H5N1

COVID-19 infects famed research lab working on at-home test

Via The New York Times: Coronavirus Infects Famed Research Lab Working on At-Home Test. Excerpt:

DAKAR, Senegal — For months, researchers at the Pasteur Institute in Dakar, a prestigious biomedical research center in Senegal, have been working to produce a low-cost, rapid, at-home test for the coronavirus — the kind that countries across Africa and elsewhere have been most eager to have.  

Now the coronavirus has infected a cluster of staff members at the institute, one of whom has died, according to its director, Dr. Amadou Sall. He did not say how many workers had tested positive, but local media reports said it was five.  

Their contacts have been isolated and the work is continuing, according to Cheikh Tidiane Diagne, a researcher at the lab.  

The center’s work has been crucial in efforts to contain the spread of the virus in West Africa: In the early stages of the outbreak, it trained laboratory staff from more than a dozen countries in how to test for the virus.  

The institute says it is now working on a test kit that would cost as little as $1, and could be used at home. In other countries like the United States, home test kits for the coronavirus have yet to be widely approved or distributed, with many public health experts concerned about whether results would be accurate. So far, the World Health Organization has not recommended them for clinical use, but only in a research setting.  

Oyewale Tomori, a virologist who leads a Nigerian government committee on Covid-19, said that if it worked, a $1 antigen test kit would be a “game-changer,” because test kits now sell for more than $50 apiece.  

But he had concerns about whether it would be sensitive enough to detect the virus, and said it should be tested in other countries as well as Senegal, to show that it could work in other environments. 

Senegal now has 3,739 confirmed cases of coronavirus, and 42 deaths. A full lockdown was never imposed, but there is a curfew, restrictions on movement between the country’s regions, and mandatory mask-wearing in public spaces.

“Whatever their level, the staff of the Dakar Pasteur Institute as well as their families are facing the same restrictions, risks and life realities as all Senegalese people, with whom they share the same living conditions,” Dr. Sall said in a statement. “The virus spares no one.” 

The British diagnostic company Mologic said it had been working with the institute to make both an antigen test, which detects whether someone has the coronavirus, and an antibody test, which shows whether a person’s immune system has been exposed to it. The diagnostic kit will have two components: a saliva test and a blood test. The 10-minute antibody test should be available first, Mologic said — in June, if production goes according to plan.

China publishes plan for dealing with future pandemics

Via Sixth Tone: China Publishes Plan for Dealing With Future Pandemics.

The COVID-19 pandemic has laid bare the shortfalls in China’s public health system, and “mending the weak parts” is now an urgent priority for the country, the Chinese government said in a policy document released Wednesday.  

Improving the country’s testing capacity for infectious pathogens is a major focus of the plan. Authorities’ efforts to respond to the initial COVID-19 outbreak in the central city of Wuhan were hampered by an inability to conduct tests quickly, according to multiple media reports.  

China will ensure there is at least one biosafety level three — or P3 — research laboratory in every province and one P2 laboratory in every city, according to the document jointly released by the National Development and Reform Commission and two other ministries. 

Laboratories are assigned biosafety levels from one to four depending on the containment measures they employ to prevent the spread of dangerous pathogens, with four indicating the highest level of protection.  

SARS-CoV-2 tests in China have to be conducted in P2 labs or above, but many primary hospitals don’t meet the requirements. The lack of eligible testing facilities was a key issue at the start of the epidemic, according to Chen Xi, associate professor of health policy and economics at the Yale School of Public Health.  

“Many people have been discussing the malfunction of the early warning system, which actually has a lot to do with the limited testing capacity at the local level,” Chen told Sixth Tone. “When you’re unclear about the nature of the virus — such as the genome sequencing of the pathogen — there’s no way to develop a testing kit. And without a testing kit, you don’t know who’s been infected.” 

The document also lays out measures to ensure that China has the health resources to cope with future public health  emergencies. It says public venues should be able to quickly convert into treatment and quarantine facilities like fangcang shelter hospitals during a crisis. It also states that China should strengthen its frontline public health facilities, including primary care facilities at the county, township, and residential community level. 

Cities have been given targets for increasing the number of hospital beds capable of accommodating patients with infectious diseases and making them available for immediate use in the event of a future outbreak. Cities with over 5 million residents, for example, must have at least 600 such beds available, according to the document. 

Many Chinese cities expanded their infectious disease hospitals in the aftermath of the 2003 SARS epidemic. During the COVID-19 outbreak, however, there was still a significant shortage of beds capable of admitting infected patients, Cai Weiping, a doctor and National People’s Congress delegate, told Chinese media outlet Caixin. 

While the plan focuses mostly on improving China’s public health facilities, the section regarding potential reforms to the China CDC lacks specific details, according to Chen. Experts have called for the organization to be given a greater role in decision making during responses to future outbreaks. 

