COVID-19s
Abstract
Background: Estimates of seroprevalence to SARS-CoV-2 vary widely and may influence vaccination response. We ascertained IgG levels across a single US metropolitan site, Chicago, from June 2020 through December 2020. Methods: Participants (n=7935) were recruited through electronic advertising and received materials for a self-sampled dried blood spot assay through the mail or a minimal contact in person method. IgG to the receptor binding domain of SARS-CoV-2 was measured using an established highly sensitive and highly specific assay. Results: Overall seroprevalence was 17.9%, with no significant difference between method of contact. Only 2.5% of participants reported having had a diagnosis of COVID-19 based on virus detection, consistent with a 7-fold greater exposure to SARS-CoV-2 measured by serology than detected by viral testing. The range of IgG level observed in seropositive participants from this community survey overlapped with the range of IgG levels associated with COVID-19 cases having a documented positive PCR positive test. From a subset of those who participated in repeat testing, half of seropositive individuals retained detectable antibodies for 3-4 months. Conclusions: Quantitative IgG measurements with a highly specific and sensitive assay indicate more widespread exposure to SARS-CoV-2 than observed by viral testing. The range of IgG concentration produced from these asymptomatic exposures is similar to IgG levels occurring after documented non-hospitalized COVID-19, which is considerably lower than that produced from hospitalized COVID-19 cases. The differing ranges of IgG response, coupled with the rate of decay of antibodies, may influence response to subsequent viral exposure and vaccine.
Authors
Alexis R. Demonbreun, Thomas W. McDade, Lorenzo L. Pesce, Lauren A. Vaught, Nina L. Reiser, Elena Bogdanovic, Matthew P. Velez, Ryan R. Hsieh, Lacy M. Simons, Rana Saber, Daniel T. Ryan, Michael G. Ison, Judd F. Hultquist, John T. Wilkins, Richard T. D'Aquila, Brian Mustanski, Elizabeth M. McNally
Abstract
The early COVID-19 pandemic was characterized by rapid global spread. In Maryland and Washington, DC, United States, more than 2500 cases were reported within 3 weeks of the first COVID-19 detection in March 2020. We aimed to use genomic sequencing to understand the initial spread of SARS-CoV-2 — the virus that causes COVID-19 — in the region. We analyzed 620 samples collected from the Johns Hopkins Health System during March 11–31, 2020, comprising 28.6% of the total cases in Maryland and Washington, DC. From these samples, we generated 114 complete viral genomes. Analysis of these genomes alongside a subsampling of over 1000 previously published sequences showed that the diversity in this region rivaled global SARS-CoV-2 genetic diversity at that time and that the sequences belong to all of the major globally circulating lineages, suggesting multiple introductions into the region. We also analyzed these regional SARS-CoV-2 genomes alongside detailed clinical metadata and found that clinically severe cases had viral genomes belonging to all major viral lineages. We conclude that efforts to control local spread of the virus were likely confounded by the number of introductions into the region early in the epidemic and the interconnectedness of the region as a whole.
