@lalani_safina (1/n) I think science literate non-specialists like myself tend to view the spike as a largely static trimeric structure - but for the harpoon-transformation that takes place when binding to the receptor. This structure and strategy, by the way, is widespread among viruses, ...
@lalani_safina (2/n) RNA, DNA, single and double stranded alike. See for example,

"When viruses infect cells, they employ molecular 'harpoons' to snare their intended target...."

12/17/1999 

Viral Harpoon Reveals Ancestry of Measles, Mumps Viruses
hhmi.org/news/lamb.html
@lalani_safina (3/n) "Recently, a team of scientists identified and determined the three-dimensional structure of the harpoon protein used by a large family of pathogenic viruses to grab hold of and fuse to host cells..."
@lalani_safina (4/n) "Surprisingly, the protein's structure suggests that viruses that cause measles and mumps may be viral cousins of HIV, influeunz and Ebola virus."
@lalani_safina (5/n) This particular type of fusion protein is a class I viral fusion protein.  For a survey of viral fusion proteins, one might look at:

ncbi.nlm.nih.gov/pmc/articles/P…
@lalani_safina (6/n) As for how the fusion proteins of such diverse viruses could have a common ancestor, it's worth recognizing that at least in the realm of bacterial viruses (bacteriophages) , viruses have a modular structure and mosaic nature.

Please see:

pnas.org/content/96/5/2…
@lalani_safina (7/n) For example, phages may insert themselves into the genome of a host during their temperate phase as a prophage and through recombination acquire a gene from another prophage.
@lalani_safina (8/n) One family of viruses which may be of interest are adenoviruses. Typically they are associated with respiratory and intestinal illness. It has been discovered that they are closely related to a phage by the name of PRD1.

Please see for example:

cell.com/fulltext/S0092…
@lalani_safina (9/n) It turns out that PRD1 and adenoviruses are also related to phages found in archaea.

Please see:

sciencedirect.com/science/articl…

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More from @TimothyChase

15 Jul
@lalani_safina (1/p) No, I've just been tied up in other things. But I'm not sure how relevant it is to the paper, which by the way I thought was very interesting, the presence of an unidentified conformational state, the existence of a statistically mixed population of states that...
@lalani_safina (2/p) changes the statistical mix of closed/open-but-unbound according to environmental variables, particularly temperature, the existence of additional epitopes that antibodies might bind to in the new state, preventing the spike from closing or attaching.
@lalani_safina Well, at this point I'm headed home, and that involves picking up groceries and spending time with Moira, etc. My commute is a mess. Currently standing by the door of my train as it's pulling to a stop at the station.
Read 5 tweets
11 Jul
@lalani_safina @maudi_ahmed @AntibioticDoc (1/n) There is going to be done variation in immune response among people who are fully vaccinated. Some people will have a stronger, more effective response than others, older people will tend to see their protection wane more quickly.
@lalani_safina @maudi_ahmed @AntibioticDoc (2/n) Although the numbers are small, breakthrough infections in Israel are happening more often among those first vaccinated, at the six month mark, but is this because the vaccines are wearing off due to it being six months or that older people were vaccinated first - or both?
@lalani_safina @maudi_ahmed @AntibioticDoc (3/n) Difficult to say at this point. But that kind of variation, while troubling, isn't as dangerous as a mix of vaccinated and unvaccinated. everyone is vaccinated, there may be some transmission, but chains of transmission will tend to burn themselves out.
Read 7 tweets
28 Jun
@lalani_safina @macroliter Lambda first found in Peru had the Pango lineage name of C.37. The deletion you are looking for is likely what the following paper refers to as the novel deletion Δ246-252 .

virological.org/t/novel-sublin…
@lalani_safina @macroliter Another paper on Lambda focusing on the mutation:

medrxiv.org/content/10.110…
@lalani_safina @macroliter As for the general significance of deletions...

medrxiv.org/content/10.110…
Read 6 tweets
7 Jun
@lalani_safina @giorgilab (1/n) Actually the T478K mutation is found in "Delta" B.1.617.2. as you can tell was the substitution from T to k we are looking at a neutrally charged amino acid being replaced by a positively charged amino acid which means that it will be more difficult...
@lalani_safina @giorgilab (2/n) for the immune system to create antibodies that will counteract it. However at least with the variant discovered in Mexico we found that this mutation has an especially high free binding energy to the ACE2 receptor. As such it binds much more tightly to the receptor and...
@lalani_safina @giorgilab (3/n) this likely explains much of the increased transmissibility.

Regarding Delta:

"In particular, the Spike protein contained 9
mutations, when compared to the D614G strain (belonging to the basal B.1 lineage) used here as a
reference, including five mutations..."
Read 8 tweets
25 May
(1/n) #B1617 #variants (dropping the dots for the hashtag) "... the B.1.617.2 variant has mutations called 452R and 478K, which Tang says are both linked to increased transmissibility. Both mutations alter the spike protein...."
nature.com/articles/d4158…
(2/n) [L]452R is believed to result in the spike binding more closely to the ACE2 receptor and may simultaneously result in a degree of Immune escape. From analysis of B.1.429 which has the same mutation...
(3/n) "This replacement is predicted to create a much stronger attachment of the virus to the human cells and also might allow it to avoid the neutralizing antibodies that try to interfere with this attachment." (2021 Feb 26)

newsroom.uw.edu/news/single-mu…
Read 21 tweets
28 Mar
@beuchelt @GYamey @rjar1980 (1/n) At least in the relevant physics communities among members publishing in the peer reviewed literature, the acceptance of Einstein's special theory of relativity was rapid. A matter of a few years.
@beuchelt @GYamey @rjar1980 (2/n) This was in part thanks to the efforts of individuals such as a Lorentz and Planck. And despite the complexity of his theory of gravity, it's acceptance in the peer reviewed literature was even more rapid.
@beuchelt @GYamey @rjar1980 (3/n) There were of course antisemite scientists, particularly in Germany with the rise of Nazism, but there protests were almost entirely a matter of the popular press and politics, not peer reviewed literature.

Darwin? His case is a little more interesting.
Read 16 tweets

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