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Turcinovic J, Kuhfeldt K, Sullivan M, Landaverde L, Platt JT, Alekseyev YO, Doucette-Stamm L, Hamer DH, Klapperich C, Landsberg HE, Connor JH. Transmission Dynamics and Rare Clustered Transmission Within an Urban University Population Before Widespread Vaccination. J Infect Dis 2024; 229:485-492. [PMID: 37856283 DOI: 10.1093/infdis/jiad397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 09/18/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND Universities returned to in-person learning in 2021 while SARS-CoV-2 spread remained high. At the time, it was not clear whether in-person learning would be a source of disease spread. METHODS We combined surveillance testing, universal contact tracing, and viral genome sequencing to quantify introductions and identify likely on-campus spread. RESULTS Ninety-one percent of viral genotypes occurred once, indicating no follow-on transmission. Less than 5% of introductions resulted in >3 cases, with 2 notable exceptions of 40 and 47 cases. Both partially overlapped with outbreaks defined by contact tracing. In both cases, viral genomics eliminated over half the epidemiologically linked cases but added an equivalent or greater number of individuals to the transmission cluster. CONCLUSIONS Public health interventions prevented within-university transmission for most SARS-CoV-2 introductions, with only 2 major outbreaks being identified January to May 2021. The genetically linked cases overlap with outbreaks identified by contact tracing; however, they persisted in the university population for fewer days and rounds of transmission than estimated via contact tracing. This underscores the effectiveness of test-trace-isolate strategies in controlling undetected spread of emerging respiratory infectious diseases. These approaches limit follow-on transmission in both outside-in and internal transmission conditions.
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Affiliation(s)
- Jacquelyn Turcinovic
- Department of Virology, Immunology, and Microbiology, Chobanian & Avedisian School of Medicine
- National Emerging Infectious Diseases Laboratories
- Program in Bioinformatics
| | | | | | - Lena Landaverde
- Department of Biomedical Engineering
- Precision Diagnostics Center
- BU Clinical Testing Laboratory, Research Department
| | | | | | | | - Davidson H Hamer
- National Emerging Infectious Diseases Laboratories
- Precision Diagnostics Center
- Department of Global Health, School of Public Health
- Section of Infectious Disease, Department of Medicine, Chobanian & Avedisian School of Medicine
- Center for Emerging Infectious Disease Policy and Research, Boston University, Massachusetts
| | - Catherine Klapperich
- Department of Biomedical Engineering
- Precision Diagnostics Center
- BU Clinical Testing Laboratory, Research Department
| | | | - John H Connor
- Department of Virology, Immunology, and Microbiology, Chobanian & Avedisian School of Medicine
- National Emerging Infectious Diseases Laboratories
- Program in Bioinformatics
- Center for Emerging Infectious Disease Policy and Research, Boston University, Massachusetts
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2
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Bouton TC, Atarere J, Turcinovic J, Seitz S, Sher-Jan C, Gilbert M, White L, Zhou Z, Hossain MM, Overbeck V, Doucette-Stamm L, Platt J, Landsberg HE, Hamer DH, Klapperich C, Jacobson KR, Connor JH. Viral Dynamics of Omicron and Delta Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants With Implications for Timing of Release from Isolation: A Longitudinal Cohort Study. Clin Infect Dis 2023; 76:e227-e233. [PMID: 35737948 PMCID: PMC9278204 DOI: 10.1093/cid/ciac510] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/15/2022] [Accepted: 06/17/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND In January 2022, US guidelines shifted to recommend isolation for 5 days from symptom onset, followed by 5 days of mask-wearing. However, viral dynamics and variant and vaccination impact on culture conversion are largely unknown. METHODS We conducted a longitudinal study on a university campus, collecting daily anterior nasal swabs for at least 10 days for reverse-transcription polymerase chain reaction (RT-PCR) testing and culture, with antigen rapid diagnostic testing (RDT) on a subset. We compared culture positivity beyond day 5, time to culture conversion, and cycle threshold trend when calculated from diagnostic test, from symptom onset, by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant, and by vaccination status. We evaluated sensitivity and specificity of RDT on days 4-6 compared with culture. RESULTS Among 92 SARS-CoV-2 RT-PCR-positive participants, all completed the initial vaccine series; 17 (18.5%) were infected with Delta and 75 (81.5%) with Omicron. Seventeen percent of participants had positive cultures beyond day 5 from symptom onset, with the latest on day 12. There was no difference in time to culture conversion by variant or vaccination status. For 14 substudy participants, sensitivity and specificity of day 4-6 RDT were 100% and 86%, respectively. CONCLUSIONS The majority of our Delta- and Omicron-infected cohort culture-converted by day 6, with no further impact of booster vaccination on sterilization or cycle threshold decay. We found that rapid antigen testing may provide reassurance of lack of infectiousness, though guidance to mask for days 6-10 is supported by our finding that 17% of participants remained culture-positive after isolation.
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Affiliation(s)
- Tara C Bouton
- Section of Infectious Diseases, Boston University School of Medicine, Boston, Massachusetts, USA.,Boston Medical Center, Boston, Massachusetts, USA
| | | | - Jacquelyn Turcinovic
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA.,BioInformatics Program, Boston University, Boston, Massachusetts, USA
| | - Scott Seitz
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Cole Sher-Jan
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Madison Gilbert
- Boston Medical Center, Boston, Massachusetts, USA.,Graduate Medical Sciences, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Laura White
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Zhenwei Zhou
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Mohammad M Hossain
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Victoria Overbeck
- Boston Medical Center, Boston, Massachusetts, USA.,Boston University School of Public Health, Boston, Massachusetts, USA
| | | | - Judy Platt
- Boston University Student Health Services, Boston, Massachusetts, USA
| | | | - Davidson H Hamer
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA.,Department of Global Health, Boston University School of Public Health, Boston, Massachusetts, USA.,Center for Emerging Infectious Disease Research and Policy, Boston University, Boston, Massachusetts, USA
| | - Catherine Klapperich
- Boston University School of Public Health, Boston, Massachusetts, USA.,Boston University Clinical Testing Laboratory, Boston, Massachusetts, USA.,Boston University Precision Diagnostics Center, Boston University, Boston, Massachusetts, USA
| | - Karen R Jacobson
- Section of Infectious Diseases, Boston University School of Medicine, Boston, Massachusetts, USA.,Boston Medical Center, Boston, Massachusetts, USA
| | - John H Connor
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA.,Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA.,BioInformatics Program, Boston University, Boston, Massachusetts, USA.,Boston University Precision Diagnostics Center, Boston University, Boston, Massachusetts, USA
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3
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Landaverde L, Turcinovic J, Doucette-Stamm L, Gonzales K, Platt J, Connor JH, Klapperich C. Comparison of BinaxNOW and SARS-CoV-2 qRT-PCR Detection of the Omicron Variant from Matched Anterior Nares Swabs. Microbiol Spectr 2022; 10:e0130722. [PMID: 36255297 PMCID: PMC9769721 DOI: 10.1128/spectrum.01307-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 09/22/2022] [Indexed: 01/05/2023] Open
Abstract
The COVID-19 pandemic has increased use of rapid diagnostic tests (RDTs). In winter 2021 to 2022, the Omicron variant surge made it apparent that although RDTs are less sensitive than quantitative reverse transcription-PCR (qRT-PCR), the accessibility, ease of use, and rapid readouts made them a sought after and often sold-out item at local suppliers. Here, we sought to qualify the Abbott BinaxNOW RDT for use in our university testing program as a method to rule in positive or rule out negative individuals quickly at our priority qRT-PCR testing site. To perform this qualification study, we collected additional swabs from individuals attending this site. All swabs were tested using BinaxNOW. Initially as part of a feasibility study, test period 1 (n = 110) samples were stored cold before testing. In test period 2 (n = 209), samples were tested immediately. Combined, 102/319 samples tested severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positive via qRT-PCR. All sequenced samples were Omicron (n = 92). We calculated 53.9% sensitivity, 100% specificity, a 100% positive predictive value, and an 82.2% negative predictive value for BinaxNOW (n = 319). Sensitivity would be improved (75.3%) by changing the qRT-PCR positivity threshold from a threshold cycle (CT) value of 40 to a CT value of 30. The receiver operating characteristic (ROC) curve shows that for qRT-PCR-positive CT values of between 24 and 40, the BinaxNOW test is of limited value diagnostically. Results suggest BinaxNOW could be used in our setting to confirm SARS-CoV-2 infection in individuals with substantial viral load, but a significant fraction of infected individuals would be missed if we used RDTs exclusively to rule out infection. IMPORTANCE Our results suggest BinaxNOW can rule in SARS-CoV-2 infection but would miss infections if RDTs were exclusively used.
