Review
Virology
Youjiang Li, Danping Ji, Wangyu Cai, Yingying Hu, Yongying Bai, Jianguo Wu, Jian Xu
Summary: The article provides a detailed description and analysis of patients who test positive again after being discharged, as well as a basis for the management and protection of these patients.
JOURNAL OF MEDICAL VIROLOGY
(2021)
Article
Virology
Fenghua Chen, Zhi Geng, Jian Wang, Wenbo Liuchang, Da Huang, Yuandong Xu, Zheng Wang, Lin Wang
Summary: The study demonstrates that the swab pooling strategy may serve as an effective and economical approach for screening SARS-CoV-2 infections in large populations, especially in countries and regions where medical resources are limited during the pandemic and may thus be potential for clinical laboratory applications.
JOURNAL OF MEDICAL VIROLOGY
(2021)
Article
Virology
Julien Favresse, Jean-Louis Bayart, Clara David, Constant Gillot, Gregoire Wieers, Gatien Roussel, Guillaume Sondag, Marc Elsen, Christine Eucher, Jean-Michel Dogne, Jonathan Douxfils
Summary: This study evaluates the kinetics of serum N antigens and compares their clinical performance with NP RT-PCR. The results suggest that sensitive detection of N antigens in serum can serve as a valuable marker for COVID-19 diagnosis and evaluation of disease severity.
Article
Multidisciplinary Sciences
Jean-Baptiste Lascarrou, Gwenhael Colin, Aurelie Le Thuaut, Nicolas Serck, Mickael Ohana, Bertrand Sauneuf, Guillaume Geri, Jean-Baptiste Mesland, Gaetane Ribeyre, Claire Hussenet, Anne Sophie Boureau, Thomas Gille
Summary: In a multicenter case-control study on COVID-19 patients, it was found that patients with symptoms of headache and fatigue/malaise were more likely to have a false-negative result in their first RT-PCR test. Conversely, patients with elevated platelet and C-reactive protein levels were at a higher risk of a false-negative first RT-PCR test result. This highlights the importance of evaluating strategies involving serial RT-PCR testing for COVID-19 diagnosis.
SCIENTIFIC REPORTS
(2021)
Article
Microbiology
Arryn Craney, Dustin Petrik, Ashley Suhku, Yuqing Qiu, Sabrina Racine-Brzostek, Hanna Rennert, Heather Piscatelli, Govardhan Rathnaiah, Alyssa Hangman, Michael Carrie, Melissa Cushing
Summary: This study evaluated the performance of the MatMaCorp COVID-19 2SF test, which offers a rapid PCR-based testing for the diagnosis of SARS-CoV-2. The test showed 100% negative percent agreement and 85.4% positive percent agreement, indicating high accuracy, and specificity.
MICROBIOLOGY SPECTRUM
(2021)
Review
Microbiology
Jia-Wen Xie, Yun He, Ya-Wen Zheng, Mao Wang, Yong Lin, Li-Rong Lin
Summary: This study assessed the diagnostic accuracy of rapid antigen tests (RAT) compared to RT-PCR for detecting SARS-CoV-2. The results showed that RAT had high sensitivity and specificity, especially in early infection and high viral load cases. Using nasal samples for antigen testing is a reliable alternative to nasopharyngeal sampling.
MICROBIOLOGICAL RESEARCH
(2022)
Article
Virology
Farahnaz Joukar, Tofigh Yaghubi Kalurazi, Mahmoud Khoshsorour, Sonbol Taramian, Lida Mahfoozi, Heydar Ali Balou, Alireza Jafarinezhad, Aydin Pourkazemi, Ezat Hesni, Mehrnaz Asgharnezhad, Mohammad Shenagari, Issa Jahanzad, Mohammadreza Naghipour, Saman Maroufizadeh, Fariborz Mansour-Ghanaei
Summary: The study aimed to investigate the persistence of SARS-CoV-2 RNA in the nasopharyngeal, blood, urine, and stool samples of COVID-19 patients. Results showed no evidence of viral genetic materials in nasopharyngeal samples immediately after discharged. Further investigations on a larger sample size in multi-center and prospective RCTs are recommended to evaluate the effects of different drugs on viral shedding.
