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Article ; Online: Bioinformatics analysis of epitope-based vaccine design against the novel SARS-CoV-2.

Chen, Hong-Zhi / Tang, Ling-Li / Yu, Xin-Ling / Zhou, Jie / Chang, Yun-Feng / Wu, Xiang

2020 Volume 9, Issue 1, Page(s) 88

Abstract: Background: An outbreak of infection caused by SARS-CoV-2 recently has brought a great challenge to public health. Rapid identification of immune epitopes would be an efficient way to screen the candidates for vaccine development at the time of pandemic. ...

Abstract	Background: An outbreak of infection caused by SARS-CoV-2 recently has brought a great challenge to public health. Rapid identification of immune epitopes would be an efficient way to screen the candidates for vaccine development at the time of pandemic. This study aimed to predict the protective epitopes with bioinformatics methods and resources for vaccine development. Methods: The genome sequence and protein sequences of SARS-CoV-2 were retrieved from the National Center for Biotechnology Information (NCBI) database. ABCpred and BepiPred servers were utilized for sequential B-cell epitope analysis. Discontinuous B-cell epitopes were predicted via DiscoTope 2.0 program. IEDB server was utilized for HLA-1 and HLA-2 binding peptides computation. Surface accessibility, antigenicity, and other important features of forecasted epitopes were characterized for immunogen potential evaluation. Results: A total of 63 sequential B-cell epitopes on spike protein were predicted and 4 peptides (Spike Conclusions: B-cell epitopes on spike protein and T-cell epitopes within nucleocapsid protein were identified and recommended for developing a protective vaccine against SARS-CoV-2.
MeSH term(s)	Amino Acid Sequence ; Betacoronavirus/genetics ; Betacoronavirus/immunology ; COVID-19 ; COVID-19 Vaccines ; Computational Biology/methods ; Coronavirus Infections/immunology ; Coronavirus Infections/prevention & control ; Coronavirus Infections/virology ; Drug Design ; Epitopes, B-Lymphocyte/chemistry ; Epitopes, B-Lymphocyte/immunology ; Epitopes, T-Lymphocyte/chemistry ; Epitopes, T-Lymphocyte/immunology ; Humans ; Immunogenicity, Vaccine/immunology ; Models, Molecular ; Pandemics/prevention & control ; Pneumonia, Viral/immunology ; Pneumonia, Viral/prevention & control ; Pneumonia, Viral/virology ; SARS-CoV-2 ; Sequence Alignment ; Sequence Analysis ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/immunology ; Viral Envelope Proteins/immunology ; Viral Vaccines/immunology
Chemical Substances	COVID-19 Vaccines ; Epitopes, B-Lymphocyte ; Epitopes, T-Lymphocyte ; Spike Glycoprotein, Coronavirus ; Viral Envelope Proteins ; Viral Vaccines ; spike protein, SARS-CoV-2
Keywords	covid19
Language	English
Publishing date	2020-07-10
Publishing country	England
Document type	Journal Article
ZDB-ID	2689396-4
ISSN	2049-9957 ; 2049-9957
ISSN (online)	2049-9957
ISSN	2049-9957
DOI	10.1186/s40249-020-00713-3
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Bioinformatics analysis of epitope-based vaccine design against the novel SARS-CoV-2

Chen, Hong-Zhi / Tang, Ling-Li / Yu, Xin-Ling / Zhou, Jie / Chang, Yun-Feng / Wu, Xiang

Infectious Diseases of Poverty

2020 Volume 9, Issue 1

Keywords	covid19
Language	English
Publisher	Springer Science and Business Media LLC
Publishing country	us
Document type	Article ; Online
ZDB-ID	2689396-4
ISSN	2049-9957
ISSN	2049-9957
DOI	10.1186/s40249-020-00713-3
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Article: Bioinformatics analysis of epitope-based vaccine design against the novel SARS-CoV-2

Chen, Hong-Zhi / Tang, Ling-Li / Yu, Xin-Ling / Zhou, Jie / Chang, Yun-Feng / Wu, Xiang

Infect Dis Poverty

Abstract: BACKGROUND: An outbreak of infection caused by SARS-CoV-2 recently has brought a great challenge to public health. Rapid identification of immune epitopes would be an efficient way to screen the candidates for vaccine development at the time of pandemic. ...

