H5N1

In Los Angeles and beyond, oxygen is the latest Covid-19 bottleneck

Via KHN.org, a report by Rae Ellen Bichell and Lauren Weber: In Los Angeles and Beyond, Oxygen Is the Latest Covid Bottleneck. Excerpt:

As Los Angeles hospitals give record numbers of covid patients oxygen, the systems and equipment needed to deliver the life-sustaining gas are faltering.  

It’s gotten so bad that Los Angeles County officials are warning paramedics to conserve it. Some hospitals are having to delay releasing patients as they don’t have enough oxygen equipment to send home with them.  

“Everybody is worried about what’s going to happen in the next week or so,” said Cathy Chidester, director of the L.A. County Emergency Medical Services Agency. 

Oxygen, which makes up 21% of the Earth’s air, isn’t running short. But covid damages the lungs, and the crush of patients in hot spots such as Los Angeles, the Navajo Nation, El Paso, Texas, and in New York last spring have needed high concentrations of it. That has stressed the infrastructure for delivering the gas to hospitals and their patients.  

The strain in those areas is caused by multiple weak links in the pandemic supply chain. In some hospitals that pipe oxygen to patients’ rooms, the massive volume of cold liquid oxygen is freezing the equipment needed to deliver it, which can block the system.  

“You can completely — literally, completely — shut down the entire hospital supply if that happens,” said Rich Branson, a respiratory therapist with the University of Cincinnati and editor-in-chief of the journal Respiratory Care.

There is also pressure on the availability of both the portable cylinders that hold oxygen and the concentrators that pull oxygen from the air. And in some cases, vendors that supply the oxygen have struggled to get enough of the gas to hospitals. Even nasal cannulas, the tubing used to deliver oxygen, are now running low. 

“It’s been nuts, absolutely nuts,” said Esteban Trejo, general manager of Syoxsa, an industrial and medical gas distributor based in El Paso. He provides oxygen to several temporary hospitals set up specifically to treat people with covid. 

In November, he said, he was answering calls in the middle of the night from customers worried about oxygen supplies. At one point, when the company’s usual supplier fell through, they were hauling oxygen from Houston, more than a 10-hour drive each way. 

Branson has been sounding the alarm about logistical limitations on critical care since the SARS pandemic nearly 20 years ago, when he and others surveyed experts about the specific equipment and infrastructure needed during a future pandemic. Oxygen was near the top of the list.

Was COVID-19 in Los Angeles last December?

Via the Journal of Medical Internet Research: Excess Patient Visits for Cough and Pulmonary Disease at a Large US Health System in the Months Prior to the COVID-19 Pandemic: Time-Series Analysis. The abstract and then a comment:

Background: Accurately assessing the regional activity of diseases such as COVID-19 is important in guiding public health interventions. Leveraging electronic health records (EHRs) to monitor outpatient clinical encounters may lead to the identification of emerging outbreaks. 

Objective: The aim of this study is to investigate whether excess visits where the word “cough” was present in the EHR reason for visit, and hospitalizations with acute respiratory failure were more frequent from December 2019 to February 2020 compared with the preceding 5 years. 

Methods: A retrospective observational cohort was identified from a large US health system with 3 hospitals, over 180 clinics, and 2.5 million patient encounters annually. Data from patient encounters from July 1, 2014, to February 29, 2020, were included. Seasonal autoregressive integrated moving average (SARIMA) time-series models were used to evaluate if the observed winter 2019/2020 rates were higher than the forecast 95% prediction intervals. The estimated excess number of visits and hospitalizations in winter 2019/2020 were calculated compared to previous seasons. 

Results: The percentage of patients presenting with an EHR reason for visit containing the word “cough” to clinics exceeded the 95% prediction interval the week of December 22, 2019, and was consistently above the 95% prediction interval all 10 weeks through the end of February 2020. Similar trends were noted for emergency department visits and hospitalizations starting December 22, 2019, where observed data exceeded the 95% prediction interval in 6 and 7 of the 10 weeks, respectively. 

