Does Cross – #Neutralization of #SARS-CoV-2 Only Relate to High Pathogenic #Coronaviruses? (Trends Immunol., summary)

[Source: Trends in Immunology, full page: (LINK). Summary, edited.]

Journal Pre-proof
Does Cross-Neutralization of SARS-CoV-2 Only Relate to High Pathogenic Coronaviruses?

Zhongren Ma, Pengfei Li, Aqsa Ikram, Qiuwei Pan

PII: S1471-4906(20)30179-4

DOI: https://doi.org/10.1016/j.it.2020.08.002

Reference: TREIMM 1717

To appear in: Trends in Immunology

Please cite this article as: Z. Ma, P. Li, A. Ikram, et al., Does Cross-Neutralization of SARS-CoV-2 Only Relate to High Pathogenic Coronaviruses?, Trends in Immunology (2020), https://doi.org/10.1016/j.it.2020.08.002

This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not  yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal  disclaimers that apply to the journal pertain.

© 2020 Published by Elsevier.

Letter

*Correspondence: Q.P. (q.pan@erasmusmc.nl)

Declaration of interests: All authors declare no competing interests.

Acknowledgements: The work was supported by the Ministry of Education of China for an Innovative Research Team in University grant (No. IRT_17R88; to Z.M.). Journal Pre- proof

___

Production of antibodies in response to viral infections constitutes an essential feature of  adaptive immunity. Great efforts have been dedicated to characterize antibody responses in patients with coronavirus disease 2019 (COVID-19), caused by severe acute  respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. A recent article by Jiang et  al, published in Trends in Immunology discussed the state of research and development  of neutralizing antibodies for the prevention and treatment of COVID-19, with a specific  emphasis on cross-reactivity with other two highly pathogenic human coronaviruses,  SARS-CoV and MERS-CoV [1]. However, the authors of this article largely disregarded the  potential cross-reactive immunity triggered by the prevalence of low pathogenic human  coronaviruses (LPH-CoV).

(…)

Keywords: SARS-CoV-2; COVID-19; Coronavirus; Immunology.

——

Common #human #coronaviruses seem at least as severe as #influenza in patients hospitalized with acute respiratory infection: results from 8-year hospital-based #surveillance in #Quebec, #Canada (J Infect Dis., abstract)

[Source: Journal of Infectious Diseases, full page: (LINK). Abstract, edited.]

Common human coronaviruses seem at least as severe as influenza in patients hospitalized with acute respiratory infection: results from 8-year hospital-based surveillance in Quebec, Canada

Rodica Gilca, Sara Carazo, Rachid Amini, Hugues Charest, Gaston De Serres

The Journal of Infectious Diseases, jiaa477, https://doi.org/10.1093/infdis/jiaa477

Published: 06 August 2020

 

Abstract

Background

Few data exist about the role of common human coronaviruses (HCoV) in patients hospitalized for acute respiratory illness (ARI) and the severity of these infections compared to influenza.

Methods

Prospective data on virus etiology of ARI hospitalizations during the peaks of 8 influenza seasons (2011-12 to 2018-19) in Quebec, Canada, was used to compare patients with HCoV to those with influenza infections; generalized estimation equations models were used for multivariate analyses.

Results

We identified 340 HCoV infections which affected 11.6%(n=136) of children and 5.2%(n=204) of adults hospitalized with ARI. The majority of children (75%) with HCoV infections were also coinfected with other respiratory viruses compared to 24% of the adults (p<0.0001). No deaths were recorded in children; 5.8% of adults with HCoV monoinfection compared to 4.2% of those with influenza monoinfection died (p=0.226). The risk of pneumonia was non-significantly lower in children with HCoV than with influenza but similarly high in adults. Markers of severity (length-of-stay, intensive-care admissions and case-fatality ratio) were comparable between these infections in multivariate analyses, both in children and adults.

Conclusions

In children and adults hospitalized with ARI, HCoV infections were less frequent than influenza infections, but HCoV monoinfections were as severe as influenza monoinfections.

common coronaviruses, influenza, respiratory  hospitalization, children, adults, severity, case-fatality ratio, coinfections

Topic:  influenza – coronavirus – adult – canada – child – inpatients – respiratory tract  infections – infections – surveillance, medical – case fatality rate – quebec

Issue Section:  Major Article

This content is only available as a PDF.

