Article
Gastroenterology & Hepatology
Jinlong Ru, Mohammadali Khan Mirzaei, Jinling Xue, Xue Peng, Li Deng
Summary: ViroProfiler is a computer analysis tool for analyzing shotgun viral metagenomic data. It can be run on a local or cloud computing environment. It uses containerization technology to ensure computational reproducibility and facilitate collaborative research.
Article
Microbiology
Li Song, Lu Zhang, Xiaodong Fang
Summary: The study on the human gut virome composition revealed that viral composition varied with age and disease type. The correlation between diseases and gut virome composition may be influenced by different factors.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Public, Environmental & Occupational Health
Wylerson Guimaraes Nogueira, Bruna Veronica Azevedo Gois, Kenny da Costa Pinheiro, Andressa de Oliveira Aragao, Ana Lidia Cavalcante Queiroz, Artur Luiz da Silva, Adriana Carneiro Folador, Rommel Thiago Juca Ramos
Summary: This study provides the first description of the virome composition and diversity in Lake Bolonha in Belem, Brazil, using a metagenomic approach. The research focuses on bacteriophages and cyanophages, and the results indicate the presence of a widely diverse viral community and phage-regulated dynamics in the lake's microbial ecosystem.
FRONTIERS IN PUBLIC HEALTH
(2022)
Article
Medicine, General & Internal
Xiang Lu, Hao Wang, Jingqi Zhang, Kexin Jin, Ling Ma, Yan Wang, Shixing Yang, Xiaochun Wang, Quan Shen, Tianji Zhou, Hui Xu, Wen Zhang
Summary: The imbalance of gut microbiota affects the immune development and regulation of individuals, leading to immune dysregulation and the development of atopic dermatitis (AD). This study assessed the composition of the virome in the gut of AD patients and healthy controls, revealing differences in diversity between the two groups. Finds provide a new perspective for understanding the effect of the gut microecological environment on AD.
FRONTIERS IN MEDICINE
(2022)
Article
Virology
Ilya Plyusnin, Olli Vapalahti, Tarja Sironen, Ravi Kant, Teemu Smura
Summary: Viruses are the main cause of emerging and re-emerging infectious diseases. Metagenomic next-generation sequencing (mNGS) is a high-throughput technology that can detect known or novel divergent viruses without prior assumptions. The Lazypipe 2 mNGS pipeline has significant improvements in code stability and transparency, with added functionality and support for new software components.
Article
Veterinary Sciences
Ying Shi, Jie Tao, Benqiang Li, Xiaohui Shen, Jinghua Cheng, Huili Liu
Summary: This study utilized metagenomics to investigate the gut virome of 45 domestic healthy dogs, revealing a diverse range of virus families. Canine coronavirus was particularly prevalent in all samples, posing a potential risk for cross-species transmission to humans. The findings contribute valuable insights into the role of companion animals in public health through viral diversity studies.
FRONTIERS IN VETERINARY SCIENCE
(2021)
Article
Microbiology
Jingjie Du, Ahmed A. Zayed, Kristina A. Kigerl, Kylie Zane, Matthew B. Sullivan, Phillip G. Popovich
Summary: Metagenomic analysis revealed changes in gut microbial population dynamics after SCI, with decreases in beneficial bacteria and increases in potentially pathogenic bacteria. The study also identified reductions in microbial genes related to essential pathways for central nervous system function and an expansion of known murine gut viral species sequence space after SCI.
Article
Virology
Hai-Chang Yin, De-Cai Wan, Hong-Yan Chen
Summary: In this study, metagenomics sequencing was used to analyze fecal samples from six forest rodent species in Northeast China, revealing a diverse virome composition. The top 10 most abundant viral families included viruses closely related to known human or animal pathogens. Additionally, a novel strain of astrovirus was discovered.
Review
Microbiology
Henryk Jurasz, Tomasz Pawlowski, Karol Perlejewski
Summary: Contamination is a common issue in viral metagenomic studies, affecting sequencing results particularly for low-biomass samples and clinical applications. Basic recommendations are proposed to reduce background noise and address the priority of reagent contamination, emphasizing the need for standards development in viral metagenomics, especially for diagnostics using viral shotgun metagenomic protocols.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Gastroenterology & Hepatology
Siwen Bao, Hao Wang, Wang Li, Haisheng Wu, Chunying Lu, Liang Yong, Qing Zhang, Xiang Lu, Min Zhao, Juan Lu, Jia Liu, Chukwudozie Kingsley Ikechukwu, Juan Xu, Ping Ni, Ying Xiong, Wen Zhang, Chenglin Zhou
Summary: This study aimed to investigate the differences in the gut virome between diarrheal children and healthy controls. Viral metagenomic analyses revealed that the alpha diversity of the diarrheal virome was not significantly different from that of the healthy virome, but the beta diversity had a significant difference. The diarrheal virome was mainly dominated by the families Adenoviridae, Astroviridae, Caliciviridae, and Picornaviridae, while the healthy virome also contains phages, including Microviridae and Caudovirales.
