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.
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
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
Multidisciplinary Sciences
Olivier Zablocki, Michelle Michelsen, Marie Burris, Natalie Solonenko, Joanna Warwick-Dugdale, Romik Ghosh, Jennifer Pett-Ridge, Matthew B. Sullivan, Ben Temperton
Summary: Microbes play important roles in natural ecosystems, but are constrained by their viral predators. Studying viruses in nature can be challenging, but using integrated short- and long-read sequencing can provide more comprehensive results.
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
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
Zoology
Mi Rong Lee, Jong-Cheol Kim, So Eun Park, Woo-Jin Kim, Jae Su Kim
Summary: Ticks are carriers of viruses that can cause disease in humans and animals. Longhorned ticks, such as Haemaphysalis longicornis, can transmit severe fever with thrombocytopenia syndrome virus (SFTSV) in humans, and their population is increasing due to climate change. This study investigated viruses in longhorned ticks collected in Korea and analyzed virus titers in ticks exposed to the fungus Metarhizium anisopliae JEF-290. The findings suggest that longhorned ticks may not only spread SFTSV but also other disease-causing viruses globally. Viral metagenome analysis can be a tool for detecting unknown viruses and managing future outbreaks caused by ticks.
JOURNAL OF INVERTEBRATE PATHOLOGY
(2023)
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
Virology
Juan Lu, Shixing Yang, Xiaodan Zhang, Xiangming Tang, Ju Zhang, Xiaochun Wang, Hao Wang, Quan Shen, Wen Zhang
Summary: This study provides insights into the diversity and stability of viral communities in the Yangtze River Delta area, with no significant differences among sampling sites and a dominance of the Caudovirales order. A unique pattern of viral community composition with a relatively high abundance of the Parvoviridae family was observed in the Nanjing region.
Article
Microbiology
Kai Song
Summary: The researcher developed a Markov model-based method, VirMC, to identify viral sequences from metagenomic data, which outperformed other two state-of-the-art methods, particularly for short contigs and contaminated metagenomic samples. This alignment-free method showed better performance in assembling viral-genome sequences and could help classify healthy and diseased statuses based on human gut metagenomes.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Xiang Lu, Xiuguo Hua, Yan Wang, Dong Zhang, Shengyao Jiang, Shixing Yang, Xiaochun Wang, Quan Shen, Tianji Zhou, Zhibing Lin, Wen Zhang, Li Cui
Summary: Calf diarrhoea is a major cause of economic losses in the global dairy industry, with factors such as pathogen infections contributing to the condition. The study found that calves with diarrhoea had significantly lower diversity of viruses compared to healthy calves, with certain viruses being associated with calf diarrhoea. The research identified specific viral families and genomic sequences that may play a role in gut virus community ecology in healthy hosts and provide a theoretical basis for understanding enteric pathogens related to calf diarrhoea.
JOURNAL OF GENERAL VIROLOGY
(2021)
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)
Review
Virology
Geng-Hao Bai, Sheng-Chieh Lin, Yi-Hsiang Hsu, Shih-Yen Chen
Summary: The human body is colonized by a wide range of microorganisms, and the field of viromics has expanded. However, there have been few studies on direct causal relationships. Current viral metagenomic analyses have biases, and most review articles focus on the gut virome without investigating the role of viromes in other body sites in human diseases.
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
Biology
Oier Pedrera, Unai Ortega, Aritz Ruiz-Gonzalez, Jose Ramon Diez Diez, Oihana Barrutia
Summary: Plant Blindness refers to the lack of awareness and knowledge about plants, which is particularly common among secondary students. Despite an increase in understanding biodiversity and plant biology during secondary education, most students still exhibit symptoms of Plant Blindness. This indicates that Plant Blindness is not only related to plants themselves, but also to biodiversity.
JOURNAL OF BIOLOGICAL EDUCATION
(2023)
Article
Biotechnology & Applied Microbiology
David F. Nieuwenhuijse, Anne van der Linden, Robert H. G. Kohl, Reina S. Sikkema, Marion P. G. Koopmans, Bas B. Oude Munnink
Summary: This study explores the importance of genetic sequencing during outbreaks for public health decision making and compares different whole genome sequencing methods on the Nanopore and Illumina platforms. The findings suggest that the choice of sequencing approach and platform depends on the purpose of genome sequencing.
