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3. Phenotypes of disease severity in a cohort of hospitalized COVID-19 patients: Results from the IMPACC study

Author

Ozonoff, Al, Schaenman, Joanna, Jayavelu, Naresh Doni, Milliren, Carly E., Calfee, Carolyn S., Cairns, Charles B., Kraft, Monica, Baden, Lindsey R., Shaw, Albert C., Krammer, Florian, van Bakel, Harm, Esserman, Denise A., Liu, Shanshan, Sesma, Ana Fernandez, Simon, Viviana, Hafler, David A., Montgomery, Ruth R., Kleinstein, Steven H., Levy, Ofer, Bime, Chris, Haddad, Elias K., Erle, David J., Pulendran, Bali, Nadeau, Kari C., Davis, Mark M, Hough, Catherine L., Messer, William B., Higuita, Nelson I. Agudelo, Metcalf, Jordan P., Atkinson, Mark A., Brakenridge, Scott C., Corry, David, Kheradmand, Farrah, Ehrlich, Lauren I.R., Melamed, Esther, McComsey, Grace A., Sekaly, Rafick, Diray-Arce, Joann, Peters, Bjoern, Augustine, Alison D., Reed, Elaine F., McEnaney, Kerry, Barton, Brenda, Lentucci, Claudia, Saluvan, Mehmet, Chang, Ana C., Hoch, Annmarie, Albert, Marisa, Shaheen, Tanzia, Kho, Alvin T., Thomas, Sanya, Chen, Jing, Murphy, Maimouna D., Cooney, Mitchell, Presnell, Scott, Fragiadakis, Gabriela K., Patel, Ravi, Guan, Leying, Gygi, Jeremy, Pawar, Shrikant, Brito, Anderson, Khalil, Zain, Maguire, Cole, Fourati, Slim, Overton, James A., Vita, Randi, Westendorf, Kerstin, Salehi-Rad, Ramin, Leligdowicz, Aleksandra, Matthay, Michael A., Singer, Jonathan P., Kangelaris, Kirsten N., Hendrickson, Carolyn M., Krummel, Matthew F., Langelier, Charles R., Woodruff, Prescott G., Powell, Debra L., Kim, James N., Simmons, Brent, Goonewardene, I. Michael, Smith, Cecilia M., Martens, Mark, Mosier, Jarrod, Kimura, Hiroki, Sherman, Amy C., Walsh, Stephen R., Issa, Nicolas C., Dela Cruz, Charles, Farhadian, Shelli, Iwasaki, Akiko, Ko, Albert I., Chinthrajah, Sharon, Ahuja, Neera, Rogers, Angela J., Artandi, Maja, Siegel, Sarah A.R., Lu, Zhengchun, Drevets, Douglas A., Brown, Brent R., Anderson, Matthew L., Guirgis, Faheem W., Thyagarajan, Rama V., Rousseau, Justin F., Wylie, Dennis, Busch, Johanna, Gandhi, Saurin, Triplett, Todd A., Yendewa, George, Giddings, Olivia, Anderson, Evan J., Mehta, Aneesh K., Sevransky, Jonathan E., Khor, Bernard, Rahman, Adeeb, Stadlbauer, Daniel, Dutta, Jayeeta, Xie, Hui, Kim-Schulze, Seunghee, Gonzalez-Reiche, Ana Silvia, van de Guchte, Adriana, Farrugia, Keith, Khan, Zenab, Maecker, Holden T., Elashoff, David, Brook, Jenny, Ramires-Sanchez, Estefania, Llamas, Megan, Rivera, Adreanne, Perdomo, Claudia, Ward, Dawn C., Magyar, Clara E., Fulcher, Jennifer A., Abe-Jones, Yumiko, Asthana, Saurabh, Beagle, Alexander, Bhide, Sharvari, Carrillo, Sidney A., Chak, Suzanna, Ghale, Rajani, Gonzalez, Ana, Jauregui, Alejandra, Jones, Norman, Lea, Tasha, Lee, Deanna, Lota, Raphael, Milush, Jeff, Nguyen, Viet, Pierce, Logan, Prasad, Priya A., Rao, Arjun, Samad, Bushra, Shaw, Cole, Sigman, Austin, Sinha, Pratik, Ward, Alyssa, Willmore, Andrew, Zhan, Jenny, Rashid, Sadeed, Rodriguez, Nicklaus, Tang, Kevin, Altamirano, Luz Torres, Betancourt, Legna, Curiel, Cindy, Sutter, Nicole, Paz, Maria Tercero, Tietje-Ulrich, Gayelan, Leroux, Carolyn, Connors, Jennifer, Bernui, Mariana, Kutzler, Michel A., Edwards, Carolyn, Lee, Edward, Lin, Edward, Croen, Brett, Semenza, Nicholas C., Rogowski, Brandon, Melnyk, Nataliya, Woloszczuk, Kyra, Cusimano, Gina, Bell, Mathew R., Furukawa, Sara, McLin, Renee, Marrero, Pamela, Sheidy, Julie, Tegos, George P., Nagle, Crystal, Mege, Nathan, Ulring, Kristen, Seyfert-Margolis, Vicki, Conway, Michelle, Francisco, Dave, Molzahn, Allyson, Erickson, Heidi, Wilson, Connie Cathleen, Schunk, Ron, Sierra, Bianca, Hughes, Trina, Smolen, Kinga, Desjardins, Michael, van Haren, Simon, Mitre, Xhoi, Cauley, Jessica, Li, Xiaofang, Tong, Alexandra, Evans, Bethany, Montesano, Christina, Licona, Jose Humberto, Krauss, Jonathan, Chang, Jun Bai Park, Izaguirre, Natalie, Chaudhary, Omkar, Coppi, Andreas, Fournier, John, Mohanty, Subhasis, Muenker, M. Catherine, Nelson, Allison, Raddassi, Khadir, Rainone, Michael, Ruff, William E., Salahuddin, Syim, Schulz, Wade L., Vijayakumar, Pavithra, Wang, Haowei, Wunder Jr., Elsio, Young, H. Patrick, Zhao, Yujiao, Saksena, Miti, Altman, Deena, Kojic, Erna, Srivastava, Komal, Eaker, Lily Q., Bermúdez-González, Maria C., Beach, Katherine F., Sominsky, Levy A., Azad, Arman R., Carreño, Juan Manuel, Singh, Gagandeep, Raskin, Ariel, Tcheou, Johnstone, Bielak, Dominika, Kawabata, Hisaaki, Mulder, Lubbertus CF, Kleiner, Giulio, Lee, Alexandra S., Do, Evan Do, Fernandes, Andrea, Manohar, Monali, Hagan, Thomas, Blish, Catherine A., Din, Hena Naz, Roque, Jonasel, Yang, Samuel, Brunton, Amanda, Sullivan, Peter E., Strnad, Matthew, Lyski, Zoe L., Coulter, Felicity J., Booth, J. Leland, Sinko, Lauren A., Moldawer, Lyle L., Borresen, Brittany, Roth-Manning, Brittney, Song, Li-Zhen, Nelson, Ebony, Lewis-Smith, Megan, Smith, Jacob, Tipan, Pablo Guaman, Siles, Nadia, Bazzi, Sam, Geltman, Janelle, Hurley, Kerin, Gabriele, Gio, Sieg, Scott, Vaysman, Tatyana, Bristow, Laurel, Hussaini, Laila, Hellmeister, Kieffer, Samaha, Hady, Cheng, Andrew, Spainhour, Christine, Scherer, Erin M., Johnson, Brandi, Bechnak, Amer, Ciric, Caroline R., Hewitt, Lauren, Carter, Erin, Mcnair, Nina, Panganiban, Bernadine, Huerta, Christopher, Usher, Jacob, Ribeiro, Susan Pereira, Altman, Matthew C., Becker, Patrice M., Rouphael, Nadine, Bime, Christian, and Davis, Mark M.

