#GISAID

[biglisbonnews]

Scientists bicker over who was first to identify covid's genome The Global Initiative on Sharing Avian Influenza Data (GISAID), a large database launched in 2008 to collect and share the genome information of influenza viruses, is a key tool for scientific cooperation at the international level. Through it, scientists have been able to access genetic information of the latest…Read more... https://qz.com/covid-genome-sequence-gisaid-debate-1850284511

[suchananewsblog]

New COVID-19 origins data point to raccoon dogs in China market

Genetic material collected at a Chinese market near where the first human cases of COVID-19 were identified show raccoon dog DNA comingled with the virus, adding evidence to the theory that the virus originated from animals, not from a lab, international experts say. “These data do not provide a definitive answer to how the pandemic began, but every piece of data is important to moving us closer…

[covid-safer-hotties]

Acquired Immune Deficiency Syndrome correlation with SARS-CoV-2 N genotypes - Published July 29, 2024

You read that right: Covid infections can result in AIDS. I've been following this preprint since 2022, and I'm so excited to see it finally published! You might remember the preprint from the original Milf-Adjacent or covidsafehotties blogs.

Highlights •Genotypes N/120 and N/152 of SARS-CoV-2 have been identified in the acquired immuno-deficiency scope caused by Sarbecovirus.

•A new binding site for the Sarbecovirus N protein is proposed as the main route of infection of lymphocytes through CD147 receptors.

•Immune dysregulation caused by infection of CD147 lymphocytes is consistent with clinical data of severe and Long Covid cases.

Abstract Background Epigenetics and clinical observations referring to Betacoronavirus lead to the conjecture that Sarbecovirus may have the ability to infect lymphocytes using a different way than the spike protein. In addition to inducing the death of lymphocytes, thus drastically reducing their population and causing a serious immune deficiency, allows it to remain hidden for long periods of latency using them as a viral reservoir in what is named Long-Covid Disease. Exploring possibilities, the hypothesis is focused on that N protein may be the key of infecting lymphocytes.

Method The present article exhibits a computational assay for the latest complete sequences reported to GISAID, correlating N genotypes with an enhancement in the affinity of the complex that causes immune deficiency in order to determine a good docking with the N protein and some receptors in lymphocytes.

Results A novel high-interaction coupling of N-RBD and CD147 is presented as the main way of infecting lymphocytes, allowing to define those genotypes involved in their affinity enhancement.

Conclusion The hypothesis is consistent with the mutagenic deriving observed on the in-silico assay, which reveals that genotypes N/120 and N/152 are determinant to reduce the Immune Response of the host infecting lymphocytes, allowing the virus persists indefinitely and causing an Acquire Immune Deficiency Syndrome.

Graphical abstract

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well i've said it once already this month but 500 covid/ml in wastewater with 5+ strains circulating, neither of which are things that have gone well in the past

(currently circulating are the six XBB strains and EG5)

deaths appear to be rising very slowly (from 470 to 550/wk), still remaining at an all time low. hospitalizations more clearly rising (to 12k/wk), which seems to suggest that the proportion of people with severe cases remains lower than any other point during the pandemic, at the moment

biobot, gisaid, cdc

[canisvesperus]

Raw milkers are cooked (no pun intended).

[moontyger]

We’ve learned that the viral load in milk from infected cows is especially high. This suggests that infection might be spread through milking machines or when the milking rooms are power washed, aerosolizing infected milk. This is why workers should wear protective gear.

Another huge problem is that cattle in the U.S. are fed poultry “litter,” a euphemism for leftover feathers, bird droppings, spilled seed, and the occasional dead mouse or rat mixed in. There is supposed to be a 15-day period before cattle are slaughtered when the broiler litter is not to be used. Because of this two-week “weaning period” before human consumption, dairy cows are not supposed to be fed bird litter.

Cow manure—based on poultry litter—is widely spread on fields as a fertilizer, including on organic farms. So, our whole agricultural supply chain could be at risk of spreading infection. At least with limited testing, it doesn't look like cows are shedding virus thru their stool.

There are other possible routes of transmission. For example, house flies and blow flies can transmit H5N1 and other avian influenza viruses. During an HPAI (H5N1) epidemic in Thailand in 2005, blood-engorged mosquitoes collected at poultry farms tested positive for H5N1 by reverse transcription-PCR. Windborne spread could explain up to 24% of the transmission over distances up to 25 km in the 2003 outbreak.

There is now apparently spread of infection from cows back to birds. Grackles, blackbirds, and chickens all showed mutations from mammals, suggesting this route.

Gaps In Response

The government’s response to this potential biothreat has been reactive and limited.

The strongest initial criticism is that, despite calls for data and sample sharing as a foundation of pandemic preparedness, the USDA has not fully shared their data. When it finally shared genetic sequences with GISAID, the international database widely used by scientists since 2008, the USDA did not say where the samples originated nor include critical timing data.

Another problem is that the testing of cows is limited to dairy cows before they are moved to a different state. We don’t know if beef cattle are infected.

Surprisingly, the government apparently has had no power to restrict the movement of cattle or to require testing or reporting of infected herds or workers. A number of farmers are reluctant to allow testing. We know how voluntary reporting and restrictions will work…

However, on April 24, the USDA’s Animal and Plant Health Inspection Service announced that dairy cows would have to be tested before interstate transport and that labs and vets would have to report positive tests in cows. APHIS also announced finding H5N1 in a lung tissue sample from an asymptomatic dairy cow in an affected herd.

While there was one recently reported case of conjunctivitis in a person, there is likely to be considerable underreporting. There have been anecdotal reports of other symptomatic workers with fever, cough, and lethargy—and who do not want to be tested or seen by doctors. Many workers are likely undocumented and have no trust in the government. Dairy owners won’t want to risk prices falling or calls to cull their herds. Cattle veterinarian Dr. Barb Petersen said there has been underreporting and fear. She told Bovine Veterinarian’s journalist Rhonda Brooks, “But every dairy that I've worked with has – with the exception of one – had sick human beings at the same time they had sick cows.” She also reported infections in people with no direct contact with dairy cows. “I'm talking owners and feeders who don't usually touch cows.”

[fox-bright]

Me: "I'm feeling like maybe we'll actually get ahead of the H5N1 thing, as long as people aren't stupid about it. We're paying a lot of attention to it, and while a really quite upsetting number of people who should know better are just handwaving it, I feel hopeful."

GISAID: "Look at this nifty E627K substitution!"

Me: "...okay, so maybe I do some more canning this weekend."

[girlfriendsofthegalaxy]

this is my very favorite shit- database drama and people who can’t keep their email aliases straight

When Jeremy Kamil started to sequence samples of the rapidly spreading pandemic coronavirus in the spring of 2020, it was clear where he should deposit the genetic data: in GISAID, a long-running database for influenza genomes that had established itself as the go-to repository for SARS-CoV-2 as well.

Kamil, a virologist at Louisiana State University’s (LSU’s) Health Sciences Center Shreveport, says he quickly struck up a friendly relationship with a Steven Meyers, who used a gisaid.org email address. The two often exchanged emails and talked on the phone, sometimes for hours, about the pandemic and data sharing—but also about music, beer, and Saturday Night Live. Meyers said he had previously worked at Time Warner and had changed jobs after his boss at that company, Peter Bogner, launched GISAID in 2008. Meyers was born in Germany and living in Santa Monica, California, just like Bogner, whom he would call “our big boss” and “the Big Cheese.”

Over time, things got a little weird, Kamil says. Emails he sent to Meyers were sometimes answered from Bogner’s email account. “I used Peter’s account as writing on my little gadget was too treacherous,” was the explanation Meyers gave in one case. “I did ask though, first 😊.” Sometimes Bogner emailed Kamil about a topic he was discussing with Meyers at that very moment. Kamil offered to come to Santa Monica to meet Meyers on one of his trips to see his parents in Los Angeles, where they lived. But Meyers never seemed keen.

