Childhood Pneumonia, SERS Detection of BoNT, Hantavirus Outbreak

Back by popular demand… the Sunday weekly wrap-up of our team picks for best reads in biodefense and health security.

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Code of Conduct for Timely Sharing of Pathogen Sequence Data During Outbreaks

WHO has just released their code of conduct to help enable the sharing of pathogen genetic sequence data during infectious disease outbreaks. A key concern in recent outbreaks has been variable timelines between the start of an outbreak and the public availability of the first and subsequent genetic sequences. While the first sequences are particularly important to identify and confirm the etiological agent, the ongoing public disclosure of sequencing data as the outbreak develops allows for monitoring of many elements of the response. Comments on the draft document are due by COB 28 January 2019. Pandora Report

House Passage of the Pandemic and All-Hazards Preparedness and Advancing Innovation Act (PAHPAI)

The legislation, which re-authorizes critical federal biodefense programs and agencies, including the BioShield Special Reserve Fund (SRF), the Biomedical Advanced Research and Development Authority (BARDA), and the Strategic National Stockpile (SNS), will help strengthen the pipeline and stockpile of medical countermeasures vital to our nation’s safety and defense. Associated Press

Ebola Readiness – A False Sense of Security?

For many of us who worked in health care during the 2014-2016 Ebola outbreak, memories of those months are filled with frantic efforts to bring ourselves and staff up to par on personal protective equipment (PPE) guidelines, confirm there were patient movement algorithms, and ensure that if someone with Ebola walked through our doors, we would rapidly identify and isolate them. To say that it was a stressful time would be an understatement. The question is: are we better off than we were in 2014? Contagion Live

A Global Cause Without Champions: The Disgraceful Neglect of Childhood Pneumonia

Lower respiratory tract infections, by which we usually mean pneumonia, are the second leading cause of death in under-5s worldwide, and the leading cause in Africa.  But pneumonia does not feature in WHO’s latest Global Programme of Work and no major donor has made the cause their own. The pneumococcal conjugate vaccine (PCV) has shown the potential to reduce the burden of mortality from S pneumoniae –influenza co-infection. Why, then, is there so little cross-disciplinary global solidarity around childhood pneumonia? The Lancet

In Epidemics, Outbreak Culture Is as Toxic as Disease

One of the most prominent among the Ebola first responders was Dr. Sheikh Humarr Khan, a global expert in tropical disease who had worked on more cases of hemorrhagic fever than perhaps anyone else in the world. In 2014, he found himself overwhelmed, at the epicenter of the Ebola outbreak, treating patients at the hospital he led in Sierra Leone. When Khan himself succumbed to the virus, there was debate among leading health experts over whether to give Khan an experimental drug that had not yet been tested on humans. “This is a man who is the most informed person on earth as to whether or not he’d take the drug,” Dr. Pardis Sabeti says. “I thought it was being given to him. I thought he was being engaged. I was devastated when I learned he wasn’t.” NonProfit Quarterly


SERS Detection of Clostridium botulinum Neurotoxin Serotypes A and B in Buffer and Serum: Towards the Development of a Biodefense Test Platform

This paper reports on the detection of inactivated Clostridium botulinum neurotoxin serotype A (BoNT-A) and serotype B (BoNT-B), the two most important markers of botulism infection, by using a sandwich immunoassay, gold nanoparticle labels, and surface-enhanced Raman scattering (SERS) within the context of two threat scenarios.  Science Direct

Trends of Human Plague, Madagascar, 1998–2016

Madagascar is more seriously affected by plague, a zoonosis caused by Yersinia pestis, than any other country. During 1998–2016, a total of 13,234 suspected cases were recorded, mainly from the central highlands; 27% were confirmed and 17% were presumptive cases. Patients with bubonic plague (median age 13 years) represented 93% of confirmed and presumptive cases, and patients with pneumonic plague (median age 29 years) represented 7%. Deaths were associated with delay of consultation, pneumonic form, contact with other cases, occurrence after 2009, and not reporting dead rats. A seasonal pattern was observed with recrudescence during September–March. Emerging Infectious Diseases