Published
2022
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5. A multicenter evaluation of computable phenotyping approaches for SARS-CoV-2 infection and COVID-19 hospitalizations

Author

Khera, Rohan, Mortazavi, Bobak J., Sangha, Veer, Warner, Frederick, Patrick Young, H., Ross, Joseph S., Shah, Nilay D., Theel, Elitza S., Jenkinson, William G., Knepper, Camille, Wang, Karen, Peaper, David, Martinello, Richard A., Brandt, Cynthia A., Lin, Zhenqiu, Ko, Albert I., Krumholz, Harlan M., Pollock, Benjamin D., and Schulz, Wade L.

Published
2022
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6. De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report

Author

Gandhi, Shiv, Klein, Jonathan, Robertson, Alexander J., Peña-Hernández, Mario A., Lin, Michelle J., Roychoudhury, Pavitra, Lu, Peiwen, Fournier, John, Ferguson, David, Mohamed Bakhash, Shah A. K., Catherine Muenker, M., Srivathsan, Ariktha, Wunder, Jr, Elsio A., Kerantzas, Nicholas, Wang, Wenshuai, Lindenbach, Brett, Pyle, Anna, Wilen, Craig B., Ogbuagu, Onyema, Greninger, Alexander L., Iwasaki, Akiko, Schulz, Wade L., and Ko, Albert I.

