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Kumar S, Kumar GS, Maitra SS, Malý P, Bharadwaj S, Sharma P, Dwivedi VD. Viral informatics: bioinformatics-based solution for managing viral infections. Brief Bioinform 2022; 23:6659740. [PMID: 35947964 DOI: 10.1093/bib/bbac326] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 06/26/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Several new viral infections have emerged in the human population and establishing as global pandemics. With advancements in translation research, the scientific community has developed potential therapeutics to eradicate or control certain viral infections, such as smallpox and polio, responsible for billions of disabilities and deaths in the past. Unfortunately, some viral infections, such as dengue virus (DENV) and human immunodeficiency virus-1 (HIV-1), are still prevailing due to a lack of specific therapeutics, while new pathogenic viral strains or variants are emerging because of high genetic recombination or cross-species transmission. Consequently, to combat the emerging viral infections, bioinformatics-based potential strategies have been developed for viral characterization and developing new effective therapeutics for their eradication or management. This review attempts to provide a single platform for the available wide range of bioinformatics-based approaches, including bioinformatics methods for the identification and management of emerging or evolved viral strains, genome analysis concerning the pathogenicity and epidemiological analysis, computational methods for designing the viral therapeutics, and consolidated information in the form of databases against the known pathogenic viruses. This enriched review of the generally applicable viral informatics approaches aims to provide an overview of available resources capable of carrying out the desired task and may be utilized to expand additional strategies to improve the quality of translation viral informatics research.
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Affiliation(s)
- Sanjay Kumar
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.,Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | - Geethu S Kumar
- Department of Life Science, School of Basic Science and Research, Sharda University, Greater Noida, Uttar Pradesh, India.,Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | | | - Petr Malý
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences v.v.i., BIOCEV Research Center, Vestec, Czech Republic
| | - Shiv Bharadwaj
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences v.v.i., BIOCEV Research Center, Vestec, Czech Republic
| | - Pradeep Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Vivek Dhar Dwivedi
- Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India.,Institute of Advanced Materials, IAAM, 59053 Ulrika, Sweden
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Shahhosseini N, Wong G, Babuadze G, Camp JV, Ergonul O, Kobinger GP, Chinikar S, Nowotny N. Crimean-Congo Hemorrhagic Fever Virus in Asia, Africa and Europe. Microorganisms 2021; 9:microorganisms9091907. [PMID: 34576803 PMCID: PMC8471816 DOI: 10.3390/microorganisms9091907] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/26/2021] [Accepted: 08/28/2021] [Indexed: 11/16/2022] Open
Abstract
The global spread of ticks and various tick-borne viruses (TBVs) suggests the possibility of new tick-borne diseases emerging. Crimean-Congo hemorrhagic fever virus (CCHFV) is an emerging TBV of the Nairoviridae family that causes serious disease that can be fatal in humans. CCHFV endemic foci can be found in Africa, Asia, the Middle East, and South-Eastern Europe, and has spread to previously unaffected regions and nations, such as Spain, over the last two decades. In this review, we discuss the current situation of CCHFV in Asia, Africa and Europe based on existing knowledge, and we discuss driving factors in the distribution and transmission of the virus, such as the spread of tick vector species and host reservoirs.
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Affiliation(s)
- Nariman Shahhosseini
- Centre for Vector-Borne Diseases, Canadian Food Inspection Agency, Lethbridge, AB T1H 6P7, Canada;
| | - Gary Wong
- Département de Microbiologie-Infectiologie et d’Immunologie, Université Laval, Québec City, QC G1V 0A6, Canada; (G.W.); (G.P.K.)
- Institut Pasteur of Shanghai, Shanghai 200031, China
| | - George Babuadze
- Department of Biological Sciences, Sunnybrook Research Institute, University of Toronto, Toronto, ON M4N 3M5, Canada;
| | - Jeremy V. Camp
- Center for Virology, Medical University of Vienna, 1090 Vienna, Austria;
| | - Onder Ergonul
- Koç University, School of Medicine and Koç University Iş Bank Center for Infectious Diseases, Istanbul 34450, Turkey;
| | - Gary P. Kobinger
- Département de Microbiologie-Infectiologie et d’Immunologie, Université Laval, Québec City, QC G1V 0A6, Canada; (G.W.); (G.P.K.)
