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Liu Z, Hu R, Cao H, Huang P, Yan H, Meng P, Xiong Z, Dai X, Yang F, Wang L, Qiu Q, Yan L, Zhang T. Identification and phylogenetic analysis of Jingmen tick virus in Jiangxi Province, China. Front Vet Sci 2024; 11:1375852. [PMID: 38756509 PMCID: PMC11096534 DOI: 10.3389/fvets.2024.1375852] [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: 01/24/2024] [Accepted: 04/10/2024] [Indexed: 05/18/2024] Open
Abstract
Jingmen tick virus (JMTV) is a newly identified segmented flavivirus that has been recognized in multiple hosts, such as humans, buffalos, bats, rodents, mosquitos and ticks. Various clinical cases and studies manifested that JMTV is a true arbovirus with wide host spectrum and showed potential threats toward public health. JMTV has been reported in multiple countries in Asia, Europe, Africa, and America. Moreover, wild boars serve as an important intermediary between humans and the wild ecological system. In China, it has been reported in nine provinces, while the prevalence and the distribution of JMTV in most regions including Jiangxi Province are still unknown. Thus, to profile the distribution of JMTV in Jiangxi Province, an epidemiological investigation was carried out from 2020 to 2022. In current study, 66 ticks were collected from 17 wild boars in Jiangxi Province. The results showed that 12 out of 66 ticks were JMTV positive, indicating JMTV is prevalent in ticks and boars in Jiangxi Province. The genome sequences of JMTV strain WY01 were sequenced to profile viral evolution of JMTV in China. Phylogenetic analysis divided JMTV strains into two genotypes, Group I and Group II. WY01 belongs to Group II and it shares the closest evolutionary relationship with the Japan strains rather than the strains from neighboring provinces in China suggesting that JMTV might have complex transmission routes. Overall, current study, for the first time, reported that JMTV is prevalent in Jiangxi Province and provided additional information concerning JMTV distribution and evolution in China.
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Affiliation(s)
- Zirui Liu
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Ruiming Hu
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
- Jiangxi Engineering Research Center for Animal Health Products, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Huabin Cao
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Peng Huang
- Jiangxi Wildlife and Plant Conservation Center, Nanchang, China
| | - Hui Yan
- Jiangxi Wildlife and Plant Conservation Center, Nanchang, China
| | - Puyan Meng
- Jiangxi Academy of Forestry, Nanchang, China
| | - Zhiwei Xiong
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
- Jiangxi Biotechnology Vocational College, Nanchang, China
| | - Xueyan Dai
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Fan Yang
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Li Wang
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Qian Qiu
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Linjie Yan
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Tao Zhang
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
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Xu X, Gao Z, Wu Y, Yin H, Ren Q, Zhang J, Liu Y, Yang S, Bayasgalan C, Tserendorj A, Yang X, Chen Z. Discovery and vertical transmission analysis of Dabieshan Tick Virus in Haemaphysalis longicornis ticks from Chengde, China. Front Microbiol 2024; 15:1365356. [PMID: 38468853 PMCID: PMC10925692 DOI: 10.3389/fmicb.2024.1365356] [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: 01/04/2024] [Accepted: 02/01/2024] [Indexed: 03/13/2024] Open
Abstract
Introduction Ticks are important blood-sucking ectoparasites that can transmit various pathogens, posing significant threats to the wellbeing of humans and livestock. Dabieshan tick virus (DBTV) was initially discovered in 2015 in Haemaphysalis longicornis ticks from the Dabieshan mountain region in Hubei Province, China. In recent years, DBTV has been discovered in various regions of China, including Shandong, Zhejiang, Liaoning, Hubei, Yunnan, and Guizhou Provinces. However, the researches on tick-borne transmission of DBTV are scarce. Methods This study utilized the small RNA sequencing (sRNA-seq) method to identify tick-associated viruses in ticks collected from Chengde in Hebei Province and Yongcheng in Henan Province, leading to the discovery of a new DBTV strain in Hebei. The complete coding genome of DBTV Hebei strain was obtained through RNA-seq and Sanger sequencing. Furthermore, the transmission experiment of DBTV in H. longicornis was examined in laboratory for the first time. Results DBTV was detected in newly molted adult H. longicornis ticks collected in Chengde, Hebei Province. Additionally, DBTV was also detected in both unfed nymphs and engorged females of H. longicornis collected from Chengde, with a positive rate of 20% and 56.25%, respectively. The complete coding genome of DBTV (OP682840 and OP716696) were obtained, and phylogenetic analysis revealed that the DBTV Hebei strain clustered with previously reported DBTV strains. Furthermore, this virus was observed in engorged females, eggs, and larvae of the subsequent generation. Discussion It is necessary to expand the scope of DBTV investigation, particularly in northern China. This study demonstrated that DBTV can be transmitted from engorged females to larvae of the next generation. Moreover, the detection of DBTV in unfed nymphs and adults (which moulted from engorged nymphs) collected from the filed of Chengde suggests that H. longicornis serves as a potential transmission host and reservoir for DBTV through transstadial and transovarial transmission. However, there remains a lack of research on the isolation and pathogenicity of DBTV, highlighting the need for further studies to mitigate potential harm to the health of animals and humans.
