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1,163 results on '"Musser, James M."'

1. SARS-COV-2 Omicron variants conformationally escape a rare quaternary antibody binding mode

Author

Goike, Jule, Hsieh, Ching-Lin, Horton, Andrew P., Gardner, Elizabeth C., Zhou, Ling, Bartzoka, Foteini, Wang, Nianshuang, Javanmardi, Kamyab, Herbert, Andrew, Abbassi, Shawn, Xie, Xuping, Xia, Hongjie, Shi, Pei-Yong, Renberg, Rebecca, Segall-Shapiro, Thomas H., Terrace, Cynthia I., Wu, Wesley, Shroff, Raghav, Byrom, Michelle, Ellington, Andrew D., Marcotte, Edward M., Musser, James M., Kuchipudi, Suresh V., Kapur, Vivek, Georgiou, George, Weaver, Scott C., Dye, John M., Boutz, Daniel R., McLellan, Jason S., and Gollihar, Jimmy D.

Published
2023
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2. Klebsiella pneumoniae clinical isolates with features of both multidrug-resistance and hypervirulence have unexpectedly low virulence

Author

Kochan, Travis J., Nozick, Sophia H., Valdes, Aliki, Mitra, Sumitra D., Cheung, Bettina H., Lebrun-Corbin, Marine, Medernach, Rachel L., Vessely, Madeleine B., Mills, Jori O., Axline, Christopher M. R., Nelson, Julia A., VanGosen, Ethan M., Ward, Timothy J., Ozer, Egon A., van Duin, David, Chen, Liang, Kreiswirth, Barry N., Long, S. Wesley, Musser, James M., Bulman, Zackery P., Wunderink, Richard G., and Hauser, Alan R.

Published
2023
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3. Systems biology analysis of human genomes points to key pathways conferring spina bifida risk

Author

Aguiar-Pulido, Vanessa, Wolujewicz, Paul, Martinez-Fundichely, Alexander, Elhaik, Eran, Thareja, Gaurav, Aleem, Alice Abdel, Chalhoub, Nader, Cuykendall, Tawny, Al-Zamer, Jamel, Lei, Yunping, El-Bashir, Haitham, Musser, James M., Al-Kaabi, Abdulla, Shaw, Gary M., Khurana, Ekta, Suhre, Karsten, Mason, Christopher E., Elemento, Olivier, Finnell, Richard H., and Ross, M. Elizabeth

Published
2021

5. Signals of Significantly Increased Vaccine Breakthrough, Decreased Hospitalization Rates, and Less Severe Disease in Patients with Coronavirus Disease 2019 Caused by the Omicron Variant of Severe Acute Respiratory Syndrome Coronavirus 2 in Houston, Texas

Author

Christensen, Paul A., Olsen, Randall J., Long, S. Wesley, Snehal, Richard, Davis, James J., Ojeda Saavedra, Matthew, Reppond, Kristina, Shyer, Madison N., Cambric, Jessica, Gadd, Ryan, Thakur, Rashi M., Batajoo, Akanksha, Mangham, Regan, Pena, Sindy, Trinh, Trina, Kinskey, Jacob C., Williams, Guy, Olson, Robert, Gollihar, Jimmy, and Musser, James M.

Published
2022
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6. Using intrahost single nucleotide variant data to predict SARS-CoV-2 detection cycle threshold values.

Author

Duesterwald, Lea, Nguyen, Marcus, Christensen, Paul, Long, S. Wesley, Olsen, Randall J., Musser, James M., and Davis, James J.