The estimated excess over the 3-month 2019/2020 winter season, obtained by either subtracting the maximum or subtracting the average of the five previous seasons from the current season, was 1.6 or 2.0 excess visits for cough per 1000 outpatient visits, 11.0 or 19.2 excess visits for cough per 1000 emergency department visits, and 21.4 or 39.1 excess visits per 1000 hospitalizations with acute respiratory failure, respectively. 

The total numbers of excess cases above the 95% predicted forecast interval were 168 cases in the outpatient clinics, 56 cases for the emergency department, and 18 hospitalized with acute respiratory failure.  

Conclusions: A significantly higher number of patients with respiratory complaints and diseases starting in late December 2019 and continuing through February 2020 suggests community spread of SARS-CoV-2 prior to established clinical awareness and testing capabilities. This provides a case example of how health system analytics combined with EHR data can provide powerful and agile tools for identifying when future trends in patient populations are outside of the expected ranges.

See this Washington Post article for a discussion of the study. It does seem clear that COVID-19 was touring the world well before New Year's Eve.

WHO: Pulse survey on continuity of essential health services during the COVID-19 pandemic

A news release from WHO about its Pulse survey on continuity of essential health services during the COVID-19 pandemic: interim report, 27 August 2020. 

The World Health Organization (WHO) today published a first indicative survey on the impact of COVID-19 on health systems based on 105 countries’ reports. Data collected from five regions over the period from March to June 2020 illustrate that almost every country (90%) experienced disruption to its health services, with low- and middle-income countries reporting the greatest difficulties. Most countries reported that many routine and elective services have been suspended, while critical care - such as cancer screening and treatment and HIV therapy – has seen high-risk interruptions in low-income countries.

"The survey shines a light on the cracks in our health systems, but it also serves to inform new strategies to improve healthcare provision during the pandemic and beyond,” said Dr Tedros Adhanom Ghebreyesus, WHO Director-General. "COVID-19 should be a lesson to all countries that health is not an ‘either-or’ equation. We must better prepare for emergencies but also keep investing in health systems that fully respond to people’s needs throughout the life course."

Services hit across the board: Based on reports from key informants, countries on average experienced disruptions in 50% of a set of 25 tracer services. The most frequently disrupted areas reported included routine immunization – outreach services (70%) and facility-based services (61%), non-communicable diseases diagnosis and treatment (69%), family planning and contraception (68%), treatment for mental health disorders (61%), cancer diagnosis and treatment (55%).

Countries also reported disruptions in malaria diagnosis and treatment (46%), tuberculosis case detection and treatment (42%) and antiretroviral treatment (32%). While some areas of health care, such as dental care and rehabilitation, may have been deliberately suspended in line with government protocols, the disruption of many of the other services is expected to have harmful effects on population health in the short- medium- and long-term.

Potentially life-saving emergency services were disrupted in almost a quarter of responding countries. Disruptions to 24-hour emergency room services for example were affected in 22% of countries, urgent blood transfusions were disrupted in 23% of countries, emergency surgery was affected in 19% of the countries.

Disruption due to a mix of supply and demand side factors. 76% of countries reported reductions in outpatient care attendance due to lower demand and other factors such as lockdowns and financial difficulties. The most commonly reported factor on the supply side was cancellation of elective services (66%). Other factors reported by countries included staff redeployment to provide COVID-19 relief, unavailability of services due to closings, and interruptions in the supply of medical equipment and health products.

Adapting service delivery strategies. Many countries have started to implement some of the WHO recommended strategies to mitigate service disruptions, such as triaging to identify priorities, shifting to on-line patient consultations, changes to prescribing practices and supply chain and public health information strategies. However, only 14% of countries reported removal of user fees, which WHO recommends to offset potential financial difficulties for patients.

The pulse survey also provides an indication of countries’ experiences in adapting strategies to mitigate the impact on service provision. Despite the limitations of such a survey, it highlights the need to improve real-time monitoring of changes in service delivery and utilization as the outbreak is likely to wax and wane over the next months, and to adapt solutions accordingly.

