H5N1

Unlocking pandemic potential: Prevalence and spatial patterns of key substitutions in avian influenza H5N1 in Egyptian isolates

Via BMC Infectious Diseases: Unlocking pandemic potential: prevalence and spatial patterns of key substitutions in avian influenza H5N1 in Egyptian isolates. The abstract and then a comment:

Background 

Avian influenza H5N1 has a high human case fatality rate, but is not yet well-adapted to human hosts. Amino acid substitutions currently circulating in avian populations may enhance viral fitness in, and thus viral adaptation to, human hosts. Substitutions which could increase the risk of a human pandemic (through changes to host specificity, virulence, replication ability, transmissibility, or drug susceptibility) are termed key substitutions (KS). Egypt represents the epicenter of human H5N1 infections, with more confirmed cases than any other country. To date, however, there have not been any spatial analyses of KS in Egypt.  

Methods 

Using 925 viral samples of H5N1 from Egypt, we aligned protein sequences and scanned for KS. We geocoded isolates using dasymetric mapping, then carried out geospatial hot spot analyses to identify spatial clusters of high KS detection rates. KS prevalence and spatial clusters were evaluated for all detected KS, as well as when stratified by phenotypic consequence.  

Results 

A total of 39 distinct KS were detected in the wild, including 17 not previously reported in Egypt. KS were detected in 874 samples (94.5%). Detection rates varied by viral protein with most KS observed in the surface hemagglutinin (HA) and neuraminidase (NA) proteins, as well as the interior non-structural 1 (NS1) protein. The most frequently detected KS were associated with increased viral binding to mammalian cells and virulence. Samples with high overall detection rates of KS exhibited statistically significant spatial clustering in two governorates in the northwestern Nile delta, Alexandria and Beheira. 

Conclusions 

KS provide a possible mechanism by which avian influenza H5N1 could evolve into a pandemic candidate. With numerous KS circulating in Egypt, and non-random spatial clustering of KS detection rates, these findings suggest the need for increased surveillance in these areas.

The need is not only for increased surveillance, but for increased reporting on surveillance findings. The Egyptians have been too reticent about H5N1.

Drug to treat smallpox approved by FDA, a move against bioterrorism

Via The New York Times: Drug to Treat Smallpox Approved by F.D.A., a Move Against Bioterrorism. Excerpt:

The Food and Drug Administration on Friday approved the first drug intended to treat smallpox — a move that could halt a lethal pandemic if the virus were to be released as a terrorist bioweapon or through a laboratory accident.  

The antiviral pill, tecovirimat, also known as Tpoxx, has never been tested in humans with smallpox because the disease was declared eradicated in 1980, three years after the last known case.  

But it was very effective at protecting animals deliberately infected with monkeypox and rabbitpox, two related diseases that can be lethal. It also caused no severe side effects when safety-tested in 359 healthy human volunteers, the F.D.A. said. 

“This new treatment affords us an additional option should smallpox ever be used as a bioweapon,” said Dr. Scott Gottlieb, the F.D.A.’s commissioner. 

Having a drug that usually cures smallpox is an important medical breakthrough, according to several medical experts not associated with the F.D.A. or the company making the drug. 

F.D.A. approval is “definitely a good thing,” said Dr. Anthony S. Fauci, director of the National Institute of Allergy and Infectious Diseases. 

Research on tecovirimat — originally designated ST-246 — began at the institute after the 9/11 terrorist attack on the World Trade Center, Dr. Fauci said. The research accompanied efforts to stretch the national stockpile of smallpox vaccine by safely diluting it.  

“It all started back then, but developing a licensed product took until today,” he added.  

The F.D.A. approval of the drug went to Siga Technologies of Corvallis, Ore., a private company that developed the medicine under a federal biomedical defense contract. 

Although circulating smallpox has been eradicated, two known stores of the virus exist in laboratory freezers — one in Russia and one at the Centers for Disease Control and Prevention in Atlanta.

Bioterrorism experts fear that other stocks may exist; for example, in 2014 several forgotten vials containing smallpox were found at the National Institutes of Health. 

More worrisome, experts say, is the possibility that a terrorist lab or even a sophisticated amateur could use modern gene-editing techniques to rebuild the virus and then unleash it, deliberately or accidentally, on an unprepared world.