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Affiliation(s)
- Xiaofeng Xu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Zhihua Gao
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Youhong Wu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Hong Yin
- State Key Laboratory of Animal Disease Prevention and Control, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, Gansu, China
| | - Qiaoyun Ren
- State Key Laboratory of Animal Disease Prevention and Control, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, Gansu, China
| | - Jie Zhang
- Hebei Key Laboratory of Preventive Veterinary Medicine, College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Yongsheng Liu
- Hebei Key Laboratory of Preventive Veterinary Medicine, College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Shunli Yang
- Hebei Key Laboratory of Preventive Veterinary Medicine, College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | | | - Ariunaa Tserendorj
- School of Veterinary Medicine, Mongolian University of Life Sciences, Ulaanbaatar, Mongolia
| | - Xiaolong Yang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Ze Chen
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
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Li W, Li R, Tang X, Cheng J, Zhan L, Shang Z, Wu J. Genomics evolution of Jingmen viruses associated with ticks and vertebrates. Genomics 2023; 115:110734. [PMID: 37890641 DOI: 10.1016/j.ygeno.2023.110734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/08/2023] [Accepted: 10/24/2023] [Indexed: 10/29/2023]
Abstract
Jingmen virus (JMV) associated with ticks and vertebrates have been found to be related to human disease. We obtained the genome of a Jingmen tick virus (JMTV) strain from Rhipicephalus microplus in Guizhou province and compared the genomes of seven JMV species associated with ticks and vertebrates to understand the evolutionary relationships. The topology of the phylogenetic tree of segment 1 and segment 3 is similar, and segment 2 and segment 4 formed two different topologies, with the main differences being between Alongshan virus (ALSV), Takachi virus, Yanggou tick virus and Pteropus lylei jingmen virus (PLJV), and the possibility of genetic reassortment among these viruses. Moreover, we detected recombination within JMTV and between PLJV and ALSV. The genetic reassortment and recombination that occurs during cross-species transmission of these JMV associated with ticks and vertebrates not only complicates their evolutionary relationships, but also raises the risk of these viruses to humans.
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Affiliation(s)
- Weiyi Li
- School of Public Health, the key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 561113, China; Key Laboratory of Modern Pathogen Biology and Characteristics, Basic Medical College, Guizhou Medical University, Guiyang, Guizhou 550025, China
| | - Rongting Li
- School of Public Health, the key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 561113, China; Key Laboratory of Modern Pathogen Biology and Characteristics, Basic Medical College, Guizhou Medical University, Guiyang, Guizhou 550025, China
| | - Xiaomin Tang
- Key Laboratory of Modern Pathogen Biology and Characteristics, Basic Medical College, Guizhou Medical University, Guiyang, Guizhou 550025, China; Department of Human Parasitology, Basic Medical College, Guizhou Medical University, Guiyang, Guizhou 550025, China
| | - Jinzhi Cheng
- Key Laboratory of Modern Pathogen Biology and Characteristics, Basic Medical College, Guizhou Medical University, Guiyang, Guizhou 550025, China; Department of Human Parasitology, Basic Medical College, Guizhou Medical University, Guiyang, Guizhou 550025, China
| | - Lin Zhan
- School of Public Health, the key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 561113, China; Central Laboratory, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550002, China
| | - Zhengling Shang
- Department of Immunology, Basic Medical College, Guizhou Medical University, Guiyang, Guizhou 550025, China
| | - Jiahong Wu
- Key Laboratory of Modern Pathogen Biology and Characteristics, Basic Medical College, Guizhou Medical University, Guiyang, Guizhou 550025, China; Department of Human Parasitology, Basic Medical College, Guizhou Medical University, Guiyang, Guizhou 550025, China.