© The Author(s) 2020. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model)

Keywords: Coronavirus; Canada; Epidemiology.

——

Cross – #reactivity towards #SARS-CoV-2: the potential role of low-pathogenic #human #coronaviruses (Lancet Microbe, summary)

[Source: Lancet Microbe, full page: (LINK). Summary, edited.]

Cross-reactivity towards SARS-CoV-2: the potential role of low-pathogenic human coronaviruses

Zhongren Ma, Pengfei Li, Yuepeng Ji, Aqsa Ikram, Qiuwei Pan

Open Access | Published: August, 2020 | DOI: https://doi.org/10.1016/S2666-5247(20)30098-7

___

The human body is capable of producing antibodies in response to severe acute  respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, the causative agent of  COVID-19. The principle of antigen-antibody reaction has been widely explored to  develop enzyme immunoassays for studying seroprevalence. Kelvin Kai-Wang To and  colleagues1  found a seropositive rate of 2·73% (53 of 1938 serum samples) in SARS-CoV-2  enzyme immunoassays for individuals who had probably not been exposed to the  virus. This finding raises the possibility of antibody cross-reactivity with other human  coronaviruses.

(…)

Keywords: SARS-CoV-2; COVID-19; Seroprevalence; Coronavirus.

——

#Selective and cross-reactive #SARS-CoV-2 T cell #epitopes in unexposed #humans (Science, abstract)

[Source: Science, full page: (LINK). Abstract, edited.]

Selective and cross-reactive SARS-CoV-2 T cell epitopes in unexposed humans

Jose Mateus1, Alba Grifoni1, Alison Tarke1, John Sidney1, Sydney I. Ramirez1,3, Jennifer M. Dan1,3, Zoe C. Burger3, Stephen A. Rawlings3, Davey M. Smith3, Elizabeth Phillips2, Simon Mallal2, Marshall Lammers1, Paul Rubiro1, Lorenzo Quiambao1, Aaron Sutherland1, Esther Dawen Yu1, Ricardo da Silva Antunes1, Jason Greenbaum1, April Frazier1, Alena J. Markmann4, Lakshmanane Premkumar5, Aravinda de Silva5, Bjoern Peters1,3, Shane Crotty1,3, Alessandro Sette1,3,*,†, Daniela Weiskopf1,*,†

1 Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA. 2 Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA 6150, Australia. 3 Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA 92037, USA. 4 Department of Medicine, Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA. 5 Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.

*Corresponding author. Email: alex@lji.org (A.S.); daniela@lji.org (D.W.)
† These authors contributed equally to this work.

Science  04 Aug 2020: eabd3871 | DOI: 10.1126/science.abd3871

 

Abstract

Many unknowns exist about human immune responses to the SARS-CoV-2 virus. SARS-CoV-2 reactive CD4+ T cells have been reported in unexposed individuals, suggesting pre-existing cross-reactive T cell memory in 20-50% of people. However, the source of those T cells has been speculative. Using human blood samples derived before the SARS-CoV-2 virus was discovered in 2019, we mapped 142 T cell epitopes across the SARS-CoV-2 genome to facilitate precise interrogation of the SARS-CoV-2-specific CD4+ T cell repertoire. We demonstrate a range of pre-existing memory CD4+ T cells that are cross-reactive with comparable affinity to SARS-CoV-2 and the common cold coronaviruses HCoV-OC43, HCoV-229E, HCoV-NL63, or HCoV-HKU1. Thus, variegated T cell memory to coronaviruses that cause the common cold may underlie at least some of the extensive heterogeneity observed in COVID-19 disease.

Keywords: SARS-CoV-2; COVID-19; Coronavirus; Immunology.

——

#Evolutionary #origins of the #SARS-CoV-2 #sarbecovirus #lineage responsible for the #COVID19 pandemic (Nat Microbiol., abstract)

[Source: Nature Microbiology, full page: (LINK). Abstract, edited.]

Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic

Maciej F. Boni, Philippe Lemey, Xiaowei Jiang, Tommy Tsan-Yuk Lam, Blair W. Perry, Todd A. Castoe, Andrew Rambaut & David L. Robertson

Nature Microbiology (2020)

 

Abstract

There are outstanding evolutionary questions on the recent emergence of human coronavirus SARS-CoV-2 including the role of reservoir species, the role of recombination and its time of divergence from animal viruses. We find that the sarbecoviruses—the viral subgenus containing SARS-CoV and SARS-CoV-2—undergo frequent recombination and exhibit spatially structured genetic diversity on a regional scale in China. SARS-CoV-2 itself is not a recombinant of any sarbecoviruses detected to date, and its receptor-binding motif, important for specificity to human ACE2 receptors, appears to be an ancestral trait shared with bat viruses and not one acquired recently via recombination. To employ phylogenetic dating methods, recombinant regions of a 68-genome sarbecovirus alignment were removed with three independent methods. Bayesian evolutionary rate and divergence date estimates were shown to be consistent for these three approaches and for two different prior specifications of evolutionary rates based on HCoV-OC43 and MERS-CoV. Divergence dates between SARS-CoV-2 and the bat sarbecovirus reservoir were estimated as 1948 (95% highest posterior density (HPD): 1879–1999), 1969 (95% HPD: 1930–2000) and 1982 (95% HPD: 1948–2009), indicating that the lineage giving rise to SARS-CoV-2 has been circulating unnoticed in bats for decades.

Keywords: SARS-CoV-2; COVID-19; Sarbecovirus; Coronavirus; Bats; Evolution.

——-

##Longitudinal #epidemiology of #human #coronavirus #OC43 in #Yamagata, #Japan, 2010–2017: two groups based on #spike gene appear one after another (J Med Virol., abstract)

[Source: Journal of Medical Virology, full page: (LINK). Abstract, edited.]

Longitudinal epidemiology of human coronavirus OC43 in Yamagata, Japan, 2010–2017: two groups based on spike gene appear one after another

Kenichi Komabayashi,  Yohei Matoba,  Shizuka Tanaka,  Junji Seto,  Yoko Aoki, Tatsuya Ikeda,  Yoshitaka Shimotai,  Yoko Matsuzaki,  Tsutomu Itagaki,  Katsumi Mizuta

First published: 28 July 2020 | DOI:  https://doi.org/10.1002/jmv.26361

This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1002/jmv.26361

 

Abstract

Human coronavirus OC43 (HCoV‐OC43) is divided into genotypes A–H based on genetic recombination including the spike (S ) gene. To investigate the longitudinal transition of phylogenetic feature of HCoV‐OC43 S gene in a community, phylogenetic analysis of the S1 region of S gene was conducted using 208 strains detected in Yamagata during 2010–2017 with reference strains of genotype. The S1 sequences were divisible into four groups: A–D. All Yamagata strains belonged to either group B or group D. In group B, 46 (90.2%) out of 51 Yamagata strains were clustered with those of genotype E reference strains (cluster E). In group D, 28 (17.8%) and 122 (77.7%) out of 157 Yamagata strains were clustered respectively with genotype F and genotype G reference strains. In cluster G, 28 strains formed a distinct cluster. Monthly distributions of HCoV‐OC43 in Yamagata in 2010–2017 revealed that group B and group D appeared one after another. In group B, the cluster E strains were prevalent recurrently. In conclusion, epidemics of HCoV‐OC43 in Yamagata, Japan might be attributable to two genetically different groups: group B showed recurrent epidemic of strains belonging to single phylogenetic cluster and group D showed epidemic strains belonging to multiple clusters.

This article is protected by copyright. All rights reserved.

Keywords: Coronavirus; HCoV-OC43; Japan.

——

LY6E impairs #coronavirus #fusion and confers #immune #control of viral disease (Nat Microbiol., abstract)

[Source: Nature Microbiology, full page: (LINK). Abstract, edited.]

