Article
Microbiology
German V. Roev, Nadezhda I. Borisova, Nadezhda V. Chistyakova, Matvey R. Agletdinov, Vasily G. Akimkin, Kamil Khafizov
Summary: Next-generation sequencing technologies have transformed virology by enabling complete viral genome sequencing, metagenomic studies, and identification of new viral pathogens. However, metagenomic sequencing faces challenges in data analysis and identifying novel viruses using traditional homology-based strategies. This study used advanced computational methods and experimental strategies to analyze bat feces from different Russian cities and identified a diverse range of viral pathogens.
Article
Chemistry, Multidisciplinary
Vasilka Chopkova, Mariana Petkova, Stefan Shilev
Summary: This study investigated the bacterial diversity of mesophilic and thermophilic phases of composting in two different sites using Illumina HiSeq sequencing and phylogenetic analysis. The results showed that the mesophilic phase had a higher number of bacterial species compared to the thermophilic phase, and there were differences in bacterial diversity between the two composting sites.
APPLIED SCIENCES-BASEL
(2023)
Article
Microbiology
Ellen C. Carbo, Anne Russcher, Margriet E. M. Kraakman, Caroline S. de Brouwer, Igor A. Sidorov, Mariet C. W. Feltkamp, Aloys C. M. Kroes, Eric C. J. Claas, Jutte J. C. de Vries
Summary: In this study, the mNGS approach was used for the identification and load monitoring of transplantation-related DNA viruses in immunocompromised patients. The results showed that the mNGS method performed comparably to qPCR in detection and viral load determination.
Review
Oncology
Nicholas Bradley Larson, Ann L. Oberg, Alex A. Adjei, Liguo Wang
Summary: Next-generation sequencing (NGS) technologies, widely used in cancer research, generate vast and diverse data that require sophisticated computational methods and bioinformatics expertise. This review provides background details of NGS technology and basic bioinformatics concepts for clinicians interested in cancer research applications, with a focus on DNA-based approaches. It introduces principles of library preparation, alignment, variant calling, variant annotations, and NGS applications for other molecular data types. The review also discusses the utility of NGS methods in NSCLC research and study design considerations for leveraging NGS technologies in clinical care.
JOURNAL OF THORACIC ONCOLOGY
(2023)
Review
Cell Biology
Heloise Tudela, Sandrine P. Claus, Maya Saleh
Summary: The gut microbiota, a diverse community of microorganisms in the gastrointestinal tract, has a significant impact on health and disease. Keystone species, essential microbes for microbiota balance, play crucial roles in maintaining essential functions and their identification is crucial for the development of microbiome-based therapeutics. Understanding the functions of keystone species is a major step towards comprehending microbiome dynamics in disease.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Microbiology
Darlene D. Wagner, Rachel L. Marine, Edward Ramos, Terry Fei Fan Ng, Christina J. Castro, Margaret Okomo-Adhiambo, Krysten Harvey, Gregory Doho, Reagan Kelly, Yatish Jain, Roman L. Tatusov, Hideky Silva, Paul A. Rota, Agha N. Khan, M. Steven Oberste
Summary: VPipe is an automated bioinformatics pipeline for analyzing NGS data and performing whole-genome assembly and species identification of viral sequences. It offers a user-friendly interface with advanced search capabilities for reviewing results. Additionally, VPipe provides a centralized system for storing and analyzing NGS data, expediting public health responses to viral outbreaks and pathogen surveillance.
MICROBIOLOGY SPECTRUM
(2022)
Review
Engineering, Environmental
Emily Garner, Benjamin C. Davis, Erin Milligan, Matthew Forrest Blair, Ishi Keenum, Ayella Maile-Moskowitz, Jin Pan, Mariah Gnegy, Krista Liguori, Suraj Gupta, Aaron J. Prussin, Linsey C. Marr, Lenwood S. Heath, Peter J. Vikesland, Liqing Zhang, Amy Pruden
Summary: The emergence of NGS technologies has revolutionized the water industry's ability to address complex microbiological challenges, although faced with barriers like cost and expertise. Research has focused on the applications of NGS in water, wastewater, and recycled water, highlighting key contributions and future directions for advancement.
