H5N1

COVID-19 in Singapore—Current experience

Via JAMA Network: COVID-19 in Singapore—Current Experience: Critical Global Issues That Require Attention and Action. Excerpt:

On December 31, 2019, China informed the World Health Organization of a novel viral pneumonia in the city of Wuhan, in Hubei Province. Singapore is an independent city-state 3400 km (2125 miles) from Wuhan, but as a major air hub had an average of 330 000 visitor arrivals from China each month in 2019. 

On January 2, 2020, Singapore’s Ministry of Health alerted all physicians to identify any patient with pneumonia and a recent travel history to Wuhan. On January 3, Singapore started temperature screening at its airport of all travelers arriving from Wuhan. Researchers in China identified a novel coronavirus as the causative agent on January 9, the genetic sequence was released on January 12, and human transmission to health care workers was confirmed on January 20. 

Singapore promptly shifted its public health response level to “enhanced preparedness” and diagnosed its first case, a tourist from Wuhan, on January 23. The range of public health measures that were instituted and rapidly escalated included aggressive contact tracing and quarantine of close contacts of confirmed cases (namely persons who had spent a prolonged period within 2 m of a confirmed case), travel advisories and then entry restrictions on people traveling from Hubei, and on January 31, entry restrictions on people who had traveled to China in the preceding 14 days. Approximately 700 recent travelers from Hubei were quarantined, and Singaporeans, permanent residents, and long-term visa holders returning from China were placed under a 14-day compulsory leave of absence from work. 

As of February 19, Singapore has 84 cases of coronavirus disease 2019 (COVID-19) infection with positive results by real-time reverse transcriptase–polymerase chain reaction (RT-PCR) tests targeting the N, S, and ORF1ab genes. Of these cases, 23 were imported cases comprising 17 visitors from China and 6 Singaporeans who had been evacuated from Wuhan. Of the 61 locally transmitted cases, 5 clusters with local transmission involving 43 patients have been identified, a further 10 patients were related, and 8 are as yet not linked to any clear exposure. 

All 84 confirmed case patients were hospitalized, and of these, 34 have been discharged, 4 are currently in intensive care, and to date there have been no deaths. 

The approach taken by Singapore, learning from its experience with the severe acute respiratory syndrome (SARS), is that all confirmed cases are isolated until 2 consecutive respiratory samples for RT-PCR (sputum or nasal/throat/nasopharyngeal swabs) become negative over 2 days. Close contacts are identified and those individuals without symptoms are quarantined for 14 days from last exposure. 

As of February 19, a total of 2593 close contacts have been identified. Of these, 1172 are currently quarantined and 1421 have completed their quarantine. Contacts with symptoms are tested for COVID-19 using RT-PCR.  

Although the number of confirmed cases is still small at present, there are noticeable similarities and differences in their clinical characteristics when compared with SARS. 

First, the clinical progression of the illness appears similar to SARS: patients developed pneumonia around the end of the first week to the beginning of the second week of illness. 

Second, symptomatic infections in children are rare and in the 3 confirmed cases who were very young (aged 6 months, 1 year, and 2 years), the symptoms were very mild. This is similar to a recent report from China. 

Third, unlike SARS, COVID-19 infection has a broader spectrum of severity ranging from asymptomatic to mildly symptomatic to severe illness that requires mechanical ventilation.  

Since its experience with the SARS outbreak in 2003 when 238 people were infected, including several health care professionals, and 33 patients died, Singapore has been systematically strengthening its ability to manage another emerging infectious disease outbreak. These include the construction of a new purpose-built National Centre for Infectious Diseases and National Public Health Laboratory; significant expansion in the number of negative-pressure isolation beds throughout the public hospital system; stockpiling of personal protective equipment (PPE) and masks; establishment of formal platforms for multi-Ministry and cross-agency coordination; development of a strong capability to perform contact tracing quickly and at scale; training of health professionals including in the correct use of PPE; and building more biosafety level 3 laboratories. 

In addition, as part of Singapore’s major investments in biomedical science and clinical research and translation capabilities, a significant focus has been placed on building expertise in infectious diseases.

Chinese institutes investigate pathogen outbreaks in lab workers

Via Nature News & Comment: Chinese institutes investigate pathogen outbreaks in lab workers. Excerpt:

Two Chinese agriculture research institutions are investigating how more than 100 students and staff became infected with the bacterium Brucella, strains of which are typically found in farm animals but can also trigger potentially fatal complications in people.  

