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Zhu B, Zhu Z, Wang J, Huang S, Li F, Wang L, Liu Y, Yan Q, Zhou S, Lu M, Yang D, Wang B. Chinese woodchucks with different susceptibility to WHV infection differ in their genetic background exemplified by cytochrome B and MHC-DRB molecules. Virol J 2018; 15:101. [PMID: 29914514 PMCID: PMC6006932 DOI: 10.1186/s12985-018-1010-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 06/03/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Chinese woodchucks (M. himalayana) were recently found to be susceptible to woodchuck hepatitis virus (WHV) infection. In this study, we aimed to determine the susceptibility to WHV infection of M. himalayana from different areas and their association with the animal genetic background exemplified by cytochrome B and MHC-DRB molecules. METHODS Animals from four different areas in Qinghai province were inoculated with WHV59 strains. The virological markers including WHV surface antigen (WHsAg), WHV core antibody (WHcAb), and WHV DNA in serum were measured by ELISA and Real-time PCR, respectively. The sequences of cytochrome B gene and MHC-DRB molecules were obtained and sorted with Clustalx software. The nucleotide variation sites were identified using MEGA5 software. RESULTS The animals from four different areas had different susceptibility to WHV infection. Animals from TR and TD areas had a high level of long-lasting viremia, while those from GD and WL areas had a low level of transient viremia after WHV inoculation. All of the animals belong to the same subspecies M. himalayana robusta identified by cytochrome B gene sequences. Based on their nucleotide variation pattern, 8 alleles of cytochrome B gene were identified, and 7 MHC-DRB alleles were identified. Allele A of cytochrome B and Allele Mamo-DRB1*02 of MHC-DRB was found to be frequent in animals from TR and TD areas, while Allele H of cytochrome B and Allele Mamo-DRB1*07 of MHC-DRB was predominant in animals from GD and WL areas. CONCLUSION Chinese woodchucks from different areas differed in their susceptibility to WHV infection, though they belong to the same subspecies M. himalayana robusta. The genetic background exemplified by cytochrome B and MHC-DRB differed in Chinese woodchucks with different susceptibility to WHV infection.
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Affiliation(s)
- Bin Zhu
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277# Jiefang Avenue, Wuhan, 430022, China
| | - Zhenni Zhu
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277# Jiefang Avenue, Wuhan, 430022, China.,Department of Pediatrics, Maternal and Child Health Hospital of Hubei Province (Women and Children's Hospital of Hubei Province), Wuhan, China
| | - Junzhong Wang
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277# Jiefang Avenue, Wuhan, 430022, China
| | - Shunmei Huang
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277# Jiefang Avenue, Wuhan, 430022, China
| | - Fanghui Li
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277# Jiefang Avenue, Wuhan, 430022, China
| | - Lu Wang
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277# Jiefang Avenue, Wuhan, 430022, China
| | - Yanan Liu
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277# Jiefang Avenue, Wuhan, 430022, China
| | - Qi Yan
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277# Jiefang Avenue, Wuhan, 430022, China
| | - Shunchang Zhou
- Laboratory Animal Center, Huazhong University of Science and Technology, Wuhan, China
| | - Mengji Lu
- Institute of Virology, University of Duisburg-Essen, Essen, Germany
| | - Dongliang Yang
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277# Jiefang Avenue, Wuhan, 430022, China
| | - Baoju Wang
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277# Jiefang Avenue, Wuhan, 430022, China.
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Evidence for selection maintaining MHC diversity in a rodent species despite strong density fluctuations. Immunogenetics 2016; 68:429-437. [PMID: 27225422 DOI: 10.1007/s00251-016-0916-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/13/2016] [Indexed: 10/21/2022]
Abstract
Strong spatiotemporal variation in population size often leads to reduced genetic diversity limiting the adaptive potential of individual populations. Key genes of adaptive variation are encoded by the immune genes of the major histocompatibility complex (MHC) playing an essential role in parasite resistance. How MHC variation persists in rodent populations that regularly experience population bottlenecks remains an important topic in evolutionary genetics. We analysed the consequences of strong population fluctuations on MHC class II DRB exon 2 diversity in two distant common vole (Microtus arvalis) populations in three consecutive years using a high-throughput sequencing approach. In 143 individuals, we detected 25 nucleotide alleles translating into 14 unique amino acid MHC alleles belonging to at least three loci. Thus, the overall allelic diversity and amino acid distance among the remaining MHC alleles, used as a surrogate for the range of pathogenic antigens that can be presented to T-cells, are still remarkably high. Both study populations did not show significant population differentiation between years, but significant differences were found between sites. We concluded that selection processes seem to be strong enough to maintain moderate levels of MHC diversity in our study populations outcompeting genetic drift, as the same MHC alleles were conserved between years. Differences in allele frequencies between populations might be the outcome of different local parasite pressures and/or genetic drift. Further understanding of how pathogens vary across space and time will be crucial to further elucidate the mechanisms maintaining MHC diversity in cyclic populations.
