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Testing for Covid-19: PCR and Rapid Antigen tests

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By M.C.M. Iqbal

Associate Research Professor

Plant and Environmental Sciences,

National Institute of Fundamental Studies, Kandy.

iqbal.mo@nifs.ac.lk

Some basic facts about the two testing methods available to identify the Covid-19 virus, would help us understand the measures taken by the health authorities to control the spread of the virus. The virus that causes the Covid-19 disease (called SARS CoV-2) should be identified not only to manage patients but also to control the spread of the virus. As soon as the genome of the virus was made known by Chinese scientists in January 2020, tests were quickly developed to identify the virus. This test, popularly known as the PCR, is a chemical reaction performed in a PCR machine under very strict laboratory conditions to avoid contaminations. It is more accurately called rT-PCR, which stands for reverse Transcriptase Polymerase Chain Reaction. The discovery of this reaction earned Kary Mullis, a US scientist, the Nobel Prize for chemistry in 1993.

The genome of the virus is a long chain of four ‘letters’ of the genetic alphabet called RNA (most genomes, such as ours, are DNA). Using a combination of these letters, a complete set of instructions are available for the virus to gain entry into cells in our body, take over the machinery of the cell to make multiple copies of itself, which burst out of the cells to infect new cells. The genome consists of a very specific sequence of ‘letters’, which is peculiar to the Covid-19 virus. These ‘letters’ are chemicals called bases. The bases are codes for amino acids which are assembled into proteins. Scientists have isolated two fragments from the genome of the Covid-19 virus (the genome is nearly 30,000 bases long), which are unique to only the Covid-19 virus and not shared with RNA from any other organism. These unique fragments of the genome serve as a fingerprint for the Covid-19 virus. Using this as a basis, scientists have designed a test to unequivocally identify the Covid-19 virus.

By now, either you have personally experienced or seen on TV a trained healthcare worker attired in PPE inserting a plastic swab tipped with artificial cotton wool into the nose or throat. The swab has a long shaft, and it is gently scraped around the back of the nose or upper part of the throat (nasopharynx region). This can be an uncomfortable experience particularly for children. This is the sampling process to conduct a test for the Covid-19 virus. The swab is immediately put into a tube with chemicals, sealed, labelled and sent to a laboratory.

Of the many tests available, two are currently used in Sri Lanka. These are the PCR test and the Rapid Antigen Test. They differ in their sensitivity, specificity, cost and rapidity of results. The PCR test is conducted in a centralized laboratory, while the Rapid Antigen Test can be carried out on the spot.

 

PCR test

The PCR test is used to diagnose if a patient is infected or not with the Covid-19 virus. It is performed on patients with symptoms or on those who do not show any symptoms but are suspected of having an infection. It is vital that the test is highly sensitive and does not miss a patient infected with the virus (called a false negative result). The test should also be very specific to the Covid-19 virus; it should not diagnose a patient who is not infected with the Covid-19 virus as positive (called a false positive result). The PCR test is able to detect very low virus numbers in the patients. The results usually take around 12 to 48 hours.

Back to the sampling. The stuff on the swab needs to be cleaned. The RNA of the Covid-19 virus should be isolated from the rest of the other stuff that was scraped out from the back of the throat. There would be other bacteria and viruses, cells from our throat and mucus. These would have their own DNA and RNA. A combination of chemicals and detergents are used to clean up the sample and also to break open the Covid-19 virus to release its RNA, which is required for testing. Once this is done the sample is loaded into the PCR machine with another set of chemicals.

The PCR test is a very accurate and a nearly foolproof test for the presence or absence of the Covid-19 virus. It requires trained laboratory personnel, a modern laboratory, expensive chemicals and equipment, and time usually one or two days depending on the workload. Since PCR testing is very sensitive, it can detect the shedding of the virus from the patient even after the incubation period, and positive results can be given up to 17 days (see the figure). The incubation period is the time from exposure to the virus to onset of symptoms, which according to the WHO is on average 5-6 days but can be as long as 14 days. However, these PCR positive patients are no longer infectious and hospitalizing or quarantining them is a waste of hospital resources and agony for the patients. The WHO recommends that patients be discharged based on clinical recovery and not on a negative PCR. It is important to note that the PCR test detects the viral RNA fragments, and not the virus capable of causing infections. Thus, a positive PCR does not necessarily mean that a person has infectious virus and is capable of transmitting the virus to others.

