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.