Immune-evasion Conferring Mutations Associated with Cases of Breakthrough SARS-CoV-2 Infection among Walk-in Patients

ABSTRACT

Introduction: India recently faced a devastating second outbreak of COVID-19 infection, in which a majority of the viral sequences were found to be of the B.1.617.2 lineage. While India and the world focused on vaccination, reports of vaccine evasion by the virus, termed 'breakthrough cases', emerged worldwide. Materials and Methods: We analysed whole genome sequences of 150 SARS-CoV-2 viral samples isolated at our laboratory. We retrospectively found 9 cases of breakthrough infection, five of whom were fully, and four partially vaccinated. We followed-up these patients and can report that the variant lineages associated with these cases were B.1.617, B.1, and A. The mutations seen in these sequences in the Spike and ORF regions would have produced amino acid changes known to improve viral replication, confer drug resistance, influence host-cell interaction, and lead to antigenic drift. Increased virulence culminating in vaccine evasion may be inferred from these mutations. India, recently faced a devastating second outbreak of COVID-19 infection, in which a majority of the viral sequences were found to be of the B.1.617.2 lineage. While India and the world focused on vaccination, reports of vaccine evasion by the virus, termed 'breakthrough cases', emerged worldwide. We isolated mRNA from SARS-CoV-2 samples and outsourced them for whole genome sequencing. Results: We noticed that nine individuals had been fully (two doses of vaccine) or partially (one dose) vaccinated at least 14 days before infection. When we examined the sequences from these individuals, we found amino acid changes in the spike and NSP proteins, which were predicted to confer increased virulence upon the virus. We report the presence of three strains in the breakthrough cases;A, B.1, and B.1.617 (Nextstrain Clade G). We found one mutation, NSP6 T77A, that was present in both A and B.1 strains in the breakthrough cases, but not in other A and B.1 strains isolated, from patients of the same city. Additionally, we found multiple changes in the non-structural NSP proteins, which enable faster viral replication. Conclusion: It is clear from our case series that the strains A, B.1, and B.1.617 can attain increased virulence culminating in vaccine evasion.