Authors
Peter M. Thielen, Shirlee Wohl, Thomas Mehoke, Srividya Ramakrishnan, Melanie Kirsche, Oluwaseun Falade-Nwulia, Nídia S. Trovão, Amanda Ernlund, Craig Howser, Norah Sadowski, C. Paul Morris, Mark Hopkins, Matthew Schwartz, Yunfan Fan, Victoria Gniazdowski, Justin Lessler, Lauren Sauer, Michael C. Schatz, Jared D. Evans, Stuart C. Ray, Winston Timp, Heba H. Mostafa
Abstract
Pre-existing cross-reactivity to SARS-CoV-2 may occur in absence of prior viral exposure. However, this has been difficult to quantify at the population level due to a lack of reliably defined seroreactivity thresholds. Using an orthogonal antibody testing approach, we estimated that ~0.6% of non-triaged adults from the greater Vancouver area, Canada between May 17th and June 19th 2020 showed clear evidence of a prior SARS-CoV-2 infection, after adjusting for false-positive and false-negative test results. Using a highly sensitive multiplex assay and positive/negative thresholds established in infants in whom maternal antibodies have waned, we determine that more than 90% of uninfected adults showed antibody reactivity against the spike, receptor-binding domain (RBD), N-terminal domains (NTD) or the nucleocapsid (N) protein from SARS-CoV-2. This sero-reactivity was evenly distributed across age and sex, correlated with circulating coronaviruses reactivity, and was partially outcompeted by soluble circulating coronaviruses’ spike. Using a custom SARS-CoV-2 peptide mapping array, we found that this antibody reactivity broadly mapped to spike, and to conserved non-structural viral proteins. We conclude that most adults display pre-existing antibody cross-reactivity against SARS-CoV-2, which further supports investigation of how this may impact the clinical severity of COVID-19 or SARS-CoV-2 vaccine responses.
Authors
Abdelilah Majdoubi, Christina Michalski, Sarah E. O’Connell, Sarah Dada, Sandeep R. Narpala, Jean P. Gelinas, Disha Mehta, Claire Cheung, Dirk F.H. Winkler, Manjula Basappa, Aaron C. Liu, Matthias Görges, Vilte E. Barakauskas, Michael A. Irvine, Jennifer Mehalko, Dominic Esposito, Inna Sekirov, Agatha N. Jassem, David M. Goldfarb, Steven Pelech, Daniel C. Douek, Adrian B. McDermott, Pascal M Lavoie
Abstract
Introduction: Coronavirus 2019 (COVID-19) clinical course is heterogeneous, ranging from mild to severe multi-organ failure and death. In this study, we analyzed cell-free DNA (cfDNA) as a biomarker of injury to define the sources of tissue injury that contribute to such different trajectories. Methods: We conducted a multi-center prospective cohort study to enroll COVID-19 patients and collect plasma samples. Plasma cfDNA was subject to bisulfite sequencing. A library of tissue-specific DNA methylation signatures was used to analyze sequence reads to quantitate cfDNA from different tissue types. We then determined the correlation of tissue-specific cfDNA measures to COVID-19 outcomes. Similar analyses was performed for healthy controls and a comparator group of patients with respiratory syncytial virus and influenza. Results: We found markedly elevated levels and divergent tissue sources of cfDNA in COVID-19 patients compared to influenza and respiratory syncytial virus patients or healthy controls. The major sources of cfDNA in COVID-19 were hematopoietic cells, vascular endothelium, hepatocyte, adipocyte, kidney, heart and lung. cfDNA levels positively correlated with COVID-19 disease severity, c reactive protein, D-Dimer. cfDNA profile at admission identified patients who subsequently required intensive care or died during hospitalization. Furthermore, the increased cfDNA in COVID-19 patients generates excessive mitochondrial reactive oxygen species (mtROS) in renal tubular cells in a concentration-dependent manner. This mtROS production was inhibited by a toll-like receptor 9 (TLR-9)-specific antagonist. Conclusion cfDNA maps tissue injury that predict COVID-19 outcomes, and may mechanistically propagates COVID-19 induced tissue injury. Funding sources: Intramural Targeted Anti-COVID-19 grant, National Institutes of Health
Authors
Temesgen E. Andargie, Naoko Tsuji, Fayaz Seifuddin, Moon Kyoo Jang, Peter S.T. Yuen, Hyesik Kong, Ilker Tunc, Komudi Singh, Ananth Charya, Kenneth J. Wilkins, Steven D. Nathan, Andrea L. Cox, Mehdi Pirooznia, Robert A. Star, Sean Agbor-Enoh
Abstract
Comorbid medical illnesses, such as obesity and diabetes, are associated with more severe COVID-19, hospitalization, and death. However, the role of the immune system in mediating these clinical outcomes has not been determined. We used multi-parameter flow cytometry and systems serology to comprehensively profile the functions of T cells and antibodies targeting spike, nucleocapsid, and envelope proteins in a convalescent cohort of COVID-19 subjects who were either hospitalized (n=20) or not hospitalized (n=40). To avoid confounding, subjects were matched by age, sex, ethnicity, and date of symptom onset. Surprisingly, we found that the magnitude and functional breadth of virus-specific CD4 T cell and antibody responses were consistently higher among hospitalized subjects, particularly those with medical comorbidities. However, an integrated analysis identified more coordination between polyfunctional CD4 T-cells and antibodies targeting the S1 domain of spike among subjects that were not hospitalized. These data reveal a functionally diverse and coordinated response between T cells and antibodies targeting SARS-CoV-2, which is reduced in the presence of comorbid illnesses that are known risk factors for severe COVID-19.
