Literature DB >> 33413610

An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets.

Daniel Ward1, Matthew Higgins2, Jody E Phelan2, Martin L Hibberd2, Susana Campino2, Taane G Clark3,4.   

Abstract

During COVID-19, diagnostic serological tools and vaccines have been developed. To inform control activities in a post-vaccine surveillance setting, we have developed an online "immuno-analytics" resource that combines epitope, sequence, protein and SARS-CoV-2 mutation analysis. SARS-CoV-2 spike and nucleocapsid proteins are both vaccine and serological diagnostic targets. Using the tool, the nucleocapsid protein appears to be a sub-optimal target for use in serological platforms. Spike D614G (and nsp12 L314P) mutations were most frequent (> 86%), whilst spike A222V/L18F have recently increased. Also, Orf3a proteins may be a suitable target for serology. The tool can accessed from: http://genomics.lshtm.ac.uk/immuno (online); https://github.com/dan-ward-bio/COVID-immunoanalytics (source code).

Entities:  

Keywords:  COVID; Cross-reactivity; Epitopes; Human-coronavirus; Immuno-informatics; Mutation; SARS-CoV-2; Surveillance

Mesh：

Substances：

Year:  2021        PMID： 33413610      PMCID： PMC7790334          DOI： 10.1186/s13073-020-00822-6

Source DB:  PubMed          Journal:  Genome Med        ISSN： 1756-994X            Impact factor:   11.117


  37 in total

1.  Prediction of continuous B-cell epitopes in an antigen using recurrent neural network.

Authors:  Sudipto Saha; G P S Raghava
Journal:  Proteins       Date:  2006-10-01

2.  Amino terminus of the SARS coronavirus protein 3a elicits strong, potentially protective humoral responses in infected patients.

Authors:  Xiaofen Zhong; Zufeng Guo; Huanghao Yang; Lisheng Peng; Yong Xie; Tin-Yau Wong; Sik-To Lai; Zhihong Guo
Journal:  J Gen Virol       Date:  2006-02       Impact factor: 3.891

3.  The COVID-19 vaccine development landscape.

Authors:  Tung Thanh Le; Zacharias Andreadakis; Arun Kumar; Raúl Gómez Román; Stig Tollefsen; Melanie Saville; Stephen Mayhew
Journal:  Nat Rev Drug Discov       Date:  2020-05       Impact factor: 84.694

4.  MAFFT multiple sequence alignment software version 7: improvements in performance and usability.

Authors:  Kazutaka Katoh; Daron M Standley
Journal:  Mol Biol Evol       Date:  2013-01-16       Impact factor: 16.240

5.  BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes.

Authors:  Martin Closter Jespersen; Bjoern Peters; Morten Nielsen; Paolo Marcatili
Journal:  Nucleic Acids Res       Date:  2017-07-03       Impact factor: 16.971

6.  Estimates of the severity of coronavirus disease 2019: a model-based analysis.

Authors:  Robert Verity; Lucy C Okell; Ilaria Dorigatti; Peter Winskill; Charles Whittaker; Natsuko Imai; Gina Cuomo-Dannenburg; Hayley Thompson; Patrick G T Walker; Han Fu; Amy Dighe; Jamie T Griffin; Marc Baguelin; Sangeeta Bhatia; Adhiratha Boonyasiri; Anne Cori; Zulma Cucunubá; Rich FitzJohn; Katy Gaythorpe; Will Green; Arran Hamlet; Wes Hinsley; Daniel Laydon; Gemma Nedjati-Gilani; Steven Riley; Sabine van Elsland; Erik Volz; Haowei Wang; Yuanrong Wang; Xiaoyue Xi; Christl A Donnelly; Azra C Ghani; Neil M Ferguson
Journal:  Lancet Infect Dis       Date:  2020-03-30       Impact factor: 25.071