- Department of Medical Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Immunology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Pathology and Laboratory Medicine, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sadegh Chinikar
- Pasteur Institute of Tehran, Tehran 1316943551, Iran
- Institute of Virology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
- Correspondence: (S.C.); (N.N.)
| | - Norbert Nowotny
- Institute of Virology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
- Department of Basic Medical Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai 505055, United Arab Emirates
- Correspondence: (S.C.); (N.N.)
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Arboviruses in the Astrakhan region of Russia for 2018 season: The development of multiplex PCR assays and analysis of mosquitoes, ticks, and human blood sera. INFECTION GENETICS AND EVOLUTION 2021; 88:104711. [PMID: 33421655 DOI: 10.1016/j.meegid.2021.104711] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 12/31/2020] [Accepted: 01/04/2021] [Indexed: 11/23/2022]
Abstract
The Astrakhan region of Russia is endemic for the number of arboviruses. In this paper, we describe the results of the detection of the list of neglected arboviruses in the Astrakhan region for the 2018 season. For the purpose of the study in-house PCR assays for detection of 18 arboviruses have been developed and validated using arboviruses obtained from Russian State Collection of Viruses. Pools of ticks (n = 463) and mosquitoes (n = 312) as well as 420 samples of human patients sera have been collected and analyzed. Using developed multiplex real-time PCR assays we were able to detect RNA of eight arboviruses (Crimean-Congo hemorrhagic fever virus, Dhori (Batken strain) virus, Batai virus, Tahyna virus, Uukuniemi virus, Inkoo virus, Sindbis virus and West Nile fever virus). All discovered viruses are capable of infecting humans causing fever and in some cases severe forms with hemorrhagic or neurologic symptoms. From PCR-positive samples, we were able to recover one isolate each of Dhori (Batken strain) virus and Crimean-Congo hemorrhagic fever virus which were further characterized by next-generation sequencing. The genomic sequences of identified Dhori (Batken strain) virus strain represent the most complete genome of Batken virus strain among previously reported.
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Li Y, Yan C, Liu D, He B, Tu C. Seroepidemiological Investigation of Crimean-Congo Hemorrhagic Fever Virus in Sheep and Camels of Inner Mongolia of China. Vector Borne Zoonotic Dis 2020; 20:461-467. [PMID: 32155395 DOI: 10.1089/vbz.2019.2529] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Crimean-Congo hemorrhagic fever (CCHF) is a highly lethal infectious disease in humans caused by tick-borne Crimean-Congo hemorrhagic fever virus (CCHFV). To determine the potential risk of CCHF in the pastoral area of Northwestern China, the presence of antibody to CCHFV in the sera of two most common tick hosts, sheep and camels, in Inner Mongolia of China was evaluated. The purified recombinant nucleocapsid protein (NP) of CCHFV was prepared from a prokaryotic vector expressing the NP encoding gene, which was employed as the antigen to probe antibody against CCHFV in tick vectors using an immunoblotting assay. In total, 58.3% (35/60) and 54% (12/22) of camels were positive of antibody to CCHFV in sera at Alxa Youqi County and Ulan Hudu Gacha Village of Inner Mongolia Province, respectively. However, only 6.7% (2/30) of sera of sheep were determined positive in antibody to CCHFV in the Wulan Hudug check area in this study. Consequently, these results indicate that 54-58.3% camels were infected by CCHFV after exposure to tick bites in Inner Mongolia, which was significantly higher than 6.7% of infection in the sheep in this area, suggesting there is a certain relationship between the serological reactivity and exposure time to ticks, range of activity, living behaviors, and breeding time. Further intensive surveillance of livestock and exposed population is required to better understand the spread of CCHFV in this area.
