Article
Chemistry, Analytical
Yugan He, Liqin Wang, Xiaoping An, Yigang Tong
Summary: An all-in-one nucleic acid testing assay was developed in this study for rapid detection of viral RNA in a single tube, showing potential as a simple, scalable, and time-saving alternative for point-of-care testing of SARS-CoV-2.
Article
Biochemistry & Molecular Biology
Bruna de Oliveira Coelho, Heloisa Bruna Soligo Sanchuki, Dalila Luciola Zanette, Jeanine Marie Nardin, Hugo Manuel Paz Morales, Bruna Fornazari, Mateus Nobrega Aoki, Lucas Blanes
Summary: This study investigates the colorimetric RT-LAMP technique for detecting SARS-CoV-2, highlighting the presence of three color clusters and the correlation between viral load and color change. Results show a sensitivity of 93.8% and specificity of 90.4%, with the novel finding of an orange color cluster indicating low viral loads. The study concludes that colorimetric RT-LAMP is efficient for COVID-19 diagnosis, particularly in the early stages of infection.
MOLECULAR MEDICINE
(2021)
Article
Medicine, General & Internal
Juan Garcia-Bernalt Diego, Pedro Fernandez-Soto, Marta Dominguez-Gil, Moncef Belhassen-Garcia, Juan Luis Munoz Bellido, Antonio Muro
Summary: The global SARS-CoV-2 pandemic has brought about a need for widespread testing for COVID-19, with RT-qPCR as the gold standard method, but facing challenges. A novel RT-LAMP method has been developed, showing promise for cost-effective, rapid, and stable detection of SARS-CoV-2.
Article
Biophysics
Yugan He, Tie Xie, Yigang Tong
Summary: The one-tube colorimetric RT-LAMP assay developed in this study integrates fast RNA extraction and rapid isothermal amplification in a single tube for the visual detection of SARS-CoV-2 RNA. The assay has a low limit of detection of 200 copies/mL and can be completed in less than 1 hour, showing 100% concordance with RT-qPCR and high specificity. This assay can be used as an alternative platform for rapid and sensitive diagnosis of COVID-19 in community clinics or township hospitals.
BIOSENSORS & BIOELECTRONICS
(2021)
Article
Chemistry, Analytical
Li Zhang, Xu Wang, Dongchen Liu, Yu Wu, Li Feng, Chunyan Han, Jiajia Liu, Ying Lu, Dmitriy V. Sotnikov, Youchun Xu, Jing Cheng
Summary: Respiratory tract infections, including COVID-19, have posed a serious threat to public health. A swing-assisted multiplexed analyzer for point-of-care respiratory tract infection testing (SMART) was proposed to achieve low-cost and multiplexed nucleic acid detection. By performing hand-swing movements, the SMART system simplified the distribution of samples into reaction chambers. It successfully detected multiple respiratory tract pathogens, including SARS-CoV-2 and respiratory bacteria, indicating its potential as a versatile tool in the diagnosis of respiratory tract infections.
Article
Medicine, General & Internal
Bruna W. W. Raddatz, Felipe J. J. Rabello, Rafael Benedetti, Gisleine J. J. Steil, Louise M. M. Imamura, Edson Y. S. Kim, Erika B. B. Santiago, Luis F. Hartmann, Joao V. Predebon, Bruna M. M. Delfino, Meri B. B. Nogueira, Jucelia S. dos Santos, Breno G. G. da Silva, Diego R. P. Nicollete, Bernardo M. M. de Almeida, Sergio R. R. Rogal Jr, Marcus V. M. Figueredo
Summary: Quick and reliable mass testing is necessary for SARS-CoV-2 containment. Point-of-Care (POC) tests using Loop-Mediated Isothermal Amplification (LAMP) have emerged as a useful diagnostic tool during the COVID-19 pandemic. However, colorimetric LAMP tests have limitations in stability and false-positive results. This study presents a portable device, Hilab Molecular, that utilizes IoT and AI to pre-analyze colorimetric data, and manufacturing procedures to increase the stability of colorimetric RT-LAMP tests.
Article
Chemistry, Analytical
Wansadaj Jaroenram, Itthi Chatnuntawech, Jantana Kampeera, Sukanya Pengpanich, Pornsawan Leaungwutiwong, Benyatip Tondee, Sarawut Sirithammajak, Rapheephat Suvannakad, Pakapreud Khumwan, Sirintip Dangtip, Narong Arunrut, Sirasate Bantuchai, Wang Nguitragool, Suchawit Wongwaroran, Paisan Khanchaitit, Jetsumon Sattabongkot, Surat Teerapittayanon, Wansika Kiatpathomchai
Summary: Colorimetric loop-mediated DNA isothermal amplification-based assays using pH-dependent indicators have been developed for COVID-19 diagnosis. The dual colorimetric RT-LAMP assay with artificial intelligence (AI) operated tool enables precise and rapid result analysis in large scale testing. The method offers a simpler, faster, and cheaper approach for COVID-19 testing and other emerging pathogens.
