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Demirev AV, Lee S, Park S, Kim H, Cho S, Lee K, Kim K, Song JW, Park MS, Kim JI. Exploring the Genetic Diversity and Molecular Evolution of Seoul and Hantaan Orthohantaviruses. Viruses 2024; 16:105. [PMID: 38257805 PMCID: PMC10818986 DOI: 10.3390/v16010105] [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: 12/08/2023] [Revised: 12/30/2023] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
Seoul (SEOV) and Hantaan (HTNV) orthohantaviruses are significant zoonotic pathogens responsible for hemorrhagic fever with renal syndrome. Here, we investigated the molecular evolution of SEOV and HTNV through phylogenetic and bioinformatic analyses using complete genome sequences of their large (L), medium (M), and small (S) gene segments. Despite similar epizootic cycles and clinical symptoms, SEOV and HTNV exhibited distinct genetic and evolutionary dynamics. The phylogenetic trees of each segment consistently showed major genetic clades associated with the geographical distribution of both viruses. Remarkably, SEOV M and S segments exhibit higher evolutionary rates, rapidly increasing genetic diversity, and a more recent origin in contrast to HTNV. Reassortment events were infrequent, but both viruses appear to utilize the M gene segment in genetic exchanges. SEOV favors the L or M segment reassortment, while HTNV prefers the M or S segment exchange. Purifying selection dominates in all three gene segments of both viruses, yet SEOV experiences an elevated positive selection in its glycoprotein Gc ectodomain. Key amino acid differences, including a positive 'lysine fence' (through residues K77, K82, K231, K307, and K310) located at the tip of the Gn, alongside the physical stability around an RGD-like motif through M108-F334 interaction, may contribute to the unique antigenic properties of SEOV. With the increasing global dispersion and potential implications of SEOV for the global public health landscape, this study highlights the unique evolutionary dynamics and antigenic properties of SEOV and HTNV in informing vaccine design and public health preparedness.
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Affiliation(s)
- Atanas V. Demirev
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul 02841, Republic of Korea (S.L.); (S.P.); (H.K.); (S.C.); (K.L.); (K.K.); (J.-W.S.)
| | - Sangyi Lee
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul 02841, Republic of Korea (S.L.); (S.P.); (H.K.); (S.C.); (K.L.); (K.K.); (J.-W.S.)
| | - Sejik Park
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul 02841, Republic of Korea (S.L.); (S.P.); (H.K.); (S.C.); (K.L.); (K.K.); (J.-W.S.)
| | - Hyunbeen Kim
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul 02841, Republic of Korea (S.L.); (S.P.); (H.K.); (S.C.); (K.L.); (K.K.); (J.-W.S.)
| | - Seunghye Cho
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul 02841, Republic of Korea (S.L.); (S.P.); (H.K.); (S.C.); (K.L.); (K.K.); (J.-W.S.)
| | - Kyuyoung Lee
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul 02841, Republic of Korea (S.L.); (S.P.); (H.K.); (S.C.); (K.L.); (K.K.); (J.-W.S.)
| | - Kisoon Kim
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul 02841, Republic of Korea (S.L.); (S.P.); (H.K.); (S.C.); (K.L.); (K.K.); (J.-W.S.)
- Vaccine Innovation Center, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Jin-Won Song
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul 02841, Republic of Korea (S.L.); (S.P.); (H.K.); (S.C.); (K.L.); (K.K.); (J.-W.S.)
- Vaccine Innovation Center, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Man-Seong Park
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul 02841, Republic of Korea (S.L.); (S.P.); (H.K.); (S.C.); (K.L.); (K.K.); (J.-W.S.)
- Vaccine Innovation Center, Korea University College of Medicine, Seoul 02841, Republic of Korea
- Biosafety Center, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Jin Il Kim
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul 02841, Republic of Korea (S.L.); (S.P.); (H.K.); (S.C.); (K.L.); (K.K.); (J.-W.S.)
- Vaccine Innovation Center, Korea University College of Medicine, Seoul 02841, Republic of Korea
- Biosafety Center, Korea University College of Medicine, Seoul 02841, Republic of Korea
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Kim J, Park K, Kim K, Noh J, Kim SG, Yang E, Cho HK, Lee SH, No JS, Lee GY, Lee D, Song DH, Gu SH, Park MS, Cho NH, Jeong ST, Kim WK, Song JW. High-resolution phylogeographical surveillance of Hantaan orthohantavirus using rapid amplicon-based Flongle sequencing, Republic of Korea. J Med Virol 2024; 96:e29346. [PMID: 38178580 DOI: 10.1002/jmv.29346] [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: 10/20/2023] [Revised: 12/04/2023] [Accepted: 12/14/2023] [Indexed: 01/06/2024]
Abstract
Orthohantaviruses, etiological agents of hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome, pose a critical public health threat worldwide. Hantaan orthohantavirus (HTNV) outbreaks are particularly endemic in Gyeonggi Province in northern area of the Republic of Korea (ROK). Small mammals were collected from three regions in the Gyeonggi Province during 2017 and 2018. Serological and molecular prevalence of HTNV was 25/201 (12.4%) and 10/25 (40%), respectively. A novel nanopore-based diagnostic assay using a cost-efficient Flongle chip was developed to rapidly and sensitively detect HTNV infection in rodent specimens within 3 h. A rapid phylogeographical surveillance of HTNV at high-resolution phylogeny was established using the amplicon-based Flongle sequencing. In total, seven whole-genome sequences of HTNV were newly obtained from wild rodents collected in Paju-si (Gaekhyeon-ri) and Yeoncheon-gun (Hyeonga-ri and Wangnim-ri), Gyeonggi Province. Phylogenetic analyses revealed well-supported evolutionary divergence and genetic diversity, enhancing the resolution of the phylogeographic map of orthohantaviruses in the ROK. Incongruences in phylogenetic patterns were identified among HTNV tripartite genomes, suggesting differential evolution for each segment. These findings provide crucial insights into on-site diagnostics, genome-based surveillance, and the evolutionary dynamics of orthohantaviruses to mitigate hantaviral outbreaks in HFRS-endemic areas in the ROK.
