Rational Design of a Pan-Coronavirus Vaccine Based on Conserved CTL Epitopes

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Abstract

With the rapid global spread of the Coronavirus Disease 2019 (COVID-19) pandemic, a safe and effective vaccine against human coronaviruses (HCoVs) is believed to be a top priority in the field of public health. Due to the frequent outbreaks of different HCoVs, the development of a pan-HCoVs vaccine is of great value to biomedical science. The antigen design is a key prerequisite for vaccine efficacy, and we therefore developed a novel antigen with broad coverage based on the genetic algorithm of mosaic strategy. The designed antigen has a potentially broad coverage of conserved cytotoxic T lymphocyte (CTL) epitopes to the greatest extent, including the existing epitopes from all reported HCoV sequences (HCoV-NL63, HCoV-229E, HCoV-OC43, HCoV-HKU1, SARS-CoV, MERS-CoV, and SARS-CoV-2). This novel antigen is expected to induce strong CTL responses with broad coverage by targeting conserved epitopes against multiple coronaviruses.

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CD-HIT: accelerated for clustering the next-generation sequencing data

Limin Fu, Beifang Niu, Zhengwei Zhu … (2012)

Summary: CD-HIT is a widely used program for clustering biological sequences to reduce sequence redundancy and improve the performance of other sequence analyses. In response to the rapid increase in the amount of sequencing data produced by the next-generation sequencing technologies, we have developed a new CD-HIT program accelerated with a novel parallelization strategy and some other techniques to allow efficient clustering of such datasets. Our tests demonstrated very good speedup derived from the parallelization for up to ∼24 cores and a quasi-linear speedup for up to ∼8 cores. The enhanced CD-HIT is capable of handling very large datasets in much shorter time than previous versions. Availability: http://cd-hit.org. Contact: liwz@sdsc.edu Supplementary information: Supplementary data are available at Bioinformatics online.

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Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals

Alba Grifoni, Daniela Weiskopf, Sydney Ramirez … (2020)

Summary Understanding adaptive immunity to SARS-CoV-2 is important for vaccine development, interpreting coronavirus disease 2019 (COVID-19) pathogenesis, and calibration of pandemic control measures. Using HLA class I and II predicted peptide ‘megapools’, circulating SARS-CoV-2−specific CD8+ and CD4+ T cells were identified in ∼70% and 100% of COVID-19 convalescent patients, respectively. CD4+ T cell responses to spike, the main target of most vaccine efforts, were robust and correlated with the magnitude of the anti-SARS-CoV-2 IgG and IgA titers. The M, spike and N proteins each accounted for 11-27% of the total CD4+ response, with additional responses commonly targeting nsp3, nsp4, ORF3a and ORF8, among others. For CD8+ T cells, spike and M were recognized, with at least eight SARS-CoV-2 ORFs targeted. Importantly, we detected SARS-CoV-2−reactive CD4+ T cells in ∼40-60% of unexposed individuals, suggesting cross-reactive T cell recognition between circulating ‘common cold’ coronaviruses and SARS-CoV-2.

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Emerging coronaviruses: Genome structure, replication, and pathogenesis

Yu Chen, Qianyun Liu, Deyin Guo (2020)

Abstract The recent emergence of a novel coronavirus (2019‐nCoV), which is causing an outbreak of unusual viral pneumonia in patients in Wuhan, a central city in China, is another warning of the risk of CoVs posed to public health. In this minireview, we provide a brief introduction of the general features of CoVs and describe diseases caused by different CoVs in humans and animals. This review will help understand the biology and potential risk of CoVs that exist in richness in wildlife such as bats.

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Author and article information

Contributors

Deborah H. Fuller: Role: Academic Editor

Journal

Journal ID (nlm-ta): Viruses

Journal ID (iso-abbrev): Viruses

Journal ID (publisher-id): viruses

Title: Viruses

Publisher: MDPI

ISSN (Electronic): 1999-4915

Publication date (Electronic): 21 February 2021

Publication date Collection: February 2021

Volume: 13

Issue: 2

Electronic Location Identifier: 333

Affiliations

[1 ]School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China; limch7@ 123456mail2.sysu.edu.cn (M.L.); zengjf7@ 123456mail2.sysu.edu.cn (J.Z.); lirt9@ 123456mail2.sysu.edu.cn (R.L.); wenzy3@ 123456mail2.sysu.edu.cn (Z.W.); shuylong@ 123456mail.sysu.edu.cn (Y.S.)

[2 ]Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou 514400, China

[3 ]Gilead Sciences, Inc. 333 Lakeside Dr, Foster City, CA 94404, USA; Jenny.cai1@ 123456gilead.com (Y.C.); Jeffrey.Wallin@ 123456gilead.com (J.W.)

Author notes

[* ]Correspondence: duxj9@ 123456mail.sysu.edu.cn (X.D.); suncaijun@ 123456mail.sysu.edu.cn (C.S.)

[†]

These authors contribute equally to this work.

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Xiangjun Du https://orcid.org/0000-0001-8184-8430

Caijun Sun https://orcid.org/0000-0002-2000-7053

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Publisher ID: viruses-13-00333

DOI: 10.3390/v13020333

PMC ID: 7926959

PubMed ID: 33670023

SO-VID: 739c112e-3997-4f69-81b1-2c625f5ddc3a

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Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

Rational Design of a Pan-Coronavirus Vaccine Based on Conserved CTL Epitopes

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Abstract

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Novel Coronavirus Disease COVID-19

Most cited references 26

CD-HIT: accelerated for clustering the next-generation sequencing data

Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals

Emerging coronaviruses: Genome structure, replication, and pathogenesis

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