Exposing and exploiting host-parasite arms race clues in SARS-CoV-2: a principally new method for improved T cell immunogenicity prediction

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00023001%3A_____%2F23%3A00084081" target="_blank" >RIV/00023001:_____/23:00084081 - isvavai.cz</a>

Alternative codes found

RIV/00216208:11310/23:10472832 RIV/00216208:11110/23:10472832 RIV/00027073:_____/23:N0000034

Result on the web

<a href="https://academic.oup.com/biomethods/article/8/1/bpad011/7230015?login=true" target="_blank" >https://academic.oup.com/biomethods/article/8/1/bpad011/7230015?login=true</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1093/biomethods/bpad011" target="_blank" >10.1093/biomethods/bpad011</a>

Result language

angličtina

Original language name

Exposing and exploiting host-parasite arms race clues in SARS-CoV-2: a principally new method for improved T cell immunogenicity prediction

Original language description

Computational prediction of T cell epitopes is a crucial component in the development of novel vaccines. T cells in a healthy vertebrate host can recognize as non-self only those peptides that are present in the parasite&apos;s proteins but absent in the host&apos;s proteins. This principle enables us to determine the current and past host specificity of a parasite and to predict peptides capable of eliciting a T cell response. Building upon the detailed mapping of T cell clone specificity for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) antigens, we employed Monte Carlo tests to determine that empirically confirmed T cell-stimulating peptides have a significantly increased proportion of pentapeptides, hexapeptides and heptapeptides not found in the human proteome (P &lt; 0.0001, Cohen&apos;s d &gt; 4.9). We observed a lower density of potential pentapeptide targets for T cell recognition in the spike protein from the human-adapted SARS-CoV-2 ancestor compared to 10 other SARS-CoV-2 proteins originating from the horseshoe bat-adapted ancestor. Our novel method for predicting T cell immunogenicity of SARS-CoV-2 peptides is four times more effective than previous approaches. We recommend utilizing our theory-based method where efficient empirically based algorithms are unavailable, such as in the development of certain veterinary vaccines, and combining it with empirical methods in other cases for optimal results.

Czech name

—

Czech description

—

Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10608 - Biochemistry and molecular biology

Project

<a href="/en/project/GA22-20785S" target="_blank" >GA22-20785S: Effects of toxoplasma and CMV infection on cognitive performance – longitudinal, cross-sectional, and case-control studies</a><br>

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2023

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Biology methods &amp; protocols

ISSN

2396-8923

e-ISSN

2396-8923

Volume of the periodical

8

Issue of the periodical within the volume

1

Country of publishing house

GB - UNITED KINGDOM

Number of pages

9

Pages from-to

"art. no. bpad011"

UT code for WoS article

001032675500001

EID of the result in the Scopus database

2-s2.0-85168001957