EC Microbiology

Opinion Volume 19 Issue 8 - 2023

Chameleon-Like Mimicry among RNA Viruses Possessing Ambisense Stacking Genes in their Genomes: Possible or Not?

OP Zhirnov1,2* and AI Chernyshova1

1The D.I. Ivanovsky Institute of Virology, N.F. Gamaleya Research Center of Epidemiology and Microbiology, Moscow, Russian Federation

2The Russian-German Academy of Medico-Social and Biotechnological Sciences, The Innovation Center of Skolkovo, Moscow, Russian Federation

*Corresponding Author: OP Zhirnov, The D.I. Ivanovsky Institute of Virology, N.F. Gamaleya Research Center of Epidemiology and Microbiology, Moscow, Russian Federation.
Received: July 27, 2023; Published: August 04, 2023



In the RNA genome of influenza viruses and coronaviruses, a novel genes were identified, that, unlike the known canonical genes in these viruses, were encoded in the opposite polarity: positive in influenza virus and negative in coronaviruses (so-called ambipolar genes). The novel ambipolar genes appear to be localized in the genome in the area of canonical genes, the so-called stacking arrangement. The discovery of new viral genes implies the existence of several alternative pathways (strategies) in the realization of the viral genome in a single virus. This variety of strategies gives the virus the ability, like a chameleon, to change the structure of the virion genome and its envelope, consisting of proteins - products of the ambisense genes and/or mosaic with canonical proteins. Structural chameleon-like variants of the virus can arise depending on the biochemical composition of the virus reproduction environment in various organs of the host organism, increasing the adaptive potential and ability of the virus to evade the host immune defense, causing various forms of disease pathogenesis, including the development of latent and persistent forms of the pathological process. The existence of stealth ambipolar viruses is still hidden from researchers, like the “dark side of the moon”. Their identification will make it possible to discover novel forms of viral diseases and develop new types of drugs and vaccines.

Keywords: Viruses; Genome Strategy; Genome Polarity; Ambisense Genes; Influenza; Covid-2019

    1. Zhirnov OP., et al. “Segment NS of influenza A virus contains an additional gene NSP in positive- sense orientation”. Doklady Biochemistry and Biophysics 414 (2007): 127-133.
    2. Zhirnov OP., et al. “Structural and evolutionary characteristics of HA, NA, NS and M genes of clinical influenza A/H3N2 viruses passaged in human and canine cells”. Journal of Clinical Virology4 (2009): 322-333.
    3. Zhirnov OP. “Unique Bipolar Gene Architecture in the RNA Genome of Influenza A Virus”. Biochemistry3 (2020): 387-392.
    4. Clifford M., et al. “Evidence for a novel gene associated with human influenza A viruses”. Journal of Virology 6 (2009): 198.
    5. Gong YN., et al. “Computational analysis and mapping of novel open reading frames in influenza A viruses”. PLoS One 9 (2014): e115016.
    6. Yang CW and Chen MF. “Uncovering the potential pan proteomes encoded by genomic strand RNAs of influenza A viruses”. PLoS One 11 (2016): e0146936.
    7. Sabath N., et al. “Is there a twelfth protein-coding gene in the genome of influenza A? A selection-based approach to the detection of overlapping genes in closely related sequences”. Journal of Molecular Evolution 73 (2011): 305-315.
    8. Zhirnov O. “Ambisense polarity of genome RNA of orthomyxoviruses and coronaviruses”. World Journal of Virology5 (2021): 256-263.
    9. Zhirnov OP and Poyarkov SV. “Novel Negative Sense Genes in the RNA Genome of Coronaviruses”. Doklady Biochemistry and Biophysics1 (2021): 27-31.
    10. Kearse MG and Wilusz JE. “Non-AUG translation: a new start for protein synthesis in eukaryotes”. Genes and Development17 (2017): 1717-1731.
    11. Acevedo JM., et al. “Changes in global translation elongation or initiation rates shape the proteome via the Kozak sequence”. Scientific Reports1 (2018): 4018.
    12. Kolekar P., et al. “IRESPred: Web Server for Prediction of Cellular and Viral Internal Ribosome Entry Site (IRES)”. Scientific Reports 6 (2016): 27436.
    13. Zhirnov OP. “The unique genome of the virus and alternative strategies for its realization”. Acta Naturae2023;15(2):14-19.
    14. Zhirnov OP., et al. “Cellular immune response in infected mice to NSP protein encoded by the negative strand NS RNA of influenza A virus”. MIR Journal1 (2019): 28-36.
    15. Zhirnov OP and Isaeva EI. “NSP Protein Encoded in Negative NS RNA Strand of Influenza A Virus Induces Cellular Immune Response in Infected Animals”. Doklady Biochemistry and Biophysics1 (2019): 201-205.
    16. Zhirnov OP., et al. “Negative-sense virion RNA of segment 8 (NS) of influenza a virus is able to translate in vitro a new viral protein”. Doklady Biochemistry and Biophysics1 (2017): 122-127.
    17. Zhirnov OP and Klenk HD. “Integration of influenza A virus NSP gene into baculovirus genome and its expression in insect cells”. Vopr Virusol2 (2010): 4-8.
    18. Zhong W., et al. “Genome-wide characterization of a viral cytotoxic T lymphocyte epitope repertoire”. Journal of Biological Chemistry46 (2003): 45135-45144.
    19. Hickman HD., et al. “Influenza A virus negative strand RNA is translated for CD8+ T cell immunosurveillance”. Journal of Immunology 201 (2019): 1222-1228.
    20. Wei J and Yewdell JW. “Flu DRiPs in MHC classI immunosurveillance”. Virologica Sinica 34 (2018): 162-167.
    21. Bartas M., et al. “Unheeded SARS-CoV-2 proteins? A deep look into negative-sense RNA”. Briefings in Bioinformatics3 (2022): bbac045.

OP Zhirnov and AI Chernyshova. “Chameleon-Like Mimicry among RNA Viruses Possessing Ambisense Stacking Genes in their Genomes: Possible or Not?”. EC Microbiology  19.8 (2023): 01-05.