 

Rapid tests for the Covid-19 virus

With a rapid surge in the numbers of infected persons, rapid tests are necessary to prevent the epidemic getting out of control. An on-the-spot testing method is necessary to decide if a bus load of people should be allowed to travel from a region with infected persons to a region which is relatively free of the Covid-19 virus. For this purpose, rapid tests have been developed that give results within 15 to 30 minutes. Similar to sampling for the PCR tests, here too a nasal or throat swab is mixed with chemicals on a paper strip to produce a colour reaction.

There are two different rapid tests for the Covid-19 virus. One is the Rapid Antigen test and the second is the Antibody test. Antigens are proteins found on the surface of the virus; being part of the virus a swab from the nose or throat will detect the virus. Antibodies are produced by our body against the virus and found in the blood, which needs a blood sample for testing. This test would tell us if our body has developed antibodies to combat the virus.

 

How does the Rapid Tests differ from the PCR?

The PCR test looks for a specific fragment of the Covid-19 viral RNA taken from the patient. Even if this is present in very small amounts the PCR machine multiplies them to high number of copies. The Rapid Antigen Test look for specific proteins on the surface of the virus. These proteins are called antigens, used in some vaccines and also recognized by our immune system to launch the defense against the virus. Unlike the PCR test, the antigens are not multiplied to sufficient levels for the test to detect the virus by the Rapid Tests. They act on the available load of the virus in the sample. The viral load in an infected person is the amount or number of virus particles in the body. Thus, if the virus load in the sample is low, the test can be negative – called a false negative. Obviously, these tiny virus particles cannot be counted; they are labelled as high, medium, or low viral loads. The progress of the viral load with time is shown in the figure.

 

Figure: Progress of infection, virus release and transmission by the patient, and periods of detection by PCR and Rapid Antigen Tests (RAT). Adapted from the references below. Days after infection are approximate.

 

Sensitivity of the tests

Sensitivity refers to how well a test is able to detect the virus – or specifically the RNA or proteins produced by the Covid-19 virus. The need for sensitivity is, however, different on what our objectives are. If the need is to diagnose a patient at the beginning of an infection cycle (see figure), then the gold standard is the PCR. If the need is to screen the population (many individuals), sensitivity is less of an issue: what is at stake is how infectious are the persons being tested. In other words, do these people have a high viral load with which they can transmit the virus? The RAT is ideally suited for this purpose: it detects high viral loads (hence infectious), many individuals can be screened, it is cheap, and results are available in 15 – 20 minutes. Thus, the primary need is not to determine if a single person with a small viral load can be accurately identified, but how efficiently infectious people can be detected in a population, who are capable of transmitting the virus to others. Thus, this would help the epidemiologist to isolate and remove infected persons and break the transmission chain. This could be people who are infected and also, importantly, those who are infected but do not show any symptoms, called asymptomatic, and those who are at the beginning of the infection cycle (see figure).

With PCR, there is a time frame from the point of sampling to the release of results during which the infection can spread. Infected persons can also spread the virus before symptoms appear. Those who do not show symptoms – asymptomatic – would also spread the virus. In this context, it is necessary to reduce the period between testing and confirmation of the results, which is not possible with PCR testing.

For the public it is important to note that a negative test results does not necessarily mean one is free of infection. If the test was performed at a point in the infection cycle (see figure) when the viral load is low the RAT would give a negative result.

Implementing the RAT more frequently, is an important tool for the epidemiologist to keep track of the spread of the virus and immediately implement isolation measures. An understanding of the infection cycle of the virus is necessary.

 

False negatives

What is of concern to the epidemiologist are false negative results – the person has the virus, but the test gives a negative result. This can happen if the Rapid Antigen test is done during the incubation period. During this period there may be insufficient viral proteins (antigen) in the nose or throat. The viral proteins are in sufficient amounts around 1 – 2 days before symptoms are seen.

 

False negatives, with PCR and RAT, can also result from incorrect sampling, if the swabs are not inserted properly and swished around in the nose and throat so that enough viral proteins or virus particles stick onto the swab. This can give a false sense of security or assurance to the person who may go around spreading the virus.