Article
Engineering, Environmental
Wenjie Huang, Kailu Wang, Chi-Tim Hung, Kai-Ming Chow, Dominic Tsang, Raymond Wai-Man Lai, Richard Huan Xu, Eng-Kiong Yeoh, Chun Chen, Kin-Fai Ho
Summary: This study evaluated the airborne transmission of SARS-CoV-2 in COVID-19 isolation wards at Prince of Wales Hospital in Hong Kong. Air and surface samples were collected and analyzed, confirming the contamination of the wards. Computational fluid dynamics simulations supported the possibility of airborne transmission. Additionally, the study found that the use of ceiling-mounted air cleaners was effective in reducing airborne transmission.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Virology
Phuong-Vi Nguyen, Ludy Registre Carmola, Ethan Wang, Leda Bassit, Anuradha Rao, Morgan Greenleaf, Julie A. Sullivan, Greg S. Martin, Wilbur A. Lam, Jesse J. Waggoner, Anne Piantadosi
Summary: The widespread use of over-the-counter rapid diagnostic tests for SARS-CoV-2 has resulted in a shortage of clinical samples for viral genomic surveillance. In this study, we assessed the RNA isolated from BinaxNOW swabs stored at room temperature for SARS-CoV-2 rRT-PCR and complete viral genome sequencing. Out of 103 samples, 81 (78.6%) yielded detectable RNA, and out of 57 samples, 46 (80.7%) produced complete genome sequences. Our findings demonstrate that SARS-CoV-2 RNA extracted from used Binax test swabs presents an important opportunity for enhancing SARS-CoV-2 genomic surveillance, investigating transmission clusters, and monitoring within-host evolution.
JOURNAL OF CLINICAL VIROLOGY
(2023)
Article
Biochemistry & Molecular Biology
G. Demyashkin, E. Kogan, D. Boldyrev, T. Demura, A. Tyatyushkina, E. Annenkova, K. Semenov, I. Zorin, A. Zverev
Summary: After the outbreak of COVID-19, scientists have gained a better understanding of the disease's pathogenesis and its impact on various organs and tissues. However, the effect of the virus on fertility remains unclear. Previous studies have provided conflicting results, and there is no evidence of a direct effect on the male reproductive organs. Further research is needed to confirm if the testicles are a target organ for SARS-CoV-2.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Microbiology
Tulio J. Lopera, Juan Carlos Alzate-Angel, Francisco J. Diaz, Maria T. Rugeles, Wbeimar Aguilar-Jimenez
Summary: While the antigen test has lower sensitivity for diagnosing SARS-CoV-2 infection compared to RT-PCR, it demonstrates high negative predictive value for contagiousness. In situations with high infection prevalence, positive results from the antigen test may not require confirmation, and it can be used to screen individuals to prevent contagion and resume daily activities.
MICROBIOLOGY SPECTRUM
(2022)
Article
Immunology
Sallie M. Long, Alexander Chern, Victoria Cooley, Sei Chung, Noah Z. Feit, Arryn Craney, Matthew S. Simon, Andrew B. Tassler
Summary: This study analyzed the nasopharyngeal and tracheal cycle threshold (Ct) values in 45 COVID-19 patients undergoing tracheostomy. The Ct values rose to 37.9 before the surgery and remained above 35 postoperatively, indicating that persistent test positivity may not be associated with persistent transmissible virus in this population.
CLINICAL INFECTIOUS DISEASES
(2022)
Article
Microbiology
Annette Audige, Juerg Boeni, Peter W. Schreiber, Thomas Scheier, Roberto Buonomano, Alain Rudiger, Dominique L. Braun, Gerhard Eich, Dagmar Keller, Barbara Hasse, Christoph Berger, Huldrych F. Guenthard, Amapola Manrique, Alexandra Trkola, Michael Huber
Summary: The study evaluated the performance of saliva as an alternative specimen for RT-PCR testing in antigen detection, with results showing that saliva cannot be recommended for use in Elecsys Anti-SARS-CoV-2 Antigen assay.