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Affiliation(s)
- Jongwoo Kim
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kyungmin Park
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kijin Kim
- Centre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Juyoung Noh
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seong-Gyu Kim
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Korea University College of Medicine, Seoul, Republic of Korea
| | - Eunyoung Yang
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Korea University College of Medicine, Seoul, Republic of Korea
| | - Hee-Kyung Cho
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seung-Ho Lee
- Chem-Bio Technology Center, Agency for Defense Development, Daejeon, Republic of Korea
| | - Jin Sun No
- Division of High-Risk Pathogens, Bureau of Infectious Diseases Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Geum-Young Lee
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
| | - Daesang Lee
- Chem-Bio Technology Center, Agency for Defense Development, Daejeon, Republic of Korea
| | - Dong-Hyun Song
- Chem-Bio Technology Center, Agency for Defense Development, Daejeon, Republic of Korea
| | - Se Hun Gu
- Chem-Bio Technology Center, Agency for Defense Development, Daejeon, Republic of Korea
| | - Man-Seong Park
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Nam-Hyuk Cho
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Seong Tae Jeong
- Chem-Bio Technology Center, Agency for Defense Development, Daejeon, Republic of Korea
| | - Won-Keun Kim
- Department of Microbiology, Hallym University, Chuncheon, Republic of Korea
- Institute of Medical Research, Hallym University, Chuncheon, Republic of Korea
| | - Jin-Won Song
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Korea University College of Medicine, Seoul, Republic of Korea
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Cintron R, Whitmer SLM, Moscoso E, Campbell EM, Kelly R, Talundzic E, Mobley M, Chiu KW, Shedroff E, Shankar A, Montgomery JM, Klena JD, Switzer WM. HantaNet: A New MicrobeTrace Application for Hantavirus Classification, Genomic Surveillance, Epidemiology and Outbreak Investigations. Viruses 2023; 15:2208. [PMID: 38005885 PMCID: PMC10675615 DOI: 10.3390/v15112208] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
Hantaviruses zoonotically infect humans worldwide with pathogenic consequences and are mainly spread by rodents that shed aerosolized virus particles in urine and feces. Bioinformatics methods for hantavirus diagnostics, genomic surveillance and epidemiology are currently lacking a comprehensive approach for data sharing, integration, visualization, analytics and reporting. With the possibility of hantavirus cases going undetected and spreading over international borders, a significant reporting delay can miss linked transmission events and impedes timely, targeted public health interventions. To overcome these challenges, we built HantaNet, a standalone visualization engine for hantavirus genomes that facilitates viral surveillance and classification for early outbreak detection and response. HantaNet is powered by MicrobeTrace, a browser-based multitool originally developed at the Centers for Disease Control and Prevention (CDC) to visualize HIV clusters and transmission networks. HantaNet integrates coding gene sequences and standardized metadata from hantavirus reference genomes into three separate gene modules for dashboard visualization of phylogenetic trees, viral strain clusters for classification, epidemiological networks and spatiotemporal analysis. We used 85 hantavirus reference datasets from GenBank to validate HantaNet as a classification and enhanced visualization tool, and as a public repository to download standardized sequence data and metadata for building analytic datasets. HantaNet is a model on how to deploy MicrobeTrace-specific tools to advance pathogen surveillance, epidemiology and public health globally.
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Affiliation(s)
- Roxana Cintron
- Laboratory Branch, Division of HIV Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA (A.S.); (W.M.S.)
| | - Shannon L. M. Whitmer
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA (M.M.); (E.S.); (J.D.K.)
| | - Evan Moscoso
- General Dynamics Information Technology, Atlanta, GA 30329, USA; (E.M.); (R.K.)
| | - Ellsworth M. Campbell
- Laboratory Branch, Division of HIV Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA (A.S.); (W.M.S.)
| | - Reagan Kelly
- General Dynamics Information Technology, Atlanta, GA 30329, USA; (E.M.); (R.K.)
| | - Emir Talundzic
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA (M.M.); (E.S.); (J.D.K.)
| | - Melissa Mobley
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA (M.M.); (E.S.); (J.D.K.)
| | - Kuo Wei Chiu
- General Dynamics Information Technology, Atlanta, GA 30329, USA; (E.M.); (R.K.)
| | - Elizabeth Shedroff
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA (M.M.); (E.S.); (J.D.K.)
| | - Anupama Shankar
- Laboratory Branch, Division of HIV Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA (A.S.); (W.M.S.)
| | - Joel M. Montgomery
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA (M.M.); (E.S.); (J.D.K.)
| | - John D. Klena
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA (M.M.); (E.S.); (J.D.K.)
| | - William M. Switzer
- Laboratory Branch, Division of HIV Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA (A.S.); (W.M.S.)