Aerosol Infection With Eastern Equine Encephalitis Virus – Susceptibility and Lethality

Eastern equine encephalitis virus is an alphavirus that naturally cycles between mosquitoes and birds or rodents in Eastern States of the US. Equine infection occurs by being bitten by cross-feeding mosquitoes, with a case fatality rate of up to 75% in humans during epizootic outbreaks. There are no licensed medical countermeasures, and with an anticipated increase in mortality when exposed by the aerosol route based on anecdotal human data and experimental animal data, it is important to understand the pathogenesis of this disease in pursuit of treatment options. This report details the clinical and pathological findings of mice infected with EEEV by the aerosol route, and use as a model for EEEV infection in humans. Virology

Insights from Bacillus anthracis Strains Isolated from Permafrost in the Tundra Zone of Russia

This article describes Bacillus anthracis strains isolated during an outbreak of anthrax on the Yamal Peninsula in the summer of 2016 and independently in Yakutia in 2015. A common feature of these strains is their conservation in permafrost, from which they were extracted either due to the thawing of permafrost (Yamal strains) or as the result of paleontological excavations (Yakut strains). BioRxiv

New Mechanism for Ribosome Rescue Can Recruit RF1 or RF2 to Nonstop Ribosomes

Francisella tularensis is a highly infectious intracellular pathogen that kills more than half of infected humans if left untreated. Recently, compounds that inhibit ribosome rescue have been shown to have antibiotic activity against F. tularensis and other important pathogens. Like all bacteria that have been studied, F. tularensis uses trans-translation as the main pathway to rescue stalled ribosomes. However, unlike most bacteria, F. tularensis can survive without any of the known factors for ribosome rescue. This research identified an F. tularensis protein, ArfT, that rescues stalled ribosomes in the absence of trans-translation using a new mechanism. These results indicate that ribosome rescue activity is essential in F. tularensis and suggest that ribosome rescue activity might be essential in all bacteria. mBio

A Single Introduction of Yersinia pestis to Brazil During the 3rd Plague Pandemic

Yersinia pestis was introduced to Brazil during the third plague pandemic and currently exists in several recognized foci. There is currently limited available phylogeographic data regarding Y. pestis in Brazil. This research summarizes whole genome sequences for 411 Y. pestis strains from six Brazilian foci to investigate the phylogeography of Y. pestis in Brazil; these strains were isolated from 1966 to 1997. All strains were assigned to a single monophyletic clade within the 1.ORI population, indicating a single Y. pestis introduction was responsible for the successful establishment of endemic foci in Brazil. Overall, the patterns observed in Brazil are similar to other locations affected during the 3rd plague pandemic such as in North America and Madagascar. PLOS One


Up to 7 Million Have Had Flu This Season, CDC Says

This is the first year in which the CDC is issuing estimates on the toll of a flu season while it is still in progress. In the past, these estimates, which are derived using mathematical models, were published once per season, after the flu activity had subsided. The plan is to issue weekly estimates of how many people have been sickened by influenza, how many went to a doctor for care, and how many became so sick they were admitted to hospital. These types of figures are easier for people to understand than some of the metrics found in the CDC’s weekly update on influenza activity, FluView.  STAT

Emergence of Extensively Drug-Resistant Salmonella Typhi Infections

The emergence of fluoroquinolone nonsusceptible strains that are resistant to third-generation cephalosporins, such as ceftriaxone, in Pakistan and other countries complicates typhoid fever treatment. Travelers to areas with endemic disease should be vaccinated against typhoid fever before traveling and follow safe food and water practices. Clinicians should be aware that most typhoid fever infections in the United States are fluoroquinolone nonsusceptible and that the XDR Typhi outbreak strain associated with travel to Pakistan is only susceptible to azithromycin and carbapenems. CDC MMWR

