Akio Adachi
Takaaki Koma
Masako NomaguchiThree years have passed since the launch of our journal “Frontiers in Virology”. It was founded to biologically and molecularly clarify the multifaceted nature of viruses by multidisciplinary approaches. Understanding and gaining ascendancy over the complex viruses is tremendously challenging. We virologists have to comprehend them in terms of virus-virus, virus-host, and virus-environment relationships, as well as their fundamental properties. Of note, some viruses are highly or moderately pathogenic for humans and also for animals and plants that are important and/or useful to humans. Furthermore, we need to work with the readily mutable and transmittable viruses. Thus, we must have numerous integral specialty sections in the journal designated “Antivirals and Vaccines”, “Bioinformatic and Predictive Virology”, “Emerging and Reemerging Viruses”, “Fundamental Virology”, “Modeling of Viral Replication and Pathogenesis”, “Systems Virology”, “Translational Virology”, “Viral Disease Investigation”, “Viral Diversification and Evolution”, and “Virus and Host Immunity”. For better grasping each section, we are currently revamping and standardizing the scopes of all sections in the journal. All the sections are supposed to coordinate organically. “Frontiers in Virology” is also considerate to authors/researchers by offering numbers of article types such as Original Research, Methods, Review, Hypothesis and Theory, Clinical Trial, Brief Research Report, Perspective, Opinion, and Case Report to increase the optionality and possibility for publication (https://www.frontiersin.org/journals/virology/for-authors/article-types). As stated in the previous Grand Challenge articles (1, 2), we have provided here in “Frontiers in Virology” an innovative platform for integrative research on the most abundant species in nature, i.e., the virus. After the journal initiation, more than 1300 researchers have joined us as editor (specialty chief editor, associate editor, guest associate editor, or review editor) and approximately 250 articles have been published.
Needless to mention, one of the most important issues for modern virology is to cope with the human diseases caused by a wide variety of viruses. Especially, viruses that spread widely/globally and seriously affect humans have been long concerned about. In light of the current world situation, there may emerge not-yet-identified new viruses with such properties at any time. We have experienced a number of repeated pandemics by the influenza virus (IFV) in the past (3). While some effective drugs and vaccines are available to date, IFV is extremely difficult to suppress due to its high mutability and its wild-bird origin. Experts are really anxious about other terrible influenza-pandemics by new type viruses. About 40 years ago, we also encountered another dreadful and readily mutable virus HIV-1 that causes AIDS. Since the AIDS outbreak began, approximately 100 million people have been infected with HIV-1 and 40 million people have died of AIDS/AIDS-related diseases. AIDS still stays pandemic and functional cure is not yet achieved (4–7). Thus, the causative virus HIV-1 needs to be studied in more detail to precisely understand viral persistent state in humans. Toward this direction, further medical investigation as well as fundamental basic virus research should be performed (8–18). Since retroviral HIV-1 genome integrates into those of infected humans to establish the inseparable virus-host relationship, firm and solid virological understanding of the intracellular events is particularly required to address and follow the significant numbers of pre-clinical and clinical issues on AIDS. And now, we are witnessing new global pandemics caused by the corona and pox viruses (SARS-CoV-2 and Mpox virus, respectively) (19–28). As a matter of course, on the basis of previous profound knowledge of various viruses, extensive efforts have been paid to understand the biology/molecular biology of the two viruses and to establish valid preventive and therapeutic measures. One problem here is that the high adaptability of the two viruses despite their quite low mutation rates (19, 28). This observation can be explained by some specific mechanisms such as recombinational mutations (the non-processive replicase-driven template switching mechanism for SARS-CoV-2) (19, 29) and transient gene duplications (the accordion model for Mpox virus) (28, 30). In any case, we have to deal with the mutant viruses appearing in the course of viral infection.
