Evidence of Air and Surface Contamination with SARS-CoV-2 in a Major Hospital in Portugal

As the third wave of the COVID-19 pandemic hit Portugal, it forced the country to reintroduce lockdown measures due to hospitals reaching their full capacities. Under these circumstances, environmental contamination by SARS-CoV-2 in different areas of one of Portugal’s major Hospitals was assessed between 21 January and 11 February 2021. Air samples (n = 44) were collected from eleven different areas of the Hospital (four COVID-19 and seven non-COVID-19 areas) using Coriolis® μ and Coriolis® Compact cyclone air sampling devices. Surface sampling was also performed (n = 17) on four areas (one COVID-19 and three non-COVID-19 areas). RNA extraction followed by a one-step RT-qPCR adapted for quantitative purposes were performed. Of the 44 air samples, two were positive for SARS-CoV-2 RNA (6575 copies/m3 and 6662.5 copies/m3, respectively). Of the 17 surface samples, three were positive for SARS-CoV-2 RNA (200.6 copies/cm2, 179.2 copies/cm2, and 201.7 copies/cm2, respectively). SARS-CoV-2 environmental contamination was found both in air and on surfaces in both COVID-19 and non-COVID-19 areas. Moreover, our results suggest that longer collection sessions are needed to detect point contaminations. This reinforces the need to remain cautious at all times, not only when in close contact with infected individuals. Hand hygiene and other standard transmission-prevention guidelines should be continuously followed to avoid nosocomial COVID-19.

Download Full-text

Development and validation of a one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) for rapid detection of ZIKV in patient samples from Brazil

Scientific Reports ◽

10.1038/s41598-021-83371-1 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Severino Jefferson Ribeiro da Silva ◽

Keith Pardee ◽

Udeni B. R. Balasuriya ◽

Lindomar Pena

Keyword(s):

Reverse Transcription ◽

Rapid Detection ◽

Quantitative Polymerase Chain Reaction ◽

Rna Extraction ◽

Lamp Assay ◽

Isothermal Amplification ◽

Serum Samples ◽

Low Resource ◽

Loop Mediated Isothermal Amplification ◽

One Step

AbstractWe have previously developed and validated a one-step assay based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) for rapid detection of the Zika virus (ZIKV) from mosquito samples. Patient diagnosis of ZIKV is currently carried out in centralized laboratories using the reverse transcription-quantitative polymerase chain reaction (RT-qPCR), which, while the gold standard molecular method, has several drawbacks for use in remote and low-resource settings, such as high cost and the need of specialized equipment. Point-of-care (POC) diagnostic platforms have the potential to overcome these limitations, especially in low-resource countries where ZIKV is endemic. With this in mind, here we optimized and validated our RT-LAMP assay for rapid detection of ZIKV from patient samples. We found that the assay detected ZIKV from diverse sample types (serum, urine, saliva, and semen) in as little as 20 min, without RNA extraction. The RT-LAMP assay was highly specific and up to 100 times more sensitive than RT-qPCR. We then validated the assay using 100 patient serum samples collected from suspected cases of arbovirus infection in the state of Pernambuco, which was at the epicenter of the last Zika epidemic. Analysis of the results, in comparison to RT-qPCR, found that the ZIKV RT-LAMP assay provided sensitivity of 100%, specificity of 93.75%, and an overall accuracy of 95.00%. Taken together, the RT-LAMP assay provides a straightforward and inexpensive alternative for the diagnosis of ZIKV from patients and has the potential to increase diagnostic capacity in ZIKV-affected areas, particularly in low and middle-income countries.