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Cobble KR, Califf KJ, Stone NE, Shuey MM, Birdsell DN, Colman RE, Schupp JM, Aziz M, Van Andel R, Rocke TE, Wagner DM, Busch JD. Genetic variation at the MHC DRB1 locus is similar across Gunnison's prairie dog (Cynomys gunnisoni) colonies regardless of plague history. Ecol Evol 2016; 6:2624-51. [PMID: 27066243 PMCID: PMC4798151 DOI: 10.1002/ece3.2077] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 02/18/2016] [Accepted: 02/22/2016] [Indexed: 01/16/2023] Open
Abstract
Yersinia pestis was introduced to North America around 1900 and leads to nearly 100% mortality in prairie dog (Cynomys spp.) colonies during epizootic events, which suggests this pathogen may exert a strong selective force. We characterized genetic diversity at an MHC class II locus (DRB1) in Gunnison's prairie dog (C. gunnisoni) and quantified population genetic structure at the DRB1 versus 12 microsatellite loci in three large Arizona colonies. Two colonies, Seligman (SE) and Espee Ranch (ES), have experienced multiple plague‐related die‐offs in recent years, whereas plague has never been documented at Aubrey Valley (AV). We found fairly low allelic diversity at the DRB1 locus, with one allele (DRB1*01) at high frequency (0.67–0.87) in all colonies. Two other DRB1 alleles appear to be trans‐species polymorphisms shared with the black‐tailed prairie dog (C. ludovicianus), indicating that these alleles have been maintained across evolutionary time frames. Estimates of genetic differentiation were generally lower at the MHC locus (FST = 0.033) than at microsatellite markers (FST = 0.098). The reduced differentiation at DRB1 may indicate that selection has been important for shaping variation at MHC loci, regardless of the presence or absence of plague in recent decades. However, genetic drift has probably also influenced the DRB1 locus because its level of differentiation was not different from that of microsatellites in an FST outlier analysis. We then compared specific MHC alleles to plague survivorship in 60 C. gunnisoni that had been experimentally infected with Y. pestis. We found that survival was greater in individuals that carried at least one copy of the most common allele (DRB1*01) compared to those that did not (60% vs. 20%). Although the sample sizes of these two groups were unbalanced, this result suggests the possibility that this MHC class II locus, or a nearby linked gene, could play a role in plague survival.
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Affiliation(s)
- Kacy R Cobble
- Center for Microbial Genetics and Genomics Northern Arizona University PO Box 4073 Flagstaff Arizona 86011 USA
| | - Katy J Califf
- Center for Microbial Genetics and Genomics Northern Arizona University PO Box 4073 Flagstaff Arizona 86011 USA
| | - Nathan E Stone
- Center for Microbial Genetics and Genomics Northern Arizona University PO Box 4073 Flagstaff Arizona 86011 USA
| | - Megan M Shuey
- Center for Microbial Genetics and Genomics Northern Arizona University PO Box 4073 Flagstaff Arizona 86011 USA
| | - Dawn N Birdsell
- Center for Microbial Genetics and Genomics Northern Arizona University PO Box 4073 Flagstaff Arizona 86011 USA
| | - Rebecca E Colman
- Translational Genomics Research Institute North 3051 W. Shamrell Blvd #106 Flagstaff Arizona 86001 USA
| | - James M Schupp
- Translational Genomics Research Institute North 3051 W. Shamrell Blvd #106 Flagstaff Arizona 86001 USA
| | - Maliha Aziz
- Translational Genomics Research Institute North 3051 W. Shamrell Blvd #106 Flagstaff Arizona 86001 USA
| | - Roger Van Andel
- University of California Berkeley MC 7150 Berkeley California 94720 USA
| | - Tonie E Rocke
- United States Geological Survey National Wildlife Health Center 6006 Schroeder Road Madison Wisconsin 53711 USA
| | - David M Wagner
- Center for Microbial Genetics and Genomics Northern Arizona University PO Box 4073 Flagstaff Arizona 86011 USA
| | - Joseph D Busch
- Center for Microbial Genetics and Genomics Northern Arizona University PO Box 4073 Flagstaff Arizona 86011 USA
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Yu JM, Li LL, Zhang CY, Lu S, Ao YY, Gao HC, Xie ZP, Xie GC, Sun XM, Pang LL, Xu JG, Lipkin WI, Duan ZJ. A novel hepatovirus identified in wild woodchuck Marmota himalayana. Sci Rep 2016; 6:22361. [PMID: 26924426 PMCID: PMC4770319 DOI: 10.1038/srep22361] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 02/12/2016] [Indexed: 12/31/2022] Open
Abstract
Hepatitis A virus (HAV) is a hepatotropic picornavirus that causes acute liver disease worldwide. Here, we report on the identification of a novel hepatovirus tentatively named Marmota Himalayana hepatovirus (MHHAV) in wild woodchucks (Marmota Himalayana) in China. The genomic and molecular characterization of MHHAV indicated that it is most closely related genetically to HAV. MHHAV has wide tissue distribution but shows tropism for the liver. The virus is morphologically and structurally similar to HAV. The pattern of its codon usage bias is also consistent with that of HAV. Phylogenetic analysis indicated that MHHAV groups with known HAVs but forms an independent branch, and represents a new species in the genus Hepatovirus within the family Picornaviridae. Antigenic site analysis suggested MHHAV has a new antigenic property to other HAVs. Further evolutionary analysis of MHHAV and primate HAVs led to a most recent common ancestor estimate of 1,000 years ago, while the common ancestor of all HAV-related viruses including phopivirus can be traced back to 1800 years ago. The discovery of MHHAV may provide new insights into the origin and evolution of HAV and a model system with which to explore the pathogenesis of HAV infection.
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Affiliation(s)
- Jie-mei Yu
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Li-li Li
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Cui-yuan Zhang
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Shan Lu
- National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, China
| | - Yuan-yun Ao
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Han-chun Gao
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Zhi-ping Xie
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Guang-cheng Xie
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Xiao-man Sun
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Li-li Pang
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Jian-guo Xu
- National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, China
| | - W Ian Lipkin
- Center for Infection and Immunity, Columbia University, New York, NY, USA
| | - Zhao-Jun Duan
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
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