Weekly coronavirus-related chat, questions, and minor updates - week of December 28

I've been watching US data for any signs of a post-Thanksgiving surge and ... I'm not really seeing it.

What there is are both:

• An ongoing case increase that had been well underway before Thanksgiving, notably in California. California's Rt was already decreasing by Thanksgiving (Nov 25).
• An inverted horizontal sigmoid deviation in case and death data, almost certainly due to delays in testing and reporting. Counts first dipped, then climbed, then resumed (for the most part) their previous trend.

This doesn't absolutely mean that there was no "Thanksgiving bump", and it's possible that there was a slight increase which will show up down the road. As it is though, daily new cases peaked on December 18 at 662/1million, and are now trending downwards. Canada follows a nearly identical trend, whilst the UK are moving sharply upward (still just below the US in incidence/million).

Otherwise ... the thing about pandemics is that they're difficult to predict, behaviour is exceedingly dependent on human response, though viral behaviour (notably mutations, of which much recent discussion) and environment (seasonal changes, other variables) can also have effects. The North American Holiday Bump so far has, thankfully, been a bust.

Another week, another reason to be pissed off at Belgium's increasingly incompetent handling of the pandemic.

Coronavirus: Vaccinations set to begin in nursing homes, health workers in March

MARCH.

HEALTH WORKERS IN MARCH.

NINE MONTHS TO PREPARE.

Seriously, nine months to prepare, and they're acting like Edward Jenner just showed up two weeks ago.

America's vaccine rollout is already a disaster

How badly are we doing? In September, President Trump promised 100 million vaccinations by the end of the year. As a country, we have only 40 million doses, and had aimed, according to Secretary of Health and Human Services Alex Azar, to vaccinate 20 million by year-end. That’s bad enough. But we have administered only 2 million of those — barely 10 percent of the goal. At this rate, achieving sufficient vaccination to reach herd immunity and bring the pandemic to a close in the U.S. will take about seven years. In Israel, they are vaccinating about one percent of the population each day, meaning the full program of population-wide vaccination will be done by this March.

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Though refrigeration capacity varies from location to location, vaccines are only cleared for 30 days of storage in the most common units (including those in which they have been shipped). States have been rushing to build out their storage capacity, but have been warned of monthslong waits for ultracold freezers that could extend shelf life to about six months. That means that, in many places, this first batch of vaccine is set to expire in late January, around the time Joe Biden, who has been criticizing the rollout and promising to accelerate it, is set to take office.

Last week, I posted about the TSA saying that on December 23 they screened the highest number of airline passengers since March.

This page on the TSA's site shows their daily numbers, and they set another record on December 27. Other than December 24th and 25th they've been in the area of 1 million - 1.2 million every day since a week before Christmas. That's still only about half of what their volume was at this time last year, but that's still a lot of people flying. The volume has been closer to 25% for most of the year.

Incoming US House representative Luke Letlow (Louisiana, Republican) died at 41 from COVID-19 complications. He was supposed to be sworn in this Sunday, as the youngest rep in the state. A doctor from the hospital was very specific that his death was caused by COVID, and that it's absolutely not a situation like, "oh, he died from something else entirely, but because he tested positive they blame it on COVID":

Asked if Letlow had any underlying conditions that would have made his death more likely, Ghali said in a text message, "none. All COVID related."

I received the first shot of the Moderna vaccine on the 31st. As a 911 dispatcher, I qualified as a first responder(Texas being one of the few states that recognize dispatchers as first responders).

The overall process was extremely smooth.

Three lines of vehicles lined up outside of the building where the shot was being given. As people got the shot and moved on, people left their vehicles where they were, ran inside, got the shot, and then went back to their vehicles where they relocated to another part of the parking lot to wait 15 minutes for reactions. An ambulance with two paramedics was waiting close by. If anyone had a reaction, all they had to do was honk their car horn and the medics would come check them out.

I was in and out in less than 30 mins, including the 15 mins waiting time

So far, I can't say I've had any real negative side effects. A slightly sore arm is about the extent of it. Although I have been told that it's after the second shot that any side effects are likely to kick in.

Why getting COVID-19 vaccines to rural Americans is harder than it looks, and how to lift the barriers

The current vaccines’ cold storage requirements and shipping rules mean many rural hospitals can’t serve as vaccination distribution hubs. That can leave rural residents – about 20% of the U.S. population in all – traveling long distances, if they’re able to travel at all.