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Qu L, Li X, Huang B, Liu Y, Li Q, Shah T, Ning Y, Li J, Lu Y, Yan L, Wang B, Xia X. Identification and Characterization of Jingmen Tick Virus in Ticks from Yunnan Imported Cattle. Vector Borne Zoonotic Dis 2023; 23:298-302. [PMID: 37172285 DOI: 10.1089/vbz.2022.0076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023] Open
Abstract
Jingmen tick virus (JMTV) is a tick-borne segmented positive-sense ssRNA virus that can cause human disease. This virus has been confirmed to be widespread, having a wide host range. In human it can cause fever, headache, lymphadenopathy, and asthenia. Therefore, JMTV poses a threat to public health. In this study, we collected 478 ticks from imported cattle on three quarantine farms near the Yunnan border to detect medically significant tick-borne viruses. Our findings show that JMTV was the only detected virus, with an incidence rate of 56.67%. Phylogenetic analysis showed that our JMTV is more closely related to previously reported JMTV strains from Yunnan Province and neighboring Laos, implying that the tick-borne virus was most likely imported from Laos. In conclusion, we identified and characterized a novel JMTV strain in tick (Rhipicephalus microplus) from Yunnan imported cattle, emphasizing the importance of arbovirus quarantine of livestock imports.
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Affiliation(s)
- Linyu Qu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, P.R. China
| | - Xiaofei Li
- The Third People's Hospital of Kunming, Kunming, P.R. China
| | - Baoyang Huang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, P.R. China
| | - Yufu Liu
- Yunnan International Travel Healthcare Center & Kunming Customs Port Outpatient Department, Kunming, P.R. China
| | - Qian Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, P.R. China
| | - Taif Shah
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, P.R. China
| | - Yuting Ning
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, P.R. China
| | - Jie Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, P.R. China
- Yunnan International Travel Healthcare Center & Kunming Customs Port Outpatient Department, Kunming, P.R. China
| | - Yunlan Lu
- Yunnan International Travel Healthcare Center & Kunming Customs Port Outpatient Department, Kunming, P.R. China
| | - Linghua Yan
- Yunnan International Travel Healthcare Center & Kunming Customs Port Outpatient Department, Kunming, P.R. China
| | - Binghui Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, P.R. China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, P.R. China
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Cai X, Cai X, Xu Y, Shao Y, Fu L, Men X, Zhu Y. Virome analysis of ticks and tick-borne viruses in Heilongjiang and Jilin Provinces, China. Virus Res 2023; 323:199006. [PMID: 36414189 PMCID: PMC10194156 DOI: 10.1016/j.virusres.2022.199006] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 11/21/2022]
Abstract
Ticks transmit diverse human and animal pathogens, leading to an increasing number of public health concerns. In the forest area of northeast China, the spread of tick-borne diseases (TBDs) is severe; however, little is known about the tick virome composition and evolution. Herein, we investigate the geographical distribution of tick species and related viruses in Heilongjiang and Jilin Provinces in Northeast China. To reveal the diversity of tick-borne viruses in parts of Heilongjiang and Jilin, ticks were collected at 9 collection points in these provinces in 2018. Morphology and molecular biology were used to identify tick species, and 1411 ticks from nine sampling sites were collected and analysed by next-generation sequencing (NGS). Four Ixodidae were identified, including Ixodes persulcatus, Haemaphysalis japonica, Dermacentor silvarum, and Haemaphysalis concinna. After removal of host genome sequences, 13,003 high-quality NGS reads were obtained and annotated as viruses. Further phylogenetic analysis based on amplicons revealed that these viral sequences belong to Beiji nairovirus, Alongshan virus, bovine parvovirus-2, and tick-associated circovirus; some distinct sequences are closely related to Songling virus, Changping tick virus, Norway luteo-like virus 2, and Norway partiti-like virus 1. In summary, this study describes the prevalence of local ticks and variety of tick-borne viruses in northeastern China, providing a basis for further research on tick-borne viruses in the future.
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Affiliation(s)
- Xianglong Cai
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150006, China
| | - Xiaojing Cai
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150006, China
| | - Yongkang Xu
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150006, China
| | - Yi Shao
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150006, China
| | - Lian Fu
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150006, China
| | - Xiaoyu Men
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150006, China
| | - Yan Zhu
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150006, China.
