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Article ; Online: Neutral Forces and Balancing Selection Interplay to Shape the Major Histocompatibility Complex Spatial Patterns in the Striped Hamster in Inner Mongolia: Suggestive of Broad-Scale Local Adaptation

Liu, Pengbo / Li, Guichang / Zhao, Ning / Song, Xiuping / Wang, Jun / Shi, Xinfei / Wang, Bin / Zhang, Lu / Dong, Li / Li, Qingduo / Liu, Qiyong / Lü, Liang

Genes (Basel). 2023 July 22, v. 14, no. 7

2023

Abstract: Background: The major histocompatibility complex (MHC) plays a key role in the adaptive immune response to pathogens due to its extraordinary polymorphism. However, the spatial patterns of MHC variation in the striped hamster remain unclear, particularly ...

Abstract	Background: The major histocompatibility complex (MHC) plays a key role in the adaptive immune response to pathogens due to its extraordinary polymorphism. However, the spatial patterns of MHC variation in the striped hamster remain unclear, particularly regarding the relative contribution of the balancing selection in shaping MHC spatial variation and diversity compared to neutral forces. Methods: In this study, we investigated the immunogenic variation of the striped hamster in four wild populations in Inner Mongolia which experience a heterogeneous parasitic burden. Our goal was to identify local adaptation by comparing the genetic structure at the MHC with that at seven microsatellite loci, taking into account neutral processes. Results: We observed significant variation in parasite pressure among sites, with parasite burden showing a correlation with temperature and precipitation. Molecular analysis revealed a similar co-structure between MHC and microsatellite loci. We observed lower genetic differentiation at MHC loci compared to microsatellite loci, and no correlation was found between the two. Conclusions: Overall, these results suggest a complex interplay between neutral evolutionary forces and balancing selection in shaping the spatial patterns of MHC variation. Local adaptation was not detected on a small scale but may be applicable on a larger scale.
Keywords	adaptive immunity ; genetic variation ; hamsters ; major histocompatibility complex ; microsatellite repeats ; parasite load ; parasites ; temperature ; China
Language	English
Dates of publication	2023-0722
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article ; Online
ZDB-ID	2527218-4
ISSN	2073-4425
ISSN	2073-4425
DOI	10.3390/genes14071500
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Immune escape of BA.2.86 is comparable to XBB subvariants from the plasma of BA.5- and BA.5-XBB-convalescent subpopulations.

Yang, Xiaoyun / Wang, Yuan / Liang, Ziteng / Cui, Tingting / Chen, Daxiang / Li, Guichang / Xu, Hao / Liu, Siyi / Zhong, Nanshan / Huang, Weijin / Wang, Zhongfang

Journal of medical virology

2024 Volume 96, Issue 1, Page(s) e29417

Abstract: The EG.5.1 variant of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been prevalent since mid-July 2023 in the United States and China. The variant BA.2.86 has become a major concern because it is 34 mutations away from the parental ... ...

Abstract	The EG.5.1 variant of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been prevalent since mid-July 2023 in the United States and China. The variant BA.2.86 has become a major concern because it is 34 mutations away from the parental variant BA.2 and >30 mutations from XBB.1.5. There is an urgent need to evaluate whether the immunity of the population and current vaccines are protective against EG.5.1 and BA.2.86. Based on a cohort of two breakthrough-infected groups, the levels of neutralizing antibodies (NAbs) against different subvariants were measured using pseudovirus-based neutralization assays. XBB.1.5, EG.5.1, and BA.2.86 are comparably immune-evasive from neutralization by the plasma of individuals recovered from BA.5 infection (BA.5-convalescent) or XBB.1.9.2/XBB.1.5 infection following BA.5 infection (BA.5-XBB-convalescent). NAb levels against EG.5.1 and BA.2.86 subvariants remained >120 geometric mean titers (GMTs) in BA.5-XBB-convalescent individuals 2 months postinfection but were <40 GMTs in BA.5-convalescent individuals. Furthermore, the XBB-targeting messenger RNA (mRNA) vaccine RQ3033 induced higher levels of NAbs against XBB.1.5, EG.5.1, and BA.2.86 than against BA.5-XBB infection. The results suggest that BA.2.86 and EG.5.1 are unlikely to cause more severe concerns than the currently circulating XBB subvariants and that the XBB.1.5-targeting mRNA vaccine tested has promising protection against EG.5.1 and BA.2.86.
MeSH term(s)	Humans ; Plasma ; Antibodies, Neutralizing ; China ; Immune Evasion ; Mutation ; RNA, Messenger ; SARS-CoV-2/genetics
Chemical Substances	Antibodies, Neutralizing ; RNA, Messenger
Language	English
Publishing date	2024-01-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.29417
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Article ; Online: Development of SARS-CoV-2 animal vaccines using a stable and efficient NDV expression system.