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Park K, Noh J, Kim K, Kim J, Cho HK, Kim SG, Yang E, Kim WK, Song JW. A Development of Rapid Whole-Genome Sequencing of Seoul orthohantavirus Using a Portable One-Step Amplicon-Based High Accuracy Nanopore System. Viruses 2023; 15:1542. [PMID: 37515228 PMCID: PMC10386077 DOI: 10.3390/v15071542] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Whole-genome sequencing provides a robust platform for investigating the epidemiology and transmission of emerging viruses. Oxford Nanopore Technologies allows for real-time viral sequencing on a local laptop system for point-of-care testing. Seoul orthohantavirus (Seoul virus, SEOV), harbored by Rattus norvegicus and R. rattus, causes mild hemorrhagic fever with renal syndrome and poses an important threat to public health worldwide. We evaluated the deployable MinION system to obtain high-fidelity entire-length sequences of SEOV for the genome identification of accurate infectious sources and their genetic diversity. One-step amplicon-based nanopore sequencing was performed from SEOV 80-39 specimens with different viral copy numbers and SEOV-positive wild rats. The KU-ONT-SEOV-consensus module was developed to analyze SEOV genomic sequences generated from the nanopore system. Using amplicon-based nanopore sequencing and the KU-ONT-consensus pipeline, we demonstrated novel molecular diagnostics for acquiring full-length SEOV genome sequences, with sufficient read depth in less than 6 h. The consensus sequence accuracy of the SEOV small, medium, and large genomes showed 99.75-100% (for SEOV 80-39 isolate) and 99.62-99.89% (for SEOV-positive rats) identities. This study provides useful insights into on-site diagnostics based on nanopore technology and the genome epidemiology of orthohantaviruses for a quicker response to hantaviral outbreaks.
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Affiliation(s)
- Kyungmin Park
- Department of Microbiology, College of Medicine, Korea University, Seoul 02841, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Juyoung Noh
- Department of Microbiology, College of Medicine, Korea University, Seoul 02841, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Kijin Kim
- Centre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Jongwoo Kim
- Department of Microbiology, College of Medicine, Korea University, Seoul 02841, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Hee-Kyung Cho
- Department of Microbiology, College of Medicine, Korea University, Seoul 02841, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Seong-Gyu Kim
- Department of Microbiology, College of Medicine, Korea University, Seoul 02841, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Eunyoung Yang
- Department of Microbiology, College of Medicine, Korea University, Seoul 02841, Republic of Korea
| | - Won-Keun Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea
- Institute of Medical Research, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea
| | - Jin-Won Song
- Department of Microbiology, College of Medicine, Korea University, Seoul 02841, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea
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Omoga DCA, Tchouassi DP, Venter M, Ogola EO, Rotich G, Muthoni JN, Ondifu DO, Torto B, Junglen S, Sang R. Divergent Hantavirus in Somali Shrews ( Crocidura somalica) in the Semi-Arid North Rift, Kenya. Pathogens 2023; 12:pathogens12050685. [PMID: 37242355 DOI: 10.3390/pathogens12050685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/21/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
Hantaviruses are zoonotic rodent-borne viruses that are known to infect humans and cause various symptoms of disease, including hemorrhagic fever with renal and cardiopulmonary syndromes. They have a segmented single-stranded, enveloped, negative-sense RNA genome and are widely distributed. This study aimed to investigate the circulation of rodent-borne hantaviruses in peridomestic rodents and shrews in two semi-arid ecologies within the Kenyan Rift Valley. The small mammals were trapped using baited folding Sherman traps set within and around houses, then they were sedated and euthanatized through cervical dislocation before collecting blood and tissue samples (liver, kidney, spleen, and lungs). Tissue samples were screened with pan-hantavirus PCR primers, targeting the large genome segment (L) encoding the RNA-dependent RNA polymerase (RdRp). Eleven of the small mammals captured were shrews (11/489, 2.5%) and 478 (97.5%) were rodents. A cytochrome b gene-based genetic assay for shrew identification confirmed the eleven shrews sampled to be Crocidura somalica. Hantavirus RNA was detected in three (3/11, 27%) shrews from Baringo County. The sequences showed 93-97% nucleotide and 96-99% amino acid identities among each other, as well as 74-76% nucleotide and 79-83% amino acid identities to other shrew-borne hantaviruses, such as Tanganya virus (TNGV). The detected viruses formed a monophyletic clade with shrew-borne hantaviruses from other parts of Africa. To our knowledge, this constitutes the first report published on the circulation of hantaviruses in shrews in Kenya.