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Affiliation(s)
- Lena Landaverde
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Clinical Testing Laboratory, Boston University, Boston, Massachusetts, USA
- Precision Diagnostics Center, Boston University, Boston, Massachusetts, USA
| | - Jacquelyn Turcinovic
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Program in Bioinformatics, Boston University, Boston, Massachusetts, USA
| | | | - Kevin Gonzales
- Student Health Services, Healthway, Boston University, Boston, Massachusetts, USA
- Office of Research, Boston University, Boston, Massachusetts, USA
| | - Judy Platt
- Student Health Services, Healthway, Boston University, Boston, Massachusetts, USA
| | - John H. Connor
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Program in Bioinformatics, Boston University, Boston, Massachusetts, USA
- Center for Emerging Infectious Disease Research and Policy, Boston University, Boston, Massachusetts, USA
| | - Catherine Klapperich
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Clinical Testing Laboratory, Boston University, Boston, Massachusetts, USA
- Precision Diagnostics Center, Boston University, Boston, Massachusetts, USA
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4
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Turcinovic J, Kuhfeldt K, Sullivan M, Landaverde L, Platt JT, Doucette-Stamm L, Hanage WP, Hamer DH, Klapperich C, Landsberg HE, Connor JH. Linking contact tracing with genomic surveillance to deconvolute SARS-CoV-2 transmission on a university campus. iScience 2022; 25:105337. [PMID: 36246573 PMCID: PMC9554197 DOI: 10.1016/j.isci.2022.105337] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 08/12/2022] [Accepted: 10/10/2022] [Indexed: 11/26/2022] Open
Abstract
Contact tracing and genomic data, approaches often used separately, have both been important tools in understanding the nature of SARS-CoV-2 transmission. Linked analysis of contact tracing and sequence relatedness of SARS-CoV-2 genomes from a regularly sampled university environment were used to build a multilevel transmission tracing and confirmation system to monitor and understand transmission on campus. Our investigation of an 18-person cluster stemming from an athletic team highlighted the importance of linking contact tracing and genomic analysis. Through these findings, it is suggestive that certain safety protocols in the athletic practice setting reduced transmission. The linking of traditional contact tracing with rapid-return genomic information is an effective approach for differentiating between multiple plausible transmission scenarios and informing subsequent public health protocols to limit disease spread in a university environment. Contact tracing and sequencing provide more information than either approach alone Primary exposures in an athletic group occurred outside structured athletic events Genomic and contact tracing data can inform effective public health decisions
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Affiliation(s)
- Jacquelyn Turcinovic
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA,National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA,Program in Bioinformatics, Boston University, Boston, MA 02215, USA
| | - Kayla Kuhfeldt
- Student Health Services, Boston University, Boston, MA 02215, USA
| | - Madison Sullivan
- Student Health Services, Boston University, Boston, MA 02215, USA
| | - Lena Landaverde
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA,Precision Diagnostics Center, Boston University, Boston, MA 02215, USA,BU Clinical Testing Laboratory, Research Department, Boston University, Boston, MA 02215, USA
| | - Judy T. Platt
- Student Health Services, Boston University, Boston, MA 02215, USA
| | - Lynn Doucette-Stamm
- BU Clinical Testing Laboratory, Research Department, Boston University, Boston, MA 02215, USA
| | - William P. Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Davidson H. Hamer
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA,Precision Diagnostics Center, Boston University, Boston, MA 02215, USA,Department of Global Health, Boston University School of Public Health, Boston, MA 02118, USA,Section of Infectious Disease, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA,Center for Emerging Infectious Disease Policy and Research, Boston University, Boston, MA 02118, USA
| | - Catherine Klapperich
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA,Precision Diagnostics Center, Boston University, Boston, MA 02215, USA
| | | | - John H. Connor
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA,National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA,Program in Bioinformatics, Boston University, Boston, MA 02215, USA,Center for Emerging Infectious Disease Policy and Research, Boston University, Boston, MA 02118, USA,Corresponding author
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5
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Kuhfeldt K, Turcinovic J, Sullivan M, Landaverde L, Doucette-Stamm L, Hamer DH, Platt JT, Klapperich C, Landsberg HE, Connor JH. Examination of SARS-CoV-2 In-Class Transmission at a Large Urban University With Public Health Mandates Using Epidemiological and Genomic Methodology. JAMA Netw Open 2022; 5:e2225430. [PMID: 35930286 PMCID: PMC9356317 DOI: 10.1001/jamanetworkopen.2022.25430] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
IMPORTANCE SARS-CoV-2, the causative agent of COVID-19, has displayed person-to-person transmission in a variety of indoor situations. This potential for robust transmission has posed significant challenges and concerns for day-to-day activities of colleges and universities where indoor learning is a focus for students, faculty, and staff. OBJECTIVE To assess whether in-class instruction without any physical distancing, but with other public health mitigation strategies, is a risk for driving SARS-CoV-2 transmission. DESIGN, SETTING, AND PARTICIPANTS This cohort study examined the evidence for SARS-CoV-2 transmission on a large urban US university campus using contact tracing, class attendance, and whole genome sequencing during the 2021 fall semester. Eligible participants were on-campus and off-campus individuals involved in campus activities. Data were analyzed between September and December 2021. EXPOSURES Participation in class and work activities on a campus with mandated vaccination and indoor masking but that was otherwise fully open without physical distancing during a time of ongoing transmission of SARS-CoV-2, both at the university and in the surrounding counties. MAIN OUTCOMES AND MEASURES Likelihood of in-class infection was assessed by measuring the genetic distance between all potential in-class transmission pairings using polymerase chain reaction testing. RESULTS More than 600 000 polymerase chain reaction tests were conducted throughout the semester, with 896 tests (0.1%) showing detectable SARS-CoV-2; there were over 850 cases of SARS-CoV-2 infection identified through weekly surveillance testing of all students and faculty on campus during the fall 2021 semester. The rolling mean average of positive tests ranged between 4 and 27 daily cases. Of more than 140 000 in-person class events and a total student population of 33 000 between graduate and undergraduate students, only 9 instances of potential in-class transmission were identified, accounting for 0.0045% of all classroom meetings. CONCLUSIONS AND RELEVANCE In this cohort study, the data suggested that under robust transmission abatement strategies, in-class instruction was not an appreciable source of disease transmission.