He, Lei / Zhong, Jiaying / Li, Guichang / Lin, Zhengfang / Zhao, Peijing / Yang, Chuhua / Wang, Hairong / Zhang, Yuhao / Yang, Xiaoyun / Wang, Zhongfang

Journal of medical virology

2022 Volume 95, Issue 1, Page(s) e28237

Abstract: With the continuation of the coronavirus disease 2019 pandemic and the emergence of new severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants, the control of the spread of the virus remains urgent. Various animals, including cats, ferrets, ...

Abstract	With the continuation of the coronavirus disease 2019 pandemic and the emergence of new severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants, the control of the spread of the virus remains urgent. Various animals, including cats, ferrets, hamsters, nonhuman primates, minks, tree shrews, fruit bats, and rabbits, are susceptible to SARS-CoV-2 infection naturally or experimentally. Therefore, to avoid animals from becoming mixing vessels of the virus, vaccination of animals should be considered. In the present study, we report the establishment of an efficient and stable system using Newcastle disease virus (NDV) as a vector to express SARS-CoV-2 spike protein/subunit for the rapid generation of vaccines against SARS-CoV-2 in animals. Our data showed that the S and S1 protein was sufficiently expressed in rNDV-S and rNDV-S1-infected cells, respectively. The S protein was incorporated into and displayed on the surface of rNDV-S viral particles. Intramuscular immunization with rNDV-S was found to induce the highest level of binding and neutralizing antibodies, as well as strong S-specific T-cell response in mice. Intranasal immunization with rNDV-S1 provoked a robust T-cell response but barely any detectable antibodies. Overall, the NDV-vectored vaccine candidates were able to induce profound humoral and cellular immunity, which will provide a good system for developing vaccines targeting both T-cell and antibody responses.
MeSH term(s)	Animals ; Mice ; Humans ; Rabbits ; COVID-19 Vaccines ; Newcastle disease virus/genetics ; SARS-CoV-2 ; COVID-19/prevention & control ; Ferrets/metabolism ; Spike Glycoprotein, Coronavirus/genetics ; Antibodies, Neutralizing/metabolism ; Antibodies, Viral/metabolism ; Viral Vaccines/genetics
Chemical Substances	COVID-19 Vaccines ; spike protein, SARS-CoV-2 ; Spike Glycoprotein, Coronavirus ; Antibodies, Neutralizing ; Antibodies, Viral ; Viral Vaccines
Language	English
Publishing date	2022-10-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.28237
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Article ; Online: Neutral Forces and Balancing Selection Interplay to Shape the Major Histocompatibility Complex Spatial Patterns in the Striped Hamster in Inner Mongolia: Suggestive of Broad-Scale Local Adaptation.