Measles Cases at Highest For 20 Years in Europe, as Anti-vaccine Movement Grows

A fresh Guardian analysis of WHO data shows that measles cases in Europe will top 60,000 this year – more than double that of 2017 and the highest this century. There have been 72 deaths, twice as many as in 2017. In Italy, for example, members of the anti-establishment Five Star Movement (M5S) and the far-right League, proclaimed vaccines unsafe before they came to power in a populist coalition government. In 2015, M5S proposed a ban, citing a spurious “link between vaccinations and specific illnesses such as leukaemia, poisoning, inflammation, immunodepression, inheritable genetic mutations, cancer, autism and allergies.”  The Guardian

Characterization of a Filovirus (Měnglà virus) From Rousettus Bats in China

This study characterizes a phylogenetically distinct bat filovirus, named Měnglà virus (MLAV). The coding-complete genome of MLAV shares 32–54% nucleotide sequence identity with known filoviruses. Phylogenetic analysis places this new virus between EBOV and MARV, suggesting the need for a new genus taxon. Nature Microbiology

American Monitored for Ebola at Medical Center Released

The patient being monitored for possible exposure to the Ebola virus at Nebraska Medicine has been released, hospital officials say. The unidentified American health care professional was providing medical assistance in the Democratic Republic of the Congo when the exposure could have happened. Nebraska Medicine said Saturday that the patient completed the required 21-day monitoring period and did not develop any symptoms. KETV Omaha

Adenovirus Can Kill. Some Scientists Think It’s Becoming More Common

Olivia died in November, killed by a virus that normally causes symptoms little worse than the common cold: adenovirus 7. It’s the same strain that killed 11 children and made 36 sick in an outbreak at a nursing home in New Jersey. Some experts believe the strain is spreading more frequently across the United States. Adenovirus 7 causes more severe symptoms — such as fever, sore throat, and diarrhea — than other strains of adenoviruses and while there is a vaccine to prevent it, it’s currently only available to the Department of Defense. NBC News

Argentina Isolates 85 People to Quell Hantavirus Outbreak

An Argentine judge has ordered 85 residents of a remote Patagonian town to stay in their homes for at least 30 days to help halt an outbreak of hantavirus in which nine people have died. Thursday’s order by Judge Martin Zacchino affects people in Epuyen who have been in contact with people who tested positive for the virus. Some people in the town of 3,000 had resisted calls for voluntary isolation. ABC News

Nearly 500 People Are Now Sick On Royal Caribbean Cruise Ship

The number of people hit with a gastrointestinal illness on a Royal Caribbean International cruise ship has swelled to nearly 500, a company spokeswoman said Friday. The increase to 475 people comes a day after the company said 277 passengers on the Oasis of the Seas had initially fallen ill. Travelers on the cruise ship — which according to Royal Caribbean’s website is a 1,187-foot long vessel and was voted the best cruise ship 2014 by Travel Weekly readers — started feeling sick after the ship departed from Port Canaveral in Brevard County, Florida, on Sunday. NBC News

New York Faces Worst Measles Outbreak in Decades

More than 167 people in the state of New York have contracted measles in the state’s largest outbreak since the 1990s, NBC reported earlier this week (January 8). The highly contagious virus, which scientists say was brought to New York by travelers returning from a visit to Israel last September, has prompted statewide efforts to vaccinate children and adults to try to prevent an epidemic. The Scientist


Recurrent Epicardial Ventricular Tachycardia Following Smallpox Vaccination

Between 1967 and 1977, a global program of smallpox vaccination resulted in the elimination of the natural disease. Following the eradication of smallpox, routine vaccination in the United States ceased by 1989. However, vaccination amongst military personnel was renewed in 2002, in response to the imminent Iraq war and fear of bioterrorism. Since the reintroduction of the vaccine, a renewed emphasis has been placed on the risk for vaccine related adverse events, of which cardiac complications (including sudden cardiac death) have emerged as the most frequent serious adverse events reported. In this report, we present a patient who developed recurrent episodes of ventricular tachycardia (VT), beginning one month after receiving the smallpox vaccine. Health Rhythm Case Reports

