Ryan Hisner Profile picture
Apr 22, 2021 17 tweets 7 min read Read on X
1/ The @nytimes has a good interactive story on the safety of flying during the pandemic, but they didn’t discuss boarding & deboarding. Judging by CO2 readings I saw on recent flights, this is the most dangerous part of flying. #covidco2 #COVIDisairborne
nytimes.com/interactive/20…
2/ By now there is overwhelming evidence #COVIDisAirborne. It’s transmitted mainly by shared air, i.e. inhaling the air others have exhaled, which contain aerosols—tiny, liquid particles that float suspended in air for seconds to hours, depending on size.
3/ There’s no easy way to measure virus levels in the air, but CO2 is a good proxy measure of risk. Outdoor CO2 levels are ~410 ppm, but since we exhale CO2, indoor concentrations are higher. The higher the CO2 level, the more air you’re sharing.
4/ I used an Aranet CO2 meter, which was tested & recommended by @jljcolorado, a top aerosol expert. I flew from Ft. Wayne, IN (FWA), to Rochester, MN (RST) with a layover at Chicago. FWA was not busy, & the CO2 ranged from 516 to 546 ppm.
5/ When we first sat down on the plane, the CO2 level was at 1424. Four minutes later, it was 1470. Over the course of the next 6 minutes, the CO2 concentration rose steadily.
6/ In the next four minutes, the CO2 level rose from 1654 ppm to 1899 to 2027 to 2255. Most IAQ experts, including @linseymarr, recommend keeping CO2 below 700 for a multitude of reasons.
7/ The next two pictures are quite blurry because the plane started to move, but you can tell the CO2 rose to 2343, then 2351 ppm.
8/ I think the ventilation system started bringing in outdoor air when the plane began taxiing but that it took a couple minutes for the CO2 to begin to decline. Two minutes after peaking at 2351 ppm, it had decreased to 2026, and two minutes after that it was 1738.
9/ By the time we took off the CO2 was around 1400 ppm, and it stayed right around that level for the entire flight.
10/ Chicago’s O’Hare Airport appeared to have quite good ventilation. The CO2 level stayed in the low-600 range where I was. I did not venture into the crowded cafeteria area nearby, where I imagine the levels were significantly higher.
11/ The next flight was to Rochester, MN, also on American Airlines. Immediately after boarding, the CO2 was already at 2096 ppm.
12/ Five minutes later, the CO2 concentration had risen to 2393 ppm, and in the next two minutes it rose further, to 2548 before peaking at 2650 ppm.
13/ At this point there was a revving noise, and CO2 levels started to decline, falling to 1820 ppm seven minutes later. 20 minutes after the peak 2650 reading, CO2 had declined to 1292 when we started taxiing.
14/ After taxiing for several minutes, we stopped. CO2 once again rose, but only to 1546, after which the plane started rolling again and levels declined.
15/ During this flight, which seemed equally crowded as the first flight and on a similarly small plane, CO2 concentrations were lower, ranging between 900-1030 ppm. Notably, relative humidity got as low as 12% later on in the flight.
16/ The Rochester Airport wasn’t very crowded, but with CO2 at 492 ppm, it still must have had good ventilation. Doors about 10 meters away likely helped.
17/ I’ll stop there for now. Later I’ll add info about the CO2 levels at Mayo Clinic and our hotel. Our return flights, again with a layover at O’Hare, are later today, and it will be interesting to see how they compare.

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More from @LongDesertTrain

May 31
An awesome preprint on the novel, unsung SARS-CoV-2 N* protein came out recently, authored by @corcoran_lab & Rory Mulloy. I’ve previously written on N*’s demise in XEC, the top variant in late 2024/early 2025. But…
1/34
…this preprint, along with another great study by the @DavidLVBauer, @theosanderson, @PeacockFlu & others prompted me to take a closer look...
2/34biorxiv.org/content/10.110…
...and for reasons I’ll describe below, I now believe rumors of N*’s death are exaggerated.

First, XEC is in terminal decline, replaced by variants with full N* expression, so N* is back in fashion.
3/34
journals.plos.org/plosbiology/ar…
Read 35 tweets
May 15
@DameSunshine @SharonBurnabyBC B.1.1.529 wasn't/isn't a real variant; it's a placeholder that represents a putative ancestor of BA.1/BA.2/BA.3.

