key: cord-0879414-jgke9yhg
authors: Ghosh, Arup; Walia, Safal; Rattan, Roma; Kanampalliwar, Amol; Jha, Atimukta; Aggarwal, Shifu; Fatma, Sana; Das, Niyati; Chayani, Nirupama; Prasad, Punit; Raghav, Sunil K.; Parida, Ajay
title: Genomic profiles of vaccine breakthrough SARS-CoV-2 strains from Odisha, India
date: 2022-03-28
journal: Int J Infect Dis
DOI: 10.1016/j.ijid.2022.03.042
sha: 017cfc79d94444c1792503a003571b6291a5bde3
doc_id: 879414
cord_uid: jgke9yhg

nan

COVISHIELD, and the indigenous inactivated virus vaccine COVAXIN by Bharat Biotech are majorly deployed through government and private healthcare centers. Both the vaccines pose tolerable safety outcomes and enhanced immune responses (Ella et al., 2021; Voysey et al., 2021) . Recent in vitro studies showed that sera from Pfizer or the AstraZeneca vaccinated individuals is less effective in neutralizing Delta variant in comparison to Alpha (B.1.1.7) (Planas et al., 2021) . In this study, we summarize 36 COVID-19 vaccine breakthrough cases, which were SARS-CoV-2 RT-PCR positive despite evidence of antibody response following vaccination.

The isolated RNA was subjected to qRT-PCR and samples with Ct values < 35 (ORF1ab & N gene) were considered for the study. Sequencing libraries were prepared with COVIDSeq kit and sequenced using NextSeq-550 platform (Illumina). Non-Host (Human) reads extracted using Kraken2 taxonomic classifier (Wood et al., 2019) , were aligned using BWA against the Wuhan-Hu-1 (NC_045512.2) reference genome. Single nucleotide variants and short INDELs were called using GATK4 Haplotypecaller. Consensus sequences generated using BCFtools consensus and regions having no aligned reads were hard-masked. Rooted (root: NC_045512.2) phylogenetic tree of 549 sequences (512 unvaccinated sequences in the same timeframe from Odisha) was constructed using the method described in (Raghav et al., 2020) .

As a part of the regular COVID-19 genomic surveillance, we identified and sequenced 36 vaccine breakthrough infection cases. The study group consisted of 12 females, 24 males with age ranging from 23 to 65 years (median = 38.50, sd = 13.58). All subjects except two were fully immunized with two doses of either COVAXIN/BBV1552(n=8) or AZD1222/ COVISHIELD (n=26). The interval between two vaccine doses ranged between 27 to 49 days with a median interval of 35 days (n = 34) and the onset of infection ranged between 6 to 98 days post vaccination (median = 74, sd = 25, n = 31). Out of 36 cases, 33 reported either single or a combination of common COVID-19 related symptoms i.e., fever, body pain, sore throat, one individual didn't report any symptoms during sample collection and for the other two samples the symptoms were not reported. The specimens were collected between March 29 to June 15, 2021.

In the study group, 19.44% patients reported comorbidities i.e., diabetes, blood pressure, rest 72.22% patients did not report any complications, disease history is not reported for three cases. Out of 36 patients, only 1 patient was hospitalized with comorbidities, 27 recovered in home isolation, for 8 individuals the treatment status is not reported. Except for three unknown cases, the rest of the patients didn't report any prior history of SARS-CoV-2 infection at the time of sample collection.

Out of the 36 cases, twenty-nine were identified as variants of concern Delta (80%), two Figure 1C ). Looking into Spike domain specific mutations, we observed an emergence of EFR156G substitution (delE156, delF157, and R158G) in N-terminus domain, which is becoming a common trait of recently reported Delta (B.1.617.2) variants (Liu et al., 2021) . Interestingly, most of the breakthrough cases shared the presence of S:L452R, S:T478K in receptor binding domain (RBD) along with S:D614G and S:P681R near S1-S2 furin cleavage site. All these spike variants have been proposed to be associated with increased infectivity through different mechanisms ( Figure 1D ) (Harvey et al., 2021) .

In this study, we found that SARS-CoV-2 variant of concern Delta (B.1.617.2) is overrepresented in the vaccine break-through cases, which could be due to its higher prevalence as well during that period. Recent studies suggested that the effectiveness of BNT162b2 (Pfizer) and ChAdOx1 (AstraZeneca) has been reduced in comparison to Alpha (B.1.1.7) variants. Also the same has been observed in the neutralizing capability of sera from fully vaccinated individuals (Lopez Bernal et al., 2021; Planas et al., 2021) . One other in vitro study suggested that S:L452R and S:E484Q present in the RDB domain of Spike protein are responsible for immune escape and thereby 3-6 fold decrease in neutralization capability of BNT162b2 sera (Ferreira et al., 2021) . 109/HEC/21). All necessary patient/participant consents have been obtained and the appropriate institutional forms have been archived.

ILS provided an intramural grant to support the study.

The authors declare no conflict of interest.

Safety and immunogenicity of an inactivated SARS-CoV-2 vaccine, BBV152: a double-blind, randomised, phase 1 trial

SARS-CoV-2 B.1.617 mutations L452 and E484Q are not synergistic for antibody evasion

SARS-CoV-2 variants, spike mutations and immune escape

BNT162b2-elicited neutralization of B.1.617 and other SARS-CoV-2 variants

Effectiveness of Covid-19 Vaccines against the B.1.617.2 (Delta) Variant

Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization

Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity

Variants of Concern responsible for SARS-CoV-2 vaccine breakthrough infections from India

Safety and efficacy of the ChAdOx1 nCoV-19 vaccine (AZD1222) against SARS-CoV-2: an interim analysis of four randomised controlled trials in Brazil, South Africa, and the UK

Improved metagenomic analysis with Kraken 2

SARS-CoV-2 variants of concern and phylogenetic analysis of vaccine breakthrough cases; (A & B) Genome wide non-synonymous mutations present in high fraction (>20%) of samples, grouped by the vaccines, (C) Phylogenetic tree (n=549) of our study genomes along with SARS-CoV-2 sequences prevalent during the same time frame from

Odisha, the tree is rooted with Wuhan-Hu-01 assembly, and (D) Non-synonymous mutations observed in different domains of Spike protein grouped by vaccination type

We would like to acknowledge the State Surveillance Officers (SSOs) of Odisha for their support in arranging the samples. Thanks to Dr. Andrew A. Lamare, Dr. Sudeep Jena, and Mr. Rahul Biswal from SCB hospital, Cuttack for the samples and the metadata.