Article
Multidisciplinary Sciences
Yuri Munsamy, Riaz Y. Seedat, Tumelo R. Sekee, Phillip A. Bester, Felicity J. Burt
Summary: This study identified sequence variations within the LCR of a South African HPV31 isolate, and found that these variations may affect the viral p97 promoter activity. Further investigation using mutagenesis and beta-galactosidase assays revealed increased transcriptional activity in mutants with a single nucleotide change within the YY1 transcription factor binding site.
Article
Multidisciplinary Sciences
Wanxin Li, Lila Kari, Yaoliang Yu, Laura A. Hug
Summary: MT-MAG is a machine learning-based software tool that provides complete or partial hierarchically-structured taxonomic classification of metagenome-assembled genomes (MAGs). It is alignment-free and uses k-mer frequencies for classification. MT-MAG is capable of classifying large and diverse metagenomic datasets. It achieves high classification accuracy and outperforms other comparable tools. It also provides additional information for unclassified sequences. Rating: 7/10
Article
Multidisciplinary Sciences
Kazuki Ichikawa, Riki Kawahara, Takeshi Asano, Shinichi Morishita
Summary: This study uses a high-precision algorithm to determine complex TR structures from long accurate sequences, revealing the abundance and diversity of TRs. It finds that complex TRs are more common than single-unit TRs, and that they tend to consist of <10-bp units. Several known disease-associated TRs are found in loci with extended TRs, making them potential candidates for disease association.
NATURE COMMUNICATIONS
(2023)
Review
Microbiology
Ryan F. Relich, Michael J. Loeffelholz
Summary: The classification of viruses remains important in various disciplines, including clinical virology. Since 2019, new taxonomic revisions have been made to known viruses and several novel human and animal viruses have been discovered. This update provides an overview of taxonomic changes for disease-causing viruses of humans between 2020 and 2022, based on recent advancements by the International Committee on Taxonomy of Viruses.
JOURNAL OF CLINICAL MICROBIOLOGY
(2023)
Review
Microbiology
Michael J. Loeffelholz, Bradley W. Fenwick
Summary: The classification of viruses is important for scientific and clinical disciplines, and recent updates on disease-causing viruses have been influenced by the International Committee on Taxonomy of Viruses.
JOURNAL OF CLINICAL MICROBIOLOGY
(2021)
Article
Immunology
Kavita Panwar, Anna Godi, Clementina E. Cocuzza, Nick Andrews, Jo Southern, Paul Turner, Elizabeth Miller, Simon Beddows
Summary: The study evaluated the antibody response of HPV vaccines against different types of human papillomavirus. The findings showed that the vaccines provided long-lasting protection against vaccine types and maintained high antibody levels against related non-vaccine types. This contributes to the evidence base supporting public health intervention.
Article
Multidisciplinary Sciences
Shan-Shan Zhou, Xue-Mei Yan, Kai-Fu Zhang, Hui Liu, Jie Xu, Shuai Nie, Kai-Hua Jia, Si-Qian Jiao, Wei Zhao, You-Jie Zhao, Ilga Porth, Yousry A. El Kassaby, Tongli Wang, Jian-Feng Mao
Summary: Researchers have constructed a plant dataset containing 2,593,685 intact LTR-RTs from 300 plant species, representing 93 families of 46 orders. This dataset includes structural and functional annotation, age determination, and classification information, providing valuable resources for investigating the evolutionary dynamics and functional implications of LTR-RTs in plant genomes.
Article
Microbiology
Shiwen Peng, Louise Ferrall, Stephanie Gaillard, Chenguang Wang, Wei-Yu Chi, Chuan-Hsiang Huang, Richard B. S. Roden, T-C Wu, Yung-Nien Chang, Chien-Fu Hung
Summary: Immunotherapy for cervical cancer targeting high-risk human papillomavirus types 16 and 18 shows promising results in preclinical studies, with pBI-11 DNA vaccine inducing strong immune responses and therapeutic effects in mouse models. Combination with TA-HPV boost and PD-1 antibody blockade improves tumor control and survival. Clinical translation of this strategy may provide a new approach for HPV16/18-associated tumors.
