H5N1

Delta is worse. This time around, Alabama is facing a two-front war

Via The Washington Post, a powerful and disturbing op-ed by Dr. Michael Saag of the University of Alabama at Birmingham: Delta is worse. This time around, Alabama is facing a two-front war. Excerpt:

As we entered into the July Fourth weekend, many Americans celebrated as if the epidemic had ended: traveling in record numbers and engaging in large gatherings with no masks and no social distancing. All the while, many of those celebrating were unvaccinated and immunologically vulnerable. With the delta variant going from zero cases in March to 60 percent of cases by mid-July, we were approaching a near-perfect storm. 

Now we are in it. Cases are exploding. Here in Alabama, the state with the lowest vaccination rate (less than 35 percent), rates of infection have risen from less than three cases per 100,000 people four weeks ago to more than 54 cases per 100,000 this week. 

Suzanne Judd at the University of Alabama at Birmingham School of Public Health generated models that show, by Labor Day, cases will skyrocket to two to three times the peak we experienced in January. At our 1,157-bed hospital in Birmingham, Alabama’s largest, we have risen from three cases in-house in mid-June to more than 67 cases on Wednesday. Statewide, the rise exceeds 500 percent since July 4. 

These trends are terrifying and, as a virologist who had covid-19 last spring, I can say they induce a kind of pre-traumatic stress in our health-care workers. We know what’s coming. We’ve experienced this trauma before. We don’t want to do this again, but the die is already cast. My fellow health-care workers are being thrown back into the fire, like servicemen and women going back for a third tour of duty in a war zone. 

This week alone, one infectious-disease colleague and four ER physicians, all fully vaccinated, have become ill with the variant. This is very different from what we experienced before. Delta is different. 

With the current spike of cases, 99 percent of deaths are occurring in unvaccinated people. Almost all of these are preventable. That is particularly troublesome to health-care workers who struggle valiantly to save the lives of those who now present to the hospital, the vast majority of whom chose not to be vaccinated. 

Making it worse is the hate we experience from a small, but very real, group of people who seek to undermine our efforts through the steady release of misinformation in social media and elsewhere. I received an inquiry this week from a person who claimed to be a CNN reporter, initially asking me for information about delta and then demanding “proof” that delta is here. Despite my best effort to explain, I was berated with accusations that I was making this up. (He later posted most of the exchange on Facebook.) 

I am not alone in suffering these types of attacks. It is this sort of behavior that has led to poor vaccine uptake among many people and resulted in this new spike of cases. 

Despite the static and misinformation, we will get it done. It will be helpful, however, if this time around we pull together as a country, ignore those who spew hate and sow mistrust of those trying to serve the public. The virus is a formidable enemy and terrifying enough. We can’t afford to be fighting a two-front war.

Estimating SARS-CoV-2 infections from deaths, confirmed cases, tests, and random surveys

Thanks to CIDRAP for alerting us to this important study in PNAS: Estimating SARS-CoV-2 infections from deaths, confirmed cases, tests, and random surveys. Excerpt, with my bolding:

Significance

The novel coronavirus SARS-CoV-2 has infected over 33 million people in the United States. Nationwide, over 600,000 have died in the COVID-19 pandemic, which has necessitated shutdowns of schools and sectors of the economy. The extent of the virus’ spread remains uncertain due to biases in test data. 

We combine multiple data sources to estimate the true number of infections in all US states. These data include representative random testing surveys from Indiana and Ohio, which provide potentially unbiased prevalence estimates. 

We find that approximately 60% of infections have gone unreported. Even so, only about 20% of the United States had been infected as of early March 2021, suggesting that the country was far from herd immunity at that point. 

