H5N1

The four Black Deaths

I had an opportunity to read this long article in The American Historical Review, and found it fascinating: Four Black Deaths. We tend to think of the Black Death as a European disaster, but medical historian Monica H. Green shows its extent was far greater. The abstract: 

The Black Death, often called the largest pandemic in human history, is conventionally defined as the massive plague outbreak of 1346 to 1353 C.E. that struck the Black Sea and Mediterranean, extended into the Middle East, North Africa, and western Europe, and killed as much as half the total population of those regions. Yet genetic approaches to plague’s history have established that Yersinia pestis, the causative organism of plague, suddenly diverged in Central Asia at some point before the Black Death, splitting into four new branches—a divergence geneticists have called the “Big Bang.” 

Drawing on a “biological archive” of genetic evidence, I trace the bacterial descendants of the Big Bang proliferation, comparing that data to historical human activities in and around the area of plague’s emergence. The Mongols, whose empire emerged in 1206, unwittingly moved plague through Central Eurasia in the thirteenth, not the fourteenth, century. Grain shipments that the Mongols brought with them to several sieges, including the siege of Baghdad, were the most likely mechanism of transmission. 

The fourteenth century plague outbreaks represent local spillover events out of the new plague reservoirs seeded by the military campaigns of the thirteenth century.

COVID-19 on Saturday morning: 102,177,365 cases, 2,209,313 deaths

A screenshot from the Johns Hopkins Coronavirus COVID-19 (2019-nCoV) dashboard:

Daily case counts remain over 600,000. At this rate, we will see 120,000,000 cases by the end of February.

Trials raise fears coronavirus is learning to resist vaccines

Via The Los Angeles Times: Trials raise fears coronavirus is learning to resist vaccines. Excerpt:

New data showing that two COVID-19 vaccines are far less effective in South Africa than in other places they were tested have heightened fears that the coronavirus is quickly finding ways to elude the world’s most powerful tools to contain it.  

The U.S. company Novavax reported this week that although its vaccine was nearly 90% effective in clinical trials conducted in Britain, the figure fell to 49% in South Africa — and that nearly all the infections the company analyzed in South Africa involved the B.1.351 variant that emerged there late last year and has spread to the United States and at least 30 other countries.  

Johnson & Johnson announced Friday that its new shot was 72% effective against preventing moderate or severe illness in the United States, compared with 66% in Latin America and 57% in South Africa. 

Laboratory tests had suggested that the vaccines authorized in the U.S. — one from Pfizer and BioNTech, the other from Moderna and the National Institutes of Health — trigger a smaller immune response to the South Africa variant. 

Now there is evidence from tests in people that some variants are less vulnerable to certain vaccines. 

“From an evolutionary biology perspective, this is totally expected and anticipated,” said Dr. Michael Mina, a Harvard epidemiologist. “But it never feels good to be validated on something so scary.” 

Researchers once believed it would take several more months, or even years, for the virus to develop resistance to vaccines. They said the speedy evolution is largely a result of the virus’ unchecked spread.  

More than 100 million people have been infected worldwide, and each of those infections is an opportunity for the virus to randomly mutate.  

A mutation that happens to give the virus an advantage — the ability to resist the body’s natural defenses, for example — can become the basis for a heartier variant.

The relationship between cultural tightness–looseness and COVID-19 cases and deaths

Via The Lancet Planetary Health: The relationship between cultural tightness–looseness and COVID-19 cases and deaths: a global analysis. The summary: 

Background 

The COVID-19 pandemic is a global health crisis, yet certain countries have had far more success in limiting COVID-19 cases and deaths. We suggest that collective threats require a tremendous amount of coordination, and that strict adherence to social norms is a key mechanism that enables groups to do so. Here we examine how the strength of social norms—or cultural tightness–looseness—was associated with countries' success in limiting cases and deaths by October, 2020. We expected that tight cultures, which have strict norms and punishments for deviance, would have fewer cases and deaths per million as compared with loose cultures, which have weaker norms and are more permissive. 

Methods 

We estimated the relationship between cultural tightness–looseness and COVID-19 case and mortality rates as of Oct 16, 2020, using ordinary least squares regression. We fit a series of stepwise models to capture whether cultural tightness–looseness explained variation in case and death rates controlling for under-reporting, demographics, geopolitical factors, other cultural dimensions, and climate. 

