Incidence and Outcome of Coinfections with SARS-CoV-2 and Rhinovirus

Background: We aimed to compare the clinical severity in patients who were coinfected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and rhinovirus or monoinfected with a single one of these viruses. Methods: The study period ranged from 1 March 2020 to 28 February 2021 (one year). SARS-CoV-2 and other respiratory viruses were identified by real-time reverse-transcription-PCR as part of the routine work at Marseille University hospitals. Bacterial and fungal infections were detected by standard methods. Clinical data were retrospectively collected from medical files. This study was approved by the ethical committee of our institute. Results: A total of 6034/15,157 (40%) tested patients were positive for at least one respiratory virus. Ninety-three (4.3%) SARS-CoV-2-infected patients were coinfected with another respiratory virus, with rhinovirus being the most frequent (62/93, 67%). Patients coinfected with SARS-CoV-2 and rhinovirus were significantly more likely to report a cough than those with SARS-CoV-2 monoinfection (62% vs. 31%; p = 0.0008). In addition, they were also significantly more likely to report dyspnea than patients with rhinovirus monoinfection (45% vs. 36%; p = 0.02). They were also more likely to be transferred to an intensive care unit and to die than patients with rhinovirus monoinfection (16% vs. 5% and 7% vs. 2%, respectively) but these differences were not statistically significant. Conclusions: A close surveillance and investigation of the co-incidence and interactions of SARS-CoV-2 and other respiratory viruses is needed. The possible higher risk of increased clinical severity in SARS-CoV-2-positive patients coinfected with rhinovirus warrants further large scale studies.

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Direct Detection of Respiratory Syncytial Virus, Parainfluenza Virus, and Adenovirus in Clinical Respiratory Specimens by a Multiplex Reverse Transcription-PCR Assay

Journal of Clinical Microbiology ◽

10.1128/jcm.36.11.3149-3154.1998 ◽

1998 ◽

Vol 36 (11) ◽

pp. 3149-3154 ◽

Cited By ~ 81

Author(s):

Carla Osiowy

Keyword(s):

Tissue Culture ◽

Respiratory Syncytial Virus ◽

Respiratory Virus ◽

Respiratory Viruses ◽

Parainfluenza Virus ◽

Rt Pcr ◽

Pcr Assay ◽

Reverse Transcription Pcr ◽

Syncytial Virus ◽

Respiratory Specimens

Diagnosis of respiratory virus infections currently involves detection by isolation or antigen detection, which usually identifies only a single suspected agent. To permit identification of more than one respiratory virus in clinical specimens, a rapid detection method involving a single-step, multiplex reverse transcription-PCR (RT-PCR) assay was developed. The assay included five primer sets that amplified the RNA of respiratory syncytial virus subtypes A and B, parainfluenza virus types 1, 2, and 3, and adenovirus types 1 to 7. Initially the assay was tested on tissue culture-grown virus and was found to be specific for all 12 prototype viruses tested, with no interassay cross amplification or amplification of other respiratory viruses. Assay sensitivity allowed a detection range of 0.2 50% tissue culture infectious dose (TCID50) for adenovirus to 250 TCID50 for parainfluenza virus type 1. The multiplex RT-PCR assay was also able to directly detect viruses in respiratory specimens, with virus being detected in 41 of 112 samples as compared to 34 of 112 samples detected by direct immunofluorescence or antigen detection following specimen culture. This suggests that the multiplex RT-PCR assay can be used as a rapid and sensitive diagnostic method for major respiratory viruses.

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Rates of asymptomatic respiratory virus infection across age groups

Epidemiology and Infection ◽

10.1017/s0950268819000505 ◽

2019 ◽

Vol 147 ◽

Cited By ~ 9

Author(s):

M. Galanti ◽

R. Birger ◽

M. Ud-Dean ◽

I. Filip ◽

H. Morita ◽

...

Keyword(s):

New York ◽

Virus Infection ◽

Large Scale ◽

Respiratory Virus ◽

Viral Infections ◽

Age Groups ◽

Respiratory Viruses ◽

Surveillance Systems ◽

Infection Frequency ◽

Respiratory Virus Infection

AbstractRespiratory viral infections are a leading cause of disease worldwide. A variety of respiratory viruses produce infections in humans with effects ranging from asymptomatic to life-treathening. Standard surveillance systems typically only target severe infections (ED outpatients, hospitalisations, deaths) and fail to track asymptomatic or mild infections. Here we performed a large-scale community study across multiple age groups to assess the pathogenicity of 18 respiratory viruses. We enrolled 214 individuals at multiple New York City locations and tested weekly for respiratory viral pathogens, irrespective of symptom status, from fall 2016 to spring 2018. We combined these test results with participant-provided daily records of cold and flu symptoms and used this information to characterise symptom severity by virus and age category. Asymptomatic infection rates exceeded 70% for most viruses, excepting influenza and human metapneumovirus, which produced significantly more severe outcomes. Symptoms were negatively associated with infection frequency, with children displaying the lowest score among age groups. Upper respiratory manifestations were most common for all viruses, whereas systemic effects were less typical. These findings indicate a high burden of asymptomatic respiratory virus infection exists in the general population.

