Old test for the diagnosis of novel corona virus infection: Role of GeneXpert in COVID-19 testing.

Abstract

Dear Editor, We are dealing with the COVID-19 pandemic of unprecedented scale with total number of cases at 8,993,659 with 469,587 deaths as per latest WHO situation report on 23thJune 2020.[1] Various tests available for diagnosis of COVID-19 infection include RT-PCR, isothermal amplification methods, antigen and antibody testing. RT-PCR is considered standard of care for diagnosis of COVID-19 and data about sensitivity and specificity are being scrutinized. Positivity rate varied based on specimen for analysis; In 205 patients tested by RT-PCR; positivity rates were 93% for bronchoalveolar lavage, 72% for sputum, 63% for nasal swabs, 46% for fibro bronchoscope brush biopsy and 32% for throat swabs.[2] However, false negative rates of COVID-19 tests range from 2-29%, placing sensitivity between 71-98%.[3] Various issues involving RT-PCR are cost, processing time and complex methodology. Testing with RT-PCR has been recommended 24 hrs before elective surgery by various surgical societies.[4] According to Indian Council of Medical Research high risk patients undergoing elective surgeries should have two negative RT-PCR tests 24 hrs apart.[5] It also has the drawback of long processing time which may lead to delay in life saving surgery or procedure. WHO has authorized the use of GeneXpert® platform for testing COVID-19 patients.[6] It can make a difference in testing strategy for COVID-19 in critical situations like emergency surgeries and other lifesaving radiological interventions, health care worker testing and testing in ICU patients. Primary care physicians play an important role in the emergency areas at community level, they come across variety of illnesses; as they are the first contact care providers. Primary care physicians can decide about need of urgency of some intervention and which test (RT-PCR vs GeneXpert) will be required as per the situation at their disposal. Various advantages include already available set up worldwide, trained manpower, less processing time (around 45 mins), around 96 tests in 24 hours, half the cost as compared to RT-PCR and use in African, Asian and Latin American countries.[6] United States Food and Drug Administration has also given emergency use authorization for Xpert ®Xpress SARS-CoV-2 testing modality. Although sensitivity specificity data is not available for GeneXpert in COVID-19, it has reliable and pathbreaking data from sputum testing in tuberculosis. When used as initial diagnostic test in place of sputum smear microscopy Xpert MTB/RIF has sensitivity of 88% and specificity of 99%.[7] Advantage of RT-PCR over GeneXpert is the ability to process larger number of samples simultaneously. So, The RT-PCR is best suitable for mass scale testing and use of GeneXpert can be lifesaving in emergency settings. Although all tests other than RT-PCR have not been standardized; GeneXpert will be a boon for testing in above discussed situations. It is being used in various hospitals and medical research institutes across India. However, we have to keep in mind issue of testing for tuberculosis in patients especially in Africa and Asia, so large scale diversion of GeneXpert testing machinery has to be avoided. Post Graduate Institute of Medical Education and Research, Chandigarh, India has taken initiative in GeneXpert testing in emergency situations like lifesaving radiological procedures and surgeries. To Summarize GeneXpert is rapid test for COVID-19 with processing time of around 45 mins and less cost Less expertise is required as already available set up for GeneXpert-MTB testing in India Can be lifesaving in emergency situations as interventions can be done at earliest. Financial support and sponsorship Nil. Conflicts of interest There are no conflicts of interest.