Article
Biochemical Research Methods
Kody A. Waldstein, Jirong Yi, Michael Myung Cho, Raghu Mudumbai, Xiaodong Wu, Steven M. Varga, Weiyu Xu
Summary: The rapid spread of SARS-CoV-2 has highlighted the need for innovative testing approaches for future pandemics. In this study, a novel sample pooling procedure based on compressed sensing theory is presented, which accurately identifies virally infected patients at high prevalence rates. The method reduces the number of tests required and provides quantification of individual sample viral load within a pool.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Chemistry, Analytical
Partha P. Sahu, Geetartha Sarma, Satyajit Das, Biswajyoti Borkakoty
Summary: Accurate and rapid detection and isolation are crucial for controlling the spread of COVID-19. Currently, the gold standard rRT-PCR tool is time-consuming and complex, requiring expensive equipment. This study focuses on developing a disposable paper capacitance sensor for simple and easy detection.
ANALYTICA CHIMICA ACTA
(2023)
Article
Multidisciplinary Sciences
Pavlo Gilchuk, Isaac Thomsen, Sandra Yoder, Eric Brady, James D. Chappell, Laura J. Stevens, Mark R. Denison, Rachel E. Sutton, Rita E. Chen, Laura A. VanBlargan, Naveenchandra Suryadevara, Seth J. Zost, Jonathan Schmitz, Jill M. Pulley, Michael S. Diamond, Jillian P. Rhoads, Gordon R. Bernard, Wesley H. Self, Todd W. Rice, Allison P. Wheeler, James E. Crowe, Robert H. Carnahan
Summary: The COVID-19 pandemic has highlighted the urgent need for rapid evaluation of neutralizing antibody responses and the development of antibody-based treatments. The currently approved serological tests do not measure antibody-mediated viral neutralization, and there is a need for standardized quantitative neutralization assays. This study presents a high-throughput two-step profiling approach for identifying neutralizing convalescent plasma. Additionally, the researchers introduce a neutralizing antibody standard reagent to calibrate antibody neutralizing activity in convalescent plasma.
Article
Multidisciplinary Sciences
Laurens Topff, Jose Sanchez-Garcia, Rafael Lopez-Gonzalez, Ana Jimenez J. Pastor, Jacob J. Visser, Merel Huisman, Julien Guiot, Regina G. H. Beets-Tan, Angel Alberich-Bayarri, Almudena R. Fuster-Matanzo, Erik R. Ranschaert
Summary: Researchers developed a deep learning-based clinical decision support system for automatic diagnosis of COVID-19 on chest CT scans. The system also provides a segmentation tool to assess lung involvement and measure disease severity. The system showed high accuracy and potential clinical utility in a retrospective multicenter study.
Article
Infectious Diseases
Akif Ayaz, Asli Guner Ozturk Demir, Gurkan Ozturk, Mehmet Kocak
Summary: Pooled RT-PCR testing strategy provides a practical way to expand the screening capacity of RT-PCR in pandemic management without reducing its sensitivity. The pool size does not significantly affect the final results, and a pool size of 20 is recommended.
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
(2022)
Review
Chemistry, Analytical
Olena Filchakova, Dina Dossym, Aisha Ilyas, Tamila Kuanysheva, Altynay Abdizhamil, Rostislav Bukasov
Summary: More than six billion tests for COVID-19 have been conducted worldwide. This article emphasizes the importance of testing for the SARS-CoV-2 virus and corresponding human antibodies, not only for medical diagnosis and treatment, but also for economic and social activities. The review discusses the parameters of these tests and compares different detection methods. While RT-PCR remains the gold standard, there is a need for alternative methods that are less expensive and more accessible.
Article
Chemistry, Analytical
Julia Martin, Noelia Tena, Agustin G. Asuero
Summary: This review discusses four main methods for diagnosing, screening and monitoring SARS-CoV-2, including RT-PCR, CT, and rapid antigen and antibody detection. RT-PCR is considered the gold standard with the highest sensitivity and specificity, while combining CT images with RT-PCR provides the most robust and accurate confirmation of COVID-19 infection.
MICROCHEMICAL JOURNAL
(2021)
Article
Biochemical Research Methods
Cristina Mendes de Oliveira, Leila Brochi, Luciano Cesar Scarpelli, Annelise Correa Wengerkievicz Lopes, Jose Eduardo Levi
Summary: Two RNA extraction-free single RT-PCR protocols on saliva samples were compared to oro/nasopharyngeal swab specimens, showing substantial agreement and an increasing positivity rate with disease progression. One of the saliva protocols had a 95% limit of detection of 9441 copies/mL, supporting its use as an alternative to nasopharyngeal swabs, especially in the early phase of symptom onset.
