At a time when Nepal’s COVID-19 detection capacity cannot keep pace with the number of people who need to be tested, a quick solution is already available and only needs to be activated.
These are GeneXpert machines that have revolutionised diagnosis of TB in Nepal since 2011, and can easily be used to test for COVID-19. There are 100 of them in hospitals across Nepal, and with new cartridges can be used to augment testing for the coronavirus without buying expensive new machines.
There are nearly 65,000 people in quarantine centres across Nepal, mainly returnees from India. More Nepalis are returning from abroad on flights, and there is also a need to test people who are contact traced. There are only 20 government labs across Nepal doing RT-PCR, and they have a backlog of 27,000 samples.
The GeneXpert system was developed by a California-based company called Cepheid which specialises in molecular diagnostics. It developed this innovative platform to simplify a highly complex, multi-stage process for the detection and analysis of nucleic acids in biological and environmental samples.
A single platform can perform many diagnoses, from cancer tests to routine critical infectious diseases and virology. Currently, 28 tests can be performed, but the menu is expected to run to 33 tests by 2022. A broader range of in-house testing ensures faster turnaround time and improved patient management.
Surprisingly, many people in Nepal, including doctors, have not heard about the GeneXpert system which is actually a real time polymerase chain reaction (RT-PCR) nucleic acid amplification technology.
It was because of GeneXpert machines that Nepal was found to have a much higher prevalence of tuberculosis (more than 400 per 100,000) than previously thought (200 per 100,000). The same machines can now be used to authentically diagnose COVID-19.
GeneXpert machines use different cartridges for different pathogens. Once an investment has been made on the machine, it can be used for various tests by purchasing the appropriate cartridges.
Furthermore, because all reagents are present in the cartridge, the extra time needed for reagent preparation in the traditional PCR machine is not required. This means that GeneXpert results are available within 30 minutes, which is important in a quick and reliable COVID-19 test before an emergency surgery, for example.
If enough COVID-19 cartridges were made available to use on the 100 GeneXpert machines all over Nepal, they could test least 8,000 extra samples a day. Interestingly, the location of these machines (see map, above) are all district hospitals in COVID-19 hotspots in Nepal.
Cepheid has set the price for a GeneXpert cartridge at $19.80 for low- and middle-income countries. The regular price in the US is $35. Médecins Sans Frontières and Cambridge Consultants have assessed that the subsidised price can come down another $5, and still generate profit for the company.
But even at the current rate of $19.80 (Rs2,500) per test, GeneXpert is still less than half the Rs5,500 that RT PCR tests cost at present in Nepal.
An even more important factor is that GeneXpert tests require minimum training as opposed to the traditional PCR tests which need well-trained technicians. And since GeneXpert cartridges are a self-contained system, often not requiring elaborate personal protection equipment, they are safer for disposal than traditional PCR plates.
The FDA (the US Food and Drug Administration) has approved this test, the World Health Organization (WHO) has recommended its use for the diagnosis of COVID-19 to the European Union.
The only challenge is to ensure an adequate supply of cartridges, and it is the Nepal government’s job to make a strong case to international donor agencies to help obtain them. Indonesia and Kenya have done so, and are using the cartridges. The GeneXpert COVID-19 test is not meant to be a replacement for the traditional RT PCR tests, but to top up existing testing.
It is common sense to make use of the GeneXpert machines we already have all over Nepal. If the country was a private company, it would make good business sense as well.
Come autumn, Nepal will have many more respiratory illnesses like seasonal flu to contend with, besides COVID-19. How will we know which is which? It is likely that even COVID-19 infections will go up as there will be more coughing and sneezing as winter approaches. We have about two months to be ready to make a prompt diagnosis of viral respiratory illnesses, and distinguish between the garden variety flu from COVID-19. Fast, reliable and inexpensive diagnostic tests are going to be the key in the months and years to come.
The COVID-19 virus does not seem to be going away quietly, as many had hoped and incorrectly predicted. Because South Asians are predisposed to diabetes, we have an even greater predilection for COVID-19. Clearly, we need to be prepared on all fronts including prompt and proper diagnosis for now and the imminent, potential winter onslaught.
Abhilahsa Karkey and Buddha Basnyat work at Oxford University Clinical Research Unit of Patan Academy of Health Science. Buddha Basnyat also writes the regular medical column, Dhanvantri in Nepali Times.
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