Covid-19

'New PCR methods may have to be developed to detect new strain'

A new strain of Sars-Cov-2 was found in Brittany.
A new strain of Sars-Cov-2 was found in Brittany. © NEXU Science Communication/via REUTERS

Globally, there are three principal variants - UK, South African and Brazilian - of Sars-Cov-2, the virus that causes Covid-19 disease. Now, a new strain of Sars-Cov-2 has been found in Brittany in western France. Eight cases have been linked to the new variant which seems to be difficult to detect by the PCR technique. 

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In an interview, Dr Camille Locht of the Institut Pasteur de Lille tells RFI, how worrisome the new strain is and how it is able to escape detection by a standard and reliable technique like the PCR. 

How worrying is the emergence of the new strain of Sars-Cov-2?

From what is known so far, the strain is still limited in terms of spreading. But what's annoying is it is apparently not detectable by the current PCR method.

It means that people who have this strain might be staying under the radar i.e. they cannot be traced by the current testing methods. It is therefore difficult to find exactly the number of individuals infected with the new strain.

So even if they may have some symptoms, the PCR test will be negative, supposedly meaning they are not infected. We cannot trace and follow them. There's no indication that the new strain is more virulent or more infectious than the other strains.  It doesn't mean people are more severely sick. But these are all unknowns for the moment. 

Which new testing methods are needed to detect the new strain?

It would be wise to develop a new PCR technique to adapt to this particular strain. PCR stands for polymerase chain reaction which involves the amplification of the genome of the virus. In this case, Sars-Cov-2 is a RNA virus that is reverse transcribed into DNA and then amplified by using reagents called primers.

The primers are specific to a specific genome sequence. So if there's a mutation in the sequence that corresponds to these primers, the PCR method won't work. Therefore, new PCR methods would have to be developed to target this particular strain.

Are you surprised that the new strain has now acquired a stealth mode? 

 It's not surprising. We know viruses mutate. An RNA virus tends to mutate faster than a DNA virus. An extreme example of an RNA virus is the HIV. Fortunately, Sars-Cov-2 isn't as extreme in terms of mutations as the HIV. 

But nevertheless, what we see with the British, South African and Brazilian strains is that there are mutations in the spike protein which increases the infectivity of the virus. Eventually, there are bound to be other random mutations. 

Every once in a while there is a mutation in the sequence that corresponds to the primers used in testing methods. Though this is the first time that it has happened to Sars-Cov-2, it wasn't unexpected.

It's just a matter of statistics or probability that there will be a mutation of the sequence that makes in undetectable to the current detection methods. 

Moreover, other mutations can happen anywhere in the genome. Most mutations are silent as in they don't change anything in terms of the virus biology. Some mutations may have an impact on its survival.  They may even kill the virus. But there are mutations that are annoying because they increase the virulence, infectivity or they may cause problems for detecting the virus. 

The PCR method can still be used for the new strain but for that we need to design new primers for the changed sequence. 

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