Mike Famulare
@famulare_mike
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Like polio, Twitter lingers on. Learning to be a father, husband, and person. Systems epidemiologist, see Google Scholar. All tweets mine alone.
Joined January 2020
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We lost.
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Apparently during the first wave 2020, in a meeting with a bunch of people, many I didn’t know, I blurted out “the idea that a respiratory virus with no population immunity doesn’t affect kids is the dumbest thing I ever heard.” I don’t remember this but my boss does. 😂
Data I was analysing on outbreak clusters from Victoria in late 2021 confirmed that schools were the source of far more clusters of cases than everywhere else combined.
Henry is right: improving ventilation in schools would have a big impact.
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The uncertainty around individual-level severity of
#Omicron
is shrinking. & what we're learning is, sadly, predictably, boring.
tl;dr: Omicron is probably about as severe as delta, or every other VOC. "Mild" is all but ruled out.
2 years & many "experts" have learned nothing
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Today’s exercise in cognitive dissonance is I’m the only person out of 200ish wearing a mask while watching talks at
#microaerosols24
@MicrobioSoc
while the CO2 in the room has more than doubled in the last hour and is still linearly increasing.
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The recent explosion in
#COVID19
cases and rising hospitalizations in WA is due to increasing prevalence in the community. Here's what we know about how many people are infected and what it means for your risk at Thanksgiving and other gatherings.
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MFW all the hot takes on SARS2, polio, transmission blocking, mucosal immunity, and community-level risk differences collide🤯
The story of polio epi today is the story of how mucosal vaccines and clean indoor air will together be transformative against respiratory infections.🧵
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If you’re in the Seattle area and want to treat yourself or a loved one to a delightful
#DavosSafe
afternoon at the spa, I heartily recommend
#ElaiaSpa
at the Hyatt Olive 8
@SeattleHyattFam
. Excellent services and facilities, in the best-ventilated business I’ve ever measured.
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I will never understand why this wasn't the default assumption three weeks ago. It's literally the Bayesian prior, and rational beliefs shouldn't be swayed much from it by weak data.
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This is great work. And one of my limitations as a thinker is I’ll never really understand why this was necessary. Filter effectiveness is like “bang rocks together make sound”-level physics.
It’s out! Our new state-of-the-science review of MASKS/RESPIRATORS in reducing transmission of respiratory infections. 13 authors (for our disciplines, see posts 3-4). 38000 words. 413 references. One conclusion: these devices work. For detail, read on. 1/
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@lukemunn
@prof_kozak
[Hidden curriculum] This is a feature from the committee’s POV. Since they often care more about who and where from than what said, having the social capital for recs from the “right people” shows you’re in the club. Not right, so I’m glad we don’t often ask for letters at IDM.
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But now I'm just tired. I'm signing off for a while after this couple-week burst of shouting into the void. Take care of yourself and your family. No one else will.
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@lisa_iannattone
The EVD-68 paralytic attack rate is roughly 100x lower than for polio, but otherwise this is a reasonable take. Regardless, this is yet another reason why we should be implementing universal programs to clean the damn indoor air.
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And so, back to expectations.
If
#Omicron
is like other VOCs in most ways, and differs mainly in breakthru and reinfection risk, then it's reasonable to expect it will be as severe in double-vaxxed and prior-infected people today as OG 2020 COVID was in unvaxxed people.
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But, we have to use them. Regulators and manufacturers have to move faster on vaccine updates and antiviral supply (as fast as it was, we have knowledge now to be faster). We have to get the tools to people everywhere. And we have to use NPIs to buy time again. And boost fast.
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As an interested amateur looking to learn about personal far UV-C as an infection prevention tool, I did some playing with the 222nm irradiance data from the UV Can Lily from
@joeyfox85
. For those interested in learning along with me, here are notes:
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If
#Omicron
plays out as is looking likely, it's probably telling us there's no going "back to normal" without sanitizing our indoor air. Ventilation and filtration for the long haul. Restructuring our built environment, changing regulations, investment.
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@EpiEllie
How much transmission is due to pre- & asymptomatic shedders today, now that most people are immunized. In 2020, peak viral loads typically preceded symptoms, but now symptoms typically start before peak viral load. This has implications for every safety and high-risk people.