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Affiliation(s)
- Kayla Kuhfeldt
- Student Health Services, Boston University, Boston, Massachusetts
| | - Jacquelyn Turcinovic
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts
- Program in Bioinformatics, Boston University, Boston, Massachusetts
| | - Madison Sullivan
- Student Health Services, Boston University, Boston, Massachusetts
| | - Lena Landaverde
- Department of Biomedical Engineering and Precision Diagnostics Center, Boston University, Boston, Massachusetts
- Boston University Clinical Testing Laboratory, Research Department, Boston University, Boston, Massachusetts
| | - Lynn Doucette-Stamm
- Boston University Clinical Testing Laboratory, Research Department, Boston University, Boston, Massachusetts
| | - Davidson H. Hamer
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts
- Department of Global Health, Boston University School of Public Health, Boston, Massachusetts
- Section of Infectious Disease, Department of Medicine, Boston University School of Medicine; Boston, Massachusetts
- Center for Emerging Infectious Disease Research and Policy, Boston University, Boston, Massachusetts
| | - Judy T. Platt
- Student Health Services, Boston University, Boston, Massachusetts
| | - Catherine Klapperich
- Department of Biomedical Engineering and Precision Diagnostics Center, Boston University, Boston, Massachusetts
| | | | - John H. Connor
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts
- Program in Bioinformatics, Boston University, Boston, Massachusetts
- Center for Emerging Infectious Disease Research and Policy, Boston University, Boston, Massachusetts
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6
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Grazon C, Chern M, Lally P, Baer RC, Fan A, Lecommandoux S, Klapperich C, Dennis AM, Galagan JE, Grinstaff MW. The quantum dot vs. organic dye conundrum for ratiometric FRET-based biosensors: which one would you chose? Chem Sci 2022; 13:6715-6731. [PMID: 35756504 PMCID: PMC9172442 DOI: 10.1039/d1sc06921g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 05/04/2022] [Indexed: 11/21/2022] Open
Abstract
Förster resonance energy transfer (FRET) is a widely used and ideal transduction modality for fluorescent based biosensors as it offers high signal to noise with a visibly detectable signal. While intense efforts are ongoing to improve the limit of detection and dynamic range of biosensors based on biomolecule optimization, the selection of and relative location of the dye remains understudied. Herein, we describe a combined experimental and computational study to systematically compare the nature of the dye, i.e., organic fluorophore (Cy5 or Texas Red) vs. inorganic nanoparticle (QD), and the position of the FRET donor or acceptor on the biomolecular components. Using a recently discovered transcription factor (TF)-deoxyribonucleic acid (DNA) biosensor for progesterone, we examine four different biosensor configurations and report the quantum yield, lifetime, FRET efficiency, IC50, and limit of detection. Fitting the computational models to the empirical data identifies key molecular parameters driving sensor performance in each biosensor configuration. Finally, we provide a set of design parameters to enable one to select the fluorophore system for future intermolecular biosensors using FRET-based conformational regulation in in vitro assays and new diagnostic devices.
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Affiliation(s)
- Chloé Grazon
- Department of Chemistry, Boston University Boston MA 02215 USA .,University Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629 F-33600 Pessac France .,University Bordeaux, CNRS, Bordeaux INP, ISM, UMR 5255 F-33400 Talence France
| | - Margaret Chern
- Division of Materials Science and Engineering, Boston University Boston MA 02215 USA
| | - Patrick Lally
- Department of Biomedical Engineering, Boston University Boston MA 02215 USA
| | - R. C. Baer
- Department of Microbiology, Boston UniversityBostonMA 02118USA,National Emerging Infectious Diseases Laboratories, Boston UniversityBostonMA 02118USA
| | - Andy Fan
- Department of Biomedical Engineering, Boston University Boston MA 02215 USA
| | | | | | - Allison M. Dennis
- Division of Materials Science and Engineering, Boston UniversityBostonMA 02215USA,Department of Biomedical Engineering, Boston UniversityBostonMA 02215USA
| | - James E. Galagan
- Department of Microbiology, Boston UniversityBostonMA 02118USA,Department of Biomedical Engineering, Boston UniversityBostonMA 02215USA,National Emerging Infectious Diseases Laboratories, Boston UniversityBostonMA 02118USA
| | - Mark W. Grinstaff
- Department of Chemistry, Boston UniversityBostonMA 02215USA,Division of Materials Science and Engineering, Boston UniversityBostonMA 02215USA,Department of Biomedical Engineering, Boston UniversityBostonMA 02215USA
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7
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Bouton TC, Atarere J, Turcinovic J, Seitz S, Sher-Jan C, Gilbert M, White L, Zhou Z, Hossain MM, Overbeck V, Doucette-Stamm L, Platt J, Landsberg HE, Hamer DH, Klapperich C, Jacobson KR, Connor JH. Viral dynamics of Omicron and Delta SARS-CoV-2 variants with implications for timing of release from isolation: a longitudinal cohort study. medRxiv 2022:2022.04.04.22273429. [PMID: 35411341 PMCID: PMC8996632 DOI: 10.1101/2022.04.04.22273429] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Background In January 2022, United States guidelines shifted to recommend isolation for 5 days from symptom onset, followed by 5 days of mask wearing. However, viral dynamics and variant and vaccination impact on culture conversion are largely unknown. Methods We conducted a longitudinal study on a university campus, collecting daily anterior nasal swabs for at least 10 days for RT-PCR and culture, with antigen rapid diagnostic testing (RDT) on a subset. We compared culture positivity beyond day 5, time to culture conversion, and cycle threshold trend when calculated from diagnostic test, from symptom onset, by SARS-CoV-2 variant, and by vaccination status. We evaluated sensitivity and specificity of RDT on days 4-6 compared to culture. Results Among 92 SARS-CoV-2 RT-PCR positive participants, all completed the initial vaccine series, 17 (18.5%) were infected with Delta and 75 (81.5%) with Omicron. Seventeen percent of participants had positive cultures beyond day 5 from symptom onset with the latest on day 12. There was no difference in time to culture conversion by variant or vaccination status. For the 14 sub-study participants, sensitivity and specificity of RDT were 100% and 86% respectively. Conclusions The majority of our Delta- and Omicron-infected cohort culture-converted by day 6, with no further impact of booster vaccination on sterilization or cycle threshold decay. We found that rapid antigen testing may provide reassurance of lack of infectiousness, though masking for a full 10 days is necessary to prevent transmission from the 17% of individuals who remain culture positive after isolation. Main Point Beyond day 5, 17% of our Delta and Omicron-infected cohort were culture positive. We saw no significant impact of booster vaccination on within-host Omicron viral dynamics. Additionally, we found that rapid antigen testing may provide reassurance of lack of infectiousness.