Published
2022
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7. A primer for quantum computing and its applications to healthcare and biomedical research.

Author

Durant, Thomas J S, Knight, Elizabeth, Nelson, Brent, Dudgeon, Sarah, Lee, Seung J, Walliman, Dominic, Young, Hobart P, Ohno-Machado, Lucila, and Schulz, Wade L

Abstract

Objectives To introduce quantum computing technologies as a tool for biomedical research and highlight future applications within healthcare, focusing on its capabilities, benefits, and limitations. Target Audience Investigators seeking to explore quantum computing and create quantum-based applications for healthcare and biomedical research. Scope Quantum computing requires specialized hardware, known as quantum processing units, that use quantum bits (qubits) instead of classical bits to perform computations. This article will cover (1) proposed applications where quantum computing offers advantages to classical computing in biomedicine; (2) an introduction to how quantum computers operate, tailored for biomedical researchers; (3) recent progress that has expanded access to quantum computing; and (4) challenges, opportunities, and proposed solutions to integrate quantum computing in biomedical applications. [ABSTRACT FROM AUTHOR]

Published
2024
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8. Effectiveness of CoronaVac among healthcare workers in the setting of high SARS-CoV-2 Gamma variant transmission in Manaus, Brazil: A test-negative case-control study

Author

Hitchings, Matt D.T., Ranzani, Otavio T., Torres, Mario Sergio Scaramuzzini, de Oliveira, Silvano Barbosa, Almiron, Maria, Said, Rodrigo, Borg, Ryan, Schulz, Wade L., de Oliveira, Roberto Dias, da Silva, Patricia Vieira, de Castro, Daniel Barros, Sampaio, Vanderson de Souza, de Albuquerque, Bernardino Cláudio, Ramos, Tatyana Costa Amorim, Fraxe, Shadia Hussami Hauache, da Costa, Cristiano Fernandes, Naveca, Felipe Gomes, Siqueira, Andre M., de Araújo, Wildo Navegantes, Andrews, Jason R., Cummings, Derek A.T., Ko, Albert I., and Croda, Julio

Published
2021
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10. Association between primary or booster COVID-19 mRNA vaccination and Omicron lineage BA.1 SARS-CoV-2 infection in people with a prior SARS-CoV-2 infection: A test-negative case-control analysis

Author

Lind, Margaret L., Robertson, Alexander J., Silva, Julio, Warner, Frederick, Coppi, Andreas C., Price, Nathan, Duckwall, Chelsea, Sosensky, Peri, Di Giuseppe, Erendira C., Borg, Ryan, Fofana, Mariam O., Ranzani, Otavio T., Dean, Natalie E., Andrews, Jason R., Croda, Julio, Iwasaki, Akiko, Cummings, Derek A. T., Ko, Albert I., Hitchings, Matt D. T., and Schulz, Wade L.

Subjects
Company distribution practices, Biological sciences
Abstract

Background The benefit of primary and booster vaccination in people who experienced a prior Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection remains unclear. The objective of this study was to estimate the effectiveness of primary (two-dose series) and booster (third dose) mRNA vaccination against Omicron (lineage BA.1) infection among people with a prior documented infection. Methods and findings We conducted a test-negative case-control study of reverse transcription PCRs (RT-PCRs) analyzed with the TaqPath (Thermo Fisher Scientific) assay and recorded in the Yale New Haven Health system from November 1, 2021, to April 30, 2022. Overall, 11,307 cases (positive TaqPath analyzed RT-PCRs with S-gene target failure [SGTF]) and 130,041 controls (negative TaqPath analyzed RT-PCRs) were included (median age: cases: 35 years, controls: 39 years). Among cases and controls, 5.9% and 8.1% had a documented prior infection (positive SARS-CoV-2 test record [greater than or equal to]90 days prior to the included test), respectively. We estimated the effectiveness of primary and booster vaccination relative to SGTF-defined Omicron (lineage BA.1) variant infection using a logistic regression adjusted for date of test, age, sex, race/ethnicity, insurance, comorbidities, social venerability index, municipality, and healthcare utilization. The effectiveness of primary vaccination 14 to 149 days after the second dose was 41.0% (95% confidence interval (CI): 14.1% to 59.4%, p 0.006) and 27.1% (95% CI: 18.7% to 34.6%, p < 0.001) for people with and without a documented prior infection, respectively. The effectiveness of booster vaccination ([greater than or equal to]14 days after booster dose) was 47.1% (95% CI: 22.4% to 63.9%, p 0.001) and 54.1% (95% CI: 49.2% to 58.4%, p < 0.001) in people with and without a documented prior infection, respectively. To test whether booster vaccination reduced the risk of infection beyond that of the primary series, we compared the odds of infection among boosted ([greater than or equal to]14 days after booster dose) and booster-eligible people ([greater than or equal to]150 days after second dose). The odds ratio (OR) comparing boosted and booster-eligible people with a documented prior infection was 0.79 (95% CI: 0.54 to 1.16, p 0.222), whereas the OR comparing boosted and booster-eligible people without a documented prior infection was 0.54 (95% CI: 0.49 to 0.59, p < 0.001). This study's limitations include the risk of residual confounding, the use of data from a single system, and the reliance on TaqPath analyzed RT-PCR results. Conclusions In this study, we observed that primary vaccination provided significant but limited protection against Omicron (lineage BA.1) infection among people with and without a documented prior infection. While booster vaccination was associated with additional protection against Omicron BA.1 infection in people without a documented prior infection, it was not found to be associated with additional protection among people with a documented prior infection. These findings support primary vaccination in people regardless of documented prior infection status but suggest that infection history may impact the relative benefit of booster doses., Author(s): Margaret L. Lind 1,*, Alexander J. Robertson 1, Julio Silva 2, Frederick Warner 3,4, Andreas C. Coppi 3,4, Nathan Price 3,4, Chelsea Duckwall 1, Peri Sosensky 1, Erendira C. [...]