Article
Medicine, General & Internal
Esteban Ortiz-Prado, Felipe Andrade, Eduardo Vasconez, Cristina Escobar-Espinosa, Alexander Paolo Vallejo-Janeta, Byron Freire-Paspuel, Barbara Coronel, Heberson Galvis, Diana Morales-Jadan, Ismar A. Rivera-Olivero, Tannya Lozada, Aquiles R. Henriquez-Trujillo, Miguel Angel Garcia-Bereguiain
Summary: Within the special forces police officers in Quito, Ecuador, a high infection rate of SARS-CoV-2 was found, with a percentage of potential super spreaders. The majority of the infected individuals were asymptomatic, highlighting the importance of regular testing for all asymptomatic essential workers.
FRONTIERS IN MEDICINE
(2022)
Article
Virology
Doyeong Kim, Jihoo Lee, Jyotiranjan Bal, Seul Ki Seo, Chom-Kyu Chong, Jong Ho Lee, Hyun Park
Summary: Antigen tests for SARS-CoV-2 offer a simpler and faster alternative to molecular tests, and clinical validation is crucial before widespread use. The GenBody (TM) COVAG025 immunoassay showed high sensitivity and specificity in both retrospective and prospective clinical studies, indicating its potential to assist in accurate diagnosis, isolation, and treatment of COVID-19 patients for better pandemic control.
Article
Immunology
Abbye E. McEwen, Seth Cohen, Chloe Bryson-Cahn, Catherine Liu, Steven A. Pergam, John Lynch, Adrienne Schippers, Kathy Strand, Estella Whimbey, Nandita S. Mani, Allison J. Zelikoff, Vanessa A. Makarewicz, Elizabeth R. Brown, Shah A. Mohamed Bakhash, Noah R. Baker, Jared Castor, Robert J. Livingston, Meei-Li Huang, Keith R. Jerome, Alexander L. Greninger, Pavitra Roychoudhury
Summary: Among 20 vaccine breakthrough cases at the institution, all infections were caused by variants of concern, with a median Ct value of 20.2. Variants of concern were significantly more prevalent in breakthrough infections compared to contemporaneous samples sequenced in the laboratory.
CLINICAL INFECTIOUS DISEASES
(2022)
Article
Pathology
Jack K. Tung, Kelly A. Devereaux, Archana Lal Erdmann, Iris Schrijver, James Zehnder, Carlos J. Suarez
Summary: This report illustrates three potential pitfalls related to amplicon-based NGS assays and highlights strategies to minimize such risks.
JOURNAL OF CLINICAL PATHOLOGY
(2023)
Article
Virology
Kate B. Juergens, John Huckabee, Alexander L. Greninger
Summary: In this study, the complete genomes of two novel viruses in the Iflaviridae family were obtained from bat guano in Washington State using metagenomic deep sequencing and RACE techniques. These viruses, named King virus and Rolda virus, share some nucleotide identity with deformed wing virus. The presence of these viruses in guano suggests a possible ecological relationship between the viruses, insectivores, and plant reproduction.
Article
Virology
Diana Avetyan, Siras Hakobyan, Maria Nikoghosyan, Lilit Ghukasyan, Gisane Khachatryan, Tamara Sirunyan, Nelli Muradyan, Roksana Zakharyan, Andranik Chavushyan, Varduhi Hayrapetyan, Anahit Hovhannisyan, Shah A. Mohamed Bakhash, Keith R. Jerome, Pavitra Roychoudhury, Alexander L. Greninger, Lyudmila Niazyan, Mher Davidyants, Gayane Melik-Andreasyan, Shushan Sargsyan, Lilit Nersisyan, Arsen Arakelyan
Summary: The sequencing of SARS-CoV-2 in Armenia revealed six clades and their transmission routes, with each clade being responsible for different waves of positive case increase. The study also showed that mutations did not affect PCR testing accuracy and that nanopore sequencing is a viable alternative for large-scale molecular epidemiology research.