Abstract	BACKGROUND: An outbreak of infection caused by SARS-CoV-2 recently has brought a great challenge to public health. Rapid identification of immune epitopes would be an efficient way to screen the candidates for vaccine development at the time of pandemic. This study aimed to predict the protective epitopes with bioinformatics methods and resources for vaccine development. METHODS: The genome sequence and protein sequences of SARS-CoV-2 were retrieved from the National Center for Biotechnology Information (NCBI) database. ABCpred and BepiPred servers were utilized for sequential B-cell epitope analysis. Discontinuous B-cell epitopes were predicted via DiscoTope 2.0 program. IEDB server was utilized for HLA-1 and HLA-2 binding peptides computation. Surface accessibility, antigenicity, and other important features of forecasted epitopes were characterized for immunogen potential evaluation. RESULTS: A total of 63 sequential B-cell epitopes on spike protein were predicted and 4 peptides (Spike315-324, Spike333-338, Spike648-663, Spike1064-1079) exhibited high antigenicity score and good surface accessibility. Ten residues within spike protein (Gly496, Glu498, Pro499, Thr500, Leu1141, Gln1142, Pro1143, Glu1144, Leu1145, Asp1146) are forecasted as components of discontinuous B-cell epitopes. The bioinformatics analysis of HLA binding peptides within nucleocapsid protein produced 81 and 64 peptides being able to bind MHC class I and MHC class II molecules respectively. The peptides (Nucleocapsid66-75, Nucleocapsid104-112) were predicted to bind a wide spectrum of both HLA-1 and HLA-2 molecules. CONCLUSIONS: B-cell epitopes on spike protein and T-cell epitopes within nucleocapsid protein were identified and recommended for developing a protective vaccine against SARS-CoV-2.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #690345
Database	COVID19

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Article ; Online: Schistosoma japonicum

Ma, Zhen Rong / Sun, Xi / Zheng, Wen Xiao / Li, Xuan Wu / Zhang, Ni / Huang, Ye Hong / Lu, Bin / Li, Zhuo Lin / Nouhoum, Di Bo / Yu, Xin Ling / Zhou, Jie / Chen, Hong Zhi / Yang, Xue Xian / Wu, Xiang

Biomedical and environmental sciences : BES

2022 Volume 35, Issue 11, Page(s) 1085–1089

MeSH term(s)	Animals ; Schistosoma japonicum ; Colitis, Ulcerative
Language	English
Publishing date	2022-11-25
Publishing country	China
Document type	Letter
ZDB-ID	645083-0
ISSN	2214-0190 ; 0895-3988
ISSN (online)	2214-0190
ISSN	0895-3988
DOI	10.3967/bes2022.138
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Article: [Influence factors of Schistosoma japonicum infection among fishermen in eastern Dongting Lake Region].

Yu, Xin-Ling / Zhou, Jie / He, Yong-Kang / Huang, Ming-Zhu / Li, Yue-Sheng

Zhongguo ji sheng chong xue yu ji sheng chong bing za zhi = Chinese journal of parasitology & parasitic diseases

2013 Volume 31, Issue 4, Page(s) 307–9, 314

Abstract: Objective: To investigate schistosome infection among the professional fishermen in Yueyang County, East Dongting Lake Region and its influence factors.: Methods: A total of 275 fishermen from two fisherman villages in Yueyang County were selected in ...