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Affiliation(s)
- Tara C Bouton
- Section of Infectious Diseases, Boston University School of Medicine, Boston, MA, USA
- Boston Medical Center, Boston, MA, USA
| | | | - Jacquelyn Turcinovic
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- BioInformatics Program, Boston University, Boston, MA, USA
| | - Scott Seitz
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA
| | - Cole Sher-Jan
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Madison Gilbert
- Boston Medical Center, Boston, MA, USA
- Graduate Medical Sciences, Boston University School of Medicine, Boston, MA, USA
| | - Laura White
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Zhenwei Zhou
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Mohammad M Hossain
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Victoria Overbeck
- Boston Medical Center, Boston, MA, USA
- Boston University School of Public Health, Boston, MA, USA
| | | | - Judy Platt
- Boston University Student Health Services, Boston, MA, USA
| | | | - Davidson H Hamer
- Department of Global Health, Boston University School of Public Health, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Center for Emerging Infectious Disease Research and Policy, Boston University, Boston, MA, USA
| | - Catherine Klapperich
- Boston University Clinical Testing Laboratory, Boston, MA, USA
- Boston University Student Health Services, Boston, MA, USA
- Boston University Precision Diagnostics Center, Boston University, Boston, MA, USA
| | - Karen R Jacobson
- Section of Infectious Diseases, Boston University School of Medicine, Boston, MA, USA
- Boston Medical Center, Boston, MA, USA
| | - John H Connor
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Boston University Precision Diagnostics Center, Boston University, Boston, MA, USA
- BioInformatics Program, Boston University, Boston, MA, USA
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8
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Kuhfeldt K, Turcinovic J, Sullivan M, Landaverde L, Doucette-Stamm L, Hamer DH, Platt J, Klapperich C, Landsberg HE, Connor JH. Minimal SARS-CoV-2 classroom transmission at a large urban university experiencing repeated into campus introduction. medRxiv 2022:2022.03.16.22271983. [PMID: 35313596 PMCID: PMC8936094 DOI: 10.1101/2022.03.16.22271983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
SARS-CoV-2, the causative agent of COVID-19, has displayed person to person transmission in a variety of indoor situations. This potential for robust transmission has posed significant challenges to day-to-day activities of colleges and universities where indoor learning is a focus. Concerns about transmission in the classroom setting have been of concern for students, faculty and staff. With the simultaneous implementation of both non-pharmaceutical and pharmaceutical control measures meant to curb the spread of the disease, defining whether in-class instruction without any physical distancing is a risk for driving transmission is important. We examined the evidence for SARS-CoV-2 transmission on a large urban university campus that mandated vaccination and masking but was otherwise fully open without physical distancing during a time of ongoing transmission of SARS-CoV-2 both at the university and in the surrounding counties. Using weekly surveillance testing of all on-campus individuals and rapid contact tracing of individuals testing positive for the virus we found little evidence of in-class transmission. Of more than 140,000 in-person class events, only nine instances of potential in-class transmission were identified. When each of these events were further interrogated by whole-genome sequencing of all positive cases significant genetic distance was identified between all potential in-class transmission pairings, providing evidence that all individuals were infected outside of the classroom. These data suggest that under robust transmission abatement strategies, in-class instruction is not an appreciable source of disease transmission.
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Affiliation(s)
- Kayla Kuhfeldt
- Student Health Services, Boston University, Boston, MA USA
| | - Jacquelyn Turcinovic
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Program in Bioinformatics, Boston University, Boston, MA, USA
| | | | - Lena Landaverde
- Department of Biomedical Engineering and Precision Diagnostics Center, Boston University, Boston, MA, USA
- BU Clinical Testing Laboratory, Research Department, Boston University, Boston, MA
| | - Lynn Doucette-Stamm
- BU Clinical Testing Laboratory, Research Department, Boston University, Boston, MA
| | - Davidson H Hamer
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Global Health, Boston University School of Public Health, Boston, MA
- Section of Infectious Disease, Department of Medicine, Boston University School of Medicine; Boston, MA
- Center for Emerging Infectious Disease Research and Policy, Boston University, Boston, MA
| | - Judy Platt
- Department of Global Health, Boston University School of Public Health, Boston, MA
| | - Catherine Klapperich
- Department of Biomedical Engineering and Precision Diagnostics Center, Boston University, Boston, MA, USA
| | | | - John H Connor
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Program in Bioinformatics, Boston University, Boston, MA, USA
- Center for Emerging Infectious Disease Research and Policy, Boston University, Boston, MA
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9
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Hamer DH, White LF, Jenkins HE, Gill CJ, Landsberg HE, Klapperich C, Bulekova K, Platt J, Decarie L, Gilmore W, Pilkington M, MacDowell TL, Faria MA, Densmore D, Landaverde L, Li W, Rose T, Burgay SP, Miller C, Doucette-Stamm L, Lockard K, Elmore K, Schroeder T, Zaia AM, Kolaczyk ED, Waters G, Brown RA. Assessment of a COVID-19 Control Plan on an Urban University Campus During a Second Wave of the Pandemic. JAMA Netw Open 2021; 4:e2116425. [PMID: 34170303 PMCID: PMC8233704 DOI: 10.1001/jamanetworkopen.2021.16425] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/03/2021] [Indexed: 01/15/2023] Open
Abstract
Importance The COVID-19 pandemic has severely disrupted US educational institutions. Given potential adverse financial and psychosocial effects of campus closures, many institutions developed strategies to reopen campuses in the fall 2020 semester despite the ongoing threat of COVID-19. However, many institutions opted to have limited campus reopening to minimize potential risk of spread of SARS-CoV-2. Objective To analyze how Boston University (BU) fully reopened its campus in the fall of 2020 and controlled COVID-19 transmission despite worsening transmission in Boston, Massachusetts. Design, Setting, and Participants This multifaceted intervention case series was conducted at a large urban university campus in Boston, Massachusetts, during the fall 2020 semester. The BU response included a high-throughput SARS-CoV-2 polymerase chain reaction testing facility with capacity to deliver results in less than 24 hours; routine asymptomatic screening for COVID-19; daily health attestations; adherence monitoring and feedback; robust contact tracing, quarantine, and isolation in on-campus facilities; face mask use; enhanced hand hygiene; social distancing recommendations; dedensification of classrooms and public places; and enhancement of all building air systems. Data were analyzed from December 20, 2020, to January 31, 2021. Main Outcomes and Measures SARS-CoV-2 diagnosis confirmed by reverse transcription-polymerase chain reaction of anterior nares specimens and sources of transmission, as determined through contact tracing. Results Between August and December 2020, BU conducted more than 500 000 COVID-19 tests and identified 719 individuals with COVID-19, including 496 students (69.0%), 11 faculty (1.5%), and 212 staff (29.5%). Overall, 718 individuals, or 1.8% of the BU community, had test results positive for SARS-CoV-2. Of 837 close contacts traced, 86 individuals (10.3%) had test results positive for COVID-19. BU contact tracers identified a source of transmission for 370 individuals (51.5%), with 206 individuals (55.7%) identifying a non-BU source. Among 5 faculty and 84 staff with SARS-CoV-2 with a known source of infection, most reported a transmission source outside of BU (all 5 faculty members [100%] and 67 staff members [79.8%]). A BU source was identified by 108 of 183 undergraduate students with SARS-CoV-2 (59.0%) and 39 of 98 graduate students with SARS-CoV-2 (39.8%); notably, no transmission was traced to a classroom setting. Conclusions and Relevance In this case series of COVID-19 transmission, BU used a coordinated strategy of testing, contact tracing, isolation, and quarantine, with robust management and oversight, to control COVID-19 transmission in an urban university setting.
