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Article ; Online: Erratum to: Multifactorial discrimination as a fundamental cause of mental health inequities.

Khan, Mariam / Ilcisin, Misja / Saxton, Katherine

International journal for equity in health

2017 Volume 16, Issue 1, Page(s) 144

Language	English
Publishing date	2017-08-15
Publishing country	England
Document type	Published Erratum
ISSN	1475-9276
ISSN (online)	1475-9276
DOI	10.1186/s12939-017-0557-3
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Article ; Online: Multifactorial discrimination as a fundamental cause of mental health inequities.

Khan, Mariam / Ilcisin, Misja / Saxton, Katherine

International journal for equity in health

2017 Volume 16, Issue 1, Page(s) 43

Abstract: Background: The theory of fundamental causes explains why health disparities persist over time, even as risk factors, mechanisms, and diseases change. Using an intersectional framework, we evaluated multifactorial discrimination as a fundamental cause ... ...

Abstract	Background: The theory of fundamental causes explains why health disparities persist over time, even as risk factors, mechanisms, and diseases change. Using an intersectional framework, we evaluated multifactorial discrimination as a fundamental cause of mental health disparities. Methods: Using baseline data from the Project STRIDE: Stress, Identity, and Mental Health study, we examined the health effects of discrimination among individuals who self-identified as lesbian, gay, or bisexual. We used logistic and linear regression to assess whether multifactorial discrimination met the four criteria designating a fundamental cause, namely that the cause: 1) influences multiple health outcomes, 2) affects multiple risk factors, 3) involves access to resources that can be leveraged to reduce consequences of disease, and 4) reproduces itself in varied contexts through changing mechanisms. Results: Multifactorial discrimination predicted high depression scores, psychological well-being, and substance use disorder diagnosis. Discrimination was positively associated with risk factors for high depression scores: chronic strain and total number of stressful life events. Discrimination was associated with significantly lower levels of mastery and self-esteem, protective factors for depressive symptomatology. Even after controlling for risk factors, discrimination remained a significant predictor for high depression scores. Among subjects with low depression scores, multifactorial discrimination also predicted anxiety and aggregate mental health scores. Conclusions: Multifactorial discrimination should be considered a fundamental cause of mental health inequities and may be an important cause of broad health disparities among populations with intersecting social identities.
MeSH term(s)	Adolescent ; Adult ; Anxiety/etiology ; Anxiety Disorders/etiology ; Continental Population Groups ; Depression/etiology ; Depressive Disorder/etiology ; Female ; Gender Identity ; Humans ; Logistic Models ; Male ; Mental Health ; Middle Aged ; Risk Factors ; Self Concept ; Sexuality ; Social Class ; Social Discrimination/psychology ; Social Identification ; Socioeconomic Factors ; Stress, Psychological/etiology ; Substance-Related Disorders/etiology ; Young Adult
Language	English
Publishing date	2017-03-04
Publishing country	England
Document type	Journal Article
ISSN	1475-9276
ISSN (online)	1475-9276
DOI	10.1186/s12939-017-0532-z
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Article ; Online: Diagnostic Accuracy of an At-Home, Rapid Self-test for Influenza: Prospective Comparative Accuracy Study.

Geyer, Rachel E / Kotnik, Jack Henry / Lyon, Victoria / Brandstetter, Elisabeth / Zigman Suchsland, Monica / Han, Peter D / Graham, Chelsey / Ilcisin, Misja / Kim, Ashley E / Chu, Helen Y / Nickerson, Deborah A / Starita, Lea M / Bedford, Trevor / Lutz, Barry / Thompson, Matthew J

JMIR public health and surveillance

2022 Volume 8, Issue 2, Page(s) e28268

Abstract: Background: Rapid diagnostic tests (RDTs) for influenza used by individuals at home could potentially expand access to testing and reduce the impact of influenza on health systems. Improving access to testing could lead to earlier diagnosis following ... ...