Article
Virology
Santiago Werbajh, Luciana Larocca, Carolina Carrillo, Fabiana Stolowicz, Lorena Ogas, Sergio Pallotto, Solange Cassara, Liliana Mammana, Ines Zapiola, Maria Belen Bouzas, Adrian A. Vojnov
Summary: A rapid and simple colorimetric RT-LAMP kit for detecting SARS-CoV-2 from nasopharyngeal swab samples without the need for RNA extraction was developed. The kit showed high sensitivity and specificity, and could detect known variants of concern, making it suitable for large-scale screening in resource-limited settings.
Article
Infectious Diseases
Pornlada Nuchnoi, Pakorn Piromtong, Saranya Siribal, Korrarit Anansilp, Peeradech Thichanpiang, Pilailuk Akkapaiboon Okada
Summary: During the third wave of COVID-19 in Thailand, the rapid spread of infections in high-risk areas necessitates the use of reliable and rapid molecular tests. This study demonstrates that RT-LAMP is a reliable assay for SARS-CoV-2 detection and can be used in emergency response situations.
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
(2023)
Article
Medicine, General & Internal
Ane Rivas-Macho, Ane Sorarrain, Jose M. Marimon, Felipe Goni-de-Cerio, Garbine Olabarria
Summary: The pandemic has increased the demand for fast, simple, and cost-effective tests for diagnosing emerging pathogens. Researchers have developed a colorimetric reverse transcription loop-mediated isothermal amplification method for saliva samples that outperforms commercial colorimetric and fluorescent methods in sensitivity and specificity, without the need for expensive equipment, demonstrating its potential for population screening.
Article
Multidisciplinary Sciences
Zhu Yang, Nicole Y. Liu, Zhiwei Zhu, Minmin Xiao, Shuzhi Zhong, Qiqi Xue, Lina Nie, Jinhong Zhao
Summary: In this study, a triple-target RT-LAMP assay was developed for the detection of SARS-CoV-2. It showed higher sensitivity compared to singleplex or duplex RT-LAMP assays and could detect as low as 11 copies of SARS-CoV-2 RNA per 25 mL reaction. The study also investigated the use of two different color indicators, hydroxy naphthol blue (HNB) and cresol red, in the colorimetric RT-LAMP assay.
Article
Infectious Diseases
Meng Yee Lai, Fatma Diyana Mohd Bukhari, Nur Zulaikha Zulkefli, Ilyiana Ismail, Nur Izati Mustapa, Tuan Suhaila Tuan Soh, Afifah Haji Hassan, Kalaiarasu M. Peariasamy, Yee Leng Lee, Jeyanthi Suppiah, Ravindran Thayan, Yee Ling Lau
Summary: This study proposes a method to prevent contamination in RT-LAMP by adding dUTP and UDG to the reaction mix, resulting in good results. The UDG RT-LAMP method is simple, fast, and suitable for medical facilities with limited equipment.
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
(2022)
Article
Engineering, Environmental
Haorui Cao, Kang Mao, Fang Ran, Pengqi Xu, Yirong Zhao, Xiangyan Zhang, Hourong Zhou, Zhugen Yang, Hua Zhang, Guibin Jiang
Summary: A portable paper device based on CRISPR/Cas12a and RT-LAMP was developed for the detection of SARS-CoV-2 in wastewater, offering high sensitivity and specificity. The device enables simultaneous detection of the N, E, and S genes through different visualization pathways, and provides semi-quantitative analysis. This study demonstrates a promising point-of-use method for wastewater-based surveillance.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Shanshan Wu, Xiyang Liu, Shenglong Ye, Jianmin Liu, Wei Zheng, Xue Dong, Xiushan Yin
Summary: The study presents a dye combination for isothermal detection of SARS-CoV-2 with expanded colorimetric spectrum, validated for its suitability and sensitivity through clinical RNA samples. This expanded color spectrum is expected to serve as an indicator for rapid detection of COVID-19.