Getting the word to rural residents about when they can be vaccinated isn’t easy either, and the extraordinary amount of misinformation downplaying the risk of the coronavirus this past year has had an impact on rural residents’ willingness to get the vaccine.

We work in rural health care settings and have been examining the barriers to health care for these patients to find ways to ensure health and safety.

And a similar story in the Washington Post:

Why a Michigan doctor is driving coronavirus vaccines from hospital to hospital in his Honda pickup truck

Tweet thread from Trevor Bedford, professor at UW and Fred Hutch here in Seattle and one of the experts I've been following since the very beginning of the pandemic:

With data that has emerged in the last week, I'm now 80-90% convinced that infections by the UK variant virus ... are more transmissible.

L.A. County hospitals turn away ambulances, put patients in gift shop: ‘I’ve never seen anything like this’

The crisis at Los Angeles County hospitals hit new levels as patients continued to stream in during the holiday weekend, and the medical system is bracing for a new wave of coronavirus spread arising from Christmas travel and gatherings. L.A. County’s cumulative COVID-19 death toll is expected to climb past 10,000 this week.

Hospitals are so inundated that they’ve resorted to placing patients in conference rooms and gift shops. But even so, many facilities are running out of space. Virtually all hospitals in L.A. County are being forced to divert ambulances with certain types of patients elsewhere during most hours. On Sunday, 94% of L.A. County hospitals that take in patients stemming from 911 calls were diverting some ambulances away.

“But soon, there won’t be any places for these ambulances to go,” said Dr. Christina Ghaly, the L.A. County health services director. “If every hospital is on diversion, then no hospital is on diversion.”

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Kaiser Permanente is postponing nonurgent and elective surgeries and procedures at its facilities throughout California. The pause will remain in effect through Jan. 10 in Kaiser’s Southern California region and through Jan. 4 in Northern California, according to statements from the healthcare consortium. In Southern California, Kaiser is not scheduling any new elective surgeries through January.

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“If there is a Christmas surge, we probably have not experienced it yet,” Spellberg said, noting that cases arising from that holiday may not show up for another week or two.

South Africa hits 1 million coronavirus cases as new variant spreads rapidly

The country’s new variant of the coronavirus, 501.V2, is more contagious and has quickly become dominant in many areas of the resurgence, according to experts.

The warning came as South Korea became the latest country to detect cases of the Covid variant that is believed to have originated in the UK.

Israel zooms past 1 million vaccinations in sprint to vanquish pandemic

The Jewish state has so far greatly outpaced other countries, per capita, with 11.55% of the population inoculated, according to statistics from the Our World in Data website operated by Oxford University. Second place is held by Bahrain with 3.45%, followed by the UK with 1.39% (though the latter’s data is a few days old). The US stands at 0.84%. The world average is 0.13%.

Israel is currently in its third nationwide lockdown to contain the outbreak. It has reported more than 426,000 cases and at least 3,338 deaths since the pandemic began.

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Israel started vaccinating on December 20, with a focus on healthcare workers and then on those over 60 and at-risk sectors.

Its globe-leading vaccination drive has been attributed to various factors, including its relatively small but densely packed population and highly professional, community-integrated health services.

43 San Jose Kaiser Staff Members Test Positive in COVID Outbreak

The hospital is investigating whether an incident in which a staff member appeared briefly in the emergency department on Christmas Day wearing an air-powered costume with a fan may have led to air droplets being spread around the hospital.

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The hospital is working to quickly test all emergency department employees and doctors for the virus, and anyone who tests positive or who has symptoms will quarantine per Centers for Disease Control guidelines, hospital officials said.

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Kaiser said some of the healthcare workers infected had received their first dose of the COVID vaccine, but they would not have been expected to reach immunity when the exposure occurred.

Are you eligible for a COVID-19 vaccine? Washington state to launch tool, rely on honor system

Washington state will rely on an honor system to determine eligibility for COVID-19 vaccinations, so those administering vaccines do not have to police who qualifies.

