H5N1

Canada: Applying the lessons of an earlier health care disaster

Via The New York Times: Canada Letter: Applying the lessons of an earlier health care disaster. Excerpt:

The SARS virus outbreak in 2003 that infected 375 people in Toronto, killing 44, left behind a widespread physical reminder of that dark time. While they have become often out of order and otherwise neglected in recent years, dispensers for hand sanitizer are still found in most public buildings at their entrances and dotted along their hallways. 

The fear that pervaded the Toronto area during SARS resurfaced this week, if to a lesser extent, as the Wuhan coronavirus continued its rapid spread in China and around the world.  

Traveling alongside that fear is xenophobia and discrimination against people of Chinese origin or people who simply appear to be from China. The public school board in York Region, north of Toronto, issued a statement effectively rebuking more than 9,000 people who signed a petition demanding that the children in a family recently returned from China be kept from their classes.

As I write this, four cases of coronavirus have been reported in Canada and the anti-Chinese sentiment appears limited. The health care system is working smoothly, and officials have been open about what they’re doing and what’s going on. That’s a marked contrast to SARS, where chaos and mistakes, all cloaked in secrecy, dominated. 

The extent of the turmoil in 2003 had dimmed in my memory until I recently read the report from an inquiry Ontario did after the outbreak.  

“Our public health and emergency infrastructures were in a sorry state of decay, starved for resources by governments of all three political parties,” Justice Archie Campbell wrote in his final report released in 2006. “The only thing that saved us from a worse disaster was the courage and sacrifice and personal initiative of those who stepped up — the nurses, the doctors, the paramedics and all the others — sometimes at great personal risk, to get us through a crisis that never should have happened.” 

Looking back, two things stand out about Toronto’s SARS outbreak. First, hospitals became the place where most people contracted SARS, 72 percent of them. And of the those patients, 45 percent were health care workers who became infected on the job.

Then, after officials believed the crisis had turned the corner — to the point where Health Canada ran advertisements to that effect — they were forced to acknowledge under questioning at a news conference that a second lethal round of infections was underway.  

SARS was even less understood than the coronavirus, which is nevertheless surrounded by many unknowns. There was not, among other things, any diagnostic test available for SARS during the outbreak.  

“The commission has not heard of any country or any health system that foresaw SARS,” the 2006 inquiry found. “SARS taught us that we must be ready for the unseen.”  

As the report repeatedly notes, Canada had an example of the right way to handle outbreaks during SARS. Vancouver’s infection control systems, its well-developed systems for protecting health care workers and its clearly defined hospital protocols for dealing with outbreaks, made it possible for the city to successfully contain its five cases, only one of which involved a health care worker.

New China virus likely at human transmission stage as infections spread, doctors say

Via the South China Morning Post: New China virus likely at human transmission stage as infections spread, doctors say. Excerpt:

The previously unknown coronavirus infection that has killed three people in the Chinese city of Wuhan may be moving by human-to-human transmission, with infections reported in other parts of the country and overseas, according to the World Health Organisation (WHO) and other doctors. 

The WHO stressed the need for countries to undertake “preparedness activities”, such as public announcements and ensuring ample testing and treatment supplies, and continuing to share information to help the international response. 

The advisory came as Chinese President Xi Jinping called on officials to do everything they could to prevent the disease from spreading. 

State broadcaster CCTV quoted Xi as saying that the virus must be “resolutely contained” and “the safety of people’s lives and their physical health should be given top priority”. 

Premier Li Keqiang also announced the creation of a national leading group to coordinate the fight against the disease. 

The virus, which causes pneumonia-like symptoms and had sickened 218 people in China as of Monday night, is thought to have originated in a seafood and animal meat market in Wuhan in the central province of Hubei. The WHO has not changed its earlier advice that it did not see grounds to restrict travel to or trade with China. 

The WHO China office said a team of experts was meeting officials in Wuhan to discuss the outbreak. 

“The mission is part of ongoing information sharing between the government of China and the WHO,” a spokesman said. 

In statements via Twitter earlier on Monday, the WHO said: “An animal source seems the most likely primary source of this novel coronavirus outbreak, with some limited human-to-human transmission occurring between close contacts.” 

Wuhan medical authorities said on Monday that a third patient had died from the infection at a hospital in the city, while also announcing a jump of more than 130 new cases alone over the weekend, taking Wuhan’s total to 198.

