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Latest PCR Developments Rapid Testing: Secret Weapon Against Covid-19

From MA Alexander Stark |

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Nearly all of us have in one way or another come into contact with PCR tests in recent months. Polymerase chain reaction (PCR) only requires a small DNA sample of the virus to detect an infection with Covid-19. In recent weeks and months, companies have successfully launched ever faster test kits — some of which we are presenting in this article.

Bosch’s rapid coronavirus test delivers results for positive samples in less than 30 minutes.
Bosch’s rapid coronavirus test delivers results for positive samples in less than 30 minutes.
(Source: Bosch)

Würzburg/Germany — Testing half the population weekly with inexpensive, rapid-turnaround Covid-19 tests would drive the virus toward elimination within weeks, according to a new study published by University of Colorado Boulder and Harvard University researchers. Such a strategy could lead to “personalized stay-at-home orders” without shutting down restaurants, bars, retail stores and schools, the authors said.

For the study, published in the journal Science Advances, the researchers scoured available literature on how viral load climbs and falls inside the body during infection, when people tend to experience symptoms, and when they become contagious. They then used mathematical modeling to forecast the impact of screening with different kinds of tests on three hypothetical scenarios: in 10,000 individuals; in a university-type setting of 20,000 people; and in a city of 8.4 million. When it came to curbing spread, they found that frequency and turnaround time are much more important than test sensitivity. The study demonstrates the power of frequent testing in shortening the pandemic and saving lives.

Developments reported in the past months show, that companies are increasingly focusing their efforts on rapid testing solutions. These are some of the latest developments in the field of PCR tests:

PCR — the Gold Standard for Covid-19 Tests

Bosch’s rapid coronavirus test delivers results for positive samples in less than 30 minutes.
Bosch’s rapid coronavirus test delivers results for positive samples in less than 30 minutes.
(Source: Bosch)

For instance, Bosch has developed a new rapid test for its Vivalytic analysis device to detect the Sars-Cov-2 pathogen. According to the company, the test provides a reliable result in 39 minutes. Results for positive samples are even delivered in less than 30 minutes. The rapid test is predestined for decentralized use in mobile test centres at freeway service stations or in airports. People who take the test can obtain a reliable result while at the testing site. The CE-approved test helps avoid time in quarantine, relieve laboratories, and make travel and work safer again. The test has a sensitivity of 98 % and a specificity of 100 %. To develop it, the Bosch subsidiary Bosch Healthcare Solutions joined forces with the German biotechnology company R-Biopharm — a leading provider of highly sensitive manual PCR tests.

The company launched the first rapid test for its Vivalytic analysis device at the end of March 2020, after just six weeks’ development. As a multiplex test, it simultaneously checks patient samples for the Sars-Cov-2 virus and nine other respiratory diseases in under two and a half hours. The new, accelerated test is exclusively for Sars-Cov-2. The advantages of Bosch’s rapid test lie not only in speedy analysis, but also in ease of use. A sample is taken from the patient’s nose and throat using a swab, and placed in the test cartridge. Then the test cartridge, which already contains all the reagents required for the test, is inserted into the Vivalytic device for automated analysis. The Vivalytic analysis device is designed to be user-friendly; medical staff require only brief training on how to operate it. The development of the Vivalytic system, which consists of an analysis device and test cartridges, grew out of a long-standing collaboration between Bosch’s corporate research and advance engineering and Bosch Healthcare Solutions.

What is a PCR Test?

The PCR test is considered the gold standard among coronavirus tests. By means of a PCR test, a sample from the mucous membranes of the respiratory tract can be used to reliably determine whether pathogens are present.

The PCR test is a standard procedure in the diagnosis of viruses. The test is based on the so-called polymerase chain reaction (PCR). In this process, the genetic material of the virus is amplified. This makes it possible to detect viruses even if only a few particles are present. The PCR test therefore has a high sensitivity and it detects the virus with a high degree of accuracy. In addition, only the genetic material of the Sars-Cov-2 coronavirus is specifically amplified. The test has a high specificity, i.e. it detects exactly the targeted virus.

Test Results within 25 Minutes

Even faster test results promises the Canadian company XPhyto with the approval of its 25-minutes test for use in the EU in March. Together with its exclusive German diagnostics development partner, 3a-diagnostics market the point-of-care Covid-19 RT-PCR test system (Covid-ID Lab). Covid-ID Lab is now registered within the European Union as a commercial in vitro diagnostic (CE-IVD) test.

The test is one of the fastest PCR-based Covid-19 tests currently approved. With a sample collection to result time of 25 minutes, Covid-ID Lab combines the speed of a rapid screening test with the accuracy of a PCR diagnostic. Covid-ID Lab is designed for point-of-care testing, particularly in satellite and small-scale labs, such as transportation hubs, borders, care facilities, schools, pharmacies, and hospitality settings.

