Skip to main content

An Unsupervised Clustering Algorithm to Cluster the New SARS-CoV-2 Virus Mutation

  • Conference paper
  • First Online:
Innovations in Computer Science and Engineering

Abstract

The Coronavirus disease 2019 SARS-CoV-2 is a disease which causes fear to human lives that has taken thousands and hundreds of lives globally. The pandemic which has resulted in a global health emergency is currently a much sought-after research topic. The frequently mutating virus which has originated from Chiroptera and subsequently got transmitted to other mammals including humans. However, at the genomic level, it is yet to be unraveled what makes humans more prone to getting infected by the coronaviruses. Here, we have implemented a Machine Learning model known as K-means Clustering that uses the combination of different features to determine the risk of infection. In this research paper, the K-means clustering method is used since it is a good performer for Clustering analysis. The algorithm can group the sequences of the dataset into five clusters based on the Elbow plot and co-linearity of co-efficient. Using dimensional reduction technique PCA is used with a 3D visualization and a heat map to showcase the correlation efficiency between the mutated and original sequence considered.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 219.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 279.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. WHO 2021

    Google Scholar 

  2. Abdelrahman Z, Li M, Wang X (2020) Comparative review of SARS-CoV-2, SARS-CoV, MERS-CoV, and influenza a respiratory viruses. Front Immunol 11:552909

    Google Scholar 

  3. Li W, Shi Z, Yu M, Ren W, Smith C, Epstein JH, Wang H, Crameri G, Hu Z, Zhang H, Zhang J, McEachern J, Field H, Daszak P, Eaton BT, Zhang S, Wang L (2005) Bats are natural reservoirs of SARS-like coronaviruses. Science 310(5748):676–679. https://doi.org/10.1126/science.1118391 Epub 2005 Sep 29

    Article  Google Scholar 

  4. Wang LF, Eaton BT (2007) Bats, civets and the emergence of SARS. Curr Top Microbiol Immunol 315:325–344. https://doi.org/10.1007/978-3-540-70962-6_13

    Article  Google Scholar 

  5. Shi Z, Hu Z (2008) A review of studies on animal reservoirs of the SARS coronavirus. Virus Res 133(1):74–87

    Article  MathSciNet  Google Scholar 

  6. Callaway E (2020) The coronavirus is mutating—does it matter? Nature 585:174–177

    Article  Google Scholar 

  7. Zhu Z, Lian X, Su X, Wu W, Marraro GA, Zeng Y (2020) From SARS and MERS to COVID-19: a brief summary and comparison of severe acute respiratory infections caused by three highly pathogenic human coronaviruses. Respir Res 21:224

    Article  Google Scholar 

  8. Patrick CY. Woo, PCY, Huang Y, Lau SKP, Yuen K-Y (2010) Coronavirus genomics and bioinformatics analysis. Viruses 2(8):1804–1820

    Google Scholar 

  9. Toyoshima Y, Nemoto K, Matsumoto S, Nakamura Y, Kiyotani K (2020) SARS-CoV-2 genomic variations associated with mortality rate of COVID-19. J Hum Genet 65(12):1075–1082

    Article  Google Scholar 

  10. Beeching NJ, Fletcher TE, Fowler R (2020). BMJ best practice coronavirus disease 2019 (COVID-19). British Med J 24. Retrieved from https://bestpractice.bmj.com/topics/en-us/3000168/investigations

  11. Plante JA, Liu Y, Liu J, Xia H, Johnson BA, Lokugamage KG et al (2021) Spike mutation D614G alters SARS-CoV-2 fitness. Nature 592:116–121

    Article  Google Scholar 

  12. Ikemura T, Wada K, Wada Y, Iwasaki Y, Abe T (2020) Unsupervised explainable AI for simultaneous molecular evolutionary study of forty thousand SARS-CoV-2 genomes. Biorxiv. https://doi.org/10.1101/2020.10.11.335406

    Article  Google Scholar 

  13. Khailany RA, Safdar M, Ozaslan M (2020) Genomic characterization of a novel SARS-CoV-2. Gene Reports, p 19. https://doi.org/10.1016/j.genrep.2020.100682

  14. James Ingram (2021, April) SARS CORONAVIRUS ACCESSION, Version 1. Retrieved Nov 25, 2020 from https://www.kaggle.com/jamzing/sars-coronavirusaccession/version/1

  15. National Center for Biotechnology Information (NCBI) [Internet]. Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information; [1988]. [cited 2021 Mar 13]. Available from https://www.ncbi.nlm.nih.gov/

  16. Zhaoqi B, Xuegong Z (2000) Pattern recognition. Beijing Tsinghua University Press

    Google Scholar 

  17. Thorndike RL (1953) Who belongs in the family? Psychometrika 18(4):267–276. https://doi.org/10.1007/BF02289263

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Smaranika Mohapatra or Kusumlata Jain .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2022 The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Rath, S.L., Sinha, C., Kasturi, S.L.N.P., Mohapatra, S., Jain, K. (2022). An Unsupervised Clustering Algorithm to Cluster the New SARS-CoV-2 Virus Mutation. In: Saini, H.S., Sayal, R., Govardhan, A., Buyya, R. (eds) Innovations in Computer Science and Engineering. Lecture Notes in Networks and Systems, vol 385. Springer, Singapore. https://doi.org/10.1007/978-981-16-8987-1_19

Download citation

Publish with us

Policies and ethics