Abstract	Objective: To investigate schistosome infection among the professional fishermen in Yueyang County, East Dongting Lake Region and its influence factors. Methods: A total of 275 fishermen from two fisherman villages in Yueyang County were selected in 2009. They were investigated by fecal examination and questionnairing. The stool-egg positive individuals were detected by B ultrasound. The multivariate unconditional Logistic regression analysis was used to explore the related factors of schistosome infection and liver in fishermen. Results: The total infection rate in fishermen was 40.4% (111/275), and the geometric mean of EPG was 17.4 +/- 4.4. B ultrasound data showed among 111 egg positive individuals, 39 (35.1%) cases manifested as hepatomegaly, 22 (19.8%) had splenomegaly, 11 (9.9%) had portal vein expansion and 65 (58.6%) had hepatic fibrosis. Multivariate unconditional Logistic regression analysis showed that age groups (OR = 0.630), fishing working years (OR = 2.470), chemotherapy frequency (OR = 0.425) and chemotherapy in 2008 (OR = 0.290) were the influence factors on schistosome infection (P < 0.01). Conclusion: Schistosome infection rate is high, Schistosoma japonicum-induced liver and spleen injuries are still severe in fisherman of Eastern Dongting Lake Region.
MeSH term(s)	Adult ; Animals ; China/epidemiology ; Epidemiologic Factors ; Female ; Humans ; Lakes ; Logistic Models ; Male ; Middle Aged ; Occupational Exposure ; Schistosoma japonicum ; Schistosomiasis japonica/epidemiology ; Schistosomiasis japonica/parasitology
Language	Chinese
Publishing date	2013-08
Publishing country	China
Document type	English Abstract ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	639272-6
ISSN	1000-7423
ISSN	1000-7423
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Article: [Infectivity difference between mice challenged by the laboratory-cultivated and field collected Schistosoma japonicum-infected Oncomelania hupensis].

Yu, Xin-Ling / Zhou, Jie / Hu, Jun-Jian / He, Yong-Kang / Li, Yue-Sheng

Zhongguo xue xi chong bing fang zhi za zhi = Chinese journal of schistosomiasis control

2012 Volume 24, Issue 5, Page(s) 579–80, 584

Abstract: Objective: To explore the infectivity difference between the mice challenged by laboratory-cultivated and field collected Schistosomajaponicum-infected Oncomelania hupensis snails.: Methods: A total of 120 Kunming mice were randomly divided into two ... ...

Abstract	Objective: To explore the infectivity difference between the mice challenged by laboratory-cultivated and field collected Schistosomajaponicum-infected Oncomelania hupensis snails. Methods: A total of 120 Kunming mice were randomly divided into two groups. S. japonicum-infected O. hupensis releasing cercariae was according to routine cercaria shedding method. Each mouse was challenged by 40 cercariae. The worm-load, the development rate, EPG of liver and EPG of feces in the mice were calculated. Results: The mean worm-load, adult worm development rate, EPG of liver and EPG of feces in the group of mice infected by field collected S. japonicum-infected snails were 27.43 +/- 3.78, 68.53 +/- 9.44, 19 800.97 +/- 6 752.59 and 196.37 +/- 11.56, respectively, which were significantly higher than those in the group challenged by cercariae from laboratory-cultivated S. japonicum-infected snails (23.93 +/- 4.93, 59.83 +/- 12.32, 5 803.69 +/-1 560.49 and 107.73 +/- 10.32) (P < 0.05). The mean worm-load, adult worm development rate and EPG of liver in the male mouse group were higher than those in the female mouse group (P < 0.05). Conclusion: The cercariae released from field collected S. japonicum-infected snails have more aggressive infection ability, compared with the cercariae released from the laboratory-cultivated S. japonicum-infected snails and the results also show male mice are more susceptibility to the schistosome infection than female mice.
MeSH term(s)	Animals ; Disease Reservoirs/parasitology ; Female ; Male ; Mice ; Schistosoma japonicum/growth & development ; Schistosoma japonicum/pathogenicity ; Schistosoma japonicum/physiology ; Schistosomiasis japonica/parasitology ; Snails/parasitology
Language	Chinese
Publishing date	2012-10
Publishing country	China
Document type	Comparative Study ; English Abstract ; Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1005-6661
ISSN	1005-6661
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: [Analysis of epidemiological characteristics of advanced schistosomiasis in Hu-nan province, 2012].