Article
Genetics & Heredity
Moritz Kohls, Magdalena Kircher, Jessica Krepel, Pamela Liebig, Klaus Jung
Summary: Estimating the taxonomic composition of viral sequences using artificial neural networks and machine learning models proved to be more accurate than traditional mapping approaches. Training data sampled from the NCBI database with a focus on the biological order of viruses allowed for a higher prediction accuracy in classifying test reads to their viral order. The use of auxiliary test sets helped to estimate conditional class probabilities and correct the prior estimation of taxonomic distribution in the test set.
Article
Multidisciplinary Sciences
Zhenli Diao, Dongsheng Han, Rui Zhang, Jinming Li
Summary: This review summarizes the potential applications and challenges of metagenomic next-generation sequencing (mNGS) in the diagnosis of lower respiratory tract infections (LRIs), aiming to promote the integration of mNGS into the management of patients with respiratory tract infections in a clinical setting.
JOURNAL OF ADVANCED RESEARCH
(2022)
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
Oncology
Ariana Rostami, Scott Bratman, Kathy Han
Summary: Liquid biopsy approaches for detecting viral DNA play a crucial role in diagnosing virally-associated cancers. The CaptHPV method based on next-generation sequencing is discussed for its potential in detecting plasma HPV DNA in HPV-associated cancers and its potential clinical utility.
CLINICAL CANCER RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Laura Ciuffreda, Hector Rodriguez-Perez, Carlos Flores
Summary: The introduction of nanopore sequencing technology has significantly improved our ability to study complex microbial samples, allowing real-time sequencing of long reads with low cost and portability. This technology plays a crucial role in resolving complex genomic structures, accessing metagenome assembled genomes, and shows great potential in environmental microbial analysis.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Review
Biochemistry & Molecular Biology
Pei Yee Tiew, Oliver W. Meldrum, Sanjay H. Chotirmall
Summary: Microbiomics has made significant advancements in the past decade due to the availability of next-generation sequencing (NGS) and multi-omic technologies. Integration of NGS and multi-omic datasets allows for comprehensive assessment of endophenotypes in chronic respiratory diseases like chronic obstructive pulmonary disease (COPD). Valuable insights have been gained into the role of microbial communities in COPD onset, progression, prognosis, and treatment response. Identifying specific microbes and metabolic signatures associated with COPD can lead to new therapeutic interventions and prognosis-related biomarkers. However, the analysis and interpretation of the large amount of data generated by these technologies remain challenging, and standardized methods are lacking.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Immunology
Ravina Kullar, Emanuele Chisari, James Snyder, Christopher Cooper, Javad Parvizi, Jason Sniffen
Summary: This article discusses the gaps in traditional culture and introduces the utility of next-generation sequencing (NGS) in diagnosing and treating peri-prosthetic joint infections. It highlights the clinical benefits of using NGS compared to culture alone and emphasizes the potential of NGS in improving the yield of identifying infective organisms in challenging cases.
CLINICAL INFECTIOUS DISEASES
(2023)
Article
Immunology
Denver T. Niles, Paula A. Revell, Daniel Ruderfer, Lucila Marquez, J. Chase McNeil, Debra L. Palazzi
Summary: Plasma metagenomic next-generation sequencing (mNGS) has the potential to detect multiple organisms with a single test. The study found that mNGS testing had the highest clinical impact in immunocompromised patients with well-defined deep-seated infections. Further research is needed to evaluate the full range of clinical scenarios for which mNGS testing is beneficial.
