AUTHOR=Sharma Ravi P. , Gautam Swati , Sharma Pratibha , Singh Ruchi , Sharma Himanshu , Parsoya Dinesh , Deeba Farah , Bhomia Neha , Pal Nita , Potdar Varsha , Yadav Pragya D. , Gupta Nivedita , Bhandari Sudhir , Kumar Abhinendra , Joshi Yash , Pandit Priyanka , Malhotra Bharti 

TITLE=Genomic profile of SARS-CoV-2 Omicron variant and its correlation with disease severity in Rajasthan

JOURNAL=Frontiers in Medicine

VOLUME=Volume 9 - 2022

YEAR=2022

URL=https://www.frontiersin.org/journals/medicine/articles/10.3389/fmed.2022.888408

DOI=10.3389/fmed.2022.888408

ISSN=2296-858X

ABSTRACT=Background: Omicron, a new variant of SARS-CoV-2 was first detected in November 2021. This was believed to be highly transmissible and was reported to evade immunity. As a result urgent need was felt to screen all positive samples so as to rapidly identify Omicron cases and isolate them to prevent spread of infection. Genomic surveillance of SARS-CoV-2 was planned to correlate disease severity with the genomic profile. 
Methodology: All the SARS- CoV-2 positive cases detected in state of Rajasthan were sent to our Lab. Samples received during 24th November 2021 to 4th January 2022 were selected for Next Generation Sequencing. Processing was done as per protocol on Ion Torrent S5 system for 1210 samples and bioinformatics analysis was done.
Results: Among the 1210 samples tested 762(62.9%) were Delta/Delta like and other lineages,   291(24%) were Omicron and 157(12.9%) were invalid or repeat samples. Within a month, the  proportion of  Delta and other variants was reversed, from 6% omicron became 81% and delta  and other variants 19%, initially all omicron cases were international travelers and their contacts but soon community transmission was seen. Majority of omicron patients were asymptomatic (56.7%) or had mild disease (33%), 9.2% had moderate symptoms and 2(0.7%) had severe disease requiring hospitalization, of which one (0.3%) died and rest (99.7%) recovered. History of vaccination was seen in 81.1%, of previous infection in 43.2%. Among the Omicron cases BA.1 (62.8%) was the predominant lineage followed by BA.2 (23.7%) and B.1.529 (13.4%),  rising trends were seen initially for BA.1 and later for BA.2 also. While 8.9 %  patients with Delta lineage during that period were hospitalized, 7.2% required oxygen and 0.9 % died.
Conclusion: Community spread of Omicron occurred in short time and became the predominant circulating variant, BA.1 was the predominant lineage detected. Most of the cases with Omicron  were  asymptomatic or had mild disease and mortality rate was very low as compared to Delta and other lineages.