The number of new cases showed there was human-to-human transmission, Guan Yi, director of the State Key Laboratory of Emerging Infectious Diseases at the University of Hong Kong, Beijing-based news outlet Caixin reported on Monday. “I admit that the virus did not pass from person to person in the early stage, but the situation has evolved for more than a month, and the number of new cases has risen. ‘Human-to-human’ is no longer a word game,” Guan was quoted as saying. 

Guan’s work led to the identification of the severe acute respiratory syndrome (Sars) coronavirus, which killed more than 700 people around the world in a 2002-03 outbreak that originated in China, according to the university’s website. 

“The virus’ ability to spread and adapt to the population, as well as its onset and pathogenicity, is similar to the way Sars developed in the early stage,” Guan said in the Caixin report. “I hope we can learn from the lessons of Sars and hope we don’t approach prevention and control of the [current] situation in a similar way as Sars, otherwise it will negatively affect people and the world.”

China confirms new coronavirus as it investigates mystery Wuhan illness

Via the South China Morning Post: China confirms new coronavirus as it investigates mystery Wuhan illness.

Chinese scientists investigating a mystery illness that has infected dozens in the central city of Wuhan have said it is a new strain of coronavirus from the same family that caused the 2002-03 Sars epidemic. 

Laboratory tests have found a new type of coronavirus and the whole genome sequence of the new virus has been obtained, state broadcaster China Central Television (CCTV) reported on Thursday, citing a task force of experts. 

Fifteen patients had tested positive for the new coronavirus, the report stated. It said the virus had been isolated from one of the 15 patients and showed “typical coronavirus morphology” under electron microscope observation. 

“The pathogen of these unexplained cases of viral pneumonia was initially identified as a new type of coronavirus,” the report quoted the expert group as saying.

There have been 59 reported cases of the mysterious virus in Wuhan since late December, some of them connected to a seafood market in which wild animals had been sold. The market has since been closed. 

Retrospective study identified that the first case had been identified on December 12 and the latest on December 29. No deaths have been reported and eight patients, no longer showing pneumonia symptoms, had been discharged from hospital by Wednesday. 

The Wuhan health authority has said that no human-to-human transmission has so far been detected.  

Coronaviruses can infect mammals such as pigs, cattle, cats, dogs, camels, bats and mice, as well as humans. Of the six previously known human coronaviruses, four were common and caused only minor respiratory symptoms similar to those of a cold.

The other two were serious respiratory diseases: the Severe Acute Respiratory Syndrome (Sars) coronavirus that killed more than 700 people worldwide after originating in China, and the Middle East Respiratory Syndrome coronavirus that had caused 449 deaths by 2015. 

The CCTV report said that the laboratory had used genomic sequencing, nucleic acid detection, virus isolation and other methods to analyse samples from patients. 

Although it is possible to find evidence of a pathogen in a short period of time, it could take years to produce a vaccine. 

The expert group said the initial identification needed to be followed up with further research, according to the television report. Professor David Hui Shu-cheong, a respiratory medicine expert from the Chinese University in Hong Kong, said some important details were still to be established. 

“Some key information, including which animal is the source of the virus, the incubation period and the transmission route, are still missing,” Hui said.

Hong Kong to hold daily updates on mystery Wuhan pneumonia

Via RTHK: Govt to hold daily updates on mystery illness. The full report and then a comment:

The government has unveiled precautionary measures it's taken in response to an outbreak of pneumonia cases in Wuhan, including daily briefings.  

On New Year's Eve, officials in Wuhan announced that several clinics and hospitals in the city had received patients suffering from pneumonia and the cause was not known. 

Twenty-seven people were reported by mainland media to have been infected, with seven of them seriously ill.  

The Hospital Authority said it had notified the government of three cases in which it treated patients for pneumonia symptoms after visiting Wuhan recently.  

The Authority said a female patient in Tuen Mun Hospital and a male teenager in Tai Po Nethersole Hospital have since been discharged, but a woman is still being treated in Princess Margaret Hospital.  

The Health Secretary, Sophia Chan, told a news briefing late on Thursday that the three cases are not linked to the mysterious Sars-like disease in Wuhan, because the patients did not visit the seafood market that's believed to be the source of the virus. 