Heartbreaking first-hand account from a nurse in the southeast US

Some healthcare workers refuse to take COVID-19 vaccine, even with priority access

At St. Elizabeth Community Hospital in Tehama County, fewer than half of the 700 hospital workers eligible for the vaccine were willing to take the shot when it was first offered. At Providence Holy Cross Medical Center in Mission Hills, one in five frontline nurses and doctors have declined the shot. Roughly 20% to 40% of L.A. County’s frontline workers who were offered the vaccine did the same, according to county public health officials.

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A recent survey by the Kaiser Family Foundation found that 29% of healthcare workers were “vaccine hesitant,” a figure slightly higher than the percentage of the general population, 27%.

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At Laguna Honda Hospital in San Francisco, about 10% of the nursing staff has opted out of the vaccine, said spokeswoman Zoe Harris.

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It’s unclear what happens when a hospital ends up with extra doses. State guidance allows hospitals to offer the vaccine to lower-priority people if frontline workers have already been offered the vaccine.

In Tehama County, unused doses at hospitals are being distributed to the next group of people who are eligible: staff and residents of assisted living and skilled nursing facilities.

Zeynep Tufekci: The Mutated Virus Is a Ticking Time Bomb

We are in a race against time, and the virus appears to be gaining an unfortunate ability to sprint just as we get closer to the finish line. Although the initial rollout of the vaccines has been slow, it is expected to increase rapidly. The U.S. may have 50 million to 100 million people vaccinated as early as March. That is a huge difference, one that could save many lives, especially since we also have perhaps that many people with some degree of postinfection immunity.

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All this means that the speed of the vaccine rollout is of enormous importance. There are already worrisome indicators of slow rollout. Vaccination of a broad population, not vaccines in and of themselves, saves lives, and epidemics are fought with logistics and infrastructure. We should put every bit of energy, funding, and relentlessness into vaccinating as many people as possible as quickly as possible.

Meanwhile, the United States was reportedly planning to hold back half the vaccine it has in freezers as a hedge against supply-chain issues, and some states may be slowed down by murky prioritization plans. Scott Gottlieb—the former FDA chief and a current board member of Pfizer—has argued that the U.S. should also go ahead with vaccinating as many people as possible right now and trust that the supply chain will be there for the booster. Researchers in Canada—where some provinces decided to vaccinate now as much as possible without holding half in reserve, and will administer the booster with future supplies—estimate that this type of front-loading can help “avert between 34 and 42 per cent more symptomatic coronavirus infections, compared with a strategy of keeping half the shipments in reserve.” (Note that this strategy, which is different from the one the United Kingdom just announced it will adopt in prioritizing the first dose, does not even necessarily involve explicitly changing booster timing protocols in order to maximize vaccination now; it just means not waiting to get shots into arms when the vaccines are currently available.) These were already important conversations to have, but given the threat posed by this new variant, they are even more urgent.

Dozens of residents die at Belgian care home after Santa visit

The outbreak followed a visit on 5 December by volunteers dressed as Saint Nicholas and his helper Zwarte Piet, organised by the nursing home’s management. The white-bearded, red-robed figure of Saint Nicholas, or Sinterklaas, brings gifts to Belgians every 6 December.

But within days, residents had displayed symptoms of coronavirus. Twenty six have since died and 85 more have tested positive for coronavirus, along with 40 staff.

L.A. homeless sites ‘overwhelmed’ by COVID-19: ‘These are the toughest times’

Though infections among the homeless have generally lagged slightly below the county’s per capita rate, belying early predictions of devastating outbreaks in shelters and encampments, the December surge has brought a spike in the homeless numbers as well, further straining the overstretched services system.

After averaging about 60 new cases each week through the fall, infections of homeless people doubled in the week after Thanksgiving and have since continued to climb sharply. On Tuesday, the Department of Public Health’s latest report showed 547 new cases in the previous week.

“The unexplainable protection that people who are homeless have had from COVID is disappearing,” Bales said. “All of skid row and many agencies/missions are hot spots. All are overwhelmed.”

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To keep up with the upsurge in cases, the agency opened four new isolation/quarantine sites in December, more than doubling the available beds.

The rapid response was partly assisted by the state’s Project Homekey program through which the county has purchased 10 motels and hotels for homeless housing. Most are being used as interim housing before being converted into permanent homes. Two have been converted temporarily into medical isolation/quarantine sites.

