Skip to main content

Application of Deep Mutational Scanning in Hepatitis C Virus

  • Protocol
  • First Online:
Hepatitis C Virus Protocols

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1911))

Abstract

Mutagenesis is one of the key techniques in virus research. The recent development of deep mutational scanning allows the assessment of replication fitness effects of a large number of viral mutants in a high-throughput manner. Here, we describe a protocol for studying hepatitis C virus (HCV) using deep mutational scanning, which includes the methodologies for mutant library construction, passaging, sequencing, and data analysis.

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

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover 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

References

  1. Qi H, Wu NC, Du Y, Wu TT, Sun R (2015) High-resolution genetic profile of viral genomes: why it matters. Curr Opin Virol 14:62–70

    Article  Google Scholar 

  2. Fowler DM, Fields S (2014) Deep mutational scanning: a new style of protein science. Nat Methods 11:801–807

    Article  CAS  Google Scholar 

  3. Arumugaswami V, Remenyi R, Kanagavel V, Sue EY, Ngoc Ho T, Liu C et al (2008) High-resolution functional profiling of hepatitis C virus genome. PLoS Pathog 4:e1000182

    Article  Google Scholar 

  4. Remenyi R, Qi H, Su SY, Chen Z, Wu NC, Arumugaswami V et al (2014) A comprehensive functional map of the hepatitis C virus genome provides a resource for probing viral proteins. MBio 5:e01469–e01414

    Article  CAS  Google Scholar 

  5. Qi H, Chu V, Wu NC, Chen Z, Truong S, Brar G et al (2017) Systematic identification of anti-interferon function on hepatitis C virus genome reveals p7 as an immune evasion protein. Proc Natl Acad Sci U S A 114:2018–2023

    Article  CAS  Google Scholar 

  6. Wu NC, Young AP, Al-Mawsawi LQ, Olson CA, Feng J, Qi H et al (2014) High-throughput profiling of influenza A virus hemagglutinin gene at single-nucleotide resolution. Sci Rep 4:4942

    Article  Google Scholar 

  7. Wu NC, Olson CA, Du Y, Le S, Tran K, Remenyi R et al (2015) Functional constraint profiling of a viral protein reveals discordance of evolutionary conservation and functionality. PLoS Genet 11:e1005310

    Article  Google Scholar 

  8. Qi H, Olson CA, Wu NC, Ke R, Loverdo C, Chu V et al (2014) A quantitative high-resolution genetic profile rapidly identifies sequence determinants of hepatitis C viral fitness and drug sensitivity. PLoS Pathog 10:e1004064

    Article  Google Scholar 

  9. Olson CA, Wu NC, Sun R (2014) A comprehensive biophysical description of pairwise epistasis throughout an entire protein domain. Curr Biol 24:2643–2651

    Article  CAS  Google Scholar 

  10. Wu NC, Grande G, Turner HL, Ward AB, Xie J, Lerner RA et al (2017) In vitro evolution of an influenza broadly neutralizing antibody is modulated by hemagglutinin receptor specificity. Nat Commun 8:15371

    Article  CAS  Google Scholar 

  11. Doud MB, Bloom JD (2016) Accurate measurement of the effects of all amino-acid mutations on influenza hemagglutinin. Viruses 8:E155

    Article  Google Scholar 

  12. Al-Mawsawi LQ, Wu NC, Olson CA, Shi VC, Qi H, Zheng X et al (2014) High-throughput profiling of point mutations across the HIV-1 genome. Retrovirology 11:124

    Article  Google Scholar 

  13. Haddox HK, Dingens AS, Bloom JD (2016) Experimental estimation of the effects of all amino-acid mutations to HIV's envelope protein on viral replication in cell culture. PLoS Pathog 12:e1006114

    Article  Google Scholar 

  14. Lindenbach BD, Evans MJ, Syder AJ, Wolk B, Tellinghuisen TL, Liu CC et al (2005) Complete replication of hepatitis C virus in cell culture. Science 309:623–626

    Article  CAS  Google Scholar 

Download references

Acknowledgment

NCW was supported by the Croucher Foundation Fellowship.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Nicholas C. Wu .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Wu, N.C., Qi, H. (2019). Application of Deep Mutational Scanning in Hepatitis C Virus. In: Law, M. (eds) Hepatitis C Virus Protocols . Methods in Molecular Biology, vol 1911. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8976-8_12

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-8976-8_12

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8975-1

  • Online ISBN: 978-1-4939-8976-8

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics