Weekly coronavirus-related chat, questions, and minor updates - week of April 5

My uncle died from covid a week or so ago. He was 70+ and had a very fragile health already. He was going to take the vaccine the next day. It's the first person I personally know to die from covid. Brazil. Very sad.

Getting my second shot this week (CureVac candidate). I hope it won't knock me out as much as the first one. I still think the fever from the first shot was amplified by lack of sleep before and after, I'll try to be well-rested when I get it.

Has anyone here gotten their second shot? What was your experience, compared to the first one, in terms of side effects?

Brazil Tops 4,000 Daily COVID-19 Deaths, Nears U.S. Peak

With less than two-thirds the population of the U.S., Brazil logged nearly 4,200 deaths on Tuesday. That is close to the peak U.S. daily death toll of 4,476 recorded on Jan. 12, according to data maintained by Johns Hopkins University.

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Intensive care units across the country have been operating at near capacity for weeks, and officials are warning that the pandemic is quickly overwhelming health care infrastructure. A bulletin issued by the Brazilian medical research institution Fiocruz on Tuesday said that the lethality of coronavirus has more than doubled to 4.2% from around 2% at the end of 2020. Fiocruz attributes the increased death rate to the inability to quickly and correctly diagnose serious cases of COVID-19 and to overloaded hospitals. It warns of the "collapse of the health care system."

Brazil has become South America’s superspreader event

In Lima [Peru], scientists have detected the variant in 40 percent of coronavirus cases. In Uruguay, it’s been found in 30 percent. In Paraguay, officials say half of cases at the border with Brazil are P.1. Other South American countries — Colombia, Argentina, Venezuela, Chile — have discovered it in their territories. Limitations in genomic sequencing have made it difficult to know the true breadth of the variant’s spread, but it has been identified in more than two dozen countries, from Japan to the United States.

Hospital systems across South America are being pushed to their limits. Uruguay, one of South America’s wealthiest nations and a success story early in the pandemic, is barreling toward a medical system failure. Health officials say Peru is on the precipice, with only 84 intensive care beds left at the end of March. The intensive care system in Paraguay, roiled by protests last month over medical shortcomings, has run out of hospital beds.

“Paraguay has little chance of stopping the spread of the P.1 variant,” said Elena Candia Florentín, president of the Paraguayan Society of Infectious Diseases.

“With the medical system collapsed, medications and supplies chronically depleted, early detection deficient, contact tracing nonexistent, waiting patients begging for treatment on social media, insufficient vaccinations for health workers, and uncertainty over when general and vulnerable populations will be vaccinated, the outlook in Paraguay is dark,” she said.

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Now that the variant has infiltrated numerous countries, stopping its spread will be difficult. Most South American countries, with the exception of Brazil, adopted stringent containment measures last year. But they have been undone by poverty, apathy, distrust and exhaustion. With national economies battered and poverty rising sharply, public health experts fear more restrictions will be difficult to maintain. In Brazil, despite record death numbers, many states are lifting restrictions.

That has left inoculation as the only way out. But coronavirus vaccines are South America’s white whale: often discussed, but rarely seen. The continent hasn’t distributed its own vaccine or negotiated a regional agreement with pharmaceutical companies. It’s one of the world’s hardest-hit regions but has administered only 6 percent of the world’s vaccine doses, according to the site Our World in Data. (The outlier is Chile, which is vaccinating residents more quickly than anywhere in the Americas — but still suffering a surge in cases.)

Got my second dose of pfizer a couple of days ago. Had a fun fever, aches, and chills the first night, and my arm has a deep pain like nothing I've felt from a shot before. It has reduced range and mobility, very painful to lift above the rest of my shoulder. Really hoping that subsides soon and never returns. I'm a bit worried it's bursitis or SIRVA.

Edit: Looks like my concerns were unwarranted and the shoulder pain cleared up in a few days. I'm thankful!

World's Biggest Vaccine Maker 'Very Stressed' As India Sees Record Spike In COVID-19

MUMBAI — India on Monday recorded its biggest daily jump in coronavirus infections, joining only a handful of countries, including the United States, to cross the threshold of 100,000 new cases in a single day.

A surge is happening across South Asia. Pakistan's prime minister and president are among those to test positive in recent weeks. A one-week lockdown began in Bangladesh on Monday.

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India is the world's biggest vaccine producer, making up to 100 million doses per month of the Oxford-AstraZeneca vaccine alone. It has diverted some exports in recent weeks to try to boost inoculations at home.

Nearly 80 million doses have been administered so far in what the Indian government calls the biggest vaccine campaign in the world. But that's still less than 5% of the population of nearly 1.4 billion. The government has said its goal is to vaccinate 300 million people by midsummer. Anyone over age 45 is currently eligible.

More than half of India's new cases are in the western state of Maharashtra, where Mumbai is the state capital. High-rise apartment blocks where residents test positive are being sealed off there and guarded by police. Authorities are commandeering private hospitals and nursing homes. On Sunday, they issued new restrictions calling for all nonessential shops to close on weekends. A night curfew remains in effect.

Vaccine Manufacturing Woes at Emergent

The current theory is that the recent J&J production run was lost because an employee did not adequately disinfect while moving from the AstraZeneca section of the plant into the J&J section. That would most certainly do it. Anyone who’s done biologics production (or who has just worked in a busy cell culture lab) will be able to tell you stories about contaminations of this sort, some disastrous and some narrowly avoided. It’s even worse than mistaking the sugar for the salt in a kitchen, because you’re dealing with things that grow and reproduce – cells and viruses. A mixup can spread catastrophically, and that’s just what seems to have happened here.

And if the hygiene at this plant is as depicted above, they’re asking for other kinds of contamination as well. Things like adventitious yeast can rip up your cell cultures, too. In research labs, people are warned about doing any home baking or brewing, and to be sure to take serious showers before setting foot in the cell culture room after anything like that. There are mycoplasma out there ready to drop in and mess with your cells, there are viruses that you haven’t even heard of before that can ruin everything (ask Genzyme people about that). . .no, cell culture work is pretty unforgiving, and the larger the scale, the larger the worries. There is only one way around this problem, and that is rigorous cleanliness. No shortcuts, no exceptions. And walking from a part of a production plant that is dealing with one kind of cell/virus combination into a part that’s dealing with a completely different one without even taking a shower is not rigorous cleanliness.

The Times reports that Emergent’s own auditors had repeatedly detected mold in a cell culture room, repeatedly had problems with bacterial growth on equipment surfaces, and so on. This stuff will happen anywhere if you are not a complete hardass about disinfection, and if you’re running a vaccine production facility there is no excuse not to be. Fungi and bacteria never take breaks and they are the living, metabolizing definition of “opportunistic”. [...]

Osaka moves Olympic torch run off public roads, declares COVID-19 emergency

The prefecture reported 878 new infections on Wednesday, a second-straight day of record numbers. Severe cases have filled about 70% of hospital beds in the region.

Osaka and the neighbouring prefectures of Hyogo and Miyagi started on Monday a month of targeted lockdown measures, to rein in a more virulent strain of the virus.

In recent days, Osaka's infections have outstripped those in Tokyo, the Japanese capital and a much larger city. Even so, Tokyo's cases are on an uptrend as well, with Wednesday's 555 new infections standing at the highest since early February.

Tokyo Governor Yuriko Koike said she was preparing to request similar emergency steps in the capital region.

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Japan's vaccination drive is far behind that of most major economies, with about 1 million people being given at least one dose since February.

That figure represents less than 1% of the population, versus almost 2% in neighbouring South Korea, which started its campaign after Japan.

More senseless delay while thousands die daily (in other countries):

Biden’s Orphaned AstraZeneca Stockpile Rises to 20 Million Doses

The administration isn’t making any decisions either way about AstraZeneca until the FDA completes its review, said an official familiar with the matter, who, like the other officials, was granted anonymity to discuss the issue.

The U.S. government last year spent $1.2 billion to accelerate research, development, production and delivery of 300 million doses of AstraZeneca’s vaccine. At the time, the Department of Health and Human Services under the Trump administration said it expected the first doses to be delivered as early as last October.

Biden didn’t change that order, so AstraZeneca began producing shots in the U.S. in anticipation of eventual FDA approval. Last month, the president agreed to send 4.2 million doses of AstraZeneca’s vaccine to Mexico and Canada, an arrangement the administration termed a “loan.” When those doses are included, the running U.S. AstraZeneca total is nearly 30 million so far, the people said.

The company expects to have 50 million doses ready by the end of this month, one of the officials said.

Supreme Court Rules For Worshippers And Against California COVID Restrictions

the court barred the state from enforcing a rule that for now limits both religious and non-religious gatherings in homes to no more than three households.

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The court has done an about-face on these issues involving worship in churches, synagogues, mosques and now homes since the arrival of Justice Barrett. Until early 2021, after her arrival, the court, by 5-4 votes had generally deferred to the judgments of health departments and scientists when it came to state COVID-19 restrictions.

Hard choices emerge as link between AstraZeneca vaccine and rare clotting disorder becomes clearer

“Causality is more of a journey to certainty than a binary decision," says Anthony Cox, an expert on pharmacovigilance at the University of Birmingham. But faced with the accumulating cases, the European Medicines Agency (EMA), which had been careful not to point fingers, acknowledged on 7 April "a probable causal association" between the syndrome and the vaccine, recently named Vaxzevria.

As the link has become clearer, a possible mechanism driven by an errant immune reaction has come into focus. Now health officials face hard questions about who should and who shouldn't get Vaxzevria, which some countries have already restricted to older age groups, upending vaccination schedules.

Researchers stress that the troubles by no means spell Vaxzevria's end. In the vast majority of cases, its benefits outweigh the risks, and the vaccine, cheap and easy to store, is still the best hope for vaccinating large numbers of people in low- and middle-income countries. And some scientists suggest that a simple strategy could reduce the risk while stretching supplies: Cut the vaccine dose in half.

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Pinpointing the mechanism is crucial to understanding whether other vaccines made from a modified adenovirus, which include those from Johnson & Johnson and CanSino as well as Russia’s Sputnik V, do something similar. On 9 April, EMA said it was investigating four cases of similar clotting seen in U.S. patients who had received the Johnson & Johnson vaccine, which has been used in the United States since early March but has yet to make its debut in Europe. The cases could be coincidence, Greinacher says, but “it’s at least very suspicious.”

An older article from March:

Mexico’s Excess Deaths Far Exceed Official Coronavirus Toll

Excess deaths in Mexico for 2020 and early 2021 exceeded 417,000, more than double the official number of fatalities from the pandemic, the federal government said in a report that also sharply raised what it called Covid-related deaths.

On Thursday Mexico became the third country with more than 200,000 confirmed Covid-19 deaths, trailing only U.S. and Brazil, countries with much larger populations.

But in a report released on Saturday, what were termed Covid-associated deaths were far higher, at 294,287 through mid-February. In all, some 71% of excess deaths were said to be “associated” with Covid based on a review of death certificates.

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Mexico is ramping up its vaccination pace, now running at about 186,000 doses per day. At that rate it would take 2.8 years to cover 75% of the country’s population with a two-dose vaccine.

The U.S. is expected to send 2.7 million doses of the AstraZeneca vaccine to Mexico, with 1.5 million due to arrive on Sunday.