Platystemon posted:

Morbus slipping on taxonomy.

Sad!

icantfindaname posted:

I had to do crimes to get novavax, last I checked you're only eligible if you are unvaccinated, they won't give it to you after an mrna, at least in the USA

Snowglobe of Doom posted:

Technically the advice is the same here in Australia but when I was booking my most recent shot online I picked Novavax anyway and the pharmacist who administered it didn't care, he just slammed it right into my arm

DickParasite posted:

Nicotine feels amazing tho

HidaO-Win posted:

Anyone have the link to the excel sheet of best performing air purifiers? I’ve gotten permission to buy some for my classrooms and we have a limited number of vendors I can go through, so I want some stats to base my choices on.

Thanks in advance.

Oracle posted:

I believe here has everything you’re looking for.

https://www.thelocal.it/20230911/italys-schools-warned-to-avoid-gatherings-as-covid-cases-rise posted:

Italy’s schools warned to ‘avoid gatherings’ as Covid cases rise
As Italy’s new school year began, masks and hand sanitiser were distributed in schools and staff were asked to prevent gatherings to help stem an increase in Covid infections.

Pupils returned to school in many parts of Italy on Monday and authorities said they were distributing masks and hand sanitiser amid a post-summer increase in the number of recorded cases of Covid–19.

"The advice coming from principals, teachers and janitors is to avoid gatherings of students, especially in these first days of school,” Mario Rusconi, head of Italy’s Principals' Association, told Rai news on Monday.

He added that local authorities in many areas were distributing masks and hand sanitizer to schools who had requested them.

"The use of personal protective equipment is recommended for teachers and students who are vulnerable,” he said, confirming that “use is not mandatory.”
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Recorded cases of Covid have increased in most Italian regions over the past three weeks, along with rates of hospitalisation and admittance to intensive care, as much of the country returns to school and work following the summer holidays.
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https://www.euronews.com/next/2023/09/11/covid-19-should-we-fear-a-new-wave posted:

COVID: Should we fear a new winter wave of infections and hospitalisations?
Since mid-July, Europe has been experiencing a resurgence in cases of COVID due in part to the emergence of new variants.
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In 16 of the 21 countries analysed, an increase in case rates was observed, particularly among people aged 80 and over.
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According to Quique Bassat, an epidemiologist and researcher at ISGlobal and ICREA, "over the last few months, during the summer, we have seen an increase in the transmission of COVID-19 in several European countries.

"In Spain, for example, we have seen a significant increase in transmission and a rise in hospitalisations linked to COVID-19. This is attributed to the emergence of new variants, which are more contagious than previous ones".

The epidemiologist also added that "every week, a new sub-variant seems to emerge, appearing more dangerous or even more contagious than the previous ones".
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"If we add to these viruses the burden of COVID-19, the healthcare system is put under severe strain. And when it's under strain, it suffers. That's what we all fear".
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"We need to adopt a cautious attitude, using common sense, without giving into paranoia about the risks of COVID-19. I think we should persevere with the good practices we have adopted over the last 12 months, namely maintaining our vigilance and constant monitoring of developments in the situation", added the expert.
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https://www.stltoday.com/news/local...8d8c7055fb.html posted:

CDC faces dilemma over recommending a new COVID booster for all

A small percentage of Americans got the most recent COVID-19 booster shot, and even fewer probably realize the federal government is preparing to recommend yet another shot as early as Tuesday.

Until a week or two ago, William Schaffner read that indifference as a sign the Centers for Disease Control and Prevention should advocate vaccinating only those most at risk from the virus.

But then Schaffner, an infectious disease specialist at Vanderbilt University Medical Center, changed his mind.

Members of the CDC’s Advisory Committee on Immunization Practices won him over to the argument that the vaccine be recommended for all Americans above 6 months of age, he said in an interview. The committee, which sets U.S. vaccination policy and helps determine insurance coverage for vaccines, will vote on the question Tuesday as it weighs the benefits of updated vaccines from Pfizer, Moderna, and Novavax.

Not all vaccine experts see it quite as Schaffner, a nonvoting liaison representative to the ACIP, does.

“I don’t plan to get it myself,” said Paul Offit, 72, the director of the Vaccine Education Center at Children’s Hospital of Philadelphia. He’s had two boosters and got COVID last year. Another vaccine might increase his protection against mild infection for a few months, but like most Americans’ immune systems, his is already familiar enough with the virus to protect him from serious disease, Offit believes.

Some of Schaffner’s scientific colleagues argue the government should be recommending the shot only for frail, older, sick, and immunocompromised people. Over 95% of the U.S. population are already COVID-immunized through vaccination, infection, or both, and the risks of serious illness for healthy younger people are not great.