Subjects
SINGLE nucleotide polymorphisms, STANDARD deviations, COVID-19 pandemic, VIRAL load, SARS-CoV-2
Abstract

Over the last four years, each successive wave of the COVID-19 pandemic has been caused by variants with mutations that improve the transmissibility of the virus. Despite this, we still lack tools for predicting clinically important features of the virus. In this study, we show that it is possible to predict the PCR cycle threshold (Ct) values from clinical detection assays using sequence data. Ct values often correspond with patient viral load and the epidemiological trajectory of the pandemic. Using a collection of 36,335 high quality genomes, we built models from SARS-CoV-2 intrahost single nucleotide variant (iSNV) data, computing XGBoost models from the frequencies of A, T, G, C, insertions, and deletions at each position relative to the Wuhan-Hu-1 reference genome. Our best model had an R2 of 0.604 [0.593–0.616, 95% confidence interval] and a Root Mean Square Error (RMSE) of 5.247 [5.156–5.337], demonstrating modest predictive power. Overall, we show that the results are stable relative to an external holdout set of genomes selected from SRA and are robust to patient status and the detection instruments that were used. This study highlights the importance of developing modeling strategies that can be applied to publicly available genome sequence data for use in disease prevention and control. [ABSTRACT FROM AUTHOR]

Published
2024
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7. Delta Variants of SARS-CoV-2 Cause Significantly Increased Vaccine Breakthrough COVID-19 Cases in Houston, Texas

Author

Christensen, Paul A., Olsen, Randall J., Long, S. Wesley, Subedi, Sishir, Davis, James J., Hodjat, Parsa, Walley, Debbie R., Kinskey, Jacob C., Ojeda Saavedra, Matthew, Pruitt, Layne, Reppond, Kristina, Shyer, Madison N., Cambric, Jessica, Gadd, Ryan, Thakur, Rashi M., Batajoo, Akanksha, Mangham, Regan, Pena, Sindy, Trinh, Trina, Yerramilli, Prasanti, Nguyen, Marcus, Olson, Robert, Snehal, Richard, Gollihar, Jimmy, and Musser, James M.

Published
2022
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8. Human M1 macrophages express unique innate immune response genes after mycobacterial infection to defend against tuberculosis

Author

Khan, Arshad, Zhang, Kangling, Singh, Vipul K., Mishra, Abhishek, Kachroo, Priyanka, Bing, Tian, Won, Jong Hak, Mani, Arunmani, Papanna, Ramesha, Mann, Lovepreet K., Ledezma-Campos, Eder, Aguillon-Duran, Genesis, Canaday, David H., David, Sunil A., Restrepo, Blanca I., Viet, Nhung Nguyen, Phan, Ha, Graviss, Edward A., Musser, James M., Kaushal, Deepak, Gauduin, Marie Claire, and Jagannath, Chinnaswamy

Published
2022
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9. Transmission history of SARS-CoV-2 in humans and white-tailed deer

Author

Willgert, Katriina, Didelot, Xavier, Surendran-Nair, Meera, Kuchipudi, Suresh V., Ruden, Rachel M., Yon, Michele, Nissly, Ruth H., Vandegrift, Kurt J., Nelli, Rahul K., Li, Lingling, Jayarao, Bhushan M., Levine, Nicole, Olsen, Randall J., Davis, James J., Musser, James M., Hudson, Peter J., Kapur, Vivek, and Conlan, Andrew J. K.

Published
2022
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10. Trajectory of Growth of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants in Houston, Texas, January through May 2021, Based on 12,476 Genome Sequences

Author

Olsen, Randall J., Christensen, Paul A., Long, S. Wesley, Subedi, Sishir, Hodjat, Parsa, Olson, Robert, Nguyen, Marcus, Davis, James J., Yerramilli, Prasanti, Saavedra, Matthew O., Pruitt, Layne, Reppond, Kristina, Shyer, Madison N., Cambric, Jessica, Gadd, Ryan, Thakur, Rashi M., Batajoo, Akanksha, Finkelstein, Ilya J., Gollihar, Jimmy, and Musser, James M.

Published
2021
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11. Significantly Decreased Mortality in a Large Cohort of Coronavirus Disease 2019 (COVID-19) Patients Transfused Early with Convalescent Plasma Containing High-Titer Anti–Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Spike Protein IgG

Author

Salazar, Eric, Christensen, Paul A., Graviss, Edward A., Nguyen, Duc T., Castillo, Brian, Chen, Jian, Lopez, Bevin V., Eagar, Todd N., Yi, Xin, Zhao, Picheng, Rogers, John, Shehabeldin, Ahmed, Joseph, David, Masud, Faisal, Leveque, Christopher, Olsen, Randall J., Bernard, David W., Gollihar, Jimmy, and Musser, James M.

