The Hindu Explains | Institutions may save money and time with pool testing protocols

The RT-PCR test is the most effective method to test for COVID-19, but it is expensive and time-consuming.   | Photo Credit: PTI

The story so far: Waves of COVID-19 pandemic are sweeping the globe, and only two measures have so far proved their worth in containing these waves – physical distancing and hand hygiene on the one side and aggressive testing and quarantining those testing positive on the other. Yes, vaccines and drugs are on their way, but these two measures have an immediacy that is irrefutable. The RT-PCR test is the most effective method to test for COVID-19, but it is expensive and time-consuming. Pooled testing of samples is a variant method that has been may reduce cost as well as time taken.

What is pooled testing and what are the different types of pooled testing?

Samples taken from the nasal swabs or throat swabs of people being tested for COVID-19 are grouped into batches or pools. The pooled samples are tested together. If a pool tests negative, all the samples in it are given negative status. If it is positive, then the samples that were pooled in it may be tested again individually to see which among the members shows a positive result. When the total number of samples to be tested is large and the number of positives is expected to be a small percentage of the total number, this mode of testing results in fewer tests being performed. This both saves time and expense.

There is also another type of pooled testing, known as a non-adaptive pooled test. In this method, with just one round of testing of all the pools, it is possible to tell which sample is positive and which is negative. This can work provided the number of positives is a small percentage of the total.

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How does a non-adaptive test work?

Let us say there are three samples, A, B and C. These can be pooled into three pools P1 = A and B, P2 = B and C and P3 = A and C, which exhausts all possible combinations of the three. Now if each of the pools is tested using an RT-PCR test, and the results are, for example, that P1 and P3 test positive and P2 is negative, knowing the combinations, it can simply be read off that A is positive and B and C are negative. Of course, in this toy example, three is the sample size and three tests have to be done anyway, even to test the samples individually. It is seen that if two of the individual samples are positive, say B and C, then all three pools will test positive and no information can be gleaned from the pooling system. Thus, a low prevalence rate or a low number of expected positives are needed for this method to yield good answers.

In the above example, there were three samples and three tests had to be done, how does this help save money or time?

The case of three was taken as a toy example to illustrate that with one round of pooled testing it will be possible to identify which among the three is positive. As the number of samples goes up, the method becomes more economical. For instance, in the case of nine samples, it can be worked out that only six tests need to be done to ascertain which of the nine is positive and which, negative. Thus, three tests are saved. The pooling of samples has to be done carefully and an algorithm has to be worked out that will “deconvolute” the results and tell us which samples from the positive pools are positive.

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Has pooled testing been tried out anywhere until now?

A famous example is China. The country had a massive campaign to screen all the 11 million residents of Wuhan city in May this year. The New York Times reported that they screened over 6.5 million people within just two days. It was possible to do this because they used pool testing. For nearly a month they had reported no new cases in Wuhan so it was a low-prevalence zone and hence the method worked. This is a demonstration of the power of pooled testing wherein a large number of people were tested in a short time. The key point is the low prevalence rate.

What is the ICMR’s stand on pooled testing?

The ICMR, in April, issued an advisory on the feasibility of using pooled samples for carrying out molecular testing for COVID-19. In the advisory, it mentions that the number of COVID-19 cases is rising exponentially, however, rates of positivity are still low in some cases. There pooled testing may be used. Based on a feasibility study conducted in Lucknow it makes the following recommendations – (1) Use in areas of low prevalence… with positivity less than 2%. (2) In areas with prevalence between 2% and 5%, sample pooling for RT-PCR may be considered only for surveillance among asymptotic people, excluding samples from those who have had direct contact with confirmed cases and from health workers. (3) The pooling of samples is not recommended for areas with prevalence rates over 5%. (4) the preferable number of samples to be pooled is five.

Also Read | Testing for COVID-19 in India

Are any pool testing protocols being developed in India?

TAPESTRY is a protocol being developed by many partners: IIT Bombay, NCBS and InStem from Bangalore, Wyss Institute for Biologically Inspired Engineering from Harvard University, Harvard Medical School, Shop101 and SASTRA University. According to Manoj Gopalakrishnan from IIT Bombay, the corresponding author of a preprint that appeared in medRxiv preprint server, the group has tested the protocol for pools of size from seven to 38. Also, the prevalence rate can be as high as 12% for the protocol to work. The protocol is now being tested and validated and is yet to be approved for use.

But if in parts there are community transmission or high prevalence of positives, is it any use to develop these protocols?

In places where repeated tests are being done, for instance in testing healthcare personnel, airlines crew, police, delivery personnel, hotel staff, such a pooling protocol may save time and expense. If someone tests negative on one day and needs to be tested again on the second day along with several such others, then chances are there is a low prevalence of positives. In such regimes, pooled testing protocols like TAPESTRY may be really useful.

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Printable version | May 6, 2021 11:54:41 AM |

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