Phylogenetic network analysis of SARS-CoV-2 genomes

[Frostbit]

Phylogenetic network analysis of SARS-CoV-2 genomes

This is a phylogenetic network of SARS-CoV-2 genomes sampled from across the world. These genomes are closely related and under evolutionary selection in their human hosts, sometimes with parallel evolution events, that is, the same virus mutation emerges in two different human hosts. This makes character-based phylogenetic networks the method of choice for reconstructing their evolutionary paths and their ancestral genome in the human host. The network method has been used in around 10,000 phylogenetic studies of diverse organisms, and is mostly known for reconstructing the prehistoric population movements of humans and for ecological studies, but is less commonly employed in the field of virology.

In light of the lengthy discussion on the definition of a "lab tech" and the obvious level of knowledge in science of the NEIP participants I figured this would be an interesting study to discuss.

Talk amongst yourselves.....

[Celeste Chalfonte]

Phylogenetic network analysis of SARS-CoV-2 genomes





In light of the lengthy discussion on the definition of a "lab tech" and the obvious level of knowledge in science of the NEIP participants I figured this would be an interesting study to discuss.

Talk amongst yourselves.....

In terms of virology, I can see the benefit of this for determining the origin of the pandemic, but does it have implications for prevention and/or treatment?

[Frostbit]

In terms of virology, I can see the benefit of this for determining the origin of the pandemic, but does it have implications for prevention and/or treatment?

Treatment perhaps since it would be one way to track any "drift" in the genetic make up of the virus. The second and especially the third wave of the 1917-18 Influenza Pandemic "drifted" to become very very deadly to young people with robust immune systems.

I posted this before but if you missed it I recommend you watch.

[Frostbit]

This study is out of China and is not peer reviewed so should be taken with a grain of salt but it appears there is significant drift occurring.

The sudden outbreak of the severe acute respiratory syndrome-coronavirus (SARS-CoV-2) has spread globally with more than 1,300,000 patients diagnosed and a death toll of 70,000. Current genomic survey data suggest that single nucleotide variants (SNVs) are abundant. However, no mutation has been directly linked with functional changes in viral pathogenicity. Here we report functional characterizations of 11 patient-derived viral isolates, all of which have at least one mutation. Importantly, these viral isolates show significant variation in cytopathic effects and viral load, up to 270-fold differences, when infecting Vero-E6 cells. We observed intrapersonal variation and 6 different mutations in the spike glycoprotein (S protein), including 2 different SNVs that led to the same missense mutation. Therefore, we provide direct evidence that the SARS-CoV-2 has acquired mutations capable of substantially changing its pathogenicity.

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

[scott]

This study is out of China and is not peer reviewed so should be taken with a grain of salt but it appears there is significant drift occurring.



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

No conclusions have been drawn so there isn't much to discuss. I could give you data from research studies all day long but without a conclusion - "did it work?" "did it fail?" "are the results inconclusive?" it's not much use. This is a preliminary and incomplete study. Useful data for someone else to build on, but that's it.

on edit:

Frosty's last post was not posted when loaded the page and got distracted doing other stuff.

So the conclusion is, "Therefore, we provide direct evidence that the SARS-CoV-2 has acquired mutations capable of substantially changing its pathogenicity" and the title is now, "Patient-derived mutations impact pathogenicity of SARS-CoV-2."

Um, duh. That's how all viral infections work. How much and how bad is what is needed, not just verifying that a virus mutates in people.