7.  Analytical sensitivity and efficiency comparisons of SARS-CoV-2 RT-qPCR primer-probe sets.

Authors:  Chantal B F Vogels; Anderson F Brito; Anne L Wyllie; Joseph R Fauver; Isabel M Ott; Chaney C Kalinich; Mary E Petrone; Arnau Casanovas-Massana; M Catherine Muenker; Adam J Moore; Jonathan Klein; Peiwen Lu; Alice Lu-Culligan; Xiaodong Jiang; Daniel J Kim; Eriko Kudo; Tianyang Mao; Miyu Moriyama; Ji Eun Oh; Annsea Park; Julio Silva; Eric Song; Takehiro Takahashi; Manabu Taura; Maria Tokuyama; Arvind Venkataraman; Orr-El Weizman; Patrick Wong; Yexin Yang; Nagarjuna R Cheemarla; Elizabeth B White; Sarah Lapidus; Rebecca Earnest; Bertie Geng; Pavithra Vijayakumar; Camila Odio; John Fournier; Santos Bermejo; Shelli Farhadian; Charles S Dela Cruz; Akiko Iwasaki; Albert I Ko; Marie L Landry; Ellen F Foxman; Nathan D Grubaugh
Journal:  Nat Microbiol       Date:  2020-07-10       Impact factor: 30.964

8.  A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2.

Authors:  Alba Grifoni; John Sidney; Yun Zhang; Richard H Scheuermann; Bjoern Peters; Alessandro Sette
Journal:  Cell Host Microbe       Date:  2020-03-16       Impact factor: 21.023

9.  An interactive web-based dashboard to track COVID-19 in real time.

Authors:  Ensheng Dong; Hongru Du; Lauren Gardner
Journal:  Lancet Infect Dis       Date:  2020-02-19       Impact factor: 25.071

10.  Antibody-dependent SARS coronavirus infection is mediated by antibodies against spike proteins.

Authors:  Sheng-Fan Wang; Sung-Pin Tseng; Chia-Hung Yen; Jyh-Yuan Yang; Ching-Han Tsao; Chun-Wei Shen; Kuan-Hsuan Chen; Fu-Tong Liu; Wu-Tse Liu; Yi-Ming Arthur Chen; Jason C Huang
Journal:  Biochem Biophys Res Commun       Date:  2014-07-26       Impact factor: 3.575
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  5 in total

1.  A systematic review on AI/ML approaches against COVID-19 outbreak.

Authors:  Onur Dogan; Sanju Tiwari; M A Jabbar; Shankru Guggari
Journal:  Complex Intell Systems       Date:  2021-07-05

2.  Machine learning research towards combating COVID-19: Virus detection, spread prevention, and medical assistance.

Authors:  Osama Shahid; Mohammad Nasajpour; Seyedamin Pouriyeh; Reza M Parizi; Meng Han; Maria Valero; Fangyu Li; Mohammed Aledhari; Quan Z Sheng
Journal:  J Biomed Inform       Date:  2021-03-24       Impact factor: 8.000

3.  COVID-profiler: a webserver for the analysis of SARS-CoV-2 sequencing data.

Authors:  Jody Phelan; Wouter Deelder; Daniel Ward; Susana Campino; Martin L Hibberd; Taane G Clark
Journal:  BMC Bioinformatics       Date:  2022-04-15       Impact factor: 3.169

4.  Computational screening for investigating the synergistic regulatory potential of drugs and phytochemicals in combination with 2-deoxy-D-glucose against SARS-CoV-2.

Authors:  Anshika Gupta; Shweta Singh Chauhan; Anamika Singh Gaur; Ramakrishnan Parthasarathi
Journal:  Struct Chem       Date:  2022-09-03       Impact factor: 1.795

5.  Cryo-EM structure of SARS-CoV-2 ORF3a in lipid nanodiscs.

Authors:  Ben Sorum; Sonali S Mali; Christopher M Hoel; David M Kern; Savitha Sridharan; Jonathan P Remis; Daniel B Toso; Abhay Kotecha; Diana M Bautista; Stephen G Brohawn
Journal:  Nat Struct Mol Biol       Date:  2021-06-22       Impact factor: 15.369
  5 in total

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