Comparative analytical evaluation of the respiratory TaqMan Array Card with real-time PCR and commercial multi-pathogen assays

Harvey, John; Chester, Stephanie; Bürke, S.; Ansbro, Marisela; Aden, Tricia; Gose, Remedios; Sciulli, Rebecca; Bai, Jing; DesJardin, Lucy E.; Benfer, Jeffrey L.; Hall, Joshua C.; Smole, Sandra; Doan, Kimberly; Popowich, Michael; George, Kirsten St.; Quinlan, Tammy; Halse, Tanya A.; Li, Zhen; Pérez-Osorio, Ailyn C.; Glover, William A.; Russell, Denny; Reisdorf, Erik; Whyte, Thomas; Whitaker, Brett; Hatcher, Cynthia; Srinivasan, Velusamy; Tatti, Kathleen M.; Tondella, M. Lucia; Wang, Xin; Winchell, Jonas M.; Mayer, Leonard W.; Jernigan, Daniel B.; Mawle, Alison C.

doi:10.1016/j.jviromet.2015.11.020

Cited by 23 publications

(29 citation statements)

References 26 publications

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“…The multi-zone model for the building with low ventilation was further used to simulate the spread of influenza A viruses by bioaerosols, and the simulation results were compared to the cumulative incidence of viral ARIs confirmed by quantitative polymerase chain reaction assay of nasal and throat swabs using a TaqMan Array Card assay (Thermo-Fisher, San Jose, CA) for a wide range of viral respiratory pathogens (Harvey et al, 2016). The detailed methodology introduces the two dormitory buildings under investigation, the distributed CO 2 monitoring system, and the multi-zone models.…”

Section: Methodsmentioning

confidence: 99%

“…At screening for self-reported symptoms, participants were asked to describe their symptoms and date the onset. They were also asked to provide nose and throat swab specimens which were evaluated within 24 h for evidence S. Zhu, et al Environment International 137 (2020) 105537 of infection with viral pathogens commonly implicated in ARIs (Harvey et al, 2016, Steensels et al, 2015 using a qRT-PCR array (TAC assay, TaqMan® Array Card, Thermo Fisher Scientific, Carlsbad, CA). Participants with confirmed infections with certain viruses including influenza A and B, human coronavirus, adenovirus, respiratory syncytial virus, parainfluenza, and human metapneumovirus (not rhinovirus, enterovirus, other respiratory viruses, or bacterial infections) were further enrolled in an in-depth evaluation and asked to provide details of their close contacts, i.e.…”

Section: Monitoring Of Ari Incidencementioning

confidence: 99%

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Ventilation and laboratory confirmed acute respiratory infection (ARI) rates in college residence halls in College Park, Maryland

Zhu

Jenkins

Addo

et al. 2020

Environment International

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A B S T R A C TStrategies to protect building occupants from the risk of acute respiratory infection (ARI) need to consider ventilation for its ability to dilute and remove indoor bioaerosols. Prior studies have described an association of increased self-reported colds and influenza-like symptoms with low ventilation but have not combined rigorous characterization of ventilation with assessment of laboratory confirmed infections. We report a study designed to fill this gap. We followed laboratory confirmed ARI rates and measured CO 2 concentrations for four months during the winter-spring of 2018 in two campus residence halls: (1) a high ventilation building (HVB) with a dedicated outdoor air system that supplies 100% of outside air to each dormitory room, and (2) a low ventilation building (LVB) that relies on infiltration as ventilation. We enrolled 11 volunteers for a total of 522 person-days in the HVB and 109 volunteers for 6069 person-days in the LVB, and tested upper-respiratory swabs from symptomatic cases and their close contacts for the presence of 44 pathogens using a molecular assay. We observed one ARI case in the HVB (0.70/person-year) and 47 in the LVB (2.83/person-year). Simultaneously, 154 CO 2 sensors distributed primarily in the dormitory rooms collected 668,390 useful data points from over 1 million recorded data points. Average and standard deviation of CO 2 concentrations were 1230 ppm and 408 ppm in the HVB, and 1492 ppm and 837 ppm in the LVB, respectively. Importantly, this study developed and calibrated multi-zone models for the HVB with 229 zones and 983 airflow paths, and for the LVB with 529 zones and 1836 airflow paths by using a subset of CO 2 data for model calibration. The models were used to calculate ventilation rates in the two buildings and potential for viral aerosol migration between rooms in the LVB. With doors and windows closed, the average ventilation rate was 12 L/s in the HVB dormitory rooms and 4 L/s in the LVB dormitory rooms. As a result, residents had on average 6.6 L/(s person) of outside air in the HVB and 2.3 L/(s person) in the LVB. LVB rooms located at the leeward side of the building had smaller average ventilation rates, as well as a somewhat higher ARI incidence rate and average CO 2 concentrations when compared to those values in the rooms located at the windward side of the building. Average ventilation rates in twenty LVB dormitory rooms increased from 2.3 L/s to 7.5 L/s by opening windows, 3.6 L/s by opening doors, and 8.8 L/s by opening both windows and doors. Therefore, opening both windows and doors in the LVB dormitory rooms can increase ventilation rates to the levels comparable to those in the HVB. But it can also have a negative effect on thermal comfort due to low outdoor temperatures. Simulation results identified an aerobiologic pathway from a room occupied by an index case of influenza A to a room occupied by a possible secondary case.