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Affiliation(s)
- Dorcus C A Omoga
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
- Zoonotic arbo and Respiratory Virus Research Program, Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health, University of Pretoria, Gezina 0031, South Africa
| | - David P Tchouassi
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
| | - Marietjie Venter
- Zoonotic arbo and Respiratory Virus Research Program, Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health, University of Pretoria, Gezina 0031, South Africa
| | - Edwin O Ogola
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
| | - Gilbert Rotich
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
| | - Joseph N Muthoni
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
| | - Dickens O Ondifu
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
| | - Baldwyn Torto
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
| | - Sandra Junglen
- Institute of Virology, Charité Universitätsmedizin Berlin, Corporate Member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Rosemary Sang
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
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Zhang X, Zhang Y, Liu H, Tang K, Zhang C, Wang M, Xue M, Jia X, Hu H, Li N, Zhuang R, Jin B, Zhang F, Zhang Y, Ma Y. IL-15 induced bystander activation of CD8 + T cells may mediate endothelium injury through NKG2D in Hantaan virus infection. Front Cell Infect Microbiol 2022; 12:1084841. [PMID: 36590594 PMCID: PMC9797980 DOI: 10.3389/fcimb.2022.1084841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/01/2022] [Indexed: 12/23/2022] Open
Abstract
Introduction Hantaan virus (HTNV) can cause endothelium injury in hemorrhagic fever with renal syndrome (HFRS) patients. Bystander activation of CD8+ T cells by virus infection has been shown that was involved in host injury, but it is unclear during HTNV infection. This project aimed to study the effect of bystander-activated CD8+ T cell responses in HTNV infection. Methods The in vitro infection model was established to imitate the injury of endothelium in HFRS patients. Flow cytometry was performed to detect the expression of markers of tetramer+ CD8+ T cells and human umbilical vein endothelial cells (HUVECs). The levels of interleukin-15 (IL-15) in serum and supermanant were detected using ELISA kit. The expression of MICA of HUVECs was respectively determined by flow cytometry and western blot. The cytotoxicity of CD8+ T cells was assessed through the cytotoxicity assay and antibody blocking assay. Results EBV or CMV-specific CD8+ T cells were bystander activated after HTNV infection in HFRS patients. HTNV-infected HUVECs in vitro could produce high levels of IL-15, which was positively correlated with disease severity and the expression of NKG2D on bystander-activated CD8+ T cells. Moreover, the elevated IL-15 could induce activation of CD122 (IL-15Rβ)+NKG2D+ EBV/CMV-specific CD8+ T cells. The expression of IL-15Rα and ligand for NKG2D were upregulated on HTNV-infected HUVECs. Bystander-activated CD8+ T cells could exert cytotoxicity effects against HTNV-infected HUVECs, which could be enhanced by IL-15 stimulation and blocked by NKG2D antibody. Discussion IL-15 induced bystander activation of CD8+ T cells through NKG2D, which may mediate endothelium injury during HTNV infection in HFRS patients.
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Affiliation(s)
- Xiyue Zhang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (The Fourth Military Medical University), Xi’an, China,Basic Medicine School, Yanan University, Yan’an, China
| | - Yusi Zhang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (The Fourth Military Medical University), Xi’an, China
| | - He Liu
- Department of Microbiology, Basic Medicine School, Air-Force Medical University (The Fourth Military Medical University), Xi’an, China
| | - Kang Tang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (The Fourth Military Medical University), Xi’an, China
| | - Chunmei Zhang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (The Fourth Military Medical University), Xi’an, China
| | - Meng Wang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (The Fourth Military Medical University), Xi’an, China,Basic Medicine School, Yanan University, Yan’an, China
| | - Manling Xue
- Department of Immunology, Basic Medicine School, Air-Force Medical University (The Fourth Military Medical University), Xi’an, China,Basic Medicine School, Yanan University, Yan’an, China
| | - Xiaozhou Jia
- Department of Infectious Diseases, Eighth Hospital of Xi'an, Xi’an, China
| | - Haifeng Hu
- Center for Infectious Diseases, Tangdu Hospital, Air-Force Medical University (The Fourth Military Medical University), Xi’an, China
| | - Na Li
- Department of Transfusion Medicine, Xijing Hospital, Air-Force Medical University (The Fourth Military Medical University), Xi’an, China
| | - Ran Zhuang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (The Fourth Military Medical University), Xi’an, China
| | - Boquan Jin
- Department of Immunology, Basic Medicine School, Air-Force Medical University (The Fourth Military Medical University), Xi’an, China
| | - Fanglin Zhang
- Department of Microbiology, Basic Medicine School, Air-Force Medical University (The Fourth Military Medical University), Xi’an, China
| | - Yun Zhang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (The Fourth Military Medical University), Xi’an, China,*Correspondence: Yun Zhang, ; Ying Ma,