The Lanzhou Veterinary Research Institute in central China confirmed on 7 December that 96 staff and students have tested positive for the infection. In a statement, the institute said most of the infected people are not experiencing signs of brucellosis, the illness caused by the bacterium, which can include fever and flu-like symptoms. 

The institute says it has closed its labs following the outbreak. Although some mice have also tested positive to the infection, an investigation has yet to announce the strain of Brucella in the infected people, or the source of the outbreak. 

On 10 December, the health commission for the province of Heilongjiang confirmed that 13 students at the Harbin Veterinary Research Institute, around 2,600 kilometres to the northeast of Lanzhou, also had the infection. The 13 students were among 49 students who had previously worked as interns at the Lanzhou institute. The Harbin institute says it is also investigating the outbreak.  

Different types of Brucella occur in many mammals species, but infections are most commonly detected in farm animals such as goats, sheep, cattle and pigs. Human infections most commonly result from the ingestion of undercooked meat or raw milk — but the bacteria can also enter the body through the lungs or skin wounds. Brucella strains are not typically transmitted from person to person. If left untreated, the infection can travel to the heart or brain and, in rare cases, be fatal. It can also cause infertility in animals and humans. 

The outbreak at the Lanzhou Veterinary Research Institute was first uncovered in November when some students in the institute‘s foot and mouth disease research unit noticed that large numbers of their lab mice were infertile, according to The Beijing News. The mice tested positive for Brucella, as did four students. The institute then tested 317 people, and found that 96 had been infected.

The Beijing News also reported that students at the institute often forgo wearing masks and taking other precautions.  

The research institutes in Harbin and Lanzhou did not respond to Nature’s questions about how the outbreak occurred, or their lab‘s safety procedures.

Uganda: Naguru Ebola treatment unit poorly equipped

Via The Independent: Naguru Ebola treatment unit poorly equipped- Medics. Excerpt:

Kampala, Uganda: The Ebola Treatment Unit-ETU at Naguru General Hospital is under equipped, URN has learnt. 

According to doctors, the unit lacks equipment and facilities needed to offer quality care to Ebola patients. Apparently, if an Ebola case was rushed to the Ebola Treatment Unit at Naguru General Hospital, health workers would find it hard to measure the blood pressure of patients, carry out continuous tests and provide them oxygen in case they can’t breathe on their own. 

Our reporter visited the unit on Friday last week and found it deserted. There was no activity in the facility, which is fenced with chain link. The doors were under lock and key. The unit comprises of three wards. Each ward is a standalone building measuring approximately 10 meters squared. 

At the triage or reception ward, an empty white 10 liter jerrycan that is supposed to contain 0.5 chlorine solution for hand washing sits on a metallic stand in a corner of the small room gathering dust.  

A one liter bottle of Saraya alcohol-based hand sanitizer also mounted on a wall gathers dust. 

Dr. Mukanga Kizito, the head of the Naguru Hospital Isolation Unit and Ebola Treatment, says they are supposed to be on standby mode, ready to handle any Ebola case that makes its way to Kampala. 

“But as we stand now, we lack a lot of equipment to say that we are ready 100 percent,” he said.  

Dr. Kizito says the first challenges they face is the space in the ETU. He explains that the ETU was initially built to offer care for health workers affected by Ebola. He says the ETU is small and wouldn’t be able to handle a big Ebola outbreak.  

Dr. Kizito says due to the limited space, so many World Health Organisation recommendations are not being adhered to, saying they are forced to work with what they have. 

“The space that we do not have is not enough. Ideally a bed is supposed to be two meters away from the next bed. Ideally each ward at their current size is supposed to have only two beds instead of the four there. As it is, a health worker would not be comfortable,” said Dr. Kizito. 

Dr. Kizito says the facility lacks key monitoring and investigative equipment at the ETU.  

Dr. Kizito explains that even if Naguru hospital has a laboratory, using the current laboratory could spread the disease to other parts of the country.

Ebola in eastern DRC

Via The Lancet Infectious Diseases, a devastatingly critical comment by Pierre E. Rollin: Ebola in eastern DRC.

When the current Ebola outbreak was declared on Aug 1, 2018, in North Kivu, Democratic Republic of the Congo (DRC), confidence was high that the hundreds of experienced responders and the new therapeutics and vaccines would be able to quickly stop this tenth outbreak in DRC. As of July 28, 2019, 2671 probable and confirmed cases and 1790 probable and confirmed deaths have been reported. Leadership and coordination shortfalls, increased insecurity, mistrust, and denial from both the community and the responders are now hallmarks of the response. 

