2. Method
An observational retrospective cohort study was conducted in the Department of Microbiology, at a tertiary care hospital where patients aged >12 years who were laboratory confirmed cases of SARS-CoV-2 diagnosed by real-time PCR performed on their nasopharyngeal swabs were enrolled in the study. Nasopharyngeal swabs were transported in viral transport media from which viral RNA was extracted using the MagNA Pure 96 DNA and Viral NA Small Volume kit (Roche, Basel, Switzerland) on the automated MagNA Pure 96 platform (Roche, Basel, Switzerland) as per manufacturer’s protocol [5] followed by Real-time RT-PCR using standardized protocols of Q-line – ER (nCoV-19) RT-PCR detection kit (POCT Service Private Ltd., India) and Check RT-PCR Omisure kit (Tata MD, India); in April 2021 and January 2022, respectively.
A sample size of 100 patients each from two different time periods (April 2021 & January 2022) was taken when the two variants were predominantly circulating. The archived positive specimens were subjected to amplicon-based nanopore sequencing using GridION MK1 sequencer (Oxford Nanopore Technologies Ltd., United Kingdom) as per standardized protocol. [6]
The study protocol was approved by the Institutional Ethics Committee, Maulana Azad Medical College, New Delhi, India (F.1/IEC/MAMC/92/04/2022/No441). Telephonic interviews were conducted, wherein a willingness to participate was verified from each participant. If the patient had been admitted in the hospital, details regarding demographics (age, gender), co-morbidities (hypertension, diabetes, chronic kidney disease, chronic liver disease, chronic obstructive pulmonary disease, chronic heart disease, malignancies), length of hospital stay, oxygen requirement and mortality outcomes of the patients were collected. Details from hospital records were collected if the patient had not survived. Patients were excluded if they did not respond to a phone call or contact number was not available. The association between the variant of SARS-CoV-2 infecting the patient and the demographics, comorbidities and diseases outcomes was determined.
All the data was collected and compiled in MS Excel and analysis was done using SPSS version 20 software. Results for quantitative variables have been expressed as median, mean and standard deviation, whereas, qualitative data as percentages. Further, analysis was done by Chi-square test for qualitative data and significance was considered if p-value <0.05. Odds risk (OR) ratio and 95% confidence interval were analyzed using SPSS version 20.