| | - Ying Ma
- Department of Immunology, Basic Medicine School, Air-Force Medical University (The Fourth Military Medical University), Xi’an, China,*Correspondence: Yun Zhang, ; Ying Ma,
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Park K, Lee SH, Kim J, Lee J, Lee GY, Cho S, Noh J, Choi J, Park J, Song DH, Gu SH, Yun H, Kim JE, Lee D, Hwang IU, Kim WK, Song JW. A Portable Diagnostic Assay, Genetic Diversity, and Isolation of Seoul Virus from Rattus norvegicus Collected in Gangwon Province, Republic of Korea. Pathogens 2022; 11:1047. [PMID: 36145479 PMCID: PMC9503505 DOI: 10.3390/pathogens11091047] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/11/2022] [Accepted: 09/12/2022] [Indexed: 11/16/2022] Open
Abstract
Seoul virus (SEOV), an etiological agent for hemorrhagic fever with renal syndrome, poses a significant public health threat worldwide. This study evaluated the feasibility of a mobile Biomeme platform for facilitating rapid decision making of SEOV infection. A total of 27 Rattus norvegicus were collected from Seoul Metropolitan City and Gangwon Province in Republic of Korea (ROK), during 2016-2020. The serological and molecular prevalence of SEOV was 5/27 (18.5%) and 2/27 (7.4%), respectively. SEOV RNA was detected in multiple tissues of rodents using the Biomeme device, with differences in Ct values ranging from 0.6 to 2.1 cycles compared to a laboratory benchtop system. Using amplicon-based next-generation sequencing, whole-genome sequences of SEOV were acquired from lung tissues of Rn18-1 and Rn19-5 collected in Gangwon Province. Phylogenetic analysis showed a phylogeographical diversity of rat-borne orthohantavirus collected in Gangwon Province. We report a novel isolate of SEOV Rn19-5 from Gangwon Province. Our findings demonstrated that the Biomeme system can be applied for the molecular diagnosis of SEOV comparably to the laboratory-based platform. Whole-genome sequencing of SEOV revealed the phylogeographical diversity of orthohantavirus in the ROK. This study provides important insights into the field-deployable diagnostic assays and genetic diversity of orthohantaviruses for the rapid response to hantaviral outbreaks in the ROK.
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Affiliation(s)
- Kyungmin Park
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea
- Department of Microbiology, College of Medicine, Korea University, Seoul 02841, Korea
| | - Seung-Ho Lee
- Chem-Bio Technology Center, Agency for Defense Development, Daejeon 34186, Korea
| | - Jongwoo Kim
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea
- Department of Microbiology, College of Medicine, Korea University, Seoul 02841, Korea
| | - Jingyeong Lee
- Department of Microbiology, College of Medicine, Korea University, Seoul 02841, Korea
| | - Geum-Young Lee
- Department of Microbiology, College of Medicine, Korea University, Seoul 02841, Korea
| | - Seungchan Cho
- Department of Microbiology, College of Medicine, Korea University, Seoul 02841, Korea
| | - Juyoung Noh
- Department of Microbiology, College of Medicine, Korea University, Seoul 02841, Korea
| | - Jeewan Choi
- Republic of Korea Armed Forces Medical Command, Seongnam 13415, Korea
| | - Juwon Park
- The Fifth Preventive Medicine Unit of Republic of Korea Army, Pocheon 11132, Korea
| | - Dong-Hyun Song
- Chem-Bio Technology Center, Agency for Defense Development, Daejeon 34186, Korea
| | - Se Hun Gu
- Chem-Bio Technology Center, Agency for Defense Development, Daejeon 34186, Korea
| | - Hyeongseok Yun
- Chem-Bio Technology Center, Agency for Defense Development, Daejeon 34186, Korea
| | - Jung-Eun Kim
- Chem-Bio Technology Center, Agency for Defense Development, Daejeon 34186, Korea
| | - Daesang Lee
- Chem-Bio Technology Center, Agency for Defense Development, Daejeon 34186, Korea
| | - Il-Ung Hwang
- Department of Orthopaedic Surgery, Sheikh Khalifa Specialty Hospital, Seoul National University Hospital, Seoul 02841, Korea
| | - Won-Keun Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon 24252, Korea
- Institute of Medical Research, College of Medicine, Hallym University, Chuncheon 24252, Korea
| | - Jin-Won Song
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea
- Department of Microbiology, College of Medicine, Korea University, Seoul 02841, Korea
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8
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Lee J, Park K, Kim J, Lee SH, Lee GY, Cho S, Kim HC, Klein TA, Kim JA, Choi J, Park J, Song DH, Gu SH, Yun H, Kim JE, Lee D, Hur GH, Jeong ST, Hwang IU, Kim WK, Song JW. Whole-genome sequencing and genetic diversity of severe fever with thrombocytopenia syndrome virus using multiplex PCR-based nanopore sequencing, Republic of Korea. PLoS Negl Trop Dis 2022; 16:e0010763. [PMID: 36094957 PMCID: PMC9499217 DOI: 10.1371/journal.pntd.0010763] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 09/22/2022] [Accepted: 08/23/2022] [Indexed: 11/19/2022] Open
Abstract
Background
Whole-genome sequencing plays a critical role in the genomic epidemiology intended to improve understanding the spread of emerging viruses. Dabie bandavirus, causing severe fever with thrombocytopenia syndrome (SFTS), is a zoonotic tick-borne virus that poses a significant public health threat. We aimed to evaluate a novel amplicon-based nanopore sequencing tool to obtain whole-genome sequences of Dabie bandavirus, also known as SFTS virus (SFTSV), and investigate the molecular prevalence in wild ticks, Republic of Korea (ROK).