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Section: Methodsmentioning

confidence: 99%

Section: Monitoring Of Ari Incidencementioning

confidence: 99%

Ventilation and laboratory confirmed acute respiratory infection (ARI) rates in college residence halls in College Park, Maryland

Zhu

Jenkins

Addo

et al. 2020

Environment International

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“…Nasopharyngeal (NP) or oropharyngeal (OP) swabs are collected from the first 10 ILI patients of each week and tested at the NYC Public Health Laboratory for influenza using the CDC real‐time RT‐PCR assay. Specimens collected from October 2011 through August 2014 were further tested for respiratory pathogens by the New York State Department of Health Wadsworth Center using Taqman Array Card (TAC, Life Technologies, Carlsbad, CA) that included influenza A virus (H1, H1N1pdm09, and H3), influenza B virus, adenovirus, coronaviruses (229E, HKu1, NL63, OC43), enterovirus, HMPV, HPIV types 1‐4, RSV, rhinovirus, Chlamydia pneumoniae , Mycoplasma pneumoniae , Bordetella pertussis , Haemophilus influenzae, Legionella pneumophila , Streptococcus pneumoniae , Streptococcus pyogenes . Discordant results in influenza virus testing between the CDC PCR testing kits and Taqman testing were assumed positive by any assay.…”

Section: Methodsmentioning

confidence: 99%

Comparison of outpatient medically attended and community‐level influenza‐like illness—New York City, 2013‐2015

Russell

Fowlkes

Stockwell

et al. 2018

Influenza Resp Viruses

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BackgroundSurveillance of influenza‐like illness (ILI) in the United States is primarily conducted through medical settings despite a significant burden of non‐medically attended ILI.ObjectivesTo assess consistency between surveillance for respiratory viruses in outpatient and community settings using ILI surveillance from the Centers for Disease Control and Prevention Influenza Incidence Surveillance Project (IISP) and the Mobile Surveillance for Acute Respiratory Infections (ARI) and Influenza‐Like Illness in the Community (MoSAIC) Study.MethodsThe Influenza Incidence Surveillance Project conducts ILI surveillance in 3 primary care clinics in New York City, and MoSAIC conducts community‐based ILI/ARI surveillance through text messaging among a cohort of New York City residents. Both systems obtain respiratory specimens from participants with ILI/ARI and test for multiple pathogens. We conducted a retrospective review of ILI cases in IISP and MoSAIC from January 2013 to May 2015 with descriptive analyses of clinical and laboratory data.ResultsFive‐hundred twelve MoSAIC and 669 IISP participants met an ILI criteria (fever with cough or sore throat) and were included. Forty percent of MoSAIC participants sought care; the majority primary care. Pathogens were detected in 63% of MoSAIC and 70% of IISP cases. The relative distribution of influenza and other respiratory viruses detected was similar; however, there were statistically significant differences in the frequency that were not explained by care seeking.ConclusionsOutpatient and community‐based surveillance in the one found similar timing and relative distribution of respiratory viruses, but community surveillance in a single neighborhood may not fully capture the variations in ILI etiology that occur more broadly.

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“…Parents will be trained at visit 2 to identify early respiratory infection symptoms and to collect and store nasal wash samples. Multiplex PCR analysis will be performed for 22 relevant respiratory viral and bacterial pathogens (see Table 5) using TaqMan assays validated by the CDC [52]. Inflammatory mechanisms will be assessed through type I interferon (IFN-α, IFN-β), IL-8, and leptin levels in nasal wash samples.…”

Section: Respiratory Tract Samplingmentioning

confidence: 99%

Genotype tailored treatment of mild symptomatic acid reflux in children with uncontrolled asthma (GenARA): Rationale and methods

Tang

Blake

Lima

et al. 2019

Contemporary Clinical Trials

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Asthma causes enormous suffering and cost for children in the US and around the world [1-3]. Comorbid gastroesophageal reflux disease (GERD) makes asthma management more difficult due to increased symptoms. Proton pump inhibitor (PPI) drugs are effective at improving to GERD symptoms, however they have demonstrated only modest and variable effects on asthma control in the setting of co-morbid GERD. Importantly, PPI metabolism and efficacy depend on CYP2C19 genotype. The Genotype Tailored Treatment of Symptomatic Acid Reflux in Children with Uncontrolled Asthma (GenARA) study is a randomized, double-blind, placebo-controlled trial to determine if genotype-tailored PPI dosing improves asthma symptoms among children with inadequately controlled asthma and GERD symptoms. This study has an innovative design to both assess the efficacy of genotype-tailored PPI dosing and perform pharmacokinetic modeling of the oral PPI Lansoprazole. Children ages 6-17 years old with clinician-diagnosed asthma and mild GERD symptoms will submit a saliva sample for CYP2C19 genotyping. Participants will undergo a two-step randomization to: (1) genotype-tailored versus conventional dosing of open-label oral lansoprazole for pharmacokinetic modeling, and (2) genotype-tailored lansoprazole daily versus placebo for 24 weeks to determine the effect of genotype-tailored PPI dosing on asthma control. Measures of asthma control, spirometry, and nasal washes during acute illnesses will be collected at 8-week intervals throughout the study. GenARA will better define the effects of CYP2C19 genotype on the dose response of lansoprazole in children and adolescents and assess if a novel dosing regimen improves GERD and asthma control. Tang et al.

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Comparative analytical evaluation of the respiratory TaqMan Array Card with real-time PCR and commercial multi-pathogen assays

Cited by 23 publications

References 26 publications

Ventilation and laboratory confirmed acute respiratory infection (ARI) rates in college residence halls in College Park, Maryland

Ventilation and laboratory confirmed acute respiratory infection (ARI) rates in college residence halls in College Park, Maryland

Comparison of outpatient medically attended and community‐level influenza‐like illness—New York City, 2013‐2015

Genotype tailored treatment of mild symptomatic acid reflux in children with uncontrolled asthma (GenARA): Rationale and methods

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