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Whole Genome Sequencing Confirmed SARS-CoV-2 Reinfections Among Healthcare Workers in India with Increased Severity in the Second Episode

30 Pages Posted: 21 Sep 2020

See all articles by Jayanthi Shastri

Jayanthi Shastri

Kasturba Hospital for Infectious Disease

Swapneil Parikh

Kasturba Hospital for Infectious Disease

Sachee Agarwal

Kasturba Hospital for Infectious Disease

Nirjhar Chatterjee

Kasturba Hospital for Infectious Disease

Manish Pathak

Kasturba Hospital for Infectious Disease

Chetan Sharma

International Centre for Genetic Engineering and Biotechnology

Akshay Kanakan

CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB)

Vivekanand A

CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB)

Janani Srinivasa Vasudevan

CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB)

Ranjeet Maurya

CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB)

Saman Fatihi

CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB)

Lipi Thukral

CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB)

Anurag Agrawal

CSIR-HRDC - Centre of Excellence for Translational Research in Asthma and Lung Diseases; CSIR-HRDC - Academy of Scientific & Innovative Research (AcSIR)

Lancelot Pinto

P. D. Hinduja Hospital; P. D. Hinduja Hospital

Rajesh Pandey

CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB)

Sujatha Sunil

International Centre For Genetic Engineering And Biotechnology (ICGEB), India

More...

Abstract

Background: Frontline healthcare workers (HCWs) are exceedingly exposed to SARS-CoV-2 and reinfections are a possibility. A RT-PCR positive test does not confirm reinfection. Whole genome sequencing (WGS) of the viral isolates from the different episodes can confirm a reinfection.

Methods: RNA was extracted from nasopharyngeal plus oropharyngeal samples from four HCWs who were SARS-CoV-2 RT-PCR positive in May/June and then again in July. Anti-NC antibody testing was performed after the second infection in three HCWs. The RNA was subjected to whole genome sequencing and comparative genome and protein-based functional annotation analyses were performed on the nucleotide and amino acid sequences.

Findings: Whole genome sequencing of the eight SARS-CoV-2 viral samples generated a genome coverage ranging from 82.55 to 98.23%. Phylogenetic analysis revealed that sequences belonged to the L clade and within this major clade; they clustered into India-specific A2a and A4 clades. A total of 39 mutations were identified within the eight genomes, including 22 non-synonymous, 16 synonymous, and 1 stop-coding substitutions. Comparative genomic and protein-based annotation analyses revealed differences in the presence and absence of specific mutations in the virus sequences from the first and second episode in all four paired samples. Three HCWs were negative for anti-NC antibodies after the second infection.

Interpretation: Genomic variations observed through whole genome sequencing coupled with clinical presentation confirm reinfections of SARS-CoV-2 in healthcare workers.

Funding: Municipal Corporation of Greater Mumbai, ICGEB core funding, MLP-2005 and Fondation Botnar grants.

Declaration of Interests: The authors declare no competing interests.

Ethics Approval Statement: The study was approved by the Institutional Review Board of Kasturba Hospital of Infectious Diseases; IRB number 015/2020. The patients provided written informed consent.

Keywords: SARS-CoV-2, COVID-19, Reinfections, Whole Genome Sequencing, Healthcare workers

Suggested Citation

Shastri, Jayanthi and Parikh, Swapneil and Agarwal, Sachee and Chatterjee, Nirjhar and Pathak, Manish and Sharma, Chetan and Kanakan, Akshay and A, Vivekanand and Srinivasa Vasudevan, Janani and Maurya, Ranjeet and Fatihi, Saman and Thukral, Lipi and Agrawal, Anurag and Pinto, Lancelot and Pandey, Rajesh and Sunil, Sujatha, Whole Genome Sequencing Confirmed SARS-CoV-2 Reinfections Among Healthcare Workers in India with Increased Severity in the Second Episode. Available at SSRN: https://ssrn.com/abstract=3688220 or http://dx.doi.org/10.2139/ssrn.3688220

Jayanthi Shastri (Contact Author)

Kasturba Hospital for Infectious Disease ( email )

Mumbai
India

Swapneil Parikh

Kasturba Hospital for Infectious Disease ( email )

Mumbai
India

Sachee Agarwal

Kasturba Hospital for Infectious Disease ( email )

Nirjhar Chatterjee

Kasturba Hospital for Infectious Disease ( email )

Manish Pathak

Kasturba Hospital for Infectious Disease

Chetan Sharma

International Centre for Genetic Engineering and Biotechnology

Akshay Kanakan

CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB) ( email )

Vivekanand A

CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB) ( email )

Janani Srinivasa Vasudevan

CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB) ( email )

Ranjeet Maurya

CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB) ( email )

Saman Fatihi

CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB) ( email )

Lipi Thukral

CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB) ( email )

Anurag Agrawal

CSIR-HRDC - Centre of Excellence for Translational Research in Asthma and Lung Diseases ( email )

New Delhi
India

CSIR-HRDC - Academy of Scientific & Innovative Research (AcSIR) ( email )

CSIR- Human Resource Development Centre, (CSIR-HRD
Ghaziabad, Uttar Pradesh
India

Lancelot Pinto

P. D. Hinduja Hospital ( email )

P. D. Hinduja Hospital ( email )

Rajesh Pandey

CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB)

Sujatha Sunil

International Centre For Genetic Engineering And Biotechnology (ICGEB), India ( email )

New Delhi, 110020
India

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