The ineffectiveness of the collection, analysis, and diffusion of epidemiological data, the centrepiece of any response, is predictive of the situation worsening. The different and mainly incomplete databases combined with the absence of accurate and up-to-date chains of transmission makes case counts, monitoring, and intervention difficult or even impossible. 

Many cases of Ebola virus disease are identified late, with many previous transits through unprepared health-care facilities, or are detected as community deaths. Most of the probable cases (death without laboratory confirmation) are not recorded. Research activities are following a parallel agenda, which often differs from timely intervention goals, with numerous data collections kept for exclusive scientific publications and to advance personal careers. 

Laboratory diagnosis is done at multiple sites by the Institut National de Recherches Biologiques. This achievement is tempered by an overconfidence in the capabilities of the laboratories, incomplete sharing of results with patient providers, low quality-control procedures, and unjustified fear of losing control. Rapid field molecular typing of the virus and bedside rapid diagnostic assays, both seen as a crucial support for the control of the 2014–16 west Africa outbreak, are not done to inform the response. 

Early in the outbreak, new therapeutics were made available first under a monitored emergency use of unregistered and investigational interventions (MEURI) protocol, then through a randomised controlled trial supported by the US National Institutes of Health, the Institut National de Recherches Biologiques, and the DRC Ministry of Health. As of July 30, 2019, 682 patients were recruited under the MEURI and 621 patients under the randomised controlled trial protocol. Late admission of cases due to fear from the community or ineffective follow-up of contacts has complicated the use of therapeutics and vaccines and analyses. 

Ring vaccination of contacts and contacts of contacts of confirmed Ebola cases using rVSV-ZEBOV was rapidly implemented. As of July 27, 2019, 178 121 people have been vaccinated, 31 016 of whom were frontline workers, the rest being contacts and contacts of contacts of Ebola cases. The epidemiological data generated by the vaccination and the contact tracing teams are mostly not shared. As a result, daily field reports have noted at least 651 identified contacts of confirmed cases who were not vaccinated and became cases (among them 205 deaths) between Dec 31, 2018, and July 30, 2019. Vaccination coverage among health-care workers is high but incomplete. 

The initial response should be to generate, maintain, and constantly update the primary databases, then sharing them among all players. Parallel databases should not exist. Because of the field difficulties and the inadequate personnel resources, a single team staffed by the most experienced partners should oversee this task. During the autumn of 2014, a Conakry informal taskforce, consisting of one member from each main partner (Guinea Ministry of Health, WHO, Médecins Sans Frontières, Centers for Disease Control and Prevention) met at least once a week, allowing real fact-based understanding and management of the Ebola situation. This approach needs to be replicated for this outbreak at each level. 

Laboratory support from national and external partners is needed and should provide timely support for clinical management of patients receiving experimental therapeutics or difficult epidemiological investigations, such as cases with multiple or unknown origins. As in the west African outbreak, point-of-care rapid diagnostic tests should be fielded, at least as an evaluation of community deaths. 

The existing vaccination strategy and implementation on the ground, should be drastically changed. A single combined team should follow and vaccinate contacts and contacts of contacts. This policy, combined with a rapid and complete inclusion of all high-risk contacts, should reduce, or at least improve the outcome of, secondary Ebola cases and affect the transmission curve. 

Even if the infection prevention and control efforts have yielded some progress, the relatively large proportion of cases due to reuse of material (eg, syringes, needles, and perfusion tubes) is unacceptable. More emphasis on the multiple risks of this practice should be advertised among the care providers and the population. 

Helping the existing local health-care providers to regain the population's confidence is crucial. This should be done by introducing a comprehensive health system with actions that encompass the health-related problems encountered daily by the population—eg, malaria, vaccine-preventable diseases, childbirth, and quality of care. 

Together with the presence of violence and insecurity, Ebola virus disease has a real chance of becoming endemic in this part of DRC. Only multiple and immediate changes, starting within the leadership and coordination of all the partners involved through inclusive, flexible, and unified response efforts, will be able to reverse the trend.

Japan to import Ebola virus for research ahead of 2020 Olympics

Via The Mainichi: Japan to import Ebola virus for research ahead of 2020 Olympics. Excerpt:

TOKYO (Kyodo) -- Japan will import strains of Ebola and four other deadly viruses for the first time for the development of diagnostic kits ahead of the next year's Olympic and Paralympic Games in Tokyo, the health ministry said Monday. 

The government will obtain the rare but often fatal viruses, which cause hemorrhagic fever, from foreign laboratories possibly in a month or two for research at the National Institute of Infectious Diseases in a Tokyo suburb, the only facility in the country equipped to handle such deadly viruses, the ministry officials said. 