Principal findings
A total of 6,593 ticks were collected from Gyeonggi and Gangwon Provinces, ROK in 2019 and 2020. Quantitative polymerase chain reaction revealed the presence of SFSTV RNA in three Haemaphysalis longicornis ticks. Two SFTSV strains were isolated from H. longicornis captured from Pocheon and Cheorwon. Multiplex polymerase chain reaction-based nanopore sequencing provided nearly full-length tripartite genome sequences of SFTSV within one hour running. Phylogenetic and reassortment analyses were performed to infer evolutionary relationships among SFTSVs. Phylogenetic analysis grouped SFTSV Hl19-31-4 and Hl19-31-13 from Pocheon with sub-genotype B-1 in all segments. SFTSV Hl20-8 was found to be a genomic organization compatible with B-1 (for L segment) and B-2 (for M and S segments) sub-genotypes, indicating a natural reassortment between sub-genotypes.
Conclusion/Significance
Amplicon-based next-generation sequencing is a robust tool for whole-genome sequencing of SFTSV using the nanopore platform. The molecular prevalence and geographical distribution of SFTSV enhanced the phylogeographic map at high resolution for sophisticated prevention of emerging SFTS in endemic areas. Our findings provide important insights into the rapid whole-genome sequencing and genetic diversity for the genome-based diagnosis of SFTSV in the endemic outbreak.
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Affiliation(s)
- Jingyeong Lee
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kyungmin Park
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jongwoo Kim
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seung-Ho Lee
- Chem-Bio Technology Center, Agency for Defense Development, Yuseong, Daejeon, Republic of Korea
| | - Geum-Young Lee
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seungchan Cho
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
| | - Heung-Chul Kim
- Force Health Protection and Preventive Medicine, Medical Department Activity-Korea/65th Medical Brigade, Unit 15281, United States of America
| | - Terry A. Klein
- Force Health Protection and Preventive Medicine, Medical Department Activity-Korea/65th Medical Brigade, Unit 15281, United States of America
| | - Jeong-Ah Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Diseases Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Jeewan Choi
- Republic of Korea Armed Forces Medical Command, Seongnam, Republic of Korea
| | - Juwan Park
- The Fifth Preventive Medicine Unit of Republic of Korea Army, Pocheon, Republic of Korea
| | - Dong-Hyun Song
- Chem-Bio Technology Center, Agency for Defense Development, Yuseong, Daejeon, Republic of Korea
| | - Se Hun Gu
- Chem-Bio Technology Center, Agency for Defense Development, Yuseong, Daejeon, Republic of Korea
| | - Hyeongseok Yun
- Chem-Bio Technology Center, Agency for Defense Development, Yuseong, Daejeon, Republic of Korea
| | - Jung-Eun Kim
- Chem-Bio Technology Center, Agency for Defense Development, Yuseong, Daejeon, Republic of Korea
| | - Daesang Lee
- Chem-Bio Technology Center, Agency for Defense Development, Yuseong, Daejeon, Republic of Korea
| | - Gyeung Haeng Hur
- Chem-Bio Technology Center, Agency for Defense Development, Yuseong, Daejeon, Republic of Korea
| | - Seong Tae Jeong
- Chem-Bio Technology Center, Agency for Defense Development, Yuseong, Daejeon, Republic of Korea
| | - Il-Ung Hwang
- Department of Orthopaedic Surgery, Sheikh Khalifa Specialty Hospital, Seoul National University Hospital, Seoul, Republic of Korea
| | - Won-Keun Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
- Institute of Medical Research, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Jin-Won Song
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
- * E-mail:
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9
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Gutiérrez Jaraa JP, Quezada MT. Modeling of hantavirus cardiopulmonary syndrome. Medwave 2022; 22:e8722. [DOI: 10.5867/medwave.2022.03.002526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 03/01/2022] [Indexed: 11/27/2022] Open
Abstract
Introduction Hantavirus cardiopulmonary syndrome is an infection caused by rodents of the Bunyanvirales family towards humans. This disease in Chile is considered endemic, which has a high fatality rate. At present, some studies show the contagion between people of the Andes virus, whose locality is concentrated in Argentina and Chile. Objectives Analyze the possibility of hantavirus transmission between humans using an SEIR-type mathematical model. Methods An SEIR (Susceptible, Exposed, Infectious and Recovered) mathematical model to express the dynamics of hantavirus disease is proposed, including the possibility of human-to-human transmission and the perception of risk. Results The peak of human-to-human contagion decreases by about 25% after increasing people’s perception of risk by reducing the rate of resistance to changeand increasing the speed of people’s reaction. Conclusions It is urgent to review risk communication strategies and prevention measures in the face of this possibility of massive human-tohuman infections, in addition to strengthening research and planning the development of a vaccine to protect populations exposed to this disease with a high fatality rate.
