Article
Immunology
Ruihe Shi, Yuan Wang, Shujuan Zhou, Yanli Zhang, Shiwei Zheng, Dingfang Zhang, Xilong Du, Weiyue Gu, Yiran Xu, Changlian Zhu
Summary: This study assessed the diagnostic accuracy of sputum using metagenomic next-generation sequencing for detecting lower respiratory tract infections. The results showed that viral detection in sputum had good sensitivity but poor specificity, while bacterial detection had poor sensitivity. Clinicians should be cautious when interpreting sputum results, particularly for bacterial detection.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
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
Chemistry, Multidisciplinary
Na Zhao, Jiabao Cao, Jiayue Xu, Beibei Liu, Bin Liu, Dingqiang Chen, Binbin Xia, Liang Chen, Wenhui Zhang, Yuqing Zhang, Xuan Zhang, Zhimei Duan, Kaifei Wang, Fei Xie, Kun Xiao, Wei Yan, Lixin Xie, Hongwei Zhou, Jun Wang
Summary: Utilizing RNA sequencing and third-generation sequencing technology for pathogen identification can improve the ratio of microbial reads and accelerate clinical diagnosis, showing significant potential.
Article
Medical Laboratory Technology
Zhenli Diao, Yuanfeng Zhang, Yuqing Chen, Yanxi Han, Lu Chang, Yu Ma, Lei Feng, Tao Huang, Rui Zhang, Jinming Li
Summary: This study evaluated the performance of mNGS assays in detecting pathogens in lower respiratory infections and identified sources of false-positive and false-negative results. The findings provide valuable insights for the improvement of method development and quality control in clinical mNGS laboratories.
CLINICAL CHEMISTRY
(2023)
Review
Virology
Xinye Wang, Sacha Stelzer-Braid, Matthew Scotch, William D. Rawlinson
Summary: NGS technologies have been successfully utilized in detecting a variety of respiratory viruses, showcasing advantages in novel virus discovery, typing, mutation identification, and infection cluster assessment. Despite technical and ethical challenges, NGS holds promise as a future tool to enhance understanding of respiratory viruses and provide more accurate diagnoses.
REVIEWS IN MEDICAL VIROLOGY
(2022)
Article
Infectious Diseases
Mengyuan Liang, Yamin Fan, Dongmei Zhang, Lian Yang, Xiaorong Wang, Sufei Wang, Juanjuan Xu, Jianchu Zhang
Summary: This study retrospectively reviewed the clinical data of patients with suspected lower respiratory tract infections at Wuhan Union Hospital. The results showed that mNGS had a high sensitivity and shorter processing time compared to culture test. Antibiotic treatment could be adjusted or confirmed based on the mNGS results, leading to significant improvement in clinical symptoms and inflammatory indicators for patients.
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
(2022)
Article
Public, Environmental & Occupational Health
Xiangyong Tian, Wenjing Duan, Xiulei Zhang, Xiaoqiang Wu, Chan Zhang, Zhiwei Wang, Guanghui Cao, Yue Gu, Fengmin Shao, Tianzhong Yan
Summary: In this study, the clinical application of metagenomic next-generation sequencing (mNGS) in detecting viral infections in kidney transplant recipients (KTRs) during the COVID-19 pandemic was investigated. The results showed a rich virus spectrum in infected KTRs, including rare viruses, and identified torque teno virus (TTV) as a potential biomarker for predicting rejection.
FRONTIERS IN PUBLIC HEALTH
(2022)
Article
Microbiology
Geum-Young Lee, Won-Keun Kim, Seungchan Cho, Kyungmin Park, Jongwoo Kim, Seung-Ho Lee, Jingyeong Lee, Young-Sun Lee, Ji Hoon Kim, Kwan Soo Byun, Jin-Won Song
Summary: This study used multiplex PCR-based NGS to obtain nearly whole-genome HAV sequences and analyze the genetic diversity and phylogenetic relationships. The VP3 region may be used to track the origin of HAV outbreaks. Additionally, a VP3-specific qPCR method was developed for molecular diagnosis of HAV infection.
Article
Immunology
Shixiao Li, Jiajia Qin, Peng Zhou, Minfei Peng, Jiao Qian, Yingying Cai, Qingxin Shi, Tao-Hsin Tung, Bo Shen, Sufei Yu
Summary: In-house mNGS has a higher detection rate and a wider spectrum of pathogens in patients with lower respiratory tract infections (LRTIs), while also shortening the turnaround time and hospitalization. It may be more suitable for clinical microbiology laboratories.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Immunology
Nanda Ramchandar, Jessica Burns, Nicole G. Coufal, Andrew Pennock, Benjamin Briggs, Rita Stinnett, John Bradley, John Arnold, George Y. Liu, Maya Pring, Vidyadhar V. Upasani, Kathleen Rickert, David Dimmock, Charles Chiu, Lauge Farnaes, Christopher Cannavino
Summary: Through a study on pediatric patients with acute osteomyelitis and/or septic arthritis, it was found that mNGS testing had higher diagnostic value in identifying pathogens compared to traditional culture and usual care testing.