Download Full-text

Evaluation of Two Surface Sampling Methods for Detection of Erwinia herbicola on a Variety of Materials by Culture and Quantitative PCR

Applied and Environmental Microbiology ◽

10.1128/aem.01825-06 ◽

2007 ◽

Vol 73 (11) ◽

pp. 3505-3510 ◽

Cited By ~ 32

Author(s):

Mark P. Buttner ◽

Patricia Cruz ◽

Linda D. Stetzenbach ◽

Tracy Cronin

Keyword(s):

Quantitative Pcr ◽

Sampling Methods ◽

Collection Efficiency ◽

Test Chamber ◽

Surface Sampling ◽

Laminate Glass ◽

Erwinia Herbicola ◽

Surface Samples ◽

Sampling Protocols ◽

Surface Materials

ABSTRACT This research was designed to evaluate surface sampling protocols for use with culture and quantitative PCR (QPCR) amplification assay for detection of the gram-negative bacterial biothreat simulant Erwinia herbicola on a variety of surface materials. Surfaces selected for evaluation were wood laminate, glass and computer monitor screens, metal file cabinets, plastic arena seats, nylon seat cushions, finished concrete flooring, and vinyl tile flooring. Laboratory and test chamber studies were performed to evaluate two sampling methods, a sponge and a macrofoam swab, for detection of E. herbicola on surface materials. In laboratory trials, seven materials were inoculated with a known concentration of E. herbicola cells and samples were collected from the surfaces of the materials to determine sampling efficiencies. Culture analysis was ineffective for assessing E. herbicola collection efficiency because very few culturable cells were obtained from surface samples. QPCR demonstrated that E. herbicola DNA was present in high concentrations on all of the surface samples, and sampling efficiencies ranged from 0.7 to 52.2%, depending on the sampling method and the surface material. The swab was generally more efficient than the sponge for collection of E. herbicola from surfaces. Test chamber trials were also performed in which E. herbicola was aerosolized into the chamber and allowed to settle onto test materials. Surface sampling results supported those obtained in laboratory trials. The results of this study demonstrate the capabilities of QPCR to enhance the detection and enumeration of biocontaminants on surface materials and provide information on the comparability of sampling methods.

Download Full-text

Robust Saliva-Based RNA Extraction-Free One-Step Nucleic Acid Amplification Test for Mass SARS-CoV-2 Monitoring

Molecules ◽

10.3390/molecules26216617 ◽

2021 ◽

Vol 26 (21) ◽

pp. 6617

Author(s):

Eva Rajh ◽

Tina Šket ◽

Arne Praznik ◽

Petra Sušjan ◽

Alenka Šmid ◽

...

Keyword(s):

Oral Cavity ◽

Reverse Transcription ◽

Screening Program ◽

Quantitative Polymerase Chain Reaction ◽

Rna Extraction ◽

Diagnostic Sensitivity ◽

Nucleic Acid Amplification ◽

Nasopharyngeal Swab ◽

Viral Spread ◽

One Step

Early diagnosis with rapid detection of the virus plays a key role in preventing the spread of infection and in treating patients effectively. In order to address the need for a straightforward detection of SARS-CoV-2 infection and assessment of viral spread, we developed rapid, sensitive, extraction-free one-step reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and reverse transcription loop-mediated isothermal amplification (RT-LAMP) tests for detecting SARS-CoV-2 in saliva. We analyzed over 700 matched pairs of saliva and nasopharyngeal swab (NSB) specimens from asymptomatic and symptomatic individuals. Saliva, as either an oral cavity swab or passive drool, was collected in an RNA stabilization buffer. The stabilized saliva specimens were heat-treated and directly analyzed without RNA extraction. The diagnostic sensitivity of saliva-based RT-qPCR was at least 95% in individuals with subclinical infection and outperformed RT-LAMP, which had at least 70% sensitivity when compared to NSBs analyzed with a clinical RT-qPCR test. The diagnostic sensitivity for passive drool saliva was higher than that of oral cavity swab specimens (95% and 87%, respectively). A rapid, sensitive one-step extraction-free RT-qPCR test for detecting SARS-CoV-2 in passive drool saliva is operationally simple and can be easily implemented using existing testing sites, thus allowing high-throughput, rapid, and repeated testing of large populations. Furthermore, saliva testing is adequate to detect individuals in an asymptomatic screening program and can help improve voluntary screening compliance for those individuals averse to various forms of nasal collections.