 

Implications for interventions

The roll out of effective vaccines would not necessarily end the pandemic. This is due to the challenges of successfully vaccinating the entire population and the resurgence of new variants with increased transmissibility, which was not anticipated earlier. In addition, there is asymptomatic transmission, and an overwhelmed health sector that is unable to attend to routine health needs of the people. Lockdowns and closures to reduce social interaction affects individual and government revenue. Hence, there is an urgent need for an early warning system on the spread of the virus in the population to deploy interventions by the state and prevent the uncontrolled spread of the virus. At present, monitoring of the virus spread is based on daily reports of PCR results, hospital admissions and random Rapid Antigen tests. This, however, does not reflect the prevalence of the virus in the broader community. The UK implemented a community-wide program to detect the resurgence of the virus at low prevalence in 2020 over six months (see Riley at al. in references). This was a real-time, country-wide population-based surveillance, that can be modified and conducted in Sri Lanka to monitor the Covid-19 virus and provide early warning. This could avoid sudden lockdowns and the inconveniences to the state, economy and the public.

 

References

McCartney  M, Sullivan  F, Heneghan  C. Information and rational decision-making: explanations to patients and citizens about personal risk of COVID-19. Evidence-Based Med, 2020. [Epub ahead of print.], doi:10.1136/bmjebm-2020-111541.

Crozier, A., Rajan, S., Buchan, I., & McKee, M. (2021). Put to the test: use of rapid testing technologies for covid-19. bmj, 372. https://doi.org/10.1136/bmj.n208 

He, X., Lau, E.H.Y., Wu, P. et al. Temporal dynamics in viral shedding and transmissibility of COVID-19. Nat Med 26, 672–675 (2020). https://doi.org/10.1038/s41591-020-0869-5

Mina, M. J., Parker, R., & Larremore, D. B. (2020). Rethinking Covid-19 test sensitivity—A strategy for containment. New England Journal of Medicine, 383(22), e120.

Guglielmi, G. (2021). Rapid coronavirus tests: a guide for the perplexed. Nature, 590(7845), 202-5.

Riley S. et al. Resurgence of SARS-CoV-2: detection by community viral surveillance. Science. 2021 6545):990-5.



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Proxy wars make unsettling comeback

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Russian armed forces in Ukraine

It’s the day of the North-East proxy war all over again. Concrete proof that this is so comes in the form of the latest military aid package approved for Ukraine by the Biden administration running into $60 billion. So substantial is this injection of assistance that it has prompted Ukrainian President Volodymyr Zelenskyy to see it as pointing to a “chance of victory”.

To the extent to which the West sees some of its best interests, such as the right to self- determination, being eroded in the Ukraine, to the same degree could the latter’s efforts to protect its independence against the Russian invasion be seen as a proxy war where the West pits itself indirectly against the East, in the form of Russia.

Only time will tell whether Zelenskyy is right in seeing the emergence of a “chance of Victory”, now that the much hoped for aid has arrived from the West, but increasingly sizeable and sophisticated arms for Ukraine foreshadow a further prolongation of the wasting war in the Ukraine. While the Russian armed forces would need to brace for an escalating and more destructive confrontation in the Ukraine, the civilians on both sides of the divide should see themselves as being placed ‘on the firing line’ as never before. Overall, the human costs of war would prove staggering.

To make matters far worse for the Russian side, the UK government too has weighed in with an aid package for Ukraine to the tune of Sterling Pounds 500 million, making the prospect of bringing early relief to the relevant suffering publics by the international community a very distant one, since the war in the Ukraine would be stepped-up several fold as a result of the influx of more arms.

It would not be irrelevant, at this juncture, to take the minds of Russia’s rulers to their Cold War failure in Afghanistan. There was nothing to gain from the long-running Afghan quagmire for both sides to the conflict. The USSR’s failed military intervention left behind an Afghanistan which has wilted in the grip of big power rivalries over the decades.

However, Afghanistan was the last of a number of Cold War era proxy wars which rendered the world an increasingly dangerous place for the majority of its peoples. We are not seeing a Cold War type ideological confrontation in the Ukraine, but it is an open question whether the Russian people, for instance, are gaining anything substantial from the war right now.

The Ukraine situation, though, points to the primacy of sovereignty and issues flowing from it in these post-Cold War times. What Ukraine impresses on ambitious global powers is the impossibility of waging colonial era type military interventions in particularly the global South at present. Ukraine, under President Zalenskyy, has decided to fight back the Russian invasion tooth-and-nail and the likelihood is that there would be no clear winners from this war of attrition.