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Insectivorous songbirds as early indicators of future defoliation by spruce budworm

Landscape Ecology ◽

10.1007/s10980-021-01300-z ◽

2021 ◽

Author(s):

Marion Germain ◽

Daniel Kneeshaw ◽

Louis De Grandpré ◽

Mélanie Desrochers ◽

Patrick M. A. James ◽

...

Keyword(s):

Large Scale ◽

Spatial Scales ◽

Spruce Budworm ◽

Detection Methods ◽

Maximum Probability ◽

Point Count ◽

Probability Of Presence ◽

Time Lagged ◽

One Year ◽

Local Sampling

Abstract Context Although the spatiotemporal dynamics of spruce budworm outbreaks have been intensively studied, forecasting outbreaks remains challenging. During outbreaks, budworm-linked warblers (Tennessee, Cape May, and bay-breasted warbler) show a strong positive response to increases in spruce budworm, but little is known about the relative timing of these responses. Objectives We hypothesized that these warblers could be used as sentinels of future defoliation of budworm host trees. We examined the timing and magnitude of the relationships between defoliation by spruce budworm and changes in the probability of presence of warblers to determine whether they responded to budworm infestation before local defoliation being observed by standard detection methods. Methods We modelled this relationship using large-scale point count surveys of songbirds and maps of cumulative time-lagged defoliation over multiple spatial scales (2–30 km radius around sampling points) in Quebec, Canada. Results All three warbler species responded positively to defoliation at each spatial scale considered, but the timing of their response differed. Maximum probability of presence of Tennessee and Cape May warbler coincided with observations of local defoliation, or provided a one year warning, making them of little use to guide early interventions. In contrast, the probability of presence of bay-breasted warbler consistently increased 3–4 years before defoliation was detectable. Conclusions Early detection is a critical step in the management of spruce budworm outbreaks and rapid increases in the probability of presence of bay-breasted warbler could be used to identify future epicenters and target ground-based local sampling of spruce budworm.

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Respiratory viral testing and antibacterial treatment in patients hospitalized with community-acquired pneumonia

Infection Control and Hospital Epidemiology ◽

10.1017/ice.2020.1312 ◽

2020 ◽

pp. 1-9

Author(s):

Michael Klompas ◽

Peter B. Imrey ◽

Pei-Chun Yu ◽

Chanu Rhee ◽

Abhishek Deshpande ◽

...

Keyword(s):

Retrospective Cohort ◽

Respiratory Virus ◽

Respiratory Viruses ◽

Community Acquired Pneumonia ◽

Blood Cultures ◽

Antibacterial Treatment ◽

Viral Pathogens ◽

Antimicrobial Utilization ◽

Viral Testing ◽

Virus Testing

Abstract Objective: Viruses are more common than bacteria in patients hospitalized with community-acquired pneumonia. Little is known, however, about the frequency of respiratory viral testing and its associations with antimicrobial utilization. Design: Retrospective cohort study. Setting: The study included 179 US hospitals. Patients: Adults admitted with pneumonia between July 2010 and June 2015. Methods: We assessed the frequency of respiratory virus testing and compared antimicrobial utilization, mortality, length of stay, and costs between tested versus untested patients, and between virus-positive versus virus-negative patients. Results: Among 166,273 patients with pneumonia on admission, 40,787 patients (24.5%) were tested for respiratory viruses, 94.8% were tested for influenza, and 20.7% were tested for other viruses. Viral assays were positive in 5,133 of 40,787 tested patients (12.6%), typically for influenza and rhinovirus. Tested patients were younger and had fewer comorbidities than untested patients, but patients with positive viral assays were older and had more comorbidities than those with negative assays. Blood cultures were positive for bacterial pathogens in 2.7% of patients with positive viral assays versus 5.3% of patients with negative viral tests (P < .001). Antibacterial courses were shorter for virus-positive versus -negative patients overall (mean 5.5 vs 6.4 days; P < .001) but varied by bacterial testing: 8.1 versus 8.0 days (P = .60) if bacterial tests were positive; 5.3 versus 6.1 days (P < .001) if bacterial tests were negative; and 3.3 versus 5.2 days (P < .001) if bacterial tests were not obtained (interaction P < .001). Conclusions: A minority of patients hospitalized with pneumonia were tested for respiratory viruses; only a fraction of potential viral pathogens were assayed; and patients with positive viral tests often received long antibacterial courses.

