Journal of The Academy of Clinical Microbiologists

Register      Login

SEARCH WITHIN CONTENT

FIND ARTICLE

Volume / Issue

Online First

Archive
Volume  26 (2024)
Volume  25 (2023)
Volume  24 (2022)
Volume  23 (2021)
Volume  22 (2020)
Volume  21 (2019)
Volume  20 (2018)
Volume  19 (2017)
Volume  18 (2016)
Volume  17 (2015)
Volume  16 (2014)
Volume  15 (2013)
Related articles

VOLUME 24 , ISSUE S1 ( December, 2022 ) > List of Articles

REVIEW ARTICLE

Role of next-generation sequencing in diagnosing, tracking and vaccine development of severe acute respiratory syndrome coronavirus 2

Nagamani Kammili, Amrithesh Kumar Arun, Winnie Thomas, Bhanuja Rani

Keywords : Coronavirus disease-2019 pandemic, next-generation sequencing, Variants of Concern, Variants of Interest

Citation Information : Kammili N, Arun AK, Thomas W, Rani B. Role of next-generation sequencing in diagnosing, tracking and vaccine development of severe acute respiratory syndrome coronavirus 2. 2022; 24 (S1):25-31.

DOI: 10.4103/jacm.jacm_18_22

License: CC BY-NC 4.0

Published Online: 11-11-2022

Copyright Statement:  Copyright © 2022; Wolters Kluwer India Pvt. Ltd.


Abstract

An objective method of detecting infections without the requirement for clinical hypotheses is provided using next-generation sequencing (NGS) technology for the diagnosis of infectious disorders. In order to inform nations and the general public about any potential changes that may be required to respond to the variant and stop its spread, the World Health Organization and its international networks of experts have been continuously monitoring changes to the virus based on NGS data throughout the current pandemic. When tracking ongoing outbreaks, monitoring for novel pathogens or spotting potentially harmful variations of well-known diseases, NGS offers substantial advantages. Due to the technology's quick creation of high-resolution sequence data, researchers and research teams can access it easily and share it with one another. Numerous candidate vaccines have been created on several platforms quickly. Many of them have worked in crisis circumstances in numerous nations worldwide. The breakthrough infections could only be tracked by the use of NGS technology. In this review, we discussed in silico analysis using current bioinformatics approaches, and sequencing reveals unique emerging severe acute respiratory syndrome coronavirus 2 variations which have the potential to cause novel illnesses in the future.