Authors
Krystle K.Q. Yu, Stephanie Fischinger, Malisa T. Smith, Caroline Atyeo, Deniz Cizmeci, Caitlin R. Wolf, Erik D. Layton, Jennifer K. Logue, Melissa S. Aguilar, Kiel Shuey, Carolin Loos, Jingyou Yu, Nicholas M. Franko, Robert Y. Choi, Anna Wald, Dan H. Barouch, David M. Koelle, Douglas Lauffenburger, Helen Y. Chu, Galit Alter, Chetan Seshadri
Abstract
We are reporting on a phase IIa study which aimed to determine the intubation rate, survival, viral clearance, and the development of endogenous antibodies in patients with COVID-19 pneumonia treated with convalescent plasma (CCP) containing high levels of neutralizing anti-SARS-CoV-2 antibodies. All 51 treated patients had COVID-19 pneumonia by radiographic and laboratory evaluation. Fresh or frozen CCP from donors with high titers of neutralizing antibodies was administered. The non-mechanically ventilated patients (n=36) had an intubation rate of 13.9% and a day-30 survival of 88.9%. The overall survival for a comparative group based on network data was 72.5% (1625/2241). Patients had rates of negative nasopharyngeal swab on day +10 and +30 of 43.8% and 73% respectively. Patients mechanically ventilated had a day-30 mortality of 46.7%; the mortality for a comparative group based on network data was 71% (369/520). All evaluable patients were found to have neutralizing antibodies on day +3 (n=47), and all but 1 had antibodies on day +30 and +60. The only adverse event was a mild rash. We are concluding that in this study of patients with COVID-19 pneumonia, CCP was safe and conferred transfer of antibodies while preserving endogenous immune response.
Authors
Michele L. Donato, Steven Park, Melissa Baker, Robert Korngold, Alison Morawski, Xue Geng, Ming Tan, Andrew Ip, Stuart Goldberg, Scott D. Rowley, Kar F. Chow, Emily Brown, Joshua Zenreich, Phyllis McKiernan, Kathryn Buttner, Anna Ullrich, Laura Long, Rena Feinman, Andrea Ricourt, Marlo Kemp, Mariefel Vendivil, Hyung C. Suh, Bindu Balani, Cristina Cicogna, Rani Sebti, Abdulla Al-Khan, Steven J. Sperber, Samit Desai, Stacey L. Fanning, Danit Arad, Ronaldo C. Go, Elizabeth Tam, Keith Rose, Sean Sadikot, David S. Siegel, Martin Gutierrez, Tatyana Feldman, Andre Goy, Andrew Pecora, Noa Biran, Lori A. Leslie, Alfred Gillio, Sarah Timmapuri, Michele S. Boonstra, Sam Singer, Sukhdeep Kaur, Ernest Richards, David S. Perlin
Abstract
The development of prophylactic and therapeutic agents for coronavirus disease 2019 (COVID-19) is a current global health priority. Here, we investigated the presence of cross-neutralizing antibodies against severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) in dromedary camels that were Middle East respiratory syndrome (MERS)-CoV-seropositive but MERS-CoV-free. The tested 229 dromedaries had anti-MERS-CoV camel antibodies with variable cross-reactivity patterns against SARS-CoV-2 proteins, including the S trimer, M, N, and E proteins. Using SARS-CoV-2 competitive immunofluorescence immunoassays and pseudovirus neutralization assays, we found medium-to-high titers of cross-neutralizing antibodies against SARS-CoV-2 in these animals. Through linear B cell epitope mapping using phage immunoprecipitation sequencing and a SARS-CoV-2 peptide/proteome microarray, we identified a large repertoire of betacoronavirus cross-reactive antibody specificities in these dromedaries and demonstrated that the SARS-CoV-2-specific VHH antibody repertoire is qualitatively diverse. This analysis revealed not only several SARS-CoV-2 epitopes that are highly immunogenic in humans, including a neutralizing epitope, but also epitopes exclusively targeted by camel antibodies. The identified SARS-CoV-2 cross-neutralizing camel antibodies are not proposed as a potential treatment for COVID-19. Rather, their presence in non-immunized camels supports the development of SARS-CoV-2 hyperimmune camels, which could be a prominent source of therapeutic agents for the prevention and treatment of COVID-19.