Article
Virology
Patricia Gil, Antoni Exbrayat, Etienne Loire, Ignace Rakotoarivony, Florian Charriat, Come Morel, Thierry Baldet, Michel Boisseau, Albane Marie, Benoit Frances, Gregory L'Ambert, Mohamed Bessat, Yehia Otify, Maria Goffredo, Giuseppe Mancini, Nuria Busquets, Lotty Birnberg, Sandra Talavera, Carles Aranda, Emna Ayari, Selma Mejri, Soufien Sghaier, Amal Bennouna, Hicham El Rhaffouli, Thomas Balenghien, Ghita Chlyeh, Ouafaa Fassi Fihri, Julie Reveillaud, Yannick Simonin, Marc Eloit, Serafin Gutierrez
Summary: Our understanding of the diversity of eukaryotic viruses is expanding, and it may have an impact on host physiology. However, the assembly processes of eukaryotic viruses in terrestrial animals are still unknown. In this study, we compared the taxonomic diversity of eukaryotic viruses in mosquitoes from different geographic locations and found differences in virus distribution depending on geography.
Review
Virology
Daan Jansen, Jelle Matthijnssens
Summary: Virome research is a rapidly growing field in the study of the microbiome, and its association with human diseases like inflammatory bowel disease (IBD) is increasingly recognized. Despite progress, there are methodological challenges that limit our understanding of the virome. This review discusses these challenges, including methodological biases and the imbalances observed in the virome of IBD patients, and highlights the need for further research to draw firm conclusions.
Article
Veterinary Sciences
Shixing Yang, Yumin He, Xu Chen, Ullah Kalim, Yan Wang, Shuyu Yang, Haifeng Qi, Hengzheng Cheng, Xiang Lu, Xiaochun Wang, Quan Shen, Wen Zhang
Summary: Raccoon dogs, as an ancient species of Canidae, carry various viruses, some of which have been detected from recent development in raccoon dog breeding. A study on the virome in raccoon dog feces from a farm in Jilin Province, China, identified DNA or RNA viruses mainly from seven families. This research contributes to a better understanding of the virome in raccoon dogs and provides valuable information for viral disease monitoring, prevention, and treatment in these animals.
FRONTIERS IN VETERINARY SCIENCE
(2021)
Article
Microbiology
Elisa M. Bolatti, Gaston Viarengo, Tomaz M. Zorec, Agustina Cerri, Maria E. Montani, Lea Hosnjak, Pablo E. Casal, Eugenia Bortolotto, Violeta Di Domenica, Diego Chouhy, Maria Belen Allasia, Ruben M. Barquez, Mario Poljak, Adriana A. Giri
Summary: This study investigated the diversity of DNA viruses in five arthropodophagous bat species from Argentina using metagenomics. Circoviridae and Genomoviridae were found to be the most prevalent viral families among vertebrate viruses. The viral diversity in T. brasiliensis colony was lower compared to other bat species. This research provides valuable insights into the global diversity of bat viruses and their importance in preventing emerging zoonotic diseases.
Article
Virology
Juliana Vanessa Cavalcante Souza, Hazerral de Oliveira Santos, Anderson Brandao Leite, Marta Giovanetti, Rafael dos Santos Bezerra, Eneas de Carvalho, Jardelina de Souza Todao Bernardino, Vincent Louis Viala, Rodrigo Haddad, Massimo Ciccozzi, Luiz Carlos Junior Alcantara, Sandra Coccuzzo Sampaio, Dimas Tadeu Covas, Simone Kashima, Maria Carolina Elias, Svetoslav Nanev Slavov
Summary: Viral metagenomics is a valuable tool for identifying emerging and re-emerging viral pathogens in clinical samples with unknown etiology. This study showcased the utility of metagenomics in identifying arboviruses in samples with inconclusive amplification results, and identified Dengue virus type 2 and Chikungunya virus in the samples.
Article
Biochemical Research Methods
Zena Cai, Yunshi Fan, Zheng Zhang, Congyu Lu, Zhaozhong Zhu, Taijiao Jiang, Tongling Shan, Yousong Peng
Summary: A systematic survey identified numerous viral circRNAs from 23 viral species, including both double-stranded DNA viruses and single-stranded RNA viruses. These viral circRNAs exhibit diverse characteristics and are involved in various cellular activities and diseases.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Virology
Shixing Yang, Tongling Shan, Yuqing Xiao, Heteng Zhang, Xiaochun Wang, Quan Shen, Yan Wang, Yuxin Yao, Qi Liu, Hao Wang, Wen Zhang
Summary: Analysis of pangolin metagenomic data suggests that pangolins may be intermediate hosts for SARS-CoV-2, but further sampling and analysis from various countries are needed for confirmation.
