COVID-19 Tests | Wish List

trader32176
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Could 3D printed swabs be used to collect COVID-19 test samples?

6/2/21


https://www.news-medical.net/news/20210 ... mples.aspx


Researchers have evaluated 3D printed sample collection swabs made in-house and found them to be a reliable alternative to commercial swabs.

The detection of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is done by collecting samples from the nose and throat. The samples are usually collected using a swab, which has fibers that help better the collection and transport of the sample. As the pandemic continues throughout the world, there is a shortage of testing reagents and sampling swabs, leading to delayed results, affecting the spread of the virus.

To overcome the supply challenge, 3D printing technology was used to rapidly build prototypes. Several teams made available open-source designs for making 3D printed swabs, and workflows were established for local printing.

Researchers from the Université de Montréal and the Université du Québec in Canada evaluated the fabrication process and clinically tested 3D printed swabs manufactured within a hospital, comparing them with commercially available swabs. They reported their results in a paper published on the medRxiv* preprint server.

Evaluating swabs

The swabs were 3D printed locally at the hospital system using the designs provided by the University of South Florida and the Northwell Health system, sterilized and immediately packed individually. The team tested the swabs at their institution’s COVID-19 screening clinic.

From the two designs available, the team selected one that had a smaller head size and greater flexibility for clinical tests. To this design, they added a breaking point some distance from the tip to enable storage and transport of the swab head with the sample.

They ensured that the swab heads were sterile by inoculating the swabs with a bacteria, subjecting them to the sterilization procedure, and testing them for bacterial growth. If the sterilization procedure was effective, no bacteria would grow on the inoculated swabs.

The team tested the swabs on 63 patients, about half of who tested negative for COVID-19. They used 3D printed swabs from three different lots for collecting samples. They found no significant statistical difference in the cycle threshold counts between the PCR results obtained using the 3D printed swabs or the commercial swabs. The overall agreement between the data obtained from the two different swabs was about 97%. The data for the two samples did not agree with each other.

Potential replacement for commercial swabs


The results indicate that if there is a shortage of commercial swabs, 3D printed swabs may be used to collect samples. This finding corresponds to results from previous studies comparing 3D printed swabs with commercial swabs.

The authors were able to take advantage of their health-related 3D printing center in their institution along with sterilization services, which allowed them to quickly perform steam sterilization. Because of the available setup and presence of staff, the cost per 3D printed swab was about 56 US cents. Further optimization can lead to increased production volume and lower production costs.

Our clinical trial has demonstrated that our local 3D printed swab production line offers a reliable local alternative to commercial swabs and therefore confirms that it is a viable local response to provide replacements in the event of pandemic supply chain disruption,” write the authors.

With SARS-CoV-2 continuing to spread in many parts of the world, there will be a need for increased testing capacity. Such local methods for making sample collection swabs may help with increased testing.

*Important Notice


medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Journal reference:

Lapierre, S. G. et al. (2021) Clinical Evaluation of In House Produced 3D Printed Nasopharyngeal Swabs for COVID-19 Testing. medRxiv. https://doi.org/10.1101/2021.05.26.21257548, https://www.medrxiv.org/content/10.1101 ... 21257548v1.
trader32176
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Scientists develop low-cost lab-on-paper device for rapid and accurate detection of SARS-CoV-2

6/18/21


https://www.news-medical.net/news/20210 ... CoV-2.aspx


A team of scientists from the University of Connecticut, USA, has developed a low-cost lab-on-paper technology to rapidly and easily detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. The work has recently been published in a Royal Society of Chemistry’s Lab on a Chip journal.

Background


Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative pathogen of the coronavirus disease 2019 (COVID-19) pandemic, is an enveloped RNA virus of the human beta-coronavirus family. Being a respiratory virus, SARS-CoV-2 primarily attacks the upper respiratory tract and gradually propagates to the lower respiratory tract to cause mild to severe infection.

Reverse transcription-polymerase chain reaction (RT-PCR)-based amplification of viral RNA in respiratory samples is considered as the golden standard method to diagnose COVID-19. However, despite high accuracy, RT-PCR is not always convenient for mass detection of SARS-CoV-2 infection at the community level because of its high turnaround time. In contrast, despite a shorter turnaround time, rapid antigen testing largely suffers from a lower accuracy level. Thus, for the better management of the COVID-19 pandemic, it is necessary to develop rapid, high accuracy diagnostic technologies that can be used for large-scale detection of SARS-CoV-2 infection.
Lab-on-paper technology

In the current study, the scientists have developed an autonomous lab-on-paper device for multiplex gene detection of SARS-CoV-2. The method, which combines reverse transcription recombinase polymerase amplification (RT-RPA) and CRISPR–Cas12a detection, can simultaneously detect nucleoprotein and spike genes of SARS-CoV-2 in a single respiratory swab sample. As an internal control, the device uses human housekeeping RNAse P gene.