However, she said the government will start giving daily updates on suspected cases it receives from the Hospital Authority, and it's also taking other measures to protect its borders 

"There are heightened procedures. There are increased procedures - surveillance procedures - that both the Hospital Authority as well as the Department of Health have taken," Chan said. 

She said at the airport and express rail terminal there would be increased surveillance for any travellers who might be unwell.  

The Sars epidemic in 2003 infected more than 1,700 people in Hong Kong and killed almost 300. The disease, which is from the same family of viruses as the common cold, emerged in Guangdong province at the end of 2002. It spread to more than 30 countries infecting over 8,000 people, with 744 deaths in total.

The Wuhan media are still silent about any medical tests, so reports today seem to focus on what other jurisdictions, like Hong Kong and Singapore, are doing. 

So we are in an "excess of caution" phase—and that includes the Chinese authorities, who are clearly being very cautious about the nature of the outbreak.

Hong Kong beefs up border checks against mystery illness

Via RTHK: HK beefs up border checks against mystery illness.

Hong Kong health authorities are beefing up health checks at border checkpoints as authorities in central China investigate an outbreak of a Sars-like disease in Wuhan that has sickened 27 – with seven in a critical condition.  

Health Secretary Sophia Chan convened a meeting with the Hospital Authority, the Health Department, and infectious diseases expert Yuen Kwok-yung on Tuesday night, before announcing that people who have acute respiratory symptoms and fever, and have travelled to Wuhan over the past fortnight, may be placed in isolation in hospital. 

Chan said Hospital Authority staff have been told to be on alert for such cases, and private doctors will be urged to refer any suspicious cases to the government. She also called on members of the public to maintain good hygiene and keep away from animals or animal droppings when travelling in the mainland. 

The minister said mainland authorities have found no indication that the disease – a viral type of pneumonia – can be spread among people, nor have any medical personnel fallen sick so far.  

Hospital Authority chief Tony Ko said no suspected case has been identified so far.  

But Professor Yuen said the current outbreak in Wuhan bears some similarities to the 1997 bird flu outbreak, and the Sars outbreak in 2003, as everyone who has fallen ill is linked to the same seafood market in the mainland city; and that around 25 percent of the victims are seriously ill. 

“At this stage, according to information from the mainland, we don’t know what kind of virus is involved. However we have reason to believe that this may be a new, emerging infectious disease that is similar to Sars or bird flu”, Yuen said. 

But he added that he thinks there’s only a “slim chance” that Hong Kong could be affected by another mass outbreak like Sars. 

He said health authorities are now much better equipped to deal with such emergencies, with much better tests, expertise on respiratory illnesses, infection controls, and communications with their mainland counterparts. 

“There’s no need to panic, but the level of alertness needs to be heightened”, he said.

See also this earlier RTHK report citing an expert saying it's too soon to suppose that SARS is back.

Pneumonic plague is diagnosed in China

The New York Times takes note: Pneumonic Plague Is Diagnosed in China. Excerpt and then a comment:

BEIJING — Two people in China were diagnosed with plague, setting off a panic on Tuesday about the potential spread of the highly infectious and fatal disease and prompting China’s government to warn citizens to take precautions to protect themselves.  

Beijing officials said the two infected people came from Inner Mongolia, a sparsely populated region of northern China. They sought treatment on Tuesday in a hospital in Beijing’s Chaoyang District, where they were diagnosed with pneumonic plague, according to the government office of the district.  

The Chinese Center for Disease Control and Prevention said on Weibo, the microblogging site, that there was no need for Beijing residents to panic and that the risks of further transmission are “extremely low.” The authorities quickly isolated the patients, conducted epidemiological investigations on the people who could have been exposed and disinfected all the relevant sites, the CDC said. They have also strengthened monitoring of patients with fever, it added. 

Pneumonic plague is one of three types of infectious disease known as plague caused by the same bacterium, Yersinia pestis. Patients diagnosed with pneumonic plague, which causes high fevers and shortness of breath, sometimes first contract the closely related and more well-known disease, bubonic plague.

Fears are mounting in China over a possible outbreak of the disease, once known as the Black Death, which killed tens of millions of people in medieval Europe, and spread through Asia and Africa. 