On 24 December 2022, when Kamil was again in Los Angeles, Meyers wrote that he would be “lucky this time around”: Kamil would have a chance to meet Bogner, along with GISAID in-house lawyer Ben Branda, in Santa Monica. Meyers himself couldn’t make it. Five days later, at a restaurant named R+D Kitchen, Kamil says he noticed Bogner had the same voice—with a hint of a German accent—as Meyers. “It wasn’t similar,” Kamil says. “It was identical.” It was the final nail, Kamil says: “I was duped.”

[excalculus]

Here we are, heading into another COVID winter.  The fucker’s still here and sadly we aren’t likely to get rid of it any time soon.  You kill diseases by cutting off transmission and slowly strangling them to death.  We tried that.  We locked down the whole world and it didn’t work.

I won’t deny that things look really ugly right now, especially with other respiratory diseases coming back.  But as the sequencing results keep coming in, it’s really starting to look like something incredible happened.

Sure, the lockdowns didn’t succeed in killing COVID.  That doesn’t mean they killed nothing.

Hey, I wonder how the influenza viruses are holding up?

There are two types of influenza that cause the epidemics we get every winter: A and B.  (C and D don’t really get up to the same level of mischief so let’s ignore them for now.)  Type A infects both animals and people, and includes things like the H1N1 bird flu pandemic strain, swine flu, et al.  The H[number]N[number] format points out which subtype of two important viral proteins it has, and usually strains are reported with that code, what animal they jumped into humans from, and where they were first sequenced.  Type B only affects humans, especially children.  It doesn’t have subtypes like Type A.  Instead it has two distinct lineages: B/Victoria and B/Yamagata. 

Today’s best flu vaccines are called “quadrivalent” because they target B/Victoria, B/Yamagata, and our best guess at which two Type A’s are going to blow up this year.  The guess is based on global sequencing of flu infections, so we have at least a decent idea of both past and current circulation logged in databases like GISAID and the WHO’s FluNet. 

Cases went way down during the lockdowns - masking and social distancing pushed spread down to a fraction of what it usually is.  Influenza in general is now back in force as people go back to their normal behavior.  There’s plenty of Type A flying around.  There’s been B/Victoria.

B/Yamagata has not been conclusively identified since March of 2020.

As early as 2021, flu researchers noticed the lack of new B/Yamagata sequences coming in and started to suspect something was fishy.  Look at this graph of GISAID flu data by lineage:

[GISAID] [paper]

Let’s, uh, check FluNet maybe?  That shows that in a typical year you see tens of thousands of cases of B/Yamagata on PCR tests.  2017 had 30,552; 2018 had 51,524.  Then... 3,464 in 2019.  364 in 2020 in only 9 countries.  It does seem like there are still signs of life in 2021 with 8 hits, but keep in mind these detections are based on simple PCR tests like what we do for COVID.  PCR tests are exquisitely sensitive, to the point where it’s been shown that giving flu vaccines and then later using the same room to give flu tests can throw a weak positive by picking up viral RNA from the vaccine.  More specifically, as of March 2022 there’s been a case of this exact thing happening with what looked like a B/Yamagata detection.  So it’s going to be more reliable to look at only the results from full sequencing, where you can yeet anything that matches the vaccine ingredients and only look at wild viruses. 

[paper]

Zero.  Nothing.  All signs point to we shot at COVID and blew up an entire flu lineage as collateral damage!  What the fuck!  We’re probably going to have to change how we do flu vaccines because fully a quarter of what they aim at looks to be gone from the face of the earth!