Regarding potential advantages, the device is capable of detecting 102 copies of viral RNA within one hour. Since two viral genes are simultaneously detected instead of a single gene, the device is expected to provide high accuracy information. Moreover, because of its simple and easy operational technique, testing with the device can be performed by any healthcare professional, making it suitable for large-scale detection of SARS-CoV-2 infection at the community level.

Operating procedure

To determine the performance of the device, the scientists collected 21 nasal swab samples from patients. Using commercially available kits, they processed these samples to isolate and purity nucleic acids. Afterward, they transferred the nucleic acid preparations to the cellulose-based paper membrane used in the device to detect SARS-CoV-2 infection. The results obtained from the device were comparable to those obtained from conventional RT-PCR testing.

The CRISPR technology used in the device is a highly sensitive and specific gene-editing technology that can alter the genome of an organism by targeting and cutting specific nucleic acid segments, such as DNA or RNA segments.

In the lab-on-paper method, CRISPR first locates the nucleoprotein and spike genes of SARS-CoV-2 and subsequently cuts them. Because of the cut, a fluorescent signal is produced on the device paper, indicating a positive test result. In addition, the device detects the human housekeeping RNAse P gene in order to validate the quality of the sample and the reliability of the result.

Potential advantages

The specialized cellulose-based paper membrane used in the device is hydrophilic in nature. Because of this property, the paper can transport samples that contain nucleic acids. This is highly advantageous as the test can be performed automatically once the sample is loaded. Moreover, because of certain specific formulations, the paper does not interfere with the biochemical reaction required for CRISPR to locate and cut the viral genes. This further reduces the risk of false negative/positive results.

By selecting specific genes of interest, the device can be used for detecting various other pathogens, including human immunodeficiency virus (HIV), human papillomavirus (HPV), or influenza virus.

The scientists have already applied for a provisional patent for the invention through the University of Connecticut Technology Commercialization Services. They are currently looking for an industrial partner to commercialize the device and expand its usage.

Journal reference:

Yin K. 2021. Autonomous lab-on-paper for multiplexed, CRISPR-based diagnostics of SARS-CoV-2. Lab on a Chip. https://doi.org/10.1039/D1LC00293G, https://pubs.rsc.org/en/content/article ... ivAbstract
trader32176
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Re: COVID-19 Tests | Wish List

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SARS-CoV-2 detection with a simple, inexpensive, and sensitive molecular test

6/23/21


https://www.news-medical.net/news/20210 ... -test.aspx


Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing along with contact tracing, isolation, and physical barriers like masks and distancing are the standard strategies used to reduce community transmission. However, insufficient testing protocols have led to failure in containing the community spread of SARS-CoV-2 in many countries. In addition, long delays in access to testing and obtaining test results have made it difficult to contain the spread of the virus. This gap in testing reduces the effectiveness of contact tracing and isolation strategies.

Despite the development of safe vaccines against the virus, the threat of transmission remains high due to the logistical difficulties of global vaccine distribution, limited supply of vaccines, and vaccine hesitancy. In addition to this, the emergence of more infectious SARS-CoV-2 variants that escape natural or vaccine-induced immunity shows that testing will remain a crucial tool in the fight against the pandemic to decrease viral transmission. Also, the absence of global vaccination coverage increases the potential for future outbreaks.

Frequent testing with ‘rapid’ tests that provide quick results is an effective strategy to monitor viral spread in the population and identify infectious individuals, thus allowing faster and safer reopening of the economy. An effective frequent testing strategy should be easy to use and self-administer, rapid, inexpensive, sensitive enough to detect most infectious people, and highly specific. Initial testing strategies for SARS-CoV-2 included deep nasopharyngeal swabs and RT-qPCR, and these tests were conducted by trained healthcare personnel.

To increase testing capacity and decrease time to test results, home-based diagnosis using ‘rapid’ tests were developed to detect viral antigens in shallow nasal swabs. While these tests offered quick results, they were not very sensitive and can only detect ~20,000 viral RNA copies per microliter.