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Assisting scalable diagnosis automatically via CT images in the combat against COVID-19

Scientific Reports ◽

10.1038/s41598-021-83424-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Bohan Liu ◽

Pan Liu ◽

Lutao Dai ◽

Yanlin Yang ◽

Peng Xie ◽

...

Keyword(s):

Large Scale ◽

Area Under The Curve ◽

Independent Set ◽

Reference Method ◽

Ct Images ◽

Loss Of Life ◽

Case Identification ◽

Reverse Transcription Pcr ◽

Using Data

AbstractThe pandemic of Coronavirus Disease 2019 (COVID-19) is causing enormous loss of life globally. Prompt case identification is critical. The reference method is the real-time reverse transcription PCR (RT-PCR) assay, whose limitations may curb its prompt large-scale application. COVID-19 manifests with chest computed tomography (CT) abnormalities, some even before the onset of symptoms. We tested the hypothesis that the application of deep learning (DL) to 3D CT images could help identify COVID-19 infections. Using data from 920 COVID-19 and 1,073 non-COVID-19 pneumonia patients, we developed a modified DenseNet-264 model, COVIDNet, to classify CT images to either class. When tested on an independent set of 233 COVID-19 and 289 non-COVID-19 pneumonia patients, COVIDNet achieved an accuracy rate of 94.3% and an area under the curve of 0.98. As of March 23, 2020, the COVIDNet system had been used 11,966 times with a sensitivity of 91.12% and a specificity of 88.50% in six hospitals with PCR confirmation. Application of DL to CT images may improve both efficiency and capacity of case detection and long-term surveillance.

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COVID-19 mitigation strategies were associated with decreases in other respiratory virus infections

Open Forum Infectious Diseases ◽

10.1093/ofid/ofab105 ◽

2021 ◽

Author(s):

Sinha Pranay ◽

Katherine Reifler ◽

Michael Rossi ◽

Manish Sagar

Keyword(s):

Respiratory Virus ◽

Respiratory Infections ◽

Respiratory Viruses ◽

Mitigation Strategies ◽

Virus Infections ◽

Time Period ◽

Viral Respiratory Infections ◽

Respiratory Virus Infections ◽

Viral Respiratory

Abstract Detection of diverse respiratory viruses in Boston was around 80% lower after practices were instituted to limit COVID-19 spread compared to the same time period during the previous five years. Continuing the strategies that lower COVID-19 dissemination may be useful in decreasing the incidence of other viral respiratory infections.

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Intermittent Iron Folate Supplementation: Impact on Hematinic Status and Growth of School Girls

ISRN Hematology ◽

10.5402/2012/482153 ◽

2012 ◽

Vol 2012 ◽

pp. 1-6 ◽

Cited By ~ 5

Author(s):

Aditi Sen ◽

Shubhada Kanani

Keyword(s):

Body Mass Index ◽

Folic Acid ◽

Weekly Dose ◽

Folate Supplementation ◽

Standard Methods ◽

Pubertal Growth ◽

School Girls ◽

Iron Folic Acid ◽

One Year ◽

The Impact

In view of high iron needs for adolescent growth, this paper studied the impact of daily vs. intermittent (once and twice weekly) iron folic acid (IFA) supplementation on hemoglobin levels and pubertal growth among primary school girls in early adolescence (9–13 years) of Vadodara, India. Methods. Hemoglobin (Hb), height and weight of the girls were assessed using standard methods. In three experimental schools (ES) IFA tablets in a dose of 100 mg Fe+0.5 mg folic acid was given either daily, once weekly or twice weekly for one year. The fourth school (control: CS) did not receive any intervention. Results. Hb levels significantly improved (P<0.01) in all ES compared to CS. Body Mass Index (BMI) increment in ES vs CS was significant (P<0.05) in twice weekly IFA and daily IFA. Within ES groups, mean Hb and BMI increments were comparable between twice weekly IFA and daily IFA. Anemic ES girls showed higher Hb and BMI increments vs. non-anemic girls. Better the Hb response, greater was the benefit on BMI. Conclusion: Twice-weekly IFA supplementation was comparable to daily IFA as regards impact on Hb and growth; at less cost and greater feasibility. Once-weekly dose was inadequate to significantly improve growth.

