Are RT-PCR tests failing to detect some coronavirus variants? What doctors say

Doctors TNM spoke to said that they are using a combination of methods to detect if a person has COVID-19 and then prescribing the necessary treatment.
COVID-19 testing at a railway station
COVID-19 testing at a railway station
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In the recent past there have been several anecdotes as well as reports of the RT-PCR test giving a false negative even for people who may be infected with the novel coronavirus. This has raised several concerns. Apart from the possible delay in getting treatment itself, there are also questions about whether the new variants of the SARS-CoV-2 virus found in India could be evading detection by RT-PCR tests.

While doctors TNM spoke to said that they believe that the RT-PCR test should still be able to detect coronavirus if an individual is infected with a variant, they also say that more research is needed to ascertain the variants’ detectability with the RT-PCR tests. They add that they are not relying on RT-PCR tests alone, and have been using a combination of methods to detect if a person has COVID-19 and then prescribing the necessary treatment.

Detectability of variants through RT-PCR tests

Dr A Velumani, the CEO of Thyrocare Technologies, a chain of diagnostics labs, explains that the RT-PCR test they do does not look for a single virus gene of the virus, but three. “The virus has a certain gene that we look for; specific sequences are the signature of the virus. There are particular locations on the gene that are used to detect if it’s SARS-CoV-2,” he says. He adds that since the RT-PCR test looks for the gene in three locations of the virus, even if it is a variant, at least two out of three locations should show up the identifying gene. “However, a three-gene test cannot identify if the virus detected is a variant. For that you need at least a five-gene indicator test,” Dr Velumani says.

Dr Siri Kamath, consultant physician at BGS Gleneagles Global Hospital in Kengeri, Bengaluru, points out that the variants have affected the spike protein of the virus, and the RT-PCR test looks for genetic material of the virus to identify it. “RT-PCR test detects the most conserved part of the genome of the virus. It is yet to be proven if variations in spike protein of the virus will affect its detection. We don’t have the correlation between false negatives being because of infection by variants,” he says. 

Dr Srivatsa Lokeshwaran, a consultant, interventional pulmonology with Aster CMI Hospital in Bengaluru, agreed, saying, “RNA viruses like the coronavirus are bound to mutate over a period of time. Despite minor mutations, RT-PCR would still detect the virus.” 

Further, Dr Velumani points out that false negatives are not new, and happened earlier also during the first wave of coronavirus infections. “It is because of variation in human response to the virus and how the virus or its variant would react with the body that causes variations in result. A laboratory can’t figure that out.”

What the research says so far 

The doctors TNM spoke to agreed that there needs to be more study into whether variants of the virus have varied detectability by RT-PCR tests as well. So far, there is limited study and reporting on the same.

In March, France had reported a new variant of the novel coronavirus from its Brittany region. Eight of the 79 COVID-19 patients had then tested negative for the disease on RT-PCR test, which is considered the gold standard. The illness was confirmed for the eight persons who subsequently died. They showed typical COVID-19 symptoms later, after blood samples and tissue in their respiratory system were analysed. In February, Finnish researchers had also found a variant of the virus that was evading detection by at least one standard RT-PCR test, though not all. A researcher was quoted as saying that this new variant did not “genetically resemble any other known variant.”

This research paper further states that mutations “may impact the diagnostic sensitivity and specialty, and therefore, they should be considered in designing new testing kits as part of the current efforts in COVID-19 testing, prevention, and control.” The study genotyped 31,421 SARS-CoV-2 genome samples collected up to July 23, 2020 and found that “essentially all of the current COVID-19 diagnostic targets have undergone mutations.”

However, American regulatory body Food and Drug Administration (FDA) in January said that genetic variants of SARS-CoV-2 may lead to false negatives in molecular tests. “[…] false negative results may occur with any molecular test for the detection of SARS-CoV-2 if a mutation occurs in the part of the virus’ genome assessed by that test,” it said, adding, “Molecular tests designed to detect multiple SARS-CoV-2 genetic targets are less susceptible to the effects of genetic variation than tests designed to detect a single genetic target.” RT-PCR is a molecular test. The FDA did not mention if variants that affect the spike protein can evade detection.  

In India, variants from the United Kingdom (B.1.1.7), South Africa (B.1.351) and Brazil (P.1) have been detected, as per the Consortium on Genomics (INSACOG), which is a group of 10 national laboratories established by the Union Ministry for Health. Further, there is also a double variant which has been found in some samples from Maharashtra, which has ‘immune escape’ qualities i.e. it may evade detection by the human immune system, hence affecting the infected individual’s capacity to generate an immunogenic response and eliminate it. 

However, it is not clear if these variants are less likely to be detected by the RT-PCR test, and medical professionals as well as scientists have called for more study into this aspect.

How doctors are tackling COVID-19 if RT-PCR test is negative

Doctors are using a combination of methods to check if a person has COVID-19 even if the individual tests negative on the RT-PCR test. Dr Anoop Amarnath, member of the Critical Care Support Unit of the Karnataka government, who works at Manipal Hospital, explains that they are looking at diagnosis from four aspects – the RT-PCR test, certain biochemical parameters, radiological parameters (such as a high-resolution CT scan), and clinical symptoms (presenting with cough, fever, breathlessness, oxygen saturation levels).

Acknowledging that they are seeing negative test results even where a person is symptomatic, Dr Anoop says, “As per the guidelines, we look at the other markers and if those suggest they have COVID-19, then they are given the relevant treatment.”

Dr Siri says that their first hint is how a person’s symptoms. “If the clinical symptoms are there, we first assume that it’s COVID-19 and advise them to isolate etc. Then even if the RT-PCR test result is negative, we see the age and vulnerability of the person. Say, if the patient is 40+, we do a CT scan of the lungs. If the person is younger and does not have serious symptoms, we may put them on appropriate medication, tell them to self-isolate at home, and keep checking their oxygen saturation levels. If it has not dropped below a certain level in the first 10 days or so, it is likely their condition will not deteriorate.”

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