Download Full-text

Investigating SARS-CoV-2 surface and air contamination in an acute healthcare setting during the peak of the COVID-19 pandemic in London

10.1101/2020.05.24.20110346 ◽

2020 ◽

Cited By ~ 2

Author(s):

Jie Zhou ◽

Jonathan A. Otter ◽

James R. Price ◽

Cristina Cimpeanu ◽

Danel Meno Garcia ◽

...

Keyword(s):

Limit Of Detection ◽

Healthcare Setting ◽

Viral Rna ◽

Cross Sectional ◽

Air Samples ◽

Air Contamination ◽

Viral Culture ◽

Air Sampler ◽

Surface Samples ◽

Acute Healthcare

ABSTRACTBackgroundEvaluation of SARS-CoV-2 surface and air contamination during the COVID-19 pandemic in London.MethodsWe performed this prospective cross-sectional observational study in a multi-site London hospital. Air and surface samples were collected from seven clinical areas, occupied by patients with COVID-19, and a public area of the hospital. Three or four 1.0 m3 air samples were collected in each area using an active air sampler. Surface samples were collected by swabbing items in the immediate vicinity of each air sample. SARS-CoV-2 was detected by RT-qPCR and viral culture; the limit of detection for culturing SARS-CoV-2 from surfaces was determined.ResultsViral RNA was detected on 114/218 (52.3%) of surfaces and 14/31 (38.7%) air samples but no virus was cultured. The proportion of surface samples contaminated with viral RNA varied by item sampled and by clinical area. Viral RNA was detected on surfaces i and in air in public areas of the hospital but was more likely to be found in areas immediately occupied by COVID-19 patients than in other areas (67/105 (63.8%) vs. 29/64 (45.3%) (odds ratio 0.5, 95% confidence interval 0.2-0.9, p=0.025, Chi squared test)). The high PCR Ct value for all samples (>30) indicated that the virus would not be culturable.ConclusionsOur findings of extensive viral RNA contamination of surfaces and air across a range of acute healthcare settings in the absence of cultured virus underlines the potential risk from environmental contamination in managing COVID-19, and the need for effective use of PPE, physical distancing, and hand/surface hygiene.

Download Full-text

One-step discrimination of BCR/ABLp210 transcript isoforms directly from RNA extraction with fusion-triggered rolling circle amplification

Analytica Chimica Acta ◽

10.1016/j.aca.2019.03.055 ◽

2019 ◽

Vol 1067 ◽

pp. 129-136 ◽

Cited By ~ 3

Author(s):

Nini Luo ◽

Qianfeng Xia ◽

Lutan Zhang ◽

Yuhong Zhang ◽

Lizhen Huang ◽

...

Keyword(s):

Rolling Circle Amplification ◽

Rna Extraction ◽

Transcript Isoforms ◽

Rolling Circle ◽

One Step

Download Full-text

Detection of Airborne Severe Acute Respiratory Syndrome (SARS) Coronavirus and Environmental Contamination in SARS Outbreak Units

The Journal of Infectious Diseases ◽

10.1086/429634 ◽

2005 ◽

Vol 191 (9) ◽

pp. 1472-1477 ◽

Cited By ~ 201

Author(s):

Timothy F. Booth ◽

Bill Kournikakis ◽

Nathalie Bastien ◽

Jim Ho ◽

Darwyn Kobasa ◽

...

Keyword(s):

Severe Acute Respiratory Syndrome ◽

Environmental Contamination ◽

Respiratory Protection ◽

Chain Reaction ◽

Air Samples ◽

Aerosol Generation ◽

Hygiene Practices ◽

Viral Aerosol ◽

Polymerase Chain ◽

Droplet Transmission

Abstract Severe acute respiratory syndrome (SARS) is characterized by a risk of nosocomial transmission; however, the risk of airborne transmission of SARS is unknown. During the Toronto outbreaks of SARS, we investigated environmental contamination in SARS units, by employing novel air sampling and conventional surface swabbing. Two polymerase chain reaction (PCR)–positive air samples were obtained from a room occupied by a patient with SARS, indicating the presence of the virus in the air of the room. In addition, several PCR-positive swab samples were recovered from frequently touched surfaces in rooms occupied by patients with SARS (a bed table and a television remote control) and in a nurses’ station used by staff (a medication refrigerator door). These data provide the first experimental confirmation of viral aerosol generation by a patient with SARS, indicating the possibility of airborne droplet transmission, which emphasizes the need for adequate respiratory protection, as well as for strict surface hygiene practices