To that end, WHO will continue to work with countries and to provide supportive tools to address the fallout from COVID-19. Given countries’ urgent demand for assistance during the pandemic response, WHO is developing the COVID19: Health Services Learning Hub, a web-based platform that will allow sharing of experiences and learning from innovative country practices that can inform the collective global response. WHO is also devising additional surveys at the sub-national level and in health facilities to gauge the longer-term impact of disruptions and help countries weigh the benefits and risks of pursuing different mitigation strategies.

How a single superspreading event sent COVID-19 across Massachusetts and the world

Via The Washington Post: How a single superspreading event sent coronavirus across Massachusetts and the world. Excerpt:

None of the biotech executives at the meeting noticed the uninvited guest. They had flown to Boston from across the globe for the annual leadership meeting of the drug company Biogen, and they were busy catching up with colleagues and hobnobbing with upper management. For two days they shook hands, kissed cheeks, passed each other the salad tongs at the hotel buffet, never realizing that one among their number carried the coronavirus in their lungs. 

By the meeting’s end on Feb. 27, the infection had infiltrated many more people: a research director, a photographer, the general manager for the company’s east division. They took the virus home with them to the Boston suburbs, Indiana and North Carolina, to Slovakia, Australia and Singapore. 

Over the following two weeks, the virus that circulated among conference attendees was implicated in at least 35 new cases. In April, the same distinctive viral sub-strain swirled through two Boston homeless shelters, where it infected 122 residents.  

Scientists know all this thanks to a mistake made during the coronavirus’s replication process — a simple switch of two letters in the virus’s 30,000-character genetic code. This mutation appeared in two elderly patients in France at almost exactly the same time that genetically matching viruses were sickening dozens of people at the Biogen meeting. After the conference, each time the infection spread, the mutation spread with it.  

Now, a sweeping study of nearly 800 coronavirus genomes, conducted by no fewer than 54 researchers at the Broad Institute, Massachusetts General Hospital, the Massachusetts Department of Public Health and several other institutions in the state, has found that viruses carrying the conference’s characteristic mutation infected hundreds of people in the Boston area, as well as victims from Alaska to Senegal to Luxembourg. As of mid-July, the variant had been found in about one-third of the cases sequenced in Massachusetts and 3 percent of all genomes studied thus far in the United States. 

The study, which was added Tuesday to the preprint website MedRxiv, is probably the largest genomic analysis of any U.S. outbreak so far and is among the most detailed looks at how coronavirus cases exploded in the pandemic’s first wave.

California's public health director resigns amid questions about COVID-19 test data

Via The Los Angeles Times: California's public health director resigns amid questions about coronavirus test data. Excerpt:

SACRAMENTO —  Gov. Gavin Newsom’s director of the California Department of Public Health resigned on Sunday, an abrupt departure of a key advisor in the state’s coronavirus battle just days after the discovery of a computer system failure that resulted in the undercounting of COVID-19 cases. 

Dr. Sonia Angell, who held the position for less than a year, announced her resignation in an email sent to department staff that was released by the California Health and Human Services Agency. 

“Since January, when we got word of repatriation flights arriving from Wuhan, China, our department has been front and center in what has become an all-of-government response of unprecedented proportions to COVID-19,” Angell wrote in the email to public health staff members. “In the final calculation, all of our work, in aggregate, makes the difference.”  

Angell’s decision to step aside comes at a crucial moment in California’s battle against the spread of the virus. More than 10,000 Californians have died from the disease, and 38 of the state’s 58 counties are on a watchlist that has required the closure of businesses that had briefly reopened in the early summer and K-12 schools as the academic year begins. Angell, who frequently has appeared alongside Newsom in his public briefings on the state’s efforts to combat the pandemic, was considered a key player in the coordination with local public health departments across the state. 

“I want to thank Dr. Angell for her service to the state and her work to help steer our public health system during this global pandemic, while never losing sight of the importance of health equity,” the governor said in a written statement Sunday night.  