Findings 

The results indicated that, compared with nations with high levels of cultural tightness, nations with high levels of cultural looseness are estimated to have had 4·99 times the number of cases (7132 per million vs 1428 per million, respectively) and 8·71 times the number of deaths (183 per million vs 21 per million, respectively), taking into account a number of controls. A formal evolutionary game theoretic model suggested that tight groups coordinate much faster and have higher survival rates than loose groups. The results suggest that tightening social norms might confer an evolutionary advantage in times of collective threat. 

Interpretation 

Nations that are tight and abide by strict norms have had more success than those that are looser as of the October, 2020. New interventions are needed to help countries tighten social norms as they continue to battle COVID-19 and other collective threats.

‘Immunological unicorn’: The Australian lab growing coronavirus – and its startling discovery

Thanks to Brenda Beagi for sending the link to this very interesting Guardian report: ‘Immunological unicorn’: the Australian lab growing coronavirus – and its startling discovery. Excerpt:

In a high security laboratory in Sydney, where a select group of researchers go to extreme lengths to work with samples of blood and swabs containing Covid-19, virologist Stuart Turville found a unicorn. 

“A beautiful, immunological unicorn,” Turville, an associate professor with the Kirby Institute at the University of New South Wales, said. 

“We found him when we were analysing samples from the Red Cross blood bank from people who have had Covid. And he had the most amazing Covid response I’ve ever seen.” 

The unicorn is a 50-year-old father of three named Damian living on the NSW Central Coast who developed symptoms of Covid-19 in March. His symptoms were severe enough to take him to the hospital emergency department, but after being given oxygen he was sent home the same day. Bizarrely, when he was tested for the virus with the gold-standard PCR nasal swab, the lab kept returning a negative result for Covid-19. 

“When they initially diagnosed him they couldn’t find virus in his nasopharyngeal area [the upper part of the throat behind the nose],” Turville told Guardian Australia. 

“So they kept on swabbing him and swabbing him, but they couldn’t find it. He kept on saying to them, ‘Look, I’m sick, my son’s got it, I have to have it’. And it was only when they looked at his blood, his serum, they said; ‘Oh, yeah, you’ve had it. And you’ve got the most amazing immune response’.”  

Most people who have Covid-19 develop a decent immune response. 

“But this guy’s response is 100 to 1,000-fold that,” Turville said.  

“His response is that good. To put it in context, we are eight or nine months out since he was infected. And he still ranks in the top 1% of responders, so what that means is if we could ever bottle a vaccine that could mimic his response, you’d want to do it. I would say that we’re going to see him responding just as well probably a year out, and maybe after about two years we might start to see some response decay.”

As Covid-19 vaccine rollout expands, Black Americans still left behind

Via NBC News, a KHN report by Hannah Recht and Lauren Weber: As Covid vaccine rollout expands, Black Americans still left behind. Excerpt:

Black Americans are still receiving Covid-19 vaccinations at dramatically lower rates than white Americans even as the chaotic rollout reaches more people, according to a new KHN analysis. 

Almost seven weeks into the vaccine rollout, states have expanded eligibility beyond front-line health care workers to more of the public — in some states to more older adults, in others to essential workers such as teachers. But new data shows that vaccination rates for Black Americans have not caught up to those of white Americans. 

Seven more states published the demographics of residents who have been vaccinated after KHN released an analysis of 16 states two weeks ago, bringing the total to 23 states with available data.  

In all 23 states, data shows white residents are being vaccinated at higher rates than Black residents, often at double the rate — or even higher. The disparities haven’t significantly changed with an additional two weeks of vaccinations.  

In Florida, for example, 5.5 percent of white residents had received at least one vaccine dose by Jan. 26, compared with 2.0 percent of Black residents. That’s about the same ratio as it was two weeks ago, when the rates were 3.1 percent and 1.1 percent, respectively. 

Black Americans are being left behind due to barriers stemming from structural racism, as well as a failure to address nuanced hesitancy and mistrust about the vaccines and the medical system overall. The ongoing vaccination gap has prompted officials from around the nation to call for action. 

“With Covid-19 continuing to take a disproportionate and deadly toll on communities of color, we need urgent solutions to address health inequities and crush this virus," said Rep. Steven Horsford (D-Nev.), first vice chair of the Congressional Black Caucus. He said he is working to pass legislation to address equity issues.