Liu, Zhao-chun / Xiao, Shui-yuan / Zhou, Jie / Yu, Xin-ling / Hu, Ben-jiao / Zhu, Jin-hua / Li, Yue-sheng

Zhongguo xue xi chong bing fang zhi za zhi = Chinese journal of schistosomiasis control

2014 Volume 26, Issue 2, Page(s) 148–152

Abstract: Objective: To understand the epidemiological characteristics of patients with advanced schistosomiasis in Hunan Province, so as to provide the evidence for formulating the advanced schistosomiasis prevention strategies and measures.: Methods: The ... ...

Abstract	Objective: To understand the epidemiological characteristics of patients with advanced schistosomiasis in Hunan Province, so as to provide the evidence for formulating the advanced schistosomiasis prevention strategies and measures. Methods: The data of advanced schistosomiasis patients were collected and analyzed retrospectively with the cross section research method and description method in Hunan Province, 2012. Results: There were 5 722 advanced schistosomiasis patients in Hunan Province, and among them, 4 112 patients were male (71.86%), and 1610 were female (28.14%). Totally 5311 patients came from the schistosomiasis endemic areas (92.82%) and 411 patients from non-schistosomiasis endemic areas (7.18%). The prevalence rate of advanced schistosomiasis was 8.46/10,000. The mean age of advanced schistosomiasis patients was 60.30 +/- 11.63 years, and the youngest was 17 years old and the oldest 92 years old. In the age composition of advanced schistosomiasis patients, the greatest number of cases was in the 60-70 years age group (32.72%). There were 3 595 cases of ascites type (62.83%), 2107 cases of splenomegaly type (36.82%), 11 cases of dwarf type (0.16%), and 11 cases of colon proliferation type (0.35%). Conclusion: The prevalence rate of advanced schistosomiasis is relatively stable in Hunan Province, and the age of the patients showed an old aging trend. The salvation of advanced schistosomiasis patients in non-endemic areas should be strengthened.
MeSH term(s)	Adult ; Age Distribution ; Aged ; Aged, 80 and over ; China/epidemiology ; Disease Progression ; Educational Status ; Female ; Humans ; Male ; Middle Aged ; Schistosomiasis/epidemiology ; Sex Distribution
Language	Chinese
Publishing date	2014-04
Publishing country	China
Document type	English Abstract ; Journal Article
ISSN	1005-6661
ISSN	1005-6661
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Article ; Online: An ultra-sensitive assay targeting the circulating anodic antigen for the diagnosis of Schistosoma japonicum in a low-endemic area, People's Republic of China.

van Dam, Govert J / Xu, Jing / Bergquist, Robert / de Dood, Claudia J / Utzinger, Jürg / Qin, Zhi-Qiang / Guan, Wei / Feng, Ting / Yu, Xin-Ling / Zhou, Jie / Zheng, Ma / Zhou, Xiao-Nong / Corstjens, Paul L A M

Acta tropica

2015 Volume 141, Issue Pt B, Page(s) 190–197

Abstract: The downward trend in prevalence and intensity of Schistosoma japonicum infection in the People's Republic of China (P.R. China) has reached a level where accurate methods are required for monitoring the national schistosomiasis control programme and to ... ...