PDF Share
  1. Alteri C, Cento V, Piralla A, Costabile V, Tallarita M, Colagrossi L, et al. Genomic epidemiology of SARS-CoV-2 reveals multiple lineages and early spread of SARS-CoV-2 infections in Lombardy, Italy. Nat Commun 2021;12:434.
  2. Shen L, Niu J, Wang C, Huang B, Wang W, Zhu N, et al. High-Throughput screening and identification of potent broad-spectrum inhibitors of coronaviruses. J Virol 2019;93:e00023-19.
  3. Chiara M, D'Erchia AM, Gissi C, Manzari C, Parisi A, Resta N, et al. Next generation sequencing of SARS-CoV-2 genomes: Challenges, applications and opportunities. Brief Bioinform 2021;22:616-30.
  4. de Mello Malta F, Amgarten D, Val FC, Cervato MC, de Azevedo BM, de Souza Basqueira M, et al. Mass molecular testing for COVID19 using NGS-based technology and a highly scalable workflow. Sci Rep 2021;11:7122.
  5. Dilliott AA, Farhan SMK, Ghani M, Sato C, Liang E, Zhang M, et al. Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease. J Vis Exp 2018;(134):57266. doi: 10.3791/57266.
  6. Forbes JD, Knox NC, Ronholm J, Pagotto F, Reimer A. Metagenomics: The next culture-independent game changer. Front Microbiol 2017;8:1069.
  7. Freed NE, Vlková M, Faisal MB, Silander OK. Rapid and inexpensive whole-genome sequencing of SARS-CoV-2 using 1200 bp tiled amplicons and Oxford Nanopore Rapid Barcoding. Biol Methods Protoc 2020;5:bpaa014.
  8. Knighton AJ, Ranade-Kharkar P, Brunisholz KD, Wolfe D, Allen L, Belnap TW, et al. Rapid implementation of a complex, multimodal technology response to COVID-19 at an integrated community-based health care system. Appl Clin Inform 2020;11:825-38.
  9. La Rosa G, Brandtner D, Mancini P, Veneri C, Bonanno Ferraro G, Bonadonna L, Lucentini L, Suffredini E. Key SARS-CoV-2 Mutations of Alpha, Gamma, and Eta Variants Detected in Urban Wastewaters in Italy by Long-Read Amplicon Sequencing Based on Nanopore Technology. Water 2021;13:2503. https://doi.org/10.3390/w13182503.
  10. Li N, Cai Q, Miao Q, Song Z, Fang Y, Hu B. High-Throughput metagenomics for identification of pathogens in the clinical settings. Small Methods 2021;5:2000792.
  11. Lu R, Zhao X, Li J, Niu P, Yang B, Wu H, et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: Implications for virus origins and receptor binding. Lancet 2020;395:565-74.
  12. Luciani F, Bull RA, Lloyd AR. Next generation deep sequencing and vaccine design: Today and tomorrow. Trends Biotechnol 2012;30:443-52.
  13. Jin Y, Yang H, Ji W, Wu W, Chen S, Zhang W, et al. Virology, epidemiology, pathogenesis, and control of COVID-19. Viruses 2020;12:E372.
  14. World Health Organization. Regional Office for the Western Pacific. Inaugural Meeting of the Western Pacific Region Emerging Molecular Pathogen Characterization Technologies (EMPaCT) Surveillance Network, Virtual meeting, 21-22 September 2021: meeting report. WHO Regional Office for the Western Pacific 2021. https://apps.who.int/iris/handle/10665/352822.
  15. Pandey, Anuj & Mishra, Sidharth & Wadgave, Yogesh & Mudgil, Nidhi & Gawande, Sonal & Dhange, Vijay. The COVID-19 variants: an overview. International Journal Of Community Medicine And Public Health 2021;8:5148. 10.18203/2394-6040.ijcmph20213826.
  16. Pattabiraman C, Prasad P, George AK, Sreenivas D, Rasheed R, Reddy NV, et al. Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian state of Karnataka. Wellcome Open Res 2021;6:110.
  17. Safiabadi Tali SH, LeBlanc JJ, Sadiq Z, Oyewunmi OD, Camargo C, Nikpour B, et al. Tools and techniques for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)/COVID-19 Detection. Clin Microbiol Rev 2021;34:e00228-20.
  18. Hurwitz AM, Huang W, Estes MK, Atmar RL, Palzkill T. Deep sequencing of phage-displayed peptide libraries reveals sequence motif that detects norovirus. Protein Eng Des Sel 2017;30:129-39.