Download Full-text

Determination of the Efficacy of Two Building Decontamination Strategies by Surface Sampling with Culture and Quantitative PCR Analysis

Applied and Environmental Microbiology ◽

10.1128/aem.70.8.4740-4747.2004 ◽

2004 ◽

Vol 70 (8) ◽

pp. 4740-4747 ◽

Cited By ~ 47

Author(s):

Mark P. Buttner ◽

Patricia Cruz ◽

Linda D. Stetzenbach ◽

Amy K. Klima-Comba ◽

Vanessa L. Stevens ◽

...

Keyword(s):

Quantitative Pcr ◽

Chlorine Dioxide ◽

Pcr Analysis ◽

Surface Sampling ◽

Chlorine Dioxide Gas ◽

Surface Samples ◽

Qpcr Analysis ◽

Environmental Background ◽

Background Material ◽

Materials Used

ABSTRACT The efficacy of currently available decontamination strategies for the treatment of indoor furnishings contaminated with bioterrorism agents is poorly understood. Efficacy testing of decontamination products in a controlled environment is needed to ensure that effective methods are used to decontaminate domestic and workplace settings. An experimental room supplied with materials used in office furnishings (i.e., wood laminate, painted metal, and vinyl tile) was used with controlled dry aerosol releases of endospores of Bacillus atrophaeus (“Bacillus subtilis subsp. niger,” also referred to as BG), a Bacillus anthracis surrogate. Studies were performed using two test products, a foam decontaminant and chlorine dioxide gas. Surface samples were collected pre- and posttreatment with three sampling methods and analyzed by culture and quantitative PCR (QPCR). Additional aerosol releases with environmental background present on the surface materials were also conducted to determine if there was any interference with decontamination or sample analysis. Culture results indicated that 105 to 106 CFU per sample were present on surfaces before decontamination. After decontamination with the foam, no culturable B. atrophaeus spores were detected. After decontamination with chlorine dioxide gas, no culturable B. atrophaeus was detected in 24 of 27 samples (89%). However, QPCR analysis showed that B. atrophaeus DNA was still present after decontamination with both methods. Environmental background material had no apparent effect on decontamination, but inhibition of the QPCR assay was observed. These results demonstrate the effectiveness of two decontamination methods and illustrate the utility of surface sampling and QPCR analysis for the evaluation of decontamination strategies.

Download Full-text

How Did Students Perceive Classroom Learning under Strict COVID-19 Pandemic Closures and Restrictions?

ENGLISH EDUCATION JOURNAL OF ENGLISH TEACHING AND RESEARCH ◽

10.29407/jetar.v6i2.16394 ◽

2021 ◽

Vol 6 (2) ◽

pp. 128-148

Author(s):

Takayoshi Sako

Keyword(s):

Collaborative Learning ◽

English Language ◽

Close Contact ◽

School Closure ◽

After School ◽

Prevention Measures ◽

Or Groups ◽

Prevention Guidelines ◽

The Impact

The COVID-19 pandemic of 2020 required strict infection prevention measures worldwide, including school closure. After school reopened, we implemented Japan’s strict COVID measures, under which close contact in pairs or groups, as well as vocalizing in unison, was proscribed, with students having to remain quiet and face the blackboard. This study’s aim is to answer the question of how students felt about learning under such extreme constraints. One of the most noticeable findings from the responses to the survey of the 2020 class was that they felt the lack of collaborative learning experiences; hence, in 2021, we implemented changes that would allow for more collaboration while still adhering to COVID prevention guidelines. Among the various collaborative learning activities in the classroom, students reported that they found value in debate activities that challenged their English language skills and critical thinking. Overall, however, students found comfort and value in a semblance of learning with their peers. It was concluded that even in a volatile and uncertain situation, such as a pandemic, it is crucial to improve environments for collaborative learning. In the future, quantitative study of the impact of collaborative learning on students’ English proficiency will be a useful follow-up study.