Abstract	The downward trend in prevalence and intensity of Schistosoma japonicum infection in the People's Republic of China (P.R. China) has reached a level where accurate methods are required for monitoring the national schistosomiasis control programme and to verify whether transmission has been interrupted. We have assessed the prevalence of active S. japonicum infection by use of an up-converting phosphor lateral-flow (UCP-LF) assay for determination of circulating anodic antigens (CAA) in urine and serum, and compared the findings with those of the Kato-Katz technique for egg detection in stool and an immunohaemagglutination assay (IHA) for specific antibodies in serum. The study was carried out in three villages located in a remaining S. japonicum-endemic area in P.R. China. Overall, 423 individuals were investigated by Kato-Katz, 395 by IHA, 371 with the UCP-LF CAA assay adapted for urine and 178 with the UCP-LF CAA assay applied on serum. The IHA showed the highest number of positive results (n=107, 27.1%). The UCP-LF CAA urine assay detected 36 CAA positives (9.7%) and the serum-based CAA assay 21 positives (11.8%). The Kato-Katz technique revealed only six positive stool samples (1.4%). Among those 166 individuals with complete data records, sensitivities of the different assays were determined versus a combined 'gold' standard, showing the highest sensitivity for the urine CAA assay (93%), followed by the serum CAA (73%) and IHA (53%), whilst triplicate Kato-Katz thick smears had a very low sensitivity (13%). Serum CAA concentrations were about 10-fold higher than in urine and were significantly correlated. Highest prevalences as determined by CAA were found in older age groups (>40 years). Half of the CAA- or egg-positive cases were negative for antibodies by IHA, thereby revealing an important obstacle for the effectiveness of the current schistosomiasis control and elimination efforts. The significantly higher prevalence of active schistosome infections as shown by the urine and serum UCP-LF CAA assays has implications for the national control and elimination programme in P.R. China, particularly in respect to case-finding and intervention strategies.
MeSH term(s)	Adolescent ; Adult ; Aged ; Aged, 80 and over ; Animals ; Antigens, Helminth/blood ; Antigens, Helminth/urine ; Child ; China/epidemiology ; Feces/parasitology ; Female ; Hemagglutination Tests ; Humans ; Male ; Middle Aged ; Prevalence ; Schistosoma japonicum/immunology ; Schistosomiasis japonica/diagnosis ; Schistosomiasis japonica/epidemiology ; Sensitivity and Specificity ; Young Adult
Chemical Substances	Antigens, Helminth
Language	English
Publishing date	2015-01
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	210415-5
ISSN	1873-6254 ; 0001-706X
ISSN (online)	1873-6254
ISSN	0001-706X
DOI	10.1016/j.actatropica.2014.08.004
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Article: [Conditions of schistosomiasis laboratories at county level].

Feng, Ting / Xu, Jing / Hang, De-Rong / Wu, Zi-Song / Tang, Li / Wang, Qi-Zhi / Yu, Xin-Ling / Zeng, Xiao-Jun / Shen, Mei-Fen / Wu, Cheng-Guo / Yuan, Yi / Guo, Jia-Gang / Zhou, Xiao-Nong

Zhongguo xue xi chong bing fang zhi za zhi = Chinese journal of schistosomiasis control

2011 Volume 23, Issue 4, Page(s) 370–376

Abstract: Objective: To understand the conditions of schistosomiasis laboratories at county level, so as to supply the information for diagnostic capacity building.: Methods: A questionnaire survey was conducted at 40 random selected counties which were in ... ...

