Article
Virology
Merlin Jayalal Lawrence Panchali, Choon-Mee Kim, Jun-Won Seo, Da-Young Kim, Na-Ra Yun, Dong-Min Kim
Summary: This study examined the presence of SARS-CoV-2 RNAemia in COVID-19 patients and found that it was highest in critical and fatal cases, suggesting that it is a predictive risk factor for disease severity and mortality.
Article
Immunology
Nikhil Ram-Mohan, David Kim, Elizabeth J. Zudock, Marjan M. Hashemi, Kristel C. Tjandra, Angela J. Rogers, Catherine A. Blish, Kari C. Nadeau, Jennifer A. Newberry, James Quinn, Ruth O'Hara, Euan Ashley, Hien Nguyen, Lingxia Jiang, Paul Hung, Andra L. Blomkalns, Samuel Yang
Summary: Measurement of SARS-CoV-2 RNA from the plasma of COVID-19 patients using digital polymerase chain reaction can predict disease severity, clinical deterioration, and extrapulmonary complications. It may guide patient triage and management effectively.
CLINICAL INFECTIOUS DISEASES
(2022)
Article
Immunology
Jana L. Jacobs, William Bain, Asma Naqvi, Brittany Staines, Priscila M. S. Castanha, Haopu Yang, Valerie F. Boltz, Simon Barratt-Boyes, Ernesto T. A. Marques, Stephanie L. Mitchell, Barbara Methe, Tolani F. Olonisakin, Ghady Haidar, Thomas W. Burke, Elizabeth Petzold, Thomas Denny, Chris W. Woods, Bryan J. McVerry, Janet S. Lee, Simon C. Watkins, Claudette M. St Croix, Alison Morris, Mary F. Kearney, Mark S. Ladinsky, Pamela J. Bjorkman, Georgios D. Kitsios, John W. Mellors
Summary: This study found that SARS-CoV-2 vRNA was detected in the plasma of COVID-19 patients, with the highest rates in ICU patients. Higher levels of vRNA were associated with more severe disease, patient outcomes, and specific inflammatory biomarkers.
CLINICAL INFECTIOUS DISEASES
(2022)
Article
Multidisciplinary Sciences
Qin Liu, Qi Su, Fen Zhang, Hein M. Tun, Joyce Wing Yan Mak, Grace Chung-Yan Lui, Susanna So Shan Ng, Jessica Y. L. Ching, Amy Li, Wenqi Lu, Chenyu Liu, Chun Pan Cheung, David S. C. Hui, Paul K. S. Chan, Francis Ka Leung Chan, Siew C. Ng
Summary: By integrating clinical features and multi-omics data, the authors identified specific gut microbiome patterns associated with disease severity and development of post-acute COVID-19 syndrome. These findings highlight the potential utility of host phenotype and multi-kingdom microbiota profiling as a prognostic tool for patients with COVID-19.
NATURE COMMUNICATIONS
(2022)
Article
Virology
Hitoshi Kawasuji, Yoshitomo Morinaga, Hideki Tani, Yoshihiro Yoshida, Yusuke Takegoshi, Makito Kaneda, Yushi Murai, Kou Kimoto, Akitoshi Ueno, Yuki Miyajima, Yasutaka Fukui, Miyuki Kimura, Hiroshi Yamada, Ippei Sakamaki, Yoshihiro Yamamoto
Summary: This study found a relatively high proportion of SARS-CoV-2 RNAemia in COVID-19 patients and its association with clinical severity, suggesting the potential utility of combining serum testing with NP tests as a prognostic indicator for COVID-19. Among patients with RNAemia, the viral loads of NP swabs were correlated with disease severity and mortality, with higher quality than each separate test.
JOURNAL OF MEDICAL VIROLOGY
(2022)
Article
Immunology
Nikhil Ram-Mohan, David Kim, Angela J. Rogers, Catherine A. Blish, Kari C. Nadeau, Andra L. Blomkalns, Samuel Yang
Summary: Determinants of Post-Acute Sequelae of COVID-19 are not known. This study found that the presence of viral RNA in blood (RNAemia) at presentation successfully predicted the occurrence of post-acute symptoms, independent of patient demographics, disease severity, and length of symptoms.
OPEN FORUM INFECTIOUS DISEASES
(2022)
Article
Immunology
Nhu Ngoc Nguyen, Linda Houhamdi, Van Thuan Hoang, Jeremy Delerce, Lea Delorme, Philippe Colson, Philippe Brouqui, Pierre-Edouard Fournier, Didier Raoult, Philippe Gautret
Summary: The reinfection rate of SARS-CoV-2 is low, and the severity of the first and second episodes of infection is similar. The severity of the second episode of COVID-19 is not higher than that of the first infection, even for patients with antibodies.