Last month, the authorities in China said they would strengthen quarantine measures to prevent plague from entering the country after Madagascar was struck by a fast-spreading outbreak of the disease. It is unclear when the cases were first detected in China but residents are asking why the authorities took so long to diagnose and disclose the problem. 

Li Jifeng, a doctor at Beijing Chaoyang Hospital where the two people sought treatment, wrote on WeChat, a social media platform, that the patients sought treatment on Nov. 3. That post, which has since been deleted, was published by CN-Healthcare, a website that covers health care news in China. Dr. Li could not be reached for comment and Beijing Chaoyang Hospital declined to comment.  

Dr. Li wrote that the patient she saw was a middle-aged man, who had a fever and complained of breathing difficulties for 10 days. He sought treatment at a hospital in Inner Mongolia but his condition did not improve. His wife also developed a fever and respiratory problems.  

“After so many years of specialist training, I’m familiar with the diagnosis and treatment of most respiratory diseases,” wrote Dr. Li. “But this time, I looked and looked at it. I couldn’t guess what pathogen caused this pneumonia. I only knew it was rare.”

On why the authorities took so long to make the announcement, Dr. Li wrote that signs of any infectious disease need to be repeatedly verified and investigated, and such announcements cannot be “transmitted casually.”  

The police quarantined the emergency room in the Chaoyang Hospital on Monday night, the news outlet Caixin reported, citing residents.  

On Tuesday, Chinese censors instructed online news aggregators in China to “block and control” online discussion related to news about the plague, according to a directive seen by The New York Times. 

Skeptical Chinese internet users have charged the government with being slow to disclose news about the disease, which is transmitted between humans and kills even faster than the more-common bubonic form. China has a history of covering up and being slow to announce infectious outbreaks, prompting many people to call for transparency this time. 

“The plague is not the most terrifying part,” one user wrote on Weibo. “What’s even scarier is the information not being made public.”

China took a deserved kicking for its suppression of SARS news, and when H7N9 avian flu suddenly appeared in Shanghai and spread across the country, the authorities almost drowned us with information—not only news reports, but research articles that made Saudi MERS studies look as pathetic as they were.

Somehow those reports dried up not long after the accession of Xi Jinping, and health problems in a nation of over 1 billion mysteriously solve themselves these days.

 

Pneumonic plague, serious as it is for the unlucky person who contracts it, is a very small problem in a large and prosperous country. (It's been endemic in US Southwest since the San Francisco plague outbreak of 1900. And antibiotics routinely beat it.) Plague in China deserves coverage as a one-off, and the Chinese authorities would look a lot better if they'd reported these cases as an interesting oddity: "in other news..."

Hong Kong: Man contracts rat hepatitis E

Via the South China Morning Post: Rat Hepatitis E: a ‘wake-up call’ for Hong Kong to shape up on public hygiene after man, 56, becomes world’s first person infected with virus. Excerpt:

Hong Kong has been put on notice to shape up on public hygiene and get rid of rodents, after a male resident became the first person in the world to be infected with a strain of Hepatitis E previously found only in animals such as rats.

The 56-year-old who lives in a public housing estate in eastern Kowloon underwent liver transplant surgery in May last year and was tested for the virus after he displayed recurring liver function problems.

Professor Yuen Kwok-yung, a top microbiologist at Hong Kong University, told a press conference on Friday that the discovery was a “wake-up call” to improve environmental hygiene and prevent rats from breeding. 

“We don’t know if in future there will be a serious outbreak of the rat Hepatitis E virus in Hong Kong,” he said. “We need to closely monitor this issue.”  

He said the city’s streets were very clean after the deadly outbreak of the Severe acute respiratory syndrome (Sars) in 2003, but public cleanliness appeared to have slipped recently. 

 “Back alleys now are very dirty with lots of rubbish. You can see rats that are bigger than cats,” Yuen said.

He led the team that had studied the patient for the past year and revealed initial information about the case on Thursday. He also informed authorities, including the Food and Environmental Hygiene Department, which responded with a clean-up operation at Choi Wan estate where the man lives on Friday.  

There is no evidence of an imminent major epidemic following the discovery of rat Hepatitis E in the patient, assured Dr Siddharth Sridhar, a clinical assistant professor from HKU’s department of microbiology involved in studying the patient.  

But researchers took any new incidence of infections jumping from animals to humans very seriously. 

