Human organoids useful for modeling COVID-19 variants of concern, finds study

First detected in the United Kingdom, the B.1.1.7 variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has exhibited heightened transmissibility compared to older strains.

A new study published on the bioRxiv* preprint server found that using human organoids could help with better characterizing the phenotype of several viral variants, including B.1.1.7. Their findings show the ribonucleic acid (RNA) shedding of the SARS-CoV-2 variant correlated with viral fitness and infectiousness.

Study: Human organoid systems reveal in vitro correlates of fitness for SARS-CoV-2 B.1.1.7. Image Credit: joshimerbin / Shutterstock

 

We report that extended shedding is an in vitro correlate of infectiousness for SARS-CoV-2 B.1.1.7, which corroborates epidemiological findings and may explain why this clade is more transmissible. Human adult stem cell-derived pulmonary and intestinal organoids thus may provide a platform for the comparison of non-cell culture-adapted SARS-CoV-2 clinical isolates,” wrote the researchers.

Airway organoids show high infectivity in B.1.1.7 variant

The researchers isolated the B.1.1.7 variant from an oropharyngeal sample, where it then grew in Calu-3 cells and spread along with another ancestral clade B isolate called Bavpat-1. They then tested the infectiousness of SARS-CoV-2 on airway organoids. While humans can shed SARS-CoV-2 for about 10 days, infected cells die after 72 hours.

To circumvent this issue, the team evaluated the replication kinetics of the B.1.1.7 and clade B isolate when infecting air-liquid interface human airway organoids 10 days post-infection. They also analyzed viral titers on Calu-3 cells to determine infectiousness.

In airway organoids, the B.1.1.7 variant showed greater viral titers than the clade B isolate. The B.1.1.7 variant had peak viral titers between days 2 and days 4 post-infection. While the peak dropped, the organoids continued to have high titers until day 10 post-infection compared to the B clade isolate, which showed decreasing titers between days 4 and 10 post-infection.

On day 3 post-infection, both viruses infected about the same number of cells. However, by day 10, the B.1.1.7 variant continued to infect an equal number of cells. The clade B isolate infected only a few cells after 10 days.

Greater viral shedding of the B.1.1.7 variant in alveolar lung cells

Alveolar cells are frequently used in research to study severe COVID-19. They established human alveolar type 2 cell organoids expressing AT2 marker genes, but not airway marker genes. AT2 cells also expressed BMP4 to prevent it from transforming into AT1 cells.

Results showed AT2 organoids were vulnerable only to SARS-CoV-2 infection compared to HTII-280+ cells that were targeted by both viruses.

The B.1.1.7 variant showed lower viral RNA titers but appeared to have slightly higher infectious titers than the clade B isolate as time progressed — though this was nonsignificant.

This discrepancy between viral RNA and infectious virus is likely to be caused by a higher peak titer for Bavpat-1 at 2 days post-infection and by the fact that in this 3D model the virus/RNA cannot be collected by daily washing of the cells,” wrote the researchers.

Because viral spread in 3D organoids is limited for long replication kinetic experiments, the team repeated the experiment using cultured AT2 cells inserted in 2D air-liquid interfaces. As before, there was more viral shedding of the clade B isolate in the first 3 days post-infection, but the B.1.1.7 titers were higher at later time points.

Chronic viral shedding in organoids post-infection

The researchers also looked at intestinal epithelial cells because they have been prone to SARS-CoV-2 infection. Results showed similar replication kinetics for B.1.1.7 compared to pulmonary cells. Similar to AT2 organoids, there were no differences in viral titers in the first three days of infection. However, there were greater B.1.1.7 viral titers in the latter stages of the infection.

After 10 days post-infection, the researchers found more infected cells from the B.1.1.7 variant than the B clade isolate. Based on the results, they suggest the B.1.1.7 is highly infectious for both lung and intestinal organoid cells.

The B.1.1.7 variant also outcompeted the clade B virus when conducting the experiment on in vitro models, indicating greater replicative fitness than ancestral viruses.

These results support an important role for social interactions in determining viral fitness. The possibility that specific virus-host interactions may be crucial in determining the outcome of experiments that measure viral fitness, and such interactions can be lost in animal models. Future studies may use reverse genetics to address the roles of these mutations in human organoid systems.”

*Important Notice

bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Written by

Jocelyn Solis-Moreira

Jocelyn Solis-Moreira graduated with a Bachelor's in Integrative Neuroscience, where she then pursued graduate research looking at the long-term effects of adolescent binge drinking on the brain's neurochemistry in adulthood.