Genomic survey of SARS-CoV-2 vaccine breakthrough infections in healthcare workers from Kerala, India.

To the editor,

Tré-Hardy et al. in this journal recently discussed the immunogenicity of mRNA-1273 in healthcare workers. Vaccines based on different strategies are being deployed across the globe to curb the recurring waves of COVID-19. Of these, inactivated SARS-CoV-2 virus-based BBV152/COVAXIN and adenoviral vector-based AZD1222/Covishield (ChAdOx1 nCoV-19) are widely used in India. , Breakthrough infections in fully vaccinated individuals have been documented in many countries including India. The emergence of SARS-CoV-2 variants threatens the continued efficacy of these vaccines with increasing reports on reduced efficacy against different SARS-CoV-2 variants of concern (VoC).

We surmise that genomic surveillance is useful to understand and monitor evolving SARS-CoV-2 variants. In this study, we describe the genomic characterization of vaccine breakthrough infections following vaccination in 6 healthcare workers (P1–P6) from Kerala, India. All 6 patients were fully vaccinated with two standard doses of the AZD1222/Covishield vaccine.

P1, a 25-year-old female, was administered the first and second dose of vaccine on January 21, and February 19, 2021, respectively. P1 was found to be positive for SARS-CoV-2 antigen on March 23 with influenza-like illness (ILI) symptoms and tested RT-PCR positive for COVID-19 on March 25.

P2, a 50-year-old male, received the two doses on January 27 and February 24 respectively. He developed fever, malaise, anosmia and headache on March 31 and tested RT-PCR positive on April 2. P2 was found to be SARS-CoV-2 IgG positive (12.94) and SARS-CoV-2 IgM negative on March 31.

P3, a 53-year-old female, received the two doses on January 29 and February 26 respectively. She developed rhinitis on March 23 and tested RT-PCR positive on March 27.

P4, a 25-year-old female, received the two doses on February 5 and 10 March respectively. She developed fever, loose stools, abdominal pain, dry cough, myalgia, rhinitis and anosmia on March 27 and tested RT-PCR positive on April 3.

P5, a 32-year-old male, received the two doses on January 28 and March 12 respectively. He tested RT-PCR positive on April 6 and developed mild nasal congestion and headache. P5 tested antigen negative after 10 days.

P6, a 33-year-old female, received the two doses on January 25 and February 22 respectively. She developed loss of smell, loose stools and rhinitis and tested RT-PCR positive on March 12. P6 tested antigen negative after 5 days. Neutralizing antibody titres for P6 were above 320 (S/Co value −14.9) on March 16.

The prognosis of the breakthrough infections in all cases shows the effective protection of the vaccine in preventing severe COVID-19. Fig. 1 A summarizes the history and timeline of infection for the 6 patients.

Fig. 1

(A) History and timelines of infection for the 6 patients and intervals between the second dose of vaccine and date of RT-PCR testing (B) Presence of variants in the genome isolates of the 6 cases (P1–P6). (C) Phylogenetic context of the 6 genome isolates with 2630 additional SARS-CoV-2 genomes from the state of Kerala.

RNA extracted from nasopharyngeal swab samples were collected as part of routine COVID-19 testing after informed consent as per the institutional ethical committee guidelines (IHEC—CSIR-IGIB/IHEC/2020–21/01) for individuals who tested positive following two doses of the AZD1222 vaccine. Antigen assay (Standard Q Covid-19 Ag Kit, SD Biosensor) was carried out in five out of six patients (Supplementary Table 1). Genomes were sequenced on NovaSeq 6000 platform following the COVIDSeq protocol with read length of 100 ´ 2 base pairs. Sequences were assembled using the NC_045512.2 reference genome. Variants were called using VarScan. Phylogenetic clustering for the isolates was done using Nextstrain with additional SARS-CoV-2 genomes isolated from Kerala. Lineages were assigned using pangolin (v2.3.9).

Genomes for the 6 isolates were assembled at a mean genome coverage of 7476.27X. 4 samples (P2-P5) had the spike variant N501Y, while P1 and P6 had spike variants E484K and S477N respectively. N501Y, E484K and S477N are key mutations in the receptor-binding domain of spike protein with substantial evidence reported in the context of immune evasion.8, 9, 10

Genomic variants present in all 6 isolates are summarized in Fig. 1B.

Isolates P1 and P6 belonged to PANGO lineage B.1.1.306 and B.1.1 respectively. P2-P5 belonged to the lineage B.1.1.7 (VOC 202012/01), defined by 6 key spike variants including N501Y. Phylogenetic context of P1–P6 with 2630 genome sequences from Kerala is summarised in Fig. 1C. P1–P5 clustered closely with other genomes from their respective lineages. Isolate P6 clustered near genomes belonging to the lineage B.1.560 which was the most prevalent lineage (N = 1130) in additional genomes included in the analysis.

All 6 patients in the study were vaccinated at an interdose interval range of 4–6 weeks and COVID-19 symptoms were observed in all at least 15 days post second dose. Considering the efficacy of AZD1222 against symptomatic COVID-19 following two standard doses is 63%, a small percentage of fully-vaccinated people may still get infected, however, it is important to note that none of the 6 patients presented with severe illness or required hospitalization. Characterization of clinically important SARS-CoV-2 variants in vaccinated individuals confers possible exploration of selection of viral escape mutants following immunization. Genome sequencing revealed that 4 patients in this study were infected by the B.1.1.7 variant of SARS-CoV-2. N501Y, a key mutation in the B.1.1.7 lineage has been reported to escape neutralization by some monoclonal antibodies (mAbs), and a small decrease in neutralization activity in patients vaccinated with Moderna (mRNA-1273) or Pfizer–BioNTech (BNT162b2). B.1.1.7 has also been shown to lower neutralising antibody titres against AZD1222 as compared to non-B.1.1.7 variants. Both E484K and S477N, found in P1 and P6 respectively, are reported to escape neutralization by a range of mAbs. E484K is also associated with a decrease in neutralizing activity of convalescent and post-vaccination (BNT162b2) sera.8, 9, 10 While it remains unclear if these breakthrough infections are related to vaccine efficacy, immune evasion, or other factors, the study highlights the importance of continued genomic surveillance for tracking emergent SARS-CoV-2 variants.

Declaration of Competing Interest

The authors report no potential conflicts of interest.