Published
2021
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13. Treatment of Coronavirus Disease 2019 (COVID-19) Patients with Convalescent Plasma

Author

Salazar, Eric, Perez, Katherine K., Ashraf, Madiha, Chen, Jian, Castillo, Brian, Christensen, Paul A., Eubank, Taryn, Bernard, David W., Eagar, Todd N., Long, S. Wesley, Subedi, Sishir, Olsen, Randall J., Leveque, Christopher, Schwartz, Mary R., Dey, Monisha, Chavez-East, Cheryl, Rogers, John, Shehabeldin, Ahmed, Joseph, David, Williams, Guy, Thomas, Karen, Masud, Faisal, Talley, Christina, Dlouhy, Katharine G., Lopez, Bevin V., Hampton, Curt, Lavinder, Jason, Gollihar, Jimmy D., Maranhao, Andre C., Ippolito, Gregory C., Saavedra, Matthew O., Cantu, Concepcion C., Yerramilli, Prasanti, Pruitt, Layne, and Musser, James M.

Published
2020
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16. Convalescent plasma anti-SARS-CoV-2 spike protein ectodomain and receptor-binding domain IgG correlate with virus neutralization

Author

Salazar, Eric, Kuchipudi, Suresh V., Christensen, Paul A., Eagar, Todd, Yi, Xin, Zhao, Picheng, Jin, Zhicheng, Long, S. Wesley, Olsen, Randall J., Chen, Jian, Castillo, Brian, Leveque, Christopher, Towers, Dalton, Lavinder, Jason, Gollihar, Jimmy, Cardona, Jose, Ippolito, Gregory, Nissly, Ruth, Bird, Ian, Greenawalt, Denver, Rossi, Randall M., Gontu, Abhinay, Srinivasan, Sreenidhi, Poojary, Indira, Cattadori, Isabella M., Hudson, Peter J., Josleyn, Nicole M., Prugar, Laura, Huie, Kathleen, Herbert, Andrew, Bernard, David W., Dye, John M., Kapur, Vivek, and Musser, James M.

Subjects
Viral proteins -- Health aspects, Epidemics -- Control -- United States, COVID-19 -- Control, Immunoglobulin G -- Health aspects, Health care industry
Abstract

The newly emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) highlights the urgent need for assays that detect protective levels of neutralizing antibodies. We studied the relationship among anti-spike ectodomain (anti-ECD), antireceptor-binding domain (anti-RBD) IgG titers, and SARS-CoV-2 virus neutralization (VN) titers generated by 2 in vitro assays using convalescent plasma samples from 68 patients with COVID-19. We report a strong positive correlation between both plasma anti-RBD and anti-ECD IgG titers and in vitro VN titers. The probability of a VN titer of [greater than or equal to] 160, the FDA-recommended level for convalescent plasma used for COVID-19 treatment, was [greater than or equal to] 80% when anti-RBD or anti-ECD titers were [greater than or equal to] 1:1350. Of all donors, 37% lacked VN titers of [greater than or equal to] 160. Dyspnea, hospitalization, and disease severity were significantly associated with higher VN titer. Frequent donation of convalescent plasma did not significantly decrease VN or IgG titers. Analysis of 2814 asymptomatic adults found 73 individuals with anti-ECD IgG titers of [greater than or equal to] 1:50 and strong positive correlation with anti-RBD and VN titers. Fourteen of these individuals had VN titers of [greater than or equal to] 1:160, and all of them had anti-RBD titers of [greater than or equal to] 1:1350. We conclude that anti-RBD or anti-ECD IgG titers can serve as a surrogate for VN titers to identify suitable plasma donors. Plasma anti-RBD or anti-ECD titers of [greater than or equal to] 1:1350 may provide critical information about protection against COVID-19 disease., Introduction The recently emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel coronavirus that causes coronavirus disease 2019 (COVID-19) disease, has spread globally and is now responsible for massive [...]