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10
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Ren D, Fu S, Yan T, Ni T, Zhang Z, Zhang M, Zhou J, Yang N, Yang Y, He Y, Chen T, Zhao Y, Liu J. The Clinical Characteristics and Outcomes of Hemorrhagic Fever With Renal Syndrome in Pregnancy. Front Med (Lausanne) 2022; 9:839224. [PMID: 35265645 PMCID: PMC8899103 DOI: 10.3389/fmed.2022.839224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 01/25/2022] [Indexed: 11/13/2022] Open
Abstract
Pregnant women with hemorrhagic fever with renal syndrome (HFRS) are a significant challenge for clinicians. The clinical characteristics of HFRS in pregnant women and its influence on both the pregnant women and fetus have yet to be clarified clearly. To highlight the specific clinical features of HFRS in pregnant women and the outcomes of pregnant women with HFRS and their fetuses, we screened pregnant women with HFRS from inception to May 1st 2021. We also conducted a comparison with non-pregnant women complicated with HFRS. Twenty-seven pregnant women and 87 non-pregnant women with complete electronic medical records were enrolled for final analyses; 55.6% (15/27) and 21.8% (19/87) were diagnosed as critical type in pregnant women and non-pregnant women, respectively. Compared with non-pregnant patients, there was a significantly higher likelihood of critical status in pregnant patients; the risk was significantly higher in late trimester (p <0.001). In addition, hypoalbuminemia and anemia were also evident in pregnant patients (p = 0.04, p <0.001, respectively). Leukocyte count, especially when higher than 15 × 109/L, was significantly correlated with disease severity (p = 0.009). After comprehensive therapy, 26 pregnant patients recovered without sequelae. Five fetal adverse events were reported during hospitalization. All adverse events were observed in mothers with critical types (p = 0.047, X2 = 4.909) and occurred in the later trimester. Collectively, our data show that pregnant woman with HFRS during the third trimester presents a more severe condition, especially those with leukocytosis. However, the majority of those pregnant patients could recover with comprehensive treatment and undergo normal labor.
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Affiliation(s)
- Danfeng Ren
- The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Shaanxi Clinical Research Center of Infectious Diseases, Xi'an, China
| | - Shan Fu
- The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Shaanxi Clinical Research Center of Infectious Diseases, Xi'an, China
| | - Taotao Yan
- The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Shaanxi Clinical Research Center of Infectious Diseases, Xi'an, China
| | - Tianzhi Ni
- The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Shaanxi Clinical Research Center of Infectious Diseases, Xi'an, China
| | - Ze Zhang
- The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Shaanxi Clinical Research Center of Infectious Diseases, Xi'an, China
| | - Mengmeng Zhang
- The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Shaanxi Clinical Research Center of Infectious Diseases, Xi'an, China
| | - Jingwen Zhou
- The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Shaanxi Clinical Research Center of Infectious Diseases, Xi'an, China
| | - Nan Yang
- The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Shaanxi Clinical Research Center of Infectious Diseases, Xi'an, China
| | - Yuan Yang
- The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Shaanxi Clinical Research Center of Infectious Diseases, Xi'an, China
| | - Yingli He
- The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Shaanxi Clinical Research Center of Infectious Diseases, Xi'an, China
| | - Tianyan Chen
- The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Shaanxi Clinical Research Center of Infectious Diseases, Xi'an, China
| | - Yingren Zhao
- The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Shaanxi Clinical Research Center of Infectious Diseases, Xi'an, China
| | - Jinfeng Liu
- The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Shaanxi Clinical Research Center of Infectious Diseases, Xi'an, China
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11
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Ismail S, Abbasi SW, Yousaf M, Ahmad S, Muhammad K, Waheed Y. Design of a Multi-Epitopes Vaccine against Hantaviruses: An Immunoinformatics and Molecular Modelling Approach. Vaccines (Basel) 2022; 10:vaccines10030378. [PMID: 35335010 PMCID: PMC8953224 DOI: 10.3390/vaccines10030378] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 02/07/2023] Open
Abstract
Hantaviruses are negative-sense, enveloped, single-stranded RNA viruses of the family Hantaviridae. In recent years, rodent-borne hantaviruses have emerged as novel zoonotic viruses posing a substantial health issue and socioeconomic burden. In the current research, a reverse vaccinology approach was applied to design a multi-epitope-based vaccine against hantavirus. A set of 340 experimentally reported epitopes were retrieved from Virus Pathogen Database and Analysis Resource (ViPR) and subjected to different analyses such as antigenicity, allergenicity, solubility, IFN gamma, toxicity, and virulent checks. Finally, 10 epitopes which cleared all the filters used were linked with each other through specific GPGPG linkers to construct a multi-antigenic epitope vaccine. The designed vaccine was then joined to three different adjuvants-TLR4-agonist adjuvant, β-defensin, and 50S ribosomal protein L7/L12-using an EAAAK linker to boost up immune-stimulating responses and check the potency of vaccine with each adjuvant. The designed vaccine structures were modelled and subjected to error refinement and disulphide engineering to enhance their stability. To understand the vaccine binding affinity with immune cell receptors, molecular docking was performed between the designed vaccines and TLR4; the docked complex with a low level of global energy was then subjected to molecular dynamics simulations to validate the docking results and dynamic behaviour. The docking binding energy of vaccines with TLR4 is -29.63 kcal/mol (TLR4-agonist), -3.41 kcal/mol (β-defensin), and -11.03 kcal/mol (50S ribosomal protein L7/L12). The systems dynamics revealed all three systems to be highly stable with a root-mean-square deviation (RMSD) value within 3 Å. To test docking predictions and determine dominant interaction energies, binding free energies of vaccine(s)-TLR4 complexes were calculated. The net binding energy of the systems was as follows: TLR4-agonist vaccine with TLR4 (MM-GBSA, -1628.47 kcal/mol and MM-PBSA, -37.75 kcal/mol); 50S ribosomal protein L7/L12 vaccine with TLR4 complex (MM-GBSA, -194.62 kcal/mol and MM-PBSA, -150.67 kcal/mol); β-defensin vaccine with TLR4 complex (MM-GBSA, -9.80 kcal/mol and MM-PBSA, -42.34 kcal/mol). Finally, these findings may aid experimental vaccinologists in developing a very potent hantavirus vaccine.