Schaffner doesn’t disagree. But lots of not-necessarily-vulnerable Americans do want the shot for themselves and their children, and, without a CDC recommendation, insurance companies wouldn’t have to pay for the vaccine.

It’s “pretty awful” that Pfizer and Moderna, the two main COVID vaccine producers, have decided to charge up to $130 a shot, compared with $30 last year for the booster, which was produced under government contract, said Kathryn Edwards, a professor of pediatrics at Vanderbilt and a member of an ACIP working group on COVID. (Pfizer spokesperson Amy Rose said the price was “consistent with the value delivered” and reflected higher expenses to provide the shots commercially.) []

But a partial recommendation could leave the very groups who suffered most during the pandemic — minorities and other disadvantaged groups — unable to get vaccinated if they want but can’t afford to.

“The last thing we need are financial barriers that would enhance disparities,” Schaffner said.
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The new vaccine is “not remotely a game changer,” said John Moore, a professor of microbiology and immunology at Weill Cornell Medical College.

For healthier adults and children, “it’s a boost in protection for a few months,” Moore said. Who exactly will benefit most is impossible to predict because the U.S. is “not a cookie-cutter population.” Its people have by now been exposed to a bewildering combination of vaccines, boosters, and different strains of the virus.
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Fearmongering has distorted the threat of the virus, Moore said. He is skeptical of the significance of the recent uptick in COVID hospitalizations, and criticized social media posters who have raised fears about new viral strains that don’t seem to pose any fundamental challenge to the new vaccines.

“Editorial FOMO drove summer surge worries,” Moore said, using an acronym for “fear of missing out.” Despite worrying comments and tweets by physicians such as Eric Topol, director of the Scripps Research Translational Institute, about a new COVID variant called BA.2.86, “it turned out to be a real nothingburger,” Moore said.
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Whether truly needed or not, the vaccines, proponents say, are safe enough that even the small benefit of taking them will outweigh the risks. The major, though rare, serious side effect of the Pfizer and Moderna vaccines — myocarditis, which particularly affected men in their teens and 20s — appears mainly to have occurred during the first two-shot series.

Paradoxically, those who most need protection from COVID are often likely to have weakened immune systems that fail to generate the hoped-for response to vaccination.

So, the vaccine is arguably most relevant for healthy people who come in frequent contact with vulnerable individuals.
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In a commentary last November, infectious disease doctors Shira Doron and Monica Gandhi said vaccination campaigns should be radically honest about the limited value of vaccines for long-term protection against infection. Such a campaign might advocate vaccinating children because even though it won’t protect durably, “it might prevent the rare case of severe disease.”
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Pingui posted:

“Editorial FOMO drove summer surge worries,” Moore said, using an acronym for “fear of missing out.” Despite worrying comments and tweets by physicians such as Eric Topol, director of the Scripps Research Translational Institute, about a new COVID variant called BA.2.86, “it turned out to be a real nothingburger,” Moore said.

https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2023.28.36.2300460 posted:

First cases of SARS-CoV-2 BA.2.86 in Denmark, 2023
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Description of the first cases
From 26 July to 21 August, surveillance detected 876 SARS-CoV-2 infections among 8,756 tested people from the 5,944,145 inhabitants of Denmark [1]. Of these, 418 were sequenced and 10 (2.4%) cases of the new variant BA.2.86 were detected. Variants EG.5.1 and XBB.1.16 were found among the majority of sequenced samples during this period (see the Supplement for a graphical distribution of the most prevalent variants).

Nine of the 10 cases were tested on clinical indication according to national guidelines [2]. The remaining case was detected by a surveillance project where individuals in several workplaces in Denmark can sign up to perform self-administered swabs at home when they have mild symptoms [3]. In total, 67 samples were tested as part of this surveillance project at workplaces from 26 July to 21 August.

Based on registry data, seven cases were female and three were male. Mean age was 57 years, median was 49 years, and five of the cases had at least one chronic condition. Seven of the cases lived in Greater Copenhagen region. All aged 18 years or above had been vaccinated against COVID-19 at least three times, with the latest vaccination 299–616 days before the BA.2.86 infection. Some of the cases had received the BA.1 updated vaccine as their fourth vaccination. Five of the cases had had a PCR-confirmed SARS-CoV-2 infection 506–556 days before the BA.2.86 infection. [ed. that would be the initial Omicron wave in Denmark, which was BA.2]

Eight of the cases were available for interview by 31 August. Interviews with these revealed that some belonged to the same household, while epidemiological links and geographical clustering were not apparent for most, including the first cases detected. For most there was no recent relevant travel history. Symptoms reported were similar to those seen for other variants, including cough, shortness of breath and fever. Some had an underlying disease or received immune-modulating treatment. None were severely ill.

