From more testing to smart testing: data-guided SARS-CoV-2 testing choices

AbstractWe present an in-depth analysis of data from drive through testing stations using rapid antigen detection tests (RDT’s), RT-PCR and virus culture, to assess the ability of RDT’s to detect infectious cases. We show that the detection limits of five commercially available RDT’s differ considerably, impacting the translation into the detection of infectious cases. We recommend careful fit-for-purpose testing before implementation of antigen RDT’s in routine testing algorithms as part of the COVID-19 response.

Download Full-text

Evaluation of three rapid lateral flow antigen detection tests for the diagnosis of SARS-CoV-2 infection

10.1101/2020.12.30.20249057 ◽

2021 ◽

Author(s):

AE Jääskeläinen ◽

MJ Ahava ◽

P Jokela ◽

L Szirovicza ◽

S Pohjala ◽

...

Keyword(s):

High Viral Load ◽

Antigen Detection ◽

Diagnostic Tools ◽

Repeated Testing ◽

Rt Pcr ◽

High Demand ◽

Overall Performance ◽

Virus Culture ◽

Regulatory Acceptance ◽

Pcr Test

AbstractIntroductionThe COVID-19 pandemic has led to high demand of diagnostic tools. Rapid antigen detection tests have been developed and many have received regulatory acceptance such as CE IVD or FDA markings. Their performance needs to be carefully assessed.Materials and Methods158 positive and 40 negative retrospective samples collected in saline and analyzed by a laboratory-developed RT-PCR test were used to evaluate Sofia (Quidel), Standard Q (SD Biosensor), and Panbio™ (Abbott) rapid antigen detection tests (RADTs). A subset of the specimens was subjected to virus culture.ResultsThe specificity of all RADTs was 100% and the sensitivity and percent agreement was 80% and 85% for Sofia, 81% and 85% for Standard Q, and 83% and 86% for Panbio™, respectively. All three RADTs evaluated in this study reached a more than 90% sensitivity for samples with a high viral load as estimated from the low Ct values in the reference RT-PCR. Virus culture was successful in 80% of specimens with a Ct value <25.ConclusionsAs expected, the RADTs were less sensitive than RT-PCR. However, they benefit from the speed and ease of testing, and lower price as compared to RT-PCR. Repeated testing in appropriate settings may improve the overall performance.

Download Full-text

In-depth Analysis of the Impurities in GaN

MRS Internet Journal of Nitride Semiconductor Research ◽

10.1557/s1092578300002064 ◽

1996 ◽

Vol 1 ◽

Cited By ~ 3

Author(s):

A. P. Kovarsky ◽

V. S. Strykanov

Keyword(s):

Secondary Ion Mass Spectrometry ◽

Dynamic Range ◽

Detection Limits ◽

Background Level ◽

Epitaxial Films ◽

Depth Analysis ◽

Lower Detection ◽

Minimum Detection Level ◽

Ion Yields ◽

Secondary Ion

GaN epitaxial films were analyzed by Secondary Ion Mass Spectrometry (SIMS). Standard implanted samples were used to determine the appropriate analytical conditions for analysis of impurities. The dose and energy of implantation for selected elements (Mg, Al, Si, Zn, Cd, H, C and O) were chosen so the maximum impurity concentration was not more than 1020 atoms/cm3. The optimum analysis conditions were ascertained from the standards for each element, and the detection limits were deduced from the background levels of the implantation profiles. We demonstate that lower detection limits of 1015 atoms/cm3 with a dynamic range 103 − 105 are possible. Zn and Cd have low ion yields, so the minimum detection level for these elements is the background level of the detector. The detection limits of the other elements are determined by the contamination of an initial GaN matrix.