True, influenza B/Yamagata could still be out there somewhere that hasn’t been sequenced.  Proving absence is hard.  But the fact that Type A and its sibling B/Victoria are back and easy to find really does suggest it’s gone, or stomped down so far it’s near impossible to find.  Time to watch and wait and feed every sample we can into the sequencers, but if we keep not finding it...

A disease is considered eradicated when we’re sure there’s no more transmission “in the wild”.  For smallpox, which was also wildly contagious and also had no nonhuman reservoir, that was three years from the last known case. 

Clock’s ticking.

[kaelio]

On 24 December 2022, when Kamil was again in Los Angeles, Meyers wrote that he would be “lucky this time around”: Kamil would have a chance to meet Bogner, along with GISAID in-house lawyer Ben Branda, in Santa Monica. Meyers himself couldn’t make it. Five days later, at a restaurant named R+D Kitchen, Kamil says he noticed Bogner had the same voice—with a hint of a German accent—as Meyers. “It wasn’t similar,” Kamil says. “It was identical.” It was the final nail, Kamil says: “I was duped.” Karthik Gangavarapu, a post-doctoral fellow at the University of California (UC), Los Angeles, who had many lengthy calls with Meyers—but never with Bogner—also suspected they were one and the same. When Science sent Gangavarapu an audio clip of Bogner talking, he replied: “This is definitely the same voice as Steven Meyers.” No one Science has spoken to in the virology community—including members of GISAID’s science advisory board—recalls ever meeting Meyers, or even seeing a picture of him.

Rest assured this isn't an anti-vax post etc. Just some absolutely insane things going on with GISAID.

[min-phone-pyae]

COVID FLiRT variants KP.3 and XEC: What you need to know

KP.3 was the 'predominant' SARS-CoV-2 variant in the US. It was also spreading in Europe. It's now joined with another variant and become XEC.

Over the European summer, the number of COVID-19 infections rose again, with test positivity for SARS-CoV-2 above 20%. Globally, test positivity was about 10%.

The US also saw a rise in hospitalizations, apparently after a wave of COVID-19 infections in Singapore.

Now, as we in the northern hemisphere move into autumn and winter, there is concern about two new variants.

The first one is known as KP.3 and its sub-variant KP.3.1.1. The second is XEC, a "recombinant" variant which is related to KP.3.

KP.3 is considered a global Variant of Concern (VOC) in the US by The US Center for Disease Control and Prevention (CDC) because KP.3 was "predominant" there in August. VOCs may spread more easily or cause more severe illness.

It's important to note that KP.3 is not a global VOC, only in the US.

The CDC recommended people get an updated 2024–2025 COVID-19 vaccine.

What are the KP.3 and XEC variants?

KP.3 is one of a group of SARS-CoV-2 variants known as FLiRT variants. SARS-CoV-2 is the base virus that causes COVID, the illness.

As the name KP.3 suggests, there are also KP.1 and KP.2 sub-variants. KP.3 became predominant because it is more infectious than other circulating sub-variants.

KP.3 and other FLiRT variants descend from the omicron variant of SARS-CoV-2.

Now, think of a family tree: The KP variants are children of the JN.1 variant. And JN.1 is, in turn, a child of omicron variant BA.2.86.

How omicron evolved into the subvariants KP.3. and XEC

This is important to know because of all the major COVID variants, omicron remains dominant, globally. You'll recall, other major variants are alpha, beta, delta, and gamma.

But omicron keeps evolving or mutating into new variants and sub-variants.

XEC the sub-variant is believed to have formed when KP.3 joined with KS.1.1. But we don't know for sure.

As Francois Balloux, Professor of Computational Systems Biology and Director at the UCL Genetics Institute, UK, told the Science Media Centre, "XEC is a likely recombinant between the subvariants KP.3.3 and KS.1.1."

XEC COVID variant in Germany

XEC has been reported as being first detected in Germany in June. But it is yet to appear on the Robert Koch Institute's COVID Dashboard.

As a spokesperson from the Robert Koch Institute implied via email, XEC may never appear on the dashboard because it is "impossible to predict how individual variants will spread."