JOURNAL OF MEDICAL VIROLOGY
(2021)
Article
Microbiology
Chuanfeng Li, Tongling Shan, Zongyan Chen, Jiewen Zhou, Hang Li, Guangzhi Tong, Guangqing Liu
Summary: In 2015, a novel duck picornavirus, named duck/AH15/CHN/2015, was isolated from Cherry Valley ducks in Anhui province of China. It shares approximately 43% amino acid sequence identity with duck hepatitis A viruses (DHAV). The virus possesses a typical picornavirus-like genomic organization and is proposed to be a member of a novel species in the genus Avihepatovirus of the family Picornaviridae.
VETERINARY MICROBIOLOGY
(2021)
Article
Microbiology
Muddassar Hameed, Abdul Wahaab, Tongling Shan, Xin Wang, Sawar Khan, Di Di, Liu Xiqian, Jun-Jie Zhang, Muhammad Naveed Anwar, Mohsin Nawaz, Beibei Li, Ke Liu, Donghua Shao, Yafeng Qiu, Jianchao Wei, Zhiyong Ma
Summary: The study conducted metagenomic analysis of mosquito samples from animal farms in Yunnan province of China, revealing a highly diverse viral community with more than 19 viral taxonomic families. The viral reads included various animal viruses, suggesting a potential circulation of these viruses in vertebrate hosts. This study provides comprehensive knowledge of diverse viral populations in Yunnan province, which may pose a potential threat to both humans and domestic animals.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Virology
Hua Wang, Xiaoyong Chen, Ning Kong, Yajuan Jiao, Dage Sun, Sujie Dong, Wenzhen Qin, Huanjie Zhai, Lingxue Yu, Hao Zheng, Wu Tong, Hai Yu, Guangzhi Tong, Tongling Shan
Summary: The study reveals that TRIM21 inhibits the proliferation of PEDV by degrading the N protein, with its overexpression suppressing viral replication and knockdown leading to increased viral titers and N protein levels. TRIM21 interacts with and colocalizes with the N protein, and its antiviral effect is dependent on its ubiquitin ligase activity, which leads to the polyubiquitination and degradation of the N protein in a proteasome-dependent manner.
ARCHIVES OF VIROLOGY
(2021)
Article
Virology
Xiaoyong Chen, Ning Kong, Jingjing Xu, Juan Wang, Mingliang Zhang, Keyue Ruan, Liwei Li, Yujiao Zhang, Hao Zheng, Wu Tong, Guoxin Li, Tongling Shan, Guangzhi Tong
Summary: OASL protein regulates PRV proliferation by enhancing RIG-I signaling and suppressing PRV infection, while the PRV UL24 protein impairs RIG-I signaling to inhibit the transcription of interferon and ISGs.
Article
Cell Biology
Dage Sun, Ning Kong, Sujie Dong, Xiaoyong Chen, Wenzhen Qin, Hua Wang, Yajuan Jiao, Huanjie Zhai, Liwei Li, Fei Gao, Lingxue Yu, Hao Zheng, Wu Tong, Hai Yu, Wen Zhang, Guangzhi Tong, Tongling Shan
Summary: This study revealed the molecular mechanisms of selective autophagy in the host against viruses and demonstrated potential viral strategies to evade the autophagic process and IFN-I signaling for successful pathogenesis.
Article
Virology
Yu Zhang, Chunmei Wang, Ce Zhu, Wei Ye, Qin Gu, Chenbin Shu, Xiping Feng, Xi Chen, Wen Zhang, Tongling Shan
Summary: This study analyzed the expression profiles of circRNAs in gingival tissues of periodontitis patients with and without Redondoviridae infection, and identified key circRNAs associated with Redondoviridae-related periodontitis. Functional annotation and enrichment analysis revealed potential alterations in biological processes and metabolism in individuals suffering from Redondoviridae-infected periodontitis.
JOURNAL OF MEDICAL VIROLOGY
(2022)
Article
Genetics & Heredity
Xiaoyong Chen, Tongling Shan, Dage Sun, Huanjie Zhai, Sujie Dong, Ning Kong, Hao Zheng, Wu Tong, Guangzhi Tong
Summary: Porcine ZCCHC3 plays an inhibitory role in the proliferation of pseudorabies virus (PRV) by regulating cellular innate immune responses. Overexpression of ZCCHC3 inhibits viral titers and protein levels, while knockdown of ZCCHC3 promotes viral growth. ZCCHC3 overexpression upregulates IFN-beta expression to suppress viral replication. PRV infection reduces endogenous expression of ZCCHC3, and PRV-encoded UL13 and UL24 proteins inhibit ZCCHC3 expression, antagonizing its antiviral effect.