Published
2022
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13. Reply to: A finding of sex similarities rather than differences in COVID-19 outcomes

Author

Takahashi, Takehiro, Ellingson, Mallory K., Wong, Patrick, Israelow, Benjamin, Lucas, Carolina, Klein, Jon, Silva, Julio, Mao, Tianyang, Oh, Ji Eun, Tokuyama, Maria, Lu, Peiwen, Venkataraman, Arvind, Park, Annsea, Liu, Feimei, Meir, Amit, Sun, Jonathan, Wang, Eric Y., Casanovas-Massana, Arnau, Wyllie, Anne L., Vogels, Chantal B. F., Earnest, Rebecca, Lapidus, Sarah, Ott, Isabel M., Moore, Adam J., Shaw, Albert, Fournier, John B., Odio, Camila D., Farhadian, Shelli, Dela Cruz, Charles, Grubaugh, Nathan D., Schulz, Wade L., Ring, Aaron M., Ko, Albert I., Omer, Saad B., and Iwasaki, Akiko

Published
2021
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14. Microfluidic Immuno‐Serolomic Assay Reveals Systems Level Association with COVID‐19 Pathology and Vaccine Protection.

Author

Kim, Dongjoo, Biancon, Giulia, Bai, Zhiliang, VanOudenhove, Jennifer, Liu, Yuxin, Kothari, Shalin, Gowda, Lohith, Kwan, Jennifer M., Buitrago‐Pocasangre, Nicholas Carlos, Lele, Nikhil, Asashima, Hiromitsu, Racke, Michael K., Wilson, JoDell E., Givens, Tara S., Tomayko, Mary M., Schulz, Wade L., Longbrake, Erin E., Hafler, David A., Halene, Stephanie, and Fan, Rong

Subjects
B cells, COVID-19, PATIENT compliance, COVID-19 vaccines, B cell lymphoma, HEMATOLOGIC malignancies
Abstract

How to develop highly informative serology assays to evaluate the quality of immune protection against coronavirus disease‐19 (COVID‐19) has been a global pursuit over the past years. Here, a microfluidic high‐plex immuno‐serolomic assay is developed to simultaneously measure50 plasma or serum samples for50 soluble markers including 35proteins, 11 anti‐spike/receptor binding domian (RBD) IgG antibodies spanningmajor variants, and controls. This assay demonstrates the quintuplicate test in a single run with high throughput, low sample volume, high reproducibilityand accuracy. It is applied to the measurement of 1012 blood samples including in‐depth analysis of sera from 127 patients and 21 healthy donors over multiple time points, either with acute COVID infection or vaccination. The protein analysis reveals distinct immune mediator modules that exhibit a reduced degree of diversity in protein‐protein cooperation in patients with hematologic malignancies or receiving B cell depletion therapy. Serological analysis identifies that COVID‐infected patients with hematologic malignancies display impaired anti‐RBD antibody response despite high level of anti‐spike IgG, which can be associated with limited clonotype diversity and functional deficiency in B cells. These findings underscore the importance to individualize immunization strategies for these high‐risk patients and provide an informative tool to monitor their responses at the systems level. [ABSTRACT FROM AUTHOR]