Liu, Pengbo / Li, Guichang / Zhao, Ning / Song, Xiuping / Wang, Jun / Shi, Xinfei / Wang, Bin / Zhang, Lu / Dong, Li / Li, Qingduo / Liu, Qiyong / Lu, Liang

Genes

2023 Volume 14, Issue 7

Abstract	Background: The major histocompatibility complex (MHC) plays a key role in the adaptive immune response to pathogens due to its extraordinary polymorphism. However, the spatial patterns of MHC variation in the striped hamster remain unclear, particularly regarding the relative contribution of the balancing selection in shaping MHC spatial variation and diversity compared to neutral forces. Methods: In this study, we investigated the immunogenic variation of the striped hamster in four wild populations in Inner Mongolia which experience a heterogeneous parasitic burden. Our goal was to identify local adaptation by comparing the genetic structure at the MHC with that at seven microsatellite loci, taking into account neutral processes. Results: We observed significant variation in parasite pressure among sites, with parasite burden showing a correlation with temperature and precipitation. Molecular analysis revealed a similar co-structure between MHC and microsatellite loci. We observed lower genetic differentiation at MHC loci compared to microsatellite loci, and no correlation was found between the two. Conclusions: Overall, these results suggest a complex interplay between neutral evolutionary forces and balancing selection in shaping the spatial patterns of MHC variation. Local adaptation was not detected on a small scale but may be applicable on a larger scale.
MeSH term(s)	Cricetinae ; Genetic Variation/genetics ; Selection, Genetic ; Major Histocompatibility Complex/genetics ; Genetic Drift ; Histocompatibility Antigens Class II/genetics ; Histocompatibility Antigens
Chemical Substances	Histocompatibility Antigens Class II ; Histocompatibility Antigens
Language	English
Publishing date	2023-07-22
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes14071500
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Article ; Online: Climate heterogeneity, season variation, and sexual dimorphism modulate the association between MHC II diversity and parasite variation in striped hamster.

Liu, Pengbo / Li, Guichang / Zhao, Ning / Liu, Qiyong / Liu, Xiaobo / Song, Xiuping / Shi, Xinfei / Lun, Xinchang / Zhang, Lu / Wang, Jun / Lu, Liang

Integrative zoology

2023

Abstract: Parasite-mediated selection is widely believed to play a crucial role in maintaining the diversity of the major histocompatibility complex (MHC) genes, which is thought to be maintained through heterozygote advantage, rare-allele advantage, and ... ...

Abstract	Parasite-mediated selection is widely believed to play a crucial role in maintaining the diversity of the major histocompatibility complex (MHC) genes, which is thought to be maintained through heterozygote advantage, rare-allele advantage, and fluctuating selection. However, the relationship between parasite pressure and MHC diversity has yielded inconsistent findings. These inconsistencies may arise from the influence of environmental factors and individual variations in traits on host-parasite interactions. To address these issues, our study extensively investigated populations of striped hamsters inhabiting regions characterized by environmental heterogeneity. The primary objective was to examine the universality of parasite-mediated selection mechanisms. Our observations revealed the presence of multiple parasite infections, accompanied by spatial and temporal variations in parasite communities and infection patterns among individual hamsters. Specifically, the temperature was found to influence all four parasite indices, while the presence of gamasid mites and parasite richness decreased with increasing precipitation. We also noted significant seasonal variation in parasite dynamics. Moreover, a significant sexual dimorphism was observed with males exhibiting a considerably higher parasite burden compared to their female counterparts. Lastly, we identified the maintenance of MHC polymorphism in striped hamsters as being driven by the heterozygote advantage and fluctuating selection mechanisms. This study underscores the significance of ecological processes in comprehending host-parasite systems and highlights the necessity of considering environmental factors and individual traits when elucidating the mechanisms underlying MHC diversity mediated by parasites.
Language	English
Publishing date	2023-12-12
Publishing country	Australia
Document type	Journal Article
ZDB-ID	2570656-1
ISSN	1749-4877 ; 1749-4869
ISSN (online)	1749-4877
ISSN	1749-4869
DOI	10.1111/1749-4877.12791
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Article: Dispersal route of the Asian house rat (Rattus tanezumi) on mainland China: insights from microsatellite and mitochondrial DNA

Guo, Song / Li, Guichang / Liu, Jinli / Wang, Jun / Lu, Liang / Liu, Qiyong

BMC genetics. 2019 Dec., v. 20, no. 1

2019

Abstract: BACKGROUND: Rattus tanezumi is a common commensal rat and an important host animal of bubonic plague in South China and Southeast Asia. The northward dispersal of this species in mainland China has been reported in recent decades, along with more recent ... ...

