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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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Features

English in Mathematics

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By R.N.A. de Silva

 

“Which subject did you have most difficulties with, having switched the medium of instruction from Sinhala to English?” I posed this question to a Sri Lankan student who was following a pre-University course in an educational institution in Hong Kong, having completed studies up to the GCE Ordinary Level programme in the Sinhala medium in a leading girls’ school in Colombo. “It is definitely mathematics,” she replied. Having served as a teacher for a long period of time at this educational institution with students from over 80 countries, I realised the above-mentioned view was shared by other students, too, who had to change the medium of instruction to English. This does not seem to make sense as one would have expected mathematics to be the easiest subject to follow as it has its own symbolic language. Why then has this situation arisen?

I would like to separate these difficulties into two categories:

1. Hastiness due to mindset

2. Vocabulary issues

Sometimes hastiness can automatically occur due to the mindset that mathematics should be easy to follow even if you change the medium of instruction as you are dealing with symbols. This attitude can cause enormous problems as students may skip instructions or avoid reading the question fully and concentrate only on the symbolic part of the problem

As an example, consider the following question.

The graphs of lines 3y = 5x + 1 and 2y = 7 – 3x intersect at point P. Find the coordinates of P.

Seeing the word ‘graphs’ and the two equations, a student maybe tempted to draw the graphs of the two lines and thereby find the point of intersection, which is a time-consuming affair. If it was read properly, the student could have noticed that the solution can be obtained by solving the two equations algebraically, which is much more efficient.

To a fast reader, obtaining the correct answer to the following question can be a problem as it may end up with just finding the value of x.

If 2x+3 = 5x-3, find the value of 2x+3.

The students need to be trained to read the question fully and understand what is required to be done, before attempting it.

The time spent to grasp the aim of the question is not wasted time.

Many children consider mathematics as an alien language consisting of symbols and expressions. Most of the difficulties that students encounter is related to vocabulary. The mathematical interpretation of the meaning of a word may differ from the meaning given to it in the English language. The word ‘find’ in mathematics means to obtain an answer showing the working while in the English language, it refers to discover or search. The following sketch shows the funny side of this difference.

Two of the words that has caused much confusion are ‘or’ and ‘and’.

In general usage, A or B is considered as either A or B but not both, as shown in picture.

However, in mathematics ‘A or B’ means ‘it can belong to A or B including intersection’. This is shown in picture.

The above, in normal usage is interpreted as ‘A and B’. However, in mathematics A and B refers to only what is common to A and B as shown in picture.

Here are the mathematical meanings of some of the other words which can have a different meaning with the English language definitions.

Determine

– Obtain the only possible answer

Plot

– Mark the position of points on a diagram

Write down

– Obtain the answer (Working need not be shown)

Constant

– A number that does not change

Similar

– Having the same shape but not the same size

Deduce

– To show a result using known information

Operation

– A procedure such as addition, subtraction, multiplication, etc.

Element

– A member of a set

Volume

– The extent of space occupied by a solid

The following illustrate some of the difficulties that the difference of meanings brings:

How odd these odd numbers are? The even numbers are even stranger.

Don’t be mean and help me to find the mean of these numbers.

Is right angle the right answer? Let me write it on the board.

The polysemous nature of some of the mathematical terms make it confusing for the students in the understanding of mathematical concepts. Mathematical terms have precise definitions to describe numerical relationships. At times these definitions resemble the everyday usage meaning but there are instances where the definitions notably differ. Consider ‘in general’ as an example. In mathematics there can be no exceptions to a result if it is considered to hold in general. However, in everyday usage, if a claim is said to be true in general, it would mean that it is true most of the time, but exceptions are possible.

To add to the problem, there are some terms such as ‘degree’ that can have many different meanings within mathematics while having a different meaning in everyday use. In mathematics, degree can refer to the measurement of an angle, the complexity of an algebraic equation and a unit of temperature.

