H5N1

Six unlearned lessons of the pandemic

The Tyee has published my article Six Unlearned Lessons of the Pandemic. Excerpt:

6. We’ll never go back to the ‘before times’  

The neoliberal world order established since the 1980s has been brutally shaken since New Year’s Eve 2019, exposing political failures ranging from worsening climate change to the migration crisis and systemic racism. Yet governments behave as if the pandemic scarcely exists. They play familiar Cold War games: Russia threatens Ukraine, China bullies its critics, the U.S. pretends it’s the leader of something called the “free world.”  

It’s understandable to yearn for a world without a pandemic. But the “before times” got us into this mess. If we did go back to before-times economies and social relations, we would soon face still more pandemics and social conflicts. Omicron’s Here.

As the pandemic continues, with occasional guest appearances by climate disasters like last summer’s heat dome and November’s floods, many of the world’s leading nations (and leaders) are hollowed-out remnants of what they once were. Internally divided, they pretend it’s business as usual. But they seem terrified of their own people and unable to define and carry out a consistent pandemic policy.  

So, having learned nothing from the pandemic, they continue as they began — unless and until we elect new governments that really have learned from the past two years.

‘Crazy’ omicron surge could peak soon, but the virus is unpredictable as the pandemic enters its third year

Via The Washington Post: ‘Crazy’ omicron surge could peak soon, but the virus is unpredictable as the pandemic enters its third year. Excerpt:

The rapid surge of omicron infections in the United States may be relatively brief, measured in weeks rather than months, according to infectious-disease experts who have been astonished by the speed of the coronavirus variant’s spread — and who are hoping this wave ebbs just as quickly. 

The idea of a rapid peak and swift decline has a precedent in South Africa, the country that revealed the presence of omicron in late November. Cases there spiked quickly and then dropped with unexpected speed after only a modest rise in hospitalizations. An especially transmissible virus tends to run out of human fuel — the susceptible portion of the population — quickly.  

Some forecasts suggest coronavirus infections could peak by mid-January.  

“Omicron will likely be quick. It won’t be easy, but it will be quick. Come the early spring, a lot of people will have experienced covid,” William Hanage, an epidemiologist at the Harvard T.H. Chan School of Public Health, said in an email Thursday.  

But this has always been an unpredictable virus, going back to when it first appeared two years ago, on Dec. 31, 2019. The virus had probably been spreading for a month or more, but that was the day infectious-disease experts around the world began hearing by email and text about an outbreak of a mysterious pathogen causing pneumonia-like respiratory infections in Wuhan, China.  

No one on that day could have known that this pathogen, initially called the “novel coronavirus” and later named SARS-CoV-2, would trigger the most brutal pandemic in a century. And no one today knows when it will be over.  

Forecasts of how the pandemic will play out have repeatedly been incorrect, to the point that some modelers have stopped trying to make caseload projections four weeks out, instead limiting their forecasts to one week ahead.  

Because beyond a week, who knows? How omicron is reshaping the pandemic Omicron is the fifth coronavirus variant of concern and is spreading rapidly around the world. 

Forecasts of the current winter wave, in which omicron has come riding in atop an existing delta wave, are somewhat more plausible. Columbia University researchers have a model that projects a peak in cases during the week beginning Jan. 9, with about 2.5 million confirmed infections in that seven-day period — and potentially as many as 5 million.  

Columbia epidemiologist Jeffrey Shaman said the infection numbers reported in recent days are already at the high-end of projections, and the peak could come sooner. Omicron is setting new daily records for infections with the virus. The seven-day average of new, officially confirmed daily cases soared to more than 300,000 Wednesday. Then came the eye-popping Thursday numbers from state health departments and the Centers for Disease Control and Prevention — 562,000 new cases, pushing the seven-day average to 343,000.  

The official number captures only a fraction of the true number of infections. People who use rapid tests at home may not report positive results. Many others never get tested when sick. And some people are infected but asymptomatic or pre-symptomatic.