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Affiliation(s)
- Davidson H. Hamer
- Department of Global Health, Boston University School of Public Health, Boston, Massachusetts
- Section of Infectious Disease, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
- National Emerging Infectious Disease Laboratory, Boston, Massachusetts
- Precision Diagnostics Center, Boston University, Boston, Massachusetts
| | - Laura F. White
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Helen E. Jenkins
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Christopher J. Gill
- Department of Global Health, Boston University School of Public Health, Boston, Massachusetts
| | - Hannah E. Landsberg
- Student Health Services, Healthway, Boston University, Boston, Massachusetts
| | - Catherine Klapperich
- Precision Diagnostics Center, Boston University, Boston, Massachusetts
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts
| | - Katia Bulekova
- Information Services and Technology, Boston University, Boston, Massachusetts
| | - Judy Platt
- Student Health Services, Healthway, Boston University, Boston, Massachusetts
| | - Linette Decarie
- Boston University Analytical Services & Institutional Research, Boston, Massachusetts
| | - Wayne Gilmore
- Information Services and Technology, Boston University, Boston, Massachusetts
| | - Megan Pilkington
- Boston University Analytical Services & Institutional Research, Boston, Massachusetts
| | - Trevor L. MacDowell
- Information Services and Technology, Boston University, Boston, Massachusetts
| | - Mark A. Faria
- Information Services and Technology, Boston University, Boston, Massachusetts
| | - Douglas Densmore
- Electrical and Computer Engineering, Boston University, Boston, Massachusetts
- Biological Design Center, Boston University, Boston, Massachusetts
| | - Lena Landaverde
- Student Health Services, Healthway, Boston University, Boston, Massachusetts
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts
| | - Wenrui Li
- Department of Mathematics and Statistics, Boston University, Boston, Massachusetts
| | - Tom Rose
- Human Resources, Boston University, Boston, Massachusetts
| | - Stephen P. Burgay
- Office of External Affairs, Boston University, Boston, Massachusetts
| | - Candice Miller
- BU Clinical Testing Laboratory, Research Department, Boston University, Boston, Massachusetts
| | - Lynn Doucette-Stamm
- BU Clinical Testing Laboratory, Research Department, Boston University, Boston, Massachusetts
| | - Kelly Lockard
- Continuous Improvement & Data Analytics, Boston University, Boston, Massachusetts
| | - Kenneth Elmore
- Office of the Provost, Boston University, Boston, Massachusetts
| | - Tracy Schroeder
- Information Services and Technology, Boston University, Boston, Massachusetts
| | - Ann M. Zaia
- Occupational Health Center, Boston University, Boston Massachusetts
| | - Eric D. Kolaczyk
- Department of Mathematics and Statistics, Boston University, Boston, Massachusetts
- Hariri Institute for Computing, Boston University, Boston, Massachusetts
| | - Gloria Waters
- Office of the Provost, Boston University, Boston, Massachusetts
- College of Health and Rehabilitation Services, Sargent College, Boston University, Boston, Massachusetts
| | - Robert A. Brown
- College of Engineering, Boston University, Boston, Massachusetts
- Office of the President, Boston University, Boston, Massachusetts
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Landaverde L, Wong W, Hernandez G, Fan A, Klapperich C. Method for the elucidation of LAMP products captured on lateral flow strips in a point of care test for HPV 16. Anal Bioanal Chem 2020; 412:6199-6209. [PMID: 32488390 PMCID: PMC7266737 DOI: 10.1007/s00216-020-02702-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/27/2020] [Accepted: 05/11/2020] [Indexed: 12/11/2022]
Abstract
Loop-mediated amplification (LAMP) is an isothermal amplification technique favored in diagnostics and point-of-care work due to its high sensitivity and ability to run in isothermal conditions. In addition, a visual readout by lateral flow strips (LFS) can be used in conjunction with LAMP, making the assay accessible at the point-of-care. However, the amplicons resulting from a LAMP reaction varied in length and shape, making them undiscernible on a double-stranded DNA intercalating dye stained gel. Standard characterization techniques also do not identify which amplicons specifically bind to the LFS, which generate the visual readout. We aimed to standardize our characterization of LAMP products during assay development by using fluorescein amidite (FAM) and biotin-tagged loop forward and backward primers during assay development. A pvuII restriction enzyme digest is applied to the LAMP products. FAM-tagged bands are directly correlated with the LFS visual readout. We applied this assay development workflow for an HPV 16 assay using both plasmid DNA and clinical samples to demonstrate proof of concept for generalized assay development work.
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Affiliation(s)
- Lena Landaverde
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA, 02215, USA
| | - Winnie Wong
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA, 02215, USA
| | - Gabriela Hernandez
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA, 02215, USA
| | - Andy Fan
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA, 02215, USA
| | - Catherine Klapperich
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA, 02215, USA.
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11
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Grazon C, Baer RC, Kuzmanović U, Nguyen T, Chen M, Zamani M, Chern M, Aquino P, Zhang X, Lecommandoux S, Fan A, Cabodi M, Klapperich C, Grinstaff MW, Dennis AM, Galagan JE. A progesterone biosensor derived from microbial screening. Nat Commun 2020; 11:1276. [PMID: 32152281 PMCID: PMC7062782 DOI: 10.1038/s41467-020-14942-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 02/03/2020] [Indexed: 01/08/2023] Open
Abstract
Bacteria are an enormous and largely untapped reservoir of biosensing proteins. We describe an approach to identify and isolate bacterial allosteric transcription factors (aTFs) that recognize a target analyte and to develop these TFs into biosensor devices. Our approach utilizes a combination of genomic screens and functional assays to identify and isolate biosensing TFs, and a quantum-dot Förster Resonance Energy Transfer (FRET) strategy for transducing analyte recognition into real-time quantitative measurements. We use this approach to identify a progesterone-sensing bacterial aTF and to develop this TF into an optical sensor for progesterone. The sensor detects progesterone in artificial urine with sufficient sensitivity and specificity for clinical use, while being compatible with an inexpensive and portable electronic reader for point-of-care applications. Our results provide proof-of-concept for a paradigm of microbially-derived biosensors adaptable to inexpensive, real-time sensor devices.
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Affiliation(s)
- Chloé Grazon
- Department of Chemistry, Boston University, Boston, MA, 02215, USA
- University Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600, Pessac, France
| | - R C Baer
- Department of Microbiology, Boston University, Boston, MA, 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, 02118, USA
| | - Uroš Kuzmanović
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Thuy Nguyen
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Mingfu Chen
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Marjon Zamani
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Margaret Chern
- Division of Materials Science and Engineering, Boston University, Boston, MA, 02215, USA
| | - Patricia Aquino
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Xiaoman Zhang
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | | | - Andy Fan
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Mario Cabodi
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Catherine Klapperich
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
- Division of Materials Science and Engineering, Boston University, Boston, MA, 02215, USA
| | - Mark W Grinstaff
- Department of Chemistry, Boston University, Boston, MA, 02215, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
- Division of Materials Science and Engineering, Boston University, Boston, MA, 02215, USA
| | - Allison M Dennis
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
- Division of Materials Science and Engineering, Boston University, Boston, MA, 02215, USA
| | - James E Galagan
- Department of Microbiology, Boston University, Boston, MA, 02118, USA.
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, 02118, USA.
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA.