Although mathematics deals essentially with symbols, it is taught through the medium of language which is the major means of communication. Students build understanding as they process ideas through language. It is important for students to give emphasis to the familiarisation with the mathematical vocabulary and at the same time understand the difference of meanings of terms mathematically and everyday usage. Teachers have an important role to play here in highlighting such terms and using them in different contexts for comfortable acclimatization. As Marcus Quintilianus quoted, “One should not aim at being possible to understand, but at being impossible to misunderstand.”

(The author is a senior mathematics examiner of the International Baccalaureate Organization and a member of the faculty of the Overseas School of Colombo.)

 

 

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Features

Success with debut single

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Fred-James Koch: Lots of airplay for ‘I’m Runnin’

 

Fred-James Koch seems to be more in the news, these days, than his illustrious father, Alston Koch.

The turning point in Fred-James career is, undoubtedly, the Hollywood film ‘Night Walk.’

His role in the film is two-fold – actor and singer.

It’s, in fact, his singing of the theme song, ‘I’m Runnin,’ that has generated quite a lot of excitement, among music lovers.

The song is now being heard, world-wide, over radio (in Sri Lanka, on Sun FM), while the video, too, has been seen by many, on social media.

An Australian magazine, ‘Music Injection,’ had this to say about Fred- James:

“Fred- James Koch has written an incredible theme song for the movie ‘Night Walk,’ called ‘I’m Runnin.’ Just released, this song is engaging and gives us a sense of urgency, as the song builds. Fred-James vocals have a unique tinge to them and with the video having scenes from ‘Night Walk,’ it encourages me to watch the movie. ‘I’m Runnin’ features AZ Sheriff.” – Jen.

Following the debut spin for ‘I’m Runnin,’ on The Music Director programme, on 88.3 Southern FM Melbourne, the track was also played on the All New Saturday Ausmosis programme.

And, guess what! It’s now No. 3 on the Australian Top 20 Download chart. and No. 2 on the Australian Top 20 Stream chart.

 

 

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Inklings of change in national reconciliation policy

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By Jehan Perera

 

The government comfortably overcame a vote of no-confidence in one of its key ministers over the rise in the price of fuel.  Those who expected to have greater numbers supporting the no-confidence motion miscalculated that the apparent differences and rivalries within the government would be uppermost.  Any government, or institution for that matter, would have its internal differences.  The current government is better secured against these differences that might otherwise split it into different competing parts on account of the familial bonds that bind the leadership together.  The President, Prime Minister, newly appointed Finance Minister, as well as the former Speaker who is now Irrigation and Internal Security Minister, are closely knit brothers who have gone through trials and tribulations together. 

An iconic photograph of recent times would be the joy on (then) President Mahinda Rajapaksa’s face when he embraced his brother (then) Defence Secretary Gotabaya Rajapaksa shortly after the latter survived a suicide bomb attack at the height of the war.  The brothers, however, have different strengths and constituencies.  They have different groups who follow and advise them, and each of these groups would prefer if their leader was the first among equals.  President Gotabaya Rajapaksa’s comment that he has another eight years in which to achieve his goals has been widely discussed.  It would send a signal to others in the polity that it would be premature to gather around another member of the family at this time in anticipation that the baton would be passed on at the conclusion of the President’s current term in 2024.

On his part, the President has been promoting the institution he once served and to which most of his confidantes belonged or continue to belong.  The institution of the military is one where the closest of human bonds can be forged, because on the battlefield each depends on the other for their lives.  In his early period in office, the President has been promoting the military, both serving and retired, wherever he can, as ambassadors to foreign nations, as Covid health guideline monitors and as a supra grade of administrators in government departments.  It is often the case that those appointed to these positions are not the best suited to the tasks they have been set to do.  But the President evidently trusts them and they are his support base.  Unlike any other president in the past, President Gotabaya Rajapaksa is not a member of a political party.  Civil society organisations have periodically called for a non-party presidency who is non-partisan in decision making. 

 

CHALLENGE EXCESSSES

However, there is a need to challenge the excesses.  The president’s pardoning of a soldier who was held by several courts, including the Supreme Court, to have deliberately killed children and (adults, eight in all), outside of the battlefield may be due to his conviction that loyalty to the military counts most.  However, the President is expected to uphold the system of checks and balances, and if he favours one institution at the expense of the others, it leads to a weakening of the entire structure of governance.  Another looming challenge is that posed to the autonomy of institutions of higher education and specifically the universities.  The government decision to vest the Kotelawala Defence University with powers to accredit other institutions of higher education is a threat to the freedom of thought and expression.  The military hierarchy who will head the KDU can be expected to have values that are important to the military, but not to democracy which is based on human rights.