Since June, the number of XEC cases in Germany has been in double-digits, but the spokesperson did not specify further. The RKI's doesn't even mention XEC on its weekly assessment, published September 18, 2024.

The focus in Germany remains on KP.3.1.1, which is dominant and considered more infectious than previous variants.

In an interview with the DPA news agency, virologist Sandra Ciesek said it was no surprise that KP.3.1.1 was more infectious.

"The virus keeps mutating in search of new ways to infect people […] but that doesn't mean that the variant causes a more severe illness," said Ciesek, who's based at the German Center for Infection Research.

How prevalent are KP.3.1.1, KS.1.1 and XEC? Up to September 3, KP.3.1.1 remains the most dominent variant, according to data provided by GISAID, the Global Initiative on Sharing All Influenza Data, and presented by outbreak.info.

KP.3.1.1 was detected worldwide 14,396 times

KP.3.3 was detected worldwide 9,157 times

KS.1.1 was detected worldwide 2,650 times

XEC was detected worldwide 95 times

[schoje]

Pesquisadores de cinco estados brasileiros sequenciaram amostras que indicam uma possível nova linhagem do novo coronavírus (SARS-CoV-2) em circulação no país, segundo informou hoje (12) o Laboratório Nacional de Computação Científica, um instituto do Ministério da Ciência e Tecnologia, Inovações (MCTI) localizado em Petrópolis, no Rio de Janeiro. Além da linhagem identificada no Reino Unido, o Brasil já tem casos confirmados de duas variantes (P.1 e P.2), que surgiram a partir de cepas que circulavam no país.  A possível nova linhagem foi encontrada no sequenciamento de três amostras, em um universo de 195 que foram analisadas por pesquisadores do Amazonas, Rio Grande do Norte, Paraíba, Bahia e Rio de Janeiro. Essa identificação, entretanto, permitiu descobrir que já havia outras amostras com as mesmas características sequenciadas. O trabalho foi organizado pelo Laboratório de Bioinformática (Labinfo) do LNCC, e também participaram quatro universidade públicas: Universidade Federal do Rio Grande do Norte (UFRN), Universidade Federal da Paraíba (UFPB), Universidade Estadual de Santa Cruz (UESC) e Universidade do Estado do Rio de Janeiro (UERJ). Ao todo, 22 pesquisadores assinam a publicação, que foi submetida a um periódico científico ao mesmo tempo em que os sequenciamentos foram depositados em uma base de dados públicos internacionais (Gisaid).  A coordenadora do Labinfo, Ana Tereza Vasconcelos, explica que os dados compartilhados serão analisados por outros pesquisadores ao redor do mundo para que a identificação da nova linhagem seja confirmada pela comunidade científica. Segundo a cientista, as amostras em que a mutação foi encontrada são de Natal, no Rio Grande do Norte, e do interior da Bahia. "Essas mutações não interferem na vacina, mas demonstram que o vírus está mudando o tempo inteiro, e quanto mais as pessoas estiverem na rua sem máscara e sem medidas de proteção individual, mais o vírus vai mudar e mais variantes vão surgir. É mais uma demonstração de que o vírus está circulando livremente", diz Ana Tereza Vasconcelos, que reforça o pedido pelo respeito às medidas de prevenção, como evitar aglomerações, usar máscaras e higienizar as mãos.  A possível nova linhagem teria se originado da linhagem B.1.1.33, já presente no Brasil desde o início de 2020. A mutação apresentada é a E484K, na proteína S, estrutura que forma a coroa de espinhos que dá nome ao novo coronavírus. Essa mutação é associada ao escape do sistema imunológico, o que, segundo a coordenadora do Labinfo, ainda precisa ser confirmado por mais estudos. "Essa mutação já foi relacionada a vírus que conseguem escapar do sistema imunológico do hospedeiro. Os vírus estão tentando sobreviver, e eles têm mecanismos de escape. A gente acredita que essa nova linhagem pode ter esse mesmo mecanismo", afirma a pesquisadora. Essa mesma mutação já foi identificada nas variantes P.1 e P.2, originadas no Brasil a partir da linhagem B.1.1.28, e também também está entre as modificações genéticas encontradas nas variantes descobertas no Reino Unido e na África do Sul.  A mutação é um processo comum na reprodução dos vírus, que se multiplicam rapidamente e podem produzir versões geneticamente diferentes nesse processo. A maior circulação do vírus faz com que mais organismos se multipliquem, o que aumenta as chances de uma mutação ocorrer. Para que uma nova linhagem surja, no entanto, é necessário que essa mutação seja identificada em diversos indivíduos de uma determinada linhagem.

