#Breakthrough #infections #CDC #Walensky

(1/n) Under Walensky the CDC stopped tracking breakthrough infections back in May if they didn't require hospitalization. It helps keep down the numbers since hospitalization is rare among the fully vaccinated.

newsweek.com/why-did-cdc-st…
(2/n) Keeping numbers low this way may have seemed reasonable at the time since they wanted people to get vaccinated and since infection with Alphav rarely resulted in infectious fully vaccinated individuals.

cnn.com/2021/08/05/hea…
(3/n) However, this means that when the effectiveness of vaccines is measured in terms of the prevention of severe COVID it misses a great deal of infections among the fully vaccinated, as was belatedly learned by a John Hopkins epidemiologist...

baltimoresun.com/opinion/op-ed/…
(4/n). Viral loads in the nose and throat are statistically indistinguishable among the infected vaccinated and unvaccinated. The fully vaccinated are likely equally able to infect others and responsible for substantial transmission.

nbcnews.com/science/scienc…
(5/n) It is common to hear that the current epidemic is an epidemic of the unvaccinated. They are after all those most likely to end up in the hospital. It is also sometimes pointed out that those whoo are unvaccinated are increasing the number of infections, giving the virus...
(6/n) ... a chance to mutate and become something even more dangerous than Delta. However, thanks to the CDC decision not to track asymptomatic and mild infections among the fully vaccinated we have been flying blind in a pandemic that had been transformed by Delta.
(7/n) Currently we have little information on how often the fully vaccinated have asymptomatic or mild infections, but what little we know from the unfortunate experience of the John's Hopkins epidemiologist and CDC's mentioned in their internal document suggests it is...
(8/n) ... quite common. So it would seem that while the unvaccinated are responsible for much of the transmission and potential evolution of the virus, the fully vaccinated bare much of this burden as well, particular when they choose not to wear masks.
(9/10) And however strongly worded the CDC's suggestion that the fully vaccinated wear masks in areas of high transmission (likely according to their state level national map, but many will likely substitute their own subjective impression), the CDCk knows most won't follow it.
(10/10) So it would seem the CDC currently shares much of the moral burden for transmission, evolution, and potentially increasing immune escape and virulence that await us in variants to come.

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More from @TimothyChase

9 Aug
@lalani_safina (1/n) They actually*replicate* in a host, but transmission, at least by droplets or aerosols tends to work better at lower temperatures because the air is dryer (the humidity of saturation roughly doubles with every 10°C, droplets tend to lose moisture, virus particles...
@lalani_safina (2/n) and remain aloft longer. Or at least that is how it works with the flu. But if everyone is immunologically naive to the pathogen then transmission can remain high even in warm weather. This is, is I remember correctly, with the "Spanish" flu that started in Kansas...
@lalani_safina (3/n) during it's second wave. And it has been what we have been seeing so far with the SARS-CoV-2, which so far has shown less dependence upon the season. At the same time, there is another seasonal effect, one less dependent upon the absolute humidity: the extent...
Read 27 tweets
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
13 Jul
@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..."
Read 9 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

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