1
|
Tian H, Han W, Li L, Shi X, Han X, Wei Y, Cai Y, Han Z, Zhang Y, Xu Y, Li Q, Liu S. The complete mitochondrial genome and phylogenetic analysis of Rattus tanezumi (Niethammer, 1975), captured from North China. Mitochondrial DNA B Resour 2024; 9:1218-1222. [PMID: 39291128 PMCID: PMC11407395 DOI: 10.1080/23802359.2024.2404211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2024] Open
Abstract
Rattus tanezumi (Niethammer, 1975) is one of the commensal rodent species in South China. With the development of transportation and climate change, R. tanezumi has gradually migrated north and become the dominant rat species for the past few years. In this study, we assembled a complete mitochondrial genome of R. tanezumi, captured from North China. The mitogenome contains 16,307 nucleotide pairs, including 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes, as well as one non-coding control region. Based on whole mitogenome phylogenetical analysis showed that R. tanezumi captured from North China had a close phylogenetic relationship with that from Japan and South Korea. These findings are valuable for further studies on the evolution, genetic diversity, and taxonomy of Asian commensal rodent.
Collapse
Affiliation(s)
- Hong Tian
- School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Weimin Han
- School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Luling Li
- School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Xiaodong Shi
- School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Xu Han
- Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, China
| | - Yamei Wei
- Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, China
| | - Yanan Cai
- Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, China
| | - Zhanying Han
- Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, China
| | - Yanbo Zhang
- Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, China
| | - Yonggang Xu
- Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, China
| | - Qi Li
- Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, China
| | - Shiyou Liu
- School of Public Health, Hebei Medical University, Shijiazhuang, China
- Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, China
| |
Collapse
|
2
|
Li J, Huang E, Wu Y, Zhu C, Li W, Ai L, Xie Q, Tian Z, Zhong W, Sun G, Zhang L, Tan W. Population structure, dispersion patterns and genetic diversity of two major invasive and commensal zoonotic disease hosts ( Rattus norvegicus and Rattus tanezumi) from the southeastern coast of China. Front Genet 2024; 14:1174584. [PMID: 38259625 PMCID: PMC10800861 DOI: 10.3389/fgene.2023.1174584] [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: 02/26/2023] [Accepted: 12/11/2023] [Indexed: 01/24/2024] Open
Abstract
Background: The invasive brownrat (Rattus norvegicus) and the Oriental rats (Rattus tanezumi) are common commensal murid that are important hosts for rodent-borne diseases in southeast Asia. Understanding their population structure and genetic diversity is essential to uncover their invasion biology and distribution dynamics that are essential for controlling rodent-borne diseases. Methods: TA total of 103 R. norvegicus and 85 R. tanezumi were collected from 13 to 9 coastal areas of six provincial monitoring sentinel sites, respectivelyto assess patterns in their microsatellite loci and their mitochondrial coxl gene region. Results: Eleven sampled populations of R. norvegicus were divided into two major clusters by region. The observed heterozygosity values of all regional populations were smaller than expected genetic diversity heterozygosity values and deviated from Hardy-Weinberg equilibrium Nine sample populations of R. tanezumi were divided into three clusters; two that included sample from Hainan and Fujian provinces, and one that included samples from the other provinces and cities. The genetic diversity of R. tanezumi was highest in samples from Jiangsu and Guangdong provinces. Conclusion: The data in this paper confirm the two invasive rodent species from the southeastern coastal region of China may have relied on maritime transport to spread from the southern region of China to the Yangtze River basin. R. tanezumi may then hanve migrated unidirectionally, along the southeastern provinces of China towards the north, while R. norvegicus spread in a complex and multidirectional manner in Hainan, Fujian, Zhejiang and Jiangsu Provinces of the country.