The KDU law needs to be opposed as indeed the Federation of University Teachers Associations (FUTA) has urged along with opposition political parties.  At the same time there are other issues on which civil society can consider giving constructive support to governmental initiatives.  For instance, they do not engage with NGOs who provide a variety of services complementing the work of the government. The most important of these is the national reconciliation process.  There are indications that the government is shifting its stance on the issues of post-war reconciliation.  President Gotabaya Rajapaksa’s election victory on a highly nationalist platform won him a big majority of votes of the Sinhalese ethnic majority.  The government felt empowered to publicly declare its intention to withdraw from the post-war reconciliation process initiated by its predecessor government with support from the international community.  This was followed by withdrawal from UNHRC resolution 30/1 of 2015 co-sponsored by the previous government. 

However, the four subsequent internationally driven resolutions against Sri Lanka, emanating from Geneva (UNHRC), Ottawa (Ontario Parliament), Washington DC (US Congress) and Brussels (EU Parliament) seem to have led to a serious rethink within the government about its policy towards post-war reconciliation.  All four make human rights and the ethnic conflict their centerpiece.  Though not yet publicly commented upon, the signs of change are two-fold.  The first is the increased visibility of the US Embassy in meeting with the leaders of the Tamil and Muslim parties.  The media has reported that US Embassy officials discussed issues of post-war reconciliation efforts, devolution of power, rule of law and the Prevention of Terrorism Act with SLMC leader Rauff Hakeem. Recently, a US Embassy delegation, led by Ambassador Alaina B. Teplitz, held similar discussions with TNA leader R. Sampanthan where the focus was on the proposed new Constitution.

 

CHANGING WINDS

The second sign of a change is the statement from the Presidential Secretariat announcing a recommendation, emanating from the President Commission of Inquiry for Appraisal of the Findings of Previous Commissions and Committees on Human Rights and the Way Forward headed by Justice AHMD Nawaz.  This is with regard to the EU call for the abolishing of the Prevention of Terrorism Act long seen by those promoting national security as part of the country’s first line of defence.  The Commission said that it cannot agree with calls for repealing the PTA but Sri Lanka’s anti-terrorism law should be reformed in line with similar laws in other countries, including the UK.  This would be aimed at affirming Sri Lankan sovereignty and national security interests, which are important to the government’s voter base, while complying with the requirements of the EU parliament which has called for the repeal of the PTA on the grounds that it violated human rights. 

The Presidential Secretariat statement also contains a significant section in which it mentioned that “It is the policy of the Government to work with the United Nations and its agencies to ensure accountability and human resource development in order to achieve lasting peace and reconciliation. The Government is committed to providing solutions for the issues to be resolved within the democratic and legal process and to ensure justice and reconciliation by implementing necessary institutional reforms.”  This is the first official indication that the Government is reconsidering its earlier position that it would blaze is own path with an indigenously generated reconciliation model which would not require international assistance. In this context it would be useful if the government focused closer attention to the achievement of the UN Sustainable Goals.

Veteran Tamil political leader V Anandasangaree, who has championed Tamil rights for a long time, and whose son is a Canadian parliamentarian, has referred to these recent developments and said that the President who holds the defence portfolio, Prime Minister and Finance Minister being members of Rajapaksa family could ensure genuine post-war reconciliation.  He also urged President Gotabaya Rajapaksa’s government not to leave the problem for a future administration to resolve, but address it now.  If the President is to successfully address the problem that has eluded a solution since independence, and been the biggest disaster to Sri Lanka’s development, he will need to broad base his support at multiple levels.  He will not only need the support of the ruling party, led by his brothers, as well as civil society, but also that of the ethnic minority parties and the opposition political parties.  This will require patience, dialogue and self-sacrifice, and the need to break from past and chart a reconciliatory course of action.

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