Huge iceberg drifts close to Greenland village, causing fears of a tsunami

Credit: Ritzau Scanpix/Magnus Kristensen via Reuters

The photo lends a new meaning to the old cliché "tip of the iceberg." Via Thomson Reuters: Huge iceberg drifts close to Greenland village, causing fears of a tsunami.

An iceberg the size of a hill has drifted close to a tiny village on the western coast of Greenland, causing fear that it could swamp the settlement with a tsunami if it calves.  

The iceberg towers over houses on a promontory in the village of Innaarsuit but it is grounded and has not moved overnight, state broadcaster KNR reported.  

A danger zone close to the coast has been evacuated and people have been moved further up a steep slope where the settlement lies, a Greenland police spokesman told Reuters. 

"We can feel the concern among the residents. We are used to big icebergs, but we haven't seen such a big one before," Susanna Eliassen, a member of the village council in Innaarsuit, told KNR. 

The government and police are on high alert and have moved a search-and-rescue (SAR) helicopter closer to the remote village with about 170 inhabitants.

Fighting drug resistance with graphene

Via HealthNews.Africa: To tackle drug resistant bacteria, scientists turn to the world's strongest material. Excerpt:

The prevalence of antimicrobial resistant bacteria, caused by the indiscriminate application and overuse of antibiotics, has been a global issue threatening human health for several decades. Antimicrobial resistance is projected to cause the death of approximately 300 million people in the next 35 years. To prevent these deaths, researchers are seeking and putting forward alternative ways to fight bacteria.  

While efforts are geared towards introducing new drugs, a recent study published in Burns & Trauma is turning the world’s attention to a composite of the world’s strongest known material, known as graphene. 

According to the study, graphene oxide-quaternary ammonium nanocomposite is a promising antimicrobial agent for infected wound management and antibacterial wound dressing.  

Graphene shot to fame due to its extraordinary mechanical strength, optical transmittance, electrical conductivity and high specific area properties. It is the world’s strongest known material. 

The researchers posited that its excellent optical transmittance enables graphene to serve as the ideal liquid crystal display material for computer, TV and cell phone display screens. It is also known as the material with the best electrical conductivity, which can replace silicon to produce supercomputers that run faster and have lower energy consumption. 

In the biomedical fields, graphene and its deviates exhibit excellent antibacterial activity against a wide range of bacteria.

“Recent advances in nanomaterials have allowed for a considerable number of applications of graphene in antibacterial sciences. Its antibacterial properties have been attributed to the combined mechanisms of bacterial membrane perturbation caused by sharp edges and oxidative stress induction. Graphene-based composite antibacterial materials have therefore become a hot topic in scientific research,” said Tengfei Liu, co-author of the research paper. 

According to him, their study focuses on the application of graphene oxide-quaternary ammonium nanocomposite (GO-QAS) for wound repair and infection control. 

Liu noted that the GO-QAS nanocomposite exhibits excellent biocompatibility and synergistic antibacterial ability against multidrug resistant bacteria through not only mechanical membrane perturbation (including wrapping, bacterial membrane insertion, and bacterial membrane perforation), but also oxidative stress induction. 

“Notably, GO-QAS topically applied on infected wounds maintained highly efficient antibacterial activity and accelerated the healing process of infected wounds by promoting re-epithelialization and granulation tissue formation. In the future, GO-QAS nanocomposite could be applied as a promising antimicrobial agent for infected wound management and antibacterial wound dressing synthesis,” Liu said.

UK schools banning school run to protect pupils from air pollution

Via The Guardian: UK schools banning school run to protect pupils from air pollution. Excerpt:

Schools across the country are moving to ban the school run amid growing concern about the devastating impact of air pollution on young people’s health. 

The Guardian has found that thousands of schools in cities and towns – from Edinburgh to London, Manchester to Ellesmere Port – are taking measures to try to deter parents using their cars. These include closing roads, setting up “park and stride” schemes, walk-to-school initiatives and “playing dead” protests. 

Kathryn Shaw, from the charity Living Streets, said more families and schools were becoming aware of the impact of air pollution on young people’s health, as well as concerns over road safety.  

“When parents drive up to the school gates, it’s not just their children they’re dropping off for the day,” she said. “The toxic fumes from the cars stay too. A lot of parents don’t want to drive all the way but feel there is no other option.”  