Static socio-ecological COVID-19 vulnerability index and vaccine hesitancy index for England

Via The Lancet Regional Health: Static Socio-Ecological COVID-19 Vulnerability Index and Vaccine Hesitancy Index for England. The summary:

Background  

Population characteristics can be used to infer vulnerability of communities to COVID-19, or to the likelihood of high levels of vaccine hesitancy. Communities harder hit by the virus, or at risk of being so, stand to benefit from greater resource allocation than their population size alone would suggest. This study reports a simple but efficacious method of ranking small areas of England by relative characteristics that are linked with COVID-19 vulnerability and vaccine hesitancy.  

Methods  

Publicly available data on a range of characteristics previously linked with either poor COVID-19 outcomes or vaccine hesitancy were collated for all Middle Super Output Areas of England (MSOA, n=6790, excluding Isles of Scilly), scaled and combined into two numeric indices. Multivariable linear regression was used to build a parsimonious model of vulnerability (static socio-ecological vulnerability index, SEVI) in 60% of MSOAs, and retained variables were used to construct two simple indices. Assuming a monotonic relationship between indices and outcomes, Spearman correlation coefficients were calculated between the SEVI and cumulative COVID-19 case rates at MSOA level in the remaining 40% of MSOAs over periods both during and out with national lockdowns. Similarly, a novel vaccine hesitancy index (VHI) was constructed using population characteristics aligned with factors identified by an Office for National Statistics (ONS) survey analysis. The relationship between the VHI and vaccine coverage in people aged 12+years (as of 2021-06-24) was determined using Spearman correlation. The indices were split into quintiles, and MSOAs within the highest vulnerability and vaccine hesitancy quintiles were mapped.  

Findings  

The SEVI showed a moderate to strong relationship with case rates in the validation dataset across the whole study period, and for every intervening period studied except early in the pandemic when testing was highly selective. The SEVI was more strongly correlated with case rates than any of its domains (rs 0·59 95% CI 0.57-0.62) and outperformed an existing MSOA-level vulnerability index. The VHI was significantly negatively correlated with COVID-19 vaccine coverage in the validation data at the time of writing (rs -0·43 95% CI -0·46 to -0·41). London had the largest number and proportion of MSOAs in quintile 5 (most vulnerable/hesitant) of SEVI and VHI concurrently.  

Interpretation  

The indices presented offer an efficacious way of identifying geographical disparities in COVID-19 risk, thus helping focus resources according to need.

German COVID incidence rate 2-3 times higher than reported - minister

Via Reuters: German COVID incidence rate 2-3 times higher than reported - minister. Excerpt:

BERLIN, Dec 29 (Reuters) - German Health Minister Karl Lauterbach said on Wednesday that the number of new coronavirus cases has been under-reported and the actual incidence rate of infections is about two or three times higher than the officially reported figure.  

Lauterbach said the under-reporting was due to fewer tests being performed at workplaces and at doctors practices during the holiday season, as well as only a few of those test results being submitted to authorities.

Lauterbach also expressed concern about a clear rise in cases of the Omicron variant and appealed to people to celebrate the New Year only in small groups.  

Hajo Zeeb of the Leibniz Institute for Prevention Research and Epidemiology also doubts the accuracy of Germany's reported figures for the coronavirus and the Omicron variant. 

"The figures now are certainly under-reported," he told the media group RedaktionsNetzwerk Deutschland.  

The Robert Koch Institute for infectious diseases on Wednesday reported 2,686 new cases of the variant, bringing the total number to 13,129. Four people have died with the variant.

The seven-day incidence rate, which has been a key metric for determining coronavirus policy, was reported as 205.5 cases per 100,000 residents, the lowest figure since early November.  

This translated into 40,043 new cases over the past 24 hours. In neighbouring France, by comparison, authorities on Wednesday reported 208,000 new cases.

A spokesperson for the German Health Ministry said earlier Wednesday that the government expects a clearer picture of the infection situation early next year.

Omicron 'going to get worse' as California hospitalizations up

Via The Los Angeles Times: Omicron 'going to get worse' as California hospitalizations up. Excerpt:

The number of COVID-19 patients hospitalized in California over the weekend reached levels not seen in months as the rapid spread of the Omicron variant caused major airline interruptions and sent throngs of people to testing sites.  