Last week, state officials confirmed that as many as 300,000 records had not been processed by the computer clearinghouse system relied upon to provide to local officials the COVID-19 test results reported by labs on a daily basis. Two separate errors were identified — one related to a computer server outage, the other to the expiration of an electronic certificate for data to be transferred from Quest Laboratories.  

Administration officials insisted they did not know the extent of the problem until after Newsom’s public event on Aug. 3 in which he expressed optimism that current case numbers — lower than some had expected — meant some progress in the state’s efforts. But some local officials were sent communications the week before from the state Department of Public Health acknowledging a problem with the CalREDIE computer system.  

Dr. Mark Ghaly, the secretary of the California Health and Human Services Agency, said on Friday that a full investigation was underway to determine what happened. And although he said that he had become aware of the “magnitude” of the problem only after Newsom’s public statements, some state officials had information on the problem earlier.

COVID-19 live updates: Cases are surging along the US Gulf Coast

Via The New York Times, a grim afternoon roundup: Coronavirus Live Updates: Cases Are Surging Along the U.S. Gulf Coast. Click or tap through to read the stories listed in the bullet points:

Known cases surpassed four million in the United States. The White House and Senate Republicans neared agreement on a proposal for the next round of virus relief.  

RIGHT NOW Another study showing that a malaria drug that was heavily promoted — and even taken — by President Trump did not improve the conditions of patients with Covid-19 was published in the New England Journal of Medicine. 

Here’s what you need to know: 

• Texas and Florida have drawn attention, but the virus is surging in Alabama, Louisiana and Mississippi too. 

• The U.S. passes four million known cases, as hospitalizations and deaths rise. 

• Draft Republican virus aid proposal reflects significant retreat by White House on tax cuts, testing and schools. 

• U.S. testing continues to falter with more shortages in lab equipment. 

• Another study shows that the drug hydroxychloroquine didn’t help Covid-19 patients. 

• As Trump calls for schools to reopen fully for in-person instruction, his son’s school says it will not. 

• ‘Untrue and unacceptable’: Officials at the W.H.O. reject reported criticism from Pompeo.

COVID-19 report: India reports record spike as cases double in South Africa

Via The Guardian: Coronavirus report: India reports record spike as cases double in South Africa. Excerpt:

India reported a record spike in coronavirus cases on Saturday, taking the national total to more than 800,000 and pushing several states to bring back lockdowns, despite the punitive economic cost. 

Now the world’s third-worst affected country by case load, it reported a spike of 27,114 cases on Saturday, although mortality rates have been lower than in other badly affected countries with confirmed death toll now 22,123.  

The country’s most populous state of Uttar Pradesh, home to nearly 230 million people, imposed a weekend lockdown. Several others announced restrictions in districts reporting large spikes. 

India is one of several countries that appeared to have had success containing Covid-19 with lockdowns but after easing controls saw the disease come roaring back.  

South Africa, which had one of the strictest lockdowns in the world but started easing it under economic pressure, has also seen confirmed cases double over the past two weeks, with extreme inequality exacerbating the outbreak. 

In Johannesburg, oxygen concentrators, which help people with Covid-19 breathe, are hard to find as private businesses and individuals are buying them up, AP reported. 

Meanwhile, South Africa’s struggling public hospitals are short on medical oxygen and are seeing a higher proportion of deaths than in private ones, the National Institute for Communicable Diseases said. 

There have been more than 12m cases worldwide and more than half a million confirmed deaths, according to data from Johns Hopkins university.  

From Texas to Johannesburg, hospitals are being overwhelmed by patients. Scenes that first played out in Wuhan in January, and became grimly familiar in Iran and Europe through the spring, are repeating around the world.  

The busiest hospitals in Houston are increasingly telling emergency responders they cannot safely accept new admissions as hundreds of coronavirus patients crowd emergency rooms, ProPublica and NBC reported.  

The Texas governor, Greg Abbott, has warned residents “the worst is yet to come” after a week in which coronavirus diagnoses exceeded 10,000 new cases per day on Tuesday.