Published
2020
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17. Limited window for donation of convalescent plasma with high live-virus neutralizing antibody titers for COVID-19 immunotherapy

Author

Gontu, Abhinay, Srinivasan, Sreenidhi, Salazar, Eric, Nair, Meera Surendran, Nissly, Ruth H., Greenawalt, Denver, Bird, Ian M., Herzog, Catherine M., Ferrari, Matthew J., Poojary, Indira, Katani, Robab, Lindner, Scott E., Minns, Allen M., Rossi, Randall, Christensen, Paul A., Castillo, Brian, Chen, Jian, Eagar, Todd N., Yi, Xin, Zhao, Picheng, Leveque, Christopher, Olsen, Randall J., Bernard, David W., Gollihar, Jimmy, Kuchipudi, Suresh V., Musser, James M., and Kapur, Vivek

Published
2021
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19. Gene fitness landscape of group A streptococcus during necrotizing myositis

Author

Zhu, Luchang, Olsen, Randall J., Beres, Stephen B., Eraso, Jesus M., Saavedra, Matthew Ojeda, Kubiak, Samantha L., Cantu, Concepcion C., Jenkins, Leslie, Charbonneau, Amelia R.L., Waller, Andrew S., and Musser, James M.

Subjects
DNA sequencing -- Usage, Myositis -- Diagnosis -- Genetic aspects -- Patient outcomes, Necrotizing fasciitis, Primates, Genomics, Amino acids, Peptides, Skeletal muscle, Blood lipids, Transposons, Infection, Genomes, Genetic research, Health care industry
Abstract

Necrotizing fasciitis and myositis are devastating infections characterized by high mortality. Group A streptococcus (GAS) is a common cause of these infections, but the molecular pathogenesis is poorly understood. We report a genome-wide analysis using serotype M1 and M28 strains that identified GAS genes contributing to necrotizing myositis in nonhuman primates (NHP), a clinically relevant model. Using transposon-directed insertion-site sequencing (TraDIS), we identified 126 and 116 GAS genes required for infection by serotype M1 and M28 organisms, respectively. For both M1 and M28 strains, more than 25% of the GAS genes required for necrotizing myositis encode known or putative transporters. Thirteen GAS transporters contributed to both M1 and M28 strain fitness in NHP myositis, including putative importers for amino acids, carbohydrates, and vitamins and exporters for toxins, quorum-sensing peptides, and uncharacterized molecules. Targeted deletion of genes encoding 5 transporters confirmed that each isogenic mutant strain was significantly (P < 0.05) impaired in causing necrotizing myositis in NHPs. Quantitative reverse-transcriptase PCR (qRT-PCR) analysis showed that these 5 genes are expressed in infected NHP and human skeletal muscle. Certain substrate-binding lipoproteins of these transporters, such as Spy0271 and Spy1728, were previously documented to be surface exposed, suggesting that our findings have translational research implications., Introduction Necrotizing fasciitis, commonly known as the flesh-eating disease, is an invasive infection with very high rates of human morbidity and mortality (1). In severe cases, contiguous muscle may be [...]

Published
2019
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32. Genome Sequence and Comparative Microarray Analysis of Serotype M18 Group A Streptococcus Strains Associated with Acute Rheumatic Fever Outbreaks

Author

Smoot, James C., Barbian, Kent D., Van Gompel, Jamie J., Smoot, Laura M., Chaussee, Michael S., Sylva, Gail L., Sturdevant, Daniel E., Ricklefs, Stacy M., Porcella, Stephen F., Parkins, Larye D., Beres, Stephen B., Campbell, David S., Smith, Todd M., Zhang, Qing, Kapur, Vivek, Daly, Judy A., Veasy, L. George, and Musser, James M.