JOURNAL OF VIROLOGICAL METHODS
(2021)
Article
Biophysics
Pengfei Zhang, Liben Chen, Jiumei Hu, Alexander Y. Trick, Fan-En Chen, Kuangwen Hsieh, Yang Zhao, Branch Coleman, Kate Kruczynski, Thomas R. Pisanic, Christopher D. Heaney, William A. Clarke, Tza-Huei Wang
Summary: The study introduces a rapid and sensitive magnetofluidic immuno-PCR platform for point-of-care serological testing of COVID-19, which achieved high sensitivity and specificity in clinical sample evaluation.
BIOSENSORS & BIOELECTRONICS
(2022)
Review
Biochemical Research Methods
Qi Song, Xindi Sun, Ziyi Dai, Yibo Gao, Xiuqing Gong, Bingpu Zhou, Jinbo Wu, Weijia Wen
Summary: COVID-19 is an acute respiratory disease caused by SARS-CoV-2 with high transmissibility, severe cases can lead to death. Currently, RT-PCR is the primary diagnostic method, yet POCT offers advantages of ease of use and timely detection, reducing the testing burden on central hospitals and facilitating early detection and treatment.
Article
Medicine, General & Internal
Victoria Hall, Sarah Foulkes, Ferdinando Insalata, Peter Kirwan, Ayoub Saei, Ana Atti, Edgar Wellington, Jameel Khawam, Katie Munro, Michelle Cole, Caio Tranquillini, Andrew Taylor-Kerr, Nipunadi Hettiarachchi, Davina Calbraith, Noshin Sajedi, Iain Milligan, Yrene Themistocleous, Diane Corrigan, Lisa Cromey, Lesley Price, Sally Stewart, Elen de Lacy, Chris Norman, Ezra Linley, Ashley D. Otter, Amanda Semper, Jacqueline Hewson, Silvia D'Arcangelo, Meera Chand, Colin S. Brown, Tim Brooks, Jasmin Islam, Andre Charlett, Susan Hopkins
Summary: This study investigated the duration and effectiveness of immunity among healthcare workers in the United Kingdom. It found that two doses of the BNT162b2 vaccine provided high short-term protection against SARS-CoV-2 infection, but this protection significantly decreased after six months. However, infection-acquired immunity boosted by vaccination remained high, even more than one year after infection.
NEW ENGLAND JOURNAL OF MEDICINE
(2022)
Article
Chemistry, Analytical
Wenyao Zhang, Kaixin Zheng, Yang Ye, Jiali Ji, Xiaoyu Cheng, Sailing He
Summary: A pipette-tip-enabled digital nucleic acid analyzer for high-performance COVID-19 testing is demonstrated in this study. By using digital LAMP technology, the ORF1a/b gene can be amplified without the need for a thermal cycler, allowing for the generation of monodisperse microdroplets with benchtop centrifugation. The method offers a significant improvement in sensitivity over nondigital techniques and compares favorably to commercial dLAMP platforms, showing potential for large-scale applications of ultrasensitive digital nucleic acid analyzers.
ANALYTICAL CHEMISTRY
(2021)
Editorial Material
Hematology
Lee M. Greenberger, Gwen L. Nichols
Summary: In this issue of Blood, Mittelman et al(1) and Pagano et al(2) demonstrate that patients with hematologic malignancies who have been fully or partially vaccinated are at a higher risk of poor clinical outcomes after COVID-19 infection compared to matched controls or the general population.
Review
Biochemistry & Molecular Biology
Davoodbasha MubarakAli
Summary: Rapid detection of viral infection is essential for preventing pandemic spread, involving sample collection for isolation and nucleic acid detection. The advancement in testing methods, such as RNA, immunologic, and radiological tests, can aid in the quick and accurate diagnosis and treatment of viral infections.
APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Carolina de la Guardia, Giselle Rangel, Alcibiades Villarreal, Amador Goodridge, Patricia L. Fernandez, Ricardo Lleonart
Summary: COVID-19 is an acute respiratory disease caused by SARS-CoV-2, resulting in high mortality and economic breakdown. ELISA assays can effectively measure specific antibodies in COVID-19 patients with high sensitivity, specificity, and congruence with RT-PCR results.