Abstract	Background: Rapid diagnostic tests (RDTs) for influenza used by individuals at home could potentially expand access to testing and reduce the impact of influenza on health systems. Improving access to testing could lead to earlier diagnosis following symptom onset, allowing more rapid interventions for those who test positive, including behavioral changes to minimize spread. However, the accuracy of RDTs for influenza has not been determined in self-testing populations. Objective: This study aims to assess the accuracy of an influenza RDT conducted at home by lay users with acute respiratory illness compared with that of a self-collected sample by the same individual mailed to a laboratory for reference testing. Methods: We conducted a comparative accuracy study of an at-home influenza RDT (Ellume) in a convenience sample of individuals experiencing acute respiratory illness symptoms. Participants were enrolled in February and March 2020 from the Greater Seattle region in Washington, United States. Participants were mailed the influenza RDT and reference sample collection materials, which they completed and returned for quantitative reverse-transcription polymerase chain reaction influenza testing in a central laboratory. We explored the impact of age, influenza type, duration, and severity of symptoms on RDT accuracy and on cycle threshold for influenza virus and ribonuclease P, a marker of human DNA. Results: A total of 605 participants completed all study steps and were included in our analysis, of whom 87 (14.4%) tested positive for influenza by quantitative reverse-transcription polymerase chain reaction (70/87, 80% for influenza A and 17/87, 20% for influenza B). The overall sensitivity and specificity of the RDT compared with the reference test were 61% (95% CI 50%-71%) and 95% (95% CI 93%-97%), respectively. Among individuals with symptom onset ≤72 hours, sensitivity was 63% (95% CI 48%-76%) and specificity was 94% (95% CI 91%-97%), whereas, for those with duration >72 hours, sensitivity and specificity were 58% (95% CI 41%-74%) and 96% (95% CI 93%-98%), respectively. Viral load on reference swabs was negatively correlated with symptom onset, and quantities of the endogenous marker gene ribonuclease P did not differ among reference standard positive and negative groups, age groups, or influenza subtypes. The RDT did not have higher sensitivity or specificity among those who reported more severe illnesses. Conclusions: The sensitivity and specificity of the self-test were comparable with those of influenza RDTs used in clinical settings. False-negative self-test results were more common when the test was used after 72 hours of symptom onset but were not related to inadequate swab collection or severity of illness. Therefore, the deployment of home tests may provide a valuable tool to support the management of influenza and other respiratory infections.
MeSH term(s)	Humans ; Influenza, Human/diagnosis ; Prospective Studies ; Ribonuclease P ; Self-Testing ; Sensitivity and Specificity
Chemical Substances	Ribonuclease P (EC 3.1.26.5)
Language	English
Publishing date	2022-02-22
Publishing country	Canada
Document type	Journal Article
ISSN	2369-2960
ISSN (online)	2369-2960
DOI	10.2196/28268
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Article: Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens.

Huddleston, John / Hadfield, James / Sibley, Thomas R / Lee, Jover / Fay, Kairsten / Ilcisin, Misja / Harkins, Elias / Bedford, Trevor / Neher, Richard A / Hodcroft, Emma B

Journal of open source software

2021 Volume 6, Issue 57

Abstract: The analysis of human pathogens requires a diverse collection of bioinformatics tools. These tools include standard genomic and phylogenetic software and custom software developed to handle the relatively numerous and short genomes of viruses and ... ...

Abstract	The analysis of human pathogens requires a diverse collection of bioinformatics tools. These tools include standard genomic and phylogenetic software and custom software developed to handle the relatively numerous and short genomes of viruses and bacteria. Researchers increasingly depend on the outputs of these tools to infer transmission dynamics of human diseases and make actionable recommendations to public health officials (Black et al., 2020; Gardy et al., 2015). In order to enable real-time analyses of pathogen evolution, bioinformatics tools must scale rapidly with the number of samples and be flexible enough to adapt to a variety of questions and organisms. To meet these needs, we developed Augur, a bioinformatics toolkit designed for phylogenetic analyses of human pathogens.
Language	English
Publishing date	2021-01-07
Publishing country	United States
Document type	Journal Article
ISSN	2475-9066
ISSN	2475-9066
DOI	10.21105/joss.02906
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Article: Interactions among 17 respiratory pathogens: a cross-sectional study using clinical and community surveillance data.