PEDIATRIC INFECTIOUS DISEASE JOURNAL
(2022)
Article
Multidisciplinary Sciences
David Olagnier, Ensieh Farahani, Jacob Thyrsted, Julia Blay-Cadanet, Angela Herengt, Manja Idorn, Alon Hait, Bruno Hernaez, Alice Knudsen, Marie Beck Iversen, Mirjam Schilling, Sofie E. Jorgensen, Michelle Thomsen, Line S. Reinert, Michael Lappe, Huy-Dung Hoang, Victoria H. Gilchrist, Anne Louise Hansen, Rasmus Ottosen, Camilla G. Nielsen, Charlotte Moller, Demi van der Horst, Suraj Peri, Siddharth Balachandran, Jinrong Huang, Martin Jakobsen, Esben B. Svenningsen, Thomas B. Poulsen, Lydia Bartsch, Anne L. Thielke, Yonglun Luo, Tommy Alain, Jan Rehwinkel, Antonio Alcami, John Hiscott, Trine Mogensen, Soren R. Paludan, Christian K. Holm
NATURE COMMUNICATIONS
(2020)
Article
Multidisciplinary Sciences
Bruno Hernaez, Graciela Alonso, Iliana Georgana, Misbah El-Jesr, Rocio Martin, Kathy H. Y. Shair, Cornelius Fischer, Sascha Sauer, Carlos Maluquer de Motes, Antonio Alcami
Article
Virology
Kai A. Kropp, Sangar Srivaratharajan, Birgit Ritter, Pengfei Yu, Simon Krooss, Felix Polten, Andreas Pich, Antonio Alcami, Abel Viejo-Borbolla
Article
Virology
Carla Mavian, Alberto Lopez-Bueno, Rocio Martin, Andreas Nitsche, Antonio Alcami
Summary: This study monitored the pathogenesis of nine ECTVs in mice and reported the full-length genome sequence of eight novel ECTV isolates or strains. The research identified genes absent in strains attenuated through serial passages in culture that may play a role in virulence, and also found a set of putative genes that may be involved in enhancing viral growth in vitro.
Article
Genetics & Heredity
Esther Camacho, Sandra Gonzalez-de la Fuente, Jose C. Solana, Alberto Rastrojo, Fernando Carrasco-Ramiro, Jose M. Requena, Begona Aguado
Summary: Leishmania major is the main causative agent of cutaneous leishmaniasis in humans. The genome sequence of the Friedlin strain (LmjF) was successfully deciphered in 2005, serving as a reference for subsequent genome assemblies in other Leishmania species. A new assembly for the LMJFC strain was generated using Illumina short-read sequencing and PacBio Single Molecular Real-Time sequencing, improving genome annotation and providing gene models for 11,238 genes.
Review
Microbiology
Francisco Javier Alvarez-de Miranda, Isabel Alonso-Sanchez, Antonio Alcami, Bruno Hernaez
Summary: TNF is an inflammatory cytokine produced in response to viral infections, promoting the recruitment and activation of leukocytes to infection sites. Poxviruses have evolved diverse molecular mechanisms to counteract TNF antiviral action, including the expression of soluble receptors or proteins that can bind and neutralize TNF.
Article
Parasitology
Inmaculada Gomez, Manuel Carlos Lopez, Alberto Rastrojo, Fabian Lorenzo-Diaz, Jose Maria Requena, Begona Aguado, Basilio Valladares, M. Carmen Thomas
Summary: The study identified Pr77-hallmark-bearing retrotransposons in the genomes of six strains of Trypanosoma cruzi, which display differences in gene copy number related to virulence processes, abundance of retrotransposons bearing the Pr77 sequence, and associations with specific genes. The distribution of these active retroelements and other Pr77-containing elements has shaped the genome architecture and may contribute to phenotypic variability among the strains.