Authors
Lotfi Chouchane, Jean-Charles Grivel, Elmoubasher Farag, Igor Pavlovski, Selma Maacha, Abbirami Sathappan, Hamad Al-Romaihi, Sirin Abuaqel, Manar Ata, Aouatef Ismail Chouchane, Sami Remadi, Najeeb M. Halabi, Arash Rafii, Mohammed Al-Thani, Nico Marr, Murugan Subramanian, Jingxuan Shan
Abstract
Convalescent plasma with severe acute respiratory disease coronavirus 2 (SARS-CoV-2) antibodies (CCP) may hold promise as treatment for Coronavirus Disease 2019 (COVID-19). We compared the mortality and clinical outcome of patients with COVID-19 who received 200mL of CCP with a Spike protein IgG titer ≥1:2,430 (median 1:47,385) within 72 hours of admission to propensity score-matched controls cared for at a medical center in the Bronx, between April 13 to May 4, 2020. Matching criteria for controls were age, sex, body mass index, race, ethnicity, comorbidities, week of admission, oxygen requirement, D-dimer, lymphocyte counts, corticosteroids, and anticoagulation use. There was no difference in mortality or oxygenation between CCP recipients and controls at day 28. When stratified by age, compared to matched controls, CCP recipients <65 years had 4-fold lower mortality and 4-fold lower deterioration in oxygenation or mortality at day 28. For CCP recipients, pre-transfusion Spike protein IgG, IgM and IgA titers were associated with mortality at day 28 in univariate analyses. No adverse effects of CCP were observed. Our results suggest CCP may be beneficial for hospitalized patients <65 years, but data from controlled trials is needed to validate this finding and establish the effect of ageing on CCP efficacy.