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Wu Z, Chen J, Zhang L, Zhang Y, Liu L, Niu G. Molecular evidence for potential transovarial transmission of Jingmen tick virus in Haemaphysalis longicornis fed on cattle from Yunnan Province, China. J Med Virol 2023; 95:e28357. [PMID: 36443647 DOI: 10.1002/jmv.28357] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 11/16/2022] [Accepted: 11/22/2022] [Indexed: 11/30/2022]
Abstract
Jingmen tick virus (JMTV) is a novel tick-borne virus first identified from Jingmen city, Hubei Province of China in 2010. It has been proved that JMTV can cause human diseases and is widely distributed both inside and outside of China. However, the survival mode and transmission characteristics of JMTV still need further research, particularly in terms of transovarial transmission. In this study, an investigation was conducted to explore the presence of JMTV from engorged female ticks to their offspring. All engorged female adult ticks were collected from domestic cattle and allowed to lay eggs in appropriate humidity and temperature conditions. Maternal ticks, eggs and larvae were screened for JMTV RNA through real-time polymerase chain reaction (RT-PCR) and nested PCR methods. The results revealed the positive rate of 10.53% (10/95) in engorged ticks, 9.09% (2/22) in eggs and 8% (4/50) in larvae pools, respectively. Phylogenetic analysis confirmed that sequences from eggs and larvae had closer relationship with those isolates from maternal engorged ticks with more than 99.7% homology and JMTV manifested with evolutional conservatism. Our study has identified for the first time that JMTV could be transmitted from mother generation to offspring of Haemaphysalis Longicornis. Nonetheless, the efficiency of transovarial transmission in JMTV and the significance of ticks as amplification hosts still need to be further illustrated.
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Affiliation(s)
- Zhen Wu
- School of Public Health, WeiFang Medical University, Weifang, China
| | - Junhao Chen
- School of Public Health, WeiFang Medical University, Weifang, China
| | | | - Yuli Zhang
- School of Public Health, WeiFang Medical University, Weifang, China
| | - Lin Liu
- Immune-Path Biotechnology (Suzhou) Co., Ltd, Suzhou, China
| | - Guoyu Niu
- School of Public Health, WeiFang Medical University, Weifang, China
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Pereira GC. An Automated Strategy to Handle Antigenic Variability in Immunisation Protocols, Part I: Nanopore Sequencing of Infectious Agent Variants. Methods Mol Biol 2023; 2575:305-321. [PMID: 36301483 DOI: 10.1007/978-1-0716-2716-7_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Infectious agents often challenge therapeutics, from antibiotics resistance to antigenic variability affecting inoculation measures. Over the last decades, genome sequencing arose as an important ally to address such challenges. In bacterial infection, whole-genome-sequencing (WGS) supports tracking pathogenic alterations affecting the human microbiome. In viral infection, the analysis of the relevant sequence of nucleotides helps with determining historical variants of a virus and elucidates details about infection clusters and their distribution. Additionally, genome sequencing is now an important step in inoculation protocols, isolating target genes to design more robust immunisation assays. Ultimately, genetic engineering has empowered repurposing at scale, allowing long-lasting repeating clinical trials to be automated within a much shorter time-frame, by adjusting existing protocols. This is particularly important during sanitary emergencies as the ones caused by the 2014 West African Ebola outbreak, the Zika virus rapid spread in both South and North America in 2015, followed by Asia in 2016, and the pandemic caused by the SARS-CoV-2, which has infected more than 187 million people and caused more than 4 million deaths, worldwide, as per July 2021 statistics. In this scenery, this chapter presents a novel fully automated strategy to handle antigenic variability in immunisation protocols. The methodology comprises of two major steps (1) nanopore sequencing of infectious agent variants - the focus is on the SARS-CoV-2 and its variants; followed by (2) mRNA vector design for immunotherapy. This chapter presents the nanopore sequencing step and Chapter 17 introduces a protocol for mRNA vector design.
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Colmant AMG, Charrel RN, Coutard B. Jingmenviruses: Ubiquitous, understudied, segmented flavi-like viruses. Front Microbiol 2022; 13:997058. [PMID: 36299728 PMCID: PMC9589506 DOI: 10.3389/fmicb.2022.997058] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/22/2022] [Indexed: 11/21/2022] Open
Abstract
Jingmenviruses are a group of viruses identified recently, in 2014, and currently classified by the International Committee on Taxonomy of Viruses as unclassified Flaviviridae. These viruses closely related to flaviviruses are unique due to the segmented nature of their genome. The prototype jingmenvirus, Jingmen tick virus (JMTV), was discovered in Rhipicephalus microplus ticks collected from China in 2010. Jingmenviruses genomes are composed of four to five segments, encoding for up to seven structural proteins and two non-structural proteins, both of which display strong similarities with flaviviral non-structural proteins (NS2B/NS3 and NS5). Jingmenviruses are currently separated into two phylogenetic clades. One clade includes tick- and vertebrate-associated jingmenviruses, which have been detected in ticks and mosquitoes, as well as in humans, cattle, monkeys, bats, rodents, sheep, and tortoises. In addition to these molecular and serological detections, over a hundred human patients tested positive for jingmenviruses after developing febrile illness and flu-like symptoms in China and Serbia. The second phylogenetic clade includes insect-associated jingmenvirus sequences, which have been detected in a wide range of insect species, as well as in crustaceans, plants, and fungi. In addition to being found in various types of hosts, jingmenviruses are endemic, as they have been detected in a wide range of environments, all over the world. Taken together, all of these elements show that jingmenviruses correspond exactly to the definition of emerging viruses at risk of causing a pandemic, since they are already endemic, have a close association with arthropods, are found in animals in close contact with humans, and have caused sporadic cases of febrile illness in multiple patients. Despite these arguments, the vast majority of published data is from metagenomics studies and many aspects of jingmenvirus replication remain to be elucidated, such as their tropism, cycle of transmission, structure, and mechanisms of replication and restriction or epidemiology. It is therefore crucial to prioritize jingmenvirus research in the years to come, to be prepared for their emergence as human or veterinary pathogens.
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Pang Z, Jin Y, Pan M, Zhang Y, Wu Z, Liu L, Niu G. Geographical distribution and phylogenetic analysis of Jingmen tick virus in China. iScience 2022; 25:105007. [PMID: 36097615 PMCID: PMC9463580 DOI: 10.1016/j.isci.2022.105007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/08/2022] [Accepted: 08/19/2022] [Indexed: 11/26/2022] Open
Abstract
Jingmen tick virus (JMTV) is a novel tick-borne segmented RNA virus that is closely related to un-segmental RNA virus in evolution. It has been confirmed that JMTV could be a causative agent of human disease. In this study, a total of 3658 ticks were sampled from 7 provinces of China and then divided into 545 pools according to the location and species. QRT-PCR and nested PCR were performed to confirm the presence of JMTV. The results showed JMTV was identified in 5 out of 7 provinces with an average infection rate of 1.4% (51/3658). Phylogenetic analysis indicated that all JMTV strains identified in this study were closely related to each other and formed a well-supported sub-lineage. Our results provide molecular evidence of JMTV in different species of ticks from endemic and non-endemic regions and demonstrate that JMTV, as a natural foci pathogen, may be widely distributed all over China. JMTV was first identified in unrecognized endemic regions of China Two complete genomes and 13 partial S1 segments of JMTV were sequenced and analyzed JMTV was relatively conservative in evolution JMTV was widely distributed in China as a potential health threat to humans and animals
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Chang J, Bei J, Shao Q, Wang H, Fan H, Yau TO, Bu W, Ruan J, Wei D, Gao S. Full-Length Genome of an Ogataea polymorpha Strain CBS4732 ura3Δ Reveals Large Duplicated Segments in Subtelomeric Regions. Front Microbiol 2022; 13:855666. [PMID: 35464988 PMCID: PMC9019687 DOI: 10.3389/fmicb.2022.855666] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 02/25/2022] [Indexed: 11/18/2022] Open
Abstract