As described above, IFV, HIV-1, SARS-CoV-2, and Mpox are highly mutable and adaptable to their restrictive hostile environments. These viruses are dexterous in being able to ingeniously modify them significantly in response to variously changing circumstances. Through genomic adaptive mutations and/or by their own viral proteins, viruses are able to circumvent the barriers such as cellular anti-viral factors, host natural/acquired immunity against viruses, antivirals, and vaccines. As an example of the viral escape mechanism other than that by viral genomic mutations, HIV-1 innately encodes for its own accessory proteins that allow it to evade cellular restriction factors (31–34). Collectively, viruses are likely to frequently change in an environment-dependent way. So far, we are able to know the entity of the virus concerned only by nucleotide sequencings. This means that we are running behind viruses, just retrospectively following viruses. Most virologists including our group have adopted this research strategy due to limitations in the laboratory virology, whereas many biologically significant results have been accumulated by exploring viruses this way. Our team has investigated the HIV-1 adaptation process to clarify the virological significance of synonymous nucleotide substitutions and the structure-function relationship of viral proteins by combining experimental virology and the data/computational science, and successfully published the results obtained in a series of articles (35–42). On one hand, quite different from the experimental approaches, a new class of virus studies based on big data of massive scope and scale have attracted attention as an unprecedented research strategy and concept in the past decade (43–52). The studies are characterized by the methods to collect and analyze large data sets, such as NSG, CRISPR-based technologies, machine learning, and various algorithms. The research targets in those studies were: epidemiology of virus and viral disease, plant viruses, virus ecology, virus adaptation and evolution, virus drug-resistance, databases in virus research, various computational tools. The data and computational sciences may aid forecasting the future virus-related issues. Big data and experimental approaches surely synergize to consolidate the predictive role of modern virology.
“Frontiers in Virology” continues to be a platform for cutting edge studies on virology. It covers all virological subjects as indicated in the names of various specialty sections. Furthermore, “Frontiers in Virology” highly appreciates articles on the leading-edge technology to precisely understand virus-related matters. The ideal goal of virology is to be able to prospectively foresee everything about the virus and its effects on hosts/environments, being beforehand with viruses. In conclusion, we “Frontiers in Virology” earnestly hope the submission of your important papers with a high scientific value.
Author contributions
AA: Conceptualization, Writing – original draft, Writing – review & editing. TK: Writing – review & editing. MN: Writing – review & editing.
Acknowledgments
The authors appreciate all the members of their department for their daily work.
Conflict of interest
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Publisher’s note
All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.
References
1. Adachi A. Grand challenge in human/animal virology: unseen, smallest replicative entities shape the whole globe. Front Microbiol. (2020) 11:431. doi: 10.3389/fmicb.2020.00431
