Transmission event of SARS-CoV-2 delta variant reveals multiple vaccine breakthrough infections

Farinholt, Timothy; Doddapaneni, Harsha; Qin, Xiang; Menon, Vipin; Meng, Qingchang; Metcalf, Ginger; Chao, Hsu; Gingras, Marie-Claude; Avadhanula, Vasanthi; Farinholt, Paige; Agrawal, Charu; Muzny, Donna M.; Piedra, Pedro A.; Gibbs, Richard A.; Petrosino, Joseph

BACKGROUND: This study aims to identify the causative strain of SARS-CoV-2 in a cluster of vaccine breakthroughs. Vaccine breakthrough by a highly transmissible SARS-CoV-2 strain is a risk to global public health. METHODS: Nasopharyngeal swabs from suspected vaccine breakthrough cases were tested for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) by qPCR (quantitative polymerase chain reaction) for Wuhan-Hu1 and alpha variant. Positive samples were then sequenced by Swift Normalase Amplicon Panels to determine the causal variant. GATK (genome analysis toolkit) variants were filtered with allele fraction ≥80 and min read depth 30x. RESULTS: Viral sequencing revealed an infection cluster of 6 vaccinated patients infected with the delta (B.1.617.2) SARS-CoV-2 variant. With no history of vaccine breakthrough, this suggests the delta variant may possess immune evasion in patients that received the Pfizer BNT162b2, Moderna mRNA-1273, and Covaxin BBV152. CONCLUSIONS: Delta variant may pose the highest risk out of any currently circulating SARS-CoV-2 variants, with previously described increased transmissibility over alpha variant and now, possible vaccine breakthrough. FUNDING: Parts of this work was supported by the National Institute of Allergy and Infectious Diseases (1U19AI144297) and Baylor College of Medicine internal funding. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12916-021-02103-4.