Trends of a syndromic approached based respiratory PCR during the second wave of the COVID 19 pandemic in a tertiary care center in Mumbai

Abstract

Purpose: The clinical presentation of COVID 19 disease caused by Severe Acute Respiratory Syndrome Related Coronavirus – 2 (SARS-CoV2) is similar to other causes of upper respiratory viral infections caused by influenza, epidemic corona viruses, Parainfluenza virus etc. This study was undertaken to study the presence of different pathogens in the nasopharyngeal samples of symptomatic patients visiting the COVID OPD or the Emergency services over six month duration. Methods & Materials: This was a prospective study from Dec 2020 to May 2021 conducted in a 220 bed tertiary care hospital in Mumbai. We are a designated COVID care hospital with 55 isolation beds including 16 beds in the COVID ICU, a dedicated OPD for symptomatic patients and Emergency services (EMS). The test was performed on a syndromic approach based respiratory PCR with 22 targets inclusive of SARS-CoV2. Nasal and a pharyngeal swab samples (NPS) were collected and the results of the test were available in 1.5 hours from sample receipt to the lab. Results: A total of 335 patient samples were received during the study period for the syndromic approach based PCR. 133 (39.7%) of the symptomatic patients had a positive test result. 87(26%) SARS-CoV2 and 27(8.05%) Rhinovirus/Enterovirus (RhV/EV) were the two common viruses that were identified during the study duration. Other viruses, like Parainfluenza 3 (PIV3), Coronavirus 229E (229E), Coronavirus HKU1 (HKU1), Influenza AH3 (AH3), H1N1, Coronavirus OC43 (OC43) and Adenovirus were also identified. We observed co-infections 1 each of RhV/EV+AH3, RhV/EV + OC43, SARS-CoV2 +PIV3 and 2 cases of SARS-CoV2+HKU1. The trend indicated the appearance of the 2nd wave of SARS-CoV2 infection that Mumbai experienced between 1st March to 15th May 2021. Other pathogens were mostly seen in the symptomatic population especially before and after the 2nd wave. Conclusion: Our study documented the appearance of the second wave in Mumbai between 1st March to 15th May 2021. Approximately,34.5% of patients has other respiratory pathogens detected in the syndromic PCR. This is the 1st study from Mumbai documenting the types of respiratory pathogens and co infections seen during the 2nd wave of the COVID 19 pandemic in Mumbai.