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Covid-ID Lab is a multiplex viral RNA probe kit based on the reverse transcriptase-polymerase chain reaction (RT-PCR) method. For assay performance, Covid-ID Lab requires only a single 20-minute PCR thermal cycle without prior RNA extraction as part of the sample preparation. Many widely available standard PCR instruments are suitable to run the test. Results are collected after the PCR cycle via easy-to-read optical indicator strips on a simple fluidics platform. The elimination of RNA extraction for sample preparation reduces the risk of cross-contamination and minimizes the need for lab materials and trained personnel. The rapid results, minimal laboratory equipment, and ease of use are expected to translate into reduced operating costs, greater convenience and portability.

In this video Thermo Fisher Scientific provides the basics about PCR:

Thermo Fisher Scientific recently announced that the U.S. Food and Drug Administration (FDA) has granted Emergency Use Authorization (EUA) for the Thermo Fisher Scientific Amplitude Solution with the Taq Path Covid-19 High-Throughput Combo Kit. The Amplitude Solution enables clinical and public health laboratories to scale gold standard PCR testing and process up to 8000 samples in a single day with minimal staffing resources and a secured supply of kits, reagents and consumables to meet their testing needs. The solution has been implemented globally including labs in Europe and Japan.

The Amplitude Solution is a molecular diagnostic testing system that helps clinical labs expand testing capacity by combining Thermo Fisher's extraction and real-time PCR instruments with liquid handling products from Tecan Group. The modular system utilizes a high-throughput version of the company's Applied Biosystems Taq Path Covid-19 Combo Kit, which received EUA in March 2020, to process samples in four steps with minimal hands-on time and laboratory space requirements. The kit's multi-gene target design and updated interpretive software may help labs detect Sars-Cov-2 variants.

Multiplex Tests for Sars-Cov-2 and Influenza

Multiplex tests, such as the Flu SC2 Multiplex Assay from Promega, can detect and differentiate RNA from Sars-Cov-2, influenza A virus, and influenza B virus from a single patient sample. This enables:

  • labs to conserve materials while also processing more tests
  • clinicians to differentiate between Covid-19 and flu, since symptoms can be similar
  • health officials to conduct ongoing flu surveillance while also testing for Sars-Cov-2

“Multiplex molecular tests are crucial as the flu season overlaps with the Covid-19 pandemic, and we’re glad that Promega is able to continue to support laboratories by providing them more options as testing evolves and advances,” says Heather Tomlinson, Director of Clinical Diagnostics at Promega.

FDA Emergency Use Authorization for Multiplex Test

Qiagen announced the Emergency Use Authorization by the U.S. FDA for the Neumo Dx Flu A-B/RSV/Sars-Cov-2 Vantage Assay that will help healthcare professionals quickly identify and differentiate individuals suspected by a healthcare provider of respiratory viral infection consistent with Covid-19.
Qiagen announced the Emergency Use Authorization by the U.S. FDA for the Neumo Dx Flu A-B/RSV/Sars-Cov-2 Vantage Assay that will help healthcare professionals quickly identify and differentiate individuals suspected by a healthcare provider of respiratory viral infection consistent with Covid-19.
(Source: Qiagen)

The significance of reliable and fast test results leads to regulatory bodies such as the FDA to react more quickly and grant emergency approvals for promising solutions. In this context it is also crucial to distinguish Covid-19 infections from other respiratory infections. That is why Qiagen announced the Emergency Use Authorization by the U.S. FDA for the Neumo Dx Flu A-B/RSV/Sars-Cov-2 Vantage Assay that is designed to help healthcare professionals quickly identify and differentiate individuals suspected by a healthcare provider of respiratory viral infection consistent with Covid-19.

As restrictions are eased and social distancing measures are reduced, respiratory viral infections are likely to increase. Clinical signs and symptoms of respiratory viral infection due to Sars-Cov-2, influenza or RSV can be similar. This makes it essential to correctly identify them in order to treat and manage patients accordingly, especially in the Covid-19 pandemic. This polymerase chain reaction (PCR) multiplex test will be an important tool for simultaneous qualitative detection and differentiation of influenzas A and B, respiratory syncytial virus (RSV) and Sars-Cov-2 infections within 80 minutes.

Qiagen launched the Neumo Dx Flu A-B/RSV/Sars-Cov-2 Vantage Test in the European Union and other markets that accept CE-IVD in November 2020 and will now begin commercialization of the test in the U.S. The company fully acquired Neumo Dx in September 2020 and made it one of its five growth drivers for the company to continue growing on a standalone basis — the others being Sample Prep, Qiacuity, QFT and Qiastat-Dx. The Neumo Dx Flu A-B/RSV/ Sars-Cov-2 Vantage Test strengthens the company’s footprint in PCR, the gold standard in coronavirus testing.