Download Full-text

PHOTOGRAMMETRY AS A PARTICIPATORY RECOVERY TOOL AFTER DISASTERS: A GROUNDED FRAMEWORK FOR FUTURE GUIDELINES

ISPRS - International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences ◽

10.5194/isprs-archives-xlii-2-w15-921-2019 ◽

2019 ◽

Vol XLII-2/W15 ◽

pp. 921-928

Author(s):

C. Pezzica ◽

A. Piemonte ◽

C. Bleil de Souza ◽

V. Cutini

Keyword(s):

Low Cost ◽

Central Italy ◽

Semantic Content ◽

Ethnographic Study ◽

Point Of View ◽

Humanitarian Response ◽

Central Italy Earthquake ◽

Depth Analysis ◽

Crowdsourced Data ◽

Fit For Purpose

Abstract. This paper identifies the application domain, context of use, processes and goals of low-cost street-level photogrammetry after urban disasters. The proposal seeks a synergy between top-down and bottom-up initiatives carried out by different actors during the humanitarian response phase in data scarce contexts. By focusing on the self-organisation capacities of local people, this paper suggests using collaborative photogrammetry to empower communities hit by disasters and foster their active participation in recovery and reconstruction planning. It shows that this task may prove technically challenging depending on the specifics of the collected imagery and develops a grounded framework to produce user-centred image acquisition guidelines and fit-for-purpose photogrammetric reconstruction workflows, useful in future post-disaster scenarios. To this end, it presents an in-depth analysis of a collaborative photographic mapping initiative undergone by a group of citizen-scientists after the 2016 Central Italy earthquake, followed by the explorative processing of some sample datasets. Specifically, the paper firstly presents a visual ethnographic study of the photographic material uploaded by participants from September 2016 to November 2018 in the two Italian municipalities of Arquata del Tronto and Norcia. Secondly, it illustrates from a technical point of view issues concerning the processing of crowdsourced data (e.g. image filtering, selection, quality, semantic content and 3D model scaling) and discusses the viability of using it to enrich the pool of geo-information available to stakeholders and decision-makers. Final considerations are discussed as part of a grounded framework for future guidelines tailored to multiple goals and data processing scenarios.

Download Full-text

The Cross Roads of Heritage

10.26686/wgtn.17148947.v1 ◽

2021 ◽

Author(s):

◽

Philippa Dalgety

Keyword(s):

New Zealand ◽

Urban Areas ◽

Large Scale ◽

Adaptive Reuse ◽

Built Form ◽

Depth Analysis ◽

Key Factor ◽

History Of ◽

Fit For Purpose ◽

The Town

This research explores an approach for adaptive reuse to enhance livability and greater connection to place within provincial towns of New Zealand. There are existing buildings which are often left in disrepair or considered too expensive to refurbish or strengthen. They are often demolished with little consideration to the building’s significance, therefore adaptive reuse has become a missed opportunity in New Zealand. Many of our provincial cities have uninhabited large-scale buildings, which need upgrading due to being outdated and no longer fit for purpose. Seismic upgrading is a key factor in why these buildings are left uninhabited. One of the urban areas which this is prevalent is Whanganui. Whanganui has the opportunity to blend the old and the new built form to create a revitalized and timeless street appearance. The regeneration of Whanganui can be achieved through adaptive reuse to enhance the crafted beauty of the town through its architecture. The revitalization of Whanganui can give guidance to other provincial cities in New Zealand while enhancing the quality of life within the town. An in-depth analysis of the history of Whanganui, will allow for heritage significance to play a major role in the redesign. This design will be developed at three different scales to demonstrate how the built form can enhance connection to place and livability. These scales are at an urban, a built and a detailed scale. The main cross roads linking the city of Whanganui to its river is surrounded by character and historical buildings. It will be used as a key area illustrating Whanganui’s past to better inform the future.

Download Full-text

Development and Evaluation of Novel and Highly Sensitive Single-Tube Nested Real-Time RT-PCR Assays for SARS-CoV-2 Detection

International Journal of Molecular Sciences ◽

10.3390/ijms21165674 ◽

2020 ◽

Vol 21 (16) ◽

pp. 5674

Author(s):

Cyril Chik-Yan Yip ◽

Siddharth Sridhar ◽

Kit-Hang Leung ◽

Anthony Chin-Ki Ng ◽

Kwok-Hung Chan ◽

...