Collapse
Affiliation(s)
- Jiaqiao Li
- Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
- School of Resources and Chemical Engineering, Sanming University, Sanming, China
- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Enjiong Huang
- Technology Center of Fuzhou Customs, Fuzhou, Fujian, China
| | - Yifan Wu
- Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
| | - Changqiang Zhu
- Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
| | - Wenhao Li
- Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
| | - Lele Ai
- Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
| | - Qinghua Xie
- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhi Tian
- Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
| | - Weiwen Zhong
- Center for Disease Control and Prevention, Longquan, Zhejiang, China
| | - Gang Sun
- School of Resources and Chemical Engineering, Sanming University, Sanming, China
| | - Lingling Zhang
- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weilong Tan
- Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
| |
Collapse
|
3
|
Chen JT, Zhan JB, Zhu MC, Li KJ, Liu MQ, Hu B, Cai K, Xiong HR, Chen SL, Tan WL, Chen LJ, Hou W. Diversity and genetic characterization of orthohantavirus from small mammals and humans during 2012-2022 in Hubei Province, Central China. Acta Trop 2024; 249:107046. [PMID: 37866727 DOI: 10.1016/j.actatropica.2023.107046] [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: 07/15/2023] [Revised: 10/03/2023] [Accepted: 10/19/2023] [Indexed: 10/24/2023]
Abstract
Hemorrhagic fever with renal syndrome (HFRS) is a significant public health problem in Hubei Province, China, where a novel strain of orthohantavirus, HV004, was reported in 2012. However, no systematic study has investigated the prevalence and variation of orthohantavirus in rodents and humans. Herein, 2137 small mammals were collected from ten HFRS epidemic areas in Hubei Province from 2012 to 2022, and 143 serum samples from patients with suspected hemorrhagic fever were collected from two hospitals from 2017 to 2021. Orthohantavirus RNA was recovered from 134 lung tissue samples from five rodent species, with a 6.27 % prevalence, and orthohantavirus was detected in serum samples from 25 patients. Genetic analyses revealed that orthohantavirus hantanense (HTNV), orthohantavirus seoulense (SEOV), and orthohantavirus dabieshanense (DBSV) are co-circulating in rodents in Hubei, and HTNV and SEOV were identified in patient serum. Phylogenetic analysis showed that most of the HTNV sequences were clustered with HV004, indicating that HV004-like orthohantavirus was the main HNTV subtype in rodents. Two genetic reassortments and six recombination events were observed in Hubei orthohantaviruses. In summary, this study identified the diversity of orthohantaviruses circulating in Hubei over the past decade, with the HV004-like subtype being the main genotype in rodents and patients. These findings highlight the need for continued attention and focus on orthohantaviruses, especially concerning newly identified strains.
Collapse
Affiliation(s)
- Jin-Tao Chen
- State Key Laboratory of Virology/Department of Laboratory Medicine/Hubei Provincial Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences/Zhongnan Hospital, Wuhan University, 185 Donghu Road, Wuhan, Hubei 430071, China
| | - Jian-Bo Zhan
- Institute of Health Inspection and Testing, Hubei Provincial Center for Disease Control & Prevention, 6 Zhuodaoquan Road, Wuhan, Hubei 430079, China
| | - Ming-Chao Zhu
- Department of Clinical Laboratory, The First People's Hospital of Tianmen, 1 Jingling Renming Road, Tianmen, Hubei 431700, China
| | - Kai-Ji Li
- State Key Laboratory of Virology/Department of Laboratory Medicine/Hubei Provincial Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences/Zhongnan Hospital, Wuhan University, 185 Donghu Road, Wuhan, Hubei 430071, China
| | - Man-Qing Liu
- Division of Virology, Wuhan Center for Disease Control & Prevention, 288 Machang Road, Wuhan, Hubei 430015, China
| | - Bin Hu
- Institute of Health Inspection and Testing, Hubei Provincial Center for Disease Control & Prevention, 6 Zhuodaoquan Road, Wuhan, Hubei 430079, China
| | - Kun Cai
- Institute of Health Inspection and Testing, Hubei Provincial Center for Disease Control & Prevention, 6 Zhuodaoquan Road, Wuhan, Hubei 430079, China
| | - Hai-Rong Xiong
- State Key Laboratory of Virology/Department of Laboratory Medicine/Hubei Provincial Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences/Zhongnan Hospital, Wuhan University, 185 Donghu Road, Wuhan, Hubei 430071, China
| | - Shu-Liang Chen
- State Key Laboratory of Virology/Department of Laboratory Medicine/Hubei Provincial Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences/Zhongnan Hospital, Wuhan University, 185 Donghu Road, Wuhan, Hubei 430071, China
| | - Wei-Long Tan
- Department of Infection Disease, Nanjing Bioengineering (Gene) Technology Center for Medicines, 293 Zhongshan East Road, Nanjing, Jiangsu 210002, China
| | - Liang-Jun Chen
- State Key Laboratory of Virology/Department of Laboratory Medicine/Hubei Provincial Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences/Zhongnan Hospital, Wuhan University, 185 Donghu Road, Wuhan, Hubei 430071, China.