2. Adachi A. Frontiers in Virology: An innovative platform for integrative virus research. Front Virol. (2021) 1:665473. doi: 10.3389/fviro.2021.665473
3. Wang D, Zhu W, Yang L, Shu Y. The epidemiology, virology, and pathogenicity of human infections with avian influenza viruses. Cold Spring Harb Perspect Med. (2021) 11:a038620. doi: 10.1101/cshperspect.a038620
4. Gasca-Capote C, Lian X, Gao C, Roseto IC, Jiménez-León MR, Gladkov G, et al. The HIV-1 reservoir landscape in persistent elite controllers and transient elite controllers. J Clin Invest. (2024) 134:e174215. doi: 10.1172/JCI174215
5. Kwaa AK, Blankson JN. Immune responses in controllers of HIV infection. Annu Rev Immunol. (2024) 42:21–33. doi: 10.1146/annurev-immunol-083122-035233
6. Armani-Tourret M, Bone B, Tan TS, Sun W, Bellefroid M, Struyve T, et al. Immune targeting of HIV-1 reservoir cells: a path to elimination strategies and cure. Nat Rev Microbiol. (2024) 22:328–44. doi: 10.1038/s41579-024-01010-8
7. Mbonye U, Karn J. The cell biology of HIV-1 latency and rebound. Retrovirology. (2024) 21:6. doi: 10.1186/s12977-024-00639-w
8. Nkolola JP, Barouch DH. Prophylactic HIV-1 vaccine trials: past, present, and future. Lancet HIV. (2024) 11:e117–24. doi: 10.1016/S2352-3018(23)00264-3
9. Williams WB, Alam SM, Ofek G, Erdmann N, Montefiori DC, Seaman MS, et al. Vaccine induction of heterologous HIV-1-neutralizing antibody B cell lineages in humans. Cell. (2024) 187:2919–2934.e20. doi: 10.1016/j.cell.2024.04.033
10. Schriek AI, Aldon YLT, van Gils MJ, de Taeye SW. Next-generation bNAbs for HIV-1 cure strategies. Antiviral Res. (2024) 222:105788. doi: 10.1016/j.antiviral.2023.105788
11. Ahmed S, Herschhorn A. mRNA-based HIV-1 vaccines. Clin Microbiol Rev. (2024) 37:e0004124. doi: 10.1128/cmr.00041-24
12. Sever B, Otsuka M, Fujita M, Ciftci H. A review of FDA-approved anti-HIV-1 drugs, anti-Gag compounds, and potential strategies for HIV-1 eradication. Int J Mol Sci. (2024) 25:3659. doi: 10.3390/ijms25073659
13. McFadden WM, Casey-Moore MC, Bare GAL, Kirby KA, Wen X, Li G, et al. Identification of clickable HIV-1 capsid-targeting probes for viral replication inhibition. Cell Chem Biol. (2024) 31:477–486.e7. doi: 10.1016/j.chembiol.2024.02.012
14. Levintov L, Vashisth H. Structural and computational studies of HIV-1 RNA. RNA Biol. (2024) 21:1–32. doi: 10.1080/15476286.2023.2289709
15. Dwivedi R, Prakash P, Kumbhar BV, Balasubramaniam M, Dash C. HIV-1 capsid and viral DNA integration. mBio. (2024) 15:e0021222. doi: 10.1128/mbio.00212-22
16. Duchon A, Hu W-S. HIV-1 RNA genome packaging: it’s G-rated. mBio. (2024) 15:e0086123. doi: 10.1128/mbio.00861-23
17. Moezpoor MR, Stevenson M. Help or hinder: protein host factors that impact HIV-1 replication. Viruses. (2024) 16:1281. doi: 10.3390/v16081281
18. Kmiec D, Kirchhoff F. Antiviral factors and their counteraction by HIV-1: many uncovered and more to be discovered. J Mol Cell Biol. (2024) 16:mjae005. doi: 10.1093/jmcb/mjae005
19. Adachi S, Koma T, Doi N, Nomaguchi M, Adachi A. Commentary: origin and evolution of pathogenic coronaviruses. Front Immunol. (2020) 11:811. doi: 10.3389/fimmu.2020.00811
20. Koma T, Adachi S, Doi N, Adachi A, Nomaguchi M. Toward understanding molecular bases for biological diversification of human coronaviruses: present status and future perspectives. Front Microbiol. (2020) 11:2016. doi: 10.3389/fmicb.2020.02016