A third site was set up in a motel that was phased out of Project Roomkey, the program to house medically vulnerable homeless people during the pandemic. A nonprofit provided the fourth site on a property it had acquired for a future project.

U.K. Delays Second Covid-19 Vaccine Dose as Europe Ponders How to Speed Up Immunization

The U.K. will focus on giving as many people as possible a first dose of a coronavirus vaccine, even if this delays administering a second one, the government said Tuesday, despite a lack of data about the extent of the immunity conferred by a single dose.

The news comes as scientists in Europe are debating whether recipients should be given one dose instead of two given the scarcity of the vaccine, the difficulties in fending off a winter surge in infections, and a rapidly mounting death toll.

The problem: While scientists say a single dose may well confer sufficient immunity to stop the spread of the virus, there isn’t sufficient data confirming this because the clinical trials for available vaccines and those nearing authorizations were all designed around a two-dose regimen.

Britain, which is coming under severe strain amid the spread of a new, more infectious variant of the virus, is the first European government to change its policy. It stressed that vaccine recipients would still get a second dose, just three months later than planned.

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A vaccine made by Pfizer Inc. and BioNTech SE was the first to be authorized in the West. It is now being unrolled globally after emergency authorizations by various regulators on the basis of a successful months-long trial that involved giving two shots to more than 20,000 volunteers. The second injection was administered 21 days after the first.

While the trial data shows that the vaccine conferred immunity to over 50% of the participants after the first dose, marketing only one shot would require a new study in which only one dose would be administered to another set of volunteers, said BioNTech Chief Executive Uğur Şahin.

“It could be that the next generation of the vaccine consists of simply one dose,” Dr. Sahin said.

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A vaccine developed by Moderna Inc., which was authorized in the U.S. and could be given a green light by the European Union regulator in January, also consists of two doses. A third vaccine, developed by Oxford University and AstraZeneca PLC and authorized by the U.K. Wednesday, similarly has two doses.

Advocates of a one-dose approach say this might be the only way to vaccinate enough people to avoid another big surge in infections next winter, because of the limited availability.

A Continent Where the Dead Are Not Counted

In 2017, only 10 percent of deaths were registered in Nigeria, by far Africa’s biggest country by population — down from 13.5 percent a decade before. In other African countries, like Niger, the percentage is even lower.

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The United Nations Statistics Division collects vital statistics from around the world. In North and most of South America, Europe and Oceania, it says at least 90 percent of deaths are registered. In Asia, coverage is patchier.

But for most African countries, the United Nations has no death data at all.

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Half a dozen coffin carpenters and funeral directors on Odunlami Street said they had noticed that business was particularly brisk in June and July.

“The mortuaries were jam-packed,” said Tope Akindeko, manager of Peak Caskets, leaning on a coffin decorated with gilded reproductions of the Last Supper. The coffins he sold then were rough, cheap models, he said, while expensive American-made steel ones shipped in from Batesville, Ind., stayed on the shelves.

Could it have been a spike in Covid-19 deaths? Or perhaps a backlog of funerals, after two months of lockdown in Lagos? Because few deaths are registered, it was hard to tell.

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[R]esearchers have just declared that there was a huge, hidden outbreak in the capital of Sudan. In the absence of a good death registration system, they used a molecular and serological survey and an online one distributed on Facebook, where people reported their symptoms and whether they’d had a test. The researchers calculated that Covid-19 killed 16,000 more people than the 477 deaths confirmed by mid-November in Khartoum, which has a population roughly the size of Wisconsin’s.

Khartoum is only one city in a vast, diverse continent with a variety of approaches to fighting the pandemic. But several factors that the researchers cited for why the Covid-19 caseload might be vastly underreported — stigma, people unable to get tested, the fact that the threshold for reacting to any disease is high — are true in many African countries.

The Worst Of COVID-19 Should Be Over For Manaus, Brazil. But It's Not

In Brazil's jungle metropolis of Manaus, nurse Francinete Simões thought she had seen the last COVID-19 death at the urgent care center where she works in July. Hospitals finally had space to take critical patients again after a violent initial wave of the virus left many of the city's dead in mass graves.

But in recent weeks, Simões says, hospitals are "filling up, and I'm seeing people die again." The state government has now ordered non-essential businesses to close between December 26 and January 10 as a virus containment measure for this city of 2.2 million.

Here is a graph on Twitter.