Abstract 

There are multiple sources of data giving information about the number of SARS-CoV-2 infections in the population, but all have major drawbacks, including biases and delayed reporting. For example, the number of confirmed cases largely underestimates the number of infections, and deaths lag infections substantially, while test positivity rates tend to greatly overestimate prevalence. Representative random prevalence surveys, the only putatively unbiased source, are sparse in time and space, and the results can come with big delays. Reliable estimates of population prevalence are necessary for understanding the spread of the virus and the effectiveness of mitigation strategies. 

We develop a simple Bayesian framework to estimate viral prevalence by combining several of the main available data sources. It is based on a discrete-time Susceptible–Infected–Removed (SIR) model with time-varying reproductive parameter. Our model includes likelihood components that incorporate data on deaths due to the virus, confirmed cases, and the number of tests administered on each day. 

We anchor our inference with data from random-sample testing surveys in Indiana and Ohio. We use the results from these two states to calibrate the model on positive test counts and proceed to estimate the infection fatality rate and the number of new infections on each day in each state in the United States. 

We estimate the extent to which reported COVID cases have underestimated true infection counts, which was large, especially in the first months of the pandemic. We explore the implications of our results for progress toward herd immunity.

Discussion

To craft and implement effective policy and mitigation strategies, policymakers need reliable assessments of the impact of previous nonpharmaceutical interventions on the transmission rate of the disease. We have developed a simple Bayesian model of the dynamics of SARS-CoV-2 transmission incorporating readily available time-series data tracking the virus, as well as statewide representative point-prevalence surveys conducted in Indiana and Ohio, which are the highest-quality random testing surveys carried out to date. We present estimates of the IFR and the time-varying viral prevalence and reproductive number r(t) in each US state on each day.

Our results indicate that a large majority of COVID infections go unreported. Even so, we find that the United States was still far from reaching herd immunity to the virus in early March 2021 from infections alone. This suggests that continued mitigation and an aggressive vaccination effort are necessary to surpass the herd-immunity threshold without incurring many more deaths due to the disease. This work demonstrates the value of random-sample testing in response to this and future pandemics.

By incorporating testing and case data aggregated over any period of time, our additive model for positive tests in Eq. 2 allows us to avoid using data at the daily level, which can be very unreliable. For example, the reported cumulative number of tests administered in a state may not be updated for up to 2 wk at a time, or it may decrease from one day to the next as data are deduplicated upon further review. The latter scenario frequently occurs with reported cases as well. Working with data at the daily level generally requires using some kind of moving average, which washes out stochasticity in the data and leads to oversmoothing inconsistent with the high overdispersion of SARS-CoV-2 transmission.

Our inference relies on daily reported deaths due to COVID in each state, as opposed to excess deaths. Because of the possibility of death misclassification, excess-death data represent a mix of confirmed COVID deaths and deaths from other causes. Nevertheless, relying on reported deaths is a potential source of bias, as they are affected by the accuracy of cause-of-death determinations. Their numbers can fall significantly below excess-death counts and may undershoot the true number of deaths due to the disease. Ascertainment of COVID deaths may vary between states, with the cumulative excess-death count since the start of the pandemic exceeding reported COVID deaths by upwards of 50% in some states, according to a New York Times analysis of Centers for Disease Control and Prevention (CDC) mortality data. Consequently, our results may underestimate viral incidence in those states.

The CDC estimated a total of 83 million infections in the United States through December 2020, which is substantially larger than our estimate of 50 million infections in that period. Their numbers are based on the work of Reese et al., who infer COVID incidence in the United States using a multiplier model to account for underdetection in the number of confirmed cases. Beyond the limitations of our study discussed above, there are a few possible explanations for the difference in our estimates. Reese at al. base their estimates on nationally reported laboratory-confirmed cases, which do not constitute a probabilistic sample of the population. To this point, the authors remark that “…some infections, such as those among healthcare workers or from outbreaks in congregate residential settings, may be more likely to be tested and nationally reported compared with the general population, and could overestimate nonhospitalized cases and infections.”