Burstein, Roy / Althouse, Benjamin M / Adler, Amanda / Akullian, Adam / Brandstetter, Elizabeth / Cho, Shari / Emanuels, Anne / Fay, Kairsten / Gamboa, Luis / Han, Peter / Huden, Kristen / Ilcisin, Misja / Izzo, Mandy / Jackson, Michael L / Kim, Ashley E / Kimball, Louise / Lacombe, Kirsten / Lee, Jover / Logue, Jennifer K /

Rogers, Julia / Chung, Erin / Sibley, Thomas R / Van Raay, Katrina / Wenger, Edward / Wolf, Caitlin R / Boeckh, Michael / Chu, Helen / Duchin, Jeff / Rieder, Mark / Shendure, Jay / Starita, Lea M / Viboud, Cecile / Bedford, Trevor / Englund, Janet A / Famulare, Michael

medRxiv : the preprint server for health sciences

2022

Abstract: Background: Co-circulating respiratory pathogens can interfere with or promote each other, leading to important effects on disease epidemiology. Estimating the magnitude of pathogen-pathogen interactions from clinical specimens is challenging because ... ...

Abstract	Background: Co-circulating respiratory pathogens can interfere with or promote each other, leading to important effects on disease epidemiology. Estimating the magnitude of pathogen-pathogen interactions from clinical specimens is challenging because sampling from symptomatic individuals can create biased estimates. Methods: We conducted an observational, cross-sectional study using samples collected by the Seattle Flu Study between 11 November 2018 and 20 August 2021. Samples that tested positive via RT-qPCR for at least one of 17 potential respiratory pathogens were included in this study. Semi-quantitative cycle threshold (Ct) values were used to measure pathogen load. Differences in pathogen load between monoinfected and coinfected samples were assessed using linear regression adjusting for age, season, and recruitment channel. Results: 21,686 samples were positive for at least one potential pathogen. Most prevalent were rhinovirus (33·5%), Conclusions: Viral load data can be used to overcome sampling bias in studies of pathogen-pathogen interactions. When applied to respiratory pathogens, we found evidence of viral-
Language	English
Publishing date	2022-02-06
Publishing country	United States
Document type	Preprint
DOI	10.1101/2022.02.04.22270474
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Article ; Online: Characteristics of COVID-19 in Homeless Shelters : A Community-Based Surveillance Study.

Annals of internal medicine

2020 Volume 174, Issue 1, Page(s) 42–49

Abstract: Background: Homeless shelters are a high-risk setting for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission because of crowding and shared hygiene facilities.: Objective: To investigate SARS-CoV-2 case counts across several ... ...

