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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.
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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
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Wei Y, Cai Y, Han X, Han Z, Zhang Y, Xu Y, Li Q. Genetic diversity and molecular evolution of Seoul virus in Hebei province, China. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 114:105503. [PMID: 37717798 DOI: 10.1016/j.meegid.2023.105503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/19/2023]
Abstract
Seoul virus (SEOV) is a major pathogen which causes hemorrhagic fever with renal syndrome (HFRS), and is present all over the world. However, there are currently few long-term systematic studies of SEOV's phylogenetic and evolutionary mechanisms in epidemic areas. Thus, in this study, we used RT-PCR combined with NGS to obtain the genomes of six SEOV viruses from 1993, as well as 56 Hebei province-specific tissue samples from 1999 to 2022. Phylogenetic analysis showed that the SEOV samples could be divided into seven groups and showed geographic clustering. The geographic region may be the main factor affecting the genetic diversity of SEOV. We also found that SEOV was subject to strong overall purifying selection and positive selection at certain sites during evolution. Recombination events and high nucleotide substitution rates were also shown to accelerate SEOV's evolution. Evolutionary feature of the L segment is more representative of complete genome. Our detailed analysis provides a deeper understanding of the genetic diversity and evolutionary drivers of SEOV within its primary epidemic areas. It will be important to further monitor epidemiological trends and drivers of variation to help increase our understanding of the pathogenicity of SEOV infections.
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Affiliation(s)
- Yamei Wei
- Hebei Medical University, Shijiazhuang, Hebei Province, China; Institute for Viral Disease Control and Prevention, Hebei Province Center for Disease Control and Prevention, Shijiazhuang, Hebei Province, China
| | - Yanan Cai
- Hebei Medical University, Shijiazhuang, Hebei Province, China; Institute for Viral Disease Control and Prevention, Hebei Province Center for Disease Control and Prevention, Shijiazhuang, Hebei Province, China
| | - Xu Han
- Institute for Viral Disease Control and Prevention, Hebei Province Center for Disease Control and Prevention, Shijiazhuang, Hebei Province, China
| | - Zhanying Han
- Institute for Viral Disease Control and Prevention, Hebei Province Center for Disease Control and Prevention, Shijiazhuang, Hebei Province, China
| | - Yanbo Zhang
- Institute for Viral Disease Control and Prevention, Hebei Province Center for Disease Control and Prevention, Shijiazhuang, Hebei Province, China
| | - Yonggang Xu
- Institute for Viral Disease Control and Prevention, Hebei Province Center for Disease Control and Prevention, Shijiazhuang, Hebei Province, China
| | - Qi Li
- Hebei Medical University, Shijiazhuang, Hebei Province, China; Institute for Viral Disease Control and Prevention, Hebei Province Center for Disease Control and Prevention, Shijiazhuang, Hebei Province, China.
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He W, Fu J, Wen Y, Cheng M, Mo Y, Chen Q. Detection and Genetic Characterization of Seoul Virus in Liver Tissue Samples From Rattus norvegicus and Rattus tanezumi in Urban Areas of Southern China. Front Vet Sci 2021; 8:748232. [PMID: 34966803 PMCID: PMC8710597 DOI: 10.3389/fvets.2021.748232] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/17/2021] [Indexed: 12/05/2022] Open
Abstract
Rodents are important hosts of hantaviruses, and lungs and kidneys are known to be the preferred organs of these viruses. Recently, hantaviruses were detected in liver samples from wild rodents in Hungary and the United States, and feeder rats in the Netherlands. However, few studies have detected hantaviruses in the liver of rats from China. In this study, hantaviruses were investigated in liver samples from R. norvegicus and R. tanezumi trapped in urban areas of southern China. A total of 461 R. norvegicus and 64 R. tanezumi were trapped. Using a pan-hantavirus PCR method, hantaviruses were detected in liver, lung, and serum samples from these animals. About 7.43% of liver samples were positive for Seoul virus (SEOV). The detection rate of SEOV in liver samples from R. norvegicus (8.24%) was higher than that from R. tanezumi (1.56%), suggesting the predominant role of R. norvegicus in the transmission of SEOV in urban areas of China. Three R. norvegicus had SEOV RNA in their liver samples but not in their lung samples, suggesting that the liver might be one of the targeted organs of SEOV. The first full SEOV protein-coding sequences (CDS) of the S and M segments, and partial CDS of the L segment from R. tanezumi were amplified. Several full and partial CDS of the S, M, and L segments from R. norvegicus were also obtained. The SEOV sequences obtained from different animals were highly similar, suggesting the cross-species transmission potential of SEOV between R. norvegicus and R. tanezumi.