[covid-safer-hotties]

New COVID Variant XEC May Outpace Others This Fall - Published Sept 18, 2024

"The virus is always going to be mutating away from what it was in order to get more efficient at infecting individuals," Adalja said. "So I think this really highlights the fact that a universal COVID vaccine, or some vaccine with different technologies, perhaps a nasal vaccine and using mucosal immunity, all of those things are important."

What if, get this, we prevented covid cases by improving ventilation, mandating air filtration, and wearing masks in public? Wouldn't that accomplish the same goal right now? Every mutation takes us further away from the current scientific fantasy of a universal covid vaccine. We have to stop cases to make this dream a reality.

by Sophie Putka

The new COVID-19 variant XEC may overtake others in circulation to become dominant in the coming months, experts said, but will not prompt a meaningful change in symptoms or vaccine response.

So far, the CDC's variant proportions tracker has not registered enough cases of XEC in the U.S. to report it. (The agency's projected estimates for the 2 weeks ending in September 14 currently show KP.3.1.1 and KP.2.3 as the leading variants, with 52.7% and 12.2% of national cases, respectively.) Another estimate using data from the variant tracker GISAID has XEC at 1.11% of U.S. cases as of September 15, with around 48 sequences reported.

First detected in Germany in June, it's been found mostly in Central Europe, representing 10% of cases, according to the U.K.'s Science Media Centre.

"XEC represents a fairly minor evolution relative to the SARS-CoV-2 diversity currently in circulation, and is not a highly derived novel variant such as those that were granted Greek letters," like Alpha, Delta, and Omicron, Francois Balloux, PhD, a computational biologist at University College London and director of the UCL Genetics Institute, said in a Science Media Centre statement.

Experts noted that while XEC may have a small advantage in transmission, available vaccines are still likely to provide protection from serious illness.

XEC is a "recombinant variant of some of the other Omicron lineages that have been around for a while, and it does appear to be more immune evasive, giving it a transmissibility advantage in the population with the immunity that it has," Amesh Adalja, MD, of the Johns Hopkins Center for Health Security in Baltimore, told MedPage Today. "But it doesn't really change anything, just like the last variant didn't change anything, or the one before that, one before that, or the one before that."

Currently available COVID vaccines target slightly different subvariants. The updated mRNA shots aimed at KP.2 from Pfizer-BioNTech (Comirnaty) and Moderna (Spikevax), as well as Novavax's vaccine targeting the JN.1 variant lineage, are still protective against the most serious consequences of COVID infections, experts said.

"If this becomes a dominant variant, it will decrease the efficacy against infection of the updated vaccines, but the updated vaccines will still be durable against severe disease [and] hospitalization, and that's what is really the primary function of our current, first-generation COVID vaccines," Adalja said.

Still, he emphasized, the rapid mutation of the virus underscores a need for a different kind of vaccine than those currently available if the goal is to protect against infection rather than just severe disease.

"The virus is always going to be mutating away from what it was in order to get more efficient at infecting individuals," Adalja said. "So I think this really highlights the fact that a universal COVID vaccine, or some vaccine with different technologies, perhaps a nasal vaccine and using mucosal immunity, all of those things are important."

