As ministry pushes for antigen tests, national lab questions direct PCR method, raising suspicionNational Public Health Laboratory says validation of direct polymerase chain reaction tests technique ‘just about satisfactory’. But experts disagree.
Amid rising calls from public health experts for expanding Covid-19 tests and exploring alternatives to detect the coronavirus in masses, the National Public Health Laboratory has said it has found the validation of direct polymerase chain reaction tests “just about satisfactory.”
“Results of direct polymerase chain reaction tests carried out at other state-run laboratories were even worse,” said Runa Jha, director at the National Public Health Laboratory.
Direct polymerase chain reaction test is a method of DNA amplification without performing DNA isolation and purification steps. In simpler terms, this is a simplified protocol where dry swab samples are collected and directly used for polymerase chain reaction tests, thereby skipping the tedious processes of carrying the samples in viral transport media and RNA extraction.
In the current methods of reverse polymerase chain reaction testing, nasal or throat swabs, needed for tests, are collected in the viral transport media, and they have to be put through the RNA extraction process, which is somewhat a lengthy and costly process.
The Ministry of Health and Population had mandated the National Public Health Laboratory to validate the direct polymerase chain reaction tests and accordingly grant permission to the laboratories to adopt the method.
The validation report furnished to the Health Ministry by the laboratory, however, said laboratories could perform the tests using the method “only if they found reliable results in their own validation”.
“As of now, no laboratory has shown interest in conducting direct polymerase chain reaction tests,” Jha told the Post. “The method can be used if we have to test a huge number of samples. As we have already acquired automated RNA extraction machines, conventional polymerase chain reaction tests, which give more accurate results, are okay for us.”
But some have questioned the laboratory’s validation process, saying direct polymerase chain reaction test is the gold standard for Covid-19 tests, is accepted worldwide and that the technique significantly reduces experimental time and costs.
“I don’t know how the National Public Health Laboratory performed validation. The technology is approved by the FDA [US Food and Drug Administration],” Dr Bhagwan Koirala, chairman of Nepal Medical Council, a national regulatory body of medical doctors, told the Post. “If the method did not give reliable results, authorities concerned should explore other methods which are reliable and cost-effective.”
According to Koirala, there are several other technologies, including loop-mediated isothermal amplification (LAMP), which does not even require biosafety level-2 lab and tests can be conducted even in the field. Tests can also be performed using GeneXpert machines, which are generally employed for tuberculosis tests. The method can detect the presence of the coronavirus in about 45 minutes.
Officials at the Department of Health Services say some at the Department, laboratories and even the Health Ministry have been pushing for continuing with the conventional polymerase chain reaction tests, as they see benefits in the purchase of testing kits.
“Even experts from outside the Health Ministry have been stressing that we should adopt new technologies including direct polymerase chain reaction tests, which are cost-effective, reliable and give results faster than the conventional method,” an official at the department told the Post on condition of anonymity. “But some of our friends are reluctant to opt for new methods, as they seem to be making profits from the purchase of the test kits that are used for the test method that we have been using.”
Even though the recovery rate has hugely increased in Nepal of late, new cases are being found daily.
As of Sunday, 102,728 people tested positive to Covid-19 in the Valley. In the last 24 hours, 2,103 people tested positive throughout the country. Of them, 1,699 people are from Kathmandu Valley.
So far, 220,308 people have tested positive for the virus nationwide, with 1,321 deaths.
To identify Covid-19 patients swiftly and treat them, the authorities must explore different ways to conduct tests, apart from the RT-PCR (reverse transcription polymerase chain reaction) technique that has been in use, according to public health experts.
The experts say without increasing tests, the status of the spread of the virus in the society won’t be known, which hampers contact tracing that eventually creates hurdles in the fight against the pandemic.
“Authorities must explore alternatives which are fast and cost-effective,” said Dr Mingmar Gyelgen Sherpa, former director-general at the Department of Health Services. “We cannot curb the infection by lessening the tests and showing reluctance in adopting new technologies used by the world.”
Just as the National Public Health Laboratory has said the validation of direct PCR tests is not up to the mark, the Health Ministry has decided to perform one million antigen-based tests throughout the country. Of them, 100,000 tests will be carried out in Kathmandu Valley, which has been a major hotspot of the coronavirus for months.
This too has raised concerns among some experts with many asking why the Nepal government is making a push for rapid antigen tests while showing reluctance to adopt the direct polymerase chain reaction technique. While rapid antigen tests can provide results faster without requiring complex machines and laboratories, their accuracy has remained questionable due to the high rate of false-positive results.
Opinions among experts, however, are divided, and in Nepal too some have called for expanding rapid antigen tests to detect the virus in the society.
Many say the focus should be on introducing globally accepted methods to fight the virus.
“If any particular laboratory fails to use the technology properly, it is a problem of the laboratory, not the technology that is validated by the world’s renowned agency,” Dr Prabhat Adhikari, an infectious disease and critical care expert, told the Post. “Validation performed at Tribhuvan University Teaching Hospital laboratory on direct PCR testing too has shown 95 percent sensitivity.”
According to Adhikari, by using the direct PCR method, coronavirus tests can be done at the price of antigen tests.
The Health Ministry’s own protocol says that polymerase chain reaction tests are needed if the result comes negative in patients having symptoms.
Adhikari said that the accuracy rate of antigen tests in asymptomatic patients is around 60 percent only.
“Why are we insisting on antigen tests when we can perform direct PCR tests at the same price, and perform more tests faster?” said Adhikari.