| | - Wei Hou
- State Key Laboratory of Virology/Department of Laboratory Medicine/Hubei Provincial Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences/Zhongnan Hospital, Wuhan University, 185 Donghu Road, Wuhan, Hubei 430071, China; School of Public Health, Wuhan University, 185 Donghu Road, Wuhan, Hubei 430071, China; School of Ecology and Environment, Tibet University, 36 Jiangsu Road, Lhasa 850000, China.
| |
Collapse
|
4
|
Yi B, Deng Q, Guo C, Li X, Wu Q, Zha R, Wang X, Lu J. Evaluating the zoonotic potential of RNA viromes of rodents provides new insight into rodent-borne zoonotic pathogens in Guangdong, China. One Health 2023; 17:100631. [PMID: 38024253 PMCID: PMC10665145 DOI: 10.1016/j.onehlt.2023.100631] [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: 05/11/2023] [Revised: 09/18/2023] [Accepted: 09/19/2023] [Indexed: 12/01/2023] Open
Abstract
Emerging and re-emerging infectious diseases have been on the rise, with a significant proportion being zoonotic. Rodents, as the natural reservoirs of numerous diverse zoonotic viruses, pose a substantial threat to human health. To investigate the diversity of known and unknown viruses harbored by rodents in Guangdong (southern province of China), we conducted a comprehensive analysis of viral genomes through metagenomic sequencing of organs from 194 rodents. Our analysis yielded 2163 viral contigs that were assigned to 25 families known to infect a wide range of hosts, including vertebrates, invertebrates, amoebas, and plants. The viral compositions vary considerably among different organs, but not in rodent species. We also assessed and prioritized zoonotic potential of those detected viruses. Ninety-two viral species that are either known to infect vertebrates and invertebrates or only vertebrates were identified, among which 21 are considered high-risk to humans. The high-risk viruses included members of the Hantavirus, Picobirnaviruses, Astroviruses and Pestivirus. The phylogenetic trees of four zoonotic viruses revealed features of novel viral genomes that seem to fit evolutionarily into a zone of viruses that potentially pose a risk of transmission to humans. Recognizing that zoonotic diseases are a One Health issue, we approached the problem of identifying the zoonotic risk from rodent-transmitted disease in the Guangdong province by performing next-generation sequencing to look for potentially zoonotic viruses in these animals.
Collapse
Affiliation(s)
- Boyang Yi
- School of Public Health, Sun Yat-Sen University, Guangzhou 510080, China
- One Health Center of Excellence for Research & Training, Sun Yat-Sen University, Guangzhou 510080, China
| | - Qiang Deng
- School of Public Health, Sun Yat-Sen University, Guangzhou 510080, China
- One Health Center of Excellence for Research & Training, Sun Yat-Sen University, Guangzhou 510080, China
| | - Cheng Guo
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York 10032, USA
| | - Xiaokang Li
- School of Public Health, Sun Yat-Sen University, Guangzhou 510080, China
- One Health Center of Excellence for Research & Training, Sun Yat-Sen University, Guangzhou 510080, China
| | - Qin Wu
- School of Public Health, Sun Yat-Sen University, Guangzhou 510080, China
- One Health Center of Excellence for Research & Training, Sun Yat-Sen University, Guangzhou 510080, China
| | - Renyun Zha
- School of Public Health, Sun Yat-Sen University, Guangzhou 510080, China
- One Health Center of Excellence for Research & Training, Sun Yat-Sen University, Guangzhou 510080, China
| | - Xianhua Wang
- School of Health Sciences, Guangzhou Xinhua University, Guangzhou 510520, China
| | - Jiahai Lu
- School of Public Health, Sun Yat-Sen University, Guangzhou 510080, China
- One Health Center of Excellence for Research & Training, Sun Yat-Sen University, Guangzhou 510080, China
- National Medical Products Administration Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, Guangzhou 510080, China
- Hainan Key Novel Thinktank “Hainan Medical University ‘One Health’ Research Center”, Haikou 571199, China
- Key Laboratory of Tropical Diseases Control, Sun Yat-Sen University, Ministry of Education, Guangzhou 510080, China
| |
Collapse
|
5
|
A long-term retrospective analysis of the haemorrhagic fever with renal syndrome epidemic from 2005 to 2021 in Jiangxi Province, China. Sci Rep 2023; 13:2268. [PMID: 36755085 PMCID: PMC9907874 DOI: 10.1038/s41598-023-29330-4] [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: 10/23/2022] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