Environmental changes are increasing the risk of virus spread, making it essential for all governments to take action to prepare for future pandemics, Chen added.  

“Public health precautions can effectively reduce the risks of a pandemic,” said Chen. “Climate change is global. This time it (the outbreak) happened in Wuhan, but we don’t know where one might emerge next time.”

COVID-19: China publishes plan for dealing with future pandemics

Via Sixth Tone: China Publishes Plan for Dealing With Future Pandemics. Excerpt:

The COVID-19 pandemic has laid bare the shortfalls in China’s public health system, and “mending the weak parts” is now an urgent priority for the country, the Chinese government said in a policy document released Wednesday.  

Improving the country’s testing capacity for infectious pathogens is a major focus of the plan. Authorities’ efforts to respond to the initial COVID-19 outbreak in the central city of Wuhan were hampered by an inability to conduct tests quickly, according to multiple media reports.  

China will ensure there is at least one biosafety level three — or P3 — research laboratory in every province and one P2 laboratory in every city, according to the document jointly released by the National Development and Reform Commission and two other ministries. 

Laboratories are assigned biosafety levels from one to four depending on the containment measures they employ to prevent the spread of dangerous pathogens, with four indicating the highest level of protection.  

SARS-CoV-2 tests in China have to be conducted in P2 labs or above, but many primary hospitals don’t meet the requirements. The lack of eligible testing facilities was a key issue at the start of the epidemic, according to Chen Xi, associate professor of health policy and economics at the Yale School of Public Health.  

“Many people have been discussing the malfunction of the early warning system, which actually has a lot to do with the limited testing capacity at the local level,” Chen told Sixth Tone. “When you’re unclear about the nature of the virus — such as the genome sequencing of the pathogen — there’s no way to develop a testing kit. And without a testing kit, you don’t know who’s been infected.” 

The document also lays out measures to ensure that China has the health resources to cope with future public health  emergencies. It says public venues should be able to quickly convert into treatment and quarantine facilities like fangcang shelter hospitals during a crisis. It also states that China should strengthen its frontline public health facilities, including primary care facilities at the county, township, and residential community level. 

Cities have been given targets for increasing the number of hospital beds capable of accommodating patients with infectious diseases and making them available for immediate use in the event of a future outbreak. Cities with over 5 million residents, for example, must have at least 600 such beds available, according to the document. 

Many Chinese cities expanded their infectious disease hospitals in the aftermath of the 2003 SARS epidemic. During the COVID-19 outbreak, however, there was still a significant shortage of beds capable of admitting infected patients, Cai Weiping, a doctor and National People’s Congress delegate, told Chinese media outlet Caixin.

ECDC: Infection prevention and control and preparedness for COVID-19 in healthcare settings - third update

ECDC has published Infection prevention and control and preparedness for COVID-19 in healthcare settings - third update. The summary:

This document aims to provide guidance to EU/EEA healthcare facilities and healthcare providers on infection prevention and control (IPC) measures for the management of suspected and confirmed cases of COVID-19 infection in healthcare settings, including long-term care facilities. It also offers guidance on the management of specimens at laboratories in the EU/EEA. This is an update of the ECDC guidance dated 31 March 2020 ‘Infection prevention and control for COVID-19 in healthcare settings'.

Five Eyes network contradicts theory COVID-19 leaked from lab

Via The Guardian: Five Eyes network contradicts theory Covid-19 leaked from lab. Excerpt:

There is no current evidence to suggest that coronavirus leaked from a Chinese research laboratory, intelligence sources have told the Guardian, contradicting recent White House claims that there is growing proof this is how the pandemic began.  

The sources also insisted that a “15-page dossier” highlighted by the Australian Daily Telegraph which accused China of a deadly cover up was not culled from intelligence from the Five Eyes network, an alliance between the UK, US, Australia, New Zealand and Canada. 

British and other Five Eyes agencies do believe that Beijing has not necessarily been open about how coronavirus initially spread in Wuhan at the turn of the year. But they are nervous about getting involved in an escalating international situation. 

On Sunday Mike Pompeo, the US secretary of state, said: “I can tell you that there is a significant amount of evidence that this came from that laboratory in Wuhan.”  

No evidence was offered by Pompeo to back up his assertion but information has been circulating over the last month in the UK, US and Australia aimed at raising questions about the high security Wuhan Institute of Virology, which has long specialised in researching coronaviruses in horseshoe bats.  

Stories have suggested that workers in the lab may not have always used full protective equipment, and that in one instance a bat urinated on a researcher who did not subsequently become ill. 

But there is nothing to indicate a leak from the lab could have caused the pandemic, sources say.  

Claims are even made that the virus was genetically engineered in Wuhan, although there is both scientific and intelligence agency agreement that there is no evidence for this.

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.