Dataset Information

A Preliminary Genomic Analysis of the Omicron Variants of SARS-CoV-2 in Central India During the third wave of the COVID-19 Pandemic.

ABSTRACT:

Background

Omicron was detected in South Africa for the first time at the month of November 2021, from then it expanded swiftly over the world, outcompeting other SARS-CoV-2 variants such as Delta. The toxicity, resistance to antiviral medicines, transmissibility, and vaccine-induced immunity of newly developed SARS-CoV-2 variants are major worldwide health concerns.

Aim of study

This study investigates the comprehensive explanation of all mutations and their evolutionary linkages between the Omicron variant and recently discovered SARS-CoV-2 variants.

Method

On Illumina MiniSeq Machine, 31 RNA isolates from clinical specimens were sequenced utilizing next-generation sequencing technique. Different bioinformatics tools have been used to analyze the mutations in omicron variant. A phylogenetic tree was constructed to determine Omicron's evolutionary relationships with other variants.

Results

In our investigation, we discovered 79 distinct types of mutations in 31 fully vaccinated COVID-19 positive samples. Mostly mutations were found in non-spike region. According to the NJ approach of phylogenetic tree revels, the nearest variants were in the order listed, based on sequence identity: Omicron, Gamma, Alpha, Delta, Mu and Beta. On the other hand as per UPGMA approach, the Omicron variation creates a novel monophyletic clade that is distinct from previous SARS-CoV-2 variants.

Conclusion

Despite the fact that some of the mutations are prevalent in Omicron and other VOCs, there are several unique mutations that have been connected to the virus's transmissibility and immune evasion, indicating a substantial shift in SARS-CoV-2 evolution.

SUBMITTER: Singh P

PROVIDER: S-EPMC9395282 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature

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Publications

A Preliminary Genomic Analysis of the Omicron Variants of SARS-CoV-2 in Central India During the third wave of the COVID-19 Pandemic.

Singh Priyanka P Negi Sanjay Singh SS Bhargava Anudita A Kolla Vara Prasad VP Arora Ripu Daman RD

Archives of medical research 20220823 6

<h4>Background</h4>Omicron was detected in South Africa for the first time at the month of November 2021, from then it expanded swiftly over the world, outcompeting other SARS-CoV-2 variants such as Delta. The toxicity, resistance to antiviral medicines, transmissibility, and vaccine-induced immunity of newly developed SARS-CoV-2 variants are major worldwide health concerns.<h4>Aim of study</h4>This study investigates the comprehensive explanation of all mutations and their evolutionary linkages ...[more]

PMID: 36123226

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Project description:BackgroundRecent studies on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reveal that Omicron variant BA.1 and sub-lineages have revived the concern over resistance to antiviral drugs and vaccine-induced immunity. The present study aims to analyze the clinical profile and genome characterization of the SARS-CoV-2 variant in eastern Uttar Pradesh (UP), North India.MethodsWhole-genome sequencing (WGS) was conducted for 146 SARS-CoV-2 samples obtained from individuals who tested coronavirus disease 2019 (COVID-19) positive between the period of 1 January 2022 and 24 February 2022, from three districts of eastern UP. The details regarding clinical and hospitalized status were captured through telephonic interviews after obtaining verbal informed consent. A maximum-likelihood phylogenetic tree was created for evolutionary analysis using MEGA7.ResultsThe mean age of study participants was 33.9 ± 13.1 years, with 73.5% accounting for male patients. Of the 98 cases contacted by telephone, 30 (30.6%) had a travel history (domestic/international), 16 (16.3%) reported having been infected with COVID-19 in past, 79 (80.6%) had symptoms, and seven had at least one comorbidity. Most of the sequences belonged to the Omicron variant, with BA.1 (6.2%), BA.1.1 (2.7%), BA.1.1.1 (0.7%), BA.1.1.7 (5.5%), BA.1.17.2 (0.7%), BA.1.18 (0.7%), BA.2 (30.8%), BA.2.10 (50.7%), BA.2.12 (0.7%), and B.1.617.2 (1.3%) lineages. BA.1 and BA.1.1 strains possess signature spike mutations S:A67V, S:T95I, S:R346K, S:S371L, S:G446S, S:G496S, S:T547K, S:N856K, and S:L981F, and BA.2 contains S:V213G, S:T376A, and S:D405N. Notably, ins214EPE (S1- N-Terminal domain) mutation was found in a significant number of Omicron BA.1 and sub-lineages. The overall Omicron BA.2 lineage was observed in 79.5% of women and 83.2% of men.ConclusionThe current study showed a predominance of the Omicron BA.2 variant outcompeting the BA.1 over a period in eastern UP. Most of the cases had a breakthrough infection following the recommended two doses of vaccine with four in five cases being symptomatic. There is a need to further explore the immune evasion properties of the Omicron variant.

Project description:IntroductionThe emergence of the Omicron SARS-CoV-2 variant from various states of India in early 2022 has caused fear of its rapid spread. The lack of such reports from Chhattisgarh (CG), a central state in India, has prompted us to identify the Omicron circulating lineages and their mutational dynamics.Materials and methodsWhole-genome sequencing (WGS) of SARS-CoV-2 was performed in 108 SARS-CoV-2 positive combined samples of nasopharyngeal and oropharyngeal swabs obtained from an equal number of patients.ResultsAll 108 SARS-CoV-2 sequences belonged to Omicron of clade 21L (84%), 22B (11%), and 22D (5%). BA.2 and its sub-lineages were predominantly found in 93.5% of patients, BA.5.2 and its sub-lineage BA.5.2.1 in 4.6% of patients, and B.1.1.529 in 2% of patients. Various BA.2 sub-lineages identified were BA.2 (38%), BA.2.38 (32%), BA.2.75 (9.25%), BA.2.56, BA.2.76, and BA.5.2.1 (5% each), BA.2.74 (4.6%), BA.5.2.1 (3.7%), BA.2.43 and B.1.1.529 (1.8% each), and BA.5.2 (0.9%). Maximum mutations were noticed in the spike (46), followed by the nucleocapsid (5), membrane (3), and envelope (2) genes. Mutations detected in the spike gene of different Omicron variants were BA.1.1.529 (32), BA.2 (44), BA.2.38 (37), BA.2.43 (38), BA.2.56 (30), BA.2.74 (31), BA.2.75 (37), BA.2.76 (32), BA.5.2, and BA.5.2.1 (38 similar mutations). The spike gene showed the signature mutations of T19I and V213G in the N-terminal domain (NTD), S373P, S375F, T376A, and D405N in receptor-binding domain (RBD), D614G, H655Y, N679K, and P681H at the furin cleavage site, N764K and D796K in fusion peptide, and Q954H and N969K in heptapeptide repeat sequence (HR)1. Notably, BA.2.43 exhibited a novel mutation of E1202Q in the C terminal. Other sites included ORF1a harboring 13 mutations followed by ORF1b (6), ORF3a (2), and ORF6 and ORF8 (1 mutation each).ConclusionBA.2 followed by BA.2.38 was the predominant Omicron lineage circulating in Chhattisgarh. BA.2.75 could supersede other Omicron due to its mutational consortium advantage. The periodical genomic monitoring of Omicron variants is thus required for real-time assessment of circulating strains and their mutational-induced severity.

Dataset Information

A Preliminary Genomic Analysis of the Omicron Variants of SARS-CoV-2 in Central India During the third wave of the COVID-19 Pandemic.

Background

Aim of study

Method

Results

Conclusion

Publications

A Preliminary Genomic Analysis of the Omicron Variants of SARS-CoV-2 in Central India During the third wave of the COVID-19 Pandemic.

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