BA.2.86 can be detected with variant-PCR
Samples from four cases were available for variant-specific qPCR analysis. The samples contained the ΔH69/V70 mutation, as detected with a BA.2.-specific allelic discrimination assay based on deletion-specific TaqMan probes [4]. The variant could be detected with a novel purpose-designed dsDNA dye-based PCR. The presence of the BA.2.86-specific S gene insertion ins16_MPLF was identified in three samples using a dsDNA dye-based PCR with insertion-specific primers, which are listed in the Supplement. The ins16_MPLF could not be detected in one sample, probably due to low viral load (E gene qPCR quantification cycle Cq = 37). Furthermore, to discriminate between the BA.2.86 variant and the two most dominant variants circulating in Denmark, EG.5 and XBB.1, we used a drop-out PCR that targets the ΔV483 mutation not present in the BA.2.86 variant to confirm the ins16_MPLF assay. We provide the PCR protocol in the Supplement.

Isolation of virus attempted in different cell lines
By 31 August 2023, virus isolation has been attempted without success from one case on Vero E6 cells and from three cases on Vero E6 cells and Vero E6 cells overexpressing angiotensin-converting enzyme 2 (ACE2) and TMPRSS2 [5].

Whole genome sequencing and molecular clock
We carried out amplicon-based whole genome sequencing using a modified ARTIC v3 primer scheme (github.com/artic-network/primer-schemes/tree/master/nCoV-2019/V3) or Arctic-midnight ONT V3, and consensus genomes were derived using a custom pipeline [6] or the pipeline wf-artic (v0.3.25) (https://github.com/epi2me-labs/wf-artic). We obtained lineage designations for each consensus genome using Nextclade (clades.nextstrain.org). Comparison of all Danish BA.2.86 genomes with others identified in global surveillance efforts from Israel, Portugal, South Africa and the US, showed 122 mutations with more than 50% conservation relative to the Wuhan-Hu1 reference genome, with a large proportion of these mutations (n = 79) in the S gene. These included a 12 nt insertion at S:16MPLF and four deletions in the S gene; the most interesting of these was S: ΔV483 in the receptor binding motif (RBM). We also observed the S:E484K mutation (also located in the RBM), which had not previously been observed in the Omicron lineage (Figure 1). We also observed several mutations in the N-terminal domain (NTD) antigenic supersite of the S gene, which suggests altered antigenicity of the S protein.
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We performed maximum-likelihood phylogenetic analysis with all 10 Danish genomes as well as eight genomes from global surveillance and representative genomes (at a redundancy threshold of 98%) of all lineages sequenced in Denmark over the sampling period of the first 10 cases. The BA.2.86 variant did not cluster with any circulating lineages and was distant from other known lineages circulating in Denmark (Figure 2). The BA.2.86 genomes fell into two distinct groups, and all genomes from Denmark grouped together with genomes from Israel and the US, suggesting parallel circulation in more than one location globally before the first samples were collected and sequenced.
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Determination of the time to most recent common ancestor (TMRCA) for this lineage used a maximum-likelihood phylogeny of BA.2.86 genomes globally as input in BEAST (v.1.10.4) with an uncorrelated relaxed clock model, a coalescent exponential growth tree prior and Markov chain Monte Carlo chains run for 10,000,000 generations [7]. The TMRCA was estimated to be 15 June 2023 with a 95% HPD between 9 April to 24 July 2023.

Wastewater surveillance
Surveillance of the new variant in wastewater was initiated after the first cases were detected. Samples from the Danish COVID-19 wastewater surveillance programme from 7 to 17 August 2023 were subjected to SARS-CoV-2 sequencing as described above (29 wastewater plants sampled twice per week, n = 116). Freyja v.1.4.5 (barcode version 08_22_2023–00–20) [8] was used to estimate lineage abundance in the samples, using 10 × as depth cutoff.

More than 50% coverage was obtained for 86 (74%) of the wastewater samples. The BA.2.86 variant was not detected by Freyja in any of the samples, but some contained multiple mutations characteristic of BA.2.86 (e.g. A7842G, C8293T and G8393A or C897A and C8293T). None of the 10 cases live in the catchment areas where the characteristic mutations were found.

The first results from wastewater surveillance of the following week (sampled on 22 and 24 August 2023) showed that characteristic mutations are continuously identified in a number of samples, and BA.2.86 was detected by Freyja at 3.6% abundance at one location.