Abstract	Background: Homeless shelters are a high-risk setting for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission because of crowding and shared hygiene facilities. Objective: To investigate SARS-CoV-2 case counts across several adult and family homeless shelters in a major metropolitan area. Design: Cross-sectional, community-based surveillance study. (ClinicalTrials.gov: NCT04141917). Setting: 14 homeless shelters in King County, Washington. Participants: A total of 1434 study encounters were done in shelter residents and staff, regardless of symptoms. Intervention: 2 strategies were used for SARS-CoV-2 testing: routine surveillance and contact tracing ("surge testing") events. Measurements: The primary outcome measure was test positivity rate of SARS-CoV-2 infection at shelters, determined by dividing the number of positive cases by the total number of participant encounters, regardless of symptoms. Sociodemographic, clinical, and virologic variables were assessed as correlates of viral positivity. Results: Among 1434 encounters, 29 (2% [95% CI, 1.4% to 2.9%]) cases of SARS-CoV-2 infection were detected across 5 shelters. Most ( Limitation: Selection bias due to voluntary participation and a relatively small case count. Conclusion: Active surveillance and surge testing were used to detect multiple cases of asymptomatic and symptomatic SARS-CoV-2 infection in homeless shelters. The findings suggest an unmet need for routine viral testing outside of clinical settings for homeless populations. Primary funding source: Gates Ventures.
MeSH term(s)	Adolescent ; Adult ; COVID-19/epidemiology ; COVID-19/transmission ; Child ; Contact Tracing ; Cross-Sectional Studies ; Female ; Homeless Persons ; Humans ; Male ; Middle Aged ; Population Surveillance ; SARS-CoV-2 ; Washington/epidemiology
Keywords	covid19
Language	English
Publishing date	2020-09-15
Publishing country	United States
Document type	Journal Article ; Multicenter Study ; Randomized Controlled Trial
ZDB-ID	336-0
ISSN	1539-3704 ; 0003-4819
ISSN (online)	1539-3704
ISSN	0003-4819
DOI	10.7326/M20-3799
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Article: SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing.

Srivatsan, Sanjay / Heidl, Sarah / Pfau, Brian / Martin, Beth K / Han, Peter D / Zhong, Weizhi / van Raay, Katrina / McDermot, Evan / Opsahl, Jordan / Gamboa, Luis / Smith, Nahum / Truong, Melissa / Cho, Shari / Barrow, Kaitlyn A / Rich, Lucille M / Stone, Jeremy / Wolf, Caitlin R / McCulloch, Denise J / Kim, Ashley E /

Brandstetter, Elisabeth / Sohlberg, Sarah L / Ilcisin, Misja / Geyer, Rachel E / Chen, Wei / Gehring, Jase / Kosuri, Sriram / Bedford, Trevor / Rieder, Mark J / Nickerson, Deborah A / Chu, Helen Y / Konnick, Eric Q / Debley, Jason S / Shendure, Jay / Lockwood, Christina M / Starita, Lea M

bioRxiv : the preprint server for biology

2021

Abstract: Background: The urgent need for massively scaled clinical testing for SARS-CoV-2, along with global shortages of critical reagents and supplies, has necessitated development of streamlined laboratory testing protocols. Conventional nucleic acid testing ... ...

Abstract	Background: The urgent need for massively scaled clinical testing for SARS-CoV-2, along with global shortages of critical reagents and supplies, has necessitated development of streamlined laboratory testing protocols. Conventional nucleic acid testing for SARS-CoV-2 involves collection of a clinical specimen with a nasopharyngeal swab in transport medium, nucleic acid extraction, and quantitative reverse transcription PCR (RT-qPCR) (1). As testing has scaled across the world, the global supply chain has buckled, rendering testing reagents and materials scarce (2). To address shortages, we developed SwabExpress, an end-to-end protocol developed to employ mass produced anterior nares swabs and bypass the requirement for transport media and nucleic acid extraction. Methods: We evaluated anterior nares swabs, transported dry and eluted in low-TE buffer as a direct-to-RT-qPCR alternative to extraction-dependent viral transport media. We validated our protocol of using heat treatment for viral activation and added a proteinase K digestion step to reduce amplification interference. We tested this protocol across archived and prospectively collected swab specimens to fine-tune test performance. Results: After optimization, SwabExpress has a low limit of detection at 2-4 molecules/uL, 100% sensitivity, and 99.4% specificity when compared side-by-side with a traditional RT-qPCR protocol employing extraction. On real-world specimens, SwabExpress outperforms an automated extraction system while simultaneously reducing cost and hands-on time. Conclusion: SwabExpress is a simplified workflow that facilitates scaled testing for COVID-19 without sacrificing test performance. It may serve as a template for the simplification of PCR-based clinical laboratory tests, particularly in times of critical shortages during pandemics.
Keywords	covid19
Language	English
Publishing date	2021-04-29
Publishing country	United States
Document type	Preprint
DOI	10.1101/2020.04.22.056283
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Article ; Online: Evaluating Specimen Quality and Results from a Community-Wide, Home-Based Respiratory Surveillance Study.