Abstract	Objective: To understand the conditions of schistosomiasis laboratories at county level, so as to supply the information for diagnostic capacity building. Methods: A questionnaire survey was conducted at 40 random selected counties which were in charge of national surveillance for schistosomiasis. The information of staffs, areas of laboratories, equipment configuration and diagnostic methods from each laboratory were collected. The serum specimens and Kato-Katz thick smears from the national surveillance sites were randomly selected and retested by provincial staffs to evaluate the testing ability of the personnel. Results: The average age of laboratory staffs was 40.93 +/- 9.56 years old, 69.39% of staffs were older than 35 years, 86.22% of them had education background below bachelor degree. Except missed professional titles of 4 persons, the staffs with primary, middle and high professional titles accounted for 56.63%, 39.29% and 2.04%, respectively. The laboratory areas varied greatly while independent schistosomiasis stations had the lowest areas with 52.81 +/- 40.08 m2, and the equipment configurations of laboratories were in a low level. The consistency rates of primary test and reexamination for serum specimens and thick smear slides were 95.89% and 99.53%, respectively, with the Kappa value over 0.90. Nine immunodiagnostic kits were used in these laboratories, and Kato-Katz technique and miracidium hatching technique were the main parasitological methods. Conclusions: The personnel structure of laboratories at primary prevention and treatment facilities for schistosomiasis is unreasonable, while the basic infrastructure of laboratories is backward and the use of diagnostic assays/methods is disordered. The diagnostic capacity building should be strengthened, and the construction and management of schistosomiasis laboratories should be standardized.
MeSH term(s)	Adult ; Animals ; China ; Clinical Laboratory Techniques/instrumentation ; Clinical Laboratory Techniques/methods ; Education ; Female ; Humans ; Laboratories/manpower ; Male ; Medical Staff/education ; Middle Aged ; Schistosoma/isolation & purification ; Schistosomiasis/diagnosis ; Schistosomiasis/parasitology
Language	Chinese
Publishing date	2011-08
Publishing country	China
Document type	English Abstract ; Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1005-6661
ISSN	1005-6661
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Article ; Online: Risk factors for helminth infections in a rural and a peri-urban setting of the Dongting Lake area, People's Republic of China.

Balen, Julie / Raso, Giovanna / Li, Yue-Sheng / Zhao, Zheng-Yuan / Yuan, Li-Ping / Williams, Gail M / Luo, Xin-Song / Shi, Meng-Zhi / Yu, Xin-Ling / Utzinger, Jürg / McManus, Donald P

International journal for parasitology

2011 Volume 41, Issue 11, Page(s) 1165–1173

Abstract: Schistosomiasis japonica and soil-transmitted helminthiasis are endemic parasitic diseases in the People's Republic of China (PR China). As very few studies have reported on the distribution and interaction of multiple species helminth infections, we ... ...

Abstract	Schistosomiasis japonica and soil-transmitted helminthiasis are endemic parasitic diseases in the People's Republic of China (PR China). As very few studies have reported on the distribution and interaction of multiple species helminth infections, we carried out a comparative study of households in a rural village and a peri-urban setting in the Dongting Lake area of Hunan province in November and December 2006 to determine the extent of single and multiple species infections, the underlying risk factors for infection, and the relationships with clinical manifestations and self-reported morbidity. In each household, stool samples were collected and subjected to the Kato-Katz method for identifying Schistosoma japonicum, Ascaris lumbricoides, hookworm and Trichuris trichiura infections. Clinical examinations were performed and questionnaire surveys conducted at both household and individual subject levels. Complete parasitological, clinical and questionnaire data were obtained for 1,298 inhabitants of the two settings. The overall prevalences of single infections of S. japonicum, A. lumbricoides, hookworm and T. trichiura were 6.5%, 5.5%, 3.0% and 0.8%, respectively; the majority of the infections were of light intensity. We found significant negative associations between wealth and infections with S. japonicum and A. lumbricoides. Clinical manifestations of splenomegaly, hepatomegaly and anaemia were prevalent (9.0%, 3.7% and 10.9%, respectively), the latter two being significantly (P<0.05) associated with schistosomiasis. Self-reported symptoms were more common among females but there was considerable under-reporting in both sexes when relying only on spontaneous recall. Our findings may guide the design and targeting of a more equitable, comprehensive and integrated parasitic disease control programme in Hunan province and in other areas of PR China.
MeSH term(s)	Adolescent ; Adult ; Aged ; Animals ; Child ; China/epidemiology ; Cross-Sectional Studies ; Feces/parasitology ; Female ; Helminthiasis/epidemiology ; Helminthiasis/parasitology ; Helminths/isolation & purification ; Helminths/physiology ; Humans ; Male ; Middle Aged ; Prevalence ; Risk Factors ; Rural Population ; Surveys and Questionnaires ; Young Adult
Language	English
Publishing date	2011-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	120518-3
ISSN	1879-0135 ; 0020-7519
ISSN (online)	1879-0135
ISSN	0020-7519
DOI	10.1016/j.ijpara.2011.07.006
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