Expected immune recognition of COVID-19 virus by memory from earlier infections with common coronaviruses in a large part of the world population.

Johannes M Dijkstra,Keiichiro Hashimoto

doi:10.12688/f1000research.23458.1

Abstract

SARS-CoV-2 is the coronavirus agent of the COVID-19 pandemic causing high mortalities. In contrast, the widely spread human coronaviruses OC43, HKU1, 229E, and NL63 tend to cause only mild symptoms. The present study shows, by in silico analysis, that these common human viruses are expected to induce immune memory against SARS-CoV-2 by sharing protein fragments (antigen epitopes) for presentation to the immune system by MHC class I. A list of such epitopes is provided. The number of these epitopes and the prevalence of the common coronaviruses suggest that a large part of the world population has some degree of specific immunity against SARS-CoV-2 already, even without having been infected by that virus. For inducing protection, booster vaccinations enhancing existing immunity are less demanding than primary vaccinations against new antigens. Therefore, for the discussion on vaccination strategies against COVID-19, the available immune memory against related viruses should be part of the consideration.

Highlights

SARS-CoV-2 and other human coronaviruses From the end of 2019, the world experienced the coronavirus disease 2019 (COVID-19) pandemic caused by the emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; aka 2019 novel coronavirus or 2019-nCoV)
In the U.S.A., a 3-year RT-PCR surveillance of respiratory samples of patients revealed that the four viruses 229E, NL63, OC43, and HKU1 were present at levels varying by season and region, with all individual viruses peaking at >3% prevalence in each investigated region (Midwest, Northeast, South, West); co-infection with other coronaviruses was found in only ~2% of infected cases, but co-infection with another respiratory virus was found in a substantial ~30% of infected cases (Killerby et al, 2018)
Many identical >9 aa stretches were found with ORF1ab encoded polyprotein, one such identical stretch was found with the N protein of the other two type II coronaviruses HCoV-OC43 and HCoV-HKU1, and no such stretches were found when comparing with any of the other gene products; ORF1ab-derived mature proteins with such stretches, expected from cleavage of the polyprotein precursor (Wu et al, 2020), were the transmembrane protein nonstructural protein 4 (NSP4), 3C-like cysteine protease NSP5, RNA binding protein NSP9, RNA dependent RNA polymerase NSP12, helicase NSP13, 3’-to-5’ exonuclease NSP14, nidoviral endoribonuclease specific for U NSP15, and S-adenosylmethionine-dependent ribose 2’-O-methyltransferase NSP16 (Table 1)

Summary

23 Apr 2020 report report

1. Anna Gil, University of Massachusetts Medical School, Worcester, USA Liisa K. Selin , University of Massachusetts Medical School, Worcester, USA. University of Rochester Medical Center, Rochester, USA David H. Smith Center for Vaccine Biology and Immunology, Rochester, USA. Any reports and responses or comments on the article can be found at the end of the article. This article is included in the Coronavirus collection

Introduction

Methods

Results and discussion