Download Full-text

SARS-CoV-2 environmental contamination from hospitalised patients with COVID-19 receiving aerosol-generating procedures

Thorax ◽

10.1136/thoraxjnl-2021-218035 ◽

2021 ◽

pp. thoraxjnl-2021-218035

Author(s):

Rebecca L Winslow ◽

Jie Zhou ◽

Ella F Windle ◽

Intesar Nur ◽

Ranjit Lall ◽

...

Keyword(s):

Environmental Contamination ◽

Quantitative Polymerase Chain Reaction ◽

Supplemental Oxygen ◽

Nasopharyngeal Swab ◽

Clinical Environment ◽

Surface Samples ◽

Hospitalised Patients ◽

Group A ◽

Fraction Of Inspired Oxygen ◽

Study Participants

BackgroundContinuous positive airways pressure (CPAP) and high-flow nasal oxygen (HFNO) are considered ‘aerosol-generating procedures’ in the treatment of COVID-19.ObjectiveTo measure air and surface environmental contamination with SARS-CoV-2 virus when CPAP and HFNO are used, compared with supplemental oxygen, to investigate the potential risks of viral transmission to healthcare workers and patients.Methods30 hospitalised patients with COVID-19 requiring supplemental oxygen, with a fraction of inspired oxygen ≥0.4 to maintain oxygen saturation ≥94%, were prospectively enrolled into an observational environmental sampling study. Participants received either supplemental oxygen, CPAP or HFNO (n=10 in each group). A nasopharyngeal swab, three air and three surface samples were collected from each participant and the clinical environment. Real-time quantitative polymerase chain reaction analyses were performed for viral and human RNA, and positive/suspected-positive samples were cultured for the presence of biologically viable virus.ResultsOverall 21/30 (70%) participants tested positive for SARS-CoV-2 RNA in the nasopharynx. In contrast, only 4/90 (4%) and 6/90 (7%) of all air and surface samples tested positive (positive for E and ORF1a) for viral RNA respectively, although there were an additional 10 suspected-positive samples in both air and surfaces samples (positive for E or ORF1a). CPAP/HFNO use or coughing was not associated with significantly more environmental contamination than supplemental oxygen use. Only one nasopharyngeal sample was culture positive.ConclusionsThe use of CPAP and HFNO to treat moderate/severe COVID-19 did not appear to be associated with substantially higher levels of air or surface viral contamination in the immediate care environment, compared with the use of supplemental oxygen.

Download Full-text

COVID-19 vaccination for patients with primary immunodeficiency

LymphoSign Journal ◽

10.14785/lymphosign-2021-0020 ◽

2021 ◽

Author(s):

Chaim M Roifman ◽

Linda Vong

Keyword(s):

Severe Acute Respiratory Syndrome ◽

Hand Hygiene ◽

Immune Responses ◽

Primary Immunodeficiency ◽

Close Contact ◽

Herd Immunity ◽

Severe Illness ◽

Third Wave ◽

Novel Coronavirus ◽

Spread Of Infection

The worldwide tally of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, causing novel coronavirus disease 2019 (COVID-19), currently approaches 149.7 million (as of April 30, 2021). Canada’s cases amount to 1,211,083 confirmed infections and 24,169 deaths. In the midst of the pandemic and a third wave of infections, programs aimed at widespread vaccination against COVID-19 remain an essential stop-gap to slow the spread of infection and help achieve protective herd immunity. Patients with primary immunodeficiency (PID) have impaired immune responses and may be at greater risk of severe illness due to COVID-19, thus, are strongly recommended to avoid interactions with those outside of their immediate household “bubble”, practice hand hygiene, and wear masks when spending time outside or in enclosed spaces where close contact with other people cannot be avoided. With the ongoing rollout of COVID-19 vaccinations, we provide here recommendations for patients with PID. It is important to note that individuals who are immunocompromised should always consult their immunologist for additional considerations/contraindications when reviewing their suitability for vaccination.

Download Full-text