Article
Virology
Tina M. Rehm, Elke Straub, Stephan Forchhammer, Ulrike Leiter, Thomas Iftner, Frank Stubenrauch
Summary: This article highlights the association of high-risk HPV with cancer and the possible link between beta-HPV and cutaneous squamous cell carcinoma. The study suggests that keratinocytes may be suitable for investigating beta-HPV replication.
JOURNAL OF VIROLOGY
(2022)
Article
Biochemistry & Molecular Biology
Supriya Khedkar, Georgy Smyshlyaev, Ivica Letunic, Oleksandr M. Maistrenko, Luis Pedro Coelho, Askarbek Orakov, Sofia K. Forslund, Falk Hildebrand, Mechthild Luetge, Thomas S. B. Schmidt, Orsolya Barabas, Peer Bork
Summary: Prokaryotic Mobile Genetic Elements (MGEs) play important roles in evolution and the spread of antibiotic resistance. However, current understanding of their global dispersal is limited. In this study, a computational framework was developed to capture different MGE types and their cargos, allowing for a better understanding of MGE dispersal. The findings were integrated into a resource, providing a valuable tool for future research on the mobile part of genomes and its horizontal dispersal.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Virology
Franziska Kuehner, Elke Straub, Thomas Iftner, Frank Stubenrauch
Summary: Productive replication of HPV16 only occurs in differentiating keratinocytes. The E8 E2 protein of HPV16 acts as a repressor of viral gene expression and genome replication, and the knock-out of E8- enhances viral late protein expression in differentiated cells. Global transcriptome analysis revealed a small number of differentially expressed genes in differentiated HPV16 wild-type and E8- cell lines, which are unrelated to cell cycle, DNA metabolism, or keratinocyte differentiation. Deregulation of these genes requires cell differentiation and is positively correlated with the expression of viral late transcripts. Knock-out of the E4 and E5 genes, which enhance productive replication, attenuates the deregulation of these host cell genes. In summary, productive HPV16 replication modulates host cell transcription.
Article
Microbiology
Anthony Duncan, Kerrie Barry, Chris Daum, Emiley Eloe-Fadrosh, Simon Roux, Katrin Schmidt, Susannah G. Tringe, Klaus U. Valentin, Neha Varghese, Asaf Salamov, Igor Grigoriev, Richard M. Leggett, Vincent Moulton, Thomas Mock
Summary: This study assembled 143 high-quality MAGs from chlorophyll a maximum layers in the surface of the Arctic and Atlantic Oceans. The results revealed strict demarcation between Arctic and Atlantic MAGs, but high similarity between adjacent sampling stations in each ocean. Eukaryotic MAGs were more diverse in the Arctic, while prokaryotic MAGs were more diverse in the Atlantic.
Editorial Material
Virology
Juan D. Ramirez, Sergio Castaneda, Nathalia Ballesteros, Marina Munoz, Matthew Hernandez, Radhika Banu, Paras Shrestha, Feng Chen, Huanzhi Shi, Harm van Bakel, Viviana Simon, Carlos Cordon-Cardo, Emilia M. Sordillo, Alberto E. Paniz-Mondolfi
Summary: The COVID-19 pandemic continues to challenge global public health systems, with the emergence of highly transmissible and immune-evading variants like Omicron. Comparative analysis of epidemiological and genomic data reveals the rapid global spread of Omicron in South Africa, the United Kingdom, and New York City, highlighting its high transmissibility. The study emphasizes the need for global authorities to prioritize equitable vaccine access and ongoing genomic surveillance. Although further research is required to fully understand the biological properties of Omicron, vaccination, large-scale testing, and infection prevention measures remain the most effective tools against the COVID-19 pandemic.