An independent country which is committed to protecting its sovereign rights has no choice but to fight back forces that are intent on destroying it and this is the task that Ukraine has set for itself right now.

On the other hand, the Russian political and military establishments are in an effort to revive the colonial project in Ukraine, which is a preposterous proposition in the present global political order which is gravitating towards political and economic liberalization. Given this backdrop it is small wonder that the West and its military arm, NATO, are firmly behind Ukraine.

Not surprisingly, the West is seeing in the Russian invasion of Ukraine a flagrant violation of all the political values that it claims to uphold and protect. There is no turning back on the moves towards political and economic liberalization that characterize the current neo-liberal age.

Moreover, by invading Ukraine it could be said that Russia is in an attempt to take the world back to some of the earliest stages in the development of modern day capitalism. Besides, if Russia’s reasons for invading Ukraine are to be accepted, any bullying big power could consider itself justified in invading its smaller neighbours, which it sees as coming under its suzerainty.

Accordingly, the world is in for a long-running East-West proxy war in the Ukraine. However, the world’s security worries would in no way end with the Ukraine because it also has other major concerns in the form of the Middle East blood-letting and the Taiwan Straits, in addition to those parts of Africa that are continuing to be weighed down by inter and intra-state turmoil.

In the Middle Eastern theatre and in the Taiwan Straits, intervention by the West is bound to continue and intensify because the latter sees some its crucial interests as being threatened in the relevant regions. Despite its keenness to extend humanitarian assistance to the war-affected populations in the Gaza, the US remains committed to protecting Israel’s best interests.

Such concern has heightened in the wake of the current hostilities between Iran and Israel. It would be in the US’ interests to keep Iran in check because the latter is a threat to Israel as well as to the West’s oil and energy supplies. Accordingly, the US would be going the extra mile to ensure Israel’s security while preventing Iran from being too great a military and political power in the Middle East.

The US could work towards the latter aims by constantly arming Israel and ensuring that the military balance in the region is constantly in favour of Israel rather than its foes’. Here too, then, is an ongoing proxy war between the West and the East; the latter taking the form of Iran which is backed by China and Russia.

Another potentially destructive proxy war between West and East is, meanwhile, working itself out in the Taiwan Straits. The US has over the years been seeing itself as a natural ally of Taiwan because the latter is a capitalist outpost in South East Asia as well as being viewed as an adversarial, break-way state by China. In its efforts to contain the power of China in Asia, the US has been seeing it to be in its interests to ensure the security of Taiwan as against China’s growing regional predominance. All this works out to more Western military aid to Taiwan, going forward.

Accordingly, proxy wars between West and East are once again surfacing unsettlingly in international politics. Military budgets of Western powers are set to grow at the expense of welfare budgets. Needless to say, the latter trend will eventually result in growing public unrest and anger towards governments.

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Artificial Intelligence: Are we getting into it with our eyes open? – Part II

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by Prof. Janendra De Costa

Senior Professor and Chair of Crop Science, Faculty of Agriculture, University of Peradeniya

How prepared is Sri Lanka for AI?

With the initiative coming from the very top, it is likely that AI will come to the fore at least in the official documents on development strategy and policy in the near future. As promised by the Minister of Education, AI is likely to make its way in to school curricula as well. Being an election year, there is a good possibility that the manifestos of all mainstream political parties in Sri Lanka will carry statements about promoting AI. Therefore, it is pertinent to ask whether Sri Lanka has the pre-requisites for successful adoption of AI in its key sectors and whether AI can be included in the school curricula from next year onwards. While confessing to be a non-expert in AI, my view, as an educator, researcher and a practitioner of Science is that Sri Lanka needs a substantial effort to first build a foundation for successful adoption of AI.

First and foremost, Sri Lanka lacks the human capital, an adequate number of trained personnel and practitioners in AI. The considerable exodus of experts in computer science and related technologies since the 2022 economic collapse and its repercussions in the aftermath have left the country significantly impoverished in terms of expertise in almost all established disciplines. The scarcity of experts would be even more acute in new, emerging disciplines such as AI. When the President and the Minister of Education talks about including AI in the school curricula, it is doubtful whether they have considered the availability adequately trained teachers to teach AI in schools or whether there has been adequate preparation in terms of computer facilities, textbooks (printed or electronic) and other learning resources.