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Friday night at the grocery store. Aboout 60% masked and relaxed. Found the cool kids. 😎
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Are we planning to roll back gloves, biohazard waste disposal, and sterilized equipment too? Healthcare-acquired infections should’ve been scandalous before the pandemic and are now very obviously unnecessary.
@WADeptHealth
should use its authority to lead permanent improvement.
Effective April 3, the Washington State Department of Health (DOH) will end the Secretary of Health Mask Order, which currently requires universal masking in healthcare, long-term care, and adult correctional facilities for people age 5+.
Read more at
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Doors open to get cross-ventilation in the room has been a staggering success!
Thank you to the pros who heard the data and responded.
#microaerosols24
@MicrobioSoc
Leadership is on it, although not sure there is much to do for the room. 🤞🏻
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Since this got a lot more attention than my usual stuff, I should add my boss is cool with it. Only brought it up once, like 3 years later. Just couldn’t not let me know he remembered. He’s one if the good ones.
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The first individual-level analysis from the UK, by
@neil_ferguson
@MRC_Outbreak
, adjusting for age, prior infection & vax, sample day, etc is out today. They find the adjusted odds ratio of hospitalization with Omicron vs mostly delta is 0.95 (0.61-1.47).
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Should we expect that we're back to the beginning?
Ooof I hope not but I'm worried.
We have new, awesome tools like antivirals that work, vaccines we can update quickly that are among the best vaccines ever developed against any disease, and NPI strategies we know work. But...
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What does 1% prevalence in WA on Thanksgiving Day mean? 76 thousand people with COVID. Between 25 to 40 thousand people who won’t yet know they are sick bringing
#COVID19
to dinner. 450 people carrying infections on Thanksgiving Day alone that will be dead by New Year’s.
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If 1% - 1 in 100 - sounds low to you, I ask how big is your group? Each person adds more risk. On average in WA, if you have dinner with 15 people, the risk of at least one bringing COVID is around 15% - 1 in 6. The same odds of catching a bullet in Russian roulette.
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@DaniBeckman
@RickABright
@davidalim
@US_FDA
Not constructive but having been closer to your side on polio and Covid, some dinosaur once-scientist bureaucrat head of a govt lab is poo-pooing this because it wasn’t invented in-house, and the lab hand who gets what you’re saying has no budget or autonomy to act on it.
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If the expectations I laid out prove roughly correct, then will need to do the first part of 2020 over again, and then the first part of 2021 over again, but better this time.
Should we expect that to happen too???
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Combine 5x reduction in airborne viral load with a 5x reduction from mucosal vaccines and R0=10ish turns into Re=0.4ish. That's a pathogen that only circulates when either vaccination isn't happening or your clean air infrastructure fails. JUST LIKE WHAT HAPPENED TO POLIO.
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@ajordannafa
As physicists say, “a tensor is thing that transforms like a tensor.” Which is to say, tensors come with rules of how it changes under coordinate transformations. A tensor can be represented as a multidimensional array in a particular coordinate system.
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If we change our behavior to stop transmission as effectively as we did in late March, we can turn this around and avoid record-shattering hospitalization, death, and chronic
#LongCovid
.
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Which is to say, basically the same intrinsic severity as delta and entirely within the range of every other VOC we've seen the last 12 months.
It's looking like
#Omicron
is in fact a SARS-CoV-2 VOC, with epidemiology similar to other VOC. Imagine that?
First, the whole class of Variants of Concern (VOCs) and many Variants of Interest are more severe relative to OG 2020 SARS-CoV-2 and its many non-VOC descendants.
(, data from
@WADeptHealth
in collab with
@paredesmig
@trvrb
and others).
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@covidsafenetwrk
Seattle: dentist James Swanson DDS all staff masked and spaces well-ventilated and with HEPA
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First, the whole class of Variants of Concern (VOCs) and many Variants of Interest are more severe relative to OG 2020 SARS-CoV-2 and its many non-VOC descendants.
(, data from
@WADeptHealth
in collab with
@paredesmig
@trvrb
and others).
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I really hope these expectations prove pessimistic, but it's unreasonable to think anything different at this point.