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12
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Ford Carleton P, Schachter S, Parrish JA, Collins JM, Crocker JB, Dixon RF, Edgman-Levitan S, Lewandrowski KB, Stahl JE, Klapperich C, Cabodi M, Gaydos CA, Rompalo AM, Manabe Y, Wang TH, Rothman R, Geddes CD, Widdice L, Jackman J, Mathura RA, Lash TB. National Institute of Biomedical Imaging and Bioengineering Point-of-Care Technology Research Network: Advancing Precision Medicine. IEEE J Transl Eng Health Med 2016; 4:2800614. [PMID: 27730014 PMCID: PMC5052024 DOI: 10.1109/jtehm.2016.2598837] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 05/16/2016] [Accepted: 05/16/2016] [Indexed: 12/28/2022]
Abstract
To advance the development of point-of-care technology (POCT), the National Institute of Biomedical Imaging and Bioengineering established the POCT Research Network (POCTRN), comprised of Centers that emphasize multidisciplinary partnerships and close facilitation to move technologies from an early stage of development into clinical testing and patient use. This paper describes the POCTRN and the three currently funded Centers as examples of academic-based organizations that support collaborations across disciplines, institutions, and geographic regions to successfully drive innovative solutions from concept to patient care.
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13
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Wong S, Drain P, Klapperich C. A point-of-care device for the rapid diagnosis of tuberculosis. Ann Glob Health 2015. [DOI: 10.1016/j.aogh.2015.02.700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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14
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Stahl JE, McGowan H, DiResta E, Gaydos CA, Klapperich C, Parrish J, Korte B. Systems Engineering and Point of Care Testing: Report from the NIBIB POCT/Systems Engineering Workshop. Point Care 2015; 14:12-24. [PMID: 25750593 PMCID: PMC4349191 DOI: 10.1097/poc.0000000000000046] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The first part of this manuscript is an introduction to systems engineering and how it may be applied to health care and point of care testing (POCT). Systems engineering is an interdisciplinary field that seeks to better understand and manage changes in complex systems and projects as whole. Systems are sets of interconnected elements which interact with each other, are dynamic, change over time and are subject to complex behaviors. The second part of this paper reports on the results of the National Institute of Biomedical Imaging and Bioengineering (NIBIB) workshop exploring the future of point of care testing and technologies and the recognition that these new technologies do not exist in isolation. That they exist within ecosystems of other technologies and systems; and these systems influence their likelihood of success or failure and their effectiveness. In this workshop, a diverse group of individuals from around the country, from disciplines ranging from clinical care, engineering, regulatory affairs and many others to members of the three major National Institutes of Health (NIH) funded efforts in the areas the Centers for POCT for sexually transmitted disease, POCT for the future of Cancer Care, POCT primary care research network, gathered together for a modified deep dive workshop exploring the current state of the art, mapping probable future directions and developing longer term goals. The invitees were broken up into 4 thematic groups: Home, Outpatient, Public/shared space and Rural/global. Each group proceeded to explore the problem and solution space for point of care tests and technology within their theme. While each thematic area had specific challenges, many commonalities also emerged. This effort thus helped create a conceptual framework for POCT as well as identifying many of the challenges for POCT going forward. Four main dimensions were identified as defining the functional space for both point of care testing and treatment, these are: Time, Location, Interpretation and Tempo. A framework is presented in this paper. There were several current and future challenges identified through the workshop. These broadly fall into the categories of technology development and implementation. More specifically these are in the areas of: 1) Design, 2) Patient driven demand and technology, 3) Information Characteristics and Presentation, 4) Health Information Systems, 5) Connectivity, 6) Workflow and implementation, 7) Maintenance/Cost, and 8) Quality Control. Definitions of these challenge areas and recommendations to address them are provided.
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Affiliation(s)
- James E Stahl
- Division of General Medicine, Medicine, MGH-Institute for Technology Assessment, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Heather McGowan
- Division of General Medicine, Medicine, MGH-Institute for Technology Assessment, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Ellen DiResta
- Division of General Medicine, Medicine, MGH-Institute for Technology Assessment, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Charlotte A Gaydos
- Division of Infectious Diseases, Medicine, Johns Hopkins University Baltimore MD
| | | | - John Parrish
- Center for Integration of Medicine and Innovative Technology (CIMIT)
| | - Brenda Korte
- National Institute of Biomedical Imaging and Bioengineering, Point-of-Care Technology Research Network; Division of Discovery Science and Technology
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15
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Huang S, Sharma S, Liu L, Fan A, Klapperich C, Rosen J. Abstract 3494: Microfluidic platform for a protein-based thyroid cancer diagnostics. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-3494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
a) The current gold-standard of care in the management of patients with thyroid nodules is ultrasound-guided fine needle aspiration biopsy (FNAB) followed by microscopic examination of cell morphology by a trained cytopathologist. Due to the lack of distinguishing morphology, 10-25% of FNAs are termed “indeterminate” and required surgery. However, only 35% of them are found to have cancer. There is a need for a more accurate and minimally invasive cancer diagnostic technology. Our objective is to develop an inexpensive, point-of-care molecular diagnostic platform to isolate and detect thyroid specific proteins to enable real-world use of biomarkers to inform patient care. b) In this study, we engineer a miniature ion exchange column within a plastic (cyclic olefin polymer), disposable lab-on-a-chip platform for sample preparation and protein purification using microfluidic channels with a specialized porous polymer monolith (PPM)-based resin bed. We capitalized on the finding that cancer cells exhibit differential protein expressional patterns compared to normal thyroid cells by targeting thyroid transcription factor (TTF-1), a thyroid specific enhancer binding protein, as a biomarker for the diagnosis of thyroid cancer. The ability to capture and release TTF-1 from the papillary thyroid cancer (PTC) cell line was evaluated via western blot. We also tested various types of thyroid samples obtained from malignant and benign human thyroid nodules. c) We compared the efficiency of a small-scale protein prep using a commercial gravity column versus our lab-on-a-chip column. Our method showed TTF-1 protein was detectable from the lysate of 5x104 cultured BCPAP cancer cell line. In contrast, it was not detectable when purified by gravity ion-exchange column. We next showed that one can maximize the concentration of protein eluted from as fewer cells as possible. We found that by titrating the elution volume per fraction down to 10 µl, the final concentration of eluted protein can be increased, and hence increase the downstream LOD to 104 cells. Next, we evaluated our extraction and purification system by using 10 mg patient thyroid tissue samples. We tested 11 human thyroid specimens for TTF-1 protein capture. They were all found to be positive which correlated with the official histopathological findings. All tissue extracts had measurable levels of TTF-1 protein and the levels of the TTF-1 were variable in the tissue specimens. We also tested one negative thyroid specimen. No TTF-1 protein was found. d) Our microfluidic protein extraction and purification system is a platform technology that may allow for optimal use of low-volume sample preparation such as we see in thyroid biopsies. This manner, when combined with an on-chip ELISA assay, would be a simple, cost effective test that gives the doctor all the needed information quickly in a single test. When mature, the device can be applied to other type of cancer based on tailored assays for specific biomarkers.
Citation Format: Shichu Huang, Siddhartha Sharma, Lena Liu, Andy Fan, Catherine Klapperich, Jennifer Rosen. Microfluidic platform for a protein-based thyroid cancer diagnostics. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3494. doi:10.1158/1538-7445.AM2014-3494
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Abstract
Fast and effective diagnostics play an important role in controlling infectious disease by enabling effective patient management and treatment. Here, we present an integrated microfluidic thermoplastic chip with the ability to amplify influenza A virus in patient nasopharyngeal (NP) swabs and aspirates. Upon loading the patient sample, the microfluidic device sequentially carries out on-chip cell lysis, RNA purification and concentration steps within the solid phase extraction (SPE), reverse transcription (RT) and polymerase chain reaction (PCR) in RT-PCR chambers, respectively. End-point detection is performed using an off-chip Bioanalyzer (Agilent Technologies, Santa Clara, CA). For peripherals, we used a single syringe pump to drive reagent and samples, while two thin film heaters were used as the heat sources for the RT and PCR chambers. The chip is designed to be single layer and suitable for high throughput manufacturing to reduce the fabrication time and cost. The microfluidic chip provides a platform to analyze a wide variety of virus and bacteria, limited only by changes in reagent design needed to detect new pathogens of interest.