EMERGING MICROBES & INFECTIONS
(2022)
Article
Multidisciplinary Sciences
Rosa Costa, Juan Alberola, Beatriz Olea, Roberto Gozalbo-Rovira, Estela Gimenez, Enric Cuevas-Ferrando, Ignacio Torres, Eliseo Albert, Nieves Carbonell, Jose Ferreres, Gloria Sanchez, Jesus Rodriguez-Diaz, Maria Luisa Blasco, David Navarro
Summary: A combined kinetic analysis was conducted on 71 critically ill COVID-19 patients to study plasma RNAemia, N-antigenemia, and virus-specific antibodies. The study found a correlation between viral components and viral load in the upper respiratory tract, and observed a parallel decrease in antibody levels with increasing RNAemia and N-antigenemia levels.
SCIENTIFIC REPORTS
(2022)
Article
Medicine, General & Internal
Mark W. Tenforde, Wesley H. Self, Katherine Adams, Manjusha Gaglani, Adit A. Ginde, Tresa McNeal, Shekhar Ghamande, David J. Douin, H. Keipp Talbot, Jonathan D. Casey, Nicholas M. Mohr, Anne Zepeski, Nathan Shapiro, Kevin W. Gibbs, D. Clark Files, David N. Hager, Arber Shehu, Matthew E. Prekker, Heidi L. Erickson, Matthew C. Exline, Michelle N. Gong, Amira Mohamed, Daniel J. Henning, Jay S. Steingrub, Ithan D. Peltan, Samuel M. Brown, Emily T. Martin, Arnold S. Monto, Akram Khan, Catherine L. Hough, Laurence W. Busse, Caitlin C. Ten Lohuis, Abhijit Duggal, Jennifer G. Wilson, Alexandra June Gordon, Nida Qadir, Steven Y. Chang, Christopher Mallow, Carolina Rivas, Hilary M. Babcock, Jennie H. Kwon, Natasha Halasa, James D. Chappell, Adam S. Lauring, Carlos G. Grijalva, Todd W. Rice, Ian D. Jones, William B. Stubblefield, Adrienne Baughman, Kelsey N. Womack, Jillian P. Rhoads, Christopher J. Lindsell, Kimberly W. Hart, Yuwei Zhu, Samantha M. Olson, Miwako Kobayashi, Jennifer R. Verani, Manish M. Patel
Summary: This study evaluated the association between mRNA COVID-19 vaccines and COVID-19 hospitalization, as well as disease progression to critical illness among hospitalized patients. The results showed that vaccination with mRNA COVID-19 vaccines significantly decreased the likelihood of COVID-19 hospitalization and disease progression to death or mechanical ventilation.
JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION
(2021)
Article
Immunology
Matthew K. Hensley, William G. Bain, Jana Jacobs, Sham Nambulli, Urvi Parikh, Anthony Cillo, Brittany Staines, Amy Heaps, Michele D. Sobolewski, Linda J. Rennick, Bernard J. C. Macatangay, Cynthia Klamar-Blain, Georgios D. Kitsios, Barbara Methe, Ashwin Somasundaram, Tullia C. Bruno, Carly Cardello, Feng Shan, Creg Workman, Prabir Ray, Anuradha Ray, Janet Lee, Rahil Sethi, William E. Schwarzmann, Mark S. Ladinsky, Pamela J. Bjorkman, Dario A. Vignali, W. Paul Duprex, Mounzer E. Agha, John W. Mellors, Kevin D. McCormick, Alison Morris, Ghady Haidar
Summary: This study reports a case of a recipient of chimeric antigen receptor-modified T-cell therapy who developed severe COVID-19 with prolonged viral replication and evolution, along with minimal immune response, suggesting the possibility of prolonged transmission from immunosuppressed patients.
CLINICAL INFECTIOUS DISEASES
(2021)
Article
Multidisciplinary Sciences
Zhongshan Cheng, Yi Cai, Ke Zhang, Jingxuan Zhang, Hongsheng Gui, Yu-Si Luo, Jie Zhou, Brian DeVeale
Summary: Through an integrative analysis of two genome-wide association studies, we identified ancestry-linked genetic risk variants associated with COVID-19 hospitalization and identified four more frequent single nucleotide polymorphisms in COVID-19-hospitalized patients with non-European ancestry. Among them, the COVID-19 risk SNP rs16831827 showed the largest difference in minor allele frequency (MAF) between populations with African and European ancestry and also exhibited higher MAF in hospitalized COVID-19 patients with mixed ancestry (odds ratio [OR] = 1.20, 95% CI: 1.10-1.30) and entirely African ancestry (OR = 1.30, 95% CI: 1.02-1.67). rs16831827 is an expression quantitative trait locus of MAP3K19, which is highly expressed in ciliated tissues including lungs, and its reduced expression may increase the risk of severe COVID-19.
