Raman signatures of type A and B influenza viruses: molecular origin of the " catch and kill" inactivation mechanism mediated by micrometric silicon nitride powder

Giuseppe Pezzotti; Yoshiki Yasukochi; Eriko Ohgitani; Maiko Nakashio; Masaharu Shin-Ya; Tetsuya Adachi; Toshiro Yamamoto; Saki Ikegami; Wenliang Zhu; Koichiro Higasa; Kazu Okuma; Osam Mazda

doi:10.1039/d4cb00237g

Raman signatures of type A and B influenza viruses: molecular origin of the " catch and kill" inactivation mechanism mediated by micrometric silicon nitride powder

RSC Chem Biol. 2025 Jan 22. doi: 10.1039/d4cb00237g. Online ahead of print.

Authors

Giuseppe Pezzotti^{1

2

3

4

5

6}, Yoshiki Yasukochi⁷, Eriko Ohgitani², Maiko Nakashio^{2

8}, Masaharu Shin-Ya², Tetsuya Adachi^{2

4

9}, Toshiro Yamamoto⁴, Saki Ikegami^{9

10}, Wenliang Zhu¹⁰, Koichiro Higasa⁷, Kazu Okuma⁹, Osam Mazda²

Affiliations

¹ Biomedical Engineering Center, Kansai Medical University 1-9-11 Shin-machi Hirakata Osaka 573-1191 Japan [email protected].
² Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine Kamigyo-ku 465 Kajii-cho Kyoto 602-8566 Japan [email protected].
³ Department of Orthopedic Surgery, Tokyo Medical University 6-7-1 Nishi-Shinjuku Shinjuku-ku 160-0023 Tokyo Japan.
⁴ Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine Kamigyo-ku Kyoto 602-8566 Japan.
⁵ Department of Molecular Science and Nanosystems, Ca' Foscari University of Venice Via Torino 155 30172 Venice Italy.
⁶ Department of Applied Science and Technology, Politecnico di Torino Corso Duca degli Abruzzi 24 10129 Torino Italy.
⁷ Department of Genome Analysis, Institute of Biomedical Science, Kansai Medical University 2-3-1 Shin-machi Hirakata Osaka 573-1191 Japan.
⁸ Department of Emergency and Critical Care Medicine, Faculty of Medicine, Fukuoka University Fukuoka 814-0180 Japan.
⁹ Department of Microbiology, Kansai Medical University, School of Medicine 2-5-1 Shinmachi Hirakata 573-1010 Osaka Prefecture Japan.
¹⁰ Ceramic Physics Laboratory, Kyoto Institute of Technology Sakyo-ku Matsugasaki 606-8585 Kyoto Japan.

Abstract

A multiomic study of the structural characteristics of type A and B influenza viruses by means of highly spectrally resolved Raman spectroscopy is presented. Three virus strains, A H1N1, A H3N2, and B98, were selected because of their known structural variety and because they have co-circulated with variable relative prevalence within the human population since the re-emergence of the H1N1 subtype in 1977. Raman signatures of protein side chains tyrosine, tryptophan, and histidine revealed unequivocal and consistent differences for pH characteristics at the virion surface, while different conformations of two C-S bond configurations in gauche and trans methionine rotamers provided distinct low-wavenumber fingerprints for different virus lineages/subtypes. Short-term exposure to a few percent fraction of silicon nitride (Si₃N₄) micrometric powder in an aqueous environment completely inactivated the influenza virions, independent of lineage/subtype dependent characteristics. The molecular-scale details of the inactivation process were studied by Raman spectroscopy and interpreted in terms of a "catch and kill" mechanism, in which the hydrolyzing ceramic surface first attracts virions with high efficiency through electrochemical interactions (mimicking cellular sialic acid) and then "poisons" the viruses by local hydrolytic elution of ammonia and nitrogen radicals. The latter event causes severe damage to the virions' structures, including structural degradation of RNA purines, rotameric scrambling of methionine residues, formation of sulfhydryl and ionized carboxyl groups, and deprotonation/torsional deformation of tyrosine, tryptophan, and histidine residues. This study confirmed the antiviral effectiveness of Si₃N₄ powder, which is safe to the human body and simply activated by water molecules. Raman spectroscopy was confirmed as a powerful tool in molecular virology, complementary to genomics and unique in providing direct information on virus structures at the molecular scale.