Chi-Jung Huang, Cheng-Yu Lo, Yu-Hsien Lee, Yung-Chuan Chen
Journal of Clinical Pathology.2025; 78(10): 678. CrossRef
In Silico Intensive Analysis for the E4 Gene Evolution of Human Adenovirus Species D
Chanhee Lee, Anyeseu Park, Jeong Yoon Lee
Journal of Microbiology.2024; 62(5): 409. CrossRef

Research Support, Non-U.S. Gov't

Molecular Detection and Characterization of Human Enteroviruses in Korean Surface Water: Gyucheol Lee , Chanhee Lee; J. Microbiol. 2008;46(3):319-324. Published online July 5, 2008; DOI: https://doi.org/10.1007/s12275-007-0232-2

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Abstract PDF

In this study, the genetic epidemiology of enteroviruses (EVs) in Korean surface water was evaluated by conducting phylogenetic analyses of the nucleotide sequences of the 5’ non-coding region (5’ NCR), which was determined by RT-PCR analysis of total culturable virus assay-positive samples. The results showed that the nucleotide sequences of the EVs could be classified into 4 genetic clusters, and that the predominant presence of Korea EVs were very similar to echoviruses type 30. Interestingly, two nucleotide sequences were very similar to those of coxsackievirus type B1 isolated from aseptic meningitis patients in Seoul, Korea, implying the possibility of a common source for the viruses circulated in water systems and humans. In addition, 3 nucleotide sequences clustered strongly with the nucleotide sequences from China or Japan, and one fell into the same cluster as echovirus type 11 from Taiwan, which suggests that EVs in Asia may have evolved in a region-specific manner. Taken together, the results of this study revealed that EVs from Korea surface waters could be genetically classified as coxsackieviruses or echoviruses, and that they evolved in Asia in a region-specific manner.

Citations

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Direct typing of human enteroviruses from wastewater samples
Wafa Ibrahim, Imène Ouerdani, Sylvie Pillet, Mahjoub Aouni, Bruno Pozzetto, Rafik Harrath
Journal of Virological Methods.2014; 207: 215. CrossRef
Incidence and molecular characterization of hepatitis A viruses in Korean surface water between 2007 and 2010
Gyu‐Cheol Lee, Min‐Jeong Kim, Sehee Nam, Chan Hee Lee
Microbiology and Immunology.2014; 58(6): 342. CrossRef
Phylogenetic analysis of the VP1 gene of Enterovirus 71 in Guangzhou during the high occurrence period of 2008
Ying-xian Yin, Zhi-ying Ou, Yi Xu, Rong Zhou, Hui-min Xia
Virus Genes.2014; 48(3): 538. CrossRef
A 5‐year survey (2007–2011) of enteric viruses in Korean aquatic environments and the use of coliforms as viral indicators
Gyu‐Cheol Lee, Weon‐Hwa Jheong, Min‐jeong Kim, Don Hyeok Choi, Kyoung‐Hee Baik
Microbiology and Immunology.2013; 57(1): 46. CrossRef
Complete genomic sequence analysis of norovirus isolated from South Korea
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Virus Genes.2012; 45(2): 225. CrossRef
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Asian Pacific Journal of Tropical Medicine.2012; 5(9): 703. CrossRef
Detection and Molecular Characterization of Human Noroviruses in Korean Groundwater Between 2008 and 2010
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Food and Environmental Virology.2012; 4(3): 115. CrossRef

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