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not much new has changed since the last time i posted my covid charts (3wks ago?), weekly deaths in the US remain slightly elevated (closer to 4k instead of the past few months' steadily below 3k) but there is one thing i can't particularly find an explanation for

there has been a HUGE bump in doses administered globally the past couple weeks. suddenly like 300m doses were given. this isn't really attributable to any one country, the bump shows up in most of europe and east asia (and not in the US). explanation is probably rather dull, maybe just because 300m doses were produced and delivered. i haven't tried very hard to dig into vaccine production and delivery, because i know from trying to find the same info for pox vaccines, that information is often hard to find and comes down to whether producers publish a press release about it

there has also been a spike in deaths globally, predating the spike in vaccinations by a week or two (possibly related...!)

this IS attributable largely to one country... china, letting go of zero covid policy

you should all know by now i don't tolerate US imperial-conspiratorial thinking here, because 80% of americans have been conditioned to abject brainrot on the subject. i'm willing to accept this as largely factual data -- sure it's possible this includes a number of recently identified past deaths or something (US numbers have had a tendency to do the opposite, where previously identified deaths are later retracted, as was the case with about 4k deaths in massachusetts in 2020 or 2021, iirc), but given that we did hear about this in the news while it was happening, and no one in the sewer of corporate-owned US news bothered to dredge up that hypothesis, it's likelier that these are simply accurate weekly numbers. i view any covid deaths as preventable tragedies, but the suddenness and scale of deaths in china is difficult to conceptualize

this does outnumber likely number of lives saved based on WHO excess deaths report, placing china at plausibly 0.01% population loss. (chart showing totals truncated at 2m, india may have 4-7m total deaths including excess. modi's government delayed the excess deaths report by several months for this reason, if you recall. US likely approaching 2.1m)

these charts can be difficult to read even if you're familiar with excess deaths (which, again, include not just plausible undiagnosed deaths from covid, but also indirectly related deaths, i.e. from delayed healthcare during a surge). i couldn't figure out a better way to structure the charts, but think of the darker gray as a possible range (or an error bar), while excess deaths were almost certainly as high as the lighter gray sections, presuming you accept the conclusions of the report

peru continues to lead by a wide margin as percentage of population (percentage chart excludes populations smaller than 10m, otherwise very small island nations like san marino and st vincent rather dubiously show up, with high uncertainty in excess). you can see why in the totals chart (which is, for contrast, untruncated) -- peru ranks 7th in number of deaths (~500k) while ranking 44th by population

there is some additional dubiousness to my methodology here, as i only have excess death data from the 2020-2021 report. i have not tried to model 2022-2023 deaths for every country, the way i have done for the US. here are those (this is what i meant hadn't changed much). they have some additional dubiousness of their own, since i am modeling excess deaths after 2021 as my own estimate, as well as only taking one possible value, somewhere in the middle, for excess deaths

biobot now showing over 50% omicron XBB in wastewater in the US

gisaid still showing slightly less XBB (22f) and more BQ1 (22e) in genetic sequencing in the US, also a new strain (23a), each about 30%

anyway i should have been asleep hours ago bye

[screenshots123]

📆 17 Oct 2023 📰 Symptoms of new Covid variants as cases increase in UK 🗞 Independent

Cases of the Pirola variant in the UK have passed 100

Covid-19 hospitalisations has increased by 24% in one week in the UK as new variant Pirola sweeps across the UK.

Data published by the UK Health Security Agency (UKHSA) from the last week of September shows the number of people testing positive for the virus increased by over 29.4% on the week before, despite a reduced testing infrastructure.

The concerning numbers come as the highly mutated new Covid variant Pirola reached over 100 cases in the UK, according to the Covid variant tracker GISAID.

Pirola, or BA.2.86, is the latest Omicron strain to appear this summer, sparking concern among experts because it has 34 more mutations...