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The Revitalization of the Historic Centre of the Town Slany

Advanced Engineering Forum ◽

10.4028/www.scientific.net/aef.12.3 ◽

2014 ◽

Vol 12 ◽

pp. 3-11

Author(s):

Zuzana Pešková

Keyword(s):

Regional Policy ◽

Large Scale ◽

Test Theory ◽

Team Members ◽

Practical Design ◽

Historic Centre ◽

Reconstruction Project ◽

One Year ◽

The Town ◽

Large Scale Project

In 2006, the town council of Slany decided to respond to the new trend of regional policy in the Central Bohemia region and focused on the revitalization of the historic core of the town. The large-scale project was assigned to a team of professionals (teachers and graduates of the Faculty of Civil Engineering of the Czech Technical University in Prague), led by Professor Sykora. Team members are to deal with issues of historical centre. The project presented a challenge to test theory, principles and procedures in practical design. The projected area featured Masaryk Square and 22 adjacent streets defined by the existing town walls. The reconstruction project of Vinarickeho Street was the first part of the overall project of revitalization of the historic core of the town chosen to implement. This reconstruction was one of the most technically, organizationally and financially complex works that have been undertaken in Slany recently. Construction started in November 2010 and lasted one year. Although this is a project of smaller scope, thanks to its complexity, sensitive approach and craftsmanship it brought the creators the price Construction of the Year 2012 in the Central Bohemia region and advanced to the second round in the competition Construction of the Year 2012 in Czech Republic.

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GaLactic and Extragalactic All-sky Murchison Widefield Array (GLEAM) survey III: South Galactic Pole data release

Publications of the Astronomical Society of Australia ◽

10.1017/pasa.2021.5 ◽

2021 ◽

Vol 38 ◽

Author(s):

T. M. O. Franzen ◽

N. Hurley-Walker ◽

S. V. White ◽

P. J. Hancock ◽

N. Seymour ◽

...

Keyword(s):

Large Scale ◽

Angular Resolution ◽

Beam Model ◽

Spectral Variability ◽

Extragalactic Source ◽

Automated Algorithm ◽

Data Release ◽

Murchison Widefield Array ◽

Source Populations ◽

One Year

Abstract We present the South Galactic Pole (SGP) data release from the GaLactic and Extragalactic All-sky Murchison Widefield Array (GLEAM) survey. These data combine both years of GLEAM observations at 72–231 MHz conducted with the Murchison Widefield Array (MWA) and cover an area of 5 113 $\mathrm{deg}^{2}$ centred on the SGP at $20^{\mathrm{h}} 40^{\mathrm{m}} < \mathrm{RA} < 05^{\mathrm{h}} 04^{\mathrm{m}}$ and $-48^{\circ} < \mathrm{Dec} < -2^{\circ} $ . At 216 MHz, the typical rms noise is ${\approx}5$ mJy beam–1 and the angular resolution ${\approx}2$ arcmin. The source catalogue contains a total of 108 851 components above $5\sigma$ , of which 77% have measured spectral indices between 72 and 231 MHz. Improvements to the data reduction in this release include the use of the GLEAM Extragalactic catalogue as a sky model to calibrate the data, a more efficient and automated algorithm to deconvolve the snapshot images, and a more accurate primary beam model to correct the flux scale. This data release enables more sensitive large-scale studies of extragalactic source populations as well as spectral variability studies on a one-year timescale.

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DIFFERENCES IN GENOTYPE OF E. FAECALIS AND E. FAECIUM CLINICAL ISOLATES REGARDING CYTOLYSIN AND GELATINASE PRODUCTION IN BULGARIAN PATIENTS

Trakia Journal of Sciences ◽

10.15547/tjs.2020.s.01.024 ◽

2020 ◽

Vol 18 (Suppl.1) ◽

pp. 130-137

Author(s):

R. Yordanova ◽

S. Stanilova

Keyword(s):

Virulence Genes ◽

Clinical Isolates ◽

University Hospitals ◽

Gelatinase Activity ◽

Non Invasive ◽

Genotypic Analysis ◽

Enterococcus Spp ◽

Virulent Gene ◽

One Year ◽

Genotype Correlation

Purpose - compare the phenotype and genotype correlation of cytolysin and gelatinase production in clinical isolates Enterococcus spp. Materials and methods - 100 Enterococcus strains collected over a period of one year from inpatients of two Bulgarian university hospitals, were tested for phenotype production of cytolysin and gelatinase. Multiplex PCR was performed to screen the presence of gelE and cylA virulence genes. Results – 17% of the enterococcal isolates demonstrated only cytolysin production phenotypically. Gelatinase activity was found in 21% of the isolates. Only E. faecalis showed combined phenotypic production of cytolysin plus gelatinase (21%). Forty-five percent of the tested enterococci were identified negative for both hemolysin and gelatinase activity. GelE was the most prevalent virulent gene (48% of the isolates). CylA gene was present alone only in four non-invasive E. faecalis isolates. Twenty-six percent of the isolates possessed both cylA and gelE genes and 21% did not harbor any of the virulence factors genotypically. Conclusion - our results prove that it is appropriate to perform both phenotypic and genotypic analysis of the enterococci virulence profile in parallel in order to better characterize the strains, which in turn may serve to develop more effective methods to limit the spread of infections caused by these microorganisms.

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