Published
2002

45. SARS-CoV-2 Omicron (B.1.1.529) Infection of Wild White-Tailed Deer in New York City

Author

Vandegrift, Kurt J., primary, Yon, Michele, additional, Surendran Nair, Meera, additional, Gontu, Abhinay, additional, Ramasamy, Santhamani, additional, Amirthalingam, Saranya, additional, Neerukonda, Sabarinath, additional, Nissly, Ruth H., additional, Chothe, Shubhada K., additional, Jakka, Padmaja, additional, LaBella, Lindsey, additional, Levine, Nicole, additional, Rodriguez, Sophie, additional, Chen, Chen, additional, Sheersh Boorla, Veda, additional, Stuber, Tod, additional, Boulanger, Jason R., additional, Kotschwar, Nathan, additional, Aucoin, Sarah Grimké, additional, Simon, Richard, additional, Toal, Katrina L., additional, Olsen, Randall J., additional, Davis, James J., additional, Bold, Dashzeveg, additional, Gaudreault, Natasha N., additional, Dinali Perera, Krishani, additional, Kim, Yunjeong, additional, Chang, Kyeong-Ok, additional, Maranas, Costas D., additional, Richt, Juergen A., additional, Musser, James M., additional, Hudson, Peter J., additional, Kapur, Vivek, additional, and Kuchipudi, Suresh V., additional

Published
2022
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47. Evolutionary pathway to increased virulence and epidemic group A Streptococcus disease derived from 3,615 genome sequences

Author

Nasser, Waleed, Beres, Stephen B., Olsen, Randall J., Dean, Melissa A., Rice, Kelsey A., Long, S. Wesley, Kristinsson, Karl G., Gottfredsson, Magnus, Vuopio, Jaana, Raisanen, Kati, Caugant, Dominique A., Steinbakk, Martin, Low, Donald E., McGeer, Allison, Darenberg, Jessica, Henriques-Normark, Birgitta, Van Beneden, Chris A., Hoffmann, Steen, and Musser, James M.

Published
2014

49. Antibody escape and cryptic cross-domain stabilization in the SARS-CoV-2 Omicron spike protein

Author

Javanmardi, Kamyab, primary, Segall-Shapiro, Thomas H., additional, Chou, Chia-Wei, additional, Boutz, Daniel R., additional, Olsen, Randall J., additional, Xie, Xuping, additional, Xia, Hongjie, additional, Shi, Pei-Yong, additional, Johnson, Charlie D., additional, Annapareddy, Ankur, additional, Weaver, Scott, additional, Musser, James M., additional, Ellington, Andrew D., additional, Finkelstein, Ilya J., additional, and Gollihar, Jimmy D., additional

Published
2022
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50. A molecular trigger for intercontinental epidemics of group A Streptococcus

Author

Zhu, Luchang, Olsen, Randall J., Nasser, Waleed, Beres, Stephen B., Vuopio, Jaana, Kristinsson, Karl G., Gottfredsson, Magnus, Porter, Adeline R., DeLeo, Frank R., and Musser, James M.

Subjects
Epidemics, Streptococcus, Genetic polymorphisms -- Analysis -- Health aspects -- Research, Health care industry
Abstract

The identification of the molecular events responsible for strain emergence, enhanced virulence, and epidemicity has been a long-pursued goal in infectious diseases research. A recent analysis of 3,615 genomes of serotype M1 group A Streptococcus strains (the so-called 'flesh-eating' bacterium) identified a recombination event that coincides with the global M1 pandemic beginning in the early 1980s. Here, we have shown that the allelic variation that results from this recombination event, which replaces the chromosomal region encoding secreted NADase and streptolysin O, is the key driver of increased toxin production and enhanced infection severity of the M1 pandemic strains. Using isoallelic mutant strains, we found that 3 polymorphisms in this toxin gene region increase resistance to killing by human polymorphonuclear leukocytes, increase bacterial proliferation, and increase virulence in animal models of pharyngitis and necrotizing fasciitis. Genome sequencing of an additional 1,125 streptococcal strains and virulence studies revealed that a highly similar recombinational replacement event underlies an ongoing intercontinental epidemic of serotype M89 group A Streptococcus infections. By identifying the molecular changes that enhance upper respiratory tract fitness, increased resistance to innate immunity, and increased tissue destruction, we describe a mechanism that underpins epidemic streptococcal infections, which have affected many millions of people., Introduction One elusive goal in infectious diseases research is identification of the genetic changes and molecular mechanisms responsible for strain emergence, enhanced virulence, and epidemicity. This goal has practical importance [...]

Published
2015
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