Article
Virology
Eline Meyers, Jeongho Park, Anja Coen, Leen Raman, Stefan Heytens, Joowon Rhee, Elizaveta Padalko, Piet Cools
Summary: During the SARS-CoV-2 pandemic, rapid and sensitive detection of the virus is crucial. A new point-of-care test system based on LAMP technology was evaluated, and it showed high clinical sensitivity and specificity for SARS-CoV-2 detection. The system's easy operation and ready-to-use reagents make it suitable for various settings, contributing to more efficient outbreak control and quarantine policies.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Multidisciplinary Sciences
Hugo Zeberg, Svante Paabo
Summary: Recent studies have identified a genetic risk factor for severe illness with COVID-19 inherited from Neandertals, but also a protective Neandertal haplotype. These genetic factors influence the need for intensive care after infection and are present in populations worldwide outside of Africa.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Stephan Riesenberg, Nelly Helmbrecht, Philipp Kanis, Tomislav Maricic, Svante Paeaebo
Summary: The authors have engineered stable gRNAs with chemical modifications to enhance genome editing efficiency regardless of target sequence composition.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Lucia Coppo, Pradeep Mishra, Nora Siefert, Arne Holmgren, Svante Paabo, Hugo Zeberg
Summary: The substitution of an amino acid in glutathione reductase in present-day humans, compared to apes and Neanderthals, has been found. This substitution does not affect the enzyme's activity and stability, but it results in the ancestral enzyme producing more reactive oxygen species and increasing cellular levels of transcripts encoding cytokines. Additionally, the ancestral enzyme has been reintroduced into the modern human gene pool through gene flow from Neanderthals and is associated with various traits in present-day people.
Article
Ecology
Samantha Brown, Diyendo Massilani, Maxim B. Kozlikin, Michael V. Shunkov, Anatoly P. Derevianko, Alexander Stoessel, Blair Jope-Street, Matthias Meyer, Janet Kelso, Svante Paeaebo, Thomas Higham, Katerina Douka
Summary: Through collagen peptide mass fingerprinting analysis of thousands of non-diagnostic bone fragments, five new hominin bones were discovered in Denisova Cave, Siberia, Russia, with three identified as Denisovan and one as Neanderthal based on mitochondrial DNA analysis. These bones, dating back to 200 ka, provide valuable insights into the material culture, behavior, and environmental adaptations of these early hominins, and have significantly expanded our understanding of Denisovan and Neanderthal interactions and archaeological signatures.
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Biology
Stephane Peyregne, Janet Kelso, Benjamin M. Peter, Svante Paeaebo
Summary: After the split from Neandertals and Denisovans, modern humans experienced an unusual number of amino acid substitutions in proteins associated with the spindle apparatus. Some of these substitutions may have been positively selected. The KNL1 gene, previously believed to be specific to modern humans, was also found in some Neandertals, suggesting gene flow between these groups.
Article
Multidisciplinary Sciences
Anneline Pinson, Lei Xing, Takashi Namba, Nereo Kalebic, Jula Peters, Christina Eugster Oegema, Sofia Traikov, Katrin Reppe, Stephan Riesenberg, Tomislav Maricic, RazVan derihaci, Pauline Wimberger, Svante Paabo, Wieland B. Huttner
Summary: This study found that the modern human variant hTKTL1, but not the Neanderthal variant, can increase the abundance of bRG without affecting bIPs, thereby affecting the generation of neocortical neurons. This indicates differences in neocortical neurogenesis between modern humans and Neanderthals.
Article
Biochemistry & Molecular Biology
Martin Lackner, Nelly Helmbrecht, Svante Paabo, Stephan Riesenberg
Summary: CRISPR nucleases can break DNA strands in specific positions in genomes, resulting in insertions, deletions, or substitutions. However, these repairs can also cause unintended effects such as larger deletions and gene conversion. This study presents a strategy called 'sequence-ascertained favorable editing' (SAFE) donor approach, which allows easy detection of unintended effects and the generation of control cells. By sequencing the target sites, different sequences indicate successful editing, while a single sequence indicates unintended effects such as deletions or gene conversion. The authors analyzed over 850 human embryonic stem cell clones and successfully detected copy number changes and most clones with gene conversion using the SAFE donor approach.
NUCLEIC ACIDS RESEARCH
(2023)
Editorial Material
Multidisciplinary Sciences
Anneline Pinson, Tomislav Maricic, Hugo Zeberg, Svante Paeaebo, Wieland B. Huttner
Article
Biochemical Research Methods
Stephan Riesenberg, Philipp Kanis, Dominik Macak, Damian Wollny, Dorothee Duesterhoeft, Johannes Kowalewski, Nelly Helmbrecht, Tomislav Maricic, Svante Paeaebo
Summary: The study introduces a high-precision method, HDRobust, for repairing DNA double-stranded breaks through homology-directed repair (HDR). By transiently inhibiting nonhomologous end joining and microhomology-mediated end joining, HDRobust achieved point mutations by HDR in up to 93% of chromosomes. Insertions, deletions, rearrangements, and unintended changes at other genomic sites were largely eliminated. The efficient correction of pathogenic mutations in cells derived from patients with anemia, sickle cell disease, and thrombophilia was validated.