Published
2023
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15. Evidence of Leaky Protection Following COVID-19 Vaccination and SARS-CoV-2 Infection in a US Correctional Facility Population

Author

Lind, Margaret L, primary, Dorion, Murilo, additional, Houde, Amy J, additional, Lansing, Mary, additional, Lapidus, Sarah, additional, Thomas, Russell, additional, Yildirim, Inci, additional, Omer, Saad B., additional, Schulz, Wade L., additional, Andrews, Jason R., additional, Hitchings, Matt DT, additional, Kennedy, Byron S., additional, Richeson, Robert P., additional, Cummings, Derek AT, additional, and Ko, Albert I, additional

Published
2023
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16. Nasal host response-based screening for undiagnosed respiratory viruses: a pathogen surveillance and detection study

Author

Cheemarla, Nagarjuna R, primary, Hanron, Amelia, additional, Fauver, Joseph R, additional, Bishai, Jason, additional, Watkins, Timothy A, additional, Brito, Anderson F, additional, Zhao, Dejian, additional, Alpert, Tara, additional, Vogels, Chantal B F, additional, Ko, Albert I, additional, Schulz, Wade L, additional, Landry, Marie L, additional, Grubaugh, Nathan D, additional, van Dijk, David, additional, and Foxman, Ellen F, additional

Published
2023
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17. Use of Whole-Genome Sequencing to Estimate the Contribution of Immune Evasion and Waning Immunity on Decreasing COVID-19 Vaccine Effectiveness

Author

Lind, Margaret L, primary, Copin, Richard, additional, McCarthy, Shane, additional, Coppi, Andreas, additional, Warner, Fred, additional, Ferguson, David, additional, Duckwall, Chelsea, additional, Borg, Ryan, additional, Muenker, M Catherine, additional, Overton, John, additional, Hamon, Sara, additional, Zhou, Anbo, additional, Cummings, Derek A T, additional, Ko, Albert I, additional, Hamilton, Jennifer D, additional, Schulz, Wade L, additional, and Hitchings, Matt D T, additional

Published
2022
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18. Microfluidic immuno-serology assay revealed a limited diversity of protection against COVID-19 in patients with altered immunity

Author

Kim, Dongjoo, primary, Biancon, Giulia, additional, Bai, Zhiliang, additional, VanOudenhove, Jennifer, additional, Liu, Yuxin, additional, Kothari, Shalin, additional, Gowda, Lohith, additional, Kwan, Jennifer M., additional, Buitrago-Pocasangre, Nicholas Carlos, additional, Lele, Nikhil, additional, Asashima, Hiromitsu, additional, Racke, Michael K., additional, Wilson, JoDell E., additional, Givens, Tara S., additional, Tomayko, Mary M., additional, Schulz, Wade L., additional, Longbrake, Erin E., additional, Hafler, David A., additional, Halene, Stephanie, additional, and Fan, Rong, additional

Published
2022
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21. The Current Landscape and Emerging Applications for Real‐World Data in Diagnostics and Clinical Decision Support and its Impact on Regulatory Decision Making

Author

Baumfeld Andre, Elodie, primary, Carrington, Nate, additional, Siami, Flora S., additional, Hiatt, Jo Carol, additional, McWilliams, Carly, additional, Hiller, Carolyn, additional, Surinach, Andy, additional, Zamorano, Alejandro, additional, Pashos, Chris L., additional, and Schulz, Wade L., additional

Published
2022
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22. Effectiveness of Primary and Booster COVID-19 mRNA Vaccination against Omicron Variant SARS-CoV-2 Infection in People with a Prior SARS-CoV-2 Infection

Author

Lind, Margaret L., primary, Robertson, Alexander James, additional, Silva, Julio, additional, Warner, Frederick, additional, Coppi, Andreas C., additional, Price, Nathan, additional, Duckwall, Chelsea, additional, Sosensky, Peri, additional, Di Giuseppe, Erendira C., additional, Borg, Ryan, additional, Fofana, Mariam O, additional, Ranzani, Otavio T., additional, Dean, Natalie E., additional, Andrews, Jason R., additional, Croda, Julio, additional, Iwasaki, Akiko, additional, Cummings, Derek A.T., additional, Ko, Albert I., additional, Hitchings, Matt DT, additional, and Schulz, Wade L., additional

Published
2022
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23. Use of whole genome sequencing to estimate the contribution of immune evasion and waning immunity on decreasing COVID-19 vaccine effectiveness.