Bad sequences and/or coinfections tend to get categorized as B.1.1.529:—they have enough Omicron muts to be ID'd as Omicron but so much dropout/mixed signals...
1/
@DameSunshine @SharonBurnabyBC ...that a specific designation isn't possible. Travel sequencing in the US is done by Ginkgo Bioworks. Their sequences are generally poor quality & they upload *pooled* sequences—against database guidelines. The B.1.1.529 here are likely low-quality/pooled sequences from GBW.
2/
@DameSunshine @SharonBurnabyBC I think it's entirely possible that a new, divergent variant will emerge this summer. There are hints with BA.3.2 & a 50-spike-mutation BQ.1.1 that has transmitted at least once. Other similar chronic infection-derived variants are undoubtedly lurking all over, unsequenced.... 3/
Read 4 tweets
May 2
Incredible how quickly @yunlong_cao & co provide us w/info on the latest emerging SARS-CoV-2 variants.

Already, we have great data on BA.3.2 (the divergent saltation lineage detected in South Africa & the Netherlands & NB.1.8.1, an emerging contender for global dominance. 1/9 Image
Image
BA.3.2 is a clear outlier on the antigenic cartography map—as expected given the enormous differences between its spike protein & every other circulating variant. 2/9
Image
It's unsurprising, therefore, that BA.3.2 evades antibodies from human sera more effectively than any other variant, though the degree of its superiority is striking. 3/9
biorxiv.org/content/10.110…Image
Read 9 tweets
Apr 25
About 1 month after this monster BQ.1.1 appeared, an even more extreme sequence has shown up in Alberta. Like the BQ, it has 50 private spike mutations, but it also has >40 AA mutations elsewhere in the genome. 1/6 Image
They include the full panoply of NSP3, NSP12, & N muts I've written about previously. ORF1a:S4398L is the most common mutation in the 4395-4398 region, this has ∆S4398, a rarity also seen in a few other extremely divergent seqs w/this constellation. 2/6 Image
In a theme that's become familiar, it's added two spike NTD glycans, N30 (via F32S) and N155 (via S155N+F157S).
Another chronic-infection leitmotif (first noted by @SolidEvidence): reversions to common or consensus residues in related Bat-CoVs, including SARS-1. 3/6 Image
Read 6 tweets
Apr 10
A fascinating SARS-CoV-2 sequence was recently uploaded—collected from a dog in Kazakhstan in July 2022.

Usher places the seq 1 nuc mut from the Wuhan ref seq—C21846T/S:T95I—i.e. pre-D614G. Could this seq somehow have a close connection to the first days of the pandemic?
1/19 Image
Of the sequences near this one on the tree, all are low-quality & clearly bad BA.1 or Delta sequences. The only genuine one is from the UK, collected April 2020. So it's likely even S:T95I was not inherited.

This sequence has several fascinating aspects. 2/ Image
(This all assumes the sequence is accurate and that C241T & C14408T (ORF1b:P314L) are genuinely absent. Its mutational characteristics make me certain this is a good sequence, though it's not impossible there's dropout not indicated hiding C241T and/or C14408T.) 3/
Read 19 tweets
Mar 12
Do you remember BA.3—the weakling cousin of BA.1 & BA.2 that seemed to take the worst from each & had weaker ACE2 binding than even the ancestral Wuhan Virus?

After 3 years, BA.3 is back.

And it is transmitting.

Who saw this coming?
1/13 Image
While the full extent of the new BA.3’s spread is not known, it’s been detected in 2 different South African regions through regular (not targeted) surveillance by @Dikeled61970012, @Tuliodna, & the invaluable South African virology community.
2/13
github.com/cov-lineages/p…
After nearly 3 years of intrahost evolution in a chronically infected person, the new BA.3 is almost unrecognizable. It has ~41 spike AA substitutions (4 of which are 2-nuc muts) to go with 14 AA deletions (∆136-147+∆243-244). We’ve seen nothing like this since 2023.
3/13 Image
Read 13 tweets

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