Authors
Hyun ah Yoon, Rachel Bartash, Inessa Gendlina, Johanna Rivera, Antonio Nakouzi, Robert H. Bortz III, Ariel S. Wirchnianski, Monika Paroder, Karen Fehn, Leana Serrano-Rahman, Rachelle Babb, Uzma N. Sarwar, Denise Haslwanter, Ethan Laudermilch, Catalina Florez, M. Eugenia Dieterle, Rohit K. Jangra, J. Maximilian Fels, Karen Tong, Margarette C. Mariano, Olivia Vergnolle, George I. Georgiev, Natalia G. Herrera, Ryan J. Malonis, Jose A. Quiroz, Nicholas C. Morano, Gregory J. Krause, Joseph M. Sweeney, Kelsie Cowman, Stephanie A. Allen, Jayabhargav Annam, Ariella Applebaum, Daniel Barboto, Ahmed Khokhar, Brianna J. Lally, Audrey Lee, Max Lee, Avinash Malaviya, Reise Sample, Xiuyi A. Yang, Yang Li, Rafael E. Ruiz, Raja Thota, Jason Barnhill, Doctor Y. Goldstein, Joan Uehlinger, Scott J. Garforth, Steven C. Almo, Jonathan R. Lai, Morayma Reyes Gil, Amy S. Fox, Kartik Chandran, Tao Wang, Johanna P. Daily, Liise-anne Pirofski
Effective virus-neutralizing activities in antisera from the first wave of severe COVID-19 survivors
Abstract
The pandemic of Coronavirus Disease 19 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become one of the worst public health crises. However, knowledge about the dynamics of antibody responses in COVID-19 patients is still poorly understood. In this study, we performed serological study with serum specimens collected at the acute and the convalescent phases from 104 severe COVID-19 patients who were the first wave of COVID-19 cases in Wuhan, China. Our findings uncovered that neutralizing antibodies to SARS-CoV-2 are persistent at least for more than 6 months in severe COVID-19 patients, despite that immunoglobulin G (IgG) levels against receptor binding domain (RBD) and nucleocapsid protein (N) IgG declined from the acute to the convalescent phase. Moreover, we demonstrate that the level of RBD-IgG is capable of correlating with SARS-CoV-2-neutralizing activities in COVID-19 serum. In summary, our findings identify the magnitude, functionality and longevity of antibody responses in COVID-19 patients, which sheds light on better understanding of humoral immune response to COVID-19, and would be beneficial for developing vaccines.
Authors
Yang Han, Peipei Liu, Yang Qiu, Jie Zhou, Ying Liu, Xujuan Hu, Qingyu Yang, Rui Huang, Xinyue Wen, Hao Song, Pengcheng Yu, Mengjie Yang, Jing Zhang, William J. Liu, Ke Peng, Guizhen Wu, Dingyu Zhang, Xi Zhou, Ying Wu
Abstract
Background: Mitochondrial DNA (MT-DNA) are intrinsically inflammatory nucleic acids released by damaged solid organs. Whether circulating cell-free MT-DNA quantitation could be used to predict the risk of poor COVID-19 outcomes remains undetermined. Methods: We measured circulating MT-DNA levels in prospectively collected, cell-free plasma samples from 97 subjects with COVID-19 at hospital presentation. Our primary outcome was mortality. ICU admission, intubation, vasopressor and renal replacement therapy requirements were secondary outcomes. Multivariate regression analysis determined whether MT-DNA levels were independent of other reported COVID-19 risk factors. Receiver operating characteristics and area under-the-curve assessment were used to compare MT-DNA levels to established and emerging inflammatory markers of COVID-19. Results: Circulating MT-DNA levels were highly elevated in patients who eventually died, required ICU admission, intubation, vasopressor use or renal replacement therapy. Multivariate regression revealed that high circulating MT-DNA is an independent risk factor for these outcomes after adjusting for age, sex, and comorbidities. We also found that circulating MT-DNA levels have a similar or superior area-under-the curve when compared against clinically-established measures of inflammation and emerging markers currently of interest as investigational targets for COVID-19 therapy. Conclusions: These results show that high circulating MT-DNA levels are a potential early indicator for poor COVID-19 outcomes. Funding: This project was supported by Washington University Institute of Clinical Translational Sciences COVID-19 Research Program. Sample procurement and patient outcome data collection was supported by the Washington University ICTS NIH grant UL1TR002345.
Authors
Davide Scozzi, Marlene Cano, Lina Ma, Dequan Zhou, Ji Hong Zhu, Jane A. O’Halloran, Charles W. Goss, Adriana M. Rauseo, Zhiyi Liu, Sanjaya Kumar Sahu, Valentina Peritore, Monica Rocco, Alberto Ricci, Rachele Amodeo, Laura Aimati, Mohsen Ibrahim, Ramsey R. Hachem, Daniel Kreisel, Philip A. Mudd, Hrishikesh S. Kulkarni, Andrew E. Gelman
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