Author

Lind, Margaret L, Copin, Richard, McCarthy, Shane, Coppi, Andreas, Warner, Fred, Ferguson, David, Duckwall, Chelsea, Borg, Ryan, Muenker, M Catherine, Overton, John, Hamon, Sara, Zhou, Anbo, Cummings, Derek A T, Ko, Albert I, Hamilton, Jennifer D, Schulz, Wade L, Hitchings, Matt D T, Cummings, Derek At, and Schulz, Wade

Subjects
SARS-CoV-2, VACCINE effectiveness, NUCLEOTIDE sequencing, CORONAVIRUS diseases, COVID-19, SARS-CoV-2 Delta variant
Abstract

Background: The impact variant-specific immune evasion and waning protection have on declining COVID-19 vaccine effectiveness remains unclear. Using whole-genome-sequencing (WGS), we examined the contribution of these factors on the decline observed following the introduction of the Delta variant. Further, we evaluated the utility of calendar-period-based classification as an alternative to WGS.Methods: We conducted a test-negative-case-control study among people who received SARS-CoV-2 RT-PCR testing in the Yale New Haven Health System between April 1 and August 24, 2021. Variant classification was performed using WGS and calendar-period.Results: Overall, 2,029 cases (RT-PCR positive, sequenced samples [infections]) and 343,985 controls (negative RT-PCRs) were included. VE 14-89 days after 2nd dose was significantly higher against WGS-classified Alpha-infection (84.4%, CI: 75.6-90.0%) than Delta-infection (68.9%, CI: 58.0-77.1%, p-value = 0.013). The odds of WGS-classified Delta-infection were significantly higher 90-149 than 14-89 days after 2nd dose (p-value = 0.003). VE estimates against calendar-period-classified infections approximated estimates against WGS-classified infections, however, calendar-period-based classification was subject to outcome misclassification (35%: Alpha-period, 4%: Delta-period).Conclusions: Both waning protection and variant-specific immune evasion contributed to the lower effectiveness. While VE estimates against calendar-period-classified infections mirrored those against WGS-classified infections, our analysis highlights the need for WGS when variants are co-circulating and misclassification is likely. [ABSTRACT FROM AUTHOR]

Published
2023
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26. A dynamic model to estimate evolving risk of major bleeding after percutaneous coronary intervention

Author

Hurley, Nathan C, primary, Desai, Nihar, additional, Dhruva, Sanket, additional, Khera, Rohan, additional, Schulz, Wade L, additional, Huang, Chenxi, additional, Curtis, Jeptha, additional, Masoudi, Frederick, additional, Rumsfeld, John, additional, Negahban, Sahand, additional, Krumholz, Harlan, additional, and Mortazavi, Bobak J, additional

Published
2021
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27. Feasibility of using real-world data in the evaluation of cardiac ablation catheters: a test-case of the National Evaluation System for Health Technology Coordinating Center

Author

Dhruva, Sanket S, primary, Jiang, Guoqian, additional, Doshi, Amit A, additional, Friedman, Daniel J, additional, Brandt, Eric, additional, Chen, Jiajing, additional, Akar, Joseph G, additional, Ross, Joseph S, additional, Ervin, Keondae R, additional, Collison Farr, Kimberly, additional, Shah, Nilay D, additional, Coplan, Paul, additional, Noseworthy, Peter A., additional, Zhang, Shumin, additional, Forsyth, Thomas, additional, Schulz, Wade L, additional, Yu, Yue, additional, and Drozda, Jr., Joseph P, additional

Published
2021
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28. De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: A case report

Author

Gandhi, Shiv, primary, Klein, Jonathan, additional, Robertson, Alexander, additional, Peña-Hernández, Mario A., additional, Lin, Michelle J, additional, Roychoudhury, Pavitra, additional, Lu, Peiwen, additional, Fournier, John, additional, Ferguson, David, additional, Mohamed Bakhash, Shah A., additional, Catherine Muenker, M., additional, Srivathsan, Ariktha, additional, Wunder, Elsio A., additional, Kerantzas, Nicholas, additional, Wang, Wenshuai, additional, Lindenbach, Brett, additional, Pyle, Anna, additional, Wilen, Craig B., additional, Ogbuagu, Onyema, additional, Greninger, Alexander L., additional, Iwasaki, Akiko, additional, Schulz, Wade L., additional, and Ko, Albert I., additional

Published
2021
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31. High burden of viruses and bacterial pathobionts drives heightened nasal innate immunity in children

Author

Watkins, Timothy A., Green, Alex B., Amat, Julien A.R., Cheemarla, Nagarjuna R., Hänsel, Katrin, Lozano, Richard, Dudgeon, Sarah N., Germain, Gregory, Landry, Marie L., Schulz, Wade L., and Foxman, Ellen F.

