SARS-CoV-2 variant spike and accessory gene mutations alter pathogenesis
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
The ongoing COVID-19 pandemic is a major public health crisis. Despite the development and deployment of vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pandemic persists. The continued spread of the virus is largely driven by the emergence of viral variants, which can evade the current vaccines through mutations in the spike protein. Although these differences in spike are important in terms of transmission and vaccine responses, these variants possess mutations in the other parts of their genome that may also affect pathogenesis. Of particular interest to us are the mutations present in the accessory genes, which have been shown to contribute to pathogenesis in the host through interference with innate immune signaling, among other effects on host machinery. To examine the effects of accessory protein mutations and other nonspike mutations on SARS-CoV-2 pathogenesis, we synthesized both viruses possessing deletions in the accessory genes as well as viruses where the WA-1 spike is replaced by each variant spike gene in a SARS-CoV-2/WA-1 infectious clone. We then characterized the in vitro and in vivo replication of these viruses and compared them to both WA-1 and the full variant viruses. Our work has revealed that the accessory proteins contribute to SARS-CoV-2 pathogenesis and the nonspike mutations in variants can contribute to replication of SARS-CoV-2 and pathogenesis in the host. This work suggests that while spike mutations may enhance receptor binding and entry into cells, mutations in accessory proteins may alter clinical disease presentation.
Article activity feed
-
-
SciScore for 10.1101/2022.05.31.494211: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IACUC: Infection of BALB/c and hACE2/k18 Mice: All animals were cared for according to the standards set forth by the Institutional Animal Care and Use Committee at the University of Maryland-Baltimore. Sex as a biological variable not detected. Randomization not detected. Blinding H/E Staining of Lungs and Pathological Scoring: Lungs were scored in a blinded fashion with a 0-5 score given, 0 being no inflammation and 5 being the highest degree of inflammation. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Virus Reconstitution: 24 hours prior to transfection, 5e4 VeroE6 cells (ATCC,Manassas, VA) were plated per … SciScore for 10.1101/2022.05.31.494211: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IACUC: Infection of BALB/c and hACE2/k18 Mice: All animals were cared for according to the standards set forth by the Institutional Animal Care and Use Committee at the University of Maryland-Baltimore. Sex as a biological variable not detected. Randomization not detected. Blinding H/E Staining of Lungs and Pathological Scoring: Lungs were scored in a blinded fashion with a 0-5 score given, 0 being no inflammation and 5 being the highest degree of inflammation. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Virus Reconstitution: 24 hours prior to transfection, 5e4 VeroE6 cells (ATCC,Manassas, VA) were plated per well in 1mL of VeroE6 media (DMEM (Quality Biological, Gaithersburg, MD), 10% FBS (Gibco, Waltham, MA), 1% Penicillin-Streptomycin (Gemini Bio Products, Sacramento, CA), 1% L-Glutamine (Gibco, Waltham, MA)). VeroE6suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)Experimental Models: Organisms/Strains Sentences Resources Infection of BALB/c and hACE2/k18 Mice: All animals were cared for according to the standards set forth by the Institutional Animal Care and Use Committee at the University of Maryland-Baltimore. BALB/csuggested: NoneThe K18-hACE2 mice were inoculated with 1e3 PFU of each virus in 50μL PBS. K18-hACE2suggested: RRID:IMSR_GPT:T037657)Recombinant DNA Sentences Resources To assemble DNA fragment clones, the TAR vectors were PCR amplified from pCC1BAC-his3 with KOD Xtreme Hot Start DNA polymerase (Millipore, Burlington, MA) using the construction primers (labeled “Con”, Table S1). pCC1BAC-his3suggested: None50 fmol of each amplicon and 15 fmol of YCpBAC vector were assembled using a standard Gibson assembly reaction (New England Biolabs, Ipswich, MA), transformed into E. coli DH10B competent cells (Thermo Fisher, Waltham, MA), and plated on LB medium with 12.5 mg/ml chloramphenicol. YCpBACsuggested: NoneFull-length genome assembly: The TAR vector for assembly of the full-length genome was amplified from pCC1BAC-ura3 using primers ConCMVpR and ConBGHtermF with KOD Xtreme Hot Start DNA polymerase (Millipore, Burlington, MA). pCC1BAC-ura3suggested: NoneSoftware and Algorithms Sentences Resources Virus Reconstitution: 24 hours prior to transfection, 5e4 VeroE6 cells (ATCC,Manassas, VA) were plated per well in 1mL of VeroE6 media (DMEM (Quality Biological, Gaithersburg, MD), 10% FBS (Gibco, Waltham, MA), 1% Penicillin-Streptomycin (Gemini Bio Products, Sacramento, CA), 1% L-Glutamine (Gibco, Waltham, MA)). Quality Biologicalsuggested: NoneThe cells were rocked every 15 minutes for 1 hour at 37°C prior to overlay with 2mL of a solid agarose overlay (EMEM (Quality Biological, Gaithersburg, MD), 10% FBS, 1% Penicillin-Streptomycin, 1% L-Glutamine, 0.4% w/v SeaKem agarose (Lonza Biosciences,Morrisville, NC). Lonza Biosciencessuggested: (Science Exchange, RRID:SCR_010620)Statistical Analysis: All statistical analyses were carried out using the GraphPad Prism software. GraphPad Prismsuggested: (GraphPad Prism, RRID:SCR_002798)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
-