Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India

Abstract

Uttar Pradesh is the densely populated state of India and is the sixth highest COVID-19 affected state with 22,904 deaths recorded on November 12, 2021. Whole-genome sequencing (WGS) is being used as a potential approach to investigate genomic evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. In this study, a total of 87 SARS-CoV-2 genomes−49 genomes from the first wave (March 2020 to February 2021) and 38 genomes from the second wave (March 2021 to July 2021) from Eastern Uttar Pradesh (E-UP) were sequenced and analyzed to understand its evolutionary pattern and variants against publicaly available sequences. The complete genome analysis of SARS-CoV-2 during the first wave in E-UP largely reported transmission of G, GR, and GH clades with specific mutations. In contrast, variants of concerns (VOCs) such as Delta (71.0%) followed by Delta AY.1 (21.05%) and Kappa (7.9%) lineages belong to G clade with prominent signature amino acids were introduced in the second wave. Signature substitution at positions S:L452R, S:P681R, and S:D614G were commonly detected in the Delta, Delta AY.1, and Kappa variants whereas S:T19R and S:T478K were confined to Delta and Delta AY.1 variants only. Vaccine breakthrough infections showed unique mutational changes at position S:D574Y in the case of the Delta variant, whereas position S:T95 was conserved among Kappa variants compared to the Wuhan isolate. During the transition from the first to second waves, a shift in the predominant clade from GH to G clade was observed. The identified spike protein mutations in the SARS-CoV-2 genome could be used as the potential target for vaccine and drug development to combat the effects of the COVID-19 disease.

Omicron BA.2 lineage predominance in severe acute respiratory syndrome coronavirus 2 positive cases during the third wave in North India

“…No. clade variants mostly the Delta and its variant Delta AY.1 and Kappa (17). Neutralization studies have also substantiated the shift of the Omicron variant as a dominant strain replacing the Delta variant (21).…”

“…Besides the curfew, other COVID-related protocols and restrictions were also implemented, including bans on gatherings of more than 200 people, cultural and religious events, etc. 1 A previous study from eastern UP has provided comprehensive information on SARS-CoV-2 variants and distinct lineage/clades in the first and second waves ( 17 ). Existing research on the clinical and genomic characteristics of Omicron cases is limited in India ( 18 – 20 ).…”

COVID‐19 transmission among vaccinated laboratory workers during the second wave in eastern Uttar Pradesh, India

“…The center is functioning as one of the nodal centers for COVID‐19 testing in the region of eastern Uttar Pradesh, India. It was on April 8, 2021, when India witnessed the second wave of COVID‐19 due to the Delta variant, 2 we received a message from a laboratory official in the group stating that “I have been tested positive for COVID‐19; all the staff should get tested!” The official was in contact with almost all of the staff working in the laboratory which was one of the COVID‐19 testing centers, which created a fearful situation. But, somewhat we were all consoled by the fact that we all have had received at least one dose of COVID‐19 vaccine shot of ChAdOx1 nCoV‐19 (correspondingly in Kaur et al, 41% had received a single shot and 19% had received both shots of vaccine) in view of the initiatives taken up by the Government of India.…”

Raman Fingerprints of the SARS-CoV-2 Delta Variant and Mechanisms of Its Instantaneous Inactivation by Silicon Nitride Bioceramics

“…This latter vibration is ∼20% lower in the Delta variant than in the Kappa one. A comparison of key residues in SARS-CoV-2 variants by Deval et al 48 significantly lower wavenumber (i.e., 959 cm −1 ) as a consequence of the different structure of the ring. 51,52 On the other hand, a cumulative signal from C−N stretching in both five-membered imidazole and six-membered pyrimidine rings of the adenine (A) purine is displayed at 1150 cm −1 .…”

“…This latter vibration is ∼20% lower in the Delta variant than in the Kappa one. A comparison of key residues in SARS-CoV-2 variants by Deval et al has shown that tryptophan was the most common residue in both Delta and Kappa variants. This notion was confirmed by the Raman data shown in this study in comparison with the spectra of two Alpha sub-variants shown in a previously published work …”