JOURNAL OF MEDICAL VIROLOGY
(2022)
Article
Virology
Ahmed Ismail, Tanuj Saini, Ahmed Al Qaffas, Ivan Erill, Steven M. Caruso, Louise Temple, Allison A. Johnson
Summary: This study explored the genome sequences of sixteen Bacillus-infecting bacteriophages through comparative genomics approaches, revealing shared and unique characteristics. These phages belong to the Salasmaviridae family with small double-stranded DNA genomes encoding 25-46 predicted open reading frames. The study observed extensive sequence divergence among core-function genes, as well as identified examples of sequence directed recombination and the introduction of novel open reading frames. These findings highlight the complex evolutionary relationships of phage genomes.
Article
Virology
Apurva T. Prabhakar, Claire D. James, Dipon Das, Christian T. Fontan, Raymonde Otoa, Xu Wang, Molly L. Bristol, Iain M. Morgan
Summary: This study reveals the role of HPV16 E2 protein in regulating transcription, replication, and segregation of the viral genome during the viral life cycle. It identifies the interaction between E2 and the host protein TopBP1 as essential for the segregation function of E2. These findings contribute to our understanding of HPV16 infection.
JOURNAL OF VIROLOGY
(2022)
Article
Public, Environmental & Occupational Health
Eliza Lai-Yi Wong, Annie Wai-Ling Cheung, Zigui Chen, Amy Yuen-Kwan Wong, Apple Chung-Man Yeung, Peter Sen-Yung Yau, Paul Kay-Sheung Chan
Summary: This study investigated HPV infection among Chinese women with cytological abnormalities and found an overall infection rate of 74%, with 2.3% being cutaneous HPV infection. The prevalence of HPV infection peaked in the 35-39 age group and gradually declined, with a second peak occurring at age 65 and above. HPV58, HPV52, HPV53, HPV16, and HPV18 were the most common high-risk genotypes among women with cytological abnormalities.
FRONTIERS IN PUBLIC HEALTH
(2022)
Article
Virology
Sile Li, Ho Yin Luk, Chichao Xia, Zigui Chen, Paul Kay Sheung Chan, Siaw Shi Boon
Summary: Esophageal carcinoma is the sixth leading cause of cancer death, with low survival rates. Infection with oncogenic viruses, notably human papillomavirus (HPV), is suspected to play a significant role in the development of esophageal carcinoma. This review explores the association between oncogenic viruses and esophageal carcinoma, with a focus on HPV. The efficacy of various treatment regimens, including immunotherapy, chemotherapy, and chemoradiotherapy, is also discussed.
TUMOUR VIRUS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Lirong Cao, Jingzhi Lou, See Yeung Chan, Hong Zheng, Caiqi Liu, Shi Zhao, Qi Li, Chris Ka Pun Mok, Renee Wan Yi Chan, Marc Ka Chun Chong, William Ka Kei Wu, Zigui Chen, Eliza Lai Yi Wong, Paul Kay Sheung Chan, Benny Chung Ying Zee, Eng Kiong Yeoh, Maggie Haitian Wang
Summary: A model that predicts the effectiveness of COVID-19 vaccines against circulating SARS-CoV-2 variants based on genetic distance was found to have high predictive accuracy. The study analyzed vaccine efficacy data and genetic sequences of the virus to establish a relationship between genetic distance and vaccine effectiveness. The model successfully predicted the protection provided by existing vaccines against new variants and can inform vaccine deployment and public health responses in real time.
Review
Oncology
Siaw Shi Boon, Ho Yin Luk, Chuanyun Xiao, Zigui Chen, Paul Kay Sheung Chan
Summary: This review discusses the timeline and development of screening, diagnosis, and treatment methods for precancer and cancer of the uterine cervix, as well as the incorporation of automation, machine learning, and state-of-the-art technologies. Cervical cancer is a major cause of cancer deaths among women worldwide, particularly in low- and middle-income countries. The review outlines the standard guidelines implemented globally and discusses the staging of cervical cancer, safety and efficacy of treatment modalities, and the use of computer-aided technologies. Concerns regarding the practicality of these advancements, such as high cost and the inability to replace trained professionals, are also addressed.