The government plans to obtain Ebola, Lassa, South American, Crimean-Congo and Marburg viruses, according to the officials.  

The mayor of Musashimurayama in western Tokyo, where the institute is located, consented to the study of the viruses at the facility in talks Monday with Health, Labor and Welfare Minister Takumi Nemoto.  

"We have come to a good level of understanding on the matter. It is a major stride toward protection" against the potential threats of the viruses as the country prepares to welcome spectators of the sporting event from all over the world, Nemoto told reporters. 

Musashimuraya Mayor Masaru Fujino said he has asked the health minister to swiftly inform the city of any mishaps involving the viruses at the research institute and to consider relocating the facility in the future. 

The research facility in Musashimurayama is the country's only laboratory in operation with the highest biosafety standard level of BSL-4. 

Its officials have repeatedly held meetings with local residents and invited them to the facility to explain about the planned virus studies.

Ultra-secure lab in Gabon equipped for Ebola studies

Google Maps

Via AFP: Ultra-secure lab in Gabon equipped for Ebola studies. Excerpt:

At a research facility in Gabon, one isolated building stands behind an electrified fence, under round-the-clock scrutiny by video cameras. The locked-down P4 lab is built to handle the world's most dangerous viruses, including Ebola.  

"Only four people, three researchers and a technician, are authorised to go inside the P4," said virologist Illich Mombo, who is in charge of the lab, one of only two in all of Africa that is authorised to handle deadly Ebola, Marburg and Crimean-Congo haemorrhagic fever viruses. The other is in Johannesburg. 

The P4 was put up 800 metres (half a mile) distant from older buildings of the Franceville International Centre for Medical Research (CIRMF), in large grounds on the outskirts of Franceville, the chief city in the southeastern Haut-Ogooue province. 

Filming the ultra-high-security lab or even taking photos is banned and the handful of people allowed inside have security badges. Backup power plants ensure an uninterruptable electricity supply. "Even the air that we breathe is filtered," Mombo explains.  

When he goes into the P4 lab to work on a sample of suspect virus such as Ebola -- which has claimed 28 lives in the Democratic Republic of Congo (DRC) during an outbreak in the past six weeks -- Mombo wears a head-to-foot biohazard suit.  

The special clothing is destroyed as soon as he has finished. Draconian measures are in force to prevent any risk of contamination, with potentially disastrous effects. 

- 'Teams on alert' -  

Once a suspect virus has been "inactivated" -- a technique that stops the sample from being contagious -- it is carefully taken from the P4 unit to other CIRMF laboratories in the compound, where it is analysed. 

Specialised teams will scrutinise it, looking to confirm its strain of Ebola and hunting for clues such as the virus's ancestry and evolution, which are vital for tracking the spread of the disease.

Status, quality and specific needs of Ebola virus diagnostic capacity and capability in European laboratories

Eurosurveillance has just published a timely article: Status, quality and specific needs of Ebola virus diagnostic capacity and capability in laboratories of the two European preparedness laboratory networks EMERGE and EVD-LabNet. Excerpt from the conclusion:

While the EBOV outbreak in West Africa was the largest on record, the risk for Europe was considered low. Nevertheless, the outbreak activated a broad laboratory and clinical response in Europe. One approach to manage such response to an outbreak with limited risks could be to centralise such diagnostics in a limited number of BSL4 laboratories. In line with this, we observed that a vast majority of the samples tested for EBOV in the European laboratories were tested by the BSL4 laboratories. 

However, while samples from patients outside Europe were most likely to be sent to the BSL4 laboratories, local suspected cases were most likely to be tested in first-line, local diagnostic laboratories without BSL4 capacity but with the possibility for confirmatory testing in BSL4 laboratories. Furthermore, in the early phases of an outbreak, it is difficult to predict whether scaled up capacity will be needed. 

Also, many specialised diagnostic laboratories of both laboratory preparedness networks provide haemorrhagic fever differential diagnostics besides the BSL4 laboratories and were called in to provide guidance for national and institutional level preparedness planning for EBOV patients.

Hungarian scientist exposed to Ebola, WHO says

Via CBC News, a report from The Associated Press: Hungarian scientist exposed to Ebola, WHO says. Excerpt:

The World Health Organization says it has co-ordinated shipment of an experimental Ebola vaccine and drugs to treat a laboratory scientist in Hungary who was exposed to the potentially deadly disease earlier this month. 

The U.N. health agency said in an emailed statement on Friday that Hungarian officials asked for help last week after a scientist working in a normally secure laboratory had an "accidental exposure" to Ebola.