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I started this thread angry about how misleading the "mild"
#Omicron
dialogue has been. & that the data are pointing to the fact that taking seriously what we have learned in the last two years may just help guess what's coming. & that bs experts are killing people yet again.
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@HannahPosted
Plus points for teaching everyone in the house a new fruit name (xigua). Minus points for that fruit being a watermelon.
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Vaccines are only one part of the solution. Only one part! I’m not even talking “lockdowns” although I think they’re worth it if the medical system will collapse. Ship everyone better masks! Ship rapid tests! Support paid sick leave! Infrastructure?? Clean the fucking indoor air.
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As RSV appears to have peaked on average in the US, I thought it would be useful to put this nasty season in context with the pre-COVID past. 🧵
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Great to see estimates of the prevalence of chronic SARS2 from scientists working with the remarkable UK
@ONS
Covid infection Survey. Chronic prevalence (>60 days) was at least 0.1-0.5% in people infected before July 2022 (thru BA.1/2).
Gonna use this moment to grind an axe...🧵
Our paper on persistent SARS-CoV-2 infections (PIs) is now published in
@Nature
!
Some key findings:
- PIs are much more common than we thought
- PIs are associated with higher odds of long COVID
- Reinfections with genetically similar viruses are rare
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Tagging some folks with wider audiences.
@trvrb
@BristOliver
@kallmemeg
@SACEMAdirector
@Tuliodna
@BallouxFrancois
@jbloom_lab
@michaelzlin
@michaelmina_lab
@florian_krammer
@EricTopol
If you found this helpful, please retweet. I'm not seeing this specific discussion elsewhere.
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@YouAreLobbyLud
Lol. We’ve got the office ventilation cranked way up (❤️❤️❤️) but it works thru lots of little vents. So I carry around my CO2 meter and complain to Facilities when I find a bad room and check that they fixed it. Going for sub-600 ppm!
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I want to say more about vaccine efficacy against severe
#COVID19
during breakthru infections. Modeler, not immunologist, so sticking to stats from trials...
tl;dr: severe efficacy given breakthru is ~independent of antibody titer and only ~60%.
Related
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This is psychotic. We talked 25th amendment for the last guy, and I don’t see a damn difference here!
Biden flat out said in his remarks today that unvaccinated people will “soon overwhelm” hospitals. Somehow boosters let us keep businesses open and “protect our economic recovery.”
He encourages shopping while noting only 60 million have had a booster.
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It’s in our control. Stay apart. Quarantine beforehand if you must gather. Always mask. Stay outside. Ventilate. Discuss risk beforehand to get past feeling shy about safety. We have the power to save lives this Thanksgiving and every day to come.
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Embarrassing for
@USDA
that it was necessary to rip metadata off a YouTube screenshot, but great work for the public to spot it and snag it.
Important update on metadata of H5N1 in cattle (and back to birds):
Thanks to the extraordinary detective skills of
@flodebarre
, we are pleased to be able to share this table containing locations and dates for several H5N1 cases in cattle and birds:
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@POTUS
Biden is choosing to do nothing—no good masks, no paid leave, no rapid tests, no isolation help—while tens of millions he’s sworn to protect get infected, at least another 100k die, and frontline workers collapse, before the one option he supports will reach half of us.
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You realize we could’ve learned something the last four years and acted under CDC leadership, right? I’d like to think we still could, but CDC is clearly irredeemably broken.
Many of us outside but adjacent knew it was rotting before 2020, but this isn’t salvageable.
If you get sick with a respiratory virus, stay home and away from others. You can return to normal activities when symptoms have been getting better overall for 24 hours, but take precaution for the next 5 days to curb the spread of illness.
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Maybe your group is extra safe. Hopefully our estimate will prove too pessimistic. But 25-40 thousand will likely have COVID on Thanksgiving and not yet know it. Only by quarantining for 14 days beforehand can you be sure you aren't one of them.
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While
#Omicron
could be better or worse, with its delta-like and (beyond)-beta-like features, I expect it is at least 2.4x more severe upon infection than 2020 SARS-CoV-2. And honestly, 6x wouldn't totally surprise me if delta-like and beta-like effects are independent.
