Clinical Characterization and Genomic Analysis of Samples from COVID-19 Breakthrough Infections during the Second Wave among the Various States of India

Abstract

From March to June 2021, India experienced a deadly second wave of COVID-19, with an increased number of post-vaccination breakthrough infections reported across the country. To understand the possible reason for these breakthroughs, we collected 677 clinical samples (throat swab/nasal swabs) of individuals from 17 states/Union Territories of the country who had received two doses (n = 592) and one dose (n = 85) of vaccines and tested positive for COVID-19. These cases were telephonically interviewed and clinical data were analyzed. A total of 511 SARS-CoV-2 genomes were recovered with genome coverage of higher than 98% from both groups. Analysis of both groups determined that 86.69% (n = 443) of them belonged to the Delta variant, along with Alpha, Kappa, Delta AY.1, and Delta AY.2. The Delta variant clustered into four distinct sub-lineages. Sub-lineage I had mutations in ORF1ab A1306S, P2046L, P2287S, V2930L, T3255I, T3446A, G5063S, P5401L, and A6319V, and in N G215C; Sub-lineage II had mutations in ORF1ab P309L, A3209V, V3718A, G5063S, P5401L, and ORF7a L116F; Sub-lineage III had mutations in ORF1ab A3209V, V3718A, T3750I, G5063S, and P5401L and in spike A222V; Sub-lineage IV had mutations in ORF1ab P309L, D2980N, and F3138S and spike K77T. This study indicates that majority of the breakthrough COVID-19 clinical cases were infected with the Delta variant, and only 9.8% cases required hospitalization, while fatality was observed in only 0.4% cases. This clearly suggests that the vaccination does provide reduction in hospital admission and mortality.

Comparison of neutralizing antibody response in first and second waves of SARS-CoV-2 pandemic in India

“… 8 Further, among the breakthrough cases during second wave infected with the Delta, majority of them did not progress to sever disease. 9 Hence, though the low cross-neutralizing antibody titers to heterologous strains (of first and second wave) were observed in this study, the data indicate that the serum of patients infected previously with one SARS-CoV-2 strain might provide protection against the rapidly emerging variants.…”

Effectiveness of BBV152 vaccine against SARS-CoV-2 infections, hospitalizations and deaths among healthcare workers in the setting of high delta variant transmission in New Delhi, India

“…From our institute, a genomic analysis study of 63 vaccine breakthrough infections (that included a sample of health care workers), 53 received BBV152 vaccine, and among them, was the predominant lineage detected in 13 fully vaccinated and 11 partially vaccinated patients (28). Similar data have been reported from other centres (29,30). Breakthrough infections against delta variant have been reported from all the settings around the world against a variety of vaccines, by now (12,13).…”

Nipah Virus Outbreak in Kerala State, India Amidst of COVID-19 Pandemic

“…Phylogenetic analyses and the amino acid variations of the retrieved NiV sequence with the other representative NiV sequences of earlier outbreaks were performed. SARS-CoV-2 positive samples were sequenced as per the method described earlier to identify the lineage in circulation ( 16 ).…”