Abstract	BACKGROUND: Rattus tanezumi is a common commensal rat and an important host animal of bubonic plague in South China and Southeast Asia. The northward dispersal of this species in mainland China has been reported in recent decades, along with more recent intercontinental expansion. Population genetics of R. tanezumi in mainland China were studied to explain the relationship between dispersal history and the ancient and modern transportation networks of China. RESULTS: In total, 502 individuals belonging to 18 populations were collected from 13 provincial areas. Nine microsatellite loci and two mtDNA sequences were analyzed. The results indicate that R. tanezumi populations from Yunnan have highest genetic diversity and populations from Tibet with lowest genetic diversity. 18 populations can be divided into four clusters, the first cluster including populations from southwest Yunnan, the second including two populations of Tibet, the third for populations from middle and east of mainland China, and the forth for two populations from north Yunnan. Both microsatellite and mtDNA data reveal that the populations from coastal areas are closely related to populations from Yunnan, whereas populations from Tibet are closely related with populations from Sichuan. CONCLUSIONS: The results suggest that early dispersal of R. tanezumi in mainland China depended on shipping transportation, with subsequent expansion from coastal areas into Central China occurring along the Yangzi River. Further, the linkages between populations in Tibet and Sichuan point to a modern era introduction via the Chuan-Zang highway, rather than along the Tea Horse Ancient Road.
Keywords	Rattus ; coasts ; genetic variation ; microsatellite repeats ; mitochondrial DNA ; plague ; population genetics ; rats ; rivers ; shipping ; transportation ; China ; South East Asia
Language	English
Dates of publication	2019-12
Size	p. 11.
Publishing place	BioMed Central
Document type	Article
ISSN	1471-2156
DOI	10.1186/s12863-019-0714-3
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Article ; Online: Dispersal route of the Asian house rat (Rattus tanezumi) on mainland China: insights from microsatellite and mitochondrial DNA.

Guo, Song / Li, Guichang / Liu, Jinli / Wang, Jun / Lu, Liang / Liu, Qiyong

BMC genetics

2019 Volume 20, Issue 1, Page(s) 11

Abstract: Background: Rattus tanezumi is a common commensal rat and an important host animal of bubonic plague in South China and Southeast Asia. The northward dispersal of this species in mainland China has been reported in recent decades, along with more recent ...

Abstract	Background: Rattus tanezumi is a common commensal rat and an important host animal of bubonic plague in South China and Southeast Asia. The northward dispersal of this species in mainland China has been reported in recent decades, along with more recent intercontinental expansion. Population genetics of R. tanezumi in mainland China were studied to explain the relationship between dispersal history and the ancient and modern transportation networks of China. Results: In total, 502 individuals belonging to 18 populations were collected from 13 provincial areas. Nine microsatellite loci and two mtDNA sequences were analyzed. The results indicate that R. tanezumi populations from Yunnan have highest genetic diversity and populations from Tibet with lowest genetic diversity. 18 populations can be divided into four clusters, the first cluster including populations from southwest Yunnan, the second including two populations of Tibet, the third for populations from middle and east of mainland China, and the forth for two populations from north Yunnan. Both microsatellite and mtDNA data reveal that the populations from coastal areas are closely related to populations from Yunnan, whereas populations from Tibet are closely related with populations from Sichuan. Conclusions: The results suggest that early dispersal of R. tanezumi in mainland China depended on shipping transportation, with subsequent expansion from coastal areas into Central China occurring along the Yangzi River. Further, the linkages between populations in Tibet and Sichuan point to a modern era introduction via the Chuan-Zang highway, rather than along the Tea Horse Ancient Road.
MeSH term(s)	Animal Distribution ; Animals ; China ; DNA, Mitochondrial/genetics ; Gene Flow ; Genetic Variation ; Linkage Disequilibrium ; Microsatellite Repeats/genetics ; Rats ; Transportation
Chemical Substances	DNA, Mitochondrial
Language	English
Publishing date	2019-01-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1471-2156
ISSN (online)	1471-2156
DOI	10.1186/s12863-019-0714-3
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Article ; Online: Spatio-temporal patterns of scrub typhus in mainland China, 2006-2017.

