"Vitat in vitro sed non evadit in vivo."
Moving most of my activity over to Blue. I will continue to monitor my account on TwiXter & occasionally respond
Mar 25 • 13 tweets • 5 min read
12-1/ My pathogen update for epi weeks 11-12 of 2025. The XEC COVID wave hasn't fully receded yet. Biobot shows that as of March 15, SARS2 wastewater levels haven't fallen to previous interwave gaps except for the Western region of the US.
12-2/ The CDC's ww numbers indicate a long tail for this wave, but it shows the West and NE back to interwave levels. These numbers are all normalized to the previous year's numbers, so I don't know if this long tail may be an artifact of the way they normalize. I trust Biobot.
Mar 11 • 13 tweets • 7 min read
10-1/ My pathogen update for epi weeks 9-10 of 2025. I'm renaming this a "pathogen update" because SARS-CoV-2 is fading into endemicity. That doesn't mean that COVID-19 won't remain a public health problem, but we've got a bunch of other pathogens that we need to keep our eye on.
10-2/ But speaking of COVID-19, the current wave is receding. Both the CDC's wastewater activity levels and Biobot's wastewater concentration chart show a downward trend in all regions of the US,
Feb 24 • 13 tweets • 5 min read
8-1/ My COVID update for epidemiological weeks 7-8 of 2025.
The current COVID wave continues to be the mildest in terms of hospitalizations and mortality since the pandemic began. And it doesn't look like LP.8.1 will break out to boost the current XEC wave.
8-2/ The CDC's wastewater survey shows SARS2 numbers are trending downward in all regions except the Midwest. Note: The CDC normalizes these against the previous year, so they don't give us absolute concentrations. Biobot does, but they haven't published an update in past 2 wks.
Feb 11 • 11 tweets • 5 min read
6-1/ My COVID update for epidemiological weeks 5-6 of 2025.
Biobot's latest wastewater numbers indicate the current XEC wave has receded a bit—but we might see a secondary bump as the numbers level off in West and Midwest, and climb a bit in the South.
6-2/ As US COVID waves go, wastewater numbers indicate this has been on the low side, but we don't really know if the viral shedding of JN.1 and its descendants has remained consistent with previous variants.
Jan 27 • 13 tweets • 5 min read
4-1/ My COVID update for epidemiological weeks 3-4 of 2025.
For the 1st time since 1952, the CDC stopped publishing its Morbidity and Mortality Weekly Report (MMRW)—the last update was on 16 Jan. Is the Trump administration emulating Chinese secrecy practices?
4-2/ Other CDC data pages seem to be up and running, though. Their wastewater numbers seem to indicate the current XEC COVID wave has peaked. Biobot hasn't published an update recently, so I don't have a reality check for CDC's data.
Jan 14 • 12 tweets • 5 min read
2-1/ Happy New Epidemiological Year! This is my COVID update for epidemiological weeks 1-2 of 2025.
Biobot shows wastewater concentrations rising steeply in the South and Midwest. 5 weeks into this wave nat'l ww concentrations have risen at ~2x rate of the previous KP.3x wave.
2-2/ CDC's ww graph shows a higher rise in the Midwest and less so in the South. Of course, the CDC normalizes its numbers against the previous year, so these are relative numbers—not avg SARS2/PMMoV concentrations in CpmL units. Biobot methodology seems more straightforward.
Dec 29, 2024 • 23 tweets • 10 min read
52-1/ COVID update for epidemiological weeks 51-52 of 2024.
Here we go again! National SARS2 wastewater numbers are climbing quickly, especially in the NE and Midwest.
52-2/ Of the big 3 respiratory viruses (per CDC), COVID still trails RSV and influenza in test positivity, but has now passed RSV in the number of ED visits.
Dec 17, 2024 • 16 tweets • 7 min read
50-1/ COVID update for epidemiological weeks 49-50 of 2024.
As of a week ago (epi week 49), COVID joined Influenza and RSV as a URTI that shows an upward trend in ED visits.
50-2/ The folks at Biobot haven't posted an update for two weeks, so I don't have any good aggregate wastewater numbers for the US (b/c the CDC doesn't publish nat'l data in CpmL units). So, let's zoom in on what's happening in some big city sewersheds. NY State first...
Dec 2, 2024 • 16 tweets • 5 min read
48-1/ COVID update for epidemiological weeks 47-48 of 2024—but since this is the season of URT infections, and COVID-19 is on hiatus, this week's update will also look at the other respiratory viruses that are making us sick at the moment.
48-2/ Today is the fifth anniversary of the COVID-19 pandemic. The symptoms of patient zero, a 55-year-old male, began on 1 December 2019. He wasn't hospitalized until the following 8 Dec. But by the end of Dec, 41 people were hospitalized with a novel form of pneumonia.
Nov 19, 2024 • 26 tweets • 10 min read
46-1/ COVID update for epidemiological weeks 45-46 of 2024.
I wanted to move these updates over to the blue skies beyond Muskland, but ThreadReader doesn't work over there yet. Also, I bookmark a lot of interesting posts, but that's not a feature over there. So here we go...
46-2/ COVID wastewater numbers remain low, but SARS2 is still circulating. XEC's growth rate has plateaued in the US (and it might be dropping), so I don't think the next wave will be an XEC.x wave. But...
Nov 4, 2024 • 34 tweets • 12 min read
44-1/ COVID update for epidemiological weeks 43-44 of 2024.
National COVID wastewater numbers dropped fast, but have probably leveled out. From the 1 Nov Biobot report...