But now schools, local councils and public health experts are beginning to take action. In Edinburgh parents have been banned from dropping their children off at nine schools. The scheme has been so successful it is now being rolled out to others across the city. In London, Hackney council has closed the roads outside five schools and the initiative is due to be extended to another 12 sites. A similar programme is to be launched in Westminster where the council says a range of options – including road closures – will be on offer from September. 

In Alloa, Scotland children lay down and played dead in the road to highlight concerns around road safety and pollution outside their school. And in Stockport one primary school has introduced a “park and stride” scheme based in a local pub car park in a bid to stop parents driving to the school gates.

Shaw said Living Streets was working with more than 2,000 schools to promote walking, cycling and scooting and that more people were becoming aware of the benefits to air quality and “children’s physical and mental health” all the time. 

The findings come amid growing concern about the illegal levels of air pollution in the UK and the impact on human health – particularly children.

CIDRAP: Cyclospora outbreaks grow in Midwest, Texas

Via CIDRAP, Stephanie Soucheray writes: Cyclospora outbreaks grow in Midwest, Texas. Excerpt:

Health departments in several states confirmed more cases in two cyclosporiasis outbreaks in the Midwest, one linked to Del Monte vegetable trays and the other to McDonald's salads. Meanwhile, more Texans are sickened in a Cyclospora outbreak with no known origin. 

Fifteen more people have been sickened with the Cyclospora parasite in the outbreak linked to pre-packaged vegetable trays from Del Monte Produce and sold at Kwik Trip gas stations in Minnesota, Wisconsin, Iowa, and Michigan, according to an update from the Centers for Disease Control and Prevention (CDC). 

There are now 227 confirmed cases of the parasitic infection, which causes intestinal illness. The number of hospitalized patients remains at 7, and no deaths have been reported.

EBOLA DRC: Evolution of the response to the Ebola epidemic as of Friday, July 13

Thanks to Helen Branswell for tweeting about this statement from the Ministry of Health: EBOLA DRC - Evolution of the response to the Ebola epidemic as of Friday, July 13, 2018. We are just about a day away from a declaration that the epidemic is over. Excerpt from the Google translation:

EPIDEMIOLOGICAL SITUATION  

Friday, July 13, 2018   

The epidemiological situation of the Ebola Virus Disease dated 13 July 2018: 

• A total of 53 cases of haemorrhagic fever were reported in the region, of which 38 were confirmed and 15 were probable. 

• 24 people have been cured of Ebola Virus Disease since the beginning of the epidemic. 

• 29 deaths were recorded, including 14 confirmed cases. 

News from the Ebola response 

Epidemiological surveillance 

• Between 29 June and 13 July 2018, 183 alerts were investigated and invalidated by surveillance teams in Equateur province and neighboring provinces. 

• Active case monitoring continues in health facilities and households.  

• Enhanced surveillance at the entry points of the cities of Kinshasa and Mbandaka will continue until the end of the epidemic is declared. However, the level of baseline surveillance at ports of entry will be permanently elevated through enhanced physical and human resources. 

Treatment of patients 

• Ebola treatment centers in Bikoro and Itipo Health Zones remain open to continue handling alerts and suspicious cases. The treatment centers and mobile laboratories will remain active for a period of 3 months after the declaration of the end of the epidemic.

Spanish scientists find a 'unicorn' Ebola antibody in three survivors

Via El Mundo: Científicos españoles desarman al virus del ébola con un anticuerpo 'unicornio' de tres supervivientes.[Spanish scientists stop Ebola virus with a 'unicorn' antibody from three survivors] Excerpt, with my translation:

Un equipo de científicos españoles ha descubierto cómo impedir la infección del virus del ébola gracias a una defensa natural que han desarrollado los supervivientes a esta enfermedad mortal. El hallazgo abre la puerta a la creación de una nueva vacuna que ya está en fase de desarrollo en un laboratorio de nuestro país.

A team of Spanish scientists have discovered how to stop infection by the Ebola virus thanks to a natural defence developed by survivors of this lethal disease. The discovery opens the door to creation of a new vaccine now under development in a Spanish laboratory.

