Application of phylogenetics (study of evolutionary relationships) and the coronavirus outbreak

pitabread · Feb 20, 2020

Figured this is relevant given the current coronavirus outbreak in China (and spreading): https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)30251-8/fulltext

The ten genome sequences of 2019-nCoV obtained from the nine patients were extremely similar, exhibiting more than 99·98% sequence identity. Notably, 2019-nCoV was closely related (with 88% identity) to two bat-derived severe acute respiratory syndrome (SARS)-like coronaviruses, bat-SL-CoVZC45 and bat-SL-CoVZXC21, collected in 2018 in Zhoushan, eastern China, but were more distant from SARS-CoV (about 79%) and MERS-CoV (about 50%). Phylogenetic analysis revealed that 2019-nCoV fell within the subgenus Sarbecovirus of the genus Betacoronavirus, with a relatively long branch length to its closest relatives bat-SL-CoVZC45 and bat-SL-CoVZXC21, and was genetically distinct from SARS-CoV.

It discusses the study of the initial viral genomes and the associated phylogenetic analysis (study of evolutionary relationships) of the virus and insights that are gained from such analysis. In particular, it discusses the possibility that this virus uses the ACE2 receptor for binding (similar to SARS).

This appears to be confirmed in this subsequent paper: Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation

Recent reports demonstrating that 2019-nCoV S and SARS-CoV S share the same functional host-cell receptor—angiotensin-converting enzyme 2 (ACE2) (22, 25–27)—prompted us to quantify the kinetics of this interaction by surface plasmon resonance (SPR). ACE2 bound to 2019-nCoV S ectodomain with ~15 nM affinity, which is approximately 10- to 20-fold higher affinity than ACE2 binding to SARS-CoV S (Fig. 3A and fig. S7) (14).

Thought this was another interesting example of how evolutionary biology is applied in real world situations to deal with real world problems.

SLP · Feb 21, 2020

pitabread said:
Figured this is relevant given the current coronavirus outbreak in China (and spreading): https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)30251-8/fulltext

It discusses the study of the initial viral genomes and the associated phylogenetic analysis (study of evolutionary relationships) of the virus and insights that are gained from such analysis. In particular, it discusses the possibility that this virus uses the ACE2 receptor for binding (similar to SARS).

This appears to be confirmed in this subsequent paper: Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation

Thought this was another interesting example of how evolutionary biology is applied in real world situations to deal with real world problems.

This is all moot since Tom Cotton says it was man-made....

civilwarbuff · Feb 28, 2020

Coronavirus more likely than Sars to bond to human cells, scientists say

pitabread · May 5, 2020

Further application of biological evolution in understand mutations and transmissibility of the coronavirus (specifically a mutated strain). This further reinforces why the Theory of Evolution is a useful science and why we continue to include it in the biological sciences:

Mutations are considered in a broader phylogenetic context, geographically, and over time, to provide an early warning system to reveal mutations that may confer selective advantages in transmission or resistance to interventions. Each one is evaluated for evidence of positive selection, and the implications of the mutation are explored through structural modeling. The mutation Spike D614G is of urgent concern; it began spreading in Europe in early February, and when introduced to new regions it rapidly becomes the dominant form. Also, we present evidence of recombination between locally circulating strains, indicative of multiple strain infections. These finding have important implications for SARS-CoV-2 transmission, pathogenesis and immune interventions.

https://www.biorxiv.org/content/10.1101/2020.04.29.069054v1.full.pdf

Application of phylogenetics (study of evolutionary relationships) and the coronavirus outbreak

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Application of phylogenetics (study of evolutionary relationships) and the coronavirus outbreak

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