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Testing for Covid-19: Australia could have been prepared

Posted By on April 30, 2020 @ 06:00

The rapid evolution of genomics over the past three decades, combined with the ‘dry runs’ of SARS, MERS and swine flu, created a genuine sense of optimism about the global capacity to respond to new threats. As each pathogen emerged, there was a competition between labs for the bragging rights of being first to decode its genetic sequence. Once the sequence was known, new tests could be instantly designed and implemented globally and without referencing real viral samples—a feature almost unique to genetic tests. There seemed to be no significant barriers to being able to respond to any new virus.

So why are nearly all countries unable to process enough Covid-19 tests? Any moderately competent graduate molecular biologist can design a working SARS-CoV-2 reverse transcription quantitative polymerase chain reaction (RT-qPCR) test—the current standard for Covid-19 testing. The principles of qPCR assay design are well known, and at the time of writing there were 295 new diagnostic kits listed at finddx.org [1].

So, if industry has responded so comprehensively, what combination of planning failures has led to even the United States still not being able to conduct enough tests? Did Australia prepare or rely on good fortune and what can be done to better prepare for the next pandemic?

After 25 years of federal and state government sponsorship of the biotechnology industry and the opening of multiple palatial research institutes in almost every state capital, Australia now no longer has the capability to manufacture these simple tests without importing major components from overseas. That problem was quickly recognised by the federal government, which put out an urgent call [2] to establish a local supplier network.

High-quality testing kits were designed and manufactured in a short time. But like nearly all countries, we rely on a limited number of global manufacturers for key components. Four that can no longer be locally sourced are PCR enzyme, DNA oligomers, plastic testing plates and the crucial nucleic acid extraction kits required to purify the virus from the sample swab. The ongoing global shortage of nucleic acid extraction kits is believed to be the core cause of test shortages, because the market is highly concentrated.

Australian industry once had the capacity to manufacture PCR enzyme and DNA oligomers, but local manufacturers have gradually been acquired and operations have moved offshore to countries that provide incentives to the biotech sector. Many manufacturers established offices in Singapore, which is a global hub for biomedical manufacturing.

More astonishing was the failure of public-health scientists to plan for and secure supply lines of testing materials in anticipation of an outbreak, even while warning others of a lack of preparedness. While Australia maintained reserves of personal protective equipment and other medical supplies, there were no national stockpiles of testing materials or even significant engagement with industry to plan. This oversight is not unique to Australia but was a global phenomenon.

The global waiting time for delivery of Covid-19 testing materials is around four to six weeks, depending on the manufacturer and country. A month is an extraordinarily long time during a pandemic, and countries that triggered their pandemic responses only a week or two after Australia are still waiting for significant shipments of materials.

The few multinational manufacturers are scaling up their operations to unprecedented levels while dealing with lockdowns around their own plants, but demand continues to grow as developing economies begin their responses. These countries are now taking desperate measures like pooling samples [3] (which reduces sensitivity) or even using rapid or point-of-care tests which do not detect early infection and which both the Royal College of Pathologists of Australasia and the World Health O [4]rganization recommend against.

Through negligence, advanced economies like Australia that could be suppliers are actually competing with the developing world for scarce resources.

But at least Australia was saved the hubris of the US Centers for Disease Control and Prevention,  which planned to take on the role of key manufacturer of testing kits in the event of an outbreak, not just for the US but also for networks of labs around the world. The inexperience of the CDC in high-quality and high-volume manufacturing was the cause of the contamination [5] issues that, combined with overzealous regulatory [6] enforcement by the US Food and Drug Administration, shut down testing in the US for three crucial weeks.

Pilot-scale biological drug manufacturing plants already established in Australia can manufacture the enzymes required, the plastics can be manufactured or stockpiled for years, and reagents can be made at scale by a number of the existing suppliers.

Thousands of qPCR instruments of essentially indistinguishable specification are dotted through research and diagnostic labs around the nation and could simply be included in a register.

Sample preparation kits could be stockpiled, or a local manufacturer could be encouraged to make them as there’s little intellectual property involved. Of all the components in a qPCR test, only the DNA oligomers couldn’t be stockpiled but would need to be manufactured as needed for each new outbreak.

Compared with the subsidies provided to the naval shipbuilding industry, it would take only miniscule incentives to encourage industry to re-establish a local DNA oligomer plant, which would immediately improve the treatment of cancer patients while speeding up research in many fields. Australia could, with a little planning, be a net contributor to pandemic preparedness for the region instead of being just another helpless island in the Pacific.

China now finds itself in the almost unique situation of having abundant capacity to manufacture testing materials and is in a position to export that technology around the globe. Even Australia is the recipient of China-made test kits, and to many developing countries China has become the indispensable ally in the fight against Covid-19.

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URL to article: https://www.aspistrategist.org.au/testing-for-covid-19-australia-could-have-been-prepared/

URLs in this post:

[1] finddx.org: https://www.finddx.org/covid-19/pipeline/

[2] urgent call: https://www.industry.gov.au/news-media/covid-19-news/call-for-australian-manufacturers-to-supply-covid-19-test-kit-components

[3] pooling samples: https://economictimes.indiatimes.com/news/politics-and-nation/centre-allows-covid-19-pool-testing-plasma-therapy-in-maharashtra/articleshow/75356883.cms

[4] World Health O: https://www.who.int/news-room/commentaries/detail/advice-on-the-use-of-point-of-care-immunodiagnostic-tests-for-covid-19

[5] contamination: https://www.washingtonpost.com/investigations/contamination-at-cdc-lab-delayed-rollout-of-coronavirus-tests/2020/04/18/fd7d3824-7139-11ea-aa80-c2470c6b2034_story.html

[6] overzealous regulatory: https://www.nytimes.com/2020/03/28/us/testing-coronavirus-pandemic.html

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