OPEN FORUM INFECTIOUS DISEASES
(2021)
Article
Virology
Manasi Majumdar, Cristina Celma, Elaine Pegg, Krunal Polra, Jake Dunning, Javier Martin
Summary: The study focused on a detection method for enteroviruses using NGS analysis of clinical samples, showing high concordance with conventional Sanger sequencing and good sensitivity and specificity for different EV types. The NGS method identified previously untyped EVs and potential co-infections, demonstrating its potential for comprehensive EV detection and genetic analysis.
Article
Medicine, General & Internal
Jinbao Huang, Heng Weng, Ling Ye, Meiqin Jiang, Yangyu Li, Hongyan Li
Summary: This study evaluated the clinical value of metagenomic next-generation sequencing (mNGS) for the screening of lower respiratory tract infections (LRTIs) and tumors. The results showed that mNGS had higher sensitivity and accuracy in pathogen diagnosis compared to traditional culture and comprehensive microbial tests (CMT). In addition, CNV detection was found to be an important auxiliary diagnostic tool for cancer.
INTERNATIONAL JOURNAL OF GENERAL MEDICINE
(2023)
Article
Immunology
Wenjing Tang, Yu Zhang, Chong Luo, Lina Zhou, Zhiyong Zhang, Xuemei Tang, Xiaodong Zhao, Yunfei An
Summary: This study evaluated the utility of mNGS for detecting pathogens in patients with PID, demonstrating its superiority over conventional methods in pathogen identification, especially in detecting rare opportunistic pathogens. Compared to traditional methods, mNGS can provide faster pathogen diagnosis, enabling clinicians to make more timely and targeted therapeutic decisions.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Medical Laboratory Technology
Chendi Jing, Hongbin Chen, Yong Liang, Ying Zhong, Qi Wang, Lifeng Li, Shijun Sun, Yifan Guo, Ruobing Wang, Zhi Jiang, Hui Wang
Summary: The mNGS workflow showed a high clinical sensitivity of 87.1%, improved clinical specificity of 80.2%, and reduced false-positive results by utilizing multiple control groups. This optimization can enhance the utility of mNGS as a powerful tool for identifying pathogens in bloodstream infections.
CLINICAL CHEMISTRY
(2021)
Article
Oncology
Tyler Shugg, Reynold C. Ly, Wilberforce Osei, Elizabeth J. Rowe, Caitlin A. Granfield, Ty C. Lynnes, Elizabeth B. Medeiros, Jennelle C. Hodge, Amy M. Breman, Bryan P. Schneider, S. Cenk Sahinalp, Ibrahim Numanagic, Benjamin A. Salisbury, Steven M. Bray, Ryan Ratcliff, Todd C. Skaar
Summary: This study assessed the accuracy of the Aldy computational method in extracting pharmacogenomics genotypes from whole genome sequencing (WGS) and whole exome sequencing (WES) data. The results showed that Aldy achieved over 99% accuracy in calling diplotypes for major pharmacogenes from both WGS and WES data, supporting its importance in clinical applications.