LY6E impairs coronavirus fusion and confers immune control of viral disease

Stephanie Pfaender, Katrina B. Mar, […] Volker Thiel

Nature Microbiology (2020)

 

Abstract

Zoonotic coronaviruses (CoVs) are substantial threats to global health, as exemplified by the emergence of two severe acute respiratory syndrome CoVs (SARS-CoV and SARS-CoV-2) and Middle East respiratory syndrome CoV (MERS-CoV) within two decades1,2,3. Host immune responses to CoVs are complex and regulated in part through antiviral interferons. However, interferon-stimulated gene products that inhibit CoVs are not well characterized4. Here, we show that lymphocyte antigen 6 complex, locus E (LY6E) potently restricts infection by multiple CoVs, including SARS-CoV, SARS-CoV-2 and MERS-CoV. Mechanistic studies revealed that LY6E inhibits CoV entry into cells by interfering with spike protein-mediated membrane fusion. Importantly, mice lacking Ly6e in immune cells were highly susceptible to a murine CoV—mouse hepatitis virus. Exacerbated viral pathogenesis in Ly6e knockout mice was accompanied by loss of hepatic immune cells, higher splenic viral burden and reduction in global antiviral gene pathways. Accordingly, we found that constitutive Ly6e directly protects primary B cells from murine CoV infection. Our results show that LY6E is a critical antiviral immune effector that controls CoV infection and pathogenesis. These findings advance our understanding of immune-mediated control of CoV in vitro and in vivo—knowledge that could help inform strategies to combat infection by emerging CoVs.

Keywords: SARS-CoV-2; COVID-19; MERS-CoV; SARS-CoV; Coronavirus; Viral pathogenesis; Immunology.

——

Evolutionary arms race between #virus and #host drives #genetic #diversity in #bat #SARS related #coronavirus #spike genes (J Virol., abstract)

[Source: Journal of Virology, full page: (LINK). Abstract, edited.]

Evolutionary arms race between virus and host drives genetic diversity in bat SARS related coronavirus spike genes

Hua Guo, Bing-Jie Hu, Xing-Lou Yang, Lei-Ping Zeng, Bei Li, Songying Ouyang, Zheng-Li Shi

DOI: 10.1128/JVI.00902-20

 

ABSTRACT

The Chinese horseshoe bat (Rhinolophus sinicus), reservoir host of severe acute respiratory syndrome coronavirus (SARS-CoV), carries many bat SARS-related CoVs (SARSr-CoVs) with high genetic diversity, particularly in the spike gene. Despite these variations, some bat SARSr-CoVs can utilize the orthologs of human SARS-CoV receptor, angiotensin-converting enzyme 2 (ACE2), for entry. It is speculated that the interaction between bat ACE2 and SARSr-CoV spike proteins drives diversity. Here, we have identified a series of R. sinicus ACE2 variants with some polymorphic sites involved in the interaction with the SARS-CoV spike protein. Pseudoviruses or SARSr-CoVs carrying different spike proteins showed different infection efficiency in cells transiently expressing bat ACE2 variants. Consistent results were observed by binding affinity assays between SARS- and SARSr-CoV spike proteins and receptor molecules from bats and humans. All tested bat SARSr-CoV spike proteins had a higher binding affinity to human ACE2 than to bat ACE2, although they showed a 10-fold lower binding affinity to human ACE2 compared with their SARS-CoV counterpart. Structure modeling revealed that the difference in binding affinity between spike and ACE2 might be caused by the alteration of some key residues in the interface of these two molecules. Molecular evolution analysis indicates that some key residues were under positive selection. These results suggest that the SARSr-CoV spike protein and R. sinicus ACE2 may have coevolved over time and experienced selection pressure from each other, triggering the evolutionary arms race dynamics.

 

Importance

Evolutionary arms race dynamics shape the diversity of viruses and their receptors. Identification of key residues which are involved in interspecies transmission is important to predict potential pathogen spillover from wildlife to humans. Previously, we have identified genetically diverse SARSr-CoV in Chinese horseshoe bats. Here, we show the highly polymorphic ACE2 in Chinese horseshoe bat populations. These ACE2 variants support SARS- and SARSr-CoV infection but with different binding affinity to different spike proteins. The higher binding affinity of SARSr-CoV spike to human ACE2 suggests that these viruses have the capacity of spillover to humans. The positive selection of residues at the interface between ACE2 and SARSr-CoV spike protein suggests a long-term and ongoing coevolutionary dynamics between them. Continued surveillance of this group of viruses in bats is necessary for the prevention of the next SARS-like disease.

Copyright © 2020 American Society for Microbiology. All Rights Reserved.

This article is made available via the PMC Open Access Subset for unrestricted noncommercial re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.

Keywords: SARS-CoV-2; COVID-19; Coronavirus; Bats; Evolution.

