Article
Microbiology
Nicholas T. Streck, Mark J. Espy, Matthew J. Ferber, Eric W. Klee, Raymund R. Razonable, Dimitri Gonzalez, Chalom Sayada, Phillip R. Heaton, Sunwen Chou, Matthew J. Binnicker
Summary: A novel next-generation sequencing (NGS) method was developed and validated in this study to accurately detect mutations in CMV genes associated with antiviral resistance. Compared to traditional Sanger sequencing, the NGS method demonstrated higher consistency and can assist in providing personalized antiviral therapy.
JOURNAL OF CLINICAL MICROBIOLOGY
(2023)
Article
Microbiology
Miaomiao Li, Shujia Liang, Chao Zhou, Min Chen, Shu Liang, Chunhua Liu, Zhongbao Zuo, Lei Liu, Yi Feng, Chang Song, Hui Xing, Yuhua Ruan, Yiming Shao, Lingjie Liao
Summary: A study conducted in China found that patients with antiretroviral therapy interruption are at risk of HIV drug resistance. Next-generation sequencing technology can detect more minority drug resistance variants, with a sharp increase in their numbers when the detection threshold is below 5%.
Article
Immunology
Shuntai Zhou, Sabrina Sizemore, Matt Moeser, Scott Zimmerman, Erika Samoff, Victoria Mobley, Simon Frost, Andy Cressman, Michael Clark, Tara Skelly, Hemant Kelkar, Umadevi Veluvolu, Corbin Jones, Joseph Eron, Myron Cohen, Julie A. E. Nelson, Ronald Swanstrom, Ann M. Dennis
Summary: The study introduces a multiplexed Primer ID-next-generation sequencing approach to identify recent HIV-1 infections among newly diagnosed patients, finding a significant portion of recent infections and certain trends, such as higher likelihood of recent infection in younger individuals and drug users. The rapid identification of recent infections and drug resistance mutations through this approach allows for prioritization of care and intervention efforts towards high-risk individuals.
JOURNAL OF INFECTIOUS DISEASES
(2021)
Article
Virology
Jocelyn Hume, Kym Lowry, David M. Whiley, Adam D. Irwin, Cheryl Bletchly, Emma L. Sweeney
Summary: This study investigates the diagnostic testing for cytomegalovirus (CMV) antiviral resistance and demonstrates the feasibility of the ViroKey? SQ FLEX Genotyping Assay. Although there were technical issues, this platform shows potential to be a useful addition to routine pathology workflows with improvement.
JOURNAL OF CLINICAL VIROLOGY
(2023)
Article
Engineering, Environmental
Zexin Tao, Xiaojuan Lin, Yao Liu, Feng Ji, Suting Wang, Ping Xiong, Li Zhang, Qing Xu, Aiqiang Xu, Ning Cui
Summary: This study collected sewage samples from Jinan, China from 2018 to 2019, and analyzed classic and novel HAstVs using real-time quantitative PCR and next generation sequencing. The results showed that sewage contains a high diversity of astroviruses, and there are multiple co-circulating lineages within each local HAstV genotype.
Article
Microbiology
V Novitsky, W. Nyandiko, R. Vreeman, A. K. DeLong, A. Manne, M. Scanlon, A. Ngeresa, J. Aluoch, F. Sang, C. Ashimosi, E. Jepkemboi, M. Orido, J. W. Hogan, R. Kantor
Summary: The study assessed the added value of using next-generation sequencing (NGS) compared to Sanger sequencing in detecting HIV-1 drug resistance mutations in Kenyan children and adolescents. It found that NGS detected more drug resistance mutations at lower thresholds, suggesting potential benefits of using NGS over existing technology.
MICROBIOLOGY SPECTRUM
(2022)
Article
Pharmacology & Pharmacy
Samuel D. Chorlton, Gordon Ritchie, Tanya Lawson, Elizabeth McLachlan, Marc G. Romney, Nancy Matic, Christopher F. Lowe
Summary: A next-generation sequencing (NGS) assay was developed for CMV antiviral drug resistance (AVDR) testing, which using MinION technology detected additional mutations compared to traditional Sanger sequencing. Through the application of an online bioinformatics pipeline, barriers associated with MinION and NGS in clinical laboratories were eliminated.
ANTIVIRAL RESEARCH
(2021)
Article
Virology
Calesta Hui Yi Teo, Nurul Hannah Binte Norhisham, Ogestelli Fabia Lee, Siyu Png, Chean Nee Chai, Gabriel Yan, Julian Wei-Tze Tang, Chun Kiat Lee
Summary: The HIV genotypic resistance test is crucial for managing HIV/AIDS patients, and high-throughput sequencing is a reliable and sensitive alternative method for detecting low-abundance covert mutations and drug resistance.