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Affiliation(s)
- Yong Li
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Academy of Military Sciences, Changchun, China.,Key Laboratory of Ministry of Education for Protection and Utilization of Special Biological Resources in the Western China, Ningxia University, Yinchuan, China.,School of Life Science, Ningxia University, Yinchuan, China
| | - Chao Yan
- School of Life Science, Ningxia University, Yinchuan, China
| | - Dongxiao Liu
- School of Life Science, Ningxia University, Yinchuan, China
| | - Biao He
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Academy of Military Sciences, Changchun, China
| | - Changchun Tu
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Academy of Military Sciences, Changchun, China
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Gruber CEM, Bartolini B, Castilletti C, Mirazimi A, Hewson R, Christova I, Avšič T, Grunow R, Papa A, Sánchez-Seco MP, Kopmans M, Ippolito G, Capobianchi MR, Reusken CBEM, Di Caro A. Geographical Variability Affects CCHFV Detection by RT-PCR: A Tool for In-Silico Evaluation of Molecular Assays. Viruses 2019; 11:E953. [PMID: 31623214 PMCID: PMC6833031 DOI: 10.3390/v11100953] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 10/15/2019] [Indexed: 01/21/2023] Open
Abstract
The Crimean-Congo hemorrhagic fever virus (CCHFV) is considered to be a major emerging infectious threat, according to the WHO R&D blueprint. A wide range of CCHFV molecular assays have been developed, employing varied primer/probe combinations. The high genetic variability of CCHFV often hampers the efficacy of available molecular tests and can affect their diagnostic potential. Recently, increasing numbers of complete CCHFV genomic sequences have become available, allowing a better appreciation of the genomic evolution of this virus. We summarized the current knowledge on molecular methods and developed a new bioinformatics tool to evaluate the existing assays for CCHFV detection, with a special focus on strains circulating in different geographical areas. Twenty-two molecular methods and 181 sequences of CCHFV were collected, respectively, from PubMed and GenBank databases. Up to 28 mismatches between primers and probes of each assay and CCHFV strains were detected through in-silico PCR analysis. Combinations of up to three molecular methods markedly decreased the number of mismatches within most geographic areas. These results supported the good practice of CCHFV detection of performing more than one assay, aimed for different sequence targets. The choice of the most appropriate tests must take into account patient's travel history and geographic distribution of the different CCHFV strains.
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Affiliation(s)
- Cesare E M Gruber
- National Institute for Infectious Diseases (INMI) "L. Spallanzani" IRCCS, WHO Collaborating Center for clinical care, diagnosis, response and training on Highly Infectious Diseases, 00149 Rome, Italy.
| | - Barbara Bartolini
- National Institute for Infectious Diseases (INMI) "L. Spallanzani" IRCCS, WHO Collaborating Center for clinical care, diagnosis, response and training on Highly Infectious Diseases, 00149 Rome, Italy.
| | - Concetta Castilletti
- National Institute for Infectious Diseases (INMI) "L. Spallanzani" IRCCS, WHO Collaborating Center for clinical care, diagnosis, response and training on Highly Infectious Diseases, 00149 Rome, Italy.
| | - Ali Mirazimi
- Public Health agency of Sweden, 17182 Solna, Sweden.
- National veterinary Institute, 75189 Uppsala, Sweden.
- Department of laboratory Medicine, Clinical Microbiology, Karolinska Institute and Karolinska, 17177 Stockholm, Sweden.
| | - Roger Hewson
- Public Health England, National Infection Service WHO Collaborating Centre for Virus Reference and Research (Special Pathogens) Porton Down, Salisbury SP40JG, UK.
| | - Iva Christova
- National Reference Laboratory on Vector-Borne Pathogens, Leptospira and Listeria, Microbiology Department, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria.
| | - Tatjana Avšič
- Faculty of Medicine, Institute of Microbiology and Immunology, 1000 Ljubljana, Slovenia.
| | - Roland Grunow
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Microorganisms (ZBS 2), Robert Koch Institute, 13353 Berlin, Germany.
| | - Anna Papa
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - María P Sánchez-Seco
- National Centre of Microbiology, Institute of Health "Carlos III", Majadahonda, 28220 Madrid, Spain.
| | - Marion Kopmans
- Erasmus MC, Department of Viroscience, WHO Collaborating Centre for arbovirus and viral hemorrhagic fever reference and research, 3015 CN Rotterdam, The Netherlands.
