COVID-19 pandemic - Cocktail of variants, a study from Northern India

The aim of the study was to identify and monitor the circulating strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the samples received at our center and update the existing national and international genomic surveillance data.

SARS-CoV-2 is no exception to the basic nature of the viruses ability to change and evolve. Since its first report in December 2019 from Wuhan, China, multiple variants of the virus have emerged and been reported. Five variants of concern have been recognized and reported by the Centers for Disease Control and Prevention, which are associated with variable degrees of transmissibility and mortality.

Nasopharyngeal and oropharyngeal swabs received in viral transport medium at the Viral Research Diagnostic Laboratory were processed for reverse transcription-polymerase chain reaction for SARS-CoV-2. Whole genome sequencing (WGS) was performed for selective positive samples using Oxford Nanopore sequencing technology, using MinKNOW software for data acquisition.

The clades were assigned using Nextclade v2.4.1 software. The statistical analysis was calculated using OpenEpi version 3, an open-source calculator, and two by two.

Variants reported over the study period included Alpha, Kappa, Delta, and Omicron. Delta dominated in the year 2021, while Omicron was the dominant variant in 2022. In both the dominant variants, asymptomatics contributed to around 30-40% of positives. Intensive care unit admissions and mortality were higher in the Delta variant, while vaccination history and travel history were higher in the patients with Omicron variant.

The trend tracking of these variants has been important in view of public health, enabling early interventions to control the spread of the disease and foresight in preparation for the situation.