Launch of Mobile Processing Laboratories to Detect Covid-19

PCR test are a crucial method to ensure the safety of people that cannot stay at home, because of different reasons and also to support efforts of reopening parts of social life and the economy that suffer from the lockdown. To do this in a safe way, mobile test centers play an important role.

Novacyt an international specialist in clinical diagnostics, in March announced the expansion of its Versalab service with the launch of mobile processing laboratories (MPL) to provide rapid turnaround PCR testing on-site. Testing will be performed using mid-nose nasal swabs, which were found to be effective and well tolerated compared to the more invasive nasopharyngeal swabs in the interim review of Queen Mary University of London’s clinical trial in care homes, as announced by the Company on 16 November 2020.

Versalab was launched in December 2020 to support private sector testing of infectious diseases, initially focused on Covid-19. This has enabled Novacyt to identify a growing number of UK and international mobile testing opportunities across the private sector.

The company’s MPLs will be fully equipped with its Promate assay and q16 PCR instruments. This product is the only direct-to-PCR Covid-19 assay approved by the Department of Health and Social Care’s Technology Validation Group. The Promate workflow, which includes a viral inactivation buffer, means the MPLs do not require a category 2 laboratory to handle the live virus. As a result, the cost of testing is reduced, as well as the risks associated with handling the live virus in a mobile testing unit. This workflow allows Novacyt to provide rapid results to patients in under 80 minutes. Novacyt is one of the first companies to offer mobile testing units to deliver same day, on-site results using the gold standard sensitivity and specificity of PCR technology. Each MPL is able to process up to 900 Covid-19 samples per day, depending on customer needs. This throughput model supports multiple use cases such as on-site testing at workplaces, schools, sporting and music events. Novacyt is also in the process of validating the use of its SNPsig portfolio with Promate to enable a mobile workflow solution that can detect the original Sars-Cov-2 strain and identify variants of concern to support healthcare providers rapidly identify the outbreak of surge infections in localized areas.

Point-of-Care Testing

The small cube-shaped device utilizes the Co-Diagnostic’s Direct Saliva extraction-free protocol in connection with Logix Smart test reagents that are pre-packaged in saliva receptacle tubes.
The small cube-shaped device utilizes the Co-Diagnostic’s Direct Saliva extraction-free protocol in connection with Logix Smart test reagents that are pre-packaged in saliva receptacle tubes.
(Source: Co-Diagnostic)

Complementing mobile test solutions, tests at home or at the point-of-care are also being developed. Here, the focus lies on usability by non-professionals. For instance, Co-Diagnostics, a molecular diagnostics company with a unique, patented platform for the development of diagnostic tests, announced in March the development of a new point-of-care/at home PCR diagnostic testing, screening and surveillance platform designed to perform Covid-19 testing at businesses, schools, homes, hotels, cruise ships, airports, airplanes and other locations.

The small cube-shaped device utilizes the company's Direct Saliva extraction-free protocol in connection with Logix Smart test reagents that are pre-packaged in saliva receptacle tubes. A person simply adds a swab or saliva sample to the receptacle tube and places the tube inside the device, which is then activated via a smartphone app and delivers rapid PCR Covid-19 results directly to the smartphone. The company believes that the convenience of displaying testing results on the smartphone empowers employees, students, travelers, and other individuals to quickly know their Covid-19 status, and may also provide a simple, straightforward way to satisfy requirements for entry into entertainment venues, clearance for airplane travel and hotel accommodations, work and school passports, and other applications.

The platform chemistry was created by Co-Diagnostics utilizing proprietary Co Primer technology, Direct Saliva extraction-free protocols, and freeze-dried reagents. The device is being developed and engineered for Co-Diagnostics by internationally renowned experts in rapid PCR applications, and whose previous medical device inventions are in widespread use around the world.

With this platform, Co-Diagnostics plans to revolutionize the availability of accurate, fast and economical PCR tests as regular Covid-19 testing becomes part of the long-term protocol for many organizations. The rapid gold-standard PCR results from this testing platform would be differentiated from less accurate antigen tests. In addition, PCR may even detect the presence of genetic material of the Sars-Cov-2 virus being carried by vaccinated patients. The Company agrees with epidemiologists that the rapid spread of the coronavirus and appearance of mutant strains mean that Covid-19 will remain with us for years, or even decades, leaving the world population to coexist with Covid-19 similar to other endemic diseases like flu, the common cold, and HIV.