Secondly, the past record of adopting new, emerging technologies in Sri Lanka tells us that the tendency will, most probably, be to adopt AI tools developed elsewhere with algorithms trained on data collected elsewhere. Only a small minority of the Sri Lankan experts is likely to take the considerably more difficult pathway of developing our own AI tools and training them on data collected specifically in a Sri Lankan context. As mentioned earlier in this article, the big, comprehensive data sets on which to train AI algorithms do not exist at present in most of the key areas where AI could make a significant positive contribution to national development of Sri Lanka. With the present and past levels of government investment on R & D in S & T (Sri Lanka with only 0.1% of its GDP invested in Science and Technology ranks among the lowest in the world in this index), there is little hope that there will be adequate and sustained support to develop our own AI tools to tackle the specific development needs of higher priority to Sri Lanka. The argument that why spend so much to develop our own AI tools when those already developed elsewhere are available will readily come from the government officials, especially those in the treasury, who have little understanding of how advancements in S & T take place via R & D.

Sri Lanka’s previous experiences in adopting new, emerging technologies

While we are about to embark on a journey to integrate AI into our national agenda, it is worth noting how similar initiatives in the past to integrate new, emerging technologies have fared. In this regard, the story of nanotechnology is especially relevant and offers valuable lessons. Nanotechnology in Sri Lanka was first promoted around 2005 as a technology that carried enormous promise for Sri Lanka to propel itself to the next level economic development via production of globally competitive nanoproducts. The initiative was spearheaded by the newly appointed Minister of Science and Technology, who was himself a former scientist and a former director of a state-sector research institute. The argument at the time was that Sri Lanka should invest its limited financial, infrastructural and humany resources on R & D in a few high potential areas rather than spreading it across all disciplines. Nanotechnology and biotechnology were the high-potential areas that were identified. The Sri Lanka Institute of Nanotechnology (SLINTEC) was established with state-of-the-art facilities on par with those available in developed countries and a select group of scientists from Sri Lanka and a few expatriate Sri Lankan scientists were employed on remuneration packages which were far superior to that enjoyed by the scientists in state sector R & D institutions. The initial funding came from a public-private partnership between the government and a few private sector organizations. It is worth noting that to provide its share of the venture, the National Science Foundation, the premier government organization that was funding S & T research in Sri Lanka diverted all its allocation for research from the treasury to the SLINTEC, thereby depriving research funding to all other areas of Science and Technology for a few years. To cut a long story short, today, after nearly 20 years, the expected nanotechnology boom along with the globally-competitive nanoproducts and the projected increase in the national GDP have not materialized while the SLINTEC, with all its state-of-the-art facilities barely survives, struggling to sustain itself financially, with all its expatriate Sri Lankan scientists gone back to their adopted countries and almost all Sri Lankan scientists who were employed initially having left for universities, in Sri Lanka and abroad. The most notable achievement of SLINTEC during this period was the development of a urea-based nanofertiliser, which when applied to the soil had the capability to release nitrogen slowly, thus facilitating its uptake by plant roots with minimum losses due to leaching. However, the US patent of this product, which was developed with a significant contribution of public funds of the Sri Lankan government was sold to a foreign company in a transaction, the details, and conditions of which are still not transparent to the general public. Ironically, after having spent so much on developing a nanofertiliser of its own, Sri Lanka had to spend another huge sum of public money to purchase a liquid nanofertiliser during the ill-fated 100% organic agriculture drive. Like the 100% organic agriculture project, the imported liquid nanofertilizer turned out to be largely ineffective.

