Beyond Diagnostics: The role of a RT-PCR laboratory in a pandemic

Abstract

Purpose: The gold standard for the detection of SARS-CoV-2 is Real Time Reverse Transcriptase PCR (rRT-PCR). A combination of nasopharyngeal and oropharyngeal swabs improves the sensitivity of detection of SARS-CoV-2 in samples. The first wave of COVID-19 impacted Chennai in May 2020 and lasted till October 2020. The second wave began in March 2021 and lasted till June 2021. The aim of this study is to compare and analyze the COVID-19 waves in 2020 and 2021 based on the data from a tertiary care centre in Chennai, India. Methods & Materials: A total of 42,374 samples were tested by rRT-PCR (Rotor Gene-Q) between March 2020 and June 2021. RNA was extracted using Zybio nucleic acid extraction kit. The target regions of the RT-PCR kits (ViroQ SARS CoV2, Bag Diagnostics, Germany) were the E-gene and RdRp gene. Quality control is maintained by routine participation in the external quality assurance scheme (EQAS). Results: In 2020, 22,905 samples were tested and 3,415 samples tested positive for COVID 19. During the first wave of COVID-19 between May-October 2020, 2989 samples tested positive for COVID 19. Between January and June 2021, 19,469 samples were tested and 2,320 samples were COVID-19 positive. A total of 2,155 samples were positive for COVID-19 in the second wave between March-June 2020. The duration of the first wave was longer with a smaller peak in incidence of COVID 19. The second wave in 2021 had a shorter duration with a more pronounced spike in COVID-19 cases in April 2021. Conclusion: The number of COVID 19 positive cases are similar between the two waves of COVID 19. However, the first wave of COVID-19 took place over a period of nearly six months, while the second wave occurred over three to four months. There is a noticeable surge in COVID-19 incidence observed in April-May 2021. This could indicate the increased infectivity of the virus as observed with the cases doubling rapidly during this time. Documenting the characteristics of the wave in terms of its rapidity of onset of disease and peaks in incidence would offer insight into the progression of COVID-19.