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Affiliation(s)
- Saba Ismail
- Foundation University Medical College, Foundation University Islamabad, Islamabad 44000, Pakistan;
| | - Sumra Wajid Abbasi
- NUMS Department of Biological Sciences, National University of Medical Sciences, Abid Majeed Rd, The Mall, Rawalpindi 46000, Pakistan;
| | - Maha Yousaf
- Department of Biosciences, COMSATS University Islamabad, Islamabad 45550, Pakistan;
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan;
| | - Khalid Muhammad
- Department of Biology, College of Science, United Arab Emirates University, Al Ain 15551, United Arab Emirates
- Correspondence: (K.M.); (Y.W.)
| | - Yasir Waheed
- Foundation University Medical College, Foundation University Islamabad, Islamabad 44000, Pakistan;
- Correspondence: (K.M.); (Y.W.)
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12
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Discovery and Genetic Characterization of Novel Paramyxoviruses Related to the Genus Henipavirus in Crocidura Species in the Republic of Korea. Viruses 2021; 13:v13102020. [PMID: 34696450 PMCID: PMC8537881 DOI: 10.3390/v13102020] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/04/2021] [Accepted: 10/04/2021] [Indexed: 12/21/2022] Open
Abstract
Paramyxoviruses, negative-sense single-stranded RNA viruses, pose a critical threat to human public health. Currently, 78 species, 17 genera, and 4 subfamilies of paramyxoviruses are harbored by multiple natural reservoirs, including rodents, bats, birds, reptiles, and fish. Henipaviruses are critical zoonotic pathogens that cause severe acute respiratory distress and neurological diseases in humans. Using reverse transcription-polymerase chain reaction, 115 Crocidura species individuals were examined for the prevalence of paramyxovirus infections. Paramyxovirus RNA was observed in 26 (22.6%) shrews collected at five trapping sites, Republic of Korea. Herein, we report two genetically distinct novel paramyxoviruses (genus: Henipavirus): Gamak virus (GAKV) and Daeryong virus (DARV) isolated from C. lasiura and C. shantungensis, respectively. Two GAKVs and one DARV were nearly completely sequenced using next-generation sequencing. GAKV and DARV contain six genes (3′-N-P-M-F-G-L-5′) with genome sizes of 18,460 nucleotides and 19,471 nucleotides, respectively. The phylogenetic inference demonstrated that GAKV and DARV form independent genetic lineages of Henipavirus in Crocidura species. GAKV-infected human lung epithelial cells elicited the induction of type I/III interferons, interferon-stimulated genes, and proinflammatory cytokines. In conclusion, this study contributes further understandings of the molecular prevalence, genetic characteristics and diversity, and zoonotic potential of novel paramyxoviruses in shrews.
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13
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Multiplex PCR-Based Nanopore Sequencing and Epidemiological Surveillance of Hantaan orthohantavirus in Apodemus agrarius, Republic of Korea. Viruses 2021; 13:v13050847. [PMID: 34066592 PMCID: PMC8148566 DOI: 10.3390/v13050847] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/01/2021] [Accepted: 05/04/2021] [Indexed: 01/02/2023] Open
Abstract
Whole-genome sequencing of infectious agents enables the identification and characterization of emerging viruses. The MinION device is a portable sequencer that allows real-time sequencing in fields or hospitals. Hantaan orthohantavirus (Hantaan virus, HTNV), harbored by Apodemus agrarius, causes hemorrhagic fever with renal syndrome (HFRS) and poses a critical public health threat worldwide. In this study, we aimed to evaluate the feasibility of using nanopore sequencing for whole-genome sequencing of HTNV from samples having different viral copy numbers. Amplicon-based next-generation sequencing was performed in A. agrarius lung tissues collected from the Republic of Korea. Genomic sequences of HTNV were analyzed based on the viral RNA copy numbers. Amplicon-based nanopore sequencing provided nearly full-length genomic sequences of HTNV and showed sufficient read depth for phylogenetic analysis after 8 h of sequencing. The average identity of the HTNV genome sequences for the nanopore sequencer compared to those of generated from Illumina MiSeq revealed 99.8% (L and M segments) and 99.7% (S segment) identities, respectively. This study highlights the potential of the portable nanopore sequencer for rapid generation of accurate genomic sequences of HTNV for quicker decision making in point-of-care testing of HFRS patients during a hantavirus outbreak.
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