Article
Virology
Brady Hueber, Alan D. Curtis, Kyle Kroll, Valerie Varner, Rhianna Jones, Sachi Pathak, Michelle Lifton, Koen K. A. Van Rompay, Kristina De Paris, R. Keith Reeves
JOURNAL OF VIROLOGY
(2020)
Article
Multidisciplinary Sciences
Koen K. A. Van Rompay, Lark L. Coffey, Tania Kapoor, Anna Gazumyan, Rebekah I. Keesler, Andrea Jurado, Avery Peace, Marianna Agudelo, Jennifer Watanabe, Jodie Usachenko, Anil Singapuri, Ramya Immareddy, Amir Ardeshir, Jackson B. Stuart, Stylianos Bournazos, Jeffrey V. Ravetch, Paul J. Balderes, Ivo C. Lorenz, Shannon R. Esswein, Jennifer R. Keeffe, Pamela J. Bjorkman, Qiao Wang, Charles M. Rice, Margaret R. MacDonald, Michel C. Nussenzweig, Davide F. Robbiani
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Multidisciplinary Sciences
Yashavanth Shaan Lakshmanappa, Sonny R. Elizaldi, Jamin W. Roh, Brian A. Schmidt, Timothy D. Carroll, Kourtney D. Weaver, Justin C. Smith, Anil Verma, Jesse D. Deere, Joseph Dutra, Mars Stone, Sergej Franz, Rebecca Lee Sammak, Katherine J. Olstad, J. Rachel Reader, Zhong-Min Ma, Nancy K. Nguyen, Jennifer Watanabe, Jodie Usachenko, Ramya Immareddy, JoAnn L. Yee, Daniela Weiskopf, Alessandro Sette, Dennis Hartigan-O'Connor, Stephen J. McSorley, John H. Morrison, Nam K. Tran, Graham Simmons, Michael P. Busch, Pamela A. Kozlowski, Koen K. A. Van Rompay, Christopher J. Miller, Smita S. Iyer
Summary: Induction of CD4 T follicular helper (Tfh) cells is crucial for antibody responses to viral infections, as shown in a rhesus macaque model of mild COVID-19 where SARS-CoV-2 infection resulted in transient accumulation of proliferating Tfh cells with a Th1 profile in peripheral blood and the generation of germinal center Tfh cells specific for viral proteins.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Ousmane H. Cisse, Liang Ma, John P. Dekker, Pavel P. Khil, Jung-Ho Youn, Jason M. Brenchley, Robert Blair, Bapi Pahar, Magali Chabe, Koen K. A. Van Rompay, Rebekah Keesler, Antti Sukura, Vanessa Hirsch, Geetha Kutty, Yueqin Liu, Li Peng, Jie Chen, Jun Song, Christiane Weissenbacher-Lang, Jie Xu, Nathan S. Upham, Jason E. Stajich, Christina A. Cuomo, Melanie T. Cushion, Joseph A. Kovacs
Summary: By sequencing and comparing the genomes of Pneumocystis species infecting different mammals, researchers gained insights into the molecular basis of host specificity in Pneumocystis.
COMMUNICATIONS BIOLOGY
(2021)
Article
Microbiology
Koen K. A. Van Rompay, Katherine J. Olstad, Rebecca L. Sammak, Joseph Dutra, Jennifer K. Watanabe, Jodie L. Usachenko, Ramya Immareddy, Anil Verma, Yashavanth Shaan Lakshmanappa, Brian A. Schmidt, Jamin W. Roh, Sonny R. Elizaldi, A. Mark Allen, Frauke Muecksch, Julio C. C. Lorenzi, Sarah Lockwood, Rachel E. Pollard, JoAnn L. Yee, Peter B. Nham, Amir Ardeshir, Jesse D. Deere, Jean Patterson, Que Dang, Theodora Hatziioannou, Paul D. Bieniasz, Smita S. Iyer, Dennis J. Hartigan-O'Connor, Michel C. Nussenzweig, J. Rachel Reader
Summary: The combination of the potent monoclonal antibodies C135-LS and C144-LS improved clinical symptoms, reduced virus replication in the respiratory tract, and significantly decreased lung inflammation in macaques infected with SARS-CoV-2. These findings suggest potential therapeutic benefits of these antibodies in early COVID-19 infection.
Article
Medicine, Research & Experimental
Mariana G. Weber, Chara J. Walters-Laird, Amir Kol, Clarissa Santos Rocha, Lauren A. Hirao, Abigail Mende, Bipin Balan, Juan Arredondo, Sonny R. Elizaldi, Smita S. Iyer, Alice F. Tarantal, Satya Dandekar
Summary: Administering MSC to SIV-infected macaques reduces viral load and enhances virus-specific responses, facilitating clearance of SIV-positive cells from gut mucosal effector sites and improving antigen presentation and immune responses. This modulates antiviral immunity predominantly through type I/II IFN signaling and B cell signature, providing insights for multipronged HIV eradication strategies.