Article
Virology
Sujie Dong, Ning Kong, Yu Zhang, Youwen Li, Dage Sun, Wenzhen Qin, Huanjie Zhai, Xueying Zhai, Xinyu Yang, Chenqian Ye, Manqing Ye, Changlong Liu, Lingxue Yu, Hao Zheng, Wu Tong, Hai Yu, Wen Zhang, Guangzhi Tong, Tongling Shan
Summary: PEDV is a highly contagious swine virus that has caused significant economic damage to the global pork industry. Current vaccines are not fully effective, making it crucial to study the interaction between PEDV and its host. TARDBP effectively suppresses PEDV replication through proteasomal and autophagic degradation pathways, while also promoting the host's innate immune response by inducing IFN expression.
JOURNAL OF VIROLOGY
(2022)
Article
Environmental Sciences
Min Zhao, Chanjuan Yue, Zijun Yang, Yunli Li, Dongsheng Zhang, Ju Zhang, Shixing Yang, Quan Shen, Xiaoyan Su, Dunwu Qi, Rui Ma, Yuqing Xiao, Rong Hou, Xia Yan, Lin Li, Yanshan Zhou, Jiabin Liu, Xiaochun Wang, Wei Wu, Wen Zhang, Tongling Shan, Songrui Liu
Summary: The study found that feline panleukopenia virus (FPV) was prevalent in both giant pandas and red pandas, and other potentially pathogenic viruses were responsible for diseases or deaths in red pandas. The study also revealed instances of interspecies jumping events between giant pandas and their associated species. These findings are important for understanding the genetic diversity and viral transmission among giant pandas, associated animals, and arthropods.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Microbiology
Tongling Shan, Shixing Yang, Haoning Wang, Hao Wang, Ju Zhang, Ga Gong, Yuqing Xiao, Jie Yang, Xiaolong Wang, Juan Lu, Min Zhao, Zijun Yang, Xiang Lu, Ziyuan Dai, Yumin He, Xu Chen, Rui Zhou, Yuxin Yao, Ning Kong, Jian Zeng, Kalim Ullah, Xiaochun Wang, Quan Shen, Xutao Deng, Jianmin Zhang, Eric Delwart, Guangzhi Tong, Wen Zhang
Summary: Using viral metagenomics, the virome of wild birds was investigated, revealing higher virus diversity compared to breeding birds. New virus families, genera, or species were identified, and potential cross-species transmission was observed.
Article
Microbiology
Juan Lu, Shixing Yang, Chunmei Wang, Hao Wang, Ga Gong, Yuan Xi, Jiamin Pan, Xiaochun Wang, Jian Zeng, Ju Zhang, Peng Li, Quan Shen, Tongling Shan, Wen Zhang
Summary: This study investigated the viral communities in the gut of highland-dwelling Phrynocephalus lizards using viral metagenomic analysis. Bacteriophages, especially of the Caudovirales order, dominated the viral communities of different lizard species. The virome of Phrynocephalus erythrurus had a unique structure with a high abundance of the Parvoviridae family. The study also identified vertebrate-infecting viruses and antibiotic resistance genes. These findings contribute to the understanding of gut viromes in highland lizards and have implications for the protection of threatened species and interspecific differences in commensal viral transmission.
MICROBIOLOGY SPECTRUM
(2022)
Article
Veterinary Sciences
Lirong Zhang, Keyue Ruan, Guoju Sang, Zhaoyang Xu, Wu Tong, Hai Yu, Tongling Shan, Fei Gao, Liwei Li, Ning Kong, Guangzhi Tong, Hao Zheng
Summary: The results of this study indicate that rats are highly susceptible to PRV infection, and the deletion of tk does not completely diminish the pathogenicity of PRV in rats.
JOURNAL OF VETERINARY RESEARCH
(2021)
Article
Immunology
Yanzi Zhou, Wangxiao Zhou, Tingting Xiao, Yunbo Chen, Tao Lv, Yuan Wang, Shuntian Zhang, Hongliu Cai, Xiaohui Chi, Xiaoyang Kong, Kai Zhou, Ping Shen, Tongling Shan, Yonghong Xiao
Summary: The study revealed interspecies and cross-regional transmission of Clostridioides difficile between animals, the environment, and humans. Community-associated strains from both farms and asymptomatic hospitalized carriers were important reservoirs of C. difficile infection in hospitals.
EMERGING MICROBES & INFECTIONS
(2021)