While it is being designed for in-home use by responsible individuals, it is anticipated that businesses, physician's offices, dental offices, schools, theaters, sporting arenas, hotels, airlines and many other locations will avail themselves of the ease, accuracy and accessibility of this testing platform.

Microarray Testing Technology

Based on its recent analysis of the global molecular testing market, Frost & Sullivan recognizes Pathogen DX with the 2021 Global Technology Innovation Leadership Award for its Detectx-Rv and Envirox-Rv tests. Pathogen Dx adapted its testing platform by combining multiplexed end-point, real-time polymerase chain reaction (RT-PCR) with DNA microarray technology to enable testing for Covid-19 in people, in the air, and on contact surfaces. The Detectx-Rv utilizes nasopharyngeal swabs, nasal aspirate or fluids, and viral RNA isolation kits and contains more probes on its microarray to drive 100 % specificity in the test.

The company's Detectx-Rv can triage patients by distinguishing among several other flu-like symptoms, such as cold and influenza A and B, from Covid-19. The test complements this accuracy with high throughput, offering 96 tests per kit. Pathogen Dx is looking to scale and maximize the throughput by enabling pooled sample testing to accommodate up to 3456 tests on six plates of the 96-well microarray and deploy continuous processing manually with four lab technicians or through automation. Furthermore, the test applies its One-step PCR that maximizes DNA amplification using similar amplification technologies, such as next-generation sequencing or Droplet Digital-PCR, leading to ten times better accuracy than with other FDA-approved PCR-based tests.

Furthermore, the test can detect viruses that spread through transmitted droplets and that remain either air-suspended for hours or on surfaces for up to three days. With at least ten times more sensitivity than existing virus-detecting technologies and with a threshold detection limit of 62 copies of the virus, Envirox-Rv delivers 98 % accuracy and detects minimal viral load, which is as low as a single copy.

New Sars-Cov-2 Variant RT-PCR Assays

Bio-Rad Laboratories announced the launch of the Sars-Cov-2 Variant RT-PCR Assays for research use only (RUO). The assays can detect Sars-Cov-2 variants of concern, including P.1, B.1.351, and B.1.1.7, by distinguishing specific mutations in Sars-Cov-2 using reverse transcription PCR (RT-PCR) often prior to a next generation sequencing (NGS) workflow for confirmation.

With the emergence of several Sars-Cov-2 variants of concern, public health researchers are looking for a quicker way to track the spread of these variants in a population. Laboratories that use NGS to track Covid-19 variants can detect these mutations more quickly and cost-effectively with the Sars-Cov-2 Variant RT-PCR Assays to more rapidly prioritize which samples to submit for NGS.

Analysis for Research Purposes

Another solution for research analysis is offered by Analytik Jena. The company offers a broad product portfolio in the field of nucleic acid extraction and PCR or real-time PCR with both extraction kits and the necessary equipment. For research purposes for the detection of Sars-Cov-2 the following workflow is suggested: Sample collection — Nucleic acid extraction — Amplification and detection.

Analytik Jena offers a choice of extraction platforms and related extraction kits for extraction of viral RNA from swabs, cell free body fluids (e.g. serum, plasma, cerebrospinal fluid) and more. The product line innuPREP AniPath allows the simultanous extraction of both bacterial and viral DNA and/or RNA from respective starting materials.

The company’s qTower product portfolio significantly reduces cost per sample while providing accurate real-time qPCR results. The thermal cycler contains state-of-the-art heating technology and homogeneity. With its flexible filter module system, researchers can simultaneously analyze 96 to 384 samples without compromising results, and perform up to six-fold multiplexing.

Automation Solutions for Sars-Cov-2 Research

Eppendorf too offers several automation solutions to cover Sars-Cov-2 related workflows. Users can automate either entire protocols or only crucial handling steps which are most tedious, time-consuming and/or error prone. Automating Sars-Cov-2 workflows can minimize exposure to potentially infectious/hazardous agents, free up time for other tasks, increase reproducibility, standardize processes and increase throughput, the company emphasizes.

Eppendorf has products designed to speed up results and to protect users:

  • Centrifuges offer innovative safety features, including fixed-angle and swing-bucket rotors with verified aerosol-tightness.
  • Range of manual pipettes and tips provides ergonomic, safe and accurate liquid handling tools.
  • CO2 incubators provide a safe, easy to sterilize environment for your cells.
  • Range of automated liquid handlers reduces human involvement, speeds up your workflows and improves result accuracy.
  • Bioprocessing solutions enable rapid progress during vaccine research and development.

In addition, the company has a variety of articles and downloadable tools that help lab workers and their colleagues learn how to work safer to minimize the risk of aerosol contamination in the laboratory.