Yue, Yujuan / Ren, Dongsheng / Liu, Xiaobo / Wang, Yujiao / Liu, Qiyong / Li, Guichang

PLoS neglected tropical diseases

2019 Volume 13, Issue 12, Page(s) e0007916

Abstract: Background: Scrub typhus, a serious public health problem in the Asia-Pacific area, is endemic in the "tsutsugamushi triangle" area. Scrub typhus has been widespread and has become a significant health concern in China. However, spatiotemporal patterns ... ...

Abstract	Background: Scrub typhus, a serious public health problem in the Asia-Pacific area, is endemic in the "tsutsugamushi triangle" area. Scrub typhus has been widespread and has become a significant health concern in China. However, spatiotemporal patterns need to be investigated further. Objective: This study aims to explore spatiotemporal patterns, diffusion characteristics and regional distribution differences of scrub typhus cases in mainland China from January 2006 to December 2017. Method: Monthly cases of scrub typhus reported at the county level during 2006-2017 were obtained. Time-series analyses, spatial distribution analyses, spatial diffusion analyses, spatial autocorrelation analyses and space-time scan statistic analyses were used to explore spatiotemporal characteristics of scrub typhus. Results: A total of 121 251 scrub typhus cases were reported in 30 provinces (or municipalities) of mainland China during 2006-2017, which rose exponentially. There were seasonal characteristics from June to November for scrub typhus. Scrub typhus had been diffused from south, southwest, southeast and eastern coasts to center, north, northeast and northwest in mainland China. Scrub typhus occurrences were from point to surrounding regions, and from south to north every year. The peak periods of scrub typhus became longer and longer from north to southwest to south in mainland China. There existed a single peak in Southwest region and North region, respectively, but existed a bimodal peak for South region. Scrub typhus cases were clustered in Yunnan, Guangdong, Guangxi, Fujian and Anhui among June to November. The scrub typhus epidemics in Guangdong and Yunnan were the most serious. Conclusions: The results in this study can be guide targeted public health interventions against scrub typhus at the county level.
MeSH term(s)	China/epidemiology ; Epidemics ; Humans ; Scrub Typhus/epidemiology ; Spatio-Temporal Analysis ; Topography, Medical
Language	English
Publishing date	2019-12-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2429704-5
ISSN	1935-2735 ; 1935-2727
ISSN (online)	1935-2735
ISSN	1935-2727
DOI	10.1371/journal.pntd.0007916
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Article ; Online: Heterologous boosting with third dose of coronavirus disease recombinant subunit vaccine increases neutralizing antibodies and T cell immunity against different severe acute respiratory syndrome coronavirus 2 variants.

Wang, Zhongfang / Zhao, Zhuxiang / Cui, Tingting / Huang, Mingzhu / Liu, Shuo / Su, Xiaoling / Li, Guichang / Song, Tao / Li, Weidong / Zhong, Nanshan / Xu, Miao / Yang, Xiaoyun / Huang, WeiJin

Emerging microbes & infections

2022 Volume 11, Issue 1, Page(s) 829–840

Abstract: Waned vaccine-induced immunity and emerging severe acute respiratory syndrome coronavirus 2 variants with potential for immune escape pose a major threat to the coronavirus disease (COVID-19) pandemic. Here, we showed that humoral immunity components, ... ...

