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The dynamics of SARS-CoV-2 infection in unvaccinated and vaccinated populations in Mumbai, India, between 28 December 2020 and 30 August 2021

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Abstract

The emergence and evolution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants that could compromise vaccine efficacy (VE) with re-infections in immunized individuals have necessitated continuous surveillance of VE. Here, the occurrence and dynamics of SARS-CoV-2 infections in the context of vaccination during the second wave of infection in Mumbai were evaluated. RT-PCR cycle threshold (Ct) values of the open reading frame (ORF)/envelope (E)/nucleocapsid (N) genes obtained from a total of 42415 samples, comprising unvaccinated (96.88%) and vaccinated cases (3.12%) were analyzed between December 28, 2020, and August 30, 2021. A lower incidence of SARS-CoV-2 infection in fully vaccinated cases (5.07%) compared to partially vaccinated cases (6.5%) and unvaccinated cases (13.453%) was recorded. VE was significant after the first dose of vaccination (ORF gene p-value = 0.003429, and E/N gene p-value = 0.000866). Furthermore, VE was observed to be significant when the post-immunization (first dose) period was stratified to within 30 days (ORF gene p-value = 0.0094 and E/N gene p-value = 0.0023) and to 60 days following the second dose of vaccination (ORF gene p-value = 0.0238). Also, significantly higher efficacy was observed within individuals receiving two doses compared to a single dose (ORF gene p-value = 0.0132 and E/N gene p-value = 0.0387). The emergence of breakthrough infections was also evident (odds ratio= 0.34; 95% confidence interval= 0.27–0.43). Interestingly, viral loads trended towards being higher in some groups of partially vaccinated individuals compared to completely vaccinated and unvaccinated populations. Finally, our results delineated a significantly higher incidence of SARS-CoV-2 acquisition in males, asymptomatic individuals, individuals with comorbidities, and those who were unvaccinated.

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Acknowledgment

This research article has been reviewed and edited to improve clarity and address language usage issues by Dr. Vainav Patel, a co-author of this manuscript (VP) and a native speaker of the English language.

We acknowledge the encouragement and support from the Indian Council of Medical Research (ICMR), the Ministry for Health & Family Welfare, the Government of India, and all the NIRRCH COVID-19 testing and reporting team, Mumbai, India.

Funding

No funding was received.

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Authors and Affiliations

  1. Genetic Research Centre, ICMR-National Institute for Research in Reproductive and Child Health, Jehangir Merwanji Street, Parel, Mumbai, 400012, India

    Venkanna Bhanothu & Shailesh Pande

  2. Department of Clinical Research, ICMR-National Institute for Research in Reproductive and Child Health, Jehangir Merwanji Street, Parel, Mumbai, 400012, India

    Kiran Munne & Shilpa Kerkar

  3. Viral Immunopathogenesis Laboratory, ICMR-National Institute for Research in Reproductive and Child Health, Jehangir Merwanji Street, Parel, Mumbai, 400012, India

    Priyanka Singh, Dimpu Gogoi, Sharad Bhagat & Vainav Patel

  4. Cellular & Structural Biology Division, ICMR-National Institute for Research in Reproductive and Child Health, Jehangir Merwanji Street, Parel, Mumbai, 400012, India

    Dhanashree Jagtap

  5. Molecular Immunology and Microbiology, ICMR-National Institute for Research in Reproductive and Child Health, Jehangir Merwanji Street, Parel, Mumbai, 400012, India

    Clara Aranha, Karan Shah & Vikrant Bhor

  6. Department of Neuroendocrinology, ICMR-National Institute for Research in Reproductive and Child Health, Jehangir Merwanji Street, Parel, Mumbai, 400012, India

    Reshma Gaonkar

  7. Department of Molecular and Cellular Biology, ICMR-National Institute for Research in Reproductive and Child Health, Jehangir Merwanji Street, Parel, Mumbai, 400012, India

    Nupur Mukherjee

  8. ICMR-National Institute for Research in Reproductive and Child Health, Jehangir Merwanji Street, Parel, Mumbai, 400012, India

    Smita D Mahale & Geetanjali Sachdeva

  9. Department of Biostatistics, ICMR-National Institute for Research in Reproductive and Child Health, Jehangir Merwanji Street, Parel, Mumbai, 400012, India

    Shahina Begum

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  1. Venkanna Bhanothu
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Corresponding authors

Correspondence to Venkanna Bhanothu or Shailesh Pande.

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Ethical approval

The study was approved by the Institutional Ethics Committee of ICMR-NIRRCH (Letter No# D/ICEC/Sci-199/214/2021).

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Communicated by Pablo Pineyro

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Supplementary Fig. S1:

(a) RT-PCR outcomes of COVID-19 suspected cases with an increase in the interval between partial vaccination and the RT-PCR test. The RT-PCR outcomes of COVID-19 suspected cases were represented as a percentage (%). (b) RT-PCR outcomes of COVID-19 suspected cases with an increase in the duration between complete vaccination and the RT-PCR test. The RT-PCR outcomes of COVID-19 suspected cases were represented as a percentage (%).

Supplementary Fig. S2:

(a) Dynamics of age (in years) in COVID-19 suspected cases with an increase in the duration between partial vaccination and the RT-PCR test. The data were represented as mean ± SD in years. (b) Dynamics of age (in years) in COVID-19 suspected cases with an increase in the duration between complete vaccination and the RT-PCR test. The data were represented as mean ± SD in years

Supplementary Fig. S3

: (a) Dynamics of Ct values of SARS-CoV-2 genes (ORF1a/b/N2 gene and E/N gene) with an increase in the duration between partial vaccination and the RT-PCR test. The data were represented as mean ± SD. (b) Dynamics of Ct values of SARS-CoV-2 genes (ORF1a/b/N2 gene and E/N gene) with an increase in the duration between full vaccination and the RT-PCR test. The data were represented as mean ± SD

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Bhanothu, V., Munne, K., Pande, S. et al. The dynamics of SARS-CoV-2 infection in unvaccinated and vaccinated populations in Mumbai, India, between 28 December 2020 and 30 August 2021. Arch Virol 168, 188 (2023). https://doi.org/10.1007/s00705-023-05815-5

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