Discussion
The SARS-CoV-2 BA.2.86 variant causes concern because a large number of mutations distinguish it from previous variants. While the limited epidemiological data available indicate that the variant is already dispersed across Denmark, the proportion of BA.2.86 among sequenced samples has been small and cannot explain the recently observed increasing transmission (see the figure about increase in the Supplement). Further, none of the 10 BA.2.86 cases have been severely ill. It is, however, crucial to underline that this is a preliminary assessment based on the first cases.
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Conclusions
Given the widespread distribution of BA.2.86 globally and within Denmark in clinical samples and in wastewater, and the high number of mutations conferring immune-evasive potential, the possibility that BA.2.86 will outcompete currently dominating variants cannot be ruled out. Our very early clinical data suggest a clinical picture in line with the typical COVID-19 illness caused by previous variants. Data are presently very preliminary and further global monitoring of BA.2.86 and other SARS-CoV-2 variants is highly warranted.
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https://www.eurosurveillance.org/de...3.28.36.2300460 posted:

Supplementary Material
The weekly number of hospitalizations due to COVID-19 in Denmark and the normalized national average concentration of SARS-CoV-2 in Denmark from 4 June 2023 to 27 August 2023. The concentration in the wastewater has grown exponentially since the beginning of July resulting in a factor 20 increase over a period of eight weeks. The rapid growth precedes the known occurrences of the new BA.2.86 variant and the low abundance among sequenced cases underlines that the observed growth is due to other variants. Preliminary analysis using logistic regression shows a positive but not significant growth in the proportion of sequenced cases. In combination with the growth seen in the wastewater then this indicates that the BA.2.86 is most likely growing in incidence.
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Pingui posted:

It should also be noted that they didn't manage to isolate the virus.

Platystemon posted:

Pingui posted:

Edit: Forgot one of the most important parts. The time to most recent common ancestor was estimated to be 15 June 2023 with a 95% HPD between 9 April to 24 July 2023. Indicating that this is an extremely new variant (as was my fear), that could have been found more or less immediately, though likely within 1½ months.

Pingui posted:

Edit: Forgot one of the most important parts. The time to most recent common ancestor was estimated to be 15 June 2023 with a 95% HPD between 9 April to 24 July 2023. Indicating that this is an extremely new variant (as was my fear), that could have been found more or less immediately, though likely within 1½ months.

NeonPunk posted:

I wonder if it's because they were using the wrong cells to isolate it since apparently someone else had a much better success using some lung cancer cells instead of the typical ACE2 kidney cells?

https://twitter.com/ShanLuLiu1/status/1701029792571592936

Pillowpants posted:

COVID Wastewater Poopsplosion

Zugzwang posted:

Wondering how we can compare this with BA.1 given the current variant landscape. BA.1 had the distinct advantage of really only having to outcompete Delta, since Delta had so thoroughly thrashed all the other variants. These two need to outcompete a bunch of other stuff.

Hm, I don't like the sound of "really good at infecting lung cells"

Thank you, Pillowpants! not sure if this is because you inserted a graphic from elsewhere into your sheet, but I can't really read the legends on the map even if I zoom in.

BusError posted:

So partner was feeling better at the end of last week, then on Sunday had a big rebound and today is feeling absolutely terrible. She is completely convinced that it's entirely due to Paxlovid, because her brother, who got got at the same time as her and did not take Pax, is feeling most of the way better now. It's very cool how I can't even succeed at accurate science communication within my own household with someone who already trusts me! I love it!

BusError posted:

So partner was feeling better at the end of last week, then on Sunday had a big rebound and today is feeling absolutely terrible. She is completely convinced that it's entirely due to Paxlovid, because her brother, who got got at the same time as her and did not take Pax, is feeling most of the way better now. It's very cool how I can't even succeed at accurate science communication within my own household with someone who already trusts me! I love it!

BusError posted:

Raskolnikov2089 posted:

Thread rec: I've been reading Immune: A Journey into the Mysterious System That Keeps You Alive by the guy who makes the Kurzgesagt youtube channel.

At first it was because I wanted to be able to make more sense of the many scientific papers that life in 2023 thrusts upon you. Now I'm simply just fascinated. It's a very layman friendly explanation of our current understanding of the immune system.

My favorite "wow" so far is that a component of sexual attraction is that we can smell our partner's immune system, and are drawn to those with different antigen presenting receptors.

NeonPunk posted:

That happens op. Like your partner remember how dumb you were for putting the toilet paper the wrong way or putting the knives in the dishwasher the wrong direction, so they do love you and cherish you but they also remember all the time you were wrong so they might not believe you when all the 'experts' say otherwise

Griz posted:

updated Pfizer/Moderna just got approved by FDA
CDC has their gatekeeping meeting tomorrow