Kim, Ashley E / Brandstetter, Elisabeth / Wilcox, Naomi / Heimonen, Jessica / Graham, Chelsey / Han, Peter D / Starita, Lea M / McCulloch, Denise J / Casto, Amanda M / Nickerson, Deborah A / Van de Loo, Margaret M / Mooney, Jennifer / Ilcisin, Misja / Fay, Kairsten A / Lee, Jover / Sibley, Thomas R / Lyon, Victoria / Geyer, Rachel E / Thompson, Matthew /

Lutz, Barry R / Rieder, Mark J / Bedford, Trevor / Boeckh, Michael / Englund, Janet A / Chu, Helen Y

Journal of clinical microbiology

2021 Volume 59, Issue 5

Abstract: While influenza and other respiratory pathogens cause significant morbidity and mortality, the community-based burden of these infections remains incompletely understood. The development of novel methods to detect respiratory infections is essential for ... ...

Abstract	While influenza and other respiratory pathogens cause significant morbidity and mortality, the community-based burden of these infections remains incompletely understood. The development of novel methods to detect respiratory infections is essential for mitigating epidemics and developing pandemic-preparedness infrastructure. From October 2019 to March 2020, we conducted a home-based cross-sectional study in the greater Seattle, WA, area, utilizing electronic consent and data collection instruments. Participants received nasal swab collection kits via rapid delivery within 24 hours of self-reporting respiratory symptoms. Samples were returned to the laboratory and were screened for 26 respiratory pathogens and a housekeeping gene. Participant data were recorded via online survey at the time of sample collection and 1 week later. Of the 4,572 consented participants, 4,359 (95.3%) received a home swab kit and 3,648 (83.7%) returned a nasal specimen for respiratory pathogen screening. The 3,638 testable samples had a mean RNase P relative cycle threshold (
MeSH term(s)	Cross-Sectional Studies ; Humans ; Influenza, Human/diagnosis ; Influenza, Human/epidemiology ; Pandemics ; Respiratory Tract Infections/diagnosis ; Respiratory Tract Infections/epidemiology ; Specimen Handling
Language	English
Publishing date	2021-04-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	390499-4
ISSN	1098-660X ; 0095-1137
ISSN (online)	1098-660X
ISSN	0095-1137
DOI	10.1128/JCM.02934-20
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Article ; Online: SwabExpress: An End-to-End Protocol for Extraction-Free COVID-19 Testing.

Clinical chemistry

2021 Volume 68, Issue 1, Page(s) 143–152

Abstract	Background: The urgent need for massively scaled clinical testing for SARS-CoV-2, along with global shortages of critical reagents and supplies, has necessitated development of streamlined laboratory testing protocols. Conventional nucleic acid testing for SARS-CoV-2 involves collection of a clinical specimen with a nasopharyngeal swab in transport medium, nucleic acid extraction, and quantitative reverse-transcription PCR (RT-qPCR). As testing has scaled across the world, the global supply chain has buckled, rendering testing reagents and materials scarce. To address shortages, we developed SwabExpress, an end-to-end protocol developed to employ mass produced anterior nares swabs and bypass the requirement for transport media and nucleic acid extraction. Methods: We evaluated anterior nares swabs, transported dry and eluted in low-TE buffer as a direct-to-RT-qPCR alternative to extraction-dependent viral transport media. We validated our protocol of using heat treatment for viral inactivation and added a proteinase K digestion step to reduce amplification interference. We tested this protocol across archived and prospectively collected swab specimens to fine-tune test performance. Results: After optimization, SwabExpress has a low limit of detection at 2-4 molecules/µL, 100% sensitivity, and 99.4% specificity when compared side by side with a traditional RT-qPCR protocol employing extraction. On real-world specimens, SwabExpress outperforms an automated extraction system while simultaneously reducing cost and hands-on time. Conclusion: SwabExpress is a simplified workflow that facilitates scaled testing for COVID-19 without sacrificing test performance. It may serve as a template for the simplification of PCR-based clinical laboratory tests, particularly in times of critical shortages during pandemics.
MeSH term(s)	COVID-19/diagnosis ; COVID-19 Nucleic Acid Testing/methods ; Clinical Laboratory Techniques ; Humans ; RNA, Viral/isolation & purification ; Real-Time Polymerase Chain Reaction ; SARS-CoV-2/isolation & purification ; Sensitivity and Specificity ; Specimen Handling
Chemical Substances	RNA, Viral
Language	English
Publishing date	2021-07-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80102-1
ISSN	1530-8561 ; 0009-9147
ISSN (online)	1530-8561
ISSN	0009-9147
DOI	10.1093/clinchem/hvab132
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Article ; Online: Interactions among 17 respiratory pathogens: a cross-sectional study using clinical and community surveillance data