New Hope with Ebola Drug Trial – Democratic Republic of the Congo

Since the start of this current outbreak in August 2018 – the tenth to hit the DRC since Ebola was discovered in 1976 – patients have had access to one of four investigational treatments on a compassionate basis. These drugs – mAb 114, Remdesivir, Zmapp and REGN-EB3 – were offered under an ethical framework developed by the World Health Organization known as the Monitored Emergency Use of Unregistered Interventions (MEURI) protocol. By 1 January, 248 patients had received one of these four drugs. While some patients seemed to improve, there was no scientific evaluation of the efficacy and safety of these drugs. So, on 24 November, the DRC’s Ministry of Public Health announced the start of a randomized control trial (RCT). WHO is coordinating the trial which is led and funded by the DRC’s Institut National de Recherche Biomédicale (INRB) and the National Institutes of Health (NIH), a part of the US Department of Health and Human Services. Other partners are MSF and ALIMA. Relief Web

Severe Flu Raises Risk of Birth Problems For Pregnant Women, Babies

A study out this week shows that pregnant women with the flu who are hospitalized in an intensive care unit are four times more likely to deliver babies prematurely and four and a half times more likely to have a baby of low birth weight. Researchers compared 490 pregnant women with the flu and 1,451 who did not have the flu. Sixty-four of the women with flu were so ill that they were admitted to a hospital ICU. NPR

Antibiotic-Resistant Infections Linked to Surgeries in Mexico

All of the travelers diagnosed with the life-threatening bacteria, carbapenem-resistant Pseudomonas aeruginosa or CRPA, had undergone invasive medical procedures. “Infections caused by this particular drug-resistant Pseudomonas are rare in the United States and difficult to treat,” the CDC said. Patients typically require long and “complex antibacterial drug combinations and courses” to defeat the infection. CNN


Proteomic Evaluation of the Acute Radiation Syndrome of the Gastrointestinal Tract in a Murine Total-body Irradiation Model

The proteomic profiling conducted here represents an untargeted systems biology approach to identify acute molecular events that will be useful for a greater understanding of animal models and may be potentially useful toward the development of medical countermeasures and/or biomarkers. Health Physics

Marines Set Up Specialist Novichok Unit In Response to Salisbury Attack

The Royal Marines have set up a unit specialising in chemical warfare skills to better prepare for incidents similar to what the UK experienced during the Novichok attack on Salisbury. Zulu Company from 45 Commando, based in Arbroath, Scotland, will be the first marines to respond to a chemical, biological, radiological or nuclear (CBRN) incident at home or abroad. The Telegraph

Watch the 2019 Doomsday Clock Announcement

The  Bulletin of the Atomic Scientists will host a live international news conference at 10 a.m. EST/1500 GMT on Thursday, January 24, 2019, to announce the 2019 time of the Doomsday Clock. The news conference will take place at the National Press Club in Washington, D.C. Watch the announcement live on their website. Bulletin of the Atomic Scientists

Healthcare Providers Should Be Ready for Nerve Agent Attacks

On the scene, emergency personnel must first recognize an exposure to sarin, cyclosarin, soman, tabun and VX. Nerve agents, which are in a similar chemical class to some insecticides, affect neurotransmitters and can severely harm the functioning of the central nervous system. This means nerve agent exposures can look similar to opioid or cyanide poisoning. Health care providers can recognize the signature symptoms of nerve agent exposure by remembering the “SLUDGE” mnemonic: salivation, lacrimation (teary eyes), urination, diarrhea, gastrointestinal cramps and emesis (vomiting). Reuters

Pediatric Considerations Before, During, and After Radiological or Nuclear Emergency

