A method to eliminate mutants in the furin cleavage site of SARS-CoV-2 in Calu-3 cells

To combat the global severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, vaccinations and treatment procedures have been developed at a breakneck pace. However, SARS-CoV-2 continues to mutate and adapt to the human population, necessitating a review of present medical countermeasures' effectiveness or the development of new ones in the near and long term. The efforts to see if the first-generation SARS-CoV-2 vaccinations are effective against the highly transmissible Delta form have highlighted this.

All of the early SARS-CoV-2 strains were grown on African Green Monkey Vero cell lines. Vero cells proliferate rapidly and express high levels of angiotensin-converting enzyme 2 (ACE2), a molecule recognized by the RBD (receptor-binding domain) of the spike protein used by SARS-CoV-2 to enter lung epithelial cells. Furin-mediated pre-activation of the spike protein improves viral entry via the ACE2 receptor. SARS-CoV-2, on the other hand, can enter Vero cells via endocytosis, making the use of the ACE2 receptor unnecessary.

Several studies have discovered that propagating SARS-CoV-2 on Vero-derived cell lines results in the rapid accumulation and loss of a functional furin cleavage site within a few passages. As a result, SARS-CoV-2 propagation on Vero cells produced challenge stocks with defects in the furin cleavage site, rendering them non-pathogenic in animals.

The authors of a new study, published in the journal Viruses, examined how the propagation of a B.1.351-related (beta variant) SARS-CoV-2 isolate in two cell types, Vero/hSLAM, and Calu-3 cells, affected viral genome sequences both within and outside of the spike gene's furin cleavage site. When the virus was grown on Vero/hSLAM cells, the authors observed an expansion of mutations in the furin cleavage site, but these were eliminated when it was grown on Calu-3 cells. In addition, distinct variants that accumulated when this virus stock was grown on Calu-3 cells were also discovered. Notably, the Calu-3-derived virus stocks remained pathogenic in hamsters, as did the Calu-3-specific variants. These findings support the growth of SARS-CoV-2 challenge stocks on Calu-3 cells prior to use in animals in order to maintain an intact furin cleavage site and viral pathogenicity.

Study: Propagation of SARS-CoV-2 in Calu-3 Cells to Eliminate Mutations in the Furin Cleavage Site of Spike. Image Credit: Pinkeyes / Shutterstock​​​​​​​
Study: Propagation of SARS-CoV-2 in Calu-3 Cells to Eliminate Mutations in the Furin Cleavage Site of Spike. Image Credit: Pinkeyes / Shutterstock

The study

Appropriate virus propagation conditions are required to keep the furin cleavage site intact in SARS-CoV-2 virus populations. The authors wanted to see if propagating a B.1.351 lineage of SARS-CoV-2 on Calu-3 cells would result in a virus stock free of furin cleavage site mutations and deletions, even if the stock had already been passaged twice on Vero cells. The authors wanted to see if propagating viruses on Calu-3 cells would eliminate accumulated virus subpopulations with mutant furin cleave site sequences and prevent the generation of viruses with new variants or deletions of this site due to cell culture adaptations.

Schematic of the passage history for the virus stocks characterized in this study. Created with BioRender.com
Schematic of the passage history for the virus stocks characterized in this study. Created with BioRender.com

The same p3 isolate of a B.1.351 virus lineage that had been passaged twice through Vero E6 cells was obtained by two different laboratories (BEI Resources and BIOQUAL). Previously accumulated mutations in the furin cleavage site were lost from the population when grown independently on Calu-3 cells at each site.

On the other hand, BEI Resources cultured the same stock on Vero-hSLAM cells and discovered that the furin cleavage site mutations survived in the population. These findings align with recent research that used Calu-3 cells to grow an early SARS-CoV-2 isolate and produced pseudovirus variants. SARS-CoV-2 viruses with an undamaged furin cleavage site infected Calu-3 cells quicker in each of these investigations.

The authors expanded on this discovery by discovering that when B.1.351 'Beta' SARS-CoV-2 variants with furin cleavage site point mutations were propagated on Calu-3 cells, they were also lost from the population. This finding suggests that when cultivated on Vero cells, all SARS-CoV-2 variants of concern will collect furin cleavage site alterations but that these can be eradicated if produced on Calu-3 before being used in animals.

The researchers infected four hamsters with the Calu-3-derived BQ-RSA-p4 strain to see if the Calu-3-specific mutations would survive in vivo. In these animals, the virus grew well, with subgenomic viral titers exceeding 107 copies/gram lung tissue, similar to the results shown in hamsters infected with the WA/2020 (Wuhan) isolate. The hamsters lost about 15% of their body weight, indicating that the Calu-3-related mutations had little effect on virus pathogenicity in hamsters.

In comparison, hamsters infected with stocks missing a furin cleavage site only lost a small amount of weight. The variations found in the Calu-3-derived stocks in the hamsters were either retained or extended. Future research will need to see if other SARS-CoV-2 lineage variants (such as B.1.617.2) acquire the same nucleotide variants when cultured on Calu-3 cells or if the nucleotide variants described here are only found in the B.1.351 lineage.

Implications

These findings confirm a process in which complete sequencing of a challenge inoculum is required to obtain a comprehensive picture of the virus population's complexity. Variant frequencies will continue to alter as SARS-CoV-2 challenge stocks adjust to cell culture settings as they are regularly propagated at multiple places. It's crucial to know whether a pathogenic viral variation found in an animal emerged from scratch or was already present in the inoculum. As a result, studying virus diversity beyond the consensus sequence is critical for identifying underlying changes that could change virus pathogenicity. From these findings, it could be suggested that every in vivo challenge study should include a characterization of the challenge stock's complexity.

Journal reference:
  • Propagation of SARS-CoV-2 in Calu-3 Cells to Eliminate Mutations in the Furin Cleavage Site of Spike, John James Baczenas, Hanne Andersen, Sujatha Rashid, David Yarmosh, Nikhita Puthuveetil, Michael Parker, Rebecca Bradford, Clint Florence, Kimberly J. Stemple, Mark G. Lewis and Shelby L. O'Connor, MDPI, 2021.12.04, https://doi.org/10.3390/v13122434, https://www.mdpi.com/1999-4915/13/12/2434  
Colin Lightfoot

Written by

Colin Lightfoot

Colin graduated from the University of Chester with a B.Sc. in Biomedical Science in 2020. Since completing his undergraduate degree, he worked for NHS England as an Associate Practitioner, responsible for testing inpatients for COVID-19 on admission.

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