Article
Clinical Neurology
Geidy E. Serrano, Jessica E. Walker, Cecilia Tremblay, Ignazio S. Piras, Matthew J. Huentelman, Christine M. Belden, Danielle Goldfarb, David Shprecher, Alireza Atri, Charles H. Adler, Holly A. Shill, Erika Driver-Dunckley, Shyamal H. Mehta, Richard Caselli, Bryan K. Woodruff, Chadwick F. Haarer, Thomas Ruhlen, Maria Torres, Steve Nguyen, Dasan Schmitt, Steven Z. Rapscak, Christian Bime, Joseph L. Peters, Ellie Alevritis, Richard A. Arce, Michael J. Glass, Daisy Vargas, Lucia Sue, Anthony J. Intorcia, Courtney M. Nelson, Javon Oliver, Aryck Russell, Katsuko E. Suszczewicz, Claryssa Borja, Madison P. Cline, Spencer J. Hemmingsen, Sanaria Qiji, Holly M. Hobgood, Joseph P. Mizgerd, Malaya K. Sahoo, Haiyu Zhang, Daniel Solis, Thomas J. Montine, Gerald J. Berry, Eric M. Reiman, Katharina Roltgen, Scott D. Boyd, Benjamin A. Pinsky, James L. Zehnder, Pierre Talbot, Marc Desforges, Michael DeTure, Dennis W. Dickson, Thomas G. Beach
Summary: Brains of 42 COVID-19 decedents and 107 non-COVID-19 controls were studied. SARS-CoV-2 viral sequences were detected in the brains of COVID-19 subjects, suggesting the possible entry of the virus through the olfactory bulb. Gene expression changes related to immune response, neuronal constituents, and olfactory/taste receptor genes were observed in the brains of COVID-19 patients.
JOURNAL OF NEUROPATHOLOGY AND EXPERIMENTAL NEUROLOGY
(2022)
Article
Medical Laboratory Technology
Ruben Yiqi Luo, Carolyn Wong, James Qiangwei Xia, Bertil E. Glader, Run-Zhang Shi, James L. Zehnder
Summary: The use of neutral-coating capillary electrophoresis coupled with high-resolution mass spectrometry has been demonstrated as an effective method for the identification of hemoglobin variants, providing significant advantages over conventional approaches.
CLINICAL CHEMISTRY
(2023)
Article
Virology
Jaydee Sereewit, Nicole A. P. Lieberman, Hong Xie, Shah A. K. Mohamed Bakhash, B. Ethan Nunley, Benjamin Chung, Margaret G. Mills, Pavitra Roychoudhury, Alexander L. Greninger
Summary: Using viral whole genome sequencing, the study identified gene inactivating mutations in monkeypox virus. These mutations may be a result of selective pressure in humans, and they pose limitations in therapeutics and diagnostic testing.
Article
Multidisciplinary Sciences
Jennifer Cable, Siddharth Balachandran, Lisa P. Daley-Bauer, Arjun Rustagi, Ferrin Antony, Justin J. Frere, Jamie Strampe, Katherine Kedzierska, Judy L. Cannon, Maureen A. McGargill, Daniela Weiskopf, Robert C. Mettelman, Julia Niessl, Paul G. Thomas, Bryan Briney, Sophie A. Valkenburg, Jesse D. Bloom, Pamela J. Bjorkman, Sho Iketani, C. Garrett Rappazzo, Chelsea M. Crooks, Kali F. Crofts, Stefan Pohlmann, Florian Krammer, Andrea J. Sant, Gary J. Nabel, Stacey Schultz-Cherry
Summary: Millions of people are infected by viruses each year, which pose ongoing threats to global public health. To develop more effective tools against viruses, a comprehensive understanding of the virus itself and our immune system's response to infection is necessary. The Keystone symposium Viral Immunity: Basic Mechanisms and Therapeutic Applications, held from June 29 to July 2, 2022, brought together researchers to discuss these topics, and this report provides concise summaries from several presenters at the symposium.
ANNALS OF THE NEW YORK ACADEMY OF SCIENCES
(2023)
Meeting Abstract
Hematology
Alicia Palomino Mosquera, Hitomi Hosoya, Michael C. Jin, Mohammad Shahrokh Esfahani, Joseph Schroers-Martin, Brian Sworder, Chih Long Liu, Elizabeth Spiteri, Yasodha Natkunam, James L. Zehnder, Henning Stehr, David M. Kurtz, Ash A. Alizadeh
Article
Cell Biology
Madeline J. Lee, Michelle W. Leong, Arjun Rustagi, Aimee Beck, Leiping Zeng, Susan Holmes, Lei S. Qi, Catherine A. Blish
Summary: SARS-CoV-2 evades direct killing by natural killer (NK) cells by downregulating ligands for the activating receptor NKG2D. The viral protein Nsp1 mediates the downregulation of NKG2D ligands and alone is sufficient to confer resistance to NK cell killing.
