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Reply to: No, the 2019-nCoV genome doesn’t actually seem engineered from HIV Posted February 1, 2020

I’m not much of a scientist, but what I would say is 1).  Correct 2.)  The Indian group identified some inserts in 2019-nCoV in the spike protein (used for cell entry) compared with its closest relative.  Having inserts is not suspicious, however they managed to identify these inserts from the HIV genome, suggesting someone might have deliberately engineered them in.  If you look at Table 1 you find 3 of the 4 inserts are located in hypervariable regions of HIV.  These are regions that are not conserved as they are not under heavy selection pressure – so there will be lots of different variations in existence.  The isolates are from Kenya, India and Thailand which suggests that the underlying database they are searching is probably very large.  If someone was searching the database for useful segments to insert into Coronavirus, then why would they chose one from Kenya, one from Thailand and two from India?  It wouldn’t be a sensible approach for bioengineering because the target proteins of the S protein and GP120 (HIV) are completely different. 3.)  No, I think the Indian authors were arguing this was a deliberate case of engineering, hence you wouldn’t expect any cases of  HIV to crop up. Just out of curiosity, India was where the story of HIV being an escaped bioweapon originally emerged back in 1983.  The US managed to stamp down on it successfully, but it looks like an oral history of it has survived among the Indian scientific community

Reply to: No, the 2019-nCoV genome doesn’t actually seem engineered from HIV Posted February 1, 2020

A long time ago, last millennium in fact, I had peripheral involvement in a project using peptides from the helical regions of the S protein to interfere with the cell fusion process.  This type of work keeps getting repeated and repeated, eg here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3849439/ Or this one https://www.nature.com/articles/ncomms4067 It always seems to work in cell assays but as far as I know no one goes on to do human tests.  For a number of reasons I think, it is not an economically attractive proposition for a drug company, peptides are comparatively expensive and not easy to administer as a pill.  Also these high profile pandemics don’t infect large numbers and then they disappear and don’t leave an easy population to run clinical trials. But I do wonder if a regulatory and market gap has opened up here.  Since the development time for locating suitable peptide agents would be very short.  Perhaps someone should just bite the bullet this time and start testing them in a clinical setting. Or perhaps some has and it hasn’t worked as well as it did in cell culture.

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Reply to: No, the 2019-nCoV genome doesn’t actually seem engineered from HIV Posted February 1, 2020

I’m not much of a scientist, but what I would say is 1).  Correct 2.)  The Indian group identified some inserts in 2019-nCoV in the spike protein (used for cell entry) compared with its closest relative.  Having inserts is not suspicious, however they managed to identify these inserts from the HIV genome, suggesting someone might have deliberately engineered them in.  If you look at Table 1 you find 3 of the 4 inserts are located in hypervariable regions of HIV.  These are regions that are not conserved as they are not under heavy selection pressure – so there will be lots of different variations in existence.  The isolates are from Kenya, India and Thailand which suggests that the underlying database they are searching is probably very large.  If someone was searching the database for useful segments to insert into Coronavirus, then why would they chose one from Kenya, one from Thailand and two from India?  It wouldn’t be a sensible approach for bioengineering because the target proteins of the S protein and GP120 (HIV) are completely different. 3.)  No, I think the Indian authors were arguing this was a deliberate case of engineering, hence you wouldn’t expect any cases of  HIV to crop up. Just out of curiosity, India was where the story of HIV being an escaped bioweapon originally emerged back in 1983.  The US managed to stamp down on it successfully, but it looks like an oral history of it has survived among the Indian scientific community

Reply to: No, the 2019-nCoV genome doesn’t actually seem engineered from HIV Posted February 1, 2020

A long time ago, last millennium in fact, I had peripheral involvement in a project using peptides from the helical regions of the S protein to interfere with the cell fusion process.  This type of work keeps getting repeated and repeated, eg here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3849439/ Or this one https://www.nature.com/articles/ncomms4067 It always seems to work in cell assays but as far as I know no one goes on to do human tests.  For a number of reasons I think, it is not an economically attractive proposition for a drug company, peptides are comparatively expensive and not easy to administer as a pill.  Also these high profile pandemics don’t infect large numbers and then they disappear and don’t leave an easy population to run clinical trials. But I do wonder if a regulatory and market gap has opened up here.  Since the development time for locating suitable peptide agents would be very short.  Perhaps someone should just bite the bullet this time and start testing them in a clinical setting. Or perhaps some has and it hasn’t worked as well as it did in cell culture.