Infection of human Nasal Epithelial Cells with SARS-CoV-2 and a 382-nt deletion isolate lacking ORF8 reveals similar viral kinetics and host transcriptional profiles

PLoS Pathog. 2020 Dec 7;16(12):e1009130. doi: 10.1371/journal.ppat.1009130. eCollection 2020 Dec.

Abstract

The novel coronavirus SARS-CoV-2 is the causative agent of Coronavirus Disease 2019 (COVID-19), a global healthcare and economic catastrophe. Understanding of the host immune response to SARS-CoV-2 is still in its infancy. A 382-nt deletion strain lacking ORF8 (Δ382 herein) was isolated in Singapore in March 2020. Infection with Δ382 was associated with less severe disease in patients, compared to infection with wild-type SARS-CoV-2. Here, we established Nasal Epithelial cells (NECs) differentiated from healthy nasal-tissue derived stem cells as a suitable model for the ex-vivo study of SARS-CoV-2 mediated pathogenesis. Infection of NECs with either SARS-CoV-2 or Δ382 resulted in virus particles released exclusively from the apical side, with similar replication kinetics. Screening of a panel of 49 cytokines for basolateral secretion from infected NECs identified CXCL10 as the only cytokine significantly induced upon infection, at comparable levels in both wild-type and Δ382 infected cells. Transcriptome analysis revealed the temporal up-regulation of distinct gene subsets during infection, with anti-viral signaling pathways only detected at late time-points (72 hours post-infection, hpi). This immune response to SARS-CoV-2 was significantly attenuated when compared to infection with an influenza strain, H3N2, which elicited an inflammatory response within 8 hpi, and a greater magnitude of anti-viral gene up-regulation at late time-points. Remarkably, Δ382 induced a host transcriptional response nearly identical to that of wild-type SARS-CoV-2 at every post-infection time-point examined. In accordance with previous results, Δ382 infected cells showed an absence of transcripts mapping to ORF8, and conserved expression of other SARS-CoV-2 genes. Our findings shed light on the airway epithelial response to SARS-CoV-2 infection, and demonstrate a non-essential role for ORF8 in modulating host gene expression and cytokine production from infected cells.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • COVID-19 / virology*
  • Chemokine CXCL10 / immunology
  • Epithelial Cells / immunology
  • Epithelial Cells / metabolism
  • Epithelial Cells / virology
  • Host-Pathogen Interactions / physiology
  • Humans
  • Kinetics
  • Nasal Mucosa / immunology
  • Nasal Mucosa / metabolism
  • Nasal Mucosa / virology*
  • SARS-CoV-2 / genetics*
  • SARS-CoV-2 / pathogenicity*
  • Transcriptome
  • Viral Proteins / genetics*
  • Viral Proteins / immunology
  • Virus Replication / physiology

Substances

  • CXCL10 protein, human
  • Chemokine CXCL10
  • ORF8 protein, SARS-CoV-2
  • Viral Proteins

Grants and funding

This research was funded by National Medical Research Council, Singapore No. MOH-COVID19RF2-0001 (to DYW, L-FW and DEA) and COVID19RF-003 (to L-FW and DEA); KST is a recipient of fellowship support from European Allergy and Clinical Immunology (EAACI) Research Fellowship 2019. AKA is a recipient of fellowship support from EAACI Research Fellowship 2017. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.