Officials said they expected Omicron’s spread to worsen in the coming weeks, with President Biden promising the federal government will do all it can to assist states facing surges in coronavirus cases. Biden acknowledged those who faced long waits for tests over the holiday and said his administration was seeking to alleviate the issue.  

“Seeing how tough it was for folks to get a test this weekend shows we have more work to do,” Biden said, “and we’re doing it.”  

There were 4,001 coronavirus patients hospitalized Sunday — California’s highest single-day total since Oct. 9 and a nearly 14% increase from last week.  

Some areas are contending with even sharper rises. Los Angeles County has seen a 30% bump in COVID-19 hospitalizations since last week. In Orange County, the patient count has swelled nearly 45% during the same period.  

Overall, the greater Southern California and Sacramento regions have posted a 20% jump in hospitalizations during the same span, while the San Francisco Bay Area has recorded a 13% increase.  

Officials and experts have long noted that hospitalizations are a lagging indicator of coronavirus spread, usually rising about two weeks after increases in infections.

That’s a potentially worrisome trend, given that California is battling a significant new spike that officials say is driven by circulation of the Omicron variant, perhaps the most heavily mutated and highly transmissible edition of the coronavirus.  

Over the last week, California reported an average of 11,914 new coronavirus cases per day, a 73% jump from two weeks ago, according to data compiled by The Times.  

The surge has been especially profound in Los Angeles County, which announced more than 20,000 combined new cases Saturday and Sunday — an eye-popping total officials say is actually an undercount because of reporting lags over the Christmas weekend.

COVID-19 on December 27: Are we just going through the motions now?

This morning's Johns Hopkins dashboard has more information than it seems to. We might settle for the big numbers at the top and click away to some other site.

Yes, we have a nice round 280 million cases, and 300 million will likely be the total in a few weeks. Deaths are at 5.4 million; we will hear a lot of comparisons to the Holocaust when the virus has killed 6 million.

But look at the US: over 4 million cases in the past 28 days, and over 1,000 deaths per day in that period. Perhaps the first year of the Trump response ensured that the Biden response would fail, but this badly? Many of these cases and deaths must be due to the active resistance to Biden's policies of many state governments and their Trumpist supporters.

Over on the right, the weekly case count is now at 5.2 million, sharply higher than the previous 4.55 million. Forty-five thousand people worldwide have died, a slight drop from the previous week. Vaccinations have dropped also. It's not much more reassuring when you click on "28-day" and see the graphs for the last 4 weeks: cases and deaths were far worse a few days ago, but vaccinations have fallen sharply.

All of these numbers are likely severe undercounts, and all of them will be higher 28 days from now, when Omicron has made itself dominant around the world. Maybe I'm just tired after two years, but they suggest to me that most governments, from municipalities to nations, are just going through the motions. 

How America's ICUs are dealing with another Christmas of death and distress

Via The New York Times: How America's ICUs Are Dealing with Another Christmas of Death and Distress. Excerpt:

INDIANAPOLIS — Of all the Covid patients that Ronda Stevenson is treating over Christmas, there’s one she cannot stop thinking about. He has been hospitalized for 10 months, and in all that time his 7-year-old daughter has never once been allowed to visit, prohibited from the hospital by age restrictions that keep families separated. Situations like this are bringing even veteran health care workers to tears.  

Ms. Stevenson, an intensive care unit nurse at Eskenazi Health in Indianapolis for the past seven years, cries as she talks about her patients and their families, making clear the grinding toll of the pandemic on already exhausted hospital work forces.  

“We’re pretty short-staffed,” Ms. Stevenson said. She added: “It’s getting harder.”  

Instead of taking holiday vacations this weekend, workers at strained hospitals across the nation are working 16-hour shifts. Some have been on the job every day for weeks. Festive meals have been replaced with protein bars and sports drinks.  

This Christmas weekend, with the United States facing another surge of illness stoked by a proportion of the population that remains unvaccinated, frontline workers are again sacrificing time at home with family to tend to Covid patients. In Indiana, which has among the highest rates of hospitalization and lowest rates of vaccination in the country, the situation is especially acute.