Furthermore, the multiplier in their model relies on documented rates of test administration and care-seeking among symptomatic COVID patients. Reese et al. note that data on rates of test administration in this group are limited, especially at the local level. As such, Reese et al. do not account for geographic variation in testing, which is a potential source of bias.

Doctors, nurses and other health groups call for mandatory vaccinations for all health workers

Via The Washington Post: Doctors, nurses and other health groups call for mandatory vaccinations for all health workers. Excerpt:

Medical groups representing millions of doctors, nurses, pharmacists and other health workers on Monday called for mandatory vaccinations of all U.S. health personnel against the coronavirus, framing the move as a moral imperative as new infections mount sharply. 

“We call for all health care and long-term care employers to require their employees to be vaccinated against covid-19,” the American Medical Association, the American Nurses Association and 55 other groups wrote in a joint statement shared with The Washington Post. “The health and safety of U.S. workers, families, communities, and the nation depends on it.” 

The statement — issued by many groups calling for a mandate for the first time — represents an increasingly tough stance by the medical and public health establishment amid the sluggish pace of national vaccinations. It comes as new cases rip through the nation, driven by the hyper-transmissible delta variant. Confirmed coronavirus infections have nearly quadrupled during July, from about 13,000 cases per day at the start of the month to more than 50,000 now, according to The Post’s tracking. Hospital leaders in states such as Alabama, Florida and Missouri have implored holdouts to get vaccinated, citing data that the shots prevent hospitalizations and even death. 

But many workers in the health field remain unvaccinated, despite having priority access to coronavirus vaccines, which first became available in December. More than 38 percent of nursing home staff were not fully vaccinated as of July 11, despite caring for patients at elevated risk from the coronavirus, according to data collected by the Centers for Medicare and Medicaid Services and analyzed by LeadingAge, which represents nonprofit nursing homes and other providers of elder care. 

An analysis by WebMD and Medscape Medical News estimated that about 25 percent of hospital workers who had contact with patients had not been vaccinated by the end of May.

Indonesia reports record number of doctor deaths from COVID-19 in July

Via Reuters: Indonesia reports record number of doctor deaths from COVID-19 in July. Excerpt:

JAKARTA, July 18 (Reuters) - Deaths of doctors from COVID-19 in Indonesia rose sharply in the first half of July, according to the profession's association, as the Delta variant of the coronavirus fuelled a surge in infections across the country. 

A total of 114 doctors died during July 1-17, the highest number reported for any period of similar length and more than 20% of the 545 total doctor deaths from COVID-19 since the beginning of the pandemic, officials from Indonesia's doctors association (IDI) said during a virtual news conference. 

Mahesa Paranadipa, a senior IDI official, said the association was concerned that the medical system may not be able to cope, according to a recording of the event. 

"We are worried about the potential of a functional collapse," Paranadipa. "This is the reported data, not yet data that may not have been reported to us."

Doctors deaths have increased in Indonesia, the world's fourth most-populous nation, despite a 95% vaccination rate among health workers. This has prompted the government to use a batch of Moderna vaccines as booster shots to China's Sinovac for healthcare workers. 

Fuelled by the spread of the more virulent Delta variant, Indonesia has reported more new coronavirus cases than any country in the world in recent days, data from the latest seven-day average from a Reuters tracker showed. It was second only to Brazil in terms of the number of deaths. 

Health experts are calling the country the new epicentre of the pandemic. Indonesia reported 44,721 cases and 1,093 new deaths from the virus on Sunday.

COVID-19 creates conditions for emergence of 'superfungus' in Brazil

Via medicalexpress.com, a FAPESP report: COVID-19 creates conditions for emergence of 'superfungus' in Brazil. Excerpt:

Fully occupied intensive care units (ICUs). Physically and mentally exhausted health workers. Chaotically overcrowded hospitals. These and similar problems posed by the COVID-19 pandemic in Brazil have created ideal conditions for the emergence of Candida auris, a microorganism some are calling a "superfungus" because of the speed with which it has developed drug resistance. 

