1887

Journal of General Virology header logo

Volume 104, Issue 5

Emergence of biased hypermutation in a heterologous additional transcription unit in recombinant lentogenic Newcastle disease virus Open Access

Abstract

Recombinant Newcastle disease virus (rNDV) strains engineered to express foreign genes from an additional transcription unit (ATU) are considered as candidate live-attenuated vector vaccines for human and veterinary use. Early during the COVID-19 pandemic we and others generated COVID-19 vaccine candidates based on rNDV expressing a partial or complete SARS-CoV-2 spike (S) protein. In our studies, a number of the rNDV constructs did not show high S expression levels in cell culture or seroconversion in immunized hamsters. Sanger sequencing showed the presence of frequent A-to-G transitions characteristic of adenosine deaminase acting on RNA (ADAR). Subsequent whole genome rNDV sequencing revealed that this biased hypermutation was exclusively localized in the ATU expressing the spike gene, and was related to deamination of adenosines in the negative strand viral genome RNA. The biased hypermutation was found both after virus rescue in chicken cell line DF-1 followed by passaging in embryonated chicken eggs, and after direct virus rescue and subsequent passaging in Vero E6 cells. Levels of biased hypermutation were higher in constructs containing codon-optimized as compared to native S gene sequences, suggesting potential association with increased GC content. These data show that deep sequencing of candidate recombinant vector vaccine constructs in different phases of development is of crucial importance in the development of NDV-based vaccines.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): ADAR1 , COVID-19 , NDV vaccine , SARS-CoV-2 and spike protein
© 2023 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
Loading

Article metrics loading...

/content/journal/jgv/10.1099/jgv.0.001851
2023-05-15
2024-05-05
Loading full text...

Full text loading...

/deliver/fulltext/jgv/104/5/jgv001851.html?itemId=/content/journal/jgv/10.1099/jgv.0.001851&mimeType=html&fmt=ahah

