Article
Biology
Francesca Marino-Merlo, Valeria Stefanizzi, Agnese Ragno, Lucia Piredda, Sandro Grelli, Beatrice Macchi, Antonio Mastino
Summary: The study developed a real-time reverse transcriptase quantitative PCR (RT-qPCR) assay to assess very low levels of HIV-1 RT activity based on previous laboratory experience. A synthetic RNA was used as a template for reverse transcription into cDNA by HIV-1 RT, and different variables were tested to optimize the assay. The optimized gD-RNA-synt-based RT assay demonstrated high sensitivity, allowing for the detection of specific cDNA reverse transcription even in the presence of 1 x 10(-9) U HIV RT. This constructed RT-qPCR assay shows promise in accurately assessing very low HIV-1 RT activity.
Article
Microbiology
Bryanna Lexus Freitas, Lynn Leach, Vishnu Chaturvedi, Sudha Chaturvedi
Summary: A new detection method has been developed to rapidly detect live multidrug-resistant yeast Candida auris in healthcare environments. This method is highly sensitive and specific, and it correlates with the results from traditional culture methods.
JOURNAL OF CLINICAL MICROBIOLOGY
(2022)
Article
Biochemical Research Methods
Yiting Zhu, Ni Hong, Liu Li, Yujie Gao, Liping Wang, Wenxing Xu, Guoping Wang
Summary: This study developed a SYBR Green-based RT-qPCR assay for the reliable detection of Pear chlorotic leaf spot associated virus (PCLSaV) infecting pear trees. This technique is important for the supervision of viral disease and the certification of pear planting materials.
JOURNAL OF VIROLOGICAL METHODS
(2022)
Article
Multidisciplinary Sciences
SungJun Park, Cheonghoon Lee, Kyuseon Cho, Hye Young Ko, Sung Jae Jang, GwangPyo Ko
Summary: The study suggests that employing inhibitor-removal treatment can improve the accuracy and sensitivity of RT-qPCR detection methods for noroviruses in water and produce.
Article
Chemistry, Analytical
Ian T. Hull, Enos C. Kline, Gaurav K. Gulati, Jack Henry Kotnik, Nuttada Panpradist, Kamal G. Shah, Qin Wang, Lisa Frenkel, James Lai, Joanne Stekler, Barry R. Lutz
Summary: The study presents a novel quantitative detection method for HIV DNA or RNA using a combination of recombinase polymerase amplification and lateral flow detection technologies, allowing for rapid and accurate testing in low-resource healthcare settings, with the potential to improve the quality of HIV treatment.
ANALYTICAL CHEMISTRY
(2022)
Article
Nanoscience & Nanotechnology
Jung Min Kim, Seungwon Jung, Eui Ju Jeon, Bong Kyun Kim, Jin Yong No, Myung Jong Kim, Heesuk Kim, Chang Seon Song, Sang Kyung Kim
Summary: This paper introduces a multiplex RT-qPCR platform using hydrogel microparticles as independent reactors, with target-specific primers and probes integrated into the particles. By harnessing the distinctive properties of boron nitride and carbon nanotubes, the platform shows high efficiency and effective suppression of non-specific reactions. Through recruiting differently coded bcPIN particles, 16-plex RT-qPCR has been achieved successfully.
ACS APPLIED MATERIALS & INTERFACES
(2021)
Article
Microbiology
Anna Andrew, Marimuthu Citartan, Kiing Aik Wong, Thean Hock Tang, Sum Magdline Sia Henry, Ewe Seng Ch'ng
Summary: A TaqMan RT-qPCR assay was developed and evaluated for detecting CHIKV in clinical samples. The assay showed high sensitivity and specificity, making it a potential diagnostic tool for CHIKV. Further validation with prospective patient samples is needed.