Background Currently, methylotrophic yeasts (e.g., Pichia pastoris, Ogataea polymorpha, and Candida boindii) are subjects of intense genomics studies in basic research and industrial applications. In the genus Ogataea, most research is focused on three basic O. polymorpha strains-CBS4732, NCYC495, and DL-1. However, the relationship between CBS4732, NCYC495, and DL-1 remains unclear, as the genomic differences between them have not be exactly determined without their high-quality complete genomes. As a nutritionally deficient mutant derived from CBS4732, the O. polymorpha strain CBS4732 ura3Δ (named HU-11) is being used for high-yield production of several important proteins or peptides. HU-11 has the same reference genome as CBS4732 (noted as HU-11/CBS4732), because the only genomic difference between them is a 5-bp insertion. Results In the present study, we have assembled the full-length genome of O. polymorpha HU-11/CBS4732 using high-depth PacBio and Illumina data. Long terminal repeat retrotransposons (LTR-rts), rDNA, 5′ and 3′ telomeric, subtelomeric, low complexity and other repeat regions were exactly determined to improve the genome quality. In brief, the main findings include complete rDNAs, complete LTR-rts, three large duplicated segments in subtelomeric regions and three structural variations between the HU-11/CBS4732 and NCYC495 genomes. These findings are very important for the assembly of full-length genomes of yeast and the correction of assembly errors in the published genomes of Ogataea spp. HU-11/CBS4732 is so phylogenetically close to NCYC495 that the syntenic regions cover nearly 100% of their genomes. Moreover, HU-11/CBS4732 and NCYC495 share a nucleotide identity of 99.5% through their whole genomes. CBS4732 and NCYC495 can be regarded as the same strain in basic research and industrial applications. Conclusion The present study preliminarily revealed the relationship between CBS4732, NCYC495, and DL-1. Our findings provide new opportunities for in-depth understanding of genome evolution in methylotrophic yeasts and lay the foundations for the industrial applications of O. polymorpha CBS4732, NCYC495, DL-1, and their derivative strains. The full-length genome of O. polymorpha HU-11/CBS4732 should be included into the NCBI RefSeq database for future studies of Ogataea spp.
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Affiliation(s)
- Jia Chang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Science, Nankai University, Tianjin, China
| | - Jinlong Bei
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Qi Shao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Science, Nankai University, Tianjin, China
| | - Hemu Wang
- Tianjin Hemu Health Biotechnological Co., Ltd., Tianjin, China
| | - Huan Fan
- Tianjin Institute of Animal Husbandry and Veterinary Research, Tianjin, China
| | - Tung On Yau
- John Van Geest Cancer Research Centre, School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom.,Department of Rural Land Use, Scotland's Rural College, Aberdeen, United Kingdom
| | - Wenjun Bu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Science, Nankai University, Tianjin, China
| | - Jishou Ruan
- School of Mathematical Sciences, Nankai University, Tianjin, China
| | - Dongsheng Wei
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Science, Nankai University, Tianjin, China
| | - Shan Gao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Science, Nankai University, Tianjin, China
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Hillary LS, Adriaenssens EM, Jones DL, McDonald JE. RNA-viromics reveals diverse communities of soil RNA viruses with the potential to affect grassland ecosystems across multiple trophic levels. ISME COMMUNICATIONS 2022; 2:34. [PMID: 36373138 PMCID: PMC8992426 DOI: 10.1038/s43705-022-00110-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/08/2022] [Accepted: 02/14/2022] [Indexed: 02/08/2023]
Abstract
The distribution and diversity of RNA viruses in soil ecosystems are largely unknown, despite their significant impact on public health, ecosystem functions, and food security. Here, we characterise soil RNA viral communities along an altitudinal productivity gradient of peat, managed grassland and coastal soils. We identified 3462 viral contigs in RNA viromes from purified virus-like-particles in five soil-types and assessed their spatial distribution, phylogenetic diversity and potential host ranges. Soil types exhibited minimal similarity in viral community composition, but with >10-fold more viral contigs shared between managed grassland soils when compared with peat or coastal soils. Phylogenetic analyses predicted soil RNA viral communities are formed from viruses of bacteria, plants, fungi, vertebrates and invertebrates, with only 12% of viral contigs belonging to the bacteria-infecting Leviviricetes class. 11% of viral contigs were found to be most closely related to members of the Ourmiavirus genus, suggesting that members of this clade of plant viruses may be far more widely distributed and diverse than previously thought. These results contrast with soil DNA viromes which are typically dominated by bacteriophages. RNA viral communities, therefore, have the potential to exert influence on inter-kingdom interactions across terrestrial biomes.
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Affiliation(s)
- Luke S. Hillary
- School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW UK
| | | | - David L. Jones
- School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW UK
- SoilsWest, Centre for Sustainable Farming Systems, Food Futures Institute, Murdoch University, Murdoch, WA 6105 Australia
| | - James E. McDonald
- School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW UK
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