BA.2 continues to do its thing in Denmark. The two most recent days of sequencing (January 20 & 21) recorded 74.2% BA.2 (285 of 384 cases). 1/9
The exponential increase in the proportion of BA.2 cases continues in the UK.
The apparent slowdown in growth in the past several days is entirely due to 0 of 8 sequences being BA.2 over the past four days & should therefore be ignored. 2/9
Similar exponential increase in the percentage of BA.2 cases in the US.
Again, the illusory plunge over the last five days is entirely due to a very small number of sequences and should be ignored. 3/9
My home state of Indiana had recorded zero BA.2 cases before last night's update, when six cases were recorded in the most recent week of sequencing, indicating a substantial percentage of BA.2. Major caveat: sample size very small. 4/9
Germany's BA.2 path is similar to what Denmark's was early on. A recent report found that 30% of cases in Berlin were BA.2, so as has been the case elsewhere, large cities with lots of international travelers are leading the way. 5/9
Japan finally has enough BA.2 to provide a decent indication of it's path. Surprise!—it's upward.
(Once again, the tiny sample sizes in recent days mean the illusory plunge at the end should be ignored.) 6/9
Not much sequencing in Portugal, but in the most recent day of sequencing, which was two weeks ago, all eight cases sequenced were BA.2. 7/9
Spain, like Portugal, has poor genetic surveillance, but is seeing a similarly steep rise in BA.2.
Small sample size makes this a pretty unreliable estimate, however. 8/9
Most of the other countries whose graphs I posted in a previous BA.2 update have seen little change. Not much has changed in Sweden, but I'll include it here since it has among the highest level of BA.2 among countries with decent sequencing. 9/9
I was rushed when putting together this thread and made a mistake in the number of BA.2 cases recorded in Indiana. There have actually been 12 BA.2 sequences in the most recent 8 days of sequencing, not 6. This gives Indiana the highest percentage of BA.2 of any US state.
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After posting this, I realized that BA.2 has a ways to go before it reaches the transmissibility of foot and mouth disease, an airborne livestock illness. How contagious is foot and mouth disease? Well... 1/4
It has been known to spread through the air, from one farm to another, over distances of HUNDREDS OF KILOMETERS. You might think I'm joking. I'm not joking. 2/4 acp.copernicus.org/articles/3/210…
I haven't investigated this issue closely, but it's believed that foot and mouth disease from farms in Brittany, France, was carried by the wind across almost the entire English Channel and infected livestock on the Isle of Wight. 3/4 daera-ni.gov.uk/articles/foot-…
This woman was triple-vaccinated, by the way. As with Delta, people with breakthrough Omicron infections are approximately as infectious as unvaccinated cases and can be superspreaders. 2/5
Reminder that the CDC decision to shorten the isolation period was exactly backward: the peak infectious period with Omicron is several days later relative to symptom onset than with previous variants. 3/5
As Omicron has washed over the US, infecting perhaps 25% of the population already & likely to reach 40% by mid-February—see thread by @trvrb below—it has driven down almost all other respiratory pathogens, with one curious exception I’ll get to later. 1/9
This is not entirely unexpected. Viral infections trigger both innate and adaptive immune responses that can prevent infection by other viruses. Behavior changes likely contribute to this pattern as well. 2/9
There have been some claims that rhinovirus infection protects against SARS-CoV-2 infection. As you can see in the graph below, SARS-CoV-2 and RV prevalence seem almost perfectly inversely related in recent months. 3/9 news.yale.edu/2021/06/15/com…
No one seems to know what BA.2 means for the world. I'm not aware of any studies on it, but I hope they come out soon. It seems apparent BA.2 will become dominant everywhere before long—as it already has in Denmark.
🧵 of graphs comparing BA.1 & BA.2 in various countries
1/16
Of all the countries with decent genetic surveillance, Denmark has the highest proportion of BA.2. 2/16
According to the Outbreak numbers compiled using @GISAID data, January 12 was when BA.2 surpassed 50% of all cases in Denmark, with 480/955 cases. 3/16
2/6 They looked at 21 cases: 19 vaxxed, 2 unvaxxed, 17 symptomatic, 4 asymptomatic. For the symptomatic, viral loads (by PCR Ct value) were much higher on days 3-6 after symptom onset than days -1 to 2. Furthermore, many samples still had high viral loads on days 7-9.
3/6 This is very different than what we'd seen with previous variants. Studies by @LucaFerrettiEvo, @DiseaseEcology, & others showed that peak infectiousness previously occurred the day before symptom onset & fell fairly rapidly thereafter. medrxiv.org/content/10.110…
Hard to believe Walensky said this out loud—apparently intentionally.
I'm pretty sure if Trump had said this, all the major media would've been in an uproar for days or weeks—and rightfully so. Why is this not a major story? Has she apologized?
I thought this was a joke tweet, but I followed the link, and there it is, on page 5 of the CDC's 152-page list of "Conditions contributing to deaths involving COVID-19" through Dec 5, 2020: bird fancier's lung.
Reminder that there are people out there who have 4+ comorbidities entirely because they had Covid & never got better. If Omicron kills one of them, what fraction of a "healthy death" is their life worth?