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. 2021 Oct 1;19(1):255.
doi: 10.1186/s12916-021-02103-4.

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

Timothy Farinholt  1 , Harsha Doddapaneni  2   3 , Xiang Qin  2   3 , Vipin Menon  2   3 , Qingchang Meng  2   3 , Ginger Metcalf  2   3 , Hsu Chao  2   3 , Marie-Claude Gingras  2   3 , Vasanthi Avadhanula  4 , Paige Farinholt  5 , Charu Agrawal  5 , Donna M Muzny  2   3 , Pedro A Piedra  4 , Richard A Gibbs  2   3 , Joseph Petrosino  4
Affiliations

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

Timothy Farinholt et al. BMC Med. .

Abstract

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.

Keywords: B.1.617.2; COVID-19; Delta variant; Infectious disease; SARS-CoV-2.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Timeline of events and spike protein mutation prevalence in SARS-CoV-2 variant lineages. a Timeline of events denoting positive tests and symptom onset for each patient (if known). b Only mutations found in greater than 50% in at least one lineage are displayed. Green text denotes a mutation found in all patients in this report and underlined mutations denote delta variant lineage defining mutations. Figure modified from Outbreak.info [7]
Fig. 2
Fig. 2
Phylogenetic analysis of SARS-CoV-2 variants. All patients (white box) cluster in a subclade of the delta variant (red). Sequences obtained from GISAID
See this image and copyright information in PMC

Update of

References

    1. New York City COVID-19 Cases Caused by SARS-CoV-2 Variants Report (3.23 .2021). https://www1.nyc.gov/assets/doh/downloads/pdf/covid/covid-19-data-varian....
    1. Ogawa J, Zhu W, Tonnu N, Singer O, Hunter T, Ryan AL, et al. The D614G mutation in the SARS-CoV2 Spike protein increases infectivity in an ACE2 receptor dependent manner. BioRxiv. 2020;90033. 10.1101/2020.07.21.214932.
    1. Hatmal MM, Alshaer W, Al-Hatamleh MAI, Hatmal M, Smadi O, Taha MO, et al. Comprehensive structural and molecular comparison of spike proteins of SARS-CoV-2, SARS-CoV and MERS-CoV, and their interactions with ACE2. Cells. 2020;9. 10.3390/cells9122638. - PMC - PubMed
    1. Harvey WT, Carabelli AM, Jackson B, Gupta RK, Thomson EC, Harrison EM, Ludden C, Reeve R, Rambaut A, COVID-19 Genomics UK (COG-UK) Consortium. Peacock SJ, Robertson DL. SARS-CoV-2 variants, spike mutations and immune escape. Nat Rev Microbiol. 2021;614(7):409–424. doi: 10.1038/s41579-021-00573-0. - DOI - PMC - PubMed
    1. Walls AC, Park YJ, Tortorici MA, Wall A, McGuire AT, Veesler D. Structure, Function, and antigenicity of the SARS-CoV-2 Spike glycoprotein. Cell. 2020;181:281–292.e6. doi: 10.1016/j.cell.2020.02.058. - DOI - PMC - PubMed

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