Using Microphysiological Systems to Study SARS-CoV-2 Variants

By Vijayalakshmidevi


The Impact of SARS-CoV-2

COVID-19 has spread through almost every country in the world and has infected over 7 million people and been linked to over 400,000 deaths (WHO, 2020 at https://covid19.who.int/). Studies to monitor the evolution and spread of the virus need to be corroborated with clinical outcomes. Since the start of the pandemic, there is a strong push to develop vaccines or antiviral drugs against different variants of SARS-CoV-2. Identifying mutations in the viral RNA genome is important for developing effective vaccines and antiviral therapies. The SARS-CoV-2 viral genome has about 6,324 identified genes; pathogenic mutations of those genes need to be identified before evaluating the impact of the mutations on viral replication and infectivity.


Mutation Sequences of SARS-CoV-2

Computational studies have been used to identify hotspot mutation sequences where changes in the genome have the potential to alter viral replication and infection. The D614G mutation in the S protein was identified using computational studies and was shown to increase viral infection by reducing S protein shedding and increasing the amount of S protein in virion particles (Zhang et al. 2020).  Other studies have  shown that coding genes such as E, M, ORF6, ORF7a, ORF7b, and ORF10 are more stable, potentially suitable to be targeted for vaccine and drug development.

Effective in vitro models, such as 3D organoids, that can recapitulate the human physiological responses can be used to study the characteristics of SARS-CoV-2 variants and evaluate the efficacy of antiviral therapies. Additionally, they can provide tools for evaluating the efficacy of vaccines in preventing the viral infections caused by different varaints.
 

Application of PerfusionPal for Molecular Studies of SARS-CoV-2
 

Recently, an air-liquid interface model that mimics the human’s airway tracheal and bronchial brushing movement, has been used to study the pathology of SARS-CoV-2 such as inflammatory response and test antiviral drug efficacy (Chugh et al. 2021). Lung organoids are another powerful tool to study the viral infection. One advantage of organoids is that they do not need an adaptation process of viruses, indicating that there is no or relatively low potential to induce genetic mutation in the viral genome. In addition, there is no potential risk of adverse effects by host cell-derived non-human protein from the virus. They provide important insights about the virus and prompt further research into the impact of viral variants (Hong et al. 2018).

PerfusionPal is a cost-effective organ-on-a-chip insert system that can be used for generating 3D lung organoids. It has multiple open-bottom wells for maintaing individual and independent 3D cell cultures, which can be used to conduct multiple assays simultaneously. PerfusionPal is equipped with a media pumping system that perfuses Blood Substitute and mimics the in vivo continuous circulation of extracellular fluid. Blood Subsitute provides oxygen to the cells and enables the long-term maitannace of the culture (Shoemaker et al. 2020). Human lung organoids developed in PerfusionPal can be infected by SARS-CoV-2 varaints to study replication and infectivity and test the efficacy of antiviral therapies. Moreover, antibodies generated in response to available vaccines can be incorporated in the culture to evaluate their efficacy in modulating response to infection.

Analyzing the virus genome sequences and their proteins is crucial for understanding the evolution of the SARS-CoV-2 virus and the impact of new viral strains.  Future studies focusing on impacts of the mutations in genome and protein functions will benefit from tools such as PerfusionPal, along with computational analysis.

References:

  1. World Health Organization. WHO coronavirus disease (COVID-19) dashboard. https ://covid 19.who.int/ (2020)
  2. Zhang L, Jackson CB, Mou H, et al. SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. Nat Commun. 2020;11(1):6013. Published 2020 Nov 26.
  3. Chugh RM, Bhanja P, Norris A, Saha S. (2021). Experimental Models to Study COVID-19 Effect in Stem Cells. Cells. 10(1):91.
  4. Hong KJ, Seo SH. Organoid as a culture system for viral vaccine strains. Clin Exp Vaccine Res. 2018;7(2):145-148. doi:10.7774/cevr.2018.7.2.145
  5. Shoemaker, J. T., Zhang, W., Atlas, S. I., Bryan, R. A., Inman, S. W., & Vukasinovic, J. (2020). A 3D Cell Culture Organ-on-a-Chip Platform With a Breathable Hemoglobin Analogue Augments and Extends Primary Human Hepatocyte Functions in vitro. Frontiers in molecular biosciences, 7, 568777.