MICROBIOLOGY SPECTRUM
(2023)
Article
Chemistry, Multidisciplinary
Jing Tu, Yi Qiao, Yuhan Luo, Naiyun Long, Zuhong Lu
Summary: DNA quantification is crucial in life sciences research, and real-time MDA technology can provide template amount information during whole-genome amplification with a very low detection limit, offering a promising tool to quantify entire DNA without sacrificing sample completeness or introducing redundant steps.
Article
Ecology
Marco Di Domenico, Valentina Curini, Riccardo Caprioli, Carla Giansante, Agata Mrugala, Michaela Mojzisova, Cesare Camma, Adam Petrusek
Summary: The study developed real-time PCR TaqMan assays to distinguish five genotype groups of A. astaci. This method may be a useful tool for investigating the natural history of crayfish plague in Europe, as well as the sources and introduction pathways of the pathogen.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2021)
Article
Veterinary Sciences
Prerana Bhande, Brigitte Sigrist, Linard Balke, Sarah Albini, Nina Wolfrum
Summary: Avian orthoavulavirus-1 (AOAV-1), also known as Newcastle disease virus, causes significant economic losses in poultry worldwide. This study demonstrates the importance of monitoring and improving diagnostic methods for detecting currently circulating AOAV-1 strains, particularly pigeon paramyxovirus-1 (PPMV-1) strains.
VETERINARY SCIENCES
(2023)
Article
Public, Environmental & Occupational Health
Jesse J. Waggoner, Victoria Stittleburg, Muktha S. Natrajan, M. Alejandra Paniagua-Avila, Desiree Bauer, Daniel Olson, Hana M. El Sahly, Edwin J. Asturias, Evan J. Anderson, Flor M. Munoz
Summary: Whole blood DENV RNA detection is sensitive for acute dengue infection and may remain positive for weeks to months.
AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE
(2021)
Article
Biochemical Research Methods
Yin-he Xia, Zi-cong Shi, Xin-wei Wang, Yong-tao Li, Zeng Wang, Hong-tao Chang, Hong-ying Liu, Lu Chen, Chuan-qing Wang, Xia Yang
Summary: GETV, a mosquito-borne virus, is increasingly posing a threat to animal safety and public health. The newly developed RT-qPCR assay for GETV has high sensitivity and reproducibility, making it suitable for rapid diagnosis and quantitative analysis of GETV infection.
MOLECULAR AND CELLULAR PROBES
(2021)
Article
Chemistry, Analytical
Lianhua Dong, Junbo Zhou, Chunyan Niu, Quanyi Wang, Yang Pan, Sitong Sheng, Xia Wang, Yongzhuo Zhang, Jiayi Yang, Manqing Liu, Yang Zhao, Xiaoying Zhang, Tao Zhu, Tao Peng, Jie Xie, Yunhua Gao, Di Wang, Xinhua Dai, Xiang Fang
Summary: The COVID-19 outbreak caused by a novel Coronavirus has spread globally. Current gold standard RT-qPCR for SARS-CoV-2 diagnosis shows varying sensitivity, highlighting the need for more accurate methods. A study on RT-dPCR demonstrated significant improvement in detection sensitivity, particularly for asymptomatic patients, making it a highly accurate method for screening suspected cases.
Article
Chemistry, Analytical
Wei Feng, Hanyong Peng, Jingyang Xu, Yanming Liu, Kanti Pabbaraju, Graham Tipples, Michael A. Joyce, Holly A. Saffran, D. Lorne Tyrrell, Shawn Babiuk, Hongquan Zhang, X. Chris Le
Summary: The study successfully integrated RT-RPA and CRISPR-Cas12a into a single tube for viral sequence detection, overcoming issues like slow initiation of RPA and non-specific amplification, significantly improving detection speed and accuracy.
ANALYTICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Catherine T. Chia, Andrew T. Bender, Lorraine Lillis, Benjamin P. Sullivan, Coleman D. Martin, Wynn Burke, Charles Landis, David S. Boyle, Jonathan D. Posner
Summary: This study reports a rapid, highly accurate, and minimally instrumented assay for HCV RNA detection using RT-RPA. The assay can detect all HCV genotypes with a limit of detection of 25 copies per reaction for genotype 1. Clinical experiments showed that the RT-RPA assay has a sensitivity and specificity of 100%. The accuracy, short runtime, and low heating demands of RT-RPA make it potentially valuable for point-of-care HCV testing.
