tetano
Editor, Senior Moderator
J Med Virol
. 2022 May 16.
doi: 10.1002/jmv.27861. Online ahead of print.
Genomics of Post-Vaccination SARS-CoV-2 Infections During the Delta Dominated Second Wave of COVID-19 Pandemic, from Mumbai Metropolitan Region (MMR), India
Kayzad Nilgiriwala[SUP] 1 [/SUP], Pratibha Kadam[SUP] 1 [/SUP], Grishma Patel[SUP] 1 [/SUP], Ambreen Shaikh[SUP] 1 [/SUP], Tejal Mestry[SUP] 1 [/SUP], Smriti Vaswani[SUP] 1 [/SUP], Shalini Sakthivel[SUP] 1 [/SUP], Aruna Poojary[SUP] 2 [/SUP], Bhavesh Gandhi[SUP] 2 [/SUP], Seema Rohra[SUP] 2 [/SUP], Zarir Udwadia[SUP] 2 [/SUP], Vikas Oswal[SUP] 3 [/SUP], Daksha Shah[SUP] 4 [/SUP], Mangala Gomare[SUP] 4 [/SUP], Kalpana Sriraman[SUP] 1 [/SUP], Nerges Mistry[SUP] 1 [/SUP]
Affiliations
Abstract
The present study was initiated to understand the proportion of predominant variants of SARS-CoV-2 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. 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-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. This article is protected by copyright. All rights reserved.
Keywords: Epidemiology; Genetics; Mutation; SARS coronavirus; Virus classification.
. 2022 May 16.
doi: 10.1002/jmv.27861. Online ahead of print.
Genomics of Post-Vaccination SARS-CoV-2 Infections During the Delta Dominated Second Wave of COVID-19 Pandemic, from Mumbai Metropolitan Region (MMR), India
Kayzad Nilgiriwala[SUP] 1 [/SUP], Pratibha Kadam[SUP] 1 [/SUP], Grishma Patel[SUP] 1 [/SUP], Ambreen Shaikh[SUP] 1 [/SUP], Tejal Mestry[SUP] 1 [/SUP], Smriti Vaswani[SUP] 1 [/SUP], Shalini Sakthivel[SUP] 1 [/SUP], Aruna Poojary[SUP] 2 [/SUP], Bhavesh Gandhi[SUP] 2 [/SUP], Seema Rohra[SUP] 2 [/SUP], Zarir Udwadia[SUP] 2 [/SUP], Vikas Oswal[SUP] 3 [/SUP], Daksha Shah[SUP] 4 [/SUP], Mangala Gomare[SUP] 4 [/SUP], Kalpana Sriraman[SUP] 1 [/SUP], Nerges Mistry[SUP] 1 [/SUP]
Affiliations
- PMID: 35578378
- DOI: 10.1002/jmv.27861
Abstract
The present study was initiated to understand the proportion of predominant variants of SARS-CoV-2 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. 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-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. This article is protected by copyright. All rights reserved.
Keywords: Epidemiology; Genetics; Mutation; SARS coronavirus; Virus classification.