“A lot of people, including myself, had scheduled time off but are now being asked to come in and pick up shifts to cover for one another and meet the increased demands of patient care,” said Dr. Graham Carlos, the executive medical director at Eskenazi, which is at capacity and has had a backlog of patients in the emergency room.  

He worries that it will only get worse. “If the numbers continue as they are, a tidal wave of infections is going to hit hospital systems, putting us in dire straits,” he said.  

Nearly two years into a pandemic that shows no sign of abating, doctors, nurses and other frontline workers have already faced the emotional toll of mass death in their hospitals. They have endured the frustration of pleading with the public to take precautions only to watch outbreaks unfold as people ignored the call for help. They have suffered the moral distress of not being able to give patients the ideal level of care.  

But this season, there is a new strain on the system: Many workers who persisted through the first year of the pandemic have departed jobs because of burnout and anxiety. And with the Omicron variant pushing case numbers up dramatically, the caregivers who remain are getting infections, too, straining staff levels in unpredictable ways.

“This is the worst I’ve ever seen it,” said Maureen May, a nurse with 37 years of experience who serves as president of the Pennsylvania Association of Staff Nurses and Allied Professionals. She canceled her own holiday plans to pick up a shift on Christmas Day so that a co-worker could have time away.

Chinese officials face punishment over Covid lockdown in Xian

Via The Guardian: Chinese officials face punishment over Covid lockdown in Xian. Excerpt:

Officials in the north-western Chinese city of Xian are facing punishment for “not doing a good job” after a Covid-19 outbreak led to the lockdown of its 13 million residents.  

All domestic flights out of Xian and most trains from the city scheduled for Friday were cancelled. Officials say the outbreak has been traced to the arrival of a plane from Pakistan.  

The Central Commission for Discipline Inspection said in a statement that 26 people in Xian were being held accountable for failing in their efforts to prevent and control Covid, but did not specify their punishment.  

New locally transmitted cases with confirmed symptoms in the city, which is famous for its terracotta warriors buried with China’s first emperor, fell to 49 for 23 December, down from 63 a day earlier - the first decline since 10 December.  

Households in Xian have been limited since Thursday to sending only one person to shop for necessities every two days.Others are not allowed leave unless they have essential jobs. The city has also launched various rounds of mass testing.  

The number of symptomatic cases in Xian - 255 between 9 and 23 December - and in China overall is tiny compared with outbreaks elsewhere. Authorities have used heavy-handed measures that have for the most part succeeded in preventing localised outbreaks from spreading.  

China is particularly determined to extinguish any outbreak as Beijing prepares to stage the Winter Olympics in February. The country has all but shut its borders to international arrivals, and those coming for the Games will be sequestered inside a strictly enforced “closed-loop”.  

China’s aggressive approach to reining in the pandemic has restricted domestic travel and consumer spending, and occasionally disrupted local industrial production. The electric vehicle maker BYD Co said on Friday that the lockdown in Xian was having an impact on its operations in the city.  

China overall confirmed 87 new symptomatic cases for 23 December, down from 100 a day earlier, the national health commission said on Friday. Fifty-five were locally transmitted, compared with 71 a day earlier.

US hospitals struggle with staffing shortages and Omicron outbreaks

Via The Guardian: US hospitals struggle with staffing shortages and Omicron outbreaks. Excerpt:

On her fourth day of Covid symptoms, Ruth woke up in the worst pain of her life. It felt like her joints were filled with broken glass; she couldn’t walk, couldn’t move. “It was worse than childbirth,” she said.  

When friends texted to check on her, she couldn’t hold the phone or move her fingers to write back. Her doctor called in medication, and it took Ruth 40 minutes to shuffle to the pharmacy half a block away.  

Ruth – who did not want her full name used – is certain that if she weren’t vaccinated and boosted, she would be in the intensive care unit or worse right now. But while she’s recovering from this “mild” case, she’s unable to work even as cases surge in her region.  

