SARS-CoV-2 Delta variant isolates from vaccinated individuals

Area of Science:

• Virology
• Genomics
• Molecular Biology

Background:

• The SARS-CoV-2 Delta variant rapidly became dominant in the U.S. due to increased transmissibility and immune evasion.
• Vaccine breakthrough infections with Delta have raised concerns about viral evolution in vaccinated populations.

Purpose of the Study:

• To investigate the genetic diversity of SARS-CoV-2 Delta variants in vaccinated individuals in the U.S.
• To identify and characterize novel mutations and their potential impact on viral properties.

Main Methods:

• Whole genome sequencing of 34 SARS-CoV-2 positive samples using Oxford Nanopore MinION.
• Evolutionary genomic analysis to identify mutations and compare isolates.

Main Results:

• Two novel mutations, ORF1b:V2354F and ORF7a:Q94*, were identified in a cluster of Delta isolates from vaccinated individuals in Colorado.
• The ORF1b:V2354F mutation may alter protein structure, while ORF7a:Q94* truncates a protein involved in transport.
• An additional mutation, S112L in the spike protein, was found in these isolates, potentially affecting antibody binding.

Conclusions:

• An emerging sub-lineage of the SARS-CoV-2 Delta variant is circulating in the U.S.
• Mutations conferring a potential advantage to the virus are likely to persist.
• Further monitoring of viral evolution in vaccinated populations is warranted.