——

#Modelling the #inactivation of #viruses from the #Coronaviridae family in response to #temperature and relative #humidity in #suspensions or #surfaces (Appl Environ Microbiol., abstract)

[Source: Applied and Environmental Microbiology, full page: (LINK). Abstract, edited.]

Modelling the inactivation of viruses from the Coronaviridae family in response to temperature and relative humidity in suspensions or surfaces.

Laurent Guillier, Sandra Martin-Latil, Estelle Chaix, Anne Thébault, Nicole Pavio, Sophie Le Poder; on behalf of Covid-19 Emergency Collective Expert Appraisal Group, Christophe Batéjat, Fabrice Biot, Lionel Koch, Don Schaffner, Moez Sanaa

DOI: 10.1128/AEM.01244-20

 

ABSTRACT

Temperature and relative humidity are major factors determining virus inactivation in the environment. This article reviews inactivation data of coronaviruses on surfaces and in liquids from published studies and develops secondary models to predict coronaviruses inactivation as a function of temperature and relative humidity. A total of 102 D-values (time to obtain a log10 reduction of virus infectivity), including values for SARS-CoV-2, were collected from 26 published studies. The values obtained from the different coronaviruses and studies were found to be generally consistent. Five different models were fitted to the global dataset of D-values. The most appropriate model considered temperature and relative humidity. A spreadsheet predicting the inactivation of coronaviruses and the associated uncertainty is presented and can be used to predict virus inactivation for untested temperatures, time points or any coronavirus strains belonging to Alphacoronavirus and Betacoronavirus genera.

 

Importance:

The prediction of the persistence of SARS-CoV-2 on fomites is essential to investigate the importance of contact transmission. This study collects available information on inactivation kinetics of coronaviruses in both solid and liquid fomites and creates a mathematical model for the impact of temperature and relative humidity on virus persistence. The predictions of the model can support more robust decision-making and could be useful in various public health contexts. Having a calculator for the natural clearance of SARS-CoV-2 depending on temperature and relative humidity could be a valuable operational tool for public authorities.

Copyright © 2020 American Society for Microbiology. All Rights Reserved.

Keywords: SARS-CoV-2; COVID-19; Coronavirus; Betacoronavirus.

——

#Global #seasonality of #human seasonal #coronaviruses: a clue for post-pandemic circulating season of #SARS-CoV-2 virus? (J Infect Dis., abstract)

[Source: Journal of Infectious Diseases, full page: (LINK). Abstract, edited.]

Global seasonality of human seasonal coronaviruses: a clue for post-pandemic circulating season of SARS-CoV-2 virus?

You Li, Xin Wang, Harish Nair

The Journal of Infectious Diseases, jiaa436, https://doi.org/10.1093/infdis/jiaa436

Published: 21 July 2020

 

Abstract

Background

The ongoing pandemic of Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 virus could recur as seasonal outbreaks, a circulating pattern observed among other pre-existing human seasonal coronaviruses (sCoV). However, little is known about seasonality of sCoV on a global scale.

Methods

We conducted a systematic review of data on seasonality of sCoV. We compared seasonality of sCoV with influenza virus and respiratory syncytial virus. We modelled monthly activity of sCoV using site-specific weather data.

Results

We included sCoV seasonality data in 40 sites from 21 countries. SCoV was prevalent in winter months in most temperate sites except for China while sCoV tended to be less seasonal in China and in tropical sites. In temperate sites excluding China, 53.1% of annual sCoV cases (Interquartile range, IQR: 34.6–61.9) occurred during influenza season and 49.6% (IQR: 30.2–60.2) of sCoV occurred during respiratory syncytial virus season. Low temperature combined with high relative humidity was associated with higher sCoV activity.

Conclusions

This is the first study that provides an overview of the global seasonality of sCoV. Our findings offer clues to the possible post-pandemic circulating season of SARS-CoV-2 and add to the knowledge pool necessary for post-pandemic preparedness for SARS-CoV-2.

COVID-19, SARS-CoV-2, seasonality, human coronavirus, temperature, relative humidity

Issue Section: Major Article

This content is only available as a PDF.

© The Author(s) 2020. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model)

Keywords: SARS-CoV-2; COVID-19; Coronavirus; RSV; Seasonal Influenza.

——