Del virus ébola, responsable de la enfermedad también conocida como fiebre hemorrágica y que es mortal en un 80-90% de los casos, se conocen cinco cepas distintas, lo que ha dificultado su investigación para inmunizar a la población expuesta o hallar una cura. Esta sería la primera vez que se ha encontrado un punto débil común para todos los tipos de este microorganismo.

Five distinct strains of Ebola virus, a hemorrhagic fever that is fatal in 80-90% of cases, are known. This has made it hard to immunize exposed populations and to find a cure. This is the first time a weak point has been found for all strains of the virus.

Los resultados de esta investigación, publicados en la revista The Journal of Infectious Diseases, los ha presentado este miércoles el doctor Rafael Delgado y su equipo del Servicio de Microbiología y del Instituto de Investigación el Hospital 12 de Octubre de Madrid. Se trata de un estudio en el que también ha colaborado la Unidad de Enfermedades Infecciosas del Hospital La Paz y el científico del Centro Nacional de Biotecnología (CNB-CSIC) Juan García Arriaza, quien lleva a cabo en su laboratorio las primeras pruebas para una posible vacuna. 

The results of this investigation, published in The Journal of Infectious Diseases, were presented on Wednesday by Dr. Rafael Delgado and his Microbiology Service team and Institute of Investigation in Madrid's October 12 Hospital. The study also had collaborators in La Paz Hospital's Infectious Diseases Unit and Juan García Arriaza of the National Biotechnology Centre, who carried out in his laboratory the first tests for a possible vaccine.

"En cuestión de un año podríamos tener la respuesta, por lo menos en el modelo de ratón, si esta estrategia cumple las expectativas que esperamos", ha asegurado a EL MUNDO Delgado.

"In perhaps a year we could know, at least for the rat model, if this strategy meets our hopes," Delgado said to El Mundo.

End Canadian immigration detention: An open letter

Via The Lancet, a letter on behalf of 2,002 individuals and 34 organizational signatories: End immigration detention: an open letter. Click or tap through for supplementary materials.

To the Honourable Ginette Petitpas Taylor, Minister of Health; the Honourable Ralph Goodale, Minister of Community Safety and Emergency Preparedness; the Honourable Ahmed D Hussen, Minister of Immigration, Refugees, and Citizenship; and the Right Honourable Prime Minister Justin Trudeau, 

Over the past 6 years, Canada has held approximately 45 000 people in immigration detention. For the first time in over a decade, Canada is projected to see a sharp rise in the total number of detainees. Children continue to be detained in Canada in large numbers, with current projections exceeding last year's total of 162 children held in immigration detention. 

We are a group of health-care providers working in Canada who—like many around the world—have been watching, with horror, the news of the separation of over 2000 child migrants from their parents in the USA. This cruelty is apparently the newest front in the Trump administration's war against asylum seekers. We've heard audio recordings of young children begging for their parents, and read first person accounts of migrants being told they will never see their children again. 

As health-care providers, we regularly see the results of childhood trauma in patients of all ages. Harm done at a young age can reverberate throughout one's life, causing intense distress and health consequences. We are not surprised that the American Academy of Pediatrics, the Canadian Paediatric Society, the American Medical Association, and the Canadian Medical Association have all come out with strong statements condemning the separation of migrant children from their families. 

In Canada, immigration detention of both adults and children, and family separation, have been a long-standing and grave concern. Canadian research and reports have repeatedly shown the severe mental health effects of even short-term detention on both adults and children. These effects can include depression, anxiety, and post-traumatic stress disorder symptoms in adults, and regression of developmental milestones, sleep disruption, anxiety, and depression in children. 

We urge our federal leaders to take action on this issue and consider how history will look back on what we as a country choose to do right now. Although Canada's practice of detaining migrant children is not new, the general public is now rapidly becoming more aware of it. To criticise the USA when children are being detained and separated from their families here in Canada is hypocrisy, actions that cause similar severe psychological trauma, which physicians and other mental health experts are now speaking out about. 

For the past few years, health-care providers in Canada have been calling for an end to the indefinite detention of migrants, the separation of families, and the detention of children. In 2017, the Canadian Medical Association passed a resolution calling for “legislative changes to protect migrants and refugees from arbitrary and indefinite detention in jails and jail-like facilities.” 