Article
Microbiology
Timothy Carroll, Douglas Fox, Neeltje van Doremalen, Erin Ball, Mary Kate Morris, Alicia Sotomayor-Gonzalez, Venice Servellita, Arjun Rustagi, Claude Kwe Yinda, Linda Fritts, Julia Rebecca Port, Zhong-Min Ma, Myndi G. Holbrook, Jonathan Schulz, Catherine A. Blish, Carl Hanson, Charles Y. Chiu, Vincent Munster, Sarah Stanley, Christopher J. Miller
Summary: New variants of SARS-CoV-2 continue to emerge globally, with the potential to cause more severe disease and evade vaccine-induced immunity. This study used a hamster model to investigate the epsilon (B.1.427/429) variant that emerged in California in late 2020. The findings suggest that this variant causes more severe disease and higher viral RNA levels in oral swabs compared to the previous B.1 (614G) variant. These results contribute to our understanding of the emergence and rapid spread of this variant in early 2021.
Article
Microbiology
Jesse D. Deere, Timothy D. Carroll, Joseph Dutra, Linda Fritts, Rebecca Lee Sammak, JoAnn L. Yee, Katherine J. Olstad, J. Rachel Reader, Amy Kistler, Jack Kamm, Clara Di Germanio, Yashavanth Shaan Lakshmanappa, Sonny R. Elizaldi, Jamin W. Roh, Graham Simmons, Jennifer Watanabe, Rachel E. Pollard, Jodie Usachenko, Ramya Immareddy, Brian A. Schmidt, Shelby L. O'Connor, Joseph DeRisi, Michael P. Busch, Smita S. Iyer, Koen K. A. Van Rompay, Dennis J. Hartigan-O'Connor, Christopher J. Miller
Summary: Clinical studies on the use of convalescent plasma (CP) for COVID-19 treatment have produced conflicting results, possibly due to varying administration timing. CP's mechanism includes neutralizing antibodies but its efficacy, minimum therapeutic titer and optimal administration timing remain unresolved. Early treatment with CP may have limited efficacy.
MICROBIOLOGY SPECTRUM
(2021)
Article
Microbiology
Koen K. A. Van Rompay, Katherine J. Olstad, Rebecca L. Sammak, Joseph Dutra, Jennifer K. Watanabe, Jodie L. Usachenko, Ramya Immareddy, Jamin W. Roh, Anil Verma, Yashavanth Shaan Lakshmanappa, Brian A. Schmidt, Clara Di Germanio, Nabeela Rizvi, Hongwei Liu, Zhong-Min Ma, Mars Stone, Graham Simmons, Larry J. Dumont, A. Mark Allen, Sarah Lockwood, Rachel E. Pollard, Rafael Ramiro de Assis, JoAnn L. Yee, Peter B. Nham, Amir Ardeshir, Jesse D. Deere, Aarti Jain, Philip L. Felgner, Lark L. Coffey, Smita S. Iyer, Dennis J. Hartigan-O'Connor, Michael P. Busch, J. Rachel Reader
Summary: The use of convalescent plasma from COVID-19 survivors as a therapeutic treatment for hospitalized patients showed only moderate efficacy, especially when administered early in infection with high neutralizing antibody titers. A macaque model of SARS-CoV-2 infection was used to study the potential therapeutic efficacy of convalescent plasma, and the results showed minimal effects on reducing virus replication in the respiratory tract but significant reduction of lung inflammation.
Article
Biology
Danielle Beckman, Adele M. H. Seelke, Jeffrey Bennett, Paige Dougherty, Koen K. A. Van Rompay, Rebekah Keesler, Patricia A. Pesavento, Lark L. A. Coffey, John H. Morrison, Eliza Bliss-Moreau
Summary: In this study, we evaluated the neuropathological consequences of fetal exposure to ZIKV in rhesus monkeys, and found that the virus can cause structural abnormalities and cell death in the developing brain. These findings may help explain why some infants born with normal sized heads during ZIKV infection experience developmental challenges as they age.
Article
Immunology
Alexandra Fowler, Koen K. A. Van Rompay, Maureen Sampson, Javier Leo, Jennifer K. Watanabe, Jodie L. Usachenko, Ramya Immareddy, Debbie M. Lovato, John T. Schiller, Alan T. Remaley, Bryce Chackerian
Summary: The study evaluated the cholesterol-lowering efficacy of virus-like particle (VLP) vaccines targeting epitopes within the LDL receptor binding domain of PCSK9. The bivalent VLP vaccine elicited strong and durable antibody responses and lowered cholesterol levels in mice and non-human primates.
Article
Microbiology
Ria Goswami, Stella J. Berendam, Shuk Hang Li, Ashley N. Nelson, Kristina De Paris, Koen K. A. Van Rompay, Sallie R. Permar, Genevieve G. Fouda