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Affiliation(s)
- Qingqing Cao
- Department of Mechanical Engineering, Boston University, Boston, Massachusetts, USA
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Abstract
Often, modern diagnostic techniques require the isolation and purification of nucleic acids directly from patient samples such as blood or stool. Many diagnostic tests are being miniaturized onto micro-sized platforms and integrated into microfluidic devices due to the economies resulting from smaller sample and reagent volumes. Often, these devices perform sample preparation in series with the diagnostic tests. The sample preparation steps are vital in order to purify the desired genetic material from potential inhibitors that can interfere with the outcome of the test. There are various techniques used to selectively capture the nucleic acids while washing away potential contamination (proteins, enzymes, lipids, etc.). Two of the most common forms of selective capture are based on nucleic acid binding to silica surface or on the precipitation of nucleic acids with or without the presence of a carrier species. Each of these methods can be performed in liquid phase or in a solid support such as an extraction column. Here we discuss both methods and address microfluidic applications.
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Affiliation(s)
- Andy Fan
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
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18
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Cao Q, Kim MC, Klapperich C. Plastic microfluidic chip for continuous-flow polymerase chain reaction: simulations and experiments. Biotechnol J 2010; 6:177-84. [PMID: 21298803 DOI: 10.1002/biot.201000100] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Revised: 09/23/2010] [Accepted: 09/29/2010] [Indexed: 11/10/2022]
Abstract
A continuous flow polymerase chain reaction (CF-PCR) device comprises a single fluidic channel that is heated differentially to create spatial temperature variations such that a sample flowing through it experiences the thermal cycling required to induce amplification. This type of device can provide an effective means to detect the presence of a small amount of nucleic acid in very small sample volumes. CF-PCR is attractive for global health applications due to its less stringent requirements for temperature control than for other designs. For mass production of inexpensive CF-PCR devices, fabrication via thermoplastic molding will likely be necessary. Here we study the optimization of a PCR assay in a polymeric CF-PCR device. Three channel designs, with varying residence time ratios for the three PCR steps (denaturation, annealing, and extension), were modeled, built, and tested. A standardized assay was run on the three different chips, and the PCR yields were compared. The temperature gradient profiles of the three designs and the residence times of simulated DNA molecules flowing through each temperature zone were predicted using computational methods. PCR performance predicted by simulation corresponded to experimental results. The effects of DNA template size and cycle time on PCR yield were also studied. The experiments and simulations presented here guided the CF-PCR chip design and provide a model for predicting the performance of new CF-PCR designs prior to actual chip manufacture, resulting in faster turn around time for new device and assay design. Taken together, this framework of combined simulation and experimental development has greatly reduced assay development time for CF-PCR in our lab.
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Affiliation(s)
- Qingqing Cao
- Department of Mechanical Engineering, Boston University, Boston, MA, USA
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19
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Abstract
To successfully perform biological experiments on bacteria in microfluidic devices, control of micron-scale cell motion in the chip-sized environment is essential. Here we describe a new method for simulating the motion of individual bacterial cells in a microfluidic device using a one-way coupling Lagrangian approach combined with rigid body theory. The cell was assumed to be an elastic, solid ellipsoid, and interactions with solid wall boundaries were considered to occur in one of two collision modes, either a "standing" or "lying" collision mode on the surface. The ordinary differential equations were solved along the cell trajectory for the thirteen unknown variables of the translational cell velocity, cell location vector, rotational angular velocity, and four Euler parameters, using the Rosenbrock method based on an adaptive time-stepping technique. As selected applications, we show how this novel simulation method may be applied to the designs of efficient hydrodynamic cell traps in a microfluidic device for bacterial applications and for cell separations. Modeled designs include optimized U-shaped sieve arrays with a single aperture for the hydrodynamic cell trapping, and three kinds of staggered micropillars for cell separations.
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Affiliation(s)
- Min-Cheol Kim
- Department of Biomedical Engineering, Boston University, MA 02215, USA
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20
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Basu A, Cheung KC, Eddington DT, Günther A, Hansen C, Huang TJ, Juncker D, Kaji H, Khademhosseini A, Khan SA, Klapperich C, Love JC, Munson M, Murthy S, Ozcan A, Ozinsky A, Spotts JM, Squires T, Takeuchi S, Wang W, Williams J. Contributors to the emerging investigators issue. Lab Chip 2010; 10:2323-2333. [PMID: 20717627 DOI: 10.1039/c0lc90044c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
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21
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Chatterjee A, Mirer PL, Zaldivar Santamaria E, Klapperich C, Sharon A, Sauer-Budge AF. RNA Isolation from Mammalian Cells Using Porous Polymer Monoliths: An Approach for High-Throughput Automation. Anal Chem 2010; 82:4344-56. [DOI: 10.1021/ac100063f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Anirban Chatterjee
- Departments of Mechanical Engineering and Biomedical Engineering, Boston University, Boston, Massachusetts 02215, and Center for Manufacturing Innovation, Fraunhofer USA, Brookline, Massachusetts 02446
| | - Paul L. Mirer
- Departments of Mechanical Engineering and Biomedical Engineering, Boston University, Boston, Massachusetts 02215, and Center for Manufacturing Innovation, Fraunhofer USA, Brookline, Massachusetts 02446
| | - Elvira Zaldivar Santamaria
- Departments of Mechanical Engineering and Biomedical Engineering, Boston University, Boston, Massachusetts 02215, and Center for Manufacturing Innovation, Fraunhofer USA, Brookline, Massachusetts 02446
| | - Catherine Klapperich
- Departments of Mechanical Engineering and Biomedical Engineering, Boston University, Boston, Massachusetts 02215, and Center for Manufacturing Innovation, Fraunhofer USA, Brookline, Massachusetts 02446
| | - Andre Sharon
- Departments of Mechanical Engineering and Biomedical Engineering, Boston University, Boston, Massachusetts 02215, and Center for Manufacturing Innovation, Fraunhofer USA, Brookline, Massachusetts 02446
| | - Alexis F. Sauer-Budge
- Departments of Mechanical Engineering and Biomedical Engineering, Boston University, Boston, Massachusetts 02215, and Center for Manufacturing Innovation, Fraunhofer USA, Brookline, Massachusetts 02446
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Gillers S, Atkinson CD, Bartoo AC, Mahalanabis M, Boylan MO, Schwartz JH, Klapperich C, Singh SK. Microscale sample preparation for PCR of C. difficile infected stool. J Microbiol Methods 2009; 78:203-7. [PMID: 19505511 DOI: 10.1016/j.mimet.2009.05.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2009] [Accepted: 05/26/2009] [Indexed: 01/22/2023]
Abstract
In this paper, we describe the design of a microfluidic sample preparation chip for human stool samples infected with Clostridium difficile. We established a polymerase chain reaction able to distinguish C. difficile in the presence of several other organisms found in the normal intestinal flora. A protocol for on-chip extraction of nucleic acids from clinical samples is described that can detect target DNA down to 5.0x10(-3) ng of template. The assay and sample preparation chip were then validated using known positive and known negative clinical samples. The work presented has potential applications in both the developed and developing world.