Review
Biotechnology & Applied Microbiology
Arijana Filipic, Ion Gutierrez-Aguirre, Gregor Primc, Miran Mozetic, David Dobnik
TRENDS IN BIOTECHNOLOGY
(2020)
Article
Microbiology
Arijana Filipic, David Dobnik, Magda Tusek Znidaric, Bojana Zegura, Alja Stern, Gregor Primc, Miran Mozetic, Maja Ravnikar, Jana Zel, Ion Gutierrez Aguirre
Summary: Water scarcity poses a major threat to human survival and quality of life, leading to an increased risk of infections from waterborne viruses. Cold atmospheric plasma (CAP) is emerging as an efficient, safe, and sustainable alternative for waterborne virus inactivation. In this study, CAP treatment successfully inactivated a resilient waterborne virus, PMMoV, without introducing any cytotoxic or genotoxic effects, showing promise for further examination as an alternative for treating potable and irrigation waters, as well as other sources of water, with a focus on inactivating various viruses, including enteric viruses.
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Biology
Valentina Levak, Tjasa Lukan, Kristina Gruden, Anna Coll
Summary: Biosensors are crucial tools for understanding plant immunity, providing effective imaging for calcium and reactive oxygen species in plants. However, there is still room for improvement in imaging the main hormonal players in immune response. The most advanced genetically encoded biosensors have made it possible to monitor multiple analytes in the same chassis, showing great potential for applications in the field of crops.
Article
Plant Sciences
Ana Vucurovic, Denis Kutnjak, Natasa Mehle, Ivana Stankovic, Anja Pecman, Aleksandra Bulajic, Branka Krstic, Maja Ravnikar
Summary: This study identified four new viruses in Serbia using high-throughput sequencing, including devastating viruses to tomatoes. The successful application of post hoc HTS testing encourages the use of this technology in research and diagnostic laboratories to discover new viruses.
Article
Dentistry, Oral Surgery & Medicine
Ales Fidler, Andrej Steyer, Damjan Manevski, Rok Gaspersic
Summary: This study developed an experimental setup to test the transmission of viruses through dental spray generated by USS and evaluated the effectiveness of antiviral coolants. Results showed that using NaOCl or EOW as coolants could effectively mitigate the spread of viruses.
JOURNAL OF PERIODONTOLOGY
(2022)
Article
Acoustics
Arijana Filipic, Tadeja Lukezic, Katarina Bacnik, Maja Ravnikar, Meta Jeselnik, Tamara Kosir, Martin Petkovsek, Mojca Zupanc, Matevz Dular, Ion Gutierrez Aguirre
Summary: Waterborne plant viruses can cause significant damage to crops, but proper water treatment strategies can prevent their spread. Hydrodynamic cavitation (HC) is an environmentally friendly method for treating recycled water, which has shown promising results in decontamination.
ULTRASONICS SONOCHEMISTRY
(2022)
Article
Microbiology
Anja Pecman, Ian Adams, Ion Gutierrez-Aguirre, Adrian Fox, Neil Boonham, Maja Ravnikar, Denis Kutnjak
Summary: Nanopore sequencing, as a novel high-throughput sequencing technology, shows similar performance to Illumina sequencing in the detection of plant viruses and viroids, while offering the advantages of faster and more affordable diagnostics.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Environmental Sciences
Olivera Maksimovic Carvalho Ferreira, Ziva Lengar, Zala Kogej, Katarina Bacnik, Irena Bajde, Mojca Milavec, Anze Zupanic, Natasa Mehle, Denis Kutnjak, Maja Ravnikar, Ion Gutierrez-Aguirre
Summary: The SARS-CoV-2 pandemic has accelerated the development of virus detection methods and overall approaches to epidemiology. Wastewater-based epidemiology has been employed to track the virus transmission dynamics. This article presents a retrospective view on the method development and implementation for a pilot monitoring in Slovenia. The study found that using Centricon filtration units coupled with Qiagen RNA extraction kit or direct RNA capture and extraction using a semi-automated kit from Promega produced the most optimal results out of the seven tested methods. The CDC's N1 and N2 assays with Fast Virus 1-mastermix were confirmed as the best performing assays among the four tested.