Letter
Infectious Diseases
Christopher K. C. Lai, Grace C. Y. Lui, Yuchen Wei, Ka Chun Chong, Zigui Chen, Lowell Ling, Rita W. Y. Ng, Siaw S. S. Boon, Wendy C. S. Ho, Apple C. M. Yeung, David S. C. Hui, Paul K. S. Chan
JOURNAL OF INFECTION
(2022)
Article
Multidisciplinary Sciences
Yue Dong, Lu Wang, Zifeng Zhang, Fengtong Ji, Tony K. F. Chan, Haojin Yang, Catherine P. L. Chan, Zhengxin Yang, Zigui Chen, Wai Tsz Chang, Jason Y. K. Chan, Joseph J. Y. Sung, Li Zhang
Summary: In this study, an endoscopy-assisted treatment procedure based on wobbling Fe2O3 helical micromachines (HMMs) was proposed for treating biofilm occlusion in T-tubes. The wobbling motion of Fe2O3 HMMs induces stronger mechanical force and fluid convections, allowing for quick destruction of biofilm and killing bacteria cells, making the procedure promising for clinical application.
Article
Oncology
Jason Y. K. Chan, Man Kit Cheung, Linlin Lan, Cherrie Ng, Eric H. L. Lau, Zenon W. C. Yeung, Eddy W. Y. Wong, Leanne Leung, Xinyu Qu, Liuyang Cai, Hengyan Zhu, Siaw Shi Boon, Robert D. Burk, Paul K. S. Chan, Zigui Chen
Summary: This study investigated the interplay among the oral microbiota, HPV infection, traditional risk factors, and patient outcomes in head and neck squamous cell carcinoma (HNSCC). The results showed that dysbiosis of the oral microbiota is closely associated with HNSCC pathogenesis, and the presence of Fusobacterium is linked to improved outcomes in OSCC patients.
Article
Microbiology
Man Kit Cheung, Sylvia L. Y. Tong, Martin C. S. Wong, Jason Y. K. Chan, Margaret Ip, Mamie Hui, Christopher K. C. Lai, Rita W. Y. Ng, Wendy C. S. Ho, Apple C. M. Yeung, Paul K. S. Chan, Zigui Chen
Summary: This study characterized the bacterial and fungal microbiomes in oral and stool samples from healthy Chinese adults. The results showed limited transmission of microbiota between the oral cavity and gut in healthy individuals, with only a few shared bacterial and fungal variants. The sharing of potentially transmissible fungal variants was associated with host factors.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Liping Lyu, Usman Asghar, Jinyu Fu, Yunyi Gao, Xue Zhang, Saleh A. Al-Farraj, Zigui Chen, Feng Gao
Summary: Ciliated protists have both germline micronucleus (MIC) and somatic macronucleus (MAC) within a single cytoplasm. Genomic sequences of ciliates remain largely unknown due to the difficulty in culturing and separating the germline from the somatic genome. Single-cell whole genome amplification techniques such as multiple displacement amplification (MDA) and multiple annealing and looping-based amplification cycles (MALBAC) have been compared in this study to characterize the germline and somatic genomes of ciliates with different genomic architectures.
EUROPEAN JOURNAL OF PROTISTOLOGY
(2023)
Review
Otorhinolaryngology
Haaron S. L. Ting, Zigui Chen, Jason Y. K. Chan
Summary: By systematically analyzing the relationship between head and neck squamous cell carcinoma (HNSCC) and the oral microbiome, similarities and inconsistencies in microbial diversities, microbiome profiles, metagenomic analysis, and host-pathogen interactions were identified. The potential clinical applications of the microbiome in screening and diagnosis of HNSCC were evaluated.