Review
Microbiology
Navisha Dookie, Azraa Khan, Nesri Padayatchi, Kogieleum Naidoo
Summary: This review discusses the potential of next generation whole genome sequencing (WGS) in accelerating individualized care for tuberculosis (TB), as well as the challenges and mechanisms of drug resistance and its implications on diagnosis and treatment.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Trinh Thi Bich Tram, Vu Thi Ngoc Ha, Le Pham Tien Trieu, Philip M. Ashton, Emily D. Crawford, Do Dang Anh Thu, Nguyen Le Quang, Guy E. Thwaites, Timothy M. Walker, Catherine Anscombe, Nguyen Thuy Thuong Thuong
Summary: FLASH technique allows for rapid detection of Mycobacterium tuberculosis (Mtb) drug resistance from clinical samples, enabling optimal and timely treatment for tuberculosis (TB) patients.
JOURNAL OF CLINICAL MICROBIOLOGY
(2023)
Article
Oncology
Yen-Ting Lin, Chi-Lu Chiang, Jen-Yu Hung, Mei-Hsuan Lee, Wu-Chou Su, Shang-Yin Wu, Yu-Feng Wei, Kang-Yun Lee, Yen-Han Tseng, Jian Su, Hsin-Pei Chung, Chih-Bin Lin, Wen-Hui Ku, Tsai-Shin Chiang, Chao-Hua Chiu, Jin-Yuan Shih
Summary: The study found that the mechanisms of ALK TKI resistance were heterogeneous, with ALK mutations being found in less than one-third of patients. In patients with simultaneous paired tissue and cfDNA samples, mutations were identified in 45% and 30% of cases, respectively, with a concordance rate of 45%.
EUROPEAN JOURNAL OF CANCER
(2021)
Article
Respiratory System
Ya-Sian Chang, Siang-Jyun Tu, Yu-Chia Chen, Ting-Yuan Liu, Ya-Ting Lee, Ju-Chen Yen, Hsin-Yuan Fang, Jan-Gowth Chang
Summary: This study identified 19 known driver mutations and new variants in Taiwanese patients with non-small cell lung cancer. EGFR mutations were found at a higher frequency compared to Caucasians, while KRAS and TP53 mutations were less common. All ClinVar pathogenic variants were trunk mutations present in the tumor regions.
RESPIRATORY RESEARCH
(2021)
Article
Virology
Laila Sara Arroyo Muhr, Daniel Guerendiain, Kate Cuschieri, Karin Sundstrom
Summary: NGS technology provides powerful opportunities for HPV genomics research, but rigorous validation and quality assurance procedures are essential to ensure reliable interpretation of results. Recommendations for optimizing sequencing data yield and curated bioinformatical procedures are crucial for robust analysis of HPV genotypes and mutations. International standards for quality assurance in HPV NGS should be developed to enhance testing and diagnostics in global efforts.
Article
Immunology
Isabelle Paula Lodding, Mette Jorgensen, Marc Bennedbaek, Nikolai Kirkby, Klaudia Naegele, Finn Gustafsson, Michael Perch, Allan Rasmussen, Henrik Sengelov, Soren Schwartz Sorensen, Hans Hirsch, Jens D. Lundgren
Summary: UL97-GCV-R is common in transplant patients with refractory CMV replication, with some patients having multiple induced mutations. The mismatch in donor/recipient CMV immunoglobulin G or failure to complete primary prophylaxis appear to increase the frequency of UL97-GCV-R, leading to the development of invasive CMV disease in many cases.
OPEN FORUM INFECTIOUS DISEASES
(2021)
Article
Biochemistry & Molecular Biology
Elisabetta Anna Tendi, Giovanna Morello, Maria Guarnaccia, Valentina La Cognata, Salvatore Petralia, Maria Anna Messina, Concetta Meli, Agata Fiumara, Martino Ruggieri, Sebastiano Cavallaro
Summary: Hyperphenylalaninemia (HPA) is a common genetic disorder characterized by serious clinical manifestations. Next-generation sequencing (NGS) technology can help identify the molecular basis of this disease due to its genetic and allelic heterogeneity. We developed a targeted NGS (tNGS) approach for detecting genetic variants associated with HPA, providing a comprehensive view and optimizing patient care.