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Affiliation(s)
- Sara Gillers
- Department of Medicine, Section of Gastroenterology, Boston University School of Medicine, Suite 504, 650 Albany Street, Boston, MA 02118, United States
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Bhattacharyya A, Kulinski D, Klapperich C. Fabrication of the thermoplastic microfluidic channels. J Vis Exp 2008:664. [PMID: 19066567 DOI: 10.3791/664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
In our lab, we have successfully isolated nucleic acids directly from microliter and submicroliter volumes of human blood, urine and stool using polymer/nanoparticle composite microscale lysis and solid phase extraction columns. The recovered samples are concentrated, small volume samples that are PCRable, without any additional cleanup. Here, we demonstrate how to fabricate thermoplastic microfluidic chips using hot embossing and heat sealing. Then, we demonstrate how to use in situ light directed surface grafting and polymerization through the sealed chip to form the composite solid phase columns. We demonstrate grafting and polymerization of a carbon nanotube/polymer composite column for bacterial cell lysis. We then show the lysis process followed by solid phase extraction of nucleic acids from the sample on chip using a silica/polymer composite column. The attached protocols contain detailed instructions on how to make both lysis and solid phase extraction columns.
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Abstract
In this interview, Dr. Klapperich discusses the fabrication of thermoplastic microfluidic devices and their application for development of new diagnostics.
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Klapperich C, Kaufman J, Wong J. Controlling and Assessing Cell–Biomaterial Interactions at the Micro- and Nanoscale. Biomaterials 2007. [DOI: 10.1201/9780849378898.ch10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Kaufman J, Wong JY, Klapperich C. Controlling and Assessing Cell–Biomaterial Interactions at the Micro- and Nanoscale: Applications in Tissue Engineering. Biomaterials 2007. [DOI: 10.1201/9780849378898-10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Niedzwiecki S, Klapperich C, Short J, Jani S, Ries M, Pruitt L. Comparison of three joint simulator wear debris isolation techniques: acid digestion, base digestion, and enzyme cleavage. J Biomed Mater Res 2001; 56:245-9. [PMID: 11340595 DOI: 10.1002/1097-4636(200108)56:2<245::aid-jbm1091>3.0.co;2-t] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Quantification of ultrahigh molecular weight polyethylene (UHMWPE) wear debris remains a challenging task in orthopedic device analysis. Currently, the weight loss method is the only accepted practice for quantifying the amount of wear generated from a PE component. This technique utilizes loaded soak controls and weight differences to account for polymeric material lost through wear mechanisms. This method enables the determination of the amount of wear in the orthopedic device, but it provides no information about debris particulate size distribution. In order to shed light on wear mechanisms, information about the wear debris and its size distribution is necessary. To date, particulate isolation has been performed using the base digestion technique. The method uses a strong base, ultracentrifugation, and filtration to digest serum constituents and to isolate PE debris from sera. It should be noted that particulate isolation methods provide valuable information about particulate size distribution and may elucidate the mechanisms of wear associated with polymeric orthopedic implants; however, these techniques do not yet provide a direct measure of the amount of wear. The aim of this study is to present alternative approaches to wear particle isolation for analysis of polymer wear in total joint replacements without recourse to ultracentrifugation. Three polymer wear debris isolation techniques (the base method, an acid treatment, and an enzymatic digestion technique) are compared for effectiveness in simulator studies. A requirement of each technique is that the wear particulate must be completely devoid of serum proteins in order to effectively image and count these particles. In all methods the isolation is performed through filtration and chemical treatment. Subsequently, the isolated polymer particles are imaged using scanning electron microscopy and quantified with digital image analysis. The results from this study clearly show that isolation can be performed without the use of ultracentrifugation and that these methods provide a viable option for wear debris analysis.
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Affiliation(s)
- S Niedzwiecki
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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Klapperich C, Pruitt L, Komvopoulos K. Chemical and biological characteristics of low-temperature plasma treated ultra-high molecular weight polyethylene for biomedical applications. J Mater Sci Mater Med 2001; 12:549-556. [PMID: 15348272 DOI: 10.1023/a:1011232032413] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Several low-temperature radio-frequency (RF) plasma surface treatments were performed on ultra-high molecular weight polyethylene (UHMWPE) used in biomedical applications. Process gases included Ar, C3F6, CH4, hexamethyldisiloxane (HMDSO), and NH4. These treatments were carried out at pressures in the range of 64-400 mTorr, RF powers of 240-1200 W, and temperatures well below the melting point of UHMWPE. X-ray photoelectron spectroscopy (XPS) was used to obtain information about the surface characteristics of UHMWPE treated with the HMDSO, C3F6, and CH4 gases as a function of treatment conditions. XPS spectra of UHMWPE treated with C3F6 and CH4 and exposed to a laboratory environment for different time periods were examined in order to assess the stability of these treatments. It was found that for the C3F6 process gas the amount of fluorine at the surface decreased over time, whereas the oxygen content of the CH4 treated samples increased as a function of time. In vitro cytotoxicity of Ar, C3F6, CH4, and NH4 plasma treated samples was studied in light of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) test results. The hemolytic nature of the various plasma treatments was evaluated using standard hemolysis tests. All of the samples tested in this study exhibited no cytotoxic and negligible hemolytic effects. The process parameters for several low-temperature plasma treatments demonstrating chemical and structural stability and good biocompatibility are discussed in conjunction with the broad applicability to other biomedical polymers.
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Affiliation(s)
- C Klapperich
- Department of Mechanical Engineering, University of California, Berkeley, CA 94720, USA
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Klapperich C, Niedzwiecki S, Ries M, Pruitt L. Fluid sorption of orthopedic grade ultrahigh molecular weight polyethylene in a serum environment is affected by the surface area and sterilization method. J Biomed Mater Res 2000; 53:73-5. [PMID: 10634955 DOI: 10.1002/(sici)1097-4636(2000)53:1<73::aid-jbm10>3.0.co;2-a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
It is shown in this work that lubricant sorption in ultrahigh molecular weight polyethylene (UHMWPE) increases with available surface area of the component. This has clinical relevance, because sliding and articulation experienced in simulator studies can result in changes in surface roughness and the creation of new surfaces. This study compares the fluid sorption of orthopedic grade UHMWPE with different surface areas (but equivalent volume) for different sterilization methods. For both the gamma radiation and nonsterile control samples, the gain in total fluid absorbed scaled proportionately with surface area. For the EtO sterilization treatment, the fluid gain was nonlinear and substantially less than the radiated and control groups. The findings from this study clearly indicate that the sterilization and surface area affect the fluid uptake and weight gain of UHMWPE.
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Affiliation(s)
- C Klapperich
- Department of Mechanical Engineering, University of California, Berkeley, California 94720, USA
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Abstract
Ultra-high-molecular weight polyethylene (UHMWPE) wear, debris-induced osteolysis is a frequent cause of failure of total hip arthroplasty. Metal-on-metal total hip arthroplasty eliminates the generation of UHMWPE particulate debris. Although the volumetric wear of a metal-on-metal articulation may be lower than a metal-UHMWPE articulation, the number of particles may be higher. Osteolysis can develop in response to metallic and UHMWPE debris. The following case of massive osteolysis associated with large amounts of cobalt-chrome wear debris shows adhesive and abrasive wear mechanisms, as well as wear caused by third-body cobalt-chrome debris and impingement of the femoral component against the rim of the acetabular cup, which led to failure of a metal-on-metal total hip arthroplasty.
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Affiliation(s)
- C Klapperich
- Department of Mechanical Engineering, University of California, Berkeley, USA
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