Keyword(s):

Real Time ◽

Limit Of Detection ◽

Rt Pcr ◽

Single Tube ◽

Highly Sensitive ◽

Testing Algorithms ◽

Pcr Assays ◽

Human Coronaviruses ◽

Pooled Sample

Sensitive molecular assays are critical for coronavirus disease 2019 (COVID-19) diagnosis. Here, we designed and evaluated two single-tube nested (STN) real-time RT-PCR assays, targeting SARS-CoV-2 RdRp/Hel and N genes. Both STN assays had a low limit of detection and did not cross react with other human coronaviruses and respiratory viruses. Using 213 initial respiratory specimens from suspected COVID-19 patients, the sensitivity of both the STN COVID-19-RdRp/Hel and the STN COVID-19-N assays was 100% (99/99), while that of the comparator non-nested N assay was 95% (94/99). Among 108 follow-up specimens from confirmed COVID-19 patients who tested negative by the non-nested COVID-19-RdRp/Hel assay, 28 (25.9%) were positive for SARS-CoV-2 by the STN COVID-19-RdRp/Hel or the STN COVID-19-N assay. To evaluate the performance of our novel STN assays in pooled specimens, we created four sample pools, with each pool consisting of one low positive specimen and 49 negative specimens. While the non-nested COVID-19-RdRp/Hel assay was positive in only one of four sample pools (25%), both of the STN assays were positive in two of four samples pools (50%). In conclusion, the STN assays are highly sensitive and specific for SARS-CoV-2 detection. Their boosted sensitivity offers advantages in non-traditional COVID-19 testing algorithms such as saliva screening and pooled sample screening during massive screening.

Download Full-text

A prospective clinical pilot study on the effects of a hydrogen peroxide mouthrinse on the intraoral viral load of SARS-CoV-2

Clinical Oral Investigations ◽

10.1007/s00784-020-03549-1 ◽

2020 ◽

Vol 24 (10) ◽

pp. 3707-3713

Author(s):

Maximilian J. Gottsauner ◽

Ioannis Michaelides ◽

Barbara Schmidt ◽

Konstantin J. Scholz ◽

Wolfgang Buchalla ◽

...

Keyword(s):

Hydrogen Peroxide ◽

Clinical Trials ◽

Viral Load ◽

Pilot Study ◽

High Risk ◽

Infection Prevention ◽

Healthcare Professionals ◽

Patient Contact ◽

Rt Pcr ◽

Virus Culture

Abstract Objectives SARS-CoV-2 is mainly transmitted by inhalation of droplets and aerosols. This puts healthcare professionals from specialties with close patient contact at high risk of nosocomial infections with SARS-CoV-2. In this context, preprocedural mouthrinses with hydrogen peroxide have been recommended before conducting intraoral procedures. Therefore, the aim of this study was to investigate the effects of a 1% hydrogen peroxide mouthrinse on reducing the intraoral SARS-CoV-2 load. Methods Twelve out of 98 initially screened hospitalized SARS-CoV-2-positive patients were included in this study. Intraoral viral load was determined by RT-PCR at baseline, whereupon patients had to gargle mouth and throat with 20 mL of 1% hydrogen peroxide for 30 s. After 30 min, a second examination of intraoral viral load was performed by RT-PCR. Furthermore, virus culture was performed for specimens exhibiting viral load of at least 103 RNA copies/mL at baseline. Results Ten out of the 12 initially included SARS-CoV-2-positive patients completed the study. The hydrogen peroxide mouthrinse led to no significant reduction of intraoral viral load. Replicating virus could only be determined from one baseline specimen. Conclusion A 1% hydrogen peroxide mouthrinse does not reduce the intraoral viral load in SARS-CoV-2-positive subjects. However, virus culture did not yield any indication on the effects of the mouthrinse on the infectivity of the detected RNA copies. Clinical relevance The recommendation of a preprocedural mouthrinse with hydrogen peroxide before intraoral procedures is questionable and thus should not be supported any longer, but strict infection prevention regimens are of paramount importance. Trial registration German Clinical Trials Register (ref. DRKS00022484)

Download Full-text

Metagenomic Sequencing To Detect Respiratory Viruses in Persons under Investigation for COVID-19

Journal of Clinical Microbiology ◽

10.1128/jcm.02142-20 ◽

2020 ◽

Vol 59 (1) ◽

pp. e02142-20

Author(s):

Ahmed Babiker ◽

Heath L. Bradley ◽

Victoria D. Stittleburg ◽

Jessica M. Ingersoll ◽

Autum Key ◽

...

