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Tabata K, Itakura Y, Ariizumi T, Igarashi M, Kobayashi H, Intaruck K, Kishimoto M, Kobayashi S, Hall WW, Sasaki M, Sawa H, Orba Y. Development of flavivirus subviral particles with low cross-reactivity by mutations of a distinct antigenic domain. Appl Microbiol Biotechnol 2023; 107:7515-7529. [PMID: 37831184 PMCID: PMC10656323 DOI: 10.1007/s00253-023-12817-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/04/2023] [Accepted: 09/25/2023] [Indexed: 10/14/2023]
Abstract
The most conserved fusion loop (FL) domain present in the flavivirus envelope protein has been reported as a dominant epitope for cross-reactive antibodies to mosquito-borne flaviviruses (MBFVs). As a result, establishing accurate serodiagnosis for MBFV infections has been difficult as anti-FL antibodies are induced by both natural infection and following vaccination. In this study, we modified the most conserved FL domain to overcome this cross-reactivity. We showed that the FL domain of lineage I insect-specific flavivirus (ISFV) has differences in antigenicity from those of MBFVs and lineage II ISFV and determined the key amino acid residues (G106, L107, or F108), which contribute to the antigenic difference. These mutations were subsequently introduced into subviral particles (SVPs) of dengue virus type 2 (DENV2), Zika virus (ZIKV), Japanese encephalitis virus (JEV), and West Nile virus (WNV). In indirect enzyme-linked immunosorbent assays (ELISAs), these SVP mutants when used as antigens reduced the binding of cross-reactive IgG and total Ig induced by infection of ZIKV, JEV, and WNV in mice and enabled the sensitive detection of virus-specific antibodies. Furthermore, immunization of ZIKV or JEV SVP mutants provoked the production of antibodies with lower cross-reactivity to heterologous MBFV antigens compared to immunization with the wild-type SVPs in mice. This study highlights the effectiveness of introducing mutations in the FL domain in MBFV SVPs with lineage I ISFV-derived amino acids to produce SVP antigens with low cross-reactivity and demonstrates an improvement in the accuracy of indirect ELISA-based serodiagnosis for MBFV infections. KEY POINTS: • The FL domain of Lineage I ISFV has a different antigenicity from that of MBFVs. • Mutated SVPs reduce the binding of cross-reactive antibodies in indirect ELISAs. • Inoculation of mutated SVPs induces antibodies with low cross-reactivity.
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Affiliation(s)
- Koshiro Tabata
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, 001-0020, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo, 001-0021, Japan
| | - Yukari Itakura
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, 001-0020, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo, 001-0021, Japan
| | - Takuma Ariizumi
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, 001-0020, Japan
| | - Manabu Igarashi
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, 001-0020, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Kita-Ku, Sapporo, N20, W10001-0020, Japan
| | - Hiroko Kobayashi
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, 001-0020, Japan
| | - Kittiya Intaruck
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, 001-0020, Japan
| | - Mai Kishimoto
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, 001-0020, Japan
- Laboratory of Veterinary Microbiology, Osaka Metropolitan University, Izumisano, 598-8531, Japan
| | - Shintaro Kobayashi
- Laboratory of Public Health, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, 060‑0818, Japan
| | - William W Hall
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Kita-Ku, Sapporo, N20, W10001-0020, Japan
- Global Virus Network, Baltimore, MD, 21201, USA
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Michihito Sasaki
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, 001-0020, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo, 001-0021, Japan
| | - Hirofumi Sawa
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo, 001-0021, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Kita-Ku, Sapporo, N20, W10001-0020, Japan
- Global Virus Network, Baltimore, MD, 21201, USA
- One Health Research Center, Hokkaido University, Sapporo, Hokkaido, 001-0020, Japan
| | - Yasuko Orba
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, 001-0020, Japan.
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo, 001-0021, Japan.
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Kita-Ku, Sapporo, N20, W10001-0020, Japan.
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Sakaguchi S, Urayama SI, Takaki Y, Hirosuna K, Wu H, Suzuki Y, Nunoura T, Nakano T, Nakagawa S. NeoRdRp: A Comprehensive Dataset for Identifying RNA-dependent RNA Polymerases of Various RNA Viruses from Metatranscriptomic Data. Microbes Environ 2022; 37. [PMID: 36002304 PMCID: PMC9530720 DOI: 10.1264/jsme2.me22001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
RNA viruses are distributed throughout various environments, and most have recently been identified by metatranscriptome sequencing. However, due to the high nucleotide diversity of RNA viruses, it is still challenging to identify novel RNA viruses from metatranscriptome data. To overcome this issue, we created a dataset of RNA-dependent RNA polymerase (RdRp) domains that are essential for all RNA viruses belonging to Orthornavirae. Genes with RdRp domains from various RNA viruses were clustered based on amino acid sequence similarities. A multiple sequence alignment was generated for each cluster, and a hidden Markov model (HMM) profile was created when the number of sequences was greater than three. We further refined 426 HMM profiles by detecting RefSeq RNA virus sequences and subsequently combined the hit sequences with the RdRp domains. As a result, 1,182 HMM profiles were generated from 12,502 RdRp domain sequences, and the dataset was named NeoRdRp. The majority of NeoRdRp HMM profiles successfully detected RdRp domains, specifically in the UniProt dataset. Furthermore, we compared the NeoRdRp dataset with two previously reported methods for RNA virus detection using metatranscriptome sequencing data. Our methods successfully identified the majority of RNA viruses in the datasets; however, some RNA viruses were not detected, similar to the other two methods. NeoRdRp may be repeatedly improved by the addition of new RdRp sequences and is applicable as a system for detecting various RNA viruses from diverse metatranscriptome data.
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Affiliation(s)
- Shoichi Sakaguchi
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University
| | - Syun-Ichi Urayama
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba
| | - Yoshihiro Takaki
- Super-cuttingedge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | | | - Hong Wu
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University
| | - Youichi Suzuki
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Takashi Nakano
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine
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