| | - Giuseppe Ippolito
- National Institute for Infectious Diseases (INMI) "L. Spallanzani" IRCCS, WHO Collaborating Center for clinical care, diagnosis, response and training on Highly Infectious Diseases, 00149 Rome, Italy.
| | - Maria R Capobianchi
- National Institute for Infectious Diseases (INMI) "L. Spallanzani" IRCCS, WHO Collaborating Center for clinical care, diagnosis, response and training on Highly Infectious Diseases, 00149 Rome, Italy.
| | - Chantal B E M Reusken
- Erasmus MC, Department of Viroscience, WHO Collaborating Centre for arbovirus and viral hemorrhagic fever reference and research, 3015 CN Rotterdam, The Netherlands.
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3721 MA Bilthoven, The Netherlands.
| | - Antonino Di Caro
- National Institute for Infectious Diseases (INMI) "L. Spallanzani" IRCCS, WHO Collaborating Center for clinical care, diagnosis, response and training on Highly Infectious Diseases, 00149 Rome, Italy.
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Fine mapping epitope on glycoprotein Gc from Crimean-Congo hemorrhagic fever virus. Comp Immunol Microbiol Infect Dis 2019; 67:101371. [PMID: 31627038 DOI: 10.1016/j.cimid.2019.101371] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 10/08/2019] [Accepted: 10/08/2019] [Indexed: 01/03/2023]
Abstract
Crimean-Congo hemorrhagic fever (CCHF) is a tick-borne zoonosis, caused by CCHF virus (CCHFV) and which there are no diagnostic or therapeutic strategies. The C-terminus of glycoprotein (Gc) encoded by the CCHFV M gene is responsible for CCHFV binding to cellular receptors and acts as a neutralizing-antibody target. In this study, a modified biosynthetic peptide technique (BSP) was used to identify fine epitopes of Gc from the CCHFV YL04057 strain using rabbit antiserum against CCHFV-Gc. Six B cell epitopes (BCEs) and one antigenic peptide (AP) were identified: E1 (88VEDASES94), E2 (117GDRQVEE123), E3 (241EIVTLH246), AP-4 (281DFQVYHVGNLLRGDKV296), E5a (370GDTP QLDL377), E5b (373PQLDLKAR380), and E6 (443HVRSSD448). Western blotting analysis showed that each epitope interacted with the positive serum of sheep that had been naturally infected with CCHFV, and the results were consistent with that of Dot-ELISA. The multiple sequence alignment (MSA) revealed high conservation of the identified epitopes among ten CCHFV strains from different areas, except for epitopes AP-4 and E6. Furthermore, three-dimensional structural modeling showed that all identified epitopes were located on the surface of the Gc "head" domain. These mapped epitopes of the CCHFV Gc would provide a basis for further increase our understanding CCHFV glycoprotein function and the development of a CCHFV epitope-based diagnostics vaccine and detection antigen.
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Vakalova EV, Butenko AM, Vishnevskaya TV, Dorofeeva TE, Gitelman AK, Kulikova LN, Lvov DK, Alkhovsky SV. [Results of investigation of ticks in Volga river delta (Astrakhan region, 2017) for Crimean-Congo hemorrhagic fever virus (Nairoviridae, Orthonairovirus, CCHFV) and other tick-borne arboviruses.]. Vopr Virusol 2019; 64:221-228. [PMID: 32167687 DOI: 10.36233/0507-4088-2019-64-5-221-228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 11/28/2019] [Indexed: 06/10/2023]
Abstract
INTRODUCTION There are natural foci of Crimean-Congo hemorrhagic fever (CCHF) that vectored by Hyalomma marginatum ticks in Volga river delta (Astrakhan region, South of Russia). The circulation of Dhori virus (DHOV) (Thogotovirus: Orthomyxoviridae) has been also shown here. We hypothesized that other tick-borne arboviruses are also likely to circulate in the region. In particular, Bhanja virus (Phlebovirus: Phenuiviridae), Wad Medani virus (Orbivirus: Reoviridae), and Tamdy virus (Orthonairovirus: Nairoviridae), which were found to circulate in neighboring regions and are vectored by Haemaphysalis spp., Dermacenter spp., and Hyalomma spp. ticks. OBJECTIVES The aim of the study was to examine ixodid ticks in Volga river delta for the presence of CCHFV, DHOV, Bhanja virus, Wad Medani virus, and Tamdy virus. MATERIAL AND METHODS Ticks were collected in Volga river delta in 2017. We used molecular genetic methods for the detection and analysis of nucleic acids (PCR, sequencing, phylogenetic analysis). RESULTS We detect CCHFV and DHOV RNA in H. marginatum ticks. The rate of infected H. marginatum ticks was 1.98% for CCHFV and 0.4% for DHOV. The results of genetic analysis showed that found DHOV strains are almost identical (99-100% in the M gene) and forms a separate genetic lineage alongside of Batken virus from Central Asia. At the same time, Bhanja virus, Wad Medani virus, and Tamdy virus were not found in ticks, collected in this region. CONCLUSIONS DHOV is circulating in the natural foci of CCHF in the Volga river delta. The ratio of infection of H. marginatum with CCHFV and DHOV was determined for the first time.
