Patient-derived mutations impact pathogenicity of SARS-CoV-2

https://www.medrxiv.org/content/10.1101/2020.04.14.20060160v1

Commentary: George Martin MD

It is well known that viruses mutate over time in large part because the replication process does not always lead to a perfect copy of the genes being replicated.  While single nucleotide variants (SNVs) are abundant in SARS-CoV-2, until this publication no mutation has been directly linked to functional changes in SARS-CoV-2 that would affect the virus’ pathogenicity.

The authors analyzed viral isolates between 1/22/2020 and 2/4/2020 from 11 patients who lived in or came in contact with viral victims from Wuhan, China. These patients by epidemiology analysis constitute 1st and 2nd generations of the viral victims based on their history. All patients survived and only 1 subject required ICU.

They identified diverse mutations in viral isolates, including 6 different mutations in the spike glycoprotein (S protein), and 2 of which are different SNVs that led to the same missense mutation.  The researchers infected Vero-E6* cells with 11 viral isolates and quantitatively assessed their viral load at 1, 2, 4, 8, 24, and 48-hours post infection and their viral cytopathic effects at 48 and 72 hours.  These mutations led to significant variations in their viral load (up to 270-fold differences in SARS-CoV-2’s ability to replicate themselves).  Higher viral loads were associated with more cell death, referred to as cytopathic effects. The authors concluded: “we provide direct evidence that the SARS-CoV-2 has acquired mutations capable of substantially changing its pathogenicity”.

It should be taken into consideration that this data is in-vitro and uses non-human cells (Vero-E6-cells) to determine pathogenicity. However, these findings raise great concern. The study highlights the observation that SARS-CoV-2 mutations are not an infrequent event and that certain SARS-CoV-2 mutations confer a greater pathogenic effect than others. The authors stressed the importance of not only identifying mutations but linking those mutations to their effect on cytopathology as was done in the study using Vero-E6-cells.
As we strive to develop anti-viral therapies and vaccines, it appears that SARS-CoV-2 may be more of a moving target than we first thought.

* Note:  Vero cells are lineages of cells used in cell cultures.  They were first isolated from kidney epithelial cells extracted from an African green monkey (Cercopithecus aethiops). The lineage was developed in 1962 by Yasumura and Kawakita . The original cell line was named “Vero” after an abbreviation of verda reno, which means “green kidney”, while vero itself means “truth” also.

Vero cells are interferon-deficient; unlike normal mammalian cells, they do not secrete interferon alpha or beta when infected by viruses.  However, they still have the Interferon-alpha/beta receptor, so they respond normally when recombinant interferon is added to their culture media.

Ref: WIKIPEDIA