Article
Immunology
Roos S. G. Sablerolles, Wim J. R. Rietdijk, Abraham Goorhuis, Douwe F. Postma, Leo G. Visser, Katharina S. Schmitz, Daryl Geers, Susanne Bogers, Eva van Haren, Marion P. G. Koopmans, Virgil A. S. H. Dalm, Neeltje A. Kootstra, Anke L. W. Huckriede, Renate Akkerman, Martin Beukema, Melvin Lafeber, Debbie van Baarle, Rory D. de Vries, P. Hugo M. van der Kuy, Corine H. GeurtsvanKessel
Summary: This study found that SARS-CoV-2-specific binding antibodies, neutralizing antibodies, and T cells remained detectable 5 months after boosting with Ad26.COV2.S vaccine, although there was a decline in antibody levels and limited cross-reactivity with Omicron BA.1.
CLINICAL INFECTIOUS DISEASES
(2023)
Article
Biochemistry & Molecular Biology
Luca M. Zaeck, Mart M. Lamers, Babs E. Verstrepen, Theo M. Bestebroer, Martin E. van Royen, Hannelore Gotz, Marc C. Shamier, Leanne P. M. van Leeuwen, Katharina S. Schmitz, Kimberley Alblas, Suzanne van Efferen, Susanne Bogers, Sandra Scherbeijn, Guus F. Rimmelzwaan, Eric C. M. van Gorp, Marion P. G. Koopmans, Bart L. Haagmans, Corine H. GeurtsvanKessel, Rory D. de Vries
Summary: In July 2022, the monkeypox outbreak was declared an international public health emergency. Historic smallpox vaccination and monkeypox virus infection can generate MPXV-neutralizing antibodies, but vaccination with MVA-BN results in lower levels of these antibodies. Further studies are needed to assess the efficacy of the MVA-BN vaccine in at-risk populations.
Article
Public, Environmental & Occupational Health
K. J. Linde, I. M. Wouters, J. A. J. W. Kluytmans, M. F. Q. Kluytmans-van den Bergh, S. D. Pas, C. H. GeurtsvanKessel, M. P. G. Koopmans, M. Meier, P. Meijer, C. R. Raben, J. Spithoven, M. H. G. Tersteeg-Zijderveld, D. J. J. Heederik, W. Dohmen
Summary: This study assessed the levels of SARS-CoV-2 in the air and on surfaces in the immediate vicinity of infected patients. The results provide evidence of environmental contamination and confirm the potential for transmission of the virus through the air.
ANNALS OF WORK EXPOSURES AND HEALTH
(2023)
Article
Infectious Diseases
Lotte Jonker, Kimberly J. Linde, Marieke L. A. de Hoog, Robin Sprado, Robin C. Huisman, Richard Molenkamp, Bas B. Oude Munnink, Wietske Dohmen, Dick J. J. Heederik, Dirk Eggink, Matthijs R. A. Welkers, Harry Vennema, Pieter L. A. Fraaij, Marion P. G. Koopmans, Inge M. Wouters, Patricia C. J. L. Bruijning-Verhagen
Summary: The study confirmed the transmission of SARS-CoV-2 within schools and substantial asymptomatic circulation, as well as multiple introductions in some cases. However, the absence of air or surface contamination during school outbreaks suggests that environmental contamination is not widespread.
BMC INFECTIOUS DISEASES
(2022)
Article
Cell Biology
Noreen Mumtaz, Amel Dudakovic, Asha Nair, Marijke Koedam, Johannes P. T. M. van Leeuwen, Marion P. G. Koopmans, Barry Rockx, Andre J. J. van Wijnen, Bram C. J. van der Eerden
Summary: Arboviruses like Zika virus affect bone development by targeting osteoblasts and altering bone remodeling. In this study, the researchers investigated the effects of Zika virus infection on mesenchymal stromal cells (MSCs) at different stages of osteogenesis. They found that late-stage infected MSCs showed elevated osteogenic markers, calcium content, and altered gene expression compared to early-stage infected MSCs.
JOURNAL OF CELLULAR PHYSIOLOGY
(2023)
Article
Virology
Reina S. S. Sikkema, Erwin de Bruin, Christian Ramakers, Robbert Bentvelsen, Wentao Li, Berend-Jan Bosch, Brenda Westerhuis, Bart Haagmans, Marion P. G. Koopmans, Pieter L. A. Fraaij
Summary: The prevention and control measures for SARS-CoV-2 have not only affected its circulation, but also the timing and prevalence of other seasonal respiratory viruses, especially in children. Limited information is available on the exposure and infections of seasonal coronaviruses and SARS-CoV-2 in children during the first year of the pandemic.