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What breaks my heart is how incredibly predictable not only the data are, but the dialogue. In 2 years, we've learned a ton about SARS-CoV-2 severity. While we haven't seen everything that might happen, it's reasonable to expect the next VOC isn't totally different than the last
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As protective antibody levels get low, infection protection goes to zero and efficacy against severe disease plateaus around 60% (and this looks the same for vaxx type and prior infection).
So, without infection protection, vax reduces severe disease risk to 0.4x of unvax risk.
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& it's the best so far but not the only analysis showing the same thing. Predicting hospitalizations from lagged cases, an idea that often works reasonably well, shows UK Omicron is either a bit more severe than Delta or hospitalizing people a bit faster.
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From cases, hospitalizations, and deaths, we use math modeling to estimate the number of people infected – the prevalence – in WA over time. Prevalence is rising quickly, roughly equal to the March peak as of Nov 6, and will hit 1% by Thanksgiving if we don’t stop it.
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We do know for sure that more antibodies are better. And so I am hopeful that people who have received boosters (or are vaccinated after surviving infection) will retain some infection protection against
#Omicron
.
But most of the world has no booster access at all.
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But sitting here watching talks? How embarrassing would it be to get sick at an aerosols and microbiology conference?! 🤦🏻♂️
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This is psychotic. What the fuck did we fight for? Scientists like me spent the last 24 months figuring out the solutions while everyone else made sacrifices big and small to buy time or suffer and too often die for the rest of our benefits. And now we’re not gonna use the tools?
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The biggest wildcard for me is boosters. Since we don't yet know how much lower
#Omicron
antibody titers will be compared to prior VOCs, I don't have good expectations for how much boosters will help and for how long.
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@SolidEvidence
You’re finding numbers similar to an adult who sheds a few hundred grams of stool per day having a completely unmitigated poliovirus infection.Asymptomatic is the norm there, so this must be doing something similar. Remarkable adaptation for SARS2 though!
@LongDesertTrain
Many papers, but shamelessly choosing one of mine, , viral loads have a huge range, from as low as 1000 copies per gram of stool in the OPV-vaccinated to 100 billion copies per gram In unvaccinated infants, with a billion copies per gram common. …
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If you and your contacts haven’t quarantined and must still get together, bundle up and stay outside. Mask up, even at the table except when physically impossible. Clear out the room, open the windows, turn on the fan. Come only for dessert and don’t stay too long.
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This is why we need to make changes again. Close high-risk commercial settings even though that causes economic distress. Eliminate social gatherings with people outside our homes when we can and always take safety measures when we can’t, even when they feel awkward.
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This also tells me it's really stupid to stop trying to reduce the spread of infectious diseases. We know a lot about stopping airborne transmission, and much non-intrusive. We know to better ventilate and filter indoor air. We can wear masks strategically, like RIGHT NOW.
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@96Henrique
@JoePostingg
This is NY boomer republicans in a nutshell. In 2007, I did an experiment with my dad once where I avoided every buzzword I could think of as we talked politics. Befitting his environment and experience, he was to the left of Obama on a bunch of stuff (especially public goods).
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Like, these people know a lot more about aerobiology than I do, so one might argue I’m the crazy one. But I’m literally watching talks about bioaersol stability that discusses specifically how this is not a great environment. Bizarre.
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Yes, the
@MRC_Outbreak
analysis has limitations. Only 24 Omi hospitalizations & the method probably under-estimates hospitalizations that haven't happened yet (which would be worse). But it adjusts for age & immunity & is based in a pop that reliably shows reproducible results.
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Anyway, of course we have to wait for more data and more careful analyses to pin down the individual-level severity of
#Omicron
. But the evidence to date rules out any reasonable definition of "mild". It's probably about as severe as delta, and at best, it's 2019-nCoV.
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Thanks to
@niket_h_thakkar
for leading the modeling and our colleagues at
@WADeptHealth
for data support and discussion on all things WA COVID epi. h/t
@trvrb
@nataliexdean
,
@dr_izzo
and
#epitwitter
for sci-comm inspiration!