Article
Immunology
Jason D. Goldman, Kai Wang, Katharina Roltgen, Sandra C. A. Nielsen, Jared C. Roach, Samia N. Naccache, Fan Yang, Oliver F. Wirz, Kathryn E. Yost, Ji-Yeun Lee, Kelly Chun, Terri Wrin, Christos J. Petropoulos, Inyoul Lee, Shannon Fallen, Paula M. Manner, Julie A. Wallick, Heather A. Algren, Kim M. Murray, Jennifer Hadlock, Daniel Chen, Chengzhen L. Dai, Dan Yuan, Yapeng Su, Joshua Jeharajah, William R. Berrington, George P. Pappas, Sonam T. Nyatsatsang, Alexander L. Greninger, Ansuman T. Satpathy, John S. Pauk, Scott D. Boyd, James R. Heath
Summary: Recovery from COVID-19 does not guarantee immunity, as reinfection with a different strain can occur. In this study, we present a case of reinfection with a variant strain carrying the D614G mutation. By analyzing antibodies, B cells, and T cells, we provide evidence of adaptive immunity during reinfection. Our findings have implications for vaccine programs and establishing benchmarks for protection against SARS-CoV-2 reinfection.
Article
Virology
Linhui Hao, Tien-Ying Hsiang, Ronit R. Dalmat, Renee Ireton, Jennifer F. Morton, Caleb Stokes, Jason Netland, Malika Hale, Chris Thouvenel, Anna Wald, Nicholas M. Franko, Kristen Huden, Helen Y. Chu, Alex Sigal, Alex L. Greninger, Sasha Tilles, Lynn K. Barrett, Wesley C. Van Voorhis, Jennifer Munt, Trevor Scobey, Ralph S. Baric, David J. Rawlings, Marion Pepper, Paul K. Drain, Michael Gale
Summary: New variants of SARS-CoV-2 continue to emerge and evade immunity. Convalescence from the ancestral virus provides limited protection against variants. Vaccination enhances immunity against viral variants, but the protection is weaker against Omicron BA.1, and a three-dose vaccine regimen provides significantly better protection against it compared to a two-dose.
Review
Hematology
James L. Zehnder, James B. Bussel, Nichola Cooper
Summary: Patients with refractory immune thrombocytopenia (rITP) have increased morbidity and mortality. Limited understanding of the refractory cause and lack of markers for treatment options. Genetic predisposition and clonal expansion of cytotoxic T cells may contribute to the pathogenesis of rITP.
BRITISH JOURNAL OF HAEMATOLOGY
(2023)
Article
Pathology
Fei Fei, Christian A. Kunder, Chandler Ho, James L. Zehnder, Gianna Tomasello, Eula Fung, Carlos J. Suarez
Summary: This study investigates the feasibility and utility of an RNA-based NGS fusion panel for solid tumors. The results demonstrate that the fusion panel can improve the accuracy of diagnosis for solid tumors and provide further clarification for the initial diagnosis. Additionally, the study finds that the overall cellularity of the tested specimen influences the success of the testing process.
AMERICAN JOURNAL OF CLINICAL PATHOLOGY
(2023)
Article
Immunology
Evann E. Hilt, James Boocock, Marisol Trejo, Catherine Q. Le, Longhua Guo, Yi Zhang, Laila Sathe, Valerie A. Arboleda, Yi Yin, Joshua S. Bloom, Pin-Chieh Wang, Joann G. Elmore, Leonid Kruglyak, Lasata Shrestha, Shah A. Mohamed Bakhash, Michelle Lin, Hong Xie, Meei-Li Huang, Pavitra Roychoudhury, Alexander Greninger, Sukantha Chandrasekaran, Shangxin Yang, Omai B. Garner
Summary: This study found evidence of the early community spread of SARS-CoV-2 in the Los Angeles area, well before widespread diagnostic testing was being conducted in early 2020. The virus was introduced into the area from both domestic and international sources as early as January.
CLINICAL INFECTIOUS DISEASES
(2022)