We call on the Canadian government to take action immediately (panel). 

Panel 

Our appeals to the Canadian Government 

• End child detention and family separation in Canada. Imprisoning children, or forcibly separating them from their parents, is simply not acceptable, no matter the migratory status of the children or their parents 

• End immigration detention in Canada. In Canada, migrants are detained in both immigration holding centres and maximum security jails; we join a group of Canada's leading physicians, academics, lawyers, community organisers, and policy makers in calling for the government to stop holding immigration detainees in maximum security correctional facilities and to end the practice of indefinite immigration detention; we join these experts in stating that, as a matter of principle, individuals should not be placed in immigration detention or separated from their families—if individuals pose a danger to themselves or to others, legal measures outside the scope of immigration policy should be used to address such situations 

• End the Safe Third Country Agreement. We join Canadian Doctors for Refugee Care in calling for an end to the Safe Third Country Agreement; the recent actions of President Trump and Attorney General Sessions have made it clear that the USA is not a safe country for migrants, refugees, and asylum seekers 

• Call on the USA to end its practice of child and family detention. Following President Trump's executive order, there is fear within the medical community that while the end of child separation is a positive step forward, more children and families will end up in immigration detention

NCDC epidemiological report, week 25

NCDC has published its Weekly Epidemiological Reports, Week 25.

PRIORITISING NIGERIA’S LASSA FEVER RESEARCH AND DEVELOPMENT ROAD-MAP 

Between January and May 2018, Nigeria experienced its largest reported outbreak of Lassa fever. In responding to the outbreak, critical questions were raised concerning the disease for which answers were either not readily available or required additional validation. 

In this regard, the Nigeria Centre for Disease Control (NCDC) has taken a leadership role to build a Research and Development (R&D) roadmap for Lassa fever in Nigeria.  

To bring the roadmap into reality, a National Lassa fever R&D Stakeholders meeting was convened between the 3rd and 4th of July 2018 in Abuja. The participants at this meeting included case management physicians from the various Lassa fever treatment centres, local and international researchers, partners including the World Health Organization and the host, NCDC. 

The meeting was aimed at identifying the key research areas for Lassa fever, developing research objectives and plans for each area and engaging partners for research implementation. The main areas of research cut across epidemiology of Lassa fever, case management, vector transmission, laboratory diagnosis and risk communications. 

The next few weeks will involve finalising the plans and mapping out resources for the research.  

The outcomes of these activities will help define the landscape with improved knowledge about Lassa fever, guide preparedness and response activities for future outbreaks and drive control/prevention measures for the disease. 

SUMMARY OF REPORTS 

In the reporting week ending on June 24, 2018: 

o There were 125 new cases of Acute Flaccid Paralysis (AFP) reported. None was confirmed as Polio. The last reported case of Polio in Nigeria was in August 2016. Active case search for AFP is being intensified as Nigeria has reinvigorated its efforts at eradicating Polio. 

o 828 suspected cases of Cholera were reported from 34 LGAs in 12 States (Adamawa – 29, Bauchi – 183, Borno – 27, FCT – 2, Gombe – 41, Jigawa – 13, Kaduna – 11, Kano – 110, Katsina – 45, Kogi – 4, Plateau - 24 & Zamfara - 339). Of these, nine were laboratory confirmed and nine deaths were recorded. 

o 24 suspected cases of Lassa fever were reported from nine LGAs in six States (Adamawa – 1, Edo – 9, Gombe – 1, Ondo – 8, Osun - 2 & Plateau – 2). Six were laboratory confirmed and two deaths were recorded.  

o There were 16 suspected cases of Cerebrospinal Meningitis (CSM) reported from 12 LGAs in eight States (Abia -1, Ebonyi – 1, Gombe – 1, Kaduna – 4, Katsina – 4, Oyo – 1, Taraba – 2 & Yobe - 2). Of these, two were laboratory confirmed and no death was recorded.  

o There were 222 suspected cases of Measles reported from 33 States. No laboratory confirmed and no death was recorded. 

In the reporting week, all States sent in their report except Taraba State. Timeliness of reporting remains 89% in both the previous and current weeks (week 24 & 25) while completeness also remains 99% at same period. It is very important for all States to ensure timely and complete reporting at all times, especially during an outbreak.