The first two cases were confirmed in December 2020 at a hospital in Salvador (state of Bahia, Northeast Brazil), and are described in the Journal of Fungi by a group of researchers led by Arnaldo Colombo, head of the Special Mycology Laboratory at the Federal University of São Paulo (UNIFESP). The study was supported by São Paulo Research Foundation—FAPESP. 

"Nine other C. auris patients have since been diagnosed at the same hospital, some colonized [with the fungus in their organism but not doing harm] and others infected," Colombo told. "No other cases have been reported in Brazil, but there are grounds for concern. We're monitoring the evolutionary characteristics of C. auris isolates from patients at the hospital in Salvador, and we've already found samples with reduced sensitivity to fluconazole and echinocandins. The latter belong to the main class of drugs used to treat invasive candidiasis." 

Except for C. auris, fungi of the genus Candida are part of the human gut microbiota and cause problems only when there are imbalances in the organism, Colombo explained. These include infections such as vaginal yeast infection and thrush (oral candidiasis), often caused by C. albicans. 

In some cases, however, the fungus enters the bloodstream and causes a systemic infection known as candidemia, the most common form of invasive candidiasis, similar to bacterial sepsis. Invasion of the bloodstream and the immune system's exacerbated response to the pathogen can cause damage to several organs and even lead to death. According to scientific evidence, mortality among candidemia patients infected by C. auris can reach 60%. 

"The species quickly becomes resistant to multiple drugs and isn't very sensitive to the disinfectants used by hospitals and clinics," Colombo said. "As a result, it's able to persist in hospitals, where it colonizes health workers and ends up infecting patients with severe COVID-19 and other long-stay critical patients."

‘It’s a little late’: US orders healthcare worker protections after thousands die

Via The Guardian: ‘It’s a little late’: US orders healthcare worker protections after thousands die. Excerpt:

US labor department officials on Thursday announced a temporary emergency standard to protect healthcare workers, saying they face “grave danger” in the workplace from the coronavirus pandemic. 

The new standard would require employers to remove workers who have Covid-19 from the workplace, notify workers of Covid exposure at work and strengthen requirements for employers to report worker deaths or hospitalizations to the Occupational Safety and Health Administration (Osha). 

“These are the workers who continue to go into work day in and day out to take care of us, to save our lives,” said Jim Frederick, acting assistant secretary of labor for occupational safety and health. “And we must make sure we do everything in our power to return the favor to protect them.” 

The new rules are set to take effect immediately after publication in the Federal Register and are expected to affect about 10.3 million healthcare workers nationwide. 

The government’s statement of reasons for the new rules cites the work of KHN and the Guardian in tallying more than 3,600 healthcare worker Covid deaths through 8 April. Journalists documented far more deaths than the limited count by the Centers for Disease Control and Prevention, which through May tallied 1,611 deaths on case-reporting forms that were often incomplete. 

The Lost on the Frontline project documented early calls for better respiratory protection for healthcare workers than loose-fitting face masks, noted serious complaints to Osha from hospital workers that went unaddressed and revealed repeated employer failures to report dozens of worker deaths. It also found that healthcare employers were often remiss in notifying workers about exposure to the coronavirus on the job. 

The new standard would address some of those problems.

50 doctors reported dead in 1 day from Covid-19 across India: Medical body

Via NDTV.com: 50 Doctors Reported Dead In 1 Day From Covid-19 Across India: Medical Body. And even that, as the end of the report suggests, is likely a severe undercount.

New Delhi: Anas Mujahid, 26, a junior Resident Doctor at Delhi's Guru Teg Bahadur Hospital  -- a dedicated Covid specialty -- died within hours of testing positive due to Covid. He is the youngest of 244 doctors who have lost their lives to Covid this year in India's second wave. Last year, 736 doctors had lost their lives during the first wave. A total of nearly 1,000 doctors across India have lost their lives due to Covid so far. 