  19. Yan Y, Wu K, Chen J, Liu H, Huang Y, Zhang Y, et al. Rapid acquisition of high-quality SARS-CoV-2 genome via amplicon-oxford nanopore sequencing. Virol Sin 2021;36:901-12.
  20. Zumla A, Al-Tawfiq JA, Enne VI, Kidd M, Drosten C, Breuer J, et al. Rapid point of care diagnostic tests for viral and bacterial respiratory tract infections – Needs, advances, and future prospects. Lancet Infect Dis 2014;14:1123-35.
  21. Li X, Song Y, Wong G, Cui J. Bat origin of a new human coronavirus: There and back again. Sci China Life Sci 2020;63:461-2.
  22. Dallavilla T, Bertelli M, Morresi A, Bushati V, Stuppia L, Beccari T, et al. Bioinformatic analysis indicates that SARS-CoV-2 is unrelated to known artificial coronaviruses. Eur Rev Med Pharmacol Sci 2020;24:4558-64.
  23. Decaro N, Lorusso A. Novel human coronavirus (SARS-CoV-2): A lesson from animal coronaviruses. Vet Microbiol 2020;244:108693.
  24. Wang R, Hozumi Y, Yin C, Wei GW. Decoding SARS-CoV-2 transmission and evolution and ramifications for COVID-19 diagnosis, vaccine, and medicine. Journal of chemical information and modeling 2020;60:5853-65.
  25. Li X, Wang L, Yan S, Yang F, Xiang L, Zhu J, et al. Clinical characteristics of 25 death cases with COVID-19: A retrospective review of medical records in a single medical center, Wuhan, China. Int J Infect Dis 2020;94:128-32.
  26. Pasik K, Domańska-Blicharz K. High-throughput sequencing in vaccine research. J Vet Res 2021;65:131-7.
  27. Ley TJ, Mardis ER, Ding L, Fulton B, McLellan MD, Chen K, et al. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature 2008;456:66-72.
  28. Margeridon-Thermet S, Shulman NS, Ahmed A, Shahriar R, Liu T, Wang C, et al. Ultra-deep pyrosequencing of hepatitis B virus quasispecies from nucleoside and nucleotide reverse-transcriptase inhibitor (NRTI)-treated patients and NRTI-naive patients. J Infect Dis 2009;199:1275-85.
  29. Ozsolak F, Milos PM. RNA sequencing: Advances, challenges and opportunities. Nat Rev Genet 2011;12:87-98.
  30. Birzele F, Fauti T, Stahl H, Lenter MC, Simon E, Knebel D, et al. Next-generation insights into regulatory T cells: Expression profiling and FoxP3 occupancy in Human. Nucleic Acids Res 2011;39:7946-60.
  31. Burwitz BJ, Ende Z, Sudolcan B, Reynolds MR, Greene JM, Bimber BN, et al. Simian immunodeficiency virus SIVmac239Deltanef vaccination elicits different Tat28-35SL8-specific CD8+T-cell clonotypes compared to a DNA prime/adenovirus type 5 boost regimen in rhesus macaques. J Virol 2011;85:3683-9.
  32. Wu X, Zhou T, Zhu J, Zhang B, Georgiev I, Wang C, et al. Focused evolution of HIV-1 neutralizing antibodies revealed by structures and deep sequencing. Science 2011;333:1593-602.
  33. Gupta N, Kaur H, Yadav PD, Mukhopadhyay L, Sahay RR, Kumar A, et al. Clinical characterization and genomic analysis of samples from COVID-19 breakthrough infections during the second wave among the various states of India. Viruses 2021;13:1782.
  34. Logunov DY, Dolzhikova IV, Zubkova OV, Tukhvatullin AI, Shcheblyakov DV, Dzharullaeva AS, et al. Safety and immunogenicity of an rAd26 and rAd5 vector-based heterologous prime-boost COVID-19 vaccine in two formulations: Two open, non-randomised phase 1/2 studies from Russia. Lancet 2020;396:887-97.
  35. CoWIN Dashboard. Available from: https://dashboard.cowin.gov.in/(22). [Last accessed on 10 May 20].
  36. Goldberg Y, Mandel M, Bar-On YM, Bodenheimer O, Freedman L, Haas EJ, et al. Waning immunity after the BNT162b2 vaccine in Israel. New England Journal of Medicine 2021;385:e85.
  37. Emary KR, Golubchik T, Aley PK, Ariani CV, Angus B, Bibi S, et al. Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 variant of concern 202012/01 (B. 1.1. 7): an exploratory analysis of a randomised controlled trial. The Lancet 2021;397:1351-62.
PDF Share
PDF Share

© Jaypee Brothers Medical Publishers (P) LTD.