Bioinformatic prediction of immunodominant regions in spike protein for early diagnosis of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

被引:6
|
作者
Zhuang, Siqi [1 ]
Tang, Lingli [1 ]
Dai, Yufeng [1 ]
Feng, Xiaojing [1 ]
Fang, Yiyuan [1 ]
Tang, Haoneng [1 ]
Jiang, Ping [1 ]
Wu, Xiang [2 ]
Fang, Hezhi [3 ]
Chen, Hongzhi [4 ,5 ]
机构
[1] Cent South Univ, Xiangya Hosp 2, Dept Lab Med, Changsha, Hunan, Peoples R China
[2] Cent South Univ, Xiangya Sch Basic Med, Dept Parasitol, Changsha, Hunan, Peoples R China
[3] Wenzhou Med Univ, Coll Lab Med & Life Sci, Key Lab Lab Med, Zhejiang Prov Key Lab Med Genet,Minist Educ, Wenzhou, Zhejiang, Peoples R China
[4] Cent South Univ, Xiangya Hosp 2, Natl Clin Res Ctr Metab Dis, Metab Syndrome Res Ctr,Minist Educ,Key Lab Diabet, Changsha, Hunan, Peoples R China
[5] Cent South Univ, Xiangya Hosp 2, Dept Metab & Endocrinol, Changsha, Hunan, Peoples R China
来源
PEERJ | 2021年 / 9卷
基金
美国国家科学基金会;
关键词
SARS-CoV-2; Spike protein; Antigen-capture; Immunodominant fragments; COVID-19; TRANSMISSIBLE GASTROENTERITIS CORONAVIRUS; IMMUNOLOGICAL DETECTION; MONOCLONAL-ANTIBODIES; SARS; CELL; EPITOPE; MUTATIONS; SEQUENCE; DESIGN; IDENTIFICATION;
D O I
10.7717/peerj.11232
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Background: To contain the pandemics caused by SARS-CoV-2, early detection approaches with high accuracy and accessibility are critical. Generating an antigen-capture based detection system would be an ideal strategy complementing the current methods based on nucleic acids and antibody detection. The spike protein is found on the outside of virus particles and appropriate for antigen detection. Methods: In this study, we utilized bioinformatics approaches to explore the immunodominant fragments on spike protein of SARS-CoV-2. Results: The S1 subunit of spike protein was identified with higher sequence specificity. Three immunodominant fragments, Spike(56-94), Spike(199-264), and Spike(577-612), located at the S1 subunit were finally selected via bioinformatics analysis. The glycosylation sites and high-frequency mutation sites on spike protein were circumvented in the antigen design. All the identified fragments present qualified antigenicity, hydrophilicity, and surface accessibility. A recombinant antigen with a length of 194 amino acids (aa) consisting of the selected immunodominant fragments as well as a universal Th epitope was finally constructed. Conclusion: The recombinant peptide encoded by the construct contains multiple immunodominant epitopes, which is expected to stimulate a strong immune response in mice and generate qualified antibodies for SARS-CoV-2 detection.
引用
收藏
页数:23
相关论文
共 50 条
  • [41] Mutation and Phylogenetic Analysis of Spike Glycoprotein of Indonesian Isolates of Severe-Acute-Respiratory-Syndrome-Coronavirus-2 (SARS-CoV-2)
    Gaffar, Shabarni
    Rahmani, Syifa Al Fauziah
    Hardianto, Ari
    MAJALAH KEDOKTERAN BANDUNG, 2021, 53 (01): : 38 - 47
  • [42] Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K
    Di Giacomo, Simone
    Mercatelli, Daniele
    Rakhimov, Amir
    Giorgi, Federico M.
    JOURNAL OF MEDICAL VIROLOGY, 2021, 93 (09) : 5638 - 5643
  • [43] Characterization of heparin and severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) spike glycoprotein binding interactions
    Kim, So Young
    Jin, Weihua
    Sood, Amika
    Montgomery, David W.
    Grant, Oliver C.
    Fuster, Mark M.
    Fu, Li
    Dordick, Jonathan S.
    Woods, Robert J.
    Zhang, Fuming
    Linhardt, Robert J.
    ANTIVIRAL RESEARCH, 2020, 181
  • [44] Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) RNA in the Human Eye
    Kamalipour, Alireza
    Ashraf, Mohammad Ali
    Moghimi, Sasan
    Moattari, Afagh
    Ashraf, Mohammad Javad
    Abbasi, Farhad
    Azodi, Farzan
    Oboudi, Shadi
    Pirbonyeh, Neda
    Mokhtaryan, Maryam
    Roshanshad, Amirhossein
    Do, Jiun L.
    Weinreb, Robert N.
    OCULAR IMMUNOLOGY AND INFLAMMATION, 2023, 31 (01) : 32 - 38
  • [45] Characteristics of Pleural Effusion in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Pneumonia
    Chong, Woon H.
    Huggins, John Terrill
    Chopra, Amit
    AMERICAN JOURNAL OF THE MEDICAL SCIENCES, 2021, 361 (02): : 281 - 284
  • [46] Hybridization Chain Reactions Targeting the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)
    Wu, Tzu-Heng
    Chang, Chia-Chen
    Yang, Ching-Hsu
    Lin, Wei-Yin
    Ee, Tan Joy
    Lin, Chii-Wann
    INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 2020, 21 (09)
  • [47] The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Epidemic in Zimbabwe: Quo Vadis?
    Katsidzira, Leolin
    Gwaunza, Lenon
    Hakim, James G.
    CLINICAL INFECTIOUS DISEASES, 2020, 71 (16) : 2180 - 2183
  • [48] Emerging Biosensors to Detect Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): A Review
    Lim, Wei Yin
    Lan, Boon Leong
    Ramakrishnan, Narayanan
    BIOSENSORS-BASEL, 2021, 11 (11):
  • [49] Is There an Association Between Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and Streptococcus pneumoniae?
    Howard, Leigh M.
    CLINICAL INFECTIOUS DISEASES, 2021, 72 (05) : E76 - E78
  • [50] Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in a Dog in Connecticut in February 2021
    Lee, Dong-Hun
    Helal, Zeinab H.
    Kim, Junwon
    Hunt, Amelia
    Barbieri, Alyza
    Tocco, Natalie
    Frasca, Salvatore, Jr.
    Kerr, Kirklyn
    Hyeon, Ji-Yeon
    Chung, David H.
    Risatti, Guillermo
    VIRUSES-BASEL, 2021, 13 (11):