The lesson that can be learnt (for those who are willing to learn) from Sri Lanka’s experience to adopt and promote nanotechnology is that successful and widespread adoption of a new technology is not possible without first establishing a broad base of R & D expertise and infrastructure in an adequately wide range of disciplines and applications. Establishing a centralised institute, however well-equipped, will not be sustainable in the long run and will not make a significant impact on national development. The adoption of biotechnology in Sri Lanka, which emerged as a discipline of high promise to Sri Lanka in the 1990s, is marginally better though nowhere near the level required to boost the national economy. When the present Minister of Education was holding the portfolio for Technology and Research under a previous administration, there was a proposal by a few academics close to him to establish a well-equipped Centre for biotechnology along the same lines as SLINTEC. The present author, as a member of the National Science and Technology Commission (NASTEC) at the time, advocated establishment of several biotechnology research groups in key areas of its applications and supporting them through equipment and other resources rather than spending on establishing one big Centre. This advice fell on deaf ears and the proposal went ahead but stalled when the Minister left his portfolio. This is illustrative of many initiatives in Sri Lanka, especially related to Science and Technology, which come from the top (i.e. the politicians). These proposals often come with a ‘sell-by-date’, which is either the next election or the period of the politician in charge of the specific Ministry. It is important to take into account all these historical facts and learn lessons from them when embarking on this new initiative to promote, develop and adopt AI.

Concluding remarks

There is no doubt that AI has the potential to bring about significant positive impacts in several key sectors of the Sri Lankan economy and many facets of the day-to-day life of the Sri Lankans. However, it is important to understand that realization of that enormous potential of AI, which is already happening in the developed world4,7, requires a substantial investment from within Sri Lanka to educate itself on the strengths and limitations of AI and develop, as much as possible, AI tools of its own or adopt those developed elsewhere only after rigorous validation within the Sri Lankan context. Adequate precautions are required to address the inherent limitations of AI, formulate and implement safeguards against the risks and illusions posed by AI and to guard against total reliance on AI once it gains the trust of its users1,5. In particular, measures are needed to prevent the loss of creativity in future generations of Sri Lankans, especially the students and other learner groups, who are highly likely to be hooked on AI tools in their learning process.

Additional Reading

1. Why scientists trust AI too much – and what to do about it. (Editorial). Nature, 627: 243. 14 March 2024. https://doi.org/10.1038/s41586-023-06221-2.

2. Alvarado, R. (2023). What kind of trust does AI deserve, if any?. AI and Ethics, 3(4): 1169-1183. https://doi.org/10.1007/s43681-022-00224-x.

3. Carroll, J. M. (2022). Why should humans trust AI?. Interactions, 29(4), 73-77. https://doi.org/10.1145/3538392.

4. Krenn, M. et al. (2022). On scientific understanding with artificial intelligence. Nature Reviews Physics, 4(12): 761-769. https://doi.org/10.1038/s42254-022-00518-3.

5. Messeri, L. & Crockett, M.J. (2024). Artificial intelligence and illusions of understanding in scientific research. Nature, 627: 49-58. https://doi.org/10.1038/s41586-024-07146-0.

6. von Eschenbach, W.J. (2021). Transparency and the Black Box problem: Why we do not trust AI. Philosophy & Technology, 34: 1607–1622. https://doi.org/10.1007/s13347-021-00477-0.

7. Wang, H. et al. (2023). Scientific discovery in the age of artificial intelligence. Nature, 620: 47-60. https://doi.org/10.1038/s41586-023-06221-2.

The writer is a Fellow of the National Academy of Sciences of Sri Lanka and has been an academic and a research scientist in Agriculture and Natural Sciences for over three decades while being based in Sri Lanka.

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Promote purple sweet potato

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By Prof. Kirthi Tennakone

The sweet potato is probably the oldest cultivated crop. Native to tropical America, Peruvians grew it 8,000 years ago. Colombus introduced sweet potatoes to Europe; later the Spanish and Portuguese dispersed the species in Asia and Africa. Today, sweet potato is one of the staple foods that alleviate starvation and malnutrition in many parts of the globe.

In the tropics, sweet potatoes produce more food per hectare than any other cultivation. Being drought – resistant and requiring minimal irrigation, fertilizer and pesticide inputs, the crop would be a promise for the world confronted by climate change.

There are highly nutritious varieties of sweet potatoes, of which sweet potato with bright purple flesh; rich in disease-fighting agents, vitamins, minerals and fiber is emerging as a superfood – chosen as the vegetable of the year 2024 by Veganuary (the organization that promotes vegetarianism by abstaining from eating animal-based food in the month of January, every year)

The sweet potato stands out as the first genetically modified vegetable people have unknowingly consumed for millennia. The modification was done not by humans, but by a bacterium found in soil. The ancestor of sweet potatoes was a creeper belonging to the Morning Glory family (Convalesce). Thousands of years ago microbe named Agrobacterium transferred a portion of its DNA (a gene) into the genome of a plant of the original kind in Ecuador, favourably altering its characteristics. In the modified plant, roots were enlarged to yield giant tubers, storing starch, proteins, minerals, water and a host of other beneficial substances. Naturally, the genetically engineered variety withstood harsh conditions and survived better. Noting the exceptional food value, South American farmers domesticated the transgenic species. The rise of Mayan and Aztec civilizations owes much to the sweet potato. Transgenic crops can do wonders!