Article
Virology
Michele M. Molendijk, My V. T. Phan, Lonneke G. M. Bode, Nikolas Strepis, Divyae K. Prasad, Nathalie Worp, David F. Nieuwenhuijse, Claudia M. E. Schapendonk, Bouke K. H. L. Boekema, Annelies Verbon, Marion P. G. Koopmans, Miranda de Graaf, Willem J. B. van Wamel
Summary: Infections caused by antibiotic resistant Staphylococcus aureus pose a significant challenge to treatment, and phages could potentially serve as an alternative to antibiotics. However, the lack of correlation between conventional in vitro and in vivo phage susceptibility assays hinders the use of phage therapy. This study assessed the susceptibility of twelve S. aureus strains to phages using four assays, and found that microcalorimetry in human serum better mimicked in vivo conditions and could be used to predict the in vivo susceptibility of S. aureus to phages.
Article
Virology
Vera C. C. Mols, Mart M. M. Lamers, Lonneke ME. Leijten, Tim I. I. Breugem, Marco WG. van de Bildt, Petra B. B. van den Doel, Peter HC. Lina, Marion PG. Koopmans, Bart L. L. Haagmans, Thijs Kuiken, Lineke Begeman
Summary: Most mammal species carry coronaviruses, with some having the ability to infect multiple hosts. A study found that a bat coronavirus in Europe has a preference for the intestines, suggesting that fecal-oral transmission is a possible route.
JOURNAL OF VIROLOGY
(2023)
Article
Biochemical Research Methods
Bas Oude B. Munnink, Marion Koopmans
Summary: Outbreak.info enables real-time monitoring and tracing of variants, as well as associated publications and resources, during the 'infodemic' of SARS-CoV-2.
Article
Environmental Sciences
Ray W. Izquierdo-Lara, Leo Heijnen, Bas B. Oude Munnink, Claudia M. E. Schapendonk, Goffe Elsinga, Jeroen Langeveld, Johan Post, Divyae K. Prasad, Christian Carrizosa, Frederic Been, Janko van Beek, Remy Schilperoort, Rianne Vriend, Ewout Fanoy, Evelien I. T. de Schepper, Reina S. Sikkema, Richard Molenkamp, Frank M. Aarestrup, Gertjan Medema, Marion P. G. Koopmans, Miranda de Graaf
Summary: Monitoring SARS-CoV-2 in wastewater has the potential to provide valuable information about viral dynamics and diversity within a population. In this study, sewage samples from different areas in Rotterdam were sequenced, and specific signature mutations were used to estimate the relative abundances of SARS-CoV-2 lineages. The results were compared with clinical genomic surveillance data to track the emergence, dominance, and replacement of specific variants of concern (VOCs). The study also demonstrated the ability to detect spatio-temporal clusters and identify mutations not captured by clinical surveillance.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Environmental Sciences
Jeroen Langeveld, Remy Schilperoort, Leo Heijnen, Goffe Elsinga, Claudia E. M. Schapendonk, Ewout Fanoy, Evelien I. T. de Schepper, Marion P. G. Koopmans, Miranda de Graaf, Gertjan Medema
Summary: During the COVID-19 pandemic from 2020 to 2022, monitoring SARS-CoV-2 RNA in wastewater has become an important tool for public health surveillance. Different normalisation methods, including electrical conductivity and crAssphage, have been studied and compared to the standard approach of using flow measurements. The results show that crAssphage can be used as a quantitative biomarker for larger populations, while electrical conductivity is useful for determining dilution rates. Overall, flow normalisation is necessary for accurately determining short-term trends in virus circulation and can be improved with additional measurements.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Multidisciplinary Sciences
Isabel Barja, Ana Pineiro, Aritz Ruiz-Gonzalez, Amaia Caro, Pilar Lopez, Jose Martin
Summary: Chemical signals in wolf feces, including aromatic compounds, steroids, and tocopherol, vary in composition and proportions between sexes and reproductive states. These compounds likely play a role in intraspecific and interspecific communication, and their levels in feces may be indicative of the wolf's sex and physiological and reproductive status.
SCIENTIFIC REPORTS
(2023)
Article
Veterinary Sciences
Katarzyna Domanska-Blicharz, Anna Orlowska, Marcin Smreczak, Bas Oude Munnink, Pawel Trebas, Wojciech Socha, Krzysztof Niemczuk, Magdalena Kawiak-Sadurska, Justyna Opolska, Anna Lisowska, Aleksandra Giza, Arkadiusz Bomba, Ewelina Iwan, Marion Koopmans, Jerzy Rola
Summary: SARS-CoV-2 infections were detected in mink on 11 farms in 8 out of 16 Polish administrative regions. Sequencing revealed that the viruses belonged to four different variants of concern (VOC) and seven different Pango lineages. Serological testing showed a high rate of seroprevalence on the single mink farm studied, indicating the potential threat of mink as virus reservoirs.
JOURNAL OF VETERINARY RESEARCH
(2022)