Tennessee: Daily COVID-19 data report delay June 28, 2020

A statement on the website of the Tennessee Department of Health: TDH Daily COVID-19 Data Report Delay June 28, 2020. The statement and then a comment:

NASHVILLE, Tenn. – The Tennessee Department of Health will not issue data on COVID-19 cases and tests on Sunday, June 28, 2020 due to an unplanned shutdown of the state surveillance system. TDH will resume daily provision of case counts and additional data once the system returns to full functionality and complete and accurate data can be provided.  

TDH uses the National Electronic Disease Surveillance System Base System, known as NBS, developed by the Centers for Disease Control and Prevention to help local, state and territorial health departments manage reportable disease data and send it to CDC. This system houses data for all reportable diseases in Tennessee, including COVID-19, and is the system health department staff members use to perform public health case investigations.  

Due to an extremely high volume of both COVID-19 and other laboratory test results being reported, there have been recent intermittent backlogs of labs in queue to be imported into the NBS system. This issue is not unique to Tennessee, and is affecting all NBS jurisdictions. The TDH team has been working closely with the NBS vendor and Tennessee State Government information technology support to quickly implement fixes that have been identified. 

At approximately 2 a.m. CDT June 28, the element of NBS that imports laboratory results encountered an unplanned shutdown. This issue was corrected by TDH and state information technology teams, and laboratory imports to NBS were restarted by 11 a.m.  

Due to the ongoing backlog and this unplanned shutdown, a limited number of COVID-19 test results were imported into NBS in the last 24 hours. TDH will not release updated COVID-19 numbers today since our data are incomplete. This will also affect our metropolitan health department partners and their data updates tomorrow. 

These technical issues may cause a delay in local public health officials contacting people recently diagnosed with COVID-19. Please consult information online or contact your local health department if you were recently diagnosed with COVID-19 and have questions about next steps.

All we need now is for the Merry Pranksters of St. Petersburg to start hacking NBS. 

COVID-19 heralds a new era for chronic diseases in primary care

An editorial in The Lancet Respiratory Medicine: COVID-19 heralds a new era for chronic diseases in primary care.

On March 23, 2020, the UK Government enforced a country-wide lockdown in response to the COVID-19 pandemic to limit transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although spread of the virus has been reduced, the lockdown has created new challenges for primary care practitioners who manage patients with chronic respiratory diseases (CRDs). However, there have also been opportunities for innovation, especially in terms of digital and remote working, and these solutions could be maintained and developed further to improve primary health-care services as we recover from the pandemic. 

The threat of COVID-19 is a serious concern for patients with CRDs and their primary care providers. Challenges that these patients already face related to their illness include an increased risk of depression, and feelings of isolation and loneliness, which might have been amplified during lockdown, without the usual support from health-care providers, family, and friends. Although the virus might have acted as a catalyst for patients with CRDs to access online support groups and self-management tools to reduce feelings of isolation, and to improve their knowledge about their illness. Improved adherence to preventer medications for those with asthma and COPD has been reported, to the extent that inhaled corticosteroid inhalers were in short supply at one point during lockdown in the UK. This shift in patient behaviour provides an opportunity for primary care providers to actively promote self-management and online support.

Confused messaging about whether patients with CRDs were at increased risk of infection with SARS-CoV-2, or development of severe disease, might also have contributed to increased levels of patient anxiety. Primary care providers, a key source of advice, might themselves have been unsure of the best guidance as concerns about increased risk were somewhat eased by emerging, reassuring data. Patient communication must be clear and efficient to help avoid misinformation and unnecessary panic, and can be difficult to convey. Efforts to ensure guidance reflects the available evidence, is up to date, and is communicated through appropriate channels is therefore essential in these unprecedented times. 

Routine check-ups were disrupted by lockdown restrictions; primary care providers had to adapt quickly to maintain care for chronically ill patients and respond to acute presentations and potential COVID-19 cases. Overnight, remote consultations (telephone, video, or online) widely replaced face-to-face appointments in the UK to allow for physical distancing and to prevent spread of infection. 97% of practices now offer video consultations and 75% offer online consultations compared with just 25% offering remote consultations last year. 

