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Affordable, scalable and sensitive viral genome-based test approach

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COVID-19 (Coronavirus 2019) caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) causes morbidity and mortality despite ongoing mitigation strategies and vaccination efforts I’m continuing. Most national attempts to combat COVID-19 shaving include social distance, blockade, limited testing, Contact tracing, And vaccine deployment. All of this helps in the fight against the pandemic.

With the aim of minimizing human suffering, financial costs, and restrictions on personal freedom caused by COVID-19, German and Austrian researchers have replaced it with an efficient population-based genome-based test. I suggested a method.

They have demonstrated an affordable, scalable, and sensitive viral genome-based testing approach developed as part of the Human Genome Project.

This test has been used to genotype billions of samples over the last decade. We achieved the same sensitivity and specificity here, but in a much more scalable way, significantly reduced the cost per sample (for very high throughput, about € 1 per PCR test).Researchers also provided a link to share notes taken in the study and the results are published in medRxiv* Preprint server before peer review..

Schematic of the SARS-CoV-2 high-throughput genome-based test pipeline.  (A) The sample tube (with barcode) is transported from the collection point to a 96-well carrier test center (see, eg, Figure 2) to prepare for a high-throughput test of SARS-CoV-2 (or other virus). Is ready. Samples are heat-inactivated prior to automatic transfer in 384-well format (b) and (c) direct RT-PCR preparation without RNA extraction, and (d) test results (positive, negative). Indicates the endpoint measurement.

Schematic of the SARS-CoV-2 high-throughput genome-based test pipeline. (A) The sample tube (with barcode) is transported from the collection point to a 96-well carrier test center (see, eg, Figure 2) to prepare for a high-throughput test of SARS-CoV-2 (or other virus). Is ready. Samples are heat-inactivated prior to automatic transfer in 384-well format (b) and (c) direct RT-PCR preparation without RNA extraction, and (d) test results (positive, negative). Indicates the endpoint measurement.

“This procedure is an EU-wide CE (European Conformity) approved for mouthwash and smear-based versions and is already used in Germany to test employees of Unilever and other companies.” The researchers said in their paper.

Discussing the results of the test, the researchers highlighted the main benefits. Infected individuals antigenRapid inspection of the base currently in use. Early detection is an important prerequisite for stopping the spread of the virus. Another advantage of this test is scalability.

“A single commercial water bath PCR system with a capacity of 100×384 PCR plates in a single run can perform over 600,000 RT-PCR reactions per day, 3 of the total PCR test capacity currently available in Germany. It will be nearly doubled. “

This approach can also be easily used to test variants. There is a second analytical cycle with a small number of additional tests on SARS-CoV-2 positive samples.

“Despite these potential benefits and the early successful testing of the strategy in the Italian city of Vò, which has 3,300 inhabitants, with the exception of Austria, we are seriously considering this as an alternative. There seems to be little government (‘alles gurglet‘), Nothing seems to support the establishment of the required infrastructure. “

To demonstrate the concept, Vienna, Austria, approved a program aimed at early disruption of the infection chain on a population scale and conducted contact tracing to prevent the spread of SARS-CoV-2. An individual self-collected and validated a mouthwash sample using a dedicated web app (www.lead-horizon.com). As an example of the distributed testing strategy used in Vienna, the researchers gave an overview (in five steps) of how population-scale testing actually works.

Reliable PCR test results were guaranteed to all residents of the community within 24 hours of sample collection. The program invited all residents to attend twice a week to ensure that people with COVID-19 can be quickly quarantined and that the chain of infections can be broken as soon as possible with regular tests. .. The local drugstore provided a validated self-collection kit for mouthwash samples, making PCR tests accessible to all residents within a 5-minute walk. The samples were packaged in a biohazard-safe sealed shipping bag and packaging and then returned to the lab for shipping.

Test logistics for the entire population. An example of a distributed testing strategy used in Vienna.

Vienna offers free sampling equipment for all residents, tourists and commuters. As a result of its success, the program is now being expanded to more pilot regions in Austria, further assessing more comprehensive national coverage. Alternatively, Alacris Theranostics has developed a similar kit that utilizes a nasal swab for high-throughput testing.

Using a model based on the established Kermack-McKendrick theory tuned to COVID-19, researchers found that if a pandemic was adopted last fall, this population-wide test approach would affect the development of the pandemic. Showed the impact. In addition, assuming certain conditions and removing some errors, we have demonstrated that the model convincingly calculated the “effectiveness of the mass test”-like Germany in early October 2020. Only under moderate contact restrictions.

They suggested that: “Even the rise of new British viral variants in early 2021 could be controlled by high-volume testing using sensitive PCR-based tests, reducing the pre-test R factor from 1.5 to very low levels. There is sex. Advanced participation. “

Importantly, they compare the effects of currently used antigen rapid tests, which detect only when an individual becomes positive after the onset of symptoms, which is a fairly late stage of infection. , Emphasized this.

From simulations performed comparing PCR with antigen-based testing, this study found that population-wide PCR-based testing was extensive, even when the participation level in the second wave (October 2020) was fairly low. Shown that it may have been done. A sharp decrease in the number of infections. In that case, it was to manage contact tracing.

In summary, the researchers showed in this study that systematic population-wide screening can eliminate COVID-19. However, keeping in mind that urgent mass testing could not be performed, supplementing vaccination could enable this mass testing infrastructure to address SARS-CoV-2 and other new similar pathogens. It was recommended to.

“The overwhelming majority of this effect, including nearly 90% of deaths, was caused by the second and third waves of the pandemic and could have been avoided by PCR-based population testing.”

Given the enormous impact this approach can have on the pandemic process, it raises the question of the mechanism that governments use to assess potential solutions to such very important issues. To do.

*Important Notices

medRxiv Publish preliminary scientific reports that should not be considered definitive as they are not peer-reviewed, guide clinical practice / health-related behaviors, and should not be treated as established information

Journal reference:

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