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For example, in the tweet above, in Washington state, we found delta is ~2.4x more likely to put an infected person in the hospital than the old non-VOC
#COVID19
and beta and gamma ~3.1x more severe. Others in the UK, South Africa, Brazil, etc have found similar.
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This simple analysis doesn't adjust for age or vaccination, but also doesn't support the idea that Omicron is much milder.
Others see the same thing. Similar quick & dirty analysis across different lags shows Omi as severe as Delta in Denmark.
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Okay, but what about prior immunity from vaccination and infection?
Expectations:
#Omicron
is probably the best at escaping antibodies of everything so far. This is both likely from the molecular bio and reinfection data in RSA .
[Thread] We have updated our preprint on SARS-CoV-2 reinfection trends in South Africa to include data through late November.
@hivepi
@jd_mathbio
@carivs
@Dr_Groome
@nicd_sa
#SACEMA
#notyetpeerreviewed
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Overall, we saw that the severity of breakthru infections in full-vax with pre-Omicron VOCs was similar to that in unvaxx with OG 2020 SARS-CoV-2. How does this make sense?
The VOCs were 1.7-3.1x worse, and vax 0.4x as severe, so overall breakthru severity is 0.7-1.3x original.
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@phealthsean
@micah_arsham
Honestly, the premise of a schedule here is flawed, other than “no less than 2 months apart.” There’s huge heterogeneity in exposure, so people’s needs vary. I wish they’d take the same “you do you” approach they’ve forced on us with masks and let adults choose for themselves.
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The second biggest wildcard is transmissibility in different populations. I was hoping that Omicron might fizzle outside southern Africa like beta mostly did, but that is looking less likely today. Rapid increase in the UK too (different immune background)
COVID-19 surveillance, England. The most recent 5 days (to 28 Nov) show an increase in S gene target failure in community testing data. An explainer follows. 🧵
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Thanksgiving isn't special in this regard. The same considerations always apply until we’re all vaccinated and can move on from this waking nightmare. The bigger the group, and more often they meet, the bigger the risk.
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I'm gonna stick my neck out and say I see evidence that the current vaccines produce less durable immunity against Omi than Delta, beyond the baseline efficacy difference. NAbs 1 month post-boost can't show the signal. We have to look ahead when thinking about vaccine updates.🧵
@kallmemeg
@UKHSA
Could you produce and share this plot with a logit y-axis? I ask because there's a hint that waning against distant variants (omi, beta) is faster than for more closely matched strains (WT, delta). Is omicron VE falling at a faster rate than delta VE?
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So far, the data for Omicron are sadly, boringly consistent with that. Omicron severity looks like every other VOC -- too damn high.
While
#Omicron
could be better or worse, with its delta-like and (beyond)-beta-like features, I expect it is at least 2.4x more severe upon infection than 2020 SARS-CoV-2. And honestly, 6x wouldn't totally surprise me if delta-like and beta-like effects are independent.
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The first germ theory revolution literally lifted our cities and has brought billions of dollars of effort toward improving water, garbage, and sewage handling throughout the world today. COVID is telling us it's time to stop ignoring the air.
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Since neutralizing antibody concentration predicts vaccine efficacy, we can expect
#Omicron
to move us to the left to worse efficacy on the graphs below.
( with
@jacohe
@michaelwhite_36
and others, but see also well-known sources
)
-lots of folks pre-judging studies underway of neutralizing antibodies as not very valuable, despite strong data linking neutralizing antibodies to efficacy of vaccines (; )
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But I feel confident enough now that if you get Omicron, vaccinated or not, it's not gonna be that much more "mild" than delta or alpha or beta or 2019-nCoV original, relative to your vaccinated status or not.
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My heart hurts so much. I’m so sad. I don’t like to show performative rage in public but I can’t just keep this in tonight. So I’m shouting into the void, and leaving to spend time with my wife since I’m lucky and privileged to be shouting instead of dying.
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But also sad, boring, and lethal is the conversation that took place among so many "experts" about how exciting it is that Omicron looks "mild." What were the 3 most obvious biases affecting early estimates of severity?
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So yeah, this quick cut at the data is consistent with RSV returning to the pre-COVID normal, and the pre-COVID normal is dumb and we should pursue the post-COVID normal.