Second Brazil COVID-19 wave strains hospitals in Sao Paulo's interior

Via The Associated Press: Second Brazil wave strains hospitals in Sao Paulo's interior. Excerpt:

JAU, Brazil (AP) — Rodinei Silva made two trips this week to the Santa Casa de Jau hospital in the interior of Brazil’s Sao Paulo state. First, he brought his wife, who was suffering COVID-19 symptoms including trouble breathing. She tested positive, but was sent home with medication because space was scarce.

“There were no beds on Tuesday,” Silva, 65, said, adding that his wife’s condition is deteriorating at home. He returned to the hospital on Thursday because he was showing symptoms. Each day, several patients like Silva turn up at the hospital in the municipality of about 152,000 people, seeking treatment. But the facility also admits COVID-19 patients from 11 surrounding cities, and it reached capacity on Jan. 18.

Just as Brazil has a glimmer of hope with the start of vaccination, it is facing a dizzying second COVID-19 wave that is straining facilities’ ability to attend to patients. Intensive-care units in public hospitals have been maxed out in several states and municipalities across the country, including two state capitals in the remote Amazon and even some cities like Jau in Sao Paulo, the nation’s wealthiest state.

“This is perhaps the most difficult moment of the entire pandemic,” said Leonardo de Avila Lins, who leads the hospital’s intensive-care ward. Sao Paulo has seen a daily average of some 11,000 cases over the past two weeks, more than were confirmed during the state’s 2020 peak, according to official data. The 14-day average of some 230 daily deaths is a few dozen shy of the toll reached last year.

At Santa Casa de Jau, arriving patients are either placed in a temporary unit, created in mid-January when intensive-care space ran out, or sent to other hospitals. Pressure is increasing by the day, said Scila Carretero, the hospital’s administrative manager.

“Our concern is not being able to transfer these patients, and not being able to absorb them into our ICU,” Carretero said, adding that transfers are challenging and they’ve managed only two since Jan. 18. That means for the most part only accepting new patients once others are discharged or die.

As of Thursday, 20 patients waited in the makeshift COVID-19 unit for a spot to open in the ICU. In the span of less than four hours, Associated Press journalists saw five people with virus symptoms arrive.

Tanzania's leader denies COVID-19, and countrymen push back

Via The Associated Press: Tanzania's leader denies COVID-19, and countrymen push back. Excerpt:

NAIROBI, Kenya (AP) — Tanzania’s president says God has eliminated COVID-19 in his country. His own church now begs to differ. 

From the local Catholic authority warning this week of a new wave of coronavirus infections, to government institutions now requiring staffers to take precautions, populist President John Magufuli is being openly questioned as the African continent fights a strong resurgence in cases and deaths.  

“We are not an island,” the Catholic secretariat of the Tanzania Episcopal Conference said in a widely shared statement this week. It urged followers, which include the president, to pray but also to adopt measures long practiced in the rest of the world, including avoiding public gatherings and close personal contact. The church’s newspaper on Friday stressed in a large front-page headline: “There is corona.” 

Tanzania has tried to be an island since April, when the East African country of 60 million people stopped updating its number of virus infections at 509 cases. Some health officials who questioned Magufuli’s stance that COVID-19 had been defeated were fired. The government promoted international tourism, eager to avoid the economic pain of neighbors who imposed lockdowns and curfews. 

The president even praised Chinese Foreign Minister Wang Yi for not wearing a face mask during a visit this month, calling it another sign that Tanzania is free of the virus.  

But pandemic concerns have returned to the spotlight in Tanzania as the world focuses on the arrival of COVID-19 vaccines. 

While other African countries seek millions of doses, Magufuli this week accused people who had been vaccinated overseas of bringing the virus back into Tanzania. He also questioned whether the vaccines work.  

“If the white man was able to come up with vaccinations, then vaccinations for AIDS would have been brought, tuberculosis would be a thing of the past, vaccines for malaria and cancer would have been found,“ he said on Wednesday.  

“Be firm,” he added. “Vaccines are inappropriate.” He urged the health ministry not to rush into vaccinations without being satisfied about their safety. He offered no evidence for his claims.

US: State lawmakers are pushing to curb governors' COVID-19 powers

Via The Associated Press: State lawmakers are pushing to curb governors' virus powers. Excerpt:

Irritated by the sweeping use of executive orders during the COVID-19 crisis, state lawmakers around the U.S. are moving to curb the authority of governors and top health officials to impose emergency restrictions such as mask rules and business shutdowns.  