Abstract

Studies during the COVID-19 pandemic showed that children had heightened nasal innate immune responses compared with adults. To evaluate the role of nasal viruses and bacteria in driving these responses, we performed cytokine profiling and comprehensive, symptom-agnostic testing for respiratory viruses and bacterial pathobionts in nasopharyngeal samples from children tested for SARS-CoV-2 in 2021–22 (n = 467). Respiratory viruses and/or pathobionts were highly prevalent (82% of symptomatic and 30% asymptomatic children; 90 and 49% for children <5 years). Virus detection and load correlated with the nasal interferon response biomarker CXCL10, and the previously reported discrepancy between SARS-CoV-2 viral load and nasal interferon response was explained by viral coinfections. Bacterial pathobionts correlated with a distinct proinflammatory response with elevated IL-1β and TNF but not CXCL10. Furthermore, paired samples from healthy 1-year-olds collected 1–2 wk apart revealed frequent respiratory virus acquisition or clearance, with mucosal immunophenotype changing in parallel. These findings reveal that frequent, dynamic host–pathogen interactions drive nasal innate immune activation in children.

Published
2024
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33. Feasibility of capturing real-world data from health information technology systems at multiple centers to assess cardiac ablation device outcomes: A fit-for-purpose informatics analysis report.

Author

Jiang, Guoqian, Dhruva, Sanket S, Chen, Jiajing, Schulz, Wade L, Doshi, Amit A, Noseworthy, Peter A, Zhang, Shumin, Yu, Yue, Young, H Patrick, Brandt, Eric, Ervin, Keondae R, Shah, Nilay D, Ross, Joseph S, Coplan, Paul, Drozda, Joseph P, and Patrick Young, H

Abstract

Objective: The study sought to conduct an informatics analysis on the National Evaluation System for Health Technology Coordinating Center test case of cardiac ablation catheters and to demonstrate the role of informatics approaches in the feasibility assessment of capturing real-world data using unique device identifiers (UDIs) that are fit for purpose for label extensions for 2 cardiac ablation catheters from the electronic health records and other health information technology systems in a multicenter evaluation.Materials and Methods: We focused on data capture and transformation and data quality maturity model specified in the National Evaluation System for Health Technology Coordinating Center data quality framework. The informatics analysis included 4 elements: the use of UDIs for identifying device exposure data, the use of standardized codes for defining computable phenotypes, the use of natural language processing for capturing unstructured data elements from clinical data systems, and the use of common data models for standardizing data collection and analyses.Results: We found that, with the UDI implementation at 3 health systems, the target device exposure data could be effectively identified, particularly for brand-specific devices. Computable phenotypes for study outcomes could be defined using codes; however, ablation registries, natural language processing tools, and chart reviews were required for validating data quality of the phenotypes. The common data model implementation status varied across sites. The maturity level of the key informatics technologies was highly aligned with the data quality maturity model.Conclusions: We demonstrated that the informatics approaches can be feasibly used to capture safety and effectiveness outcomes in real-world data for use in medical device studies supporting label extensions. [ABSTRACT FROM AUTHOR]

Published
2021
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35. Impact of COVID-19 vaccination on symptoms and immune phenotypes in vaccine-naïve individuals with Long COVID.

Author

Grady CB, Bhattacharjee B, Silva J, Jaycox J, Lee LW, Monteiro VS, Sawano M, Massey D, Caraballo C, Gehlhausen JR, Tabachnikova A, Mao T, Lucas C, Peña-Hernandez MA, Xu L, Tzeng TJ, Takahashi T, Herrin J, Güthe DB, Akrami A, Assaf G, Davis H, Harris K, McCorkell L, Schulz WL, Grffin D, Wei H, Ring AM, Guan L, Cruz CD, Iwasaki A, and Krumholz HM