FRONTIERS IN ONCOLOGY
(2023)
Article
Multidisciplinary Sciences
Eyal Shteyer, Louis Shekhtman, Tal Zinger, Sheri Harari, Inna Gafanovich, Dana Wolf, Hefziba Ivgi, Rima Barsuk, Ilana Dery, Daniela Armoni, Mila Rivkin, Rahul Pipalia, Michal Cohen Eliav, Yizhak Skorochod, Gabriel S. Breuer, Ran Tur-kaspa, Yonit Weil Wiener, Adi Stern, Scott J. Cotler, Harel Dahari, Yoav Lurie
Correction
Multidisciplinary Sciences
Eyal Shteyer, Louis Shekhtman, Tal Zinger, Sheri Harari, Inna Gafanovich, Dana Wolf, Hefziba Ivgi, Rima Barsuk, Ilana Dery, Daniela Armoni, Mila Rivkin, Rahul Pipalia, Michal Cohen Eliav, Yizhak Skorochod, Gabriel S. Breuer, Ran Tur-Kaspa, Yonit Weil Wiener, Adi Stern, Scott J. Cotler, Harel Dahari, Yoav Lurie
Article
Biochemistry & Molecular Biology
Guy Ling, Danielle Miller, Rasmus Nielsen, Adi Stern
MOLECULAR BIOLOGY AND EVOLUTION
(2020)
Article
Biochemistry & Molecular Biology
Talia Kustin, Adi Stern
Summary: RNA viruses exhibit a trend towards A-rich coding sequences during evolution, mainly influenced by selection pressures, which contribute to the advancement of genome evolution. Research findings suggest that single-stranded RNA viruses undergo selective pressure resulting in the presence of A-rich coding sequences in their genomes.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Moran Meir, Noam Harel, Danielle Miller, Maoz Gelbart, Avigdor Eldar, Uri Gophna, Adi Stern
Article
Virology
Maoz Gelbart, Adi Stern
Article
Biology
Florian Mattenberger, Victor Latorre, Omer Tirosh, Adi Stern, Ron Geller
Summary: This study comprehensively defines the effects of mutations on the capsid of a human picornavirus, identifying key structural and sequence determinants that predict mutational fitness effects. It also introduces a bioinformatic approach for identifying host proteins targeted by viral proteases based on capsid-encoded protease cleavage sites, shedding light on important aspects of viral biology, evolution, and host interactions.
Article
Biotechnology & Applied Microbiology
Alessio D. Nahmad, Cicera R. Lazzarotto, Natalie Zelikson, Talia Kustin, Mary Tenuta, Deli Huang, Inbal Reuveni, Daniel Nataf, Yuval Raviv, Miriam Horovitz-Fried, Iris Dotan, Yaron Carmi, Rina Rosin-Arbesfeld, David Nemazee, James E. Voss, Adi Stern, Shengdar Q. Tsai, Adi Barzel
Summary: In vivo engineering of B cells to secrete anti-HIV antibodies is a safe, potent, and scalable method that can be used for the treatment of infectious and noncommunicable diseases.
NATURE BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Sheri Harari, Maayan Tahor, Natalie Rutsinsky, Suzy Meijer, Danielle Miller, Oryan Henig, Ora Halutz, Katia Levytskyi, Ronen Ben-Ami, Amos Adler, Yael Paran, Adi Stern
Summary: In immunocompromised patients with chronic SARS-CoV-2 infection, adaptive evolution occurs and some mutations may lead to the emergence of variants of concern. However, certain mutations associated with global transmission are absent in chronic infections. The study also found a strong correlation between viral rebound and antibody evasion. The findings suggest a tradeoff between antibody evasion and transmissibility, highlighting the importance of monitoring chronic infections for understanding the emergence of variants of concern.
Article
Multidisciplinary Sciences
Danielle Miller, Adi Stern, David Burstein
Summary: In this study, the authors propose a concept to reveal the function of uncharacterized genes using deep learning methods adopted from natural language processing. By repurposing NLP algorithms to model gene semantics, they are able to predict functional categories for genes and demonstrate the potential of combining microbial genomics and language models to discover gene functions in microbes.
NATURE COMMUNICATIONS
(2022)
Article
Virology
Itamar Caspi, Moran Meir, Nadav Ben Nun, Reem Abu Rass, Uri Yakhini, Adi Stern, Yoav Ram
Summary: RNA viruses have high genetic diversity due to mutation and natural selection, but separating these forces is challenging. This study developed a method to infer the mutation rate and selection parameters from full haplotype sequences using neural networks. Applying this method to MS2 bacteriophage data, a mutation rate of approximately 0.2 mutations per genome per replication cycle was estimated. Additionally, evidence of reciprocal sign epistasis between beneficial mutations was found. In summary, this study provides insights into the mutation rate and selection parameters of RNA viruses using a novel approach.
Article
Multidisciplinary Sciences
Danielle Miller, Michael A. Martin, Noam Harel, Omer Tirosh, Talia Kustin, Moran Meir, Nadav Sorek, Shiraz Gefen-Halevi, Sharon Amit, Olesya Vorontsov, Avraham Shaag, Dana Wolf, Avi Peretz, Yonat Shemer-Avni, Diana Roif-Kaminsky, Naama M. Kopelman, Amit Huppert, Katia Koelle, Adi Stern
NATURE COMMUNICATIONS
(2020)
Article
Virology
Tal Zinger, Maoz Gelbart, Danielle Miller, Pleuni S. Pennings, Adi Stern
Article
Microbiology
Maoz Gelbart, Sheri Harari, Ya'ara Ben-Ari, Talia Kustin, Dana Wolf, Michal Mandelboim, Orna Mor, Pleuni S. Pennings, Adi Stern