The push is underway in such states as Arizona, Michigan, Ohio, Maryland, Kentucky, Indiana and Pennsylvania, where legislators are seeking a constitutional amendment to strip the governor of many of his emergency powers. 

Pennsylvania Republican Sen. Wayne Langerholc said the amendment would “make it unequivocally clear that our General Assembly is a co-equal branch ... that we are not a monarchy and that our voices matter.”  

Democratic Gov. Tom Wolf and some of his counterparts around the country have argued that they need authority to act quickly and decisively against the fast-changing threat. 

The coronavirus has killed an estimated 430,000 Americans and is going through its most lethal phase yet, despite the rollout of vaccines, with new and more contagious variants from abroad turning up in the U.S.

State legislatures generally took on lesser roles after the pandemic hit, with many suspending work or adjourning. It has been governors or their top health officials who have set many of the policies — imposing mask mandates, limiting public gatherings and shutting down dine-in restaurants, gyms, hair salons and other businesses. 

Lawmakers in more than half the states have filed bills this year to limit gubernatorial powers during the pandemic and other emergencies, according to the National Conference of State Legislatures. Most legislatures began their sessions this month.

Vietnam: 91 new COVID-19 cases confirmed on January 28

Via VietnamPlus, bad news: 91 new COVID-19 cases confirmed on January 28. A second report is posted below this one.

Hanoi (VNA) – Vietnam recorded 91 new COVID-19 cases in the past 24 hours to 6pm on January 28, including 84 domestically-transmitted cases and seven imported cases, according to the National Steering Committee on COVID-19 Prevention and Control. 

The locally-transmitted cases were detected in the northern provinces of Hai Duong and Quang Ninh, with the first two cases being Patient No. 1,552, a 34-year-old woman in Hung Dao commune, Hai Duong’s Chi Linh city, and Patient No. 1,553, a 31-year-old man in Hong Ha ward, Quang Ninh’s Ha Long city. 

Meanwhile, the seven imported cases were a Costa Rican expert entering Vietnam from the US on January 24, and six Vietnamese returning home from the US on January 13.  

So far, Vietnam has seen 777 domestically-transmitted cases. Also on January 28, five patients were given the all-clear, bringing the total number of recoveries to 1,430. Death toll has maintained at 35. 

Among patients undergoing treatment at medical establishments across the country, 10 have been tested negative for the coronavirus once, 14 others twice and 12 thrice.  

At present, 21,636 people who had close contact with COVID-19 patients or entered Vietnam from pandemic-hit areas are under quarantine.

Vietnam Weekly has an update. An excerpt:

There’s no other way to put it: this is bad. After going 55 days without any known community transmission of the coronavirus, a huge outbreak has arrived. Yesterday, the Ministry of Health announced a staggering 98 new cases - the most in a single day since the pandemic began. Two community cases had been announced Wednesday evening.

And late last night, state media two more community infections: one in Bac Ninh Province, and one in Hanoi, both linked to Hai Duong. The health ministry hadn’t confirmed these cases at the time of writing (11:30pm), but this brings the day’s community transmission figure to 100.

This story started to develop on Wednesday, when Vietnamese media reported that a 32 year-old woman from Hai Duong Province tested positive for the UK variant of the coronavirus upon arrival in Japan on January 17. (For some reason local authorities in Hai Duong reportedly didn’t find out about this until 10 days later.) The woman had been working at a factory in Hai Duong and was sent to Japan on a labor contract, and her flight left Hanoi and connected through Singapore.

There were several instances last year when someone arriving in Japan from Vietnam tested positive for COVID-19, only to test negative on subsequent tests, and I was certainly hoping this was the case again, though it was worrying that Japanese health officials detailed a specific viral strain.

Following that news, her contacts were traced, leading to one new case Wednesday evening - a worker at the same factory, now Patient 1,552.

The second Wednesday case, a 31 year-old man, is apparently unrelated: he works at Van Don International Airport in Quang Ninh Province, which has handled numerous repatriation flights where passengers tested positive for COVID-19 in quarantine. It’s likely he caught it from a passenger, but it’s not known how much time passed between transmission and the onset of his symptoms, which include a fever, sore throat and coughing. He tested positive after visiting a health clinic, becoming Patient 1,553.