Abstract	Waned vaccine-induced immunity and emerging severe acute respiratory syndrome coronavirus 2 variants with potential for immune escape pose a major threat to the coronavirus disease (COVID-19) pandemic. Here, we showed that humoral immunity components, including anti-S + N, anti-RBD IgG, and neutralizing antibodies (NAbs), gradually waned and decreased the neutralizing capacity against emerging Omicron variants at 3 and 6 months after two inactivated COVID-19 vaccinations. We evaluated two boosting strategies with either a third dose of inactivated vaccine (homologous, I-I-I) or a recombinant subunit vaccine (heterologous, I-I-S). Both strategies induced the production of high levels of NAbs with a broad neutralizing capacity and longer retention. Interestingly, I-I-S induced 3.5-fold to 6.8-fold higher NAb titres than I-I-I, with a broader neutralizing capacity against six variants of concern, including Omicron. Further immunological analysis revealed that the two immunization strategies differ considerably, not only in the magnitude of total NAbs produced, but also in the composite pattern of NAbs and the population of virus-specific CD4+ T cells produced. Additionally, in some cases, heterologous boosted immunity induced the production of more effective epitopes than natural infection. The level of I-I-S-induced NAbs decreased to 48% and 18% at 1 and 3 months after booster vaccination, respectively. Overall, our data provide important evidence for vaccination strategies based on available vaccines and may help guide future global vaccination plans.
MeSH term(s)	Antibodies, Neutralizing ; Antibodies, Viral ; COVID-19/prevention & control ; COVID-19 Vaccines/immunology ; Humans ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/genetics ; T-Lymphocytes/immunology ; Vaccination ; Vaccines, Subunit
Chemical Substances	Antibodies, Neutralizing ; Antibodies, Viral ; COVID-19 Vaccines ; Spike Glycoprotein, Coronavirus ; Vaccines, Subunit ; spike protein, SARS-CoV-2
Language	English
Publishing date	2022-03-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	2681359-2
ISSN	2222-1751 ; 2222-1751
ISSN (online)	2222-1751
ISSN	2222-1751
DOI	10.1080/22221751.2022.2048969
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Article ; Online: SARS-CoV-2-specific CD4

Wang, Zhongfang / Yang, Xiaoyun / Mei, Xinyue / Zhou, Yumin / Tang, Zhiqiang / Li, Guichang / Zhong, Jiaying / Yu, Mengqiu / Huang, Mingzhu / Su, Xiaoling / Lin, Bijia / Cao, Pengxing / Yang, Ji / Ran, Pixin

Signal transduction and targeted therapy

2022 Volume 7, Issue 1, Page(s) 132

Abstract: Understanding the decay and maintenance of long-term SARS-CoV-2 neutralizing antibodies in infected or vaccinated people and how vaccines protect against other SARS-CoV-2 variants is critical for assessing public vaccination plans. Here, we measured ... ...

Abstract	Understanding the decay and maintenance of long-term SARS-CoV-2 neutralizing antibodies in infected or vaccinated people and how vaccines protect against other SARS-CoV-2 variants is critical for assessing public vaccination plans. Here, we measured different plasm antibody levels 2 and 12 months after disease onset, including anti-RBD, anti-N, total neutralizing antibodies, and two neutralizing-antibody clusters. We found that total neutralizing antibodies declined more slowly than total anti-RBD and anti-N IgG, and the two neutralizing-antibody clusters decayed even more slowly than total neutralizing antibodies. Interestingly, the level of neutralizing antibodies at 12 months after disease onset was significantly lower than that at 2 months but more broadly neutralized SARS-CoV-2 variants, including Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Lambda (C.37). Significant immune escape by the Omicron variant (B.1.1.529) was also observed 2 months post-recovery. Furthermore, we revealed that a high percentage of virus-specific CD4
MeSH term(s)	Antibodies, Neutralizing/genetics ; Antibodies, Viral/genetics ; CD4-Positive T-Lymphocytes ; COVID-19 ; Humans ; SARS-CoV-2 ; T-Lymphocytes
Chemical Substances	Antibodies, Neutralizing ; Antibodies, Viral
Language	English
Publishing date	2022-04-23
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2886872-9
ISSN	2059-3635 ; 2095-9907
ISSN (online)	2059-3635
ISSN	2095-9907
DOI	10.1038/s41392-022-00978-0
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