Jiangxi is one of the provinces in China most seriously affected by the haemorrhagic fever with renal syndrome (HFRS) epidemic. The aim of this paper was to systematically explore the HFRS epidemic in Jiangxi from the perspective of Hantavirus (HV) prevalence in rodents and humans and virus molecular characteristics. Individual information on all HFRS cases in Jiangxi from 2005 to 2021 was extracted from the China Information System for Disease Control and Prevention. All S and M fragment sequences of the Seoul virus and Hantan virus strains uploaded by Jiangxi and its neighbouring provinces and some representative sequences from provinces in China or some countries of Southeast Asia with the highest HV prevalence were retrieved and downloaded from NCBI GenBank. Periodogram and spatial autocorrelation were adopted for temporal periodicity and spatial clustering analysis of the HFRS epidemic. Joinpoint regression was utilized to explore the changing morbidity trend patterns of HFRS. Multiple sequence alignment and amino acid variation analysis were used to explore the homology and variation of strain prevalence in Jiangxi. Based on monthly morbidity time series, the periodogram analysis showed that the prevalence of HFRS had periodicities of 6 months and 12 months. Spatial autocorrelation analysis showed that HFRS distributed in Jiangxi was not random, with a "High-High" clustering area around Gaoan County. HFRS morbidity among the 0 ~ 15-year-old and ~ 61-year-old or older populations in Jiangxi increased significantly during the period of 2008-2015. Generally, HFRS morbidity was significantly positively correlated with the index of rat with virus (IRV) (r = 0.742) in the counties surrounding Gaoan from 2005 to 2019. HTNV strains in Jiangxi were in one independent branch, while the SEOV strains in Jiangxi were relatively more diverse. Both the YW89-15 and GAW30/2021 strains shared approximately 85% nucleotide homology and approximately 97% amino acid homology with their corresponding standard strains and vaccine strains. GAW30/2021 and YW89-15 had some amino acid site variations in nucleoprotein, glycoprotein precursor and RNA-dependent polymerase with their corresponding vaccine strains Z10 (HTNV) and Z37 (SEOV). The HFRS epidemic in Jiangxi has obvious temporal periodicity and spatial clustering, and the significant increase in the non-Immunization Expanded Program (EPI) targeted population (children and elderly) suggests that HFRS vaccination in this population needs to be considered. Although applying the EPI played a certain role in curbing the incidence of HFRS in Jiangxi from the perspective of ecological epidemiology, HTNV and SEOV strains prevalent in Jiangxi have some amino acid site variations compared to their corresponding vaccine strains, suggesting that HV variation needs to be continuously monitored in the future to observe vaccine protective efficiency.
Collapse
|
6
|
Wang N, Yin JX, Zhang Y, Wu L, Li WH, Luo YY, Li R, Li ZW, Liu SQ. Genetic Evolution Analysis and Host Characteristics of Hantavirus in Yunnan Province, China. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:13433. [PMID: 36294012 PMCID: PMC9603364 DOI: 10.3390/ijerph192013433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/08/2022] [Accepted: 10/14/2022] [Indexed: 06/16/2023]
Abstract
For a long time, the epidemic situation of hemorrhagic fever with renal syndrome (HFRS) caused by hantavirus (HV) in Yunnan Province of China has been relatively severe. The molecular epidemiology and host characteristics of HV in Yunnan Province are still not completely clear, and the systematic and long-term investigation of the epidemic area is very limited. In this study, a total of 488 murine-shaped animals were captured in the three regions of Mile City, Mangshi City and Lianghe County in Yunnan Province, and then the type of HV was identified by multiplex real-time RT-PCR and sequenced. The results indicate that 2.46% of the murine-shaped animal specimens were infected with HV. A new subtype of Seoul virus (SEOV) was found in the rare rat species Rattus nitidus in Lianghe County, and the two strains of this new subtype were named YNLH-K40 and YNLH-K53. Through the phylogenetic analysis of this new subtype, it is shown that this new subtype is very similar to the type S5 of SEOV, which is previously described as the main cause for the high incidence of HFRS in Longquan City, Zhejiang Province, China. This new subtype is highly likely to cause human infection and disease. Therefore, in addition to further promoting the improvement of the HV gene database and strengthening the discovery and monitoring of the host animals in Yunnan Province, more attention should be paid to the pathogenic potential of the newly discovered HV type.
Collapse
|