Please join me in bringing about a better future!
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Rental car counter only had a Volvo XC90 to give me last week. It had a Clean Air menu! Built-in filtration system with indoor and outdoor particle counters and a screen that shows you the data.
Forest fires 🤝 pandemics
Well, the upper end of society is beginning to take notice and make adjustments.
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1) Growth rate and the delay between infections and bad outcomes. This biases raw comparisons of cases and hospitalizations low. If you're interviewing an expert that doesn't get this, they aren't an expert.
@paulmromer
@TWenseleers
@trvrb
Yes, it is possible to do this right, as some of us did in Feb 2020 , , and as understood in the before-times.
But people who know better are still ignoring this. I don’t know why, but so many bloody hands.
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On a plane during boarding. How clean is the air on this plane?
Great for particles, despite CO2 and lots of HCHO.
The HEPA filtration is working great, but I’m surrounded by big engines and lots of people.
With a v-flex and the filtered air blowing on my face, I feel safe.
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Good thread on antiviral nasal sprays. The evidence for prophylactic effect is very weak, but also side effect risk is all but negligible. So, we burn disposable income on enovid for high-risk situations, but I rarely discuss these since I won’t be surprised if they’re useless.🧵
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Data on breakthru infections with VOCs supports this inference from vax trials. Given infection, we saw that the risk of hospitalization among confirmed, fully vaxxed (2-dose mRNA or J&J) cases was 0.36x that of the unvaccinated. This did not depend on VOC
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@gothspiderbitch
I'm convinced this is the start of a novel in which you become obsessed with it until you try to destroy it or it destroys you 😮
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Reasonable analysis of the COVID reinfection rate. Uncontrolled spread has infected the average person once a year.
Annual all-ages reinfection is unprecedented for a single viral pathogen. SARS2 remains the nastiest of the bunch. This is a permanent hit to human flourishing.
Lets just be really clear about this.
When we look at population level, COVID is *not* infecting people 2 to 3 times per year or more, it has *never* infected people 2-3 times per year or more, nor is it going to.
We have *evidence* for this.
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Leaving the WA
#COVID19
beat for a moment and looking nationally, remember that no matter how out of control your local epidemic is, hunkering down tight will not only stop the growth but prevent infections long after loosening up again. How do we know? Snow in Seattle taught us!
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Clean air and mucosal vaccines working together is also more tolerant to the transient failure of either one. Say a new variant pops up and infection-blocking immunity goes to zero. We still have Re=2ish and very low prevalence. That gives more time to update vaccines. Better.
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@LongDesertTrain
I don’t have the energy for a detailed thread, but there’s a lot of parallels in polio. Immunocompromised people can shed OPV symptom-free for years. and their viruses (call iVDPV, for immunocompromised vax-derived poliovirus) are often found in sewers.
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3) Age of infected. For those looking at South Africa from the USA or UK, it's a younger country, and so raw hospitalization rates will be lower. Within the UK, the early Omicron cases are younger than average. Proper stats adjust for this. Experts know to do the stats.
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2) Prior immunity. Most people are immunized now, one way or another. Immunity in breakthru infections reduces severe outcomes by roughly a factor of 3, and this seems to hold across variants. This can be known from pre-Omicron data. Experts should know.
Data on breakthru infections with VOCs supports this inference from vax trials. Given infection, we saw that the risk of hospitalization among confirmed, fully vaxxed (2-dose mRNA or J&J) cases was 0.36x that of the unvaccinated. This did not depend on VOC
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Not to mention, Omicron raw case-hospitalization rate vs delta is only ~2x lower despite very different growth rates. After 2 years, we all know fast growth biases raw CHR down, yes? And factor of 2 isn't "mild", it's 2019-nCoV.
Faster growth gives negative bias to naive estimate of omicron severity. Using recent rates of growth from
@trvrb
and
@twenseleers
, the bias is by an order of magnitude.
This graph gives a qualitative explanation. Blog post calculates the numbers.
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Close reporting on H5N1.
Why do I think this article is worth promoting? It’s for the industry—written to inform people with skin in the game and who know their cows and farms well. Strong incentives for honest reporting.
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