Genomics of postvaccination SARS‐CoV‐2 infections during the Delta dominated second wave of COVID‐19 pandemic, from Mumbai Metropolitan Region (MMR), India

Abstract

The present study was initiated to understand the proportion of predominant variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in postvaccination infections during the Delta dominated second wave of coronavirus disease 2019 (COVID-19) in the Mumbai Metropolitan Region (MMR) in India and to understand any mutations selected in the postvaccination infections or showing association with any patient demographics. Samples were collected (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 and the data of 136 viral genomes were analyzed for clade/lineage and for identifying mutations. 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-October 2021). Associations of six mutations (two in spike, three in orf1a, and one in nucleocapsid) were shown with milder forms of the disease and one mutation (in orf1a) with partial vaccination status. The results indicate a trend toward reduction in disease severity as the wave progressed.

SARS-CoV-2 VOCs, Mutational diversity and clinical outcome: Are they modulating drug efficacy by altered binding strength?

“…Furthermore, we found the co-presence of five mutations (P309L in NSP2, P1640L in NSP3, A3209V in NSP4, V3718A in NSP6, and R385K in the N gene) in the Delta mortality patients, which has been recently reported to be more prevalent in the symptomatic patients than the asymptomatic ones [ 4 ]. On the other hand, three co-occurring mutations, G142D in the Spike, P2287S in the Nsp3 and T3255I in the Nsp4 region of the ORF1ab were observed in the Delta recovered patients, which has been previously reported for their correlation with milder infectious cases of SARS-CoV-2 [ 38 ].…”

Impact of COVID‐19 vaccination on transmission risk of breakthrough infections: Lessons from adapted N95 mask sampling for emerging variants and interventions

“…Tables 1 and depict the demographics, COVID‐ 19 clinical characteristics, and mask sampling scores based on the vaccination status. WGS data analysis confirmed that the SARS‐CoV‐2 positive samples were either Delta (88%) or Delta derivative (Table ) 19 …”

“…WGS data analysis confirmed that the SARS-CoV-2 positive samples were either Delta (88%) or Delta derivative (Table S2). 19…”

Sequence analysis of SARS-CoV-2 Delta variant isolated from Makassar, South Sulawesi, Indonesia

“…This observation supports previous study by Nilgriwala et al that associated the mutation of S G142D with mild cases of Delta infection. This mutation alters the supersite epitope to which antibodies with N-terminal domains bind, which suggests that the hosts evade the viral infection through their immune responses to the infection [ 40 ]. Thus, it is strongly suggested that further study should be conducted to understand the association of this mutation with the clinical outcome of patients infected by the Delta variant, while also understanding the importance of closely monitoring the low-frequency mutation in the genome of the virus with the immune escape mechanism in SARS-CoV-2 variants of interest.…”