Genomics of Post-Vaccination SARS-CoV-2 Infections During the Delta Dominated Second Wave of COVID-19 Pandemic, from Mumbai Metropolitan Region (MMR), India

Abstract

Vaccination against SARS-CoV-2 was launched in India in January 2021. Though vaccination reduced hospitalization and mortality due to COVID-19, vaccine breakthrough infections have become common. The present study was initiated in May 2021 to understand the proportion of predominant variants in post-vaccination infections during the Delta dominated second wave of COVID-19 in the Mumbai Metropolitan Region (MMR) in India and to understand any mutations selected in the post-vaccination infections or showing association with any patient demographics. We collected samples (n=166) from severe/moderate/mild COVID-19 patients who were either vaccinated (COVISHIELD/COVAXIN; partial/fully vaccinated) or unvaccinated, from a city hospital and from home isolation patients in MMR. A total of 150 viral genomes were sequenced by Oxford Nanopore sequencing (using MinION) and the data of 136 viral genomes were analyzed for clade/lineage and for identifying mutations in all the genomes. The sequences belonged to three clades (21A, 21I and 21J) and their lineage was identified as either Delta (B.1.617.2) or Delta+ (B.1.617.2 + K417N) or sub-lineages of Delta variant (AY.120/AY.38/AY.99). A total of 620 mutations were identified of which 10 mutations showed an increase in trend with time (May-Oct 2021). Associations of 6 mutations (2 in spike, 3 in orf1a and 1 in nucleocapsid) were shown with milder forms of the disease and one mutation (in orf1a) with partial vaccination status. The results indicate a trend towards reduction in disease severity as the wave progressed.

Population genetics in the early emergence of the Omicron SARS-CoV-2 variant in the provinces of South Africa

“…CC-BY-NC-ND 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted February 10, 2023. ; https://doi.org/10.1101/2023.02.09.527920 doi: bioRxiv preprint mutations in the Omicron lineage, there is evidence linking them to increased fitness, such as spike:D614G by enhancing transmission [28], epitope loss that could lead to immunological scape, such as orf1ab:P4715L [29]; reduction in severity of COVID -19 cases, such as orf1ab:T3255I [30]. Although the synonymous mutations orf1ab:F924F or nuc:C3037T do not cause changes in any protein, there is a strong allelic association with other non-synonymous mutations such as orf1ab:P47I15L and spike:D614G [31,32], which may contribute to the maintenance of virus integrity.…”

“…Two of them are unique to Omicron, namely orf1ab:P4751L and spike:H655Y. For some of these four common mutations in the Omicron lineage, there is evidence linking them to increased fitness, such as spike:D614G by enhancing transmission [28], epitope loss that could lead to immunological scape, such as orf1ab:P4715L [29]; reduction in severity of COVID -19 cases, such as orf1ab:T3255I [30]. Although the synonymous mutations orf1ab:F924F or nuc:C3037T do not cause changes in any protein, there is a strong allelic association with other non-synonymous mutations such as orf1ab:P47I15L and spike:D614G [31,32], which may contribute to the maintenance of virus integrity.…”