“These kinds of unusual infections, rare infections, first instances – even one case is enough to make public health authorities and researchers very alert about the implications,” he said.

Hong Kong: ‘Another outbreak is a certainty’

Via The Guardian: ‘Another outbreak is a certainty’: are we ready for a superbug epidemic? Excerpt:

It has been 15 years since an outbreak of severe acute respiratory syndrome (Sars) in Hong Kong killed 299 people and infected 1,755. The wildfire spread of the deadly virus through densely packed housing estates stunned the city’s health authorities and traumatised residents. Now the city’s top microbiologist thinks more deaths are on the way. 

“It’s very likely we’ll see an epidemic on the scale of Sars,” says Professor KY Yuen, chair of infectious diseases at the University of Hong Kong. He cites two key reasons for this, both applicable to cities around the world. The first is population density. “Our population is increasing. The number of people living in subdivided flats is now at least 200,000, maybe as high as 600,000,” says Yuen. 

The second is the rise of antibiotic-resistant superbugs. One new superbug infection is reported every 18 minutes in the city’s public hospitals. “The level of antimicrobial resistance in Hong Kong far exceeds that in other developed countries, with resistance to some antibiotics over 20 times higher than in the UK or Sweden,” says Yuen.

That situation is “very likely to get worse” without urgent action to tackle overuse of antibiotics, he says. A government survey revealed half of Hongkongers had taken antibiotics in the past year, with 2% admitting sourcing them illegally. Some argue that pressure to free up hospital bed space leads to oversubscription of antibiotics, as doctors try to shift patients out the door.  

A 2016 report backed by the British government found that drug-resistant infections cause 700,000 deaths globally each year. The same report projected that death toll could rise to 10 million a year by 2050 – more people than die annually from cancer. The authors put the economic cost of such a catastrophe at $100tn (£75tn). The World Health Organisation (WHO) has described rising resistance levels to antibiotics as a “global crisis”, while England’s chief medical officer has warned of a coming “post-antibiotic apocalypse”.

Cities, in particular the world’s growing megacities, are especially vulnerable. Densely populated urban areas make ideal incubators for new epidemics. A high concentration of people means a greater risk of exposure to bacteria and a higher likelihood that infectious diseases will spread.  

“Once transmitted to a human, an airborne virus could pass from that one infected individual to 25,000 others within a week, and to more than 700,000 within the first month,” Dr Jonathan D Quick, chair of the Harvard Medical School’s global health council, warned this year. 

“Within three months, it could spread to every major urban centre in the world. And by six months, it could infect more than 300 million people and kill more than 30 million.”

Pandemics: Spend on surveillance, not prediction

Via Nature News & Comment, an important comment by Edward C. Holmes, Andrew Rambaut, and Kristian G. Andersen: Pandemics: spend on surveillance, not prediction. Excerpt:

Currently, the most effective and realistic way to fight outbreaks is to monitor human populations in the countries and locations that are most vulnerable to infectious disease. This can be done by local clinicians, health workers in non-governmental organizations such as Médecins Sans Frontières (MSF; also known as Doctors Without Borders), and global institutions such as the World Health Organization (WHO).  

We advocate the detailed screening of people who are exhibiting symptoms that cannot easily be diagnosed. Such tests should use the latest sequencing technologies to characterize all the pathogens that have infected an individual — the human ‘infectome’. To track previous infections, investigators should also assess each person’s immune response, by analysing components of their blood using broad-scale serology.  

Emerging diseases are commonly associated with population expansions — when people encroach on habitats occupied by animals — as well as with environmental disturbances and climate change. Deforestation, for instance, can promote human interactions with animals that carry new threats, and can increase encounters with new vector species such as ticks and mosquitoes. Animal die-offs, for example that of bar-headed geese (Anser indicus) at Lake Qinghai in China in 2005 (which was caused by the H5N1 influenza virus), can also flag problem regions or emerging pathogens. Surveillance efforts should therefore focus on communities that live and work in such environments. 

Identifying which pathogen is causing an outbreak is no longer the bottleneck it once was. It took researchers two years to determine HIV as the cause of AIDS in the early 1980s using microscopy and other techniques. By contrast, in 2012 it took only weeks for investigators using genomic technologies to discover the coronavirus that caused Middle East respiratory syndrome (MERS).  

