How to find a SARS-CoV-2 variant

Detecting COVID-19 in a population is usually done in two ways: by testing antibodies or running a PCR test. But neither can find variants.

PCR is a fantastic technique for identifying the presence of a viral species (such as SARS-CoV-2) in a sample, but it can’t detect variants because it isn’t sensitive enough to give the more specific genetic sequence that sets it apart.

Think of it this way: it’s like identifying that someone is part of a particular family from their surname, but not being able to determine which family member it is.

We need more specific data. To find variants, we need sequencing.

What is sequencing?

Sequencing is a technique that will show the individual identity of a sample by revealing each nucleotide (unit of genetic information) in the genetic chain. Most of the nucleotide will be the same, but very small nucleotide differences can end up having a big effect on how easily the virus spreads.

For SARS-CoV-2, which is made of ribonucleic acid (RNA), PCR targets and amplifies a small region unique to this species of coronavirus. It will not pick up any other type of virus and ignores the other six known species of coronavirus. 

However, while distinct coronaviruses are genetically different enough to be separated by a PCR test, variants differ by only just a few nucleotides and require a much more sensitive test – sequencing.

More simply, PCR shows that SARS-CoV-2 is present, and sequencing shows which variant it is.

Sequencing is the step that occurs after a PCR, so it takes a few extra days to receive the results. This is why information on the origin or variant involved in an outbreak is ‘on delay’ after identifying that an outbreak has occurred.

Sequencing can tell us two things: firstly, whether the virus may have mutated in a concerning way, and secondly, where the outbreak originated by tracing the movements and lineages of variant strains.

Because sequencing can identify and track tiny changes to viral RNA, it is only used for positive COVID-19 samples.

Is sequencing used in India to find variants?

Currently, there are many different variants of SARS-CoV-2 that arise from mutations, as shown through sequencing.

This reveals where exactly the mutations occur in the RNA sequence, to see whether the mutation is likely to change the characteristics of COVID-19 symptoms or the transmission of the virus. It can also help track the ‘migration’ of strains through a population.

One of these variants, B1.617, was first identified in India in October 2020, and is now under investigation as a potential variant of note in the current COVID-19 wave spreading through the country.

The strain has around 15 mutations, but not all mutations are necessarily concerning. B1.617 is called a ‘double mutant’ because only two of its mutations are of particular note; they occur in the 452nd and 484th position of the nucleotide chain, and both are parts of the spike proteins that help the virus break into our cells.

These individual mutations were both found in other variants, the former in the US and the latter in the UK and South Africa, but this particular variant cropping up in India contains both mutations together.

This is why the variant is now under investigation. However, it is still unclear whether the variant contributes to the rise in cases seen today.

The difficulty is that the variant can only be detected through the sequencing of a PCR sample. This is time-consuming and expensive, so only a small selection of samples will be sent for sequencing.

This means that the true number and variety of variants in a population cannot be accurately estimated unless the sample size is big enough. This becomes increasingly problematic when testing resources are scarce.

For example, even though sequencing requires samples from a PCR test, many states and regions in India are using antibody testing instead; in Uttar Pradesh, 60% of tests were this type.

In addition, less than 5% of the PCR tests are being sequenced, presumably due to a lack of resources. Between January and March 2021, less than 1% of positive COVID-19 samples were sequenced, or about 7500 out of over a million samples.

So while the variant has been detected in India, there is no accurate reflection of whether it is contributing to the rise in cases or to mortality.

This means the B1.617 variant is still well and truly in the ‘unknown’ zone, and so is still under investigation.

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