This move towards a digital era will likely continue for non-urgent cases as lockdown restrictions are lifted, and care providers can then prioritise face-to-face consultations for patients who need them. Ideally, in the future, patients—in collaboration with their clinician—will have a choice in the mode of appointment that's most suitable. Some primary care practices have adopted strategies to enable patients to safely visit the facility—eg, with designated shielded sites reserved for vulnerable patients, in which physical distancing is strictly observed, or red sites where people with suspected COVID-19 can attend. Now that the peak of the pandemic might have passed, and demand for face-to-face appointments is increasing, health-care providers can adapt these measures to reflect the reducing threat of infection. 

Potential misdiagnosis of patients with CRDs being infected with COVID-19 has been a challenge for primary care physicians owing to overlapping symptoms and the initial lack of widespread testing available in primary care facilities. Physicians have to decide whether an appointment in person is necessary and worth the risk of exposing the patient to infection. 

Policy makers must learn from this experience for future pandemic preparedness, to manage any second waves, and to ensure sufficient and efficient testing is readily available in primary health-care facilities. This will not only allow improved management of individual suspected cases, but can also help physicians make key decisions about patients with respiratory illnesses, as well as identifying the risk to the general population as lockdown measures are eased. 

Although the pandemic is far from over in many countries, it is time to reflect on what we have learned from a primary health-care perspective in the management of CRDs. The shift towards increased self-management and use of digital tools could help initiate a new era in primary care—one of improved health for patients together with the flexible and comprehensive use of all available resources.

WHO: How local testing sped up response to new Ebola outbreak

Via ReliefWeb, a WHO news release: How local testing sped up response to new Ebola outbreak. Excerpt:

Mbandaka – When a young man in his town died of a haemorrhagic fever, Fabien Impanda Boliko had to act fast. The 56-year-old laboratory technician in Mbandaka tested and identified the first case of the Democratic Republic of the Congo’s (DRC) 11th Ebola outbreak in the western Equateur province. 

The sudden death caused concern among local health officials who raised an alert: perhaps the haemorrhagic fever was Ebola or, maybe it was caused by another disease. Boliko accompanied a rapid response team to obtain a sample and find out.  

“I could feel the pressure. As soon as I got back to the laboratory in Mbandaka, I started to do some tests,” said Boliko. “The results came back positive [for Ebola].” On 1 June, just one day later, the DRC government officially declared a new outbreak and response efforts began.  

Boliko credits his swift actions to training he and 25 other laboratory technicians received in 2018 following an outbreak of Ebola there, DRC’s 9th. They were trained by World Health Organization (WHO) on sample collection and testing possible Ebola cases. They learned how to use a GeneXpert machine, which can provide test results in just under two hours. 

“The training strengthened our ability to use the GeneXpert machine and test. Otherwise, if we didn’t know how to test here in Mbandaka or didn’t have the technology, the city could have experienced several weeks of uncertainty,” Boliko explained.  

The DRC’s National Institute for Biomedical Research (INRB), based in the capital of Kinshasa, is responsible for verifying the results of such tests. But, as Boliko pointed out, it can take time for a sample to reach the INRB’s more-equipped laboratories.  

“Equateur Province is able to use local resources to collect, handle, and test samples in strict compliance with biosafety rules. This is ideal,” said INRB medical biologist and laboratory expert, Dr Meris Matondo. Being able to provide accurate preliminary results at the provincial level means that local health authorities can take immediate preventive precautions even before there is a national, official declaration of a new public health emergency. 

Boliko’s quick identification of the disease translated into a swift response. Just four days after the outbreak was declared, the Ministry of Health and WHO began vaccination to stem the spread of Ebola. As of 22 June 2020, more than 4 700 people had been vaccinated. Screening for travellers at designated points of control had also been ramped up.  

“DRC has often been confronted with Ebola outbreaks. I know that this one in June 2020 won’t be our last,” Boliko said. An outbreak of Ebola between May and July 2018 in the same province was the third in the Grand Equateur region (Yambuku in 1976, Tandala in 1977 and Djera in 2014]. The 2018 outbreak claimed 33 lives, but 21 patients survived.