Article
Multidisciplinary Sciences
Manon Ragonnet-Cronin, Olivia Boyd, Lily Geidelberg, David Jorgensen, Fabricia F. Nascimento, Igor Siveroni, Robert A. Johnson, Marc Baguelin, Zulma M. Cucunuba, Elita Jauneikaite, Swapnil Mishra, Oliver J. Watson, Neil Ferguson, Anne Cori, Christl A. Donnelly, Erik Volz
Summary: The study indicates that early implementation of strong non-pharmaceutical interventions can reduce COVID-19 morbidity and mortality. The time elapsed between epidemic origin and intervention is associated with epidemic severity and explains part of the variance in reported deaths. Delay in implementing interventions resulted in more severe epidemics.
NATURE COMMUNICATIONS
(2021)
Article
Immunology
Rafael Luis Luporini, Henrique Pott-Junior, Maria Carolina B. Di Medeiros Leal, Alex Castro, Antonio Gilberto Ferreira, Marcia Regina Cominetti, Fernanda de Freitas Anibal
Summary: The study found that serum phenylalanine levels are positively correlated with disease severity in COVID-19 patients, independent of inflammatory cytokines. Patients with mild disease have lower serum phenylalanine levels in the early stages of the disease.
INTERNATIONAL IMMUNOPHARMACOLOGY
(2021)
Article
Virology
Fainareti N. Zervou, Ping Louie, Anna Stachel, Ioannis M. Zacharioudakis, Yadira Ortiz-Mendez, Kristen Thomas, Maria E. Aguero-Rosenfeld
Summary: The timing of antibody detection after viral infection varies, with IgA being the predominant immunoglobulin in early disease and IgG remaining detectable up to two months after infection.
JOURNAL OF MEDICAL VIROLOGY
(2021)
Review
Microbiology
Tiago Bertola Lobato, Matheus Gennari-Felipe, Janaina Ribeiro Barbosa Pauferro, Ilana Souza Correa, Beatriz Ferreira Santos, Beatriz Belmiro Dias, Joao Carlos de Oliveira Borges, Camila Soares dos Santos, Elvirah Samantha de Sousa Santos, Maria Janaina Leite de Araujo, Liliane Araujo Ferreira, Sara Araujo Pereira, Tamires Duarte Afonso Serdan, Adriana Cristina Levada-Pires, Elaine Hatanaka, Leandro Borges, Maria Fernanda Cury-Boaventura, Marco Aurelio Ramirez Vinolo, Tania Cristina Pithon-Curi, Laureane Nunes Masi, Rui Curi, Sandro Massao Hirabara, Renata Gorjao
Summary: This review explores the impact of obesity and type 2 diabetes on metabolic changes in leukocytes during SARS-CoV-2 infection, and highlights that obese and diabetic patients are at higher risk of worse prognosis, possibly due to the occurrence of cytokine storms.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Chemistry, Analytical
Nobuyuki Futai, Yuto Fukazawa, Tomohiro Kashiwagi, Shogo Tamaki, Riho Sakai, Catherine A. Hogan, Kanagavel Murugesan, Ashwin Ramachandran, Niaz Banaei, Juan G. Santiago
Summary: This study presents a method for the high-efficiency separation and extraction of short cfDNA fragments, using a millimeter-scale fluidic device to extract the fragments into solid agarose gel slabs from liquid human plasma samples. The method demonstrates high sensitivity in cfDNA detection.
ANALYTICA CHIMICA ACTA
(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
Virology
Lu M. Yang, Cristina Costales, Muthukumar Ramanathan, Philip L. Bulterys, Kanagavel Murugesan, Joseph Schroers-Martin, Ash A. Alizadeh, Scott D. Boyd, Janice M. Brown, Kari C. Nadeau, Sruti S. Nadimpalli, Aileen X. Wang, Stephan Busque, Benjamin A. Pinsky, Niaz Banaei
Summary: Humoral and cellular immune responses to SARS-CoV-2 vaccination differ among immunosuppressed patient groups. Factors associated with poor humoral response after primary vaccination include anti-CD20 monoclonal antibodies, S1P receptor modulators, mycophenolate, and B cell lymphoma, while S1P receptor modulators and mycophenolate are associated with poor cellular response. Some patients with poor humoral response to primary vaccination had significantly higher response after booster dose.
JOURNAL OF CLINICAL VIROLOGY
(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
Microbiology
Jacky Lu, Kanagavel Murugesan, Fiona Senchyna, Indre Budvytiene, Niaz Banaei
Summary: This study evaluated the sensitivity and specificity of QuantiFERON-TB Gold (QFT) in tuberculosis (TB) and non-tuberculous mycobacteria (NTM) patients. The results showed that QFT had a sensitivity of 78.0% in TB patients, with 86.0% in immunocompetent patients and 69.2% in immunocompromised patients. The specificity of QFT in NTM patients was 76.1%, but after excluding NTM patients with risk factors for latent TB infection, the specificity increased to 94.4%.
JOURNAL OF CLINICAL MICROBIOLOGY
(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.