HEAD AND NECK-JOURNAL FOR THE SCIENCES AND SPECIALTIES OF THE HEAD AND NECK
(2023)
Article
Oncology
Hengyan Zhu, Hon Chi Yip, Man Kit Cheung, Hiu Ching Chan, Cherrie Ng, Eric H. L. Lau, Zenon W. C. Yeung, Eddy W. Y. Wong, Leanne Leung, Xinyu Qu, Daijuanru Wang, Liuyang Cai, Paul K. S. Chan, Jason Y. K. Chan, Zigui Chen
Summary: By sequencing the microbial communities in samples from patients with primary esophageal squamous cell carcinoma (ESCC) and oral cavity squamous cell carcinoma (OSCC), this study found that these two cancers displayed similar patterns of dysbiosis in their upper aerodigestive microbiota. Certain bacterial genera were commonly enriched or depleted in both types of cancer, suggesting a potential role in the pathogenesis of malignancies.
INTERNATIONAL JOURNAL OF CANCER
(2023)
Article
Public, Environmental & Occupational Health
Man Kit Cheung, Rita W. Y. Ng, Christopher K. C. Lai, Chendi Zhu, Eva T. K. Au, Jennifer W. K. Yau, Carmen Li, Ho Cheong Wong, Bonnie C. K. Wong, Kin On Kwok, Zigui Chen, Paul K. S. Chan, Grace C. Y. Lui, Margaret Ip
Summary: International travel increases the risk of acquiring antibiotic-resistant bacteria and antibiotic resistance genes (ARGs). This study found that traveling to low- or middle-income countries, Africa or Southeast Asia, a long travel duration, and the use of alcohol-based hand sanitizer or doxycycline as antimalarial prophylaxis are important risk factors for the acquisition/enrichment of ARGs during international travel.
JOURNAL OF TRAVEL MEDICINE
(2023)
Article
Multidisciplinary Sciences
Bei Huang, Steven W. H. Chau, Yaping Liu, Joey W. Y. Chan, Jing Wang, Suk Ling Ma, Jihui Zhang, Paul K. S. Chan, Yun Kit Yeoh, Zigui Chen, Li Zhou, Sunny Hei Wong, Vincent C. T. Mok, Ka Fai To, Hei Ming Lai, Simon Ng, Claudia Trenkwalder, Francis K. L. Chan, Yun Kwok Wing
Summary: The study reveals that the gut microbiota compositions are significantly altered in early PD and RBD compared with control and RBD-FDR. The depletion of butyrate-producing bacteria and the enrichment of pro-inflammatory Collinsella have emerged in RBD and RBD-FDR after controlling potential confounders. The study also identifies 12 microbial markers that can effectively distinguish RBD from control.
NATURE COMMUNICATIONS
(2023)
Article
Oncology
Siaw Shi Boon, Yin Ching Lee, Ka Lai Yip, Ho Yin Luk, Chuanyun Xiao, Man Kin Yim, Zigui Chen, Paul Kay Sheung Chan
Summary: This study identified Aurora kinase B (AurB) as a novel interacting partner of human papillomavirus E6, and investigated the molecular mechanism of how E6 recruits AurB to induce cell immortalization and proliferation, leading to eventual cancer development. The study also evaluated the efficacy of Aurora kinase inhibitors in halting HPV-mediated carcinogenesis. The findings revealed the potential for specific and selective inhibitors to be developed for the treatment of HPV-related cancers.
Article
Microbiology
Yehao Chen, Yuping Song, Zigui Chen, Jennifer Wing Ki Yau, Kate Ching Ching Chan, Agnes Sze Yin Leung, Oi Man Chan, Apple Chung Man Yeung, Connie Lai Yuk Yuen, Paul Kay Sheung Chan, Wing Hung Tam, Ting Fan Leung
Summary: This study investigated the early-life evolution of the skin microbiome in Chinese children and its association with eczema phenotypes. The results showed that atopic sensitization at 12 months was strongly associated with persistent eczema at 24 months. Children with atopic eczema had reduced alpha diversity at 12 months and transiently higher abundance of the genus Janibacter at 6 months compared to those with non-atopic eczema. These findings suggest that atopic sensitization at 12 months may predict persistent eczema, and atopic eczema is associated with unique skin microbiome profiles at different time points. Non-invasive skin-microbiome profiling may have predictive value for atopic eczema.