A cheap, rapid, sensitive, and specific molecular test for the detection of SARS-CoV-2 in saliva

Researchers from the US recently described a rapid molecular test named WHotLAMP for the detection of SARS-CoV-2 in saliva. WHotLAMP is easy to use, very sensitive at 3.6 viral RNA copies per microliter of saliva, specific, and inexpensive. This study is published on the medRxiv*preprint serve.

WHotLAMP does not use toxic chemicals or special equipment and can be performed in point-of-care settings. WHotLAMP can also be adapted for home use. It can also be adapted for diagnostic assays for detecting other pathogens and is thus useful for potential future outbreaks.

WHotLAMP is a single-tube test with primers highly specific to SARS-CoV-2

WHotLAMP testing can be performed in a single 1.7 mL microfuge tube. The viral RNA is preserved with the help of a non-hazardous RNA stabilizer and extracted through a brief Proteinase K digestion.
Heating the sample to 95 – 155oC inactivates Proteinase K as well as SARS-CoV-2 virions, thus increasing the biosafety of the saliva sample.

The researchers designed LAMP primer sets throughout the SARS-CoV-2 genome and targeted the primer set (ZI-1, targeting ORF 1a) with the lowest predicted propensity for primer-dimer formation. They also tested a panel of 22 inactivated respiratory pathogens such as SARS-CoV-1, MERS, H1N1 influenza, and common respiratory coronaviruses to evaluate the specificity of the ZI-1 primers. They detected SARS-CoV-2 RNA in samples with encapsulated SARS-CoV-2 RNA particles, but not in samples with only the other respiratory pathogens, illustrating the primers’ specificity to SARS-CoV-2.

WHotLAMP is a broadly useful diagnostic assay that can also be adapted to detect pathogens other than SARS-CoV-2

In this study, the authors describe WHotLAMP, a simple, affordable molecular test that does not need special lab equipment to detect SARS-CoV-2 in saliva. They show that WHotLAMP can detect low levels of SARS-CoV-2 virus present in saliva in about 30 minutes. Its low false-positive rate permits deployment in low prevalence conditions, where high test specificity is critical to obtain high positive predictive values. This assay design is applicable to point-of-care settings, and the single-tube format of the test requires no centrifugation, thus making it easy to scale to 96-well formats.

“While here we focused on a test for SARS-CoV-2, this technology could be used to detect other pathogens that are present in saliva by substituting primers, making WHotLAMP a broadly useful diagnostic assay.”

*Important Notice


medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Journal reference:

WHotLAMP: A simple, inexpensive, and sensitive molecular test for the detection of SARS-CoV-2 in saliva, David Ng, Ana Pinharanda, Merly C Vogt, Ashok Litwin-Kumar, Kyle N Stearns, Urvashi V Thopte, Enrico Cannavo, Armen Enikolopov, Felix Fiederling, Stylianos Kosmidis, Barbara Noro, Ines Rodrigues-Vaz, Hani J Shayya, Peter Andolfatto, Darcy S Peterka, Tanya Tabachnik, Jeanine D'Armiento, Monica P Goldklang, Andres Bendesky, medRxiv, 2021.06.17.21259050; doi: https://doi.org/10.1101/2021.06.17.21259050, https://www.medrxiv.org/content/10.1101 ... 21259050v2
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Kids misusing soft drinks to corrupt SARS-CoV-2 tests

7/8/21


https://www.news-medical.net/news/20210 ... tests.aspx


The global coronavirus 2019 (COVID-19) pandemic has caused a momentous effect on society, with public health notices from the government encouraging adults to work from home and schools shifting to online learning platforms to teach their students. As lockdown has eased in many countries around the world, schools and workplaces have similarly returned to their normal setting.

What are LFDs?

Many workplaces look different now as compared to before lockdowns were first initiated due to the presence of masks and rigorous testing requirements for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Much of the testing that is conducted in these settings include lateral flow tests that are followed by a reverse transcriptase-polymerase chain reaction (RT-PCR) RT-PCR test, if necessary.

The mass use of rapid lateral flow tests, which has been supported by the World Health Organization (WHO), has enabled some semblance of normality at both work and school. The benefits of using lateral flow devices (LFDs) include their low costs and ease of use.

Throughout the United Kingdom, LFDs have been used by schools since March of 2021. These schools often utilize these devices to test students twice weekly with the aim of preventing the spread of infection in the event that a student(s) tests positive for SARS-CoV-2.

