A STUDY OF DETECTION AND GENOME SEQUENCING OF SARS-COV-2 FROM CLINICAL SAMPLES IN A TERTIARY CARE HOSPITAL

Main Article Content

Mohd Aadam Bin Najeeb
Dr. Madhurendra Singh
Dr. Narayan Kamath

Keywords

SARS-CoV-2, genomic surveillance, mutations, clinical outcomes, public health, vaccine

Abstract

Background: The continuous evolution of SARS-CoV-2 necessitates ongoing genomic surveillance to understand its transmission dynamics, mutation patterns, and impacts on public health measures and clinical outcomes.


Objectives: To analyse the distribution of SARS-CoV-2 variants and mutations within a tertiary care setting and assess their association with clinical outcomes to inform public health responses and treatment strategies.


Methods: This study conducted comprehensive genomic sequencing of SARS-CoV-2 from 400 clinical samples collected in a tertiary care hospital, employing RT-PCR for initial detection and Oxford-Nanopore Sequencing for whole-genome sequencing. Molecular analyses, including phylogenetic analysis and identification of unique genetic variants, were performed to elucidate the virus's evolution and transmission dynamics. Statistical analyses were conducted to explore the correlation between genomic variants and clinical outcomes, including disease severity and viral shedding.


Results: The study identified a high RT-PCR positivity rate (87.5%) with significant genomic diversity among the sequenced viruses. The Delta variant showed the highest mutation frequency in the Spike protein, suggesting increased transmissibility and potential vaccine escape. Unique genetic variants were identified in 28.1% of sequences, providing crucial insights into the virus's evolution. Statistical analysis revealed significant associations between specific genomic variants and clinical outcomes, particularly the increased risk of severe disease.


Conclusion: The findings highlight the complexity of SARS-CoV-2's evolution and its implications for disease transmission, diagnostic sensitivity, and vaccine efficacy. The study underscores the importance of genomic surveillance in detecting emergent mutations and informing targeted public health interventions and vaccine strategies. Continuous global collaboration and genomic analysis are essential to adapt to the evolving pandemic and mitigate the impact of COVID-19.


 

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References

1. Zhu N, Zhang D, Wang W, et al. A Novel Coronavirus from Patients with Pneumonia in China, 2019. N Engl J Med. 2020;382(8):727-733.
2. World Health Organization. WHO Coronavirus (COVID-19) Dashboard. [Internet]. 2023 [cited year month day]. Available from: https://covid19.who.int
3. Centers for Disease Control and Prevention. Genomic Surveillance for SARS-CoV-2. [Internet]. 2021 [cited year month day]. Available from: https://www.cdc.gov/coronavirus/2019- ncov/cases-updates/variant-surveillance.html
4. Davies NG, Abbott S, Barnard RC, et al. Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science. 2021;372(6538).
5. Smith E, Zumla A, McHugh TD. The Global Response to the COVID-19 Pandemic: How Have Immunology Societies Contributed? Lancet Immunol. 2020;21(8):1004- 1006.
6. Greaney AJ, Loes AN, Crawford KHD, et al. Comprehensive mapping of mutations in the SARS- CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies. Cell Host Microbe. 2021;29(3):463-476.e6.
7. Choi JY, Smith DM. SARS-CoV-2 Variants of Concern. Yonsei Med J. 2021 Nov;62(11):961- 968. doi: 10.3349/ymj.2021.62.11.961. PMID: 34672129; PMCID: PMC8542474.
8. El-Gilany AH. COVID-19 caseness: An epidemiologic perspective. J Infect Public Health. 2021 Jan;14(1):61-65. doi: 10.1016/j.jiph.2020.11.003. Epub 2020 Dec 9. PMID: 33352377; PMCID: PMC7832429.
9. Roque Mazoni S, Andrade J, da Silva Antonio P, Baraldi S, Frates Cauduro FL, Fernandes Dos

Santos PH, Ribeiro de Sousa P, Moura Pinho DL. Triage Strategies for COVID-19 Cases: A Scope Review. Inquiry. 2022 Jan-Dec;59:469580221095824. doi: 10.1177/00469580221 095824. PMID: 35549576; PMCID: PMC9109280.
10. Suthar AB, Schubert S, Garon J, Couture A, Brown AM, Charania S. Coronavirus Disease Case Definitions, Diagnostic Testing Criteria, and Surveillance in 25 Countries with Highest Reported Case Counts. Emerg Infect Dis. 2022 Jan;28(1):148-156. doi: 10.3201/eid2801.211082. PMID: 34932450; PMCID: PMC8714223.
11. Teymouri M, Mollazadeh S, Mortazavi H, Naderi Ghale-Noie Z, Keyvani V, Aghababaei F, Hamblin MR, Abbaszadeh-Goudarzi G, Pourghadamyari H, Hashemian SMR, Mirzaei H. Recent advances and challenges of RT-PCR tests for the diagnosisof COVID-19. Pathol Res Pract. 2021 May;221:153443. doi: 10.1016/j.prp.2021.153443. Epub 2021 Apr 14. PMID: 33930607; PMCID: PMC8045416.
12. Sule WF, Oluwayelu DO. Real-time RT-PCR for COVID-19 diagnosis: challenges and prospects. Pan Afr Med J. 2020 Jul 21;35(Suppl 2):121. doi: 10.11604/pamj.supp.2020.35.24 258. PMID: 33282076; PMCID: PMC7687508.
13. Liu T, Chen Z, Chen W, Chen X, Hosseini M, Yang Z, Li J, Ho D, Turay D, Gheorghe CP, Jones W, Wang C. A benchmarking study of SARS-CoV-2 whole-genome sequencing protocols using COVID-19 patient samples. iScience. 2021 Aug 20;24(8):102892. doi: 10.1016/j.isci.20 21.102892. Epub 2021 Jul 21. PMID: 34308277; PMCID: PMC8294598.
14. Kousathanas, A., Pairo-Castineira, E., Rawlik, K. et al. Whole-genome sequencing reveals host factors underlying critical COVID-19. Nature 607, 97–103 (2022). https://doi.org/10.1038/s41586-022-04576-6
15. Kunal S, Aditi, Gupta K, Ish P. COVID-19 variants in India: Potential role in second wave and impact on vaccination. Heart Lung. 2021 Nov-Dec;50(6):784-787. doi: 10.1016/j.hrtlng.2021. 05.008. Epub 2021 Jun 3. PMID: 34217989; PMCID: PMC8173455.
16. Aleem A, Akbar Samad AB, Vaqar S. Emerging Variants of SARS-CoV-2 and Novel Therapeutics Against Coronavirus (COVID-19). 2023 May 8. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2024 Jan–. PMID: 34033342.
17. Wruck W, Adjaye J. Detailed phylogenetic analysis tracks transmission of distinct SARS-COV- 2 variants from China and Europe to West Africa. Sci Rep. 2021 Oct 26;11(1):21108. doi: 10.1038/s41598-021-00267-w. PMID: 34702899; PMCID: PMC8548492.