Today, thousands of cultivars of sweet potato exist, generally described by the colour of the skin and flesh of the yam. The skin colours of white, brown, pink, yellow and purple are common, and the flesh colours vary from white, yellow and orange to purple. These colours originate from two types of pigments known as carotenes and anthocyanins.

Apart from chlorophyll, which imparts green colour to leaves, plants carry two other pigment types: carotenes yellowish orange in colour and anthocyanins displaying hues ranging from red to blue. As we all know, in leaves chlorophyll harvests sunlight and utilizes trapped energy to fix carbon dioxide synthesizing carbohydrates. Carotene and anthocyanins, present in leaves and other plant tissue play an important role in photosynthesis and other plant biochemical processes and give conspicuous colours to flowers, fruits and yams.

Nowadays, people are told to eat coloured vegetables and fruits, because carotenes and anthocyanins have numerous health benefits, including the prevention of cancer, heart disease, diabetes and dementia. What is the secret of coloured produce? A condition that greatly contributes to the above complications is oxidative stress, a side effect of the indispensable oxygen we continuously breathe. Oxygen burns carbohydrates and fat in our bodies, liberating energy and releasing water and carbon dioxide. However, this chemical reaction creates highly reactive molecular species, known as free radicals. Free radicals damage DNA and attack cellular tissue, causing disease and aging. Fortunately, there are agents called antioxidants that scavenge free radicals before they do any harm. Carotenes and anthocyanins act as superb antioxidants.

Current research reveals anthocyanins, the red and blue pigments in vegetables and fruits have a myriad of health benefits because they are water soluble and transmissible throughout the body after absorption from the gut. They effectively quench free radicals, reducing DNA and cellular damage – a primary cause of cancer and inflammatory diseases. Anthocyanins cross the blood-brain barrier and possess a protective action against neurodegenerative cognitive impairments such as Parkinsonism and Alzheimer’s disease. With the increase in human longevity, these illnesses pose a major health issue for which no curative treatments are available. Recent investigations provide evidence for the beneficial effect of consuming anthocyanins rich vegetables in reducing the risk of developing these debilitating conditions.

The brilliantly coloured purple sweet potatoes are gaining recognition as a superfood because of the exceptionally high anthocyanin content, and the remarkable stability of the pigment and its resistance to cooking. The Spanish seemed to have collected this special variety of sweet potatoes from the Aztecs in Peru and planted it in the Philippines around the 1400s and from there, it spread to China and Japan. The climate on the island of Okinawa was ideal for sweet potatoes, a staple food for the islanders, who preferred the purple variety. Okinawans obtain more than 50% of their calorie requirements from sweet potatoes. The incidence of cancer, heart disease and dementia stand remarkably low in this land and people live relatively long compared to other regions of the world. Are purple sweet potatoes the secret of Okinawan longevity and healthiness?

Of course, other factors such as lifestyle and assortments in the diet would contribute to the good health and longevity of the people of Okinawa. As more and more studies confirm the consumption of purple sweet potatoes is indeed an important cause, the world is rushing to cultivate this crop and promote its consumption.

Purple-fleshed sweet potatoes are rare in Sri Lanka. The farmers and consumers are largely unaware of its value.

The author was fascinatingly attracted to purple sweet potato, because of his interest in anthocyanin pigments, which he used to demonstrate a novel solar cell concept for the first time now pursued worldwide. He successfully grew this plant in his home garden, Hantana, Kandy, and obtained a good yield; some tubers weighed more than a kilo. Purple sweet prefers colder night temperatures. Our Central Highlands are probably best suited to cultivating this crop. He wishes Sri Lankans will cultivate this crop and promote its consumption.

(The author is a theoretical physicist, formerly working at the Institute of Fundamental Studies, Sri Lanka. He can be reached via email: ktenna@yahoo.co.uk)

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