Breakthrough Infections of E484K-Harboring SARS-CoV-2 Delta Variant, Lombardy, Italy

The Delta variant of concern of severe acute respiratory syndrome coronavirus 2 is dominant worldwide. We report a case cluster caused by Delta sublineage B.1.617.2 harboring the mutation E484K in Italy during July 11–July 29, 2021. This mutation appears to affect immune response and vaccine efficacy; monitoring its appearance is urgent.


RESEARCH LETTERS
The Delta variant of concern of severe acute respiratory syndrome coronavirus 2 is dominant worldwide. We report a case cluster caused by Delta sublineage B.1.617.2 harboring the mutation E484K in Italy during July 11-July 29, 2021. This mutation appears to affect immune response and vaccine efficacy; monitoring its appearance is urgent.
S ince the beginning of 2021, a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant originally described in India has become the predominant circulating variant of the coronavirus disease pandemic. This variant of concern (VOC) was renamed Delta by the World Health Organization and consists to date of 5 different sublineages (B.1.617.2, AY.1, AY.2, AY.3, and AY.3.1, according to PANGOLIN phylogeny) that share T478K and L452R as the main mutations of concern (MOCs) within the spike protein. B.1.617.2 (also known as VUI-21APR-02) is by far the most represented Delta sublineage. None of the 5 sublineages are to date characterized by the occurrence of the other MOC E484K, which causes resistance to monoclonal antibodies and reduced vaccine efficacy. However, given the widespread convergent evolution of the spike protein observed across clades, the occurrence of MOC E484K and its widespread circulation is largely expected. A clade simultaneously harboring all such MOCs is likely to be of extreme concern because of theoretical increased immune escape. We report a cluster of B.1.617.2 and E484K occurring in Lombardy, Italy. All cases were first tested by realtime reverse transcription PCR and, if positive, sequenced as previously reported (1).
On July 11, 2021, a 41-year-old man from a small village in northern Lombardy (vaccinated with BNT162b2 [Pfizer-BioNTech, https://www. pfizer.com] on June 12 and July 12) began experiencing cough, fever, and malaise; a nasopharyngeal swab specimen tested positive on July 14 by the SARS-CoV-2 Variants Elite MGB Kit (EliTech Group, https://www.elitechgroup.com); cycle threshold (C t ) was 21 for open reading frame (ORF) 1ab gene and 21 for the nucleocapsid (N) gene. He fully recovered without need for hospital admission; whole-genome sequencing confirmed B.1.617.2 that harbored E484K. His 80-year-old mother (vaccinated with mRNA-1273 [Moderna, https://www.modernatx.com] on April 9 and May 7) experienced fatigue, headache, myalgia, and dyspnea beginning July 17 and tested positive on July 24 (C t 22 for ORF1ab gene and C t 21 for N gene). She likely further infected (while playing cards) a 77-year-old man (vaccinated with BNT162b2 on April 26 and May 17) who began experiencing fever July 21 and tested positive on July 23 (C t 20 for ORF1ab gene and C t 19 for N gene) and an 83-year-old woman (vaccinated with BNT162b2 on April 3 and April 24) who experienced fever, fatigue, ageusia, and anosmia beginning July 21 and tested positive July 24 (C t 18 for both genes). None required hospital admission. An unrelated patient from the same village, an 81-year-old woman (vaccinated with mRNA-1273 on May 7 and June 9), experienced dyspnea, fever, myalgia, and fatigue beginning July 24. On July 29, she tested positive for SARS-CoV-2 RNA (C t 23 for ORF1ab gene and C t 21 for N gene), and she was admitted to the hospital. All sequences obtained in this study have been deposited into GISAID (https://www.gisaid.org; accession nos. EPI_ISL_3462078, EPI_ISL_3462074, EPI_ISL_3462072, EPI_ISL_346208).
E484K is the hallmark MOC of VOCs Beta and Gamma, in addition to having been reported in a minor sublineage of VOC Alpha, in variants of interest Eta and Iota, and at frequencies >50% in 38 more strains. E484K causes resistance to many class 2 RBDdirected antibodies (2), including bamlanivimab (3). The most potent mRNA vaccine-elicited monoclonal antibodies were >10-fold less effective against pseudotyped viruses carrying the E484K mutation (Z. Wang  E484K mutation represents a critical evolutionary event that leads to immune escape, although its consequences on viral fitness are unclear. Surveillance by genome sequencing should be maintained (T. Farinholt et al., unpub. data, https://www.medrxiv.org/ content/10.1101/2021.06.28.21258780v4).

About the Author
Dr. Baj is a medical research scientist at University of Insubria, Varese, Italy. Her research interests include persistent and emerging viral infections.