FOOD AND ENVIRONMENTAL VIROLOGY
(2022)
Review
Microbiology
Andrej Steyer, Dusanka Micetic-Turk, Sabina Fijan
Summary: This review summarizes the latest scientific evidence on the antiviral properties of probiotics against rotavirus gastroenteric infections in children. The study found that probiotics can shorten the duration of diarrhea by enhancing immune function and modulating intestinal microbiota. However, the effectiveness of probiotics may be influenced by factors such as dosage, duration of treatment, quality, and other factors.
Article
Microbiology
Sabina Fijan, Primoz Kocbek, Andrej Steyer, Polona Maver Vodicar, Maja Strauss
Summary: The skin microbiota plays an important role in protecting the skin, and disruption of this microbiota can lead to skin infections. Probiotics and their metabolites have been found to have antimicrobial effects against skin pathogens. This study evaluated the antimicrobial effects of seven multi-strain dietary supplements and eleven single-strain microbes containing probiotics against 15 clinical wound pathogens. The results showed that the multi-strain dietary supplements were more effective against the wound pathogens compared to single-strain microbes, with lactobacilli-containing supplements and single-strain microbes being the most efficient.
Article
Microbiology
Dragan Brnic, Ivana Lojkic, Nina Kresic, Vida Zrncic, Lea Ruzanovic, Tina Mikuletic, Martin Bosilj, Andrej Steyer, Tomislav Keros, Boris Habrun, Lorena Jemersic
Summary: Bats in Croatia are found to have the circulation of SARS-CoV-related coronaviruses. Guano samples tested positive for E-gene Sarebeco RT-qPCR, while bat droppings were negative. Further analysis revealed the presence of bat alphacoronaviruses and betacoronaviruses. Phylogenetic analysis confirmed the clustering of betaCoV sequence with SARS-CoV-related bat sarbecoviruses. The results indicate the first evidence of these coronaviruses in bats from Croatia.
Article
Microbiology
Urska Glinsek Biskup, Andrej Steyer, Lara Lusa, Franc Strle, Marko Pokorn, Tatjana Mrvic, Stefan Grosek, Miroslav Petrovec, Monika Jevsnik Virant
Summary: This study determines the frequency of human mastadenovirus (HAdV) in children with acute bronchiolitis, acute gastroenteritis, and febrile seizures, and identifies the types of HAdVs associated with each syndrome. HAdVs were detected in both nasopharyngeal swabs and stool samples, with certain genotypes found exclusively in stool samples. HAdVs were more commonly detected in stool samples, particularly in children with acute bronchiolitis and gastroenteritis.
Article
Biochemical Research Methods
Katarina Bacnik, Denis Kutnjak, Barbara Jeric Kokelj, Nika Tuta, Tan Loncar, Matjaz Vogelsang, Maja Ravnikar
Summary: This study utilized high-throughput sequencing to detect viral-like sequences in CHO cell lines, showing that sequencing of ribosomal RNA depleted total RNA is the most promising approach. No adventitious viral agents were found in the investigated cell lines, indicating a background of virus-like nucleic acids originating from expression vectors, endogenized viral elements, and residuals of bacteriophages.
Article
Biology
Katja Stare, Anna Coll, Ion Gutierrez-Aguirre, Magda Tusek Znidaric, Maja Ravnikar, Andreja Kezar, Luka Kavcic, Marjetka Podobnik, Kristina Gruden