Article
Immunology
Jessica A. Grembi, Audrie Lin, Md Abdul Karim, Md Ohedul Islam, Rana Miah, Benjamin F. Arnold, Elizabeth T. Rogawski McQuade, Shahjahan Ali, Md Ziaur Rahman, Zahir Hussain, Abul K. Shoab, Syeda L. Famida, Md Saheen Hossen, Palash Mutsuddi, Mahbubur Rahman, Leanne Unicomb, Rashidul Haque, Mami Taniuchi, Jie Liu, James A. Platts-Mills, Susan P. Holmes, Christine P. Stewart, Jade Benjamin-Chung, John M. Colford Jr, Eric R. Houpt, Stephen P. Luby
Summary: We evaluated the impact of water, sanitation, and handwashing (WSH) and nutrition interventions on enteropathogens in children in Bangladesh. WSH interventions were associated with fewer enteric viruses compared to controls. There was no difference in bacterial and protozoan pathogens for WSH or nutrition interventions.
JOURNAL OF INFECTIOUS DISEASES
(2023)
Article
Statistics & Probability
Claire Donnat, Susan Holmes
Summary: This study examines the evaluation of the reproductive number R for COVID-19 from a Bayesian perspective, explores the impact of heterogeneity on uncertainty quantification, and demonstrates the significant effects of heterogeneity through simulations of transmission and the impact of social distancing strategies.
JOURNAL OF APPLIED STATISTICS
(2023)
Article
Medical Laboratory Technology
Hannah Wang, Catherine A. Hogan, Michelle Verghese, Daniel Solis, Mamdouh Sibai, ChunHong Huang, Katharina Roltgen, Bryan A. Stevens, Fumiko Yamamoto, Malaya K. Sahoo, James Zehnder, Scott D. Boyd, Benjamin A. Pinsky
Summary: This study found that the concentration of nucleocapsid antigen in plasma is associated with the severity of COVID-19, particularly with ICU admission. Antigenemia showed comparable diagnostic performance to upper respiratory NAAT, aiding in triaging patients for optimized intensive care utilization.
CLINICAL CHEMISTRY
(2022)
Article
Microbiology
Priscilla S-W Yeung, Hannah Wang, Mamdouh Sibai, Daniel Solis, Fumiko Yamamoto, Naomi Iwai, Becky Jiang, Nathan Hammond, Bernadette Truong, Selamawit Bihon, Suzette Santos, Marilyn Mar, Claire Mai, Kenji O. Mfuh, Jacob A. Miller, ChunHong Huang, Malaya K. Sahoo, James L. Zehnder, Benjamin A. Pinsky
Summary: This study developed and validated an RT-qPCR-based detection method that can accurately distinguish different SARS-CoV-2 variants. The method showed high accuracy in identifying various variants and can be used in clinical laboratories for epidemiological surveillance and clinical decision-making.
JOURNAL OF CLINICAL MICROBIOLOGY
(2022)
Letter
Virology
Mamdouh Sibai, Hannah Wang, Priscilla S-W Yeung, Malaya K. Sahoo, Daniel Solis, Kenji O. Mfuh, ChunHong Huang, Fumiko Yamamoto, Benjamin A. Pinsky
JOURNAL OF CLINICAL VIROLOGY
(2022)
Article
Mathematics, Interdisciplinary Applications
Kris Sankaran, Susan P. Holmes
Summary: By linking conceptual theories with observed data, generative models serve as a crucial tool in various fields such as molecular biology, particle physics, and epidemiology. This article introduces the underlying concepts of generative models and discusses their applications in experimental design, model refinement, goodness-of-fit evaluation, and agent based simulation. The article emphasizes the flexibility of recombining generative mechanisms in different problem contexts and provides practical illustrations and code examples.
ANNUAL REVIEW OF STATISTICS AND ITS APPLICATION
(2023)
Article
Immunology
Kaiming Tao, Soo-Yon Rhee, Philip L. Tzou, Susan P. Holmes, Robert W. Shafer
Summary: During population-based genotypic drug resistance testing, HIV-1 pol nucleotide ambiguities that encode amino acid mixtures are common. This study examines the validity of sequences with fully ambiguous codons (FACs), which can translate to more than four amino acids. The findings indicate a strong correlation between FACs and HLA-associated positions as well as drug-resistance positions, suggesting that FACs are likely to result from antiviral or immune selection pressure in the context of population-based genotypic resistance testing.
AIDS RESEARCH AND HUMAN RETROVIRUSES
(2023)
Article
Multidisciplinary Sciences
Dari Shalon, Rebecca Neal Culver, Jessica A. Grembi, Jacob Folz, Peter V. Treit, Handuo Shi, Florian A. Rosenberger, Les Dethlefsen, Xiandong Meng, Eitan Yaffe, Andres Aranda-Diaz, Philipp E. Geyer, Johannes B. Mueller-Reif, Sean Spencer, Andrew D. Patterson, George Triadafilopoulos, Susan P. Holmes, Matthias Mann, Oliver Fiehn, David A. Relman, Kerwyn Casey Huang
Summary: This study developed an ingestible device that can collect samples from multiple regions of the human intestinal tract during normal digestion. Multi-omics analysis of the collected samples revealed significant differences in bacteria, phages, host proteins, and metabolites between the intestines and stool. The study provides insights into the roles of the gut microbiome and metabolome in human physiology and disease through non-invasive longitudinal profiling of microorganisms, proteins, and bile acids along the intestinal tract.