Review
Microbiology
Mari Cruz Martin-Delgado, Francisco Javier Martin Sanchez, Manuel Martinez-Selles, Jose Maria Molero Garcia, Santiago Moreno Guillen, Fernando Rodriguez-Artalejo, Julian Ruiz-Galiana, Rafael Canton, Pilar De Lucas Ramos, Alejandra Garcia-Botella, Alberto Garcia-Lledo, Teresa Hernandez-Sampelayo, Javier Gomez-Pavon, Juan Gonzalez del Castillo, Patricia Munoz, Maricela Valerio, Pilar Catalan, Almudena Burillo, Alejandro Cobo, Antonio Alcami, Emilio Bouza
Summary: Infection caused by Monkeypox Virus (MPVX) is primarily found in small rodents but can infect monkeys and humans. The virus is capable of passing from monkeys to humans and has caused outbreaks in various countries. The disease has an incubation period of 5-15 days and presents with pustules, fever, malaise, and headache. Diagnosis can be confirmed through PCR testing or by demonstrating the presence of the virus in other body fluids or tissues. Treatment options are available, and the prognosis is generally good, with low mortality rates.
REVISTA ESPANOLA DE QUIMIOTERAPIA
(2022)
Article
Environmental Sciences
Cristina del Alamo, Angela Vazquez-Calvo, Antonio Alcami, Juan Sanchez-Garcia-Casarrubios, Jose Luis Perez-Diaz
Summary: The experience of the COVID-19 pandemic has highlighted the importance of preventing the spread of biological agents in the air and on surfaces. This study investigates the effectiveness of the COUNTERFOG (R) technology in disinfecting viral-contaminated surfaces and measures the required disinfection time. The results show that COUNTERFOG (R) can rapidly and efficiently eliminate viruses using sodium hypochlorite solution, with the concentration and exposure time playing a critical role in disinfection efficacy.
FOOD AND ENVIRONMENTAL VIROLOGY
(2022)
Article
Medicine, Research & Experimental
Lara Rodriguez-Outeirino, Francisco Hernandez-Torres, Felicitas Ramirez de Acuna, Alberto Rastrojo, Carlota Creus, Alejandra Carvajal, Luis Salmeron, Marisol Montolio, Patricia Soblechero-Martin, Virginia Arechavala-Gomeza, Diego Franco, Amelia Eva Aranega
Summary: miR-106b inhibits cell proliferation in muscle stem cells and its down-regulation is required for muscle repair and engraftment of muscle stem cells, while it is increased in dystrophic muscle.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2022)
Article
Environmental Sciences
Cristina del Alamo, Angela Vazquez-Calvo, Africa Sanchiz, Gil Rodriguez-Caravaca, Rocio Martin, Bruno Hernaez, Pablo Mendez-Vigo-Carranza, Juan Sanchez Garcia-Casarrubios, Antonio Alcami, Jose Luis Perez-Diaz
Summary: The COVID-19 pandemic has brought attention to the dangers of airborne transmission of pathogens. This study explores a fast method for capturing bioaerosols in air samples, which allows for quick detection of transient levels of aerosols and has revealed the presence of SARS-CoV-2 RNA in hospital rooms. The results show that the distribution of SARS-CoV-2-containing aerosols is not homogeneous, and this technology provides a valuable tool for fast decision-making and better understanding of aerosols dynamics.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
(2023)
Editorial Material
Multidisciplinary Sciences
Antonio Alcami
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Materials Science, Multidisciplinary
Castor Salgado, Raquel Cue, Vanesa Yuste, Laura Montalvillo-Jimenez, Pilar Prendes, Senen Paz, Angela Vazquez-Calvo, Antonio Alcami, Carolina Garcia, Enrique Martinez-Campos, Paula Bosch
Summary: Commercial polyurethane coatings were modified with 1-(hydroxymethyl)-5,5-dimethylhydantoin to enhance their antiviral activity. The modified coatings showed high inactivation of Staphylococcus aureus and human coronaviruses HCoV-229E and SARS-CoV-2. The coatings were rechargeable and maintained their virucidal activity even after multiple infection cycles.
APPLIED MATERIALS TODAY
(2023)
Article
Microbiology
Alberto Domingo Lopez-Munoz, Alberto Rastrojo, Rocio Martin, Antonio Alcami
Summary: This study reveals that HSV-1 and HSV-2 exhibit different levels of genetic diversity and mutation rates under in vitro culture conditions, with HSV-2 mutating faster. The newly emerged minor variants largely impact the coding diversity of HSV-2, possibly contributing to the evolutionary divergence of HSV-1 and HSV-2 in adapting to different anatomical niche.