Rapid identification of viruses can be achieved only if such technologies — and the people trained to use them — are globally available, including in resource-limited regions where the risk of outbreaks might be higher. Thankfully, relevant capacity-building programmes are now beginning to be established, such as the Human Heredity and Health in Africa (H3Africa) Initiative, run by the UK Wellcome Trust and the US National Institutes of Health1.  

Once an emerging outbreak virus has been identified, it needs to be analysed quickly to establish what type it is; which molecular mechanisms (such as receptor type) enable it to jump between individuals; how it spreads through human populations; and how it affects those infected.

In other words, at least four kinds of analysis are needed: genomic, virological, epidemiological and clinical. And the data must be passed to key stakeholders, from researchers and health workers on the ground to international agencies such as the WHO and the MSF. Data must be kept as free of restrictions as possible, within the constraints of protections of patient privacy and other ethical issues.  

This will best be achieved through an established global network of highly trained local researchers, such as the WHO Global Outbreak Alert and Response Network (GOARN). Real-time tools for reconstructing and tracking outbreaks at the genomic level, such as portable sequencing devices, are improving fast. Information gathered during recent outbreaks has quickly had tangible impacts on public-health decisions, largely owing to data generation and analysis by many research teams within days of people being infected. 

For instance, in the 2013–16 Ebola epidemic, genome sequencing of the virus proved that a person could sexually transmit the disease more than a year after becoming infected. This prompted the WHO to increase its recommended number of tests for persistent infection in survivors of the disease.  

Ultimately, the challenge is to link genomic, clinical and epidemiological data within days of an outbreak being detected, including information about how people in an affected community are interacting. Such an open, collaborative approach to tackling the emergence of infectious disease is now possible. This is partly thanks to technology, but is mainly due to a shift in perception about the importance of this approach. At least in genomic epidemiology, there is a growing move towards real-time, open-access data and analysis, aided by the use of preprint servers and wikis such as Virological (http://virological.org). This type of collaborative effort can complement the work of agencies including the WHO and the MSF, which focus predominantly on providing information, isolating those who have been infected, and so on.

CIDRAP: New SARS-like virus from bats implicated in China pig die-off

Via CIDRAP, Lisa Schnirring writes: New SARS-like virus from bats implicated in China pig die-off. Excerpt:

A novel coronavirus that killed nearly 25,000 piglets at four farms in Guangdong province in 2016 and 2017 came from horseshoe bats and bears other striking similarities to the emergence of SARS, researchers reported yesterday in a letter to Nature. 

The outbreaks in piglets occurred only about 62 miles from where the SARS (severe acute respiratory syndrome) index case-patient lived. The SARS epidemic—also caused by a novel coronavirus (CoV) thought to have originated in the same bat species—began in southern China in 2002, sickening nearly 8,100 people, 774 of them fatally, in 37 countries.  

The new findings are the result of an investigation into a fatal outbreak that got worse, even after porcine epidemic diarrhea virus (PEDV), involved in the initial phase of the event, was no longer turning up in samples from dead piglets. Researchers from China, EcoHealth Alliance, and Duke-NUS Medical School collaborated on the study, which was supported by the National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health.  

So far, only six CoVs are known to infect humans, but only two have been linked to large fatal outbreaks: SARS and Middle East respiratory syndrome coronavirus (MERS-CoV).  

Similarities to earlier bat coronavirus 

Symptoms of the disease were similar to other known swine enteric CoV, but tests for other known viruses were negative, suggesting a novel disease. Similar outbreaks spread to three other pig farms not far from the index location, and by May 2017, the disease had killed 24,693 piglets on the four affected farms. Separating sick piglets and sows from herds helped curb the outbreak in May.  

Using next-generation genetic sequencing on a sample from the small intestine of a sick piglet, the researchers identified sequences that matched bat CoV HKU2, which was first identified in Chinese horseshoe bats from Guangdong province and Hong Kong in 2007. They found the new virus, which they called swine acute diarrhea syndrome coronavirus (SADS-CoV), on all four of the farms.  

Peter Daszak, PhD, study coauthor and EcoHealth Alliance president, said in a press release, from the group, "This is a really unexpected finding: a brand new virus from the same bats that harbor SARS-like viruses, but this time causing a major outbreak in pig farms."