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Affiliation(s)
- E V Vakalova
- Astrakhan Anti-plague Station, Astrakhan, 414024, Russia
- Astrakhan State Medical University, Astrakhan, 414011, Russia
- A.M. Nichogi Regional Infectious Clinical Hospital, Astrakhan, 414011, Russia
| | - A M Butenko
- D.I. Ivanovsky Institute of Virology National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya, Moscow, 123098, Russia
| | - T V Vishnevskaya
- D.I. Ivanovsky Institute of Virology National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya, Moscow, 123098, Russia
| | - T E Dorofeeva
- D.I. Ivanovsky Institute of Virology National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya, Moscow, 123098, Russia
| | - A K Gitelman
- D.I. Ivanovsky Institute of Virology National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya, Moscow, 123098, Russia
| | - L N Kulikova
- Center of Hygiene and Epidemiology in Astrakhan region, Astrakhan, 414057, Russia
| | - D K Lvov
- D.I. Ivanovsky Institute of Virology National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya, Moscow, 123098, Russia
| | - S V Alkhovsky
- D.I. Ivanovsky Institute of Virology National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya, Moscow, 123098, Russia
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Mapping of B-cell epitopes on the N- terminal and C-terminal segment of nucleocapsid protein from Crimean-Congo hemorrhagic fever virus. PLoS One 2018; 13:e0204264. [PMID: 30235312 PMCID: PMC6147494 DOI: 10.1371/journal.pone.0204264] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 09/04/2018] [Indexed: 02/06/2023] Open
Abstract
Crimean-Congo hemorrhagic fever virus (CCHFV) is a tick-borne pathogen that causes severe disease in humans. CCHFV is widely distributed in more than 30 countries and distinct regions, which means that it poses a serious threat to human health. The nucleocapsid protein (NP) encoded by the CCHFV S gene is the primary detectable antigen in infected cells, which makes it an important viral antigen and a clinical diagnostic target. In this study, the modified biosynthetic peptide (BSP) method was used to identify the fine epitopes on the N- and C- terminals of NP from the CCHFV YL04057 strain using rabbit antiserum against CCHFV-NP. Nine epitopes were identified: E1a (178NLILNRGG185), E1b (184GGDENP189), E2 (352PLKWGKK358), E3 (363FADDS367), E4 (399NPDDAA404), E5a (447DIVASEHL454), E5b (452EHLLHQSL459), E6 (464SPFQNAY470) and E7 (475NATSANII482). Western blotting analysis showed that each epitope interacted with the positive serum of sheep that had been naturally infected with CCHFV. Amino acid sequence alignment between each epitope and their homologous proteins showed that they were almost 100% conserved among 12 CCHFV sequences from different lineages, except for epitopes E1a, E1b and E2. Three-dimensional structural modeling analysis showed that all identified epitopes were located on the surface of the NP "head" domain. This study identified fine epitopes on the N- and C- terminals of NP, which will increase the understanding of the structure and function of NP, and it could lay the foundation for the design and development of a CCHFV multi-epitope peptide vaccine and detection antigen.
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