Article
Virology
Mohamed S. H. Hassan, Ahmed Ali, Motamed Elsayed Mahmoud, Danah Altakrouni, Shahnas M. Najimudeen, Mohamed Faizal Abdul-Careem
Summary: This study compared the efficacy of different vaccination programs against Canadian DMV/1639 IBV and found that the autogenous inactivated DMV/1639 vaccine was more effective in reducing viral loads and boosting virus neutralization titers. Both vaccination programs provided significant protection against pathological effects.
Article
Virology
Wanda Christ, Jonas Klingstrom, Janne Tynell
Summary: The integrated stress response (ISR) is activated in response to SARS-CoV-2 infection, triggering translational arrest and inhibiting stress granule formation. However, the stress-responsive transcription factors ATF4 and CHOP are not induced. Different SARS-CoV-2 variants show variant-specific differences in ISR activation, suggesting potential impacts on pathogenesis and treatment strategies.
Article
Virology
Xiao Han, Hankun Xu, Yifan Weng, Rong Chen, Jidong Xu, Tong Cao, Renjie Sun, Ying Shan, Fang He, Weihuan Fang, Xiaoliang Li
Summary: Classical swine fever virus (CSFV) can inhibit the host innate immunity by decreasing the level of high mobility group box 1 (HMGB1), and CSFV Npro can evade host antiviral immune response through upregulating HMGB1 acetylation.
Article
Virology
Sunjian Lyu, Fulei Xiong, Tianpeng Qi, Weifeng Shen, Qi Guo, Mingming Han, Li Liu, Weishao Bu, Julin Yuan, Bao Lou
Summary: This study identified and characterized a novel temperate A. hydrophila phage, P05B, which has strong lytic ability and stability across different temperatures and pH values.
Article
Virology
Siyuan Liu, Wei Chen, Raphael Nyaruaba, Shunlong Wang, Cihan Yang, Qun Wu, Ying Liu, Puyu Liu, Fei Wang, Jingling Wang, Zhiming Yuan, Dingwei Sun, Han Xia
Summary: Specific, sensitive, and reliable RT-qPCR assays for the detection of OYAV and EBIV have been successfully developed in this study. These assays hold great promise for their potential application in clinical and field samples in the future.
Article
Virology
Rui Wang, Qiang Sun, Jinbo Xiao, Congcong Wang, Xiaoliang Li, Jichen Li, Yang Song, Huanhuan Lu, Ying Liu, Shuangli Zhu, Zhijun Liu, Yong Zhang
Summary: Coxsackievirus A6 (CVA6) has emerged as an important agent causing hand, foot, and mouth disease (HFMD). Mutations in residue 64 of the virus have been found to increase resistance to ribavirin and decrease sensitivity to guanidine hydrochloride. This mutation also leads to increased replication fidelity and reduced pathogenicity. These findings provide a foundation for the development of a safe and effective live attenuated CVA6 vaccine.
Article
Virology
Yao Xiong, Keran Ma, Xiao Zou, Yantao Liang, Kaiyang Zheng, Tiancong Wang, Hong Zhang, Yue Dong, Ziyue Wang, Yundan Liu, Hongbing Shao, Andrew Mcminn, Min Wang
Summary: This study isolated a novel virus, vB_VviC_ZQ26, infecting Vibrio cyclitrophicus from coastal waters near Qingdao, China. It was found that vB_VviC_ZQ26 belongs to a new vibriophage-specific family, Coheviridae, and is mainly found in temperate and tropical epipelagic zones.
Article
Virology
Xing Li, Zhiping Ye, Ewan P. Plant
Summary: By analyzing clinical and cultured samples using the same bioinformatic pipeline, it was found that 5' copyback DVGs are prevalent in human clinical samples but not in cultured samples. Furthermore, there are differences in DVG production and composition between in vivo and in vitro infections.
