Article
Environmental Sciences
Aikaterini Galani, Athina Markou, Lampros Dimitrakopoulos, Aikaterini Kontou, Marios Kostakis, Vasileios Kapes, Marios A. Diamantopoulos, Panagiotis G. Adamopoulos, Margaritis Avgeris, Evi Lianidou, Andreas Scorilas, Dimitrios Paraskevis, Sotirios Tsiodras, Meletios-Athanasios Dimopoulos, Nikolaos Thomaidis
Summary: Wastewater analysis is an attractive alternative for quantifying and profiling the variants of SARS-CoV-2. RT-qPCR assays can monitor infection dynamics, while NGS provides evidence for the presence of existing or emerging variants. The study reports the infection dynamics in Attica since June 1st, 2021, and monitors omicron and delta variants using novel Nested-Seq and RT-PCR methods.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Engineering, Environmental
Albert Carcereny, Adan Martinez-Velazquez, Albert Bosch, Ana Allende, Pilar Truchado, Jenifer Cascales, Jesus L. Romalde, Marta Lois, David Polo, Gloria Sanchez, Alba Perez-Cataluna, Azahara Diaz-Reolid, Andres Anton, Josep Gregori, Damir Garcia-Cehic, Josep Quer, Margarita Palau, Cristina Gonzalez Ruano, Rosa M. Pinto, Susana Guix
Summary: The study developed a RT-qPCR assay to track the spread of SARS-CoV-2 variants in Spain, finding that the B.1.1.7 variant was detected earlier in wastewater surveillance than in clinical reports, showing good correlation with clinical data.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Nikita D. Yolshin, Andrey B. Komissarov, Kirill V. Varchenko, Tamila D. Musaeva, Artem V. Fadeev, Dmitry A. Lioznov
Summary: Whole genome sequencing is the best tool to track virus evolution and variant spread, but its ability to analyze a large number of samples is still inferior to qPCR. Advanced qPCR methods are needed for epidemiological and clinical research to quickly and affordably identify emerging variants and collect data on their spread. This study designed a one-step RT-qPCR assay for multiplex detection of the Omicron lineage, which showed high sensitivity and specificity and was cross-validated by WGS.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Eduarda Carvalho-Correia, Carla Calcada, Fernando Branca, Nuria Estevez-Gomez, Loretta De Chiara, Nair Varela, Pilar Gallego-Garcia, David Posada, Hugo Sousa, Joao Sousa, Maria Isabel Veiga, Nuno S. Osorio
Summary: This study developed a new multiplex RT-qPCR method (OmniSARS2) based on SARS-CoV-2 genomic knowledge for rapid and efficient virus detection, showing high sensitivity and specificity without cross-reactivity with other coronaviruses or common pathogens.
Review
Biotechnology & Applied Microbiology
Praveen Rai, Ballamoole Krishna Kumar, Vijaya Kumar Deekshit, Indrani Karunasagar, Iddya Karunasagar
Summary: COVID-19 is a disease caused by SARS-CoV-2 that has spread globally, requiring collaborative efforts for accurate diagnosis and prevention. While RT-qPCR detection is considered the gold standard for early virus detection, challenges such as technical complexity and limited applicability have led to the development of portable POC tests.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Editorial Material
Biochemistry & Molecular Biology
Stephen Bustin, Reinhold Mueller, Gregory Shipley, Tania Nolan
Summary: This commentary aims to clarify the true strengths and limitations of molecular testing technology, especially RT-qPCR, and to address and help stop the unfounded speculation surrounding its use.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Environmental Sciences
Diego A. Padilla-Reyes, Mario Moises Alvarez, Abrahan Mora, Pabel A. Cervantes-Aviles, Manish Kumar, Frank J. Loge, Jurgen Mahlknecht
Summary: Wastewater-based epidemiology is an effective and cost-effective method for monitoring the spread of SARS-CoV-2, providing early warning of outbreaks in the population. The study found a correlation between viral load in wastewater and clinical cases, with wastewater surveillance able to provide a 2-7 day early warning. The detection rate of SARS-CoV-2 in wastewater was relatively low, with one detection for every 14,300 reported new cases. Prevalence estimates during the study period ranged from 0.02% to 4.6%. The application of wastewater-based epidemiology for COVID-19 surveillance is generally consistent and feasible, with room for improvement.