Despite their utility, there has been considerable controversy surrounding the use of LFDs, as some students have reported that the application of soft drinks instead of their own sample can result in a positive test. To that end, a group of collaborating researchers from Liverpool systematically tested a variety of different soft drinks to determine their ability to create false-positive results.

LFDs and SARS-CoV-2

LFDs are designed as cartridges that comprise a nitrocellulose membrane strip and absorbent paper that contains dried test reagents. When these reagents are mixed with the analyte from a test sample, they migrate through the nitrocellulose strip and over the test line where the SARS-CoV-2 monoclonal antibody is fixed.

Two lines can be produced in a lateral flow test. One line is the control line that confirms that the test is functioning properly and its validity, whereas the other line is produced if the sample tests positive for SARS-CoV-2.

The Innova SARS-CoV-2 antigen rapid qualitative test was one of the first devices that completed the multi-stage evaluation process. As a result, this test was used in pilot testing in communities within Liverpool.

LFDs have been used for large-scale community open-access testing due to their ability to accurately distinguish between individuals who are presenting with a higher viral load of SARS-CoV-2. While RT-PCR tests are more sensitive to the virus than lateral flow tests, the widespread availability of LFDs is generally much better than that of RT-PCR tests.

Additionally, LFDs only require about 30 minutes to provide test results, which is comparable to the 48 hours needed to obtain RT-PCR results. This is a significant advantage, as it can allow individuals who test positive to remain in their house to isolate and prevent the spread of the infectious virus while they follow-up with an RT-PCR test.

Rapid testing in schools

With schools reopening on March 8, 2021, LFDs were introduced for rapid asymptomatic testing in secondary schools to allow for students and staff to be tested for SARS-CoV-2 twice weekly. Those who had tested positive through these tests were made to isolate, along with individuals who had been in close contact with them. A subsequent RT-PCR test was to be booked for these individuals within 48 hours of receiving the positive result.

However, after three months of regular testing, a school in Merseyside had reports of students who had found that either drinking fruit-flavored juice or misusing them as an analyte had the potential to provide a false-positive result. To that end, Liverpool-based researchers have undertaken a study to evaluate a variety of soft drinks and determine their ability to be misused as an analyte and provide a false-positive result for SARS-CoV-2.

False-positive tests

The team had investigated 14 brands of common non-alcoholic soft drinks, consisting of:

Highlands Spring Water
Robinsons Hydro Fruit Shoot Blackcurrant Spring Water
Robinsons Fruit Shoot Blackcurrant and Apple
Robinsons Fruit Shoot Orange
Robinsons Fruit Shoot Apple
Coca-Cola
Diet Coca-Cola
Sprite
Fanta
Appletiser
Blackcurrant Concentrated Juice
Pineapple Concentrated Juice
Orange Concentrated Juice
Apple Concentrated Juice.

Each of the drink samples was allowed to stand for two hours before analysis to allow for them to reach room temperature. One milliliter (ml) of each sample was then drawn into the extractor tube of the Innova kit. The sugar quantity and ingredients of each sample were also noted. The acidity was also tested using a urinalysis strip which included pH quantification.

In addition to these drinks, four sweeteners were also tested, which included Splenda, Canderel, Sweetex, and Hubbard’s Foodstore. To prepare the sweeteners, the researchers dissolved one tablet of the sweetener into 20 ml of spring water, of which 1 ml was used for actual testing.

Study results


Mixed findings were reported in this study, with spring water having a definite negative result, 3 out of 14 drink samples producing void LFD results which mainly included drinks from fruit concentrate, and 10 out of 14 drinks producing a positive test result. The researchers found that the drink samples that produced false-positive test results were all similar in their sugar and pH levels. Additionally, all four sweeteners that were included in this study resulted in negative LFD tests.

The researchers concluded that, in line with the user guide provided, food and drinks should not be consumed 30 minutes prior to taking the test. They recommended that the test be performed in the morning and with possible supervision.

The actual mechanism of the false positives that were identified in this study remains unclear and will therefore require further research and analysis, as the acidity and sugar content of the drinks did not appear to have any effect on the results. The researchers suggest that future studies evaluate the preservatives present in these drinks in order to determine their role in contributing to the occurrence of these false positives.

*Important Notice

medrxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Journal reference:


Oni, L., Hawcutt, D., Buchan, I. & Semple, M. (2021). Soft drinks can be misused to give false positive SARS-CoV-2 lateral flow device results. medrxiv. doi:10.1101/2021.07.05.21260003. https://www.medrxiv.org/content/10.1101 ... 21260003v1
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