44-2/ I'll point out again: COVID interwave ww concentrations are order of magnitude higher than flu and RSV ww concentrations (peak Flu A is that little red X under COVID)—perhaps due to differences in their viral shedding? But SARS2 is always circulating relatively high levels.
Oct 22, 2024 • 12 tweets • 6 min read
42-1/ COVID update for epidemiological weeks 41-42 of 2024.
COVID is down down down—at least in the US. And my bad, Biobot hasn't switched to a monthly report. They still seem to be reporting weekly. My neuro-atypical mind missed the dropdown report menu button.
42-2/ COVID ED visits are following the downward wastewater trend. Although there may be delays in tabulation, weekly deaths (per 100k) may clock in at the lowest any time since the start of the pandemic. Hospitalizations dropping, too.
Oct 7, 2024 • 33 tweets • 12 min read
40-1/ COVID update for epidemiological weeks 37-40 of 2024. Note: I skipped my last biweekly update for personal reasons. This will summarize the past month of COVID activity—plus some updates on H5N1 and some other pathogens of concern.
So, back to the COVID data mines...
40-2/ The KP.3.x wave is receding. Biobot released their update for September (I guess they're only publishing monthly updates now). Their data indicates that the SARS2 wastewater activity is still high but falling. However...
Sep 10, 2024 • 15 tweets • 7 min read
36-1/ COVID update for epidemiological weeks 35-36 of 2024.
Biobot hasn't released a new report in 4 wks. I'll use the CDC wastewater chart even though I think it runs "hot" compared to Biobot. With the exception of the Midwest the KP wave peaked the 1st or 2nd week of Aug.
36-2/ ED visits seem to have peaked as well—although the 5-17 age cohort is lagging other age groups—probably due to the opening of schools across the US. But crude death rate rose to .3/100K the 3rd week of August. They may be dropping now (or not yet).
Aug 26, 2024 • 15 tweets • 7 min read
34-1/ COVID update for epidemiological weeks 33-34 of 2024.
Were the Paris Olympics a superspreader event? Lots of claims that it was—but I can't find any data to support this. As of week 33 France's Sentinelles network shows Paris region's cases falling for last 8 weeks.
34-2/ O/c, Sentinelle tracks aggregated ARI numbers—COVID isn't broken out of the stats—but if COVID cases had increased due to the Olympics, they weren't high enough to impact the overall ARI numbers. Worth noting that the summer KP.x wave seems to have minimally affected FR.
Aug 13, 2024 • 16 tweets • 5 min read
32-1/ COVID update for epidemiological weeks 31-32 of 2024.
Both Biobot and CDC wastewater numbers indicate the current wave is still on the rise, but looking at some cities it seems to have passed its peak (next slide)...
32-2/ For instance, NYC's (Manhattan's) wave started late, showed a sharp upward trend, and now it's dropping off quickly. Boston's wave started earlier, and was less pronounced, but it's dropping off...
Jul 29, 2024 • 17 tweets • 7 min read
30-1/ COVID update for epidemiological weeks 29-30 of 2024.
COVID wastewater numbers are still rising at a steady rate. CDC's wastewater chart shows more significant rise than Biobot, but (as I said before) I don't really trust the CDC's methodology and lack of transparency.
30-2/ The current wave is manifesting itself unevenly across different sewersheds. For instance, San Jose shows the current wave as big as the last one, but 40 miles up the road, Oakland doesn't show much of wave at all...
Dec 25, 2023 • 13 tweets • 6 min read
51-1/ Summary of COVID trends as of epidemiological weeks 50 & 51.
Wastewater numbers continue to rise. Biobot and CDC agree (but I suspect they're using the same sewersheds for their data). OTOH, before we freak out, we should zoom out...
51-2/ This wave is shaping up to surpass, the BQ.1 wave at the end of last year. But despite JN.1's immune evasiveness (at least in vitro) and ACE2 binding scores (at least in vitro) which are lightyears beyond Omicron, it's not another Omicron. Zooming out...
Dec 10, 2023 • 20 tweets • 8 min read
49-1/ Summary of COVID trends as of epidemiological weeks 48 & 49.
Biobot shows our wastewater numbers are climbing quickly, indicating a rapid spread of the virus (probably all due to JN.1). NE and Midwest showing the largest increases.
49-2/ CDC's NWSS says the same w/ Midwest having highest ww activity. Biobot and NWSS numbers are 10-14 days old. We probably haven't reached BQ.1 territory, yet, but soon will.
Sep 30, 2023 • 52 tweets • 21 min read
39-1/ Summary of COVID trends as of Epidemiological Weeks 38-39. Good news—the current wave in the US has definitely peaked and is starting to drop off. Biobot wastewater shows a sharp drop-off in 3 out of 4 regions—and 4th, the NE US, is starting to drop, too...
39-2/ Emergency Department visits are falling. Hospitalizations may trail the ED curve by a week or two, but they seem to have peaked as well...
Sep 16, 2023 • 15 tweets • 7 min read
37-1/ Summary of COVID trends as of Epidemiological Weeks 36-37. This week's update will be brief because I'm traveling. The main question on my mind is has the current wave peaked, yet? Nat'l wastewater avgs have dropped off 12% in last 2 weeks.
37-2/ Midwest still climbing, but the South—where case rates were 2x higher than the rest of the US 3-4 weeks ago—has the sharpest drop in wastewater numbers. The CDC's ww percent change category chart shows things leveling off, too. I never found that metric useful because…