Mujahid is survived by his parents and four siblings. 

A week has gone by, but his friend and colleague Dr Aamir Sohail is still struggling to come to terms with the loss. 

Mujahid had minor symptoms like sore throat and tested positive in an antigen test at the hospital. In a rare case of sudden progression, he collapsed soon after and died due to intracranial bleeding. He had not been vaccinated. 

"It was shocking. He had no comorbidity. His parents also told us that he has never faced any health issue. We just could not understand how it happened," Dr Aamir Sohail said. 

"He had not been vaccinated. Many colleagues here, including me, have not taken the jab. Our process of getting vaccinated while being on Covid duty, is long. We have to inform superiors and get their signature etc. He was planning to get the jab in the next few days." 

Dr Sohail added that he got infected last month and had moderate symptoms and is now doing fine. But he said it was hard to comprehend how his friend, who seemed perfectly fine hours ago, suddenly faced such severe issues and died. 

According to the Indian Medical Association, 244 doctors have lost their lives due to Covid in the second wave. Of them, 50 deaths were recorded yesterday. The highest number of fatalities have been reported from Bihar (69) followed by Uttar Pradesh (34) and Delhi (27). 

Only 3 per cent of these doctors were fully vaccinated. 

Five months into India's vaccination drive, only 66 per cent of India's healthcare workers have been fully vaccinated. The IMA said it is making all possible efforts to encourage doctors to take the jab. 

Dr Jayesh Lele, the General Secretary of IMA, told NDTV, "It is very unfortunate that we lost 50 doctors yesterday across India and 244 in the second wave since the first week of April". 

The IMA, he said, has found that many doctors have not taken the vaccine and the organisation will do everything it can to ensure that all doctors who are on the frontline take the jab. PromotedListen to the latest songs, only on JioSaavn.com 

"Secondly we want to highlight that doctors are understaffed and overworked. They sometimes work for 48 hours at a stretch without any rest. This adds to the viral load and they ultimately succumb to the infection. The government needs to take measures to boost the healthcare workforce," he added. 

While the IMA says that a thousand doctors have died due to Covid so far, the actual numbers may be far higher. The IMA only keeps a record of its nearly 3.5 lakh members. India, however, has more than 12 lakh doctors.

Vietnam: The outbreak grows

Via Mike Tatarski's excellent Vietnam Weekly: The Outbreak Grows. Excerpt:

Before Friday’s infection updates, the Ministry of Health had logged 120 local COVID-19 cases since this new wave began on April 29. That has now grown to 411 cases of community infection: 120 in Hanoi, 85 in Bac Ninh, 52 in Vinh Phuc and 37 in Bac Giang. Those neighboring provinces make up the bulk of cases, though Da Nang has turned into a hotspot of its own with 48 infections. 

Overall, cases have been found in 26 provinces and cities, while almost 60,000 people nationwide are in some form of quarantine due to exposure to known cases. 

Here in Ho Chi Minh City, the situation is still in good shape, though this week will be different since schools are now closed. 

One concerning aspect of this latest outbreak is its spread into medical facilities: at least 10 hospitals in Hanoi (including a public cancer hospital) and elsewhere are currently locked down. Hospital clusters are what made the Da Nang outbreak last fall so dangerous. In fact, all 35 of Vietnam’s COVID-19 deaths came from that. 

It’s been hard to keep track of exactly where all these cases came from, though we know that many are linked to foreign experts who tested positive after completing quarantine. A karaoke bar in Vinh Phuc has also been linked to a number of cases. 

Nationwide contact tracing is ongoing, and hundreds of direct and indirect contacts have been found for a known patient who went to Da Lat over the Reunification Day holiday - that city was absolutely packed at the time. 

Minister of Health Nguyen Thanh Long has warned of the dangers of this outbreak given the presence of different strains and also multiple initial infection points (the index patient hasn’t been found in some areas). 

