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

Abstract

BackgroundOmicron, a new variant of Severe Acute Respiratory Syndrome-Coronavirus 2 (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, an urgent need was felt to screen all positive samples so as to rapidly identify Omicron cases and isolate them to prevent the spread of infection. Genomic surveillance of SARS-CoV-2 was planned to correlate disease severity with the genomic profile.MethodsAll the SARS-CoV-2 positive cases detected in the state of Rajasthan were sent to our Lab. Samples received from 24 November 2021 to 4 January 2022 were selected for Next-Generation Sequencing (NGS). Processing was done as per protocol on the Ion Torrent S5 System for 1,210 samples and bioinformatics analysis was done.ResultsAmong the 1,210 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, 6% Omicron became 81%, and Delta and other variants became 19%, initially all Omicron cases were seen in international travelers and their contacts but soon community transmission was seen. The majority of patients with Omicron were asymptomatic (56.7%) or had mild disease (33%), 9.2% had moderate symptoms, and two (0.7%) had severe disease requiring hospitalization, of which one (0.3%) died and the rest were (99.7%) recovered. History of vaccination was seen in 81.1%, of the previous infection in 43.2% of cases. 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. Although 8.9% of patients with Delta lineage during that period were hospitalized, 7.2% required oxygen, and 0.9% died. To conclude, the community spread of Omicron occurred in a 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 the mortality rate was very low as compared to Delta and other lineages.

Effectiveness of a booster dose of COVID-19 vaccines during an outbreak of SARS-CoV-2 Omicron BA.2 in China: A case-control study

“…A growing number of reports indicated that the Omicron-associated COVID-19 disease was less severe than the Delta-associated COVID-19 disease, resulting in more asymptomatic patients [30,31] . A study from India showed that the majority of patients infected with Omicron were asymptomatic (56.7%) [32] , consistent with our study. The Faroe Islands study reported that in over half the cases, patients assessed their illness as asymptomatic or mild [33] .…”

Effectiveness of a booster dose of COVID-19 vaccines during an outbreak of SARS-CoV-2 Omicron BA.2.2 in China: A case–control study

“…A growing number of reports indicated that the Omicron-associated COVID-19 disease was less severe than the Delta-associated COVID-19 disease, resulting in more asymptomatic patients. 30 , 31 A study from India showed that the majority of patients infected with Omicron were asymptomatic (56.7%), 32 consistent with our study. The Faroe Islands study reported that in over half the cases, patients assessed their illness as asymptomatic or mild.…”

Genomic surveillance of SARS-CoV-2 and emergence of XBB.1.16 variant in Rajasthan

“…Library preparation was done by Ion AmpliSeq library kit plus, template preparation, enrichment and chip loading was done on Ion Chef system (Life Technologies) and loaded chips were sequenced on the Ion torrent S5 system(Life Technologies). NGS data analysis was done as described previously [10]. The FASTA files obtained on sequencing were aligned withWuhan-Hu-1/2019 (genbank: MN908947) as reference using Nextclade (https://clades.Nextstrain.org).…”