Kiki’s Comments May 2020
Episode 609: A coronavirus chronology with Susan Weiss
*it is very unlikely that this coronavirus (SARS-CoV-2) escape or was released from a lab
*we need to fund more research into the origin of CoV-2
*no direct evidence that CoV-2 can enter the brain (no known neurotropism)
*the furin site and TMPRSS2 site are important for CoV-2 entry and cleavage
*the endgame is a vaccine for CoV-2 and therapeutics will be useful
*Contact tracing, personal protective equipment, and social distancing will help to control potential flare-ups to allow some things to open up
*Basic corona virology: sub-genomic messenger RNAs are made from subgenomic negative RNAs. For CoV-2 the furin site is interesting for identifying parent or precursor viruses. The pangolin virus does not have the same furin site, although it has a similar RBD. We need more research into this.
Genome: Difference in the accessory proteins; the replicase (20kb), the structural proteins (in the same order in all the viruses in all the genera), and the accessory proteins (each sub-lineage is different, e.g. the accessory proteins set is different for each beta coronavirus)
Receptor interaction: SARS-1 and SARS-2 use ACE2 (both beta coronaviruses), but so does another virus that is alpha, so we have both alpha and beta coronaviruses using the same receptor—this might mean we are overemphasizing importance in pathogenesis
*SARS-2 (CoV-2) vs SARS-1: Why is it different from SARS-1? Going to be really hard to figure out from the genomes. How it differs in interaction with the host immune system will be important (SARS-1 shut down the host interferon response).
*CoV-2 man-made? Human made or escaped from lab for COVID-19, this is most likely incorrect
*Why Bats? One of the only flying mammals (except for humans), so it is no wonder that bats are a common origin species for zoonotic viruses. Different bat species have different viruses. There doesn’t need to be an intermediate between bat to human transmission for CoV-2, although it is probable that there is.
*What is the endgame? Vaccine. Currently there are 8 in trial and around 50 in production. Hopefully we will have some therapeutics before the vaccine is ready that will allow people to begin to leave quarantine. Contact tracing (critical), personal protective equipment, and social distancing will help to control potential flare-ups to allow some things to open up. Maybe combination of an antibody and IL-6 will make it easier to leave the house
Re-infections: OC43 (common human coronavirus) you can get multiple infections. It would be really anti-dogmatic if the immunity went away completely for CoV-2—the PCR can be very misleading.
n.b. out in the actual world, RNA is much more stable.
Cleavage of Spike and furin vs TMPRSS2: Some spikes have furin sites and some don’t. During morphogenesis and processing of the spike, there are furin protease around the Golgi and intracellular membranes, and spikes that have furin can be cleaved there—they are primed for fusion. There have to be two cleavages for fusion; one is between S1 and S2, and this is generally a furin site, and there is another downstream cleavage at S2 that reveals the fusion peptide. The cleavages can happen in different places—on the membrane, during assembly, and in the endosome during entry. Depending on where the cleavages happen directs the virus into one of two entry pathways: 1) through endosomes, cathepsin being the cleaving protease, 2) through the surface, which is where TMPRSS is active. For SARS-CoV-2, you need both furin to cut between S1 and S2 and TMPRSS2 to cut the S2’. This is very cell-type dependent, but CoV-2 clearly has to have the two cleavages. The viruses that do not have the furin site have to have more cleavages upon entry, while the ones with the furin site semi-made it already. SARS-1 did not have a furin site—this is why everyone is paying so much attention to this fusion site. MERS and MHV, on the other hand, do have this furin site, while generally viruses of the SARS lineage do not. The furin is probably not important to the pathogenesis in humans.
n.b. if it enters through the endosome, hydrochloroquine only targets the endosomal site and TMPRSS-inhibitors only target the cell membrane site, so neither one of them should work completely unless the virus doesn’t follow normal patterns. It is likely both cell cleavage sites would have to be targeted. Spikes that have furin sites can activate cell-to-cell fusion—we are seeing tons of cell-to-cell fusion in CoV-2. Spike entry is not the only determinant of tropism.
Neurotropism: No direct evidence that CoV-2 can enter the brain. We do not have evidence for SARS-1 either.
Phosphodiesterases: Found in lineage A and C coronaviruses (MHC and MERS, but not SARS). Enzymes that need 2’ and 5’ linkages. During infection, usually double-stranded RNA (dsRNA) produced by most viruses is recognized by a bunch of receptors, one of which is oligoadenylate synthase. When they recognize dsRNA they produce 2’5’A—a small oligoadenylate—and this activates ribonuclease L, which cleaves single-stranded RNA (ssRNA), both viral and cellular, and is thus antiviral because it kills RNA and stops protein synthesis, causing apoptosis. MHV shuts down this pathway completely and becomes completely apathogenic. This pathway is very important for pathways that shut down the interferon pathway.
ADARs: Adenosine Deaminases Acting on RNA (ADAR) is an RNA editing enzyme that causes mutation, but it also prevents dsRNA from accumulating. In the absence of ADAR, disease can manifest; in the absence, RNA is activated and leads to apoptosis. This is an interferonopathy.