Article
Biotechnology & Applied Microbiology
Aaron J. Wilk, Alex K. Shalek, Susan Holmes, Catherine A. Blish
Summary: A flexible and scalable framework called Scriabin is presented to analyze cell-cell communication at single-cell resolution. It accurately recovers expected communication edges and uncovers spatial features of interaction. The approach is applicable to various datasets and provides insights into niche-phenotype relationships in health and disease.
NATURE BIOTECHNOLOGY
(2023)
Article
Virology
Kaiming Tao, Soo-Yon Rhee, Philip L. Tzou, Zachary A. Osman, Sergei L. Kosakovsky Pond, Susan P. Holmes, Robert W. Shafer
Summary: In order to manage individuals with detectable viremia and experience with the HIV-1 capsid inhibitor lenacapavir, capsid sequencing is required. By analyzing the published HIV-1 group M capsid sequences, the variability of amino acids at each position and the influence of subtype and cytotoxic T lymphocyte (CTL) selection pressure were characterized.
Article
Multidisciplinary Sciences
Makeda L. Robinson, David R. Glass, Veronica Duran, Olga Lucia Agudelo Rojas, Ana Maria Sanz, Monika Consuegra, Malaya Kumar Sahoo, Felix J. Hartmann, Marc Bosse, Rosa Margarita Gelvez, Nathalia Bueno, Benjamin A. Pinsky, Jose G. Montoya, Holden Maecker, Maria Isabel Estupinan Cardenas, Luis Angel Villar Centeno, Elsa Marina Rojas Garrido, Fernando Rosso, Sean C. Bendall, Shirit Einav
Summary: Approximately 5 million dengue virus-infected patients progress to severe dengue (SD) infection annually. This study reveals uncoordinated immune responses in SD patients and provides insights into SD pathogenesis in humans with potential implications for prediction and treatment.
Article
Microbiology
Jordan Mah, Chun Hong Huang, Malaya K. Sahoo, Benjamin A. Pinsky
Summary: Human adenoviruses (HAdVs) cause severe disease in immunocompromised patients. Quantitation of HAdV DNA in peripheral blood is used to assess the risk of disseminated disease and to monitor response to therapy. The semiautomated AltoStar adenovirus quantitative PCR provides accurate quantitation of HAdV DNA and is well suited for virological testing following transplantation.
MICROBIOLOGY SPECTRUM
(2023)
Article
Multidisciplinary Sciences
Elizabeth K. K. Costello, Daniel B. B. DiGiulio, Anna Robaczewska, Laura Symul, Ronald J. J. Wong, Gary M. M. Shaw, David K. K. Stevenson, Susan P. P. Holmes, Douglas S. S. Kwon, David A. A. Relman
Summary: Childbirth leads to vaginal inflammation and a decrease in Lactobacillus dominance, which continues to affect women for up to one year postpartum. Only 49.4% of women were able to recover from this disturbance by the end of the first postpartum year, indicating a significant impact on women's health and future pregnancies.
NATURE COMMUNICATIONS
(2023)
Article
Environmental Sciences
Winnie Zambrana, David Catoe, Mhara M. Coffman, Sooyeol Kim, Archana Anand, Daniel Solis, Malaya K. Sahoo, Benjamin A. Pinsky, Ami S. Bhatt, Alexandria B. Boehm, Marlene K. Wolfe
Summary: Monitoring wastewater for SARS-CoV-2 RNA can help identify small spatial areas with COVID-19 infections outside the scope of wastewater treatment plants. This study demonstrates that wastewater monitoring can aid the public health response at the subsewershed level.
Letter
Immunology
Cristina Costales, Malaya K. Sahoo, ChunHong Huang, Carolina V. Guimaraes, Donald Born, Lauren Kushner, Hayley A. Gans, Thuy A. Doan, Benjamin A. Pinsky
Summary: This article reports a fatal case of vaccine-associated measles encephalitis in an immunocompromised child in California, USA. The infection was confirmed by whole-genome RNA sequencing of measles virus from brain tissue. Biased matrix-gene hypermutation consistent with persistent measles virus central nervous system infection was observed.
EMERGING INFECTIOUS DISEASES
(2022)