ABSTRACT
Emerging reports of SARS-CoV-2 breakthrough infections entail methodical genomic surveillance for determining the efficacy of vaccines. This study elaborates genomic analysis of isolates from breakthrough infections following vaccination with AZD1222/Covishield and BBV152/Covaxin. Variants of concern B.1.617.2 and B.1.1.7 responsible for cases surge in April-May 2021 in Delhi, were the predominant lineages among breakthrough infections.
Subject(s)
COVID-19/virology , SARS-CoV-2/genetics , Adult , Aged , Aged, 80 and over , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19 Vaccines , ChAdOx1 nCoV-19/administration & dosage , Female , Genome, Viral/genetics , Genomics , Humans , India/epidemiology , Male , Middle Aged , Phylogeny , SARS-CoV-2/immunology , SARS-CoV-2/isolation & purification , Vaccination , Vaccines, Inactivated/administration & dosage , Young AdultSubject(s)
COVID-19 , Vaccines , COVID-19 Vaccines/adverse effects , Health Personnel , Humans , SARS-CoV-2ABSTRACT
Ever since the breakout of COVID-19 disease, ceaseless genomic research to inspect the epidemiology and evolution of the pathogen has been undertaken globally. Large scale viral genome sequencing and analysis have uncovered the functional impact of numerous genetic variants in disease pathogenesis and transmission. Emerging evidence of mutations in spike protein domains escaping antibody neutralization is reported. We have built a database with precise collation of manually curated variants in SARS-CoV-2 from literature with potential escape mechanisms from a range of neutralizing antibodies. This comprehensive repository encompasses a total of 5258 variants accounting for 2068 unique variants tested against 230 antibodies, patient convalescent plasma and vaccine breakthrough events. This resource enables the user to gain access to an extensive annotation of SARS-CoV-2 escape variants which would contribute to exploring and understanding the underlying mechanisms of immune response against the pathogen. The resource is available at http://clingen.igib.res.in/esc/.
Subject(s)
COVID-19/therapy , Databases, Factual , SARS-CoV-2/immunology , Antibodies, Neutralizing/immunology , COVID-19/immunology , COVID-19/virology , Epitopes, B-Lymphocyte/immunology , Epitopes, T-Lymphocyte/immunology , Genetic Variation , Humans , Immune Evasion , Immunization, Passive , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/immunology , User-Computer Interface , COVID-19 SerotherapySubject(s)
COVID-19 , SARS-CoV-2 , Antibody Formation , COVID-19 Vaccines , Genomics , Health Personnel , Humans , India/epidemiology , RNA, MessengerABSTRACT
Coronavirus disease 2019 (COVID-19) rapidly spread from a city in China to almost every country in the world, affecting millions of individuals. The rapid increase in the COVID-19 cases in the state of Kerala in India has necessitated the understanding of SARS-CoV-2 genetic epidemiology. We sequenced 200 samples from patients in Kerala using COVIDSeq protocol amplicon-based sequencing. The analysis identified 166 high-quality single-nucleotide variants encompassing four novel variants and 89 new variants in the Indian isolated SARS-CoV-2. Phylogenetic and haplotype analysis revealed that the virus was dominated by three distinct introductions followed by local spread suggesting recent outbreaks and that it belongs to the A2a clade. Further analysis of the functional variants revealed that two variants in the S gene associated with increased infectivity and five variants mapped in primer binding sites affect the efficacy of RT-PCR. To the best of our knowledge, this is the first and most comprehensive report of SARS-CoV-2 genetic epidemiology from Kerala.