Ruth is an emergency nurse in Washington DC. Her case of breakthrough Covid shows what may happen when the more contagious variant hits health workers all over the country – and the pressures Omicron will put on a US health system already groaning under the weight of the pandemic. In this wave, it’s not a shortage of beds but a shortage of qualified workers to care for people in those beds that is raising alarm bells.  

“What do you do when you have a tidal wave coming at you in a little paddle boat?” Ruth asked. “There’s going to be a huge uptick. Our entire waiting room is going to be all Covid-positive.”  

In Washington DC the infection curve looks like a straight line up. On Saturday, the city nearly tripled its previous record-high number of cases. At least two of Ruth’s colleagues were already out sick with Covid.  

In a matter of weeks, Omicron has become the dominant variant in the United States. It accounts for 73% of sequenced cases, six times higher than last week. As the holidays approach, officials and experts warn of an unmanageable crush of patients and potentially catastrophic staffing shortages.  

“This is a big concern,” said Marcus Plescia, the chief medical officer at the Association of State and Territorial Health Officials. “This is a highly contagious variant, and we really think it could cause significant issues with the workforce.”  

Omicron is spreading like wildfire and slamming into hospitals, and “​​there’s no question that this is going to be on us, really in the next week or so”, Plescia said.  

Others agreed. “There’s no question” that Omicron outbreaks among healthcare workers are “significantly diminishing the workforce”, said Georges Benjamin, executive director of the American Public Health Association. “It has profound implications for our ability to not just take care of people with Covid but [also] the other diseases that are out there.”  

The American Nurses Association is urging US officials to declare the nursing shortage a national crisis, and the American College of Emergency Physicians has expressed concerns the shortage will affect patient care.

Early assessment of the clinical severity of the SARS-CoV-2 Omicron variant in South Africa

Via medRxiv, some encouraging news: Early assessment of the clinical severity of the SARS-CoV-2 Omicron variant in South Africa. The abstract and then a comment:

Background  

The SARS-CoV-2 Omicron variant of concern (VOC) almost completely replaced other variants in South Africa during November 2021, and was associated with a rapid increase in COVID-19 cases. We aimed to assess clinical severity of individuals infected with Omicron, using S Gene Target Failure (SGTF) on the Thermo Fisher Scientific TaqPath COVID-19 PCR test as a proxy.

Methods

We performed data linkages for (i) SARS-CoV-2 laboratory tests, (ii) COVID-19 case data, (iii) genome data, and (iv) the DATCOV national hospital surveillance system for the whole of South Africa. For cases identified using Thermo Fisher TaqPath COVID-19 PCR, infections were designated as SGTF or non-SGTF. Disease severity was assessed using multivariable logistic regression models comparing SGTF-infected individuals diagnosed between 1 October to 30 November to (i) non-SGTF in the same period, and (ii) Delta infections diagnosed between April and November 2021.

Results  

From 1 October through 6 December 2021, 161,328 COVID-19 cases were reported nationally; 38,282 were tested using TaqPath PCR and 29,721 SGTF infections were identified. The proportion of SGTF infections increased from 3% in early October (week 39) to 98% in early December (week 48). On multivariable analysis, after controlling for factors associated with hospitalisation, individuals with SGTF infection had lower odds of being admitted to hospital compared to non-SGTF infections (adjusted odds ratio (aOR) 0.2, 95% confidence interval (CI) 0.1-0.3).

Among hospitalised individuals, after controlling for factors associated with severe disease, the odds of severe disease did not differ between SGTF-infected individuals compared to non-SGTF individuals diagnosed during the same time period (aOR 0.7, 95% CI 0.3-1.4).

Compared to earlier Delta infections, after controlling for factors associated with severe disease, SGTF-infected individuals had a lower odds of severe disease (aOR 0.3, 95% CI 0.2-0.6).

Conclusion

Early analyses suggest a reduced risk of hospitalisation among SGTF-infected individuals when compared to non-SGTF infected individuals in the same time period, and a reduced risk of severe disease when compared to earlier Delta-infected individuals. Some of this reducton is likely a result of high population immunity.

Reuters has a report on this study, which offers some hope that Omicron's impact will be hard but transient.