WHO said it helped get the scientist immunized with an experimental vaccine. It also helped send two unlicensed drugs.

See also this Reuters report, which offers more details.

Safety blunders expose lab staff to potentially lethal diseases in UK

Via The Guardian: Safety blunders expose lab staff to potentially lethal diseases in UK. Excerpt:

Safety breaches at UK labs that handle harmful bacteria, viruses and fungi have spread infections to staff and exposed others to potentially lethal diseases, the Guardian has learned. 

The Health and Safety Executive (HSE) has investigated a series of mistakes over the past two years that led to scientists falling ill at specialist labs run by hospitals, private companies, and even Public Health England (PHE), the government agency which exists to protect and improve the nation’s health and wellbeing. 

One scientist at a PHE laboratory became sick after contracting Shigella, a highly contagious bacterial infection that causes most cases of dysentery in Britain. The incident led the HSE to send the agency an enforcement letter to improve its health and safety practices. 

The HSE held formal investigations into more than 40 mishaps at specialist laboratories between June 2015 and July 2017, amounting to one every two to three weeks. Beyond the breaches that spread infections were blunders that led to dengue virus – which kills 20,000 people worldwide each year – being posted by mistake; staff handling potentially lethal bacteria and fungi with inadequate protection; and one occasion where students at the University of the West of England unwittingly studied live meningitis-causing germs which they thought had been killed by heat treatment. 

Of the scientists who became infected in the line of work, one was admitted to hospital after falling ill with salmonella poisoning at Pall Life Sciences, a private medical company. Another picked up a paratyphoid infection at Nottingham University Hospitals NHS Trust; four contracted Shigella at Brighton and Sussex University Hospitals NHS Trust, and a biomedical scientist at The Royal Free Hospital in London became sick with two different strains of gastrointestinal bug after testing an infected stool sample.

In Britain, microbes that are a risk to human health are ranked by hazard groups. The most harmful are listed in groups 3 and 4. Group 3 bugs, such as those that cause anthrax and leprosy, can pose a serious hazard to employees, and may spread to the community, but there is usually a vaccine or treatment. Group 4 pathogens, such as Ebola, are more dangerous. These are a serious threat to employees and the community, and there is often no vaccine or treatment. The germs must be handled in labs that meet strict safety and security requirements. 

The HSE investigated a number of close shaves. In August 2015, scientists at Bristol University accidentally posted live dengue virus – a group 3 germ carried by mosquitoes in south-east Asia – to Glasgow University’s Centre for Virus Research. Because the person who packed the material had no idea it contained live dengue, the parcel did not meet safety requirements for posting dangerous agents. With luck, the package did not leak; it arrived in one piece and was spotted on arrival at the lab, where staff destroyed the material. 

On another occasion, a diagnostic lab called Viapath posted a hazard group 3 bacteria called Chlamydia psittaci, which can cause pneumonia, to PHE’s infectious disease unit in north London. The sample was improperly labelled and, on arrival, was handled in a way that could have infected the PHE lab worker. The HSE found failings on both sides.

CIDRAP: CDC appoints permanent lab safety chief

Via CIDRAP, Lisa Schnirring writes: CDC appoints permanent lab safety chief. Excerpt:

The US Centers for Disease Control and Prevention (CDC) today announced the permanent appointment of its first associate director for laboratory science and safety, the agency's latest step in addressing a string of safety breaches. 

The appointment of Stephan Monroe, PhD, who was named as the acting associate director for laboratory science and safety in May, marks the first time the agency's top lab administrator has reported directly to the CDC director. 

Creation of a single point person for lab safety accountability first surfaced in a series of steps the CDC announced in July 2014 in the wake an anthrax incident the month before at one of its labs. At around the same time, the CDC revealed that a lab sample unintentionally cross-contaminated with highly pathogenic H5N1 avian influenza had been shipped to a US Department of Agriculture lab. 

Problems at other federal facilities have kept lab safety issue in the headlines. Last summer, decades-old smallpox samples that were found to contain live virus were found abandoned in a Food and Drug Administration lab on the National Institutes of Health campus, and more recently, investigations by USA Today detailed problems at Department of Defense labs, including the shipment of live Bacillus anthracis samples—the bacterium that causes anthrax—to dozens of outside labs over the past decade. 

At the end of 2014, the CDC said the search for a chief of lab safety was under way, and that CDC microbiologist Leslie Dauphin, PhD, had been appointed to oversee the task until the position was permanently filled. 

Monroe, who replaced Dauphin in May, takes on the task at a time when high-profile lab safety problems have been swept up in the gain-of-function research debate and garnered the attention of Congress.