21. Beladiya J, Kumar A, Vasava Y, Parmar K, Patel D, Patel S, et al. Safety and efficacy of COVID-19 vaccines: a systematic review and meta-analysis of controlled and randomized clinical trials. Rev Med Virol. (2024) 34:e2507. doi: 10.1002/rmv.2507
22. Steiner S, Kratzel A, Barut GT, Lang RM, Moreira EA, Thomann L, et al. SARS-CoV-2 biology and host interactions. Nat Rev Microbiol. (2024) 22:206–25. doi: 10.1038/s41579-023-01003-z
23. Peluso MJ, Deeks SG. Mechanisms of long COVID and the path toward therapeutics. Cell. (2024) S0092-8674:00886–9. doi: 10.1016/j.cell.2024.07.054
24. Huang Y, Mu L, Wang W. Monkeypox: epidemiology, pathogenesis, treatment and prevention. Signal Transduct Target Ther. (2022) 7:373. doi: 10.1038/s41392-022-01215-4
25. Gessain A, Nakoune E, Yazdanpanah Y. Monkeypox. N Engl J Med. (2022) . 387:1783–93. doi: 10.1056/NEJMra2208860
26. Lu J, Xing H, Wang C, Tang M, Wu C, Ye F, et al. Mpox (formerly monkeypox): pathogenesis, prevention, and treatment. Signal Transduct Target Ther. (2023) 8:458. doi: 10.1038/s41392-023-01675-2
27. Alakunle E, Kolawole D, Diaz-Canova D, Alele F, Adegboye O, Moens U, et al. A comprehensive review of monkeypox virus and mpox characteristics. Front Cell Infect Microbiol. (2024) 14:1360586. doi: 10.3389/fcimb.2024.1360586
28. Moss B. Understanding the biology of monkeypox virus to prevent future outbreaks. Nat Microbiol. (2024) 9:1408–16. doi: 10.1038/s41564-024-01690-1
29. Lai MMC. RNA recombination in animal and plant viruses. Microbiol Rev. (1992) 56:61–79. doi: 10.1128/mr.56.1.61-79.1992
30. Elde NC, Child SJ, Eickbush MT, Kitzman JO, Rogers KS, Shendure J, et al. Poxviruses deploy genomic accordions to adapt rapidly against host antiviral defenses. Cell. (2012) 150:831–41. doi: 10.1016/j.cell.2012.05.049
31. Malim MH, Emerman M. HIV-1 accessory proteins–ensuring viral survival in a hostile environment. Cell Host Microbe. (2008) 3:388–98. doi: 10.1016/j.chom.2008.04.008
32. Strebel K. HIV accessory proteins versus host restriction factors. Curr Opin Virol. (2013) 3:692–9. doi: 10.1016/j.coviro.2013.08.004
33. Simon V, Bloch N, Landau NR. Intrinsic host restrictions to HIV-1 and mechanisms of viral escape. Nat Immunol. (2015) 16:546–53. doi: 10.1038/ni.3156
34. Sauter D, Kirchhoff F. Multilayered and versatile inhibition of cellular antiviral factors by HIV and SIV accessory proteins. Cytokine Growth Factor Rev. (2018) 40:3–12. doi: 10.1016/j.cytogfr.2018.02.005
35. Nomaguchi M, Yokoyama M, Kono K, Nakayama EE, Shioda T, Saito A, et al. Gag-CA Q110D mutation elicits TRIM5-independent enhancement of HIV-1mt replication in macaque cells. Microbes Infect. (2013) 15:56–65. doi: 10.1016/j.micinf.2012.10.013
36. Nomaguchi M, Doi N, Fujiwara S, Saito A, Akari H, Nakayama EE, et al. Systemic biological analysis of the mutations in two distinct HIV-1mt genomes occurred during replication in macaque cells. Microbes Infect. (2013) 15:319–28. doi: 10.1016/j.micinf.2013.01.005
37. Nomaguchi M, Yokoyama M, Kono K, Nakayama EE, Shioda T, Doi N, et al. Generation of rhesus macaque-tropic HIV-1 clones that are resistant to major anti-HIV-1 restriction factors. J Virol. (2013) 87:11447–61. doi: 10.1128/JVI.01549-13
38. Nomaguchi M, Miyake A, Doi N, Fujiwara S, Miyazaki Y, Tsunetsugu-Yokota Y, et al. Natural single-nucleotide polymorphisms in the 3’ region of the HIV-1 pol gene modulate viral replication ability. J Virol. (2014) 88:4145–60. doi: 10.1128/JVI.01859-13