Abstract

Background: Long COVID contributes to the global burden of disease. Proposed root cause hypotheses include the persistence of SARS-CoV-2 viral reservoir, autoimmunity, and reactivation of latent herpesviruses. Patients have reported various changes in Long COVID symptoms after COVID-19 vaccinations, leaving uncertainty about whether vaccine-induced immune responses may alleviate or worsen disease pathology., Methods: In this prospective study, we evaluated changes in symptoms and immune responses after COVID-19 vaccination in 16 vaccine-naïve individuals with Long COVID. Surveys were administered before vaccination and then at 2, 6, and 12 weeks after receiving the first vaccine dose of the primary series. Simultaneously, SARS-CoV-2-reactive TCR enrichment, SARS-CoV-2-specific antibody responses, antibody responses to other viral and self-antigens, and circulating cytokines were quantified before vaccination and at 6 and 12 weeks after vaccination., Results: Self-report at 12 weeks post-vaccination indicated 10 out of 16 participants had improved health, 3 had no change, 1 had worse health, and 2 reported marginal changes. Significant elevation in SARS-CoV-2-specific TCRs and Spike protein-specific IgG were observed 6 and 12 weeks after vaccination. No changes in reactivities were observed against herpes viruses and self-antigens. Within this dataset, higher baseline sIL-6R was associated with symptom improvement, and the two top features associated with non-improvement were high IFN-β and CNTF, among soluble analytes., Conclusions: Our study showed that in this small sample, vaccination improved the health or resulted in no change to the health of most participants, though few experienced worsening. Vaccination was associated with increased SARS-CoV-2 Spike protein-specific IgG and T cell expansion in most individuals with Long COVID. Symptom improvement was observed in those with baseline elevated sIL-6R, while elevated interferon and neuropeptide levels were associated with a lack of improvement.

Published
2024
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36. Microfluidic immuno-serology assay revealed a limited diversity of protection against COVID-19 in patients with altered immunity.

Author

Kim D, Biancon G, Bai Z, VanOudenhove J, Liu Y, Kothari S, Gowda L, Kwan JM, Buitrago-Pocasangre NC, Lele N, Asashima H, Racke MK, Wilson JE, Givens TS, Tomayko MM, Schulz WL, Longbrake EE, Hafler DA, Halene S, and Fan R

Abstract

The immune response to SARS-CoV-2 for patients with altered immunity such as hematologic malignancies and autoimmune disease may differ substantially from that in general population. These patients remain at high risk despite wide-spread adoption of vaccination. It is critical to examine the differences at the systems level between the general population and the patients with altered immunity in terms of immunologic and serological responses to COVID-19 infection and vaccination. Here, we developed a novel microfluidic chip for high-plex immuno-serological assay to simultaneously measure up to 50 plasma or serum samples for up to 50 soluble markers including 35 plasma proteins, 11 anti-spike/RBD IgG antibodies spanning all major variants, and controls. Our assay demonstrated the quintuplicate test in a single run with high throughput, low sample volume input, high reproducibility and high accuracy. It was applied to the measurement of 1,012 blood samples including in-depth analysis of sera from 127 patients and 21 healthy donors over multiple time points, either with acute COVID infection or vaccination. The protein association matrix analysis revealed distinct immune mediator protein modules that exhibited a reduced degree of diversity in protein-protein cooperation in patients with hematologic malignancies and patients with autoimmune disorders receiving B cell depletion therapy. Serological analysis identified that COVID infected patients with hematologic malignancies display impaired anti-RBD antibody response despite high level of anti-spike IgG, which could be associated with limited clonotype diversity and functional deficiency in B cells and was further confirmed by single-cell BCR and transcriptome sequencing. These findings underscore the importance to individualize immunization strategy for these high-risk patients and provide an informative tool to monitor their responses at the systems level.

Published
2022
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37. De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: A case report.

Author

Gandhi S, Klein J, Robertson A, Peña-Hernández MA, Lin MJ, Roychoudhury P, Lu P, Fournier J, Ferguson D, Mohamed Bakhash SA, Catherine Muenker M, Srivathsan A, Wunder EA, Kerantzas N, Wang W, Lindenbach B, Pyle A, Wilen CB, Ogbuagu O, Greninger AL, Iwasaki A, Schulz WL, and Ko AI

Abstract

SARS-CoV-2 remdesivir resistance mutations have been generated in vitro but have not been reported in patients receiving treatment with the antiviral agent. We present a case of an immunocompromised patient with acquired B-cell deficiency who developed an indolent, protracted course of SARS-CoV-2 infection. Remdesivir therapy alleviated symptoms and produced a transient virologic response, but her course was complicated by recrudescence of high-grade viral shedding. Whole genome sequencing identified a mutation, E802D, in the nsp12 RNA-dependent RNA polymerase, which was not present in pre-treatment specimens. In vitro experiments demonstrated that the mutation conferred a ∼6-fold increase in remdesivir IC50 but resulted in a fitness cost in the absence of remdesivir. Sustained clinical and virologic response was achieved after treatment with casirivimab-imdevimab. Although the fitness cost observed in vitro may limit the risk posed by E802D, this case illustrates the importance of monitoring for remdesivir resistance and the potential benefit of combinatorial therapies in immunocompromised patients with SARS-CoV-2 infection.

Published
2021
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