ENVIRONMENTAL RESEARCH
(2022)
Article
Virology
Nanako Matsuzaki, Yuta Orihara, Masahiro Kodana, Yutaro Kitagawa, Masaru Matsuoka, Rieko Kawamura, Shinichi Takeuchi, Kazuo Imai, Norihito Tarumoto, Shigefumi Maesaki, Takuya Maeda
Summary: The VITROS(R) antigen detection test was found to be satisfactory for diagnosing contagious COVID-19 patients in the clinical setting. Additionally, the VITROS(R) test demonstrated reliable detection performance when using nasopharyngeal swab specimens with lower Ct values.
JOURNAL OF MEDICAL VIROLOGY
(2021)
Article
Environmental Sciences
G. La Rosa, M. Iaconelli, C. Veneri, P. Mancini, G. Bonanno Ferraro, D. Brandtner, L. Lucentini, L. Bonadonna, M. Rossi, M. Grigioni, S. A. R. I. network SARI network, E. Suffredini
Summary: This study developed a real-time RT-PCR assay for detecting the Omicron variant of SARS-CoV-2 and found that the variant spread rapidly based on the analysis of sewage samples collected in Italy. The study confirmed the effectiveness of sewage monitoring in tracking the spread of the virus.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Virology
Reza Soleimani, Corentin Deckers, Te-Din Huang, Pierre Bogaerts, Stephanie Evrard, Isaline Wallemme, Boutaina Habib, Pauline Rouze, Olivier Denis
Summary: This study evaluated the performances of two rapid antigen testing devices in detecting SARS-CoV-2 in nasopharyngeal samples, showing relatively high sensitivity, especially with lower cycle threshold values, and 100% specificity for both devices.
JOURNAL OF MEDICAL VIROLOGY
(2021)
Review
Chemistry, Multidisciplinary
Hossein Rahimi, Marziyeh Salehiabar, Murat Barsbay, Mohammadreza Ghaffarlou, Taras Kavetskyy, Ali Sharafi, Soodabeh Davaran, Subhash C. Chauhan, Hossein Danafar, Saeed Kaboli, Hamed Nosrati, Murali M. Yallapu, Joao Conde
Summary: The emergence of COVID-19 in 2019 has become a global pandemic, leading to serious concerns worldwide. The development of CRISPR-based diagnostic systems has reshaped molecular diagnosis and inspired researchers to develop more efficient methods for COVID-19 detection and treatment. The advantages of CRISPR-based COVID-19 diagnostic systems include high detection speed, sensitivity, precision, portability, and the elimination of the need for specialized laboratory equipment.
Review
Chemistry, Analytical
Sulaiman Alsalameh, Khalid Alnajjar, Tariq Makhzoum, Noor Al Eman, Ismail Shakir, Tanveer Ahmad Mir, Khaled Alkattan, Raja Chinnappan, Ahmed Yaqinuddin
Summary: This article reviews the recent advances and advantages of using biosensors for COVID-19 diagnosis. Traditional methods have limitations, while biosensors are sensitive, specific, rapid, and user-friendly, with the potential to go beyond traditional standards in diagnostics.
Review
Medicine, General & Internal
Debashis Dutta, Sarah Naiyer, Sabanaz Mansuri, Neeraj Soni, Vandana Singh, Khalid Hussain Bhat, Nishant Singh, Gunjan Arora, M. Shahid Mansuri
Summary: This article reviews the natural history, pathology, molecular biology, and efficient diagnostic methods of COVID-19, with a focus on the gold standard RT-qPCR method for COVID-19 diagnosis. It emphasizes the importance of the COVID-19 pandemic and aims to raise awareness about the disease and its management.
Review
Microbiology
Jessica A. Plante, Brooke M. Mitchell, Kenneth S. Plante, Kari Debbink, Scott C. Weaver, Vineet D. Menachery
Summary: Despite the development of vaccines, COVID-19 caused by SARS-CoV-2 continues to be a global concern due to the emergence of new variants, raising worries about increased spread and potential impacts on immunity.