39. Yokoyama M, Nomaguchi M, Doi N, Kanda T, Adachi A, Sato H. In silico analysis of HIV-1 Env-gp120 reveals structural bases for viral adaptation in growth-restrictive cells. Front Microbiol. (2016) 7:110. doi: 10.3389/fmicb.2016.00110
40. Nomaguchi M, Doi N, Yoshida T, Koma T, Adachi S, Ode H, et al. Production of HIV-1 vif mRNA is modulated by natural nucleotide variations and SLSA1 RNA structure in SA1D2prox genomic region. Front Microbiol. (2017) 8:2542. doi: 10.3389/fmicb.2017.02542
41. Doi N, Yokoyama M, Koma T, Kotani O, Sato H, Adachi A, et al. Concomitant enhancement of HIV-1 replication potential and neutralization-resistance in concert with three adaptive mutations in Env V1/C2/C4 domains. Front Microbiol. (2019) 10:2. doi: 10.3389/fmicb.2019.00002
42. Koma T, Yokoyama M, Kotani O, Doi N, Nakanishi N, Okubo H, et al. Species-specific valid ternary interactions of HIV-1 Env-gp120, CD4, and CCR5 as revealed by an adaptive single-amino acid substitution at the V3 loop tip. J Virol. (2021) 95:e0217720. doi: 10.1128/JVI.02177-20
43. Kao RR, Haydon DT, Lycett SJ, Murcia PR. Supersize me: how whole-genome sequencing and big data are transforming epidemiology. Trends Microbiol. (2014) 22:282–91. doi: 10.1016/j.tim.2014.02.011
44. Sharma D, Priyadarshini P, Vrati S. Unraveling the web of viroinformatics: computational tools and databases in virus research. J Virol. (2015) 89:1489–501. doi: 10.1128/JVI.02027-14
45. Dolan PT, Whitfield ZJ, Andino R. Mapping the evolutionary potential of RNA viruses. Cell Host Microbe. (2018) 23:435–46. doi: 10.1016/j.chom.2018.03.012
46. Rocklöv J, Tozan Y, Ramadona A, Sewe MO, Sudre B, Garrido J, et al. Using big data to monitor the introduction and spread of Chikungunya, Europe, 2017. Emerg Infect Dis. (2019) 25:1041–9. doi: 10.3201/eid2506.180138
47. McLeish MJ, Fraile A, García-Arenal F. Population genomics of plant viruses: the ecology and evolution of virus emergence. Phytopathology. (2021) 111:32–9. doi: 10.1094/PHYTO-08-20-0355-FI
48. Goettsch W, Beerenwinkel N, Deng L, Dölken L, Dutilh BE, Florian Erhard F, et al. ITN-VIROINF: understanding (harmful) virus-host interactions by linking virology and bioinformatics. Viruses. (2021) 13:766. doi: 10.3390/v13050766
49. Knyazev S, Hughes L, Skums P, Zelikovsky A. Epidemiological data analysis of viral quasispecies in the next-generation sequencing era. Brief Bioinform. (2021) . 22:96–108. doi: 10.1093/bib/bbaa101
50. Blassel L, Tostevin A, Villabona-Arenas CJ, Peeters M, Hué S, Gascuel O, et al. Using machine learning and big data to explore the drug resistance landscape in HIV. PloS Comput Biol. (2021) 17:e1008873. doi: 10.1371/journal.pcbi.1008873
51. Markov PV, Ghafari M, Beer M, Lythgoe K, Simmonds P, Stilianakis NI, et al. The evolution of SARS-CoV-2. Nat Rev Microbiol. (2023) . 21:361–79. doi: 10.1038/s41579-023-00878-2
Keywords: viruses, specialty sections of virology, pathogenic viruses, viral diseases, data science, computational science, experimental virology
Citation: Adachi A, Koma T and Nomaguchi M (2024) The 3rd anniversary of Frontiers in Virology: aiming to consolidate the virus research. Front. Virol. 4:1505809. doi: 10.3389/fviro.2024.1505809
Received: 03 October 2024; Accepted: 07 October 2024;
Published: 25 October 2024.
Edited and Reviewed by:
Mario Clerici, University of Milan, ItalyCopyright © 2024 Adachi, Koma and Nomaguchi. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Akio Adachi, YWRhY2hpQHRva3VzaGltYS11LmFjLmpw