In vaccine news, 851,513 Oxford/AstraZeneca doses have been injected, meaning the health ministry has used almost all of the 917,600 doses it has received thus far. There is no word on when more deliveries may arrive. Last Friday, Vietnam reported its first death related to the vaccine, a 35 year-old medical worker in An Giang Province. She died of anaphylaxis.

Outbreak Brief 4: Ebola virus disease (EVD) outbreak

Via Africa CDC and published on March 16: Outbreak Brief 4: Ebola virus disease (EVD) Outbreak.

Outbreak Update: Since the last brief (9 March 2021), one new probable case, two new deaths, and four new recoveries of Ebola virus disease (EVD) have been reported from the Democratic Republic of Congo (DR Congo) and Guinea. Cumulatively, 30 EVD cases, 15 deaths (CFR: 50%), and eight recoveries have been reported from DR Congo (12 cases; 6 deaths; 2 recoveries) and Guinea (18; 9; 6). Seven healthcare workers are amongst the confirmed cases: DR Congo (2) and Guinea (5). 

● DR Congo updates: Since the last brief, one new probable case, one new death, and no new recoveries from EVD have been reported. Cumulatively, 12 cases (11 confirmed and 1 probable) with six deaths (CFR: 50%), and two recoveries have been reported. See Table 1 for the breakdown by health zone. 

● Guinea updates: Since the last brief, no new confirmed cases or deaths have been reported. However, four new recoveries have been reported in Nzérékoré. Cumulatively, 18 cases (14 confirmed, 4 probable), nine deaths (CFR: 50%), and six recoveries have been reported. See Table 1 for the breakdown by region and sub-prefecture. 

● Cross-border updates: Between 15 February to 12 March 2021, 18 EVD-related alerts were reported in Sierra Leone. All alerts were investigated and tested negative for EVD by PCR. As of today no confirmed case has been reported from Sierra Leone.

6 deaths from Ebola in Guinea: A serious mistake that costs money?

Via Guineematin.com: 6 deaths from Ebola in Guinea: a serious mistake that costs money? Now the question is: Where and how did the old woman, nurse Lucie Haba's stepmother, acquire Ebola? The Google translation:

A serious error by the agents of the Gouéké health center would have favored the spread of the Ebola virus, which reappeared recently in this sub-prefecture located more than 40 kilometers from the city of N'Zérékoré (in southern Guinea). The latter would have made a false diagnosis on a patient they received in December 2020 and who would be the first case of Ebola.

It was the health authorities of N'Zérékoré who announced the news on Wednesday, February 17, 2021, reports the correspondent of Guineematin.com on the spot. Contrary to what has been announced so far, the Ebola virus did not reappear at the end of January in Guinea, but long before. The nurse who died between January 27 and January 2021 is therefore not the first victim of this disease. 

Her stepmother, a 70-year-old who died in December 2020 at the Gouéké health center, is said to be patient zero (the first case). In any case, this is what the daily report of the Ebola hemorrhagic fever response teams published this Wednesday, February 17 in N'Zérékoré. 

According to this report, the old woman was hospitalized at the Gouéké health center after developing a vaginal hemorrhage. Health workers who diagnosed her concluded that she had "severe anemia". But, a few weeks after her death, the nurse who was caring for her and who happened to be her stepdaughter fell ill and also died. Several people who attended her funeral subsequently fell ill and three of them died. 

This is why, a few days after the tests which revealed the presence of the Ebola virus disease in Gouéké, the health authorities decided to count the old woman among the victims of Ebola. Which makes 6 deaths caused by the epidemic since its resurgence in Guinea. Deaths, most of which are believed to be due to the false diagnosis made by the health workers who received the first patient and which led to new contaminations. 

As for contacts, they went from 164 to 216 in N'Zérékoré, announce the health authorities.