This report summarizes newer scientific data from studies of the Chernobyl and the Fukushima Daiichi nuclear power plant events, use of improvised radiologic dispersal devices, exposures from inappropriate disposal of radiotherapy equipment, and potential health effects from residential proximity to nuclear plants. Also included are recommendations from epidemiological studies and biokinetic models to address mitigation efforts. The report includes major emphases on acute radiation syndrome, acute and long-term psychological effects, cancer risks, and other late tissue reactions after low-to-high levels of radiation exposure.  American Academy of Pediatrics

Nuclear Safety Group to Look at Stockpiling Anti-radiation Pills in More Toronto Schools

In greater Toronto, there are two nuclear plants — Pickering, about 30 kilometres from Toronto’s Yonge St., and Darlington, which is about 60 kilometres away. The safety commission currently requires that anyone who lives or works within a 10-kilometre radius of the plants receive the potassium iodide pills. Anyone living or working in a radius beyond that and up to 50 kilometres can ask for the pills. The Toronto Star The Toronto Star


Gene-Editing Tool CRISPR Repurposed to Develop Better Antibiotics

The technique, known as Mobile-CRISPRi, allows scientists to screen for antibiotic function in a wide range of pathogenic bacteria. Using a form of bacterial sex, the researchers transferred Mobile-CRISPRi from common laboratory strains into diverse bacteria, even including a little-studied microbe making its home on cheese rinds. This ease of transfer makes the technique a boon for scientists studying any number of bacteria that cause disease or promote health.

DoD Selects Smiths Detection for Advanced Development of Aerosol and Vapor Chemical Agent Detector

Intended as the next generation chemical detector, the AVCAD is designed to detect, identify, alarm and report the presence of traditional and advanced threat vapors and aerosols. Using a wireless remote alarm capability and both mounted and portable configurations, AVCAD will support missions for the U.S. Army, Air Force, Navy and Marine Corps. SDI is partnered with subcontractor 908 Devices Inc. to use High-Pressure Mass Spectrometry (HPMS) for the AVCAD. CBRNE Central

India: ELISA Kits Developed by National Research Centre for Glanders and EIA Released

Glanders is a fatal infectious and notifiable disease of equines that includes horses, donkeys and mules. The disease is caused by a bacterium known as Burkholderia mallei and has zoonotic potential. After continuous research efforts of more than 8 years, NRCE has been able to develop a recombinant Hep1 antigen ELISA as an alternate to Complement-Fixation Test (CFT). The ELISA has been duly validated in India and the OIE Reference Laboratory, Germany and showed excellent sensitivity (97.2%) and specificity (99.6%). The assay has a huge potential for international commercialization as recombinant protein-based ELISA is not available in any other country. Krishi Jagran

Sandia Microneedles Technique May Mean Quicker Diagnoses of Major Illnesses

A new technique using microneedles able to draw relatively large amounts of interstitial fluid — a liquid that lurks just under the skin — opens new possibilities. Previously, microneedles — tiny, hollow, stainless steel needles — have drained tiny amounts of interstitial fluid needed to analyze electrolyte levels but could not draw enough fluid to make more complicated medical tests practical. The new method’s larger draws could be more effective in rapidly measuring exposure to chemical and biological warfare agents as well as diagnosing cancer and other diseases Sandia National Laboratories


APHL/CDC Fellowships

Masters and post-doctoral graduates may apply now through February 28, 2019 for the following two fellowships: Association of Public Health Laboratories (APHL) – CDC Antimicrobial Resistance Fellowship Program, and the APHL – CDC Bioinformatics Fellowship Program. Each are 12 months in duration, with the possibility of extension.  Wadsworth Center

Federal Biosurveillance Programs

DHS Awards $75.2M BioWatch Contract to PAE

Medical Countermeasure Development

BARDA Looks to Expand Clinical Studies Network for Biodefense Countermeasures