Burstein, Roy / Althouse, Bejamin M / Adler, Amanda / Akullian, Adam / Brandstetter, Elizabeth / Cho, Shari / Chung, Erin / Emmanuels, Anne / Fay, Kairsten / Gamboa, Luis / Han, Peter / Huden, Kristen / Ilcisin, Misja / Izzo, Mandy / Jackson, Michael L / Kim, Ashley E / Kimball, Louise / Lacombe, Kirstein / Lee, Jover /

Logue, Jennifer K / Rogers, Julia / Sibley, Thomas R / Van Raay, Katrina / Wenger, Edward / Wolf, Caitlin R / Boeckh, Michael / Chu, Helen / Duchin, Jeff / Reider, Mark / Shendure, Jay / Starita, Lea M / Viboud, Cecile / Bedfor, Trevor / Englund, Janet A / Famulare, Michael / Seattle Flu Study and SCAN Investigators

medRxiv

Abstract: Background Co-circulating respiratory pathogens can interfere with or promote each other, leading to important effects on disease epidemiology. Estimating the magnitude of pathogen-pathogen interactions from clinical specimens is challenging because ... ...

Abstract	Background Co-circulating respiratory pathogens can interfere with or promote each other, leading to important effects on disease epidemiology. Estimating the magnitude of pathogen-pathogen interactions from clinical specimens is challenging because sampling from symptomatic individuals can create biased estimates. Methods We conducted an observational, cross-sectional study using samples collected by the Seattle Flu Study between 11 November 2018 and 20 August 2021. Samples that tested positive via RT-qPCR for at least one of 17 potential respiratory pathogens were included in this study. Semi-quantitative cycle threshold (Ct) values were used to measure pathogen load. Differences in pathogen load between monoinfected and coinfected samples were assessed using linear regression adjusting for age, season, and recruitment channel. Results 21,686 samples were positive for at least one potential pathogen. Most prevalent were rhinovirus (33.5%), Streptococcus pneumoniae (SPn, 29.0%), SARS-CoV-2 (13.8%) and influenza A/H1N1 (9.6%). 140 potential pathogen pairs were included for analysis, and 56 (40%) pairs yielded significant Ct differences (p < 0.01) between monoinfected and co-infected samples. We observed no virus-virus pairs showing evidence of significant facilitating interactions, and found significant viral load decrease among 37 of 108 (34%) assessed pairs. Samples positive with SPn and a virus were consistently associated with increased SPn load. Conclusions Viral load data can be used to overcome sampling bias in studies of pathogen-pathogen interactions. When applied to respiratory pathogens, we found evidence of viral-SPn facilitation and several examples of viral-viral interference. Multipathogen surveillance is a cost-efficient data collection approach, with added clinical and epidemiological informational value over single-pathogen testing, but requires careful analysis to mitigate selection bias.
Keywords	covid19
Language	English
Publishing date	2022-02-06
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2022.02.04.22270474
Database	COVID19

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