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CSIR- Institute of Genomics and Integrative Biology, Sukhdev Vihar Mathura Road, New Delhi 110025, IndiaAcademy for Scientific and Innovative Research, Human Resource Development Centre, Campus, Ghaziabad, Uttar Pradesh 201002, India
CSIR- Institute of Genomics and Integrative Biology, Sukhdev Vihar Mathura Road, New Delhi 110025, IndiaAcademy for Scientific and Innovative Research, Human Resource Development Centre, Campus, Ghaziabad, Uttar Pradesh 201002, India
CSIR- Institute of Genomics and Integrative Biology, Sukhdev Vihar Mathura Road, New Delhi 110025, IndiaAcademy for Scientific and Innovative Research, Human Resource Development Centre, Campus, Ghaziabad, Uttar Pradesh 201002, India
CSIR- Institute of Genomics and Integrative Biology, Sukhdev Vihar Mathura Road, New Delhi 110025, IndiaAcademy for Scientific and Innovative Research, Human Resource Development Centre, Campus, Ghaziabad, Uttar Pradesh 201002, India
CSIR- Institute of Genomics and Integrative Biology, Sukhdev Vihar Mathura Road, New Delhi 110025, IndiaAcademy for Scientific and Innovative Research, Human Resource Development Centre, Campus, Ghaziabad, Uttar Pradesh 201002, India
CSIR- Institute of Genomics and Integrative Biology, Sukhdev Vihar Mathura Road, New Delhi 110025, IndiaAcademy for Scientific and Innovative Research, Human Resource Development Centre, Campus, Ghaziabad, Uttar Pradesh 201002, India
CSIR- Institute of Genomics and Integrative Biology, Sukhdev Vihar Mathura Road, New Delhi 110025, IndiaAcademy for Scientific and Innovative Research, Human Resource Development Centre, Campus, Ghaziabad, Uttar Pradesh 201002, India
Corresponding authors at: Knowledge Centre for Genome Informatics, CSIR- Institute of Genomics and Integrative Biology, Sukhdev Vihar Mathura Road, New Delhi 110025, India.
CSIR- Institute of Genomics and Integrative Biology, Sukhdev Vihar Mathura Road, New Delhi 110025, IndiaAcademy for Scientific and Innovative Research, Human Resource Development Centre, Campus, Ghaziabad, Uttar Pradesh 201002, India
SARS-CoV-2 infections and COVID-19 vaccines have been suggested to elicit immune response and reduce the predisposition to infections as well as severe disease. Reinfections
though rare, are now independently documented, but there is a paucity of literature on reinfections in fully vaccinated individuals. Here we describe a 28 year old male healthcare worker who was re-infected after being previously infected with SARS-CoV-2 and after completing the full course of Covishield/ChAdOx1 vaccine.
Safety and efficacy of the ChAdOx1 nCoV-19 vaccine (AZD1222) against SARS-CoV-2: an interim analysis of four randomised controlled trials in Brazil, South Africa, and the UK.
The patient initially tested positive for SARS-CoV-2 on routine surveillance (TaqPath COVID-19 Combo kit by Thermofisher) with cycle threshold (CT) values of 22. Subsequently, he developed fever for 2 days, breathlessness which lasted for seven days along with cough, bodyache and sore throat for ten days. On the seventh day of illness the patient suffered a brief drop in the oxygen saturation (SpO2) to 94% which recovered spontaneously on the next day. High-resolution Computed Tomography (HR-CT) revealed no abnormality and the patient tested negative for SARS-CoV-2 on reverse transcription-PCR (RT-PCR). Antibody titres two weeks aftertesting negative on RT-PCR, revealed a moderate level of antibodies (Elecsys Anti SARS-CoV-2, Roche Diagnostics) to spike protein (12). The patient then proceeded to take the first dose of Covishield/ChAdOx1 vaccine and subsequently the second dose four weeks later. He suffered mild post-vaccine effects including body aches and injection site pain lasting two days after both doses. A month after receiving the second dose, the patient again developed fever and tested positive on RT-PCR (CT of 13) for SARS-CoV-2.
In the second episode of the infection, the patient had fever for four days, and cough, bodyache, headache, sore throat, loss of smell and taste for twelve days. The SpO2 level was around 94,95%, and the patient had mild difficulty in breathing throughout the symptomatic period. His HR-CT was normal and he had no evidence of primary or secondary immunodeficiencies. The clinical course and timelines are summarised in Fig. 1A and the clinical parameters are summarised in Table 1.
Fig. 1(A) Summary of timelines and the clinical course for the patient. (B) Phylogenetic context of the genome isolate with other genomes sampled from the state of Maharashtra. (C) Genomic context of the mutations found in the genome isolate.
SARS-CoV-2 RNA isolated from the nasopharyngeal specimen of the patient during the post-vaccination episode of infection was taken up for genome sequencing following an amplicon-based COVIDSeq assay (Illumina Inc,) as per the previously described protocol.
The sequencing was performed on the Novaseq6000 platform (Illumina Inc.) to generate 100 × 2 base paired end reads. After quality checks, trimmed reads were aligned against the human reference genome (GRCh38). The unmapped reads were extracted and aligned to the SARS-CoV-2 reference genome NC_045512. Mutations were filtered at a minimum coverage depth of 5 reads and a minimum frequency of 50%. Bases with quality lower than 20 were masked from the consensus sequence. Lineage assignment for the sequence was done using Pangolin (v3.1.11, pangoLEARN version 2021–08–09).
Genome sequence for the viral isolate was assembled at a mean depth of coverage of 30460X, with genome coverage of 99.9%. Genomic analysis suggests the infection was caused by a virus belonging to the lineage B.1.617.2 (Delta) of SARS-CoV-2 (Fig. 1B). The sequence had a total of 30 distinct genetic mutations, 8 of which were in the Spike protein of the virus (Fig. 1C).
While a number of cases of reinfections and vaccine breakthrough infections have been reported, including in healthcare workers, infections following a previous infection and complete course of SARS-CoV-2 vaccines have previously not been documented. We also highlight that variants of concern, especially B.1.617.2 (Delta), have been previously suggested to escape immunity due to previous infections as well as vaccination.
SARS-CoV-2 infection rates of antibody-positive compared with antibody-negative health-care workers in England: a large, multicentre, prospective cohort study (SIREN).
To the best of our knowledge this is the first report on a combination of both reinfection as well as vaccine breakthrough infection in an individual. This report therefore highlights the need for close follow-up of rare and unusual cases of vaccine breakthroughs as well as reinfections especially in high-risk frontline workers.
Ethics
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).
Funding
Authors acknowledge funding from CSIR India through grant MLP005. Authors BJ AND MKD acknowledges research fellowships from CSIR India. VG and SJA acknowledge research fellowships from University Grants Commission (UGC), India.
Declaration of Competing Interest
Authors declare no conflicts of interest. The funders had no role in the preparation of the manuscript or decision to publish.
References
Philomina J B.
Jolly B.
John N.
Bhoyar R.C.
Majeed N.
Senthivel V.
et al.
Genomic survey of SARS-CoV-2 vaccine breakthrough infections in healthcare workers from Kerala, India.
Safety and efficacy of the ChAdOx1 nCoV-19 vaccine (AZD1222) against SARS-CoV-2: an interim analysis of four randomised controlled trials in Brazil, South Africa, and the UK.
SARS-CoV-2 infection rates of antibody-positive compared with antibody-negative health-care workers in England: a large, multicentre, prospective cohort study (SIREN).
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