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Affiliation(s)
- Wenqiao He
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, China
| | - Jiaqi Fu
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, China
| | - Yuqi Wen
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, China
| | - Mingji Cheng
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, China
| | - Yun Mo
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, China
| | - Qing Chen
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, China
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Li N, Li A, Liu Y, Wu W, Li C, Yu D, Zhu Y, Li J, Li D, Wang S, Liang M. Genetic diversity and evolution of Hantaan virus in China and its neighbors. PLoS Negl Trop Dis 2020; 14:e0008090. [PMID: 32817670 PMCID: PMC7462299 DOI: 10.1371/journal.pntd.0008090] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 09/01/2020] [Accepted: 07/08/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Hantaan virus (HTNV; family Hantaviridae, order Bunyavirales) causes hemorrhagic fever with renal syndrome (HFRS), which has raised serious concerns in Eurasia, especially in China, Russia, and South Korea. Previous studies reported genetic diversity and phylogenetic features of HTNV in different parts of China, but the analyses from the holistic perspective are rare. METHODOLOGY AND PRINCIPAL FINDINGS To better understand HTNV genetic diversity and gene evolution, we analyzed all available complete sequences derived from the small (S) and medium (M) segments with bioinformatic tools. Eleven phylogenetic groups were defined and showed geographic clustering; 42 significant amino acid variant sites were found, and 19 of them were located in immune epitopes; nine recombinant events and eight reassortments with highly divergent sequences were found and analyzed. We found that sequences from Guizhou showed high genetic divergence, contributing to multiple lineages of the phylogenetic tree and also to the recombination and reassortment events. Bayesian stochastic search variable selection analysis revealed that Heilongjiang, Shaanxi, and Guizhou played important roles in HTNV evolution and migration; the virus may originate from Zhejiang Province in the eastern part of China; and the virus population size expanded from the 1980s to 1990s. CONCLUSIONS/SIGNIFICANCE These findings revealed the original and evolutionary features of HTNV, which will help to illustrate hantavirus epidemic trends, thus aiding in disease control and prevention.
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Affiliation(s)
- Naizhe Li
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of People's Republic of China, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Aqian Li
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of People's Republic of China, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yang Liu
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of People's Republic of China, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wei Wu
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of People's Republic of China, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Chuan Li
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of People's Republic of China, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Dongyang Yu
- Department of Microbiology, Anhui Medical University, Hefei, China
| | - Yu Zhu
- Department of Microbiology, Anhui Medical University, Hefei, China
| | - Jiandong Li
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of People's Republic of China, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Dexin Li
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of People's Republic of China, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shiwen Wang
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of People's Republic of China, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- China CDC-WIV Joint Research Center for Emerging Diseases and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, P. R. China
- * E-mail: (SW); (ML)
| | - Mifang Liang
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of People's Republic of China, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- China CDC-WIV Joint Research Center for Emerging Diseases and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, P. R. China
- * E-mail: (SW); (ML)
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Su Q, Chen Y, Li M, Ma J, Wang B, Luo J, He H. Genetic Characterization and Molecular Evolution of Urban Seoul Virus in Southern China. Viruses 2019; 11:v11121137. [PMID: 31835357 PMCID: PMC6950471 DOI: 10.3390/v11121137] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 12/06/2019] [Accepted: 12/07/2019] [Indexed: 01/03/2023] Open
Abstract
Seoul virus (SEOV), which causes hemorrhagic fever with renal syndrome (HFRS) in humans, has spread all over the world, especially in mainland China. Understanding basic mechanisms of SEOV evolution is essential to better combat and prevent viral diseases. Here, we examined SEOV prevalence and evolution in the residential area of four districts in Guangzhou city, China. The carriage of SEOV was observed in 33.33% of the sampled rodents, with 35.96% of the sampled Rattus norvegicus and 13.33% of R. tanezumi. Based on the comprehensive analyses of large (L), medium (M), and small (S) segments, our study first demonstrated that the genetic characterization of urban SEOV was shaped by high nucleotide substitution rates, purifying selection, and recombination. Additionally, we detected mutational saturation in the S segment of SEOV, which may lead to the biases of genetic divergence and substitution rates in our study. Importantly, we have filled the gap of SEOV evolution in the urban area. The genetic variation of SEOV may highlight the risk of HFRS, which merits further investigation.
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Affiliation(s)
- Qianqian Su
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (Q.S.); (M.L.); (J.M.); (B.W.); (J.L.)
- University of Chinese Academy of Sciences, Beijing 100101, China;
| | - Yi Chen
- University of Chinese Academy of Sciences, Beijing 100101, China;
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Meng Li
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (Q.S.); (M.L.); (J.M.); (B.W.); (J.L.)
| | - Jiajun Ma
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (Q.S.); (M.L.); (J.M.); (B.W.); (J.L.)
| | - Bo Wang
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (Q.S.); (M.L.); (J.M.); (B.W.); (J.L.)
- University of Chinese Academy of Sciences, Beijing 100101, China;
| | - Jing Luo
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (Q.S.); (M.L.); (J.M.); (B.W.); (J.L.)
| | - Hongxuan He
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (Q.S.); (M.L.); (J.M.); (B.W.); (J.L.)
- Correspondence:
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