References

  1. de Buhr H, S. de Leeuw O, Harders F, P. Peeters B, L. de Swart R. Emergence of biased hypermutation in a heterologous additional transcription unit in recombinant lentogenic Newcastle disease virus Microbiology Society figshare 2023 https://doi.org/10.6084/m9.figshare.22587823.v1
     [Google Scholar]
  2. Rima B, Balkema-Buschmann A, Dundon WG, Duprex P, Easton A et al. ICTV Virus Taxonomy Profile: Paramyxoviridae. J Gen Virol 2019; 100:1593–1594 [View Article]
     [Google Scholar]
  3. Alexander DJ. Newcastle disease and other avian paramyxoviruses. Rev Sci Tech 2000; 19:443–462 [View Article] [PubMed]
     [Google Scholar]
  4. Peeters BP, de Leeuw OS, Koch G, Gielkens AL. Rescue of Newcastle disease virus from cloned cDNA: evidence that cleavability of the fusion protein is a major determinant for virulence. J Virol 1999; 73:5001–5009 [View Article] [PubMed]
     [Google Scholar]
  5. Dimitrov KM, Afonso CL, Yu Q, Miller PJ. Newcastle disease vaccines-a solved problem or a continuous challenge?. Vet Microbiol 2017; 206:126–136 [View Article] [PubMed]
     [Google Scholar]
  6. Bello MB, Yusoff K, Ideris A, Hair-Bejo M, Jibril AH et al. Exploring the prospects of engineered Newcastle disease virus in modern vaccinology. Viruses 2020; 12:451 [View Article] [PubMed]
     [Google Scholar]
  7. de Swart RL, de Leeuw OS, Oreshkova N, Gerhards NM, Albulescu IC et al. Intranasal administration of a live-attenuated recombinant Newcastle disease virus expressing the SARS-CoV-2 Spike protein induces high neutralizing antibody levels and protects from experimental challenge infection in hamsters. Vaccine 2022; 40:4676–4681 [View Article] [PubMed]
     [Google Scholar]
  8. DiNapoli JM, Kotelkin A, Yang L, Elankumaran S, Murphy BR et al. Newcastle disease virus, a host range-restricted virus, as a vaccine vector for intranasal immunization against emerging pathogens. Proc Natl Acad Sci 2007; 104:9788–9793 [View Article] [PubMed]
     [Google Scholar]
  9. Fulber JPC, Farnós O, Kiesslich S, Yang Z, Dash S et al. Process development for Newcastle disease virus-vectored vaccines in serum-free vero cell suspension cultures. Vaccines 2021; 9:1335 [View Article] [PubMed]
     [Google Scholar]
  10. Song B, Shiromoto Y, Minakuchi M, Nishikura K. The role of RNA editing enzyme ADAR1 in human disease. Wiley Interdiscip Rev RNA 2022; 13:e1665 [View Article] [PubMed]
     [Google Scholar]
  11. Bazak L, Haviv A, Barak M, Jacob-Hirsch J, Deng P et al. A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes. Genome Res 2014; 24:365–376 [View Article] [PubMed]
     [Google Scholar]
  12. Quin J, Sedmík J, Vukić D, Khan A, Keegan LP et al. ADAR RNA modifications, the epitranscriptome and innate immunity. Trends Biochem Sci 2021; 46:758–771 [View Article] [PubMed]
     [Google Scholar]
  13. Tan MH, Li Q, Shanmugam R, Piskol R, Kohler J et al. Dynamic landscape and regulation of RNA editing in mammals. Nature 2017; 550:249–254 [View Article] [PubMed]
     [Google Scholar]
  14. Pfaller CK, George CX, Samuel CE. Adenosine Deaminases Acting on RNA (ADARs) and viral infections. Annu Rev Virol 2021; 8:239–264 [View Article] [PubMed]
     [Google Scholar]
  15. Lamers MM, van den Hoogen BG, Haagmans BL. ADAR1: “Editor-in-Chief” of cytoplasmic innate immunity. Front Immunol 2019; 10:1763 [View Article] [PubMed]
     [Google Scholar]
  16. Piontkivska H, Wales-McGrath B, Miyamoto M, Wayne ML. ADAR editing in viruses: an evolutionary force to reckon with. Genome Biol Evol 2021; 13:evab240 [View Article] [PubMed]
     [Google Scholar]
  17. Stinnett RC, Beck AS, Lopareva EN, McNall RJ, Latner DR et al. Functional characterization of circulating mumps viruses with stop codon mutations in the small hydrophobic protein. mSphere 2020; 5:e00840-20 [View Article] [PubMed]
     [Google Scholar]
  18. Shabman RS, Jabado OJ, Mire CE, Stockwell TB, Edwards M et al. Deep sequencing identifies noncanonical editing of Ebola and Marburg virus RNAs in infected cells. mBio 2014; 5:e02011 [View Article] [PubMed]
     [Google Scholar]
  19. Pfaller CK, Donohue RC, Nersisyan S, Brodsky L, Cattaneo R. Extensive editing of cellular and viral double-stranded RNA structures accounts for innate immunity suppression and the proviral activity of ADAR1p150. PLoS Biol 2018; 16:e2006577 [View Article] [PubMed]
     [Google Scholar]
  20. Pfaller CK, Mastorakos GM, Matchett WE, Ma X, Samuel CE et al. Measles virus defective interfering RNAs are generated frequently and early in the absence of C protein and can be destabilized by adenosine deaminase acting on RNA-1-like hypermutations. J Virol 2015; 89:7735–7747 [View Article] [PubMed]
     [Google Scholar]
  21. Pfaller CK, Radeke MJ, Cattaneo R, Samuel CE. Measles virus C protein impairs production of defective copyback double-stranded viral RNA and activation of protein kinase R. J Virol 2014; 88:456–468 [View Article] [PubMed]
     [Google Scholar]
  22. Satoh Y, Higuchi K, Nishikawa D, Wakimoto H, Konami M et al. M protein of subacute sclerosing panencephalitis virus, synergistically with the F protein, plays a crucial role in viral neuropathogenicity. J Gen Virol 2021; 102:001682 [View Article] [PubMed]
     [Google Scholar]
  23. Cattaneo R, Schmid A, Eschle D, Baczko K, ter Meulen V et al. Biased hypermutation and other genetic changes in defective measles viruses in human brain infections. Cell 1988; 55:255–265 [View Article] [PubMed]
     [Google Scholar]
  24. Baczko K, Lampe J, Liebert UG, Brinckmann U, ter Meulen V et al. Clonal expansion of hypermutated measles virus in a SSPE brain. Virology 1993; 197:188–195 [View Article] [PubMed]
     [Google Scholar]
  25. Watanabe S, Shirogane Y, Sato Y, Hashiguchi T, Yanagi Y. New insights into measles virus brain infections. Trends Microbiol 2019; 27:164–175 [View Article] [PubMed]
     [Google Scholar]
  26. Otani S, Ayata M, Takeuchi K, Takeda M, Shintaku H et al. Biased hypermutation occurred frequently in a gene inserted into the IC323 recombinant measles virus during its persistence in the brains of nude mice. Virology 2014; 462–463:91–97 [View Article] [PubMed]
     [Google Scholar]
  27. Eggington JM, Greene T, Bass BL. Predicting sites of ADAR editing in double-stranded RNA. Nat Commun 2011; 2:319 [View Article] [PubMed]
     [Google Scholar]
  28. Meier JC, Kankowski S, Krestel H, Hetsch F. RNA editing-systemic relevance and clue to disease mechanisms?. Front Mol Neurosci 2016; 9:124 [View Article] [PubMed]
     [Google Scholar]
  29. Green TJ, Cox R, Tsao J, Rowse M, Qiu S et al. Common mechanism for RNA encapsidation by negative-strand RNA viruses. J Virol 2014; 88:3766–3775 [View Article] [PubMed]
     [Google Scholar]
  30. Kuttan A, Bass BL. Mechanistic insights into editing-site specificity of ADARs. Proc Natl Acad Sci 2012; 109:E3295–E3304 [View Article] [PubMed]
     [Google Scholar]
  31. Riedmann EM, Schopoff S, Hartner JC, Jantsch MF. Specificity of ADAR-mediated RNA editing in newly identified targets. RNA 2008; 14:1110–1118 [View Article] [PubMed]
     [Google Scholar]
  32. Pecori R, Di Giorgio S, Paulo Lorenzo J, Nina Papavasiliou F. Functions and consequences of AID/APOBEC-mediated DNA and RNA deamination. Nat Rev Genet 2022; 23:505–518 [View Article] [PubMed]
     [Google Scholar]
  33. Kolakofsky D, Pelet T, Garcin D, Hausmann S, Curran J et al. Paramyxovirus RNA synthesis and the requirement for hexamer genome length: the rule of six revisited. J Virol 1998; 72:891–899 [View Article] [PubMed]
     [Google Scholar]
  34. Song X, Shan H, Zhu Y, Hu S, Xue L et al. Self-capping of nucleoprotein filaments protects the Newcastle disease virus genome. Elife 2019; 8:e45057 [View Article]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/jgv.0.001851
Loading
Emergence of biased hypermutation in a heterologous additional transcription unit in recombinant lentogenic Newcastle disease virus
J. Gen. Virol. 104, 001851 (2023); https://doi.org/10.1099/jgv.0.001851
/content/journal/jgv/10.1099/jgv.0.001851
/content/journal/jgv/10.1099/jgv.0.001851
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error