Abstract
AbstractWith increasing demand for large numbers of testing during the coronavirus disease 2019 pandemic, alternative protocols were developed with shortened turn-around time. We evaluated the performance of such a protocol wherein 1138 consecutive clinic attendees were enrolled; 584 and 554 respectively from two independent study sites in the cities of Pune and Kolkata. Paired nasopharyngeal and oropharyngeal swabs were tested by using both reference and index methods in a blinded fashion. Prior to conducting real-time polymerase chain reaction, swabs collected in viral transport medium (VTM) were processed for RNA extraction (reference method) and swabs collected in a dry tube without VTM were incubated in Tris–EDTA–proteinase K buffer for 30 min and heat-inactivated at 98 °C for 6 min (index method). Overall sensitivity and specificity of the index method were 78.9% (95% confidence interval (CI) 71–86) and 99% (95% CI 98–99.6), respectively. Agreement between the index and reference method was 96.8% (k= 0.83,s.e.= 0.03). The reference method exhibited an enhanced detection of viral genes (E, N and RNA-dependent RNA polymerase) with lower Ct values compared to the index method. The index method can be used for detecting severe acute respiratory syndrome corona virus-2 infection with an appropriately chosen primer–probe set and heat treatment approach in pressing time; low sensitivity constrains its potential wider use.
Highlights
The COVID-19 pandemic swept through the world with unprecedented speed and impact on lives and livelihoods [1]
Study settings and participants The present investigation was conducted at two sites in India namely, the ICMR-National AIDS Research Institute (ICMR-NARI), Pune in the western state of Maharashtra and the School of Tropical Medicine (STM), Kolkata in the eastern state of West Bengal
Information obtained from 584 participants by ICMR-NARI and 554 participants by STM, Kolkata were included in the analyses
Summary
The COVID-19 pandemic swept through the world with unprecedented speed and impact on lives and livelihoods [1]. Within four months of its onset, more than 118,000 cases and 4,291 deaths were reported from 114 countries All of these happened following an outbreak of ‘unusual cases of pneumonia’ notified for the first time from the Wuhan city of Hubei province, China in December 2019 [2]. Such a rapid spread of the causative virus SARS-CoV-2 reminded humankind of the influenza pandemic causing havoc about 100 year ago [3,4]. The combination of two gene targets is recommended to enhance accuracy of diagnosis in the context of possible viral genetic variability; one from the conserved region of the virus and another from SARS CoV-2 specific region of the genome [8]
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