Article
Virology
Shreya Banerjee, Rakesh Sarkar, Arpita Mukherjee, Suvrotoa Mitra, Animesh Gope, Mamta Chawla-Sarkar
Summary: Rotavirus is a major cause of viral gastroenteritis in infants and continues to be a severe issue in underdeveloped nations. Recent research has shown that a long non-coding RNA called SLC7A11-AS1 is upregulated during rotavirus infection and plays a role in facilitating the virus's propagation by regulating intracellular glutathione and lipid peroxidation.
Article
Virology
Eiichi Hondo, Tetsufumi Katta, Ayato Sato, Naoya Kadofusa, Tomoki Ishibashi, Hiroshi Shimoda, Hirokazu Katoh, Atsuo Iida
Summary: Bat-borne emerging viruses, such as the Ebola virus and Nipah virus, pose a significant threat to public health. In this study, we identified micafungin as a potential antiviral drug against Pteropine orthoreovirus (PRV) and found that it inhibits viral release in human cells through activating the endoplasmic reticulum stress response pathway. This research provides valuable insights into the development of effective treatments for future virus pandemics.
Article
Virology
M. Joubert, N. van den Berg, J. Theron, V. Swart
Summary: This study investigated the host gene expression in asymptomatic avocado nursery trees infected with Avocado sunblotch viroid (ASBVd) using RNA sequencing. The results showed that 631 genes were differentially expressed during infection, with 63% upregulated. ASBVd infection significantly affected plant defence responses, phytohormone networks, gene expression pathways, secondary metabolism, cellular transport, as well as protein modification and degradation. This study provides insights into the molecular interactions underlying avsunviroid-host interactions.
Article
Virology
Wanling Zhang, Haiyan Yang, Zhengyun Liu, Shengyu Wang, Tianyang Chen, Hong Song, Yunbin Xu, Fajin Li, Guo Luo, Huan Wang
Summary: EV71 infection leads to changes in mitochondrial morphology and dynamics in human neuroblastoma cells, resulting in mitochondrial dysfunction that may contribute to nervous system dysfunction.
Article
Virology
Mikhail Oliveira Leastro, Elliot Watanabe Kitajima, Vicente Pallas, Jesus Angel Sanchez- Navarro
Summary: This study reports the construction and validation of an infectious cDNA clone of Citrus leprosis virus C (CiLV-C) based on an agroinfection system. Agro-injected Nicotiana benthamiana plants showed localized lesions similar to the natural infection process. The virus recovered from the infected plant tissue could be mechanically transmitted between plants. The CiLV-C reverse genetic system provides a powerful molecular tool for unraveling the peculiarities of the citrus leprosis pathosystem.
Article
Virology
Manel Essaidi-Laziosi, Francisco J. Perez-Rodriguez, Catia Alvarez, Pascale Sattonnet-Roche, Giulia Torriani, Meriem Bekliz, Kenneth Adea, Matthias Lenk, Tasnim Suliman, Wolfgang Preiser, Marcel A. Mueller, Christian Drosten, Laurent Kaiser, Isabella Eckerle
Summary: This study found that the Omicron variant has different replication characteristics compared to other variants of concern, being able to efficiently produce infectious virus in nasal cells but not lung cells. In addition, the Delta and Omicron variants showed increased infection efficiency in A549 cells. These findings suggest that the variants of concern have better adaptation to humans but do not have an extended host range.
Article
Virology
Martin Faye, Modeste Name Faye, Babacar Ndiaye, Moussa Moise Diagne, Safietou Sankhe, Ndeye Marieme Top, Amadou Diallo, Cheikh Loucoubar, Ndongo Dia, Amadou Alpha Sall, Ousmane Faye
Summary: Genomic surveillance in Senegal since March 2020 has detected the emergence of Omicron BA.4 and BA.5 sublineages in June 2022. Next-generation sequencing and phylogeny analysis of isolates from a cluster of cases in Northern Senegal in July 2022 revealed that the BA.4 cases originated from a XAS recombinant, marking the first reported sequence of this variant from Senegal. Continuous genomic surveillance of positive SARS-CoV-2 samples is crucial.