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Jakarta Post

PCR tests can give useful information beyond yes-no answer to infection

  • Ardila Syakriah
    Ardila Syakriah

    The Jakarta Post

Jakarta   /   Fri, October 9, 2020   /   07:15 pm
PCR tests can give useful information beyond yes-no answer to infection To the nose it goes: A medical worker takes a sample from a man’s nose during a COVID-19 swab test in Jakarta recently. Indonesia has a limited capacity for conducting swab tests due to a lack of labs, equipment and trained personnel. (JP/Dhoni Setiawan)

The gold standard test to detect the novel coronavirus that causes COVID-19 provides a yes or no answer as to whether someone is infected.

But experts have said it could also help estimate viral load, which will be useful in evaluating treatment, as well as estimating infectivity, which can be helpful in containment efforts. One record that might provide this information is the so-called cycle threshold (CT) value.

In order to discover the virus, reverse transcription-polymerase chain reaction (RT-PCR) devices amplify the sample’s genetic material in cycles. The fewer cycles required to spot the virus, or the lower the CT value is, the higher the estimated viral load a sample may contain.

Now, although studies are still limited, it is believed that the lower the CT value is -- also indicating a higher viral load -- the more infectious a person is, and vice versa.

"The RT-PCR [for novel coronavirus] is qualitative, meaning it only shows a positive or a negative [...] But the CT value then becomes, quote, unquote, semi-quantitative; not purely quantitative as it only estimates [viral load]," said clinical pathology professor Aryati.

PCR devices in Indonesia set varying limits to the cycles -- ranging between 31 and 45 cycles -- but many in the country are set at a cutoff of 40 cycles, according to experts, who have also cautioned against comparing results between different devices.

This means that if the cycles required to spot the virus run past the cutoff, then the results will come back negative. If not, then they will be positive. For example, with a device that has a cutoff of 40 cycles, taking 35 cycles to spot the virus means the result will be positive.

But experts say the only way to discover infectivity is through viral culture -- if the virus can be cultured, it means it is still infectious. But this requires more advanced labs and also much more time, said Aryati who also chairs Indonesia's Clinical Pathology and Laboratory Medicine (PDS PatKLIn) specialists.

Read also: PCR tests remain gold standard, but many factors affect results

Several studies, however, have linked CT values to infectivity. In late September, a study published in the journal Clinical Infectious Diseases, a team of researchers found that from 3,790 samples with identified CT values, 70 percent of samples with CT values of 25 or below could be cultured. The number dropped to 20 percent for samples with CT values of 30, while at CT values of 35, less than 3 percent of cultures were negative.

An earlier study published in the European Journal of Clinical Microbiology and Infectious Diseases involving 183 samples targeting a specific E gene of the virus found that samples with CT values of between 13 and 17 all led to positive cultures. Culture positivity rates then decreased progressively according to CT values, to reach 12 percent at a 33 CT value. No culture was obtained from samples with a CT value of above 34.

Maria Lucia Inge Lusida, a clinical microbiology professor who leads Airlangga University's Institute of Tropical Diseases, said the CT value could be useful for doctors and patients in evaluating treatment. Results showing higher CT values over time might indicate an improvement, Inge said.

"Asymptomatic cases usually have high CT values," she added.

Read also: Indonesia sets COVID-19 swab test price ceiling at Rp 900,000

Aryati agreed, though she noted that this would require that reagents used to test a patient's samples be the same throughout the evaluation, otherwise she advised against comparing the results. The problem was reagents supplied by the government often changed from time to time, she said.

Even if they were used for such a purpose, Aryati emphasized that these numbers were only an estimation and hence were not always conclusive.

CT values could also provide useful epidemiological information; those with low CT values must be isolated to avoid further transmission, she said.

She said that in government-run isolation facilities, where suspected and confirmed cases could share the same room, it would be important to ensure that people whose test results showed high CT values were separated from suspected cases.

In terms of contact tracing, CT values can also provide possible information on who infected whom. For instance, in a group of people infected by the virus, higher CT values, such as 34, might indicate that the person had been infected earlier than others with a lower number, say, 15.

"But not all labs can provide results quickly within a day [...] There are labs that need five to eight days, and even three weeks at the beginning of the pandemic. There are labs still overwhelmed with samples, some exceeding their capacity and with device limitations," Aryati said.

Read also: Use antigen tests for screening but with caution: Experts

Some doctors and lab operators have said not all test results provide CT values. Lab doctors interpret the number to determine whether someone has the virus or not, but it is not yet commonly used for other measures.

Inge and Aryati said devices used by their labs could provide this information automatically in the results and at the request of doctors, but some devices used by other labs would require manual reading and interpretation by operators, which would mean even more work for the already overwhelmed labs.

Jakarta regional health laboratory (Labkesda) head Endra Muryanto said there was no instruction to attach CT values to test results, but he said his lab would do so if requested. He conceded however that it would increase the workload of lab operators.

In an August in a statement responding to requests from clinicians that labs provide CT value information on test results, with the number being used as criteria for discharging patients, the Indonesian Association of Clinical Microbiologists (PAMKI) said that CT values should be interpreted and used carefully. The group suggested that lab test results did not have to attach CT values, but if deemed necessary clinicians could request them from the labs.