Keyword(s):

Influenza A ◽

Viral Infections ◽

Respiratory Viruses ◽

Human Metapneumovirus ◽

Molecular Testing ◽

Metagenomic Sequencing ◽

Rt Pcr ◽

Human Coronavirus ◽

Testing Algorithms ◽

Syncytial Virus

ABSTRACTBroad testing for respiratory viruses among persons under investigation (PUIs) for SARS-CoV-2 has been performed inconsistently, limiting our understanding of alternative viral infections and coinfections in these patients. RNA metagenomic next-generation sequencing (mNGS) offers an agnostic tool for the detection of both SARS-CoV-2 and other RNA respiratory viruses in PUIs. Here, we used RNA mNGS to assess the frequencies of alternative viral infections in SARS-CoV-2 RT-PCR-negative PUIs (n = 30) and viral coinfections in SARS-CoV-2 RT-PCR-positive PUIs (n = 45). mNGS identified all viruses detected by routine clinical testing (influenza A [n = 3], human metapneumovirus [n = 2], and human coronavirus OC43 [n = 2], and human coronavirus HKU1 [n = 1]). mNGS also identified both coinfections (1, 2.2%) and alternative viral infections (4, 13.3%) that were not detected by routine clinical workup (respiratory syncytial virus [n = 3], human metapneumovirus [n = 1], and human coronavirus NL63 [n = 1]). Among SARS-CoV-2 RT-PCR-positive PUIs, lower cycle threshold (CT) values correlated with greater SARS-CoV-2 read recovery by mNGS (R2, 0.65; P < 0.001). Our results suggest that current broad-spectrum molecular testing algorithms identify most respiratory viral infections among SARS-CoV-2 PUIs, when available and implemented consistently.

Download Full-text

Transcriptional Profiling of Methyltransferase Genes during Growth of Methanosarcina mazei on Trimethylamine

Journal of Bacteriology ◽

10.1128/jb.00420-09 ◽

2009 ◽

Vol 191 (16) ◽

pp. 5108-5115 ◽

Cited By ~ 17

Author(s):

Christian Krätzer ◽

Paul Carini ◽

Raymond Hovey ◽

Uwe Deppenmeier

Keyword(s):

Transcriptional Profiling ◽

Expression Patterns ◽

Pcr Analysis ◽

Exponential Growth Phase ◽

Methane Formation ◽

Rt Pcr ◽

Transcript Levels ◽

Methanosarcina Mazei ◽

Depth Analysis ◽

Genes Encoding

ABSTRACT The genomic expression patterns of Methanosarcina mazei growing with trimethylamine were measured in comparison to those of cells grown with methanol. We identified a total of 72 genes with either an increased level (49 genes) or a decreased level (23 genes) of mRNA during growth on trimethylamine with methanol-grown cells as the control. Major differences in transcript levels were observed for the mta, mtb, mtt, and mtm genes, which encode enzymes involved in methane formation from methanol and trimethylamine, respectively. Other differences in mRNA abundance were found for genes encoding enzymes involved in isopentenyl pyrophosphate synthesis and in the formation of aromatic amino acids, as well as a number of proteins with unknown functions. The results were verified by in-depth analysis of methyltransferase genes using specific primers for real-time quantitative reverse transcription-PCR (RT-PCR). The monitored transcript levels of genes encoding corrinoid proteins involved in methyl group transfer from methylated C1 compounds (mtaC, mtbC, mttC, and mtmC) indicated increased amounts of mRNA from the mtaBC1, mtaBC2, and mtaBC3 operons in methanol-grown cells, whereas mRNA of the mtb1-mtt1 operon was found in high concentrations during trimethylamine consumption. The genes of the mtb1-mtt1 operon encode methyltransferases that are responsible for sequential demethylation of trimethylamine. The analysis of product formation of trimethylamine-grown cells at different optical densities revealed that large amounts of dimethylamine and monomethylamine were excreted into the medium. The intermediate compounds were consumed only in the very late exponential growth phase. RT-PCR analysis of key genes involved in methanogenesis led to the conclusion that M. mazei is able to adapt to changing trimethylamine concentrations and the consumption of intermediate compounds. Hence, we assume that the organism possesses a regulatory network for optimal substrate utilization.

Download Full-text