CELL HOST & MICROBE
(2021)
Article
Engineering, Environmental
Xiaoqing Xu, Yu Deng, Xiawan Zheng, Shuxian Li, Jiahui Ding, Yu Yang, Hei Yin On, Rong Yang, Ho-Kwong Chui, Chung In Yau, Hein Min Tun, Alex W. H. Chin, Leo L. M. Poon, Malik Peiris, Gabriel M. Leung, Tong Zhang
Summary: Sewage surveillance is a valuable supplementary tool for COVID-19 control, and the interpretation of sewage data is crucial. This study compared the performance of seven commonly used primer-probe sets in RT-qPCR and evaluated their usefulness in a sewage surveillance program in Hong Kong. The results showed that the N1 primer-probe set was the best in detecting signals from new cases and convalescent patients in the community.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2022)
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
Genetics & Heredity
Yiran E. Liu, Sirle Saul, Aditya Manohar Rao, Makeda Lucretia Robinson, Olga Lucia Agudelo Rojas, Ana Maria Sanz, Michelle Verghese, Daniel Solis, Mamdouh Sibai, Chun Hong Huang, Malaya Kumar Sahoo, Rosa Margarita Gelvez, Nathalia Bueno, Maria Isabel Estupinan Cardenas, Luis Angel Villar Centeno, Elsa Marina Rojas Garrido, Fernando Rosso, Michele Donato, Benjamin A. Pinsky, Shirit Einav, Purvesh Khatri
Summary: The study integrated multiple datasets and developed an XGBoost model based on 8 genes, which accurately predicted the progression of severe dengue. The model performed well in predicting during the early febrile stage.
Letter
Microbiology
ChunHong Huang, Malaya K. Sahoo, Michelle Verghese, Mamdouh Sibai, Daniel Solis, Kenji O. Mfuh, Jason Kurzer, Catherine A. Hogan, Thuy A. Doan, Benjamin A. Pinsky
MICROBIOLOGY SPECTRUM
(2022)
Article
Medicine, General & Internal
Aslam Khan, Caroline Ichura, Hannah Wang, Izabela Rezende, Malaya K. Sahoo, ChunHong Huang, Daniel Solis, Mamdouh Sibai, Fumiko Yamamoto, Sindiso Nyathi, Bethel Bayrau, Benjamin A. Pinsky, A. Desiree LaBeaud
Summary: This study aimed to characterize the clinical severity and host factors associated with disease by different SARS-CoV-2 variants and evaluate if there are differences in disease severity caused by circulating variants. The results indicated that the delta variant was associated with severe/critical disease compared to other studied variants. The model also revealed that underlying respiratory disease and diabetes were risk factors for progression to severe disease.
FRONTIERS IN MEDICINE
(2022)
Article
Pharmacology & Pharmacy
Marwah Karim, Sirle Saul, Luca Ghita, Malaya Kumar Sahoo, Chengjin Ye, Nishank Bhalla, Chieh-Wen Lo, Jing Jin, Jun-Gyu Park, Belen Martinez-Gualda, Michael Patrick East, Gary L. Johnson, Benjamin A. Pinsky, Luis Martinez-Sobrido, Christopher R. M. Asquith, Aarthi Narayanan, Steven De Jonghe, Shirit Einav
Summary: This study investigates the functional relevance of NAKs in SARS-CoV-2 infection and demonstrates that pharmacological inhibition of NAKs can be a potential approach to treat COVID-19.
ANTIVIRAL RESEARCH
(2022)
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
Biochemistry & Molecular Biology
Jacob A. Miller, Malaya K. Sahoo, Fumiko Yamamoto, ChunHong Huang, Hannah Wang, James L. Zehnder, Quynh-Thu Le, Benjamin A. Pinsky
Summary: By detecting EBV BALF2 gene polymorphisms in plasma, screening for EBV-associated nasopharyngeal carcinoma can be improved by reducing false positives and repeated testing. There is a significant association between BALF2 haplotypes and NPC, which can be leveraged to develop screening programs that improve screening accuracy.
Article
Virology
Malaya K. Sahoo, ChunHong Huang, Mamdouh Sibai, Daniel Solis, Benjamin A. Pinsky
Summary: Calibration to the WHO standard improves inter-assay agreement and provides more reliable estimation of viral burden.
JOURNAL OF CLINICAL VIROLOGY
(2022)
Article
Virology
Philip L. Tzou, Kaiming Tao, Malaya K. Sahoo, Sergei L. Kosakovsky Pond, Benjamin A. Pinsky, Robert W. Shafer
Summary: Sierra SARS-CoV-2 is a program designed to analyze viral genomic data, helping laboratories assess sequence quality, select mutation detection thresholds, and report on the potential clinical significance of mutations in the targets of antiviral therapy.
JOURNAL OF CLINICAL VIROLOGY
(2022)
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
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)