Medical News Blog Information

Ebola - the lesser transmission risks are still risks...

The United Nations (UN) Foundation blog has used some pretty strong language in their latest post of the 5 Things to Know on Ebola This Week.

Number 2 on their list stated (by highlighting)...
First detected case of Ebola transmitted through sexual intercourse
Earlier research suggested that three months of abstinence or condom use among male survivors would suffice to prevent the transmission of Ebola through intercourse. But an Ebola patient in Liberia who died last week had just one known risk factor: her boyfriend was an Ebola survivor, treated last September. This is the first case detected of the Ebola virus being transmitted through sexual intercourse, which has necessitated updated recommendations. Read the full story here: http://unfoundationblog.org/ebola/5-things-to-know-on-ebola-this-week-10/#sthash.2HkUbbYT.dpuf
While there is reported to be ongoing testing (and presumably virus genotyping), I've yet to hear publicly the outcome of such testing. 

Perhaps the results are known behind closed doors and perhaps that testing has firmly pointed to a sexual transmission route. The UN post above certainly seems very sure and it also seems that this event has triggered an update to recommendations. There is solid literature about the presence of infectious Ebola virus in seminal fluids so the possibility shouldn't be far beyond belief.[4]

Another possible, albeit also unproven, transmission route is urine. This fluid seems to me to be a far more likely source of trouble. One cannot abstain from urination. So why worry about urine as a risk for transmission of Ebola virus? An EVD case study last year showed very nicely that infectious Ebola virus could be cultured from urine for about 12 days longer than it could be from blood.[1] Viral RNA has also been found in urine for four weeks.[1,2] 

Perhaps urine should be a more noteworthy concern for its potential to remain infectious after blood test become negative. This concern might be greater wherever toilet and hand-washing facilities and sewers, are minimal or poorly maintained.

Urine and seminal fluids are not considered to be major transmission routes for Ebola virus. But let's not forget that it was probably an unlikely transmission event, and route - a single jump from an animal to a human - that triggered >25,000 EVD cases in this epidemic. Even a rare risk must be given serious consideration when such a large public health impact can realistically result.

References...

  1. Kreuels B, Wichmann D, Emmerich P et al. A Case of Severe Ebola Virus Infection Complicated by Gram-Negative Septicemia. N Engl J Med. 2014 Oct 22. 371:2394-2401
  2. Lyon GM, Mehta AK, Varkey JB et al. Clinical Care of Two Patients with Ebola Virus Disease in the United States.  N Engl J Med. 2014 Nov 12. 371:2401-2409
  3. Ebola Virus Disease (EVD). Key questions and answers concerning water, sanitation and hygiene. World Health Organization. http://apps.who.int/iris/bitstream/10665/137181/1/WHO_EVD_WSH_14_eng.pdf?ua=1
  4. Mackay IM, Arden KE. Ebola virus in the semen of convalescent men. Lancet Infect Dis. 2015 Feb;15(2):149-50.

Compa�eros en Salud � a model for rural primary care in Chiapas, Mexico

Week 3

Compa�eros en Salud

The Mexican branch of Partners in Health, also known as CES or Compa�eros en salud is based in Jaltenango, surrounded by a number of rural communities in the sierra of Chiapas, where new Mexican medical school graduates (pasantes) are placed to fulfill their one year obligatory service posts. Currently there are 10 pasantes in 10 communities, each about 1 to 3 hours from Jaltenango on rough rugged roads. CES maintains a relatively lean budget, using it to supplement the government support of the pasantes so that they do not need to rely on the goodwill of community members to host them free of charge (the government provides US$150/month and CES effectively doubles this stipend). The budget also supports several supervisors, all of whom recently completed the CES pasante program, who travel between communities to support, precept, and teach the current pasantes. Many of these supervisors will be living in Boston in the upcoming years to complete master�s degrees in global health and public health. Additionally, the budget allows CES to supplement the often inconsistent and meager medication supplies provided by the government, and to help ensure that the pasanteshave the basic medical equipment they need to provide care. Several short and long-term volunteers also support CES, mostly from the U.S., with a medical director who recently graduated from Brigham and Women�s medicine residency program.

My role over the coming weeks is to offer support to several pasantes in two communities (Laguna and Monterrey), accompanying during visits and providing feedback and suggestions throughout the course of clinical visits. A major goal of the CES program is to improve the training of Mexican doctors, through direct clinical practice and observation, as well as through monthly didactics that take place in Jaltenango. During this month�s course, we discussed topics of biopoder (biopower), nutrition, diabetes, and tuberculosis. One pasantepresented an M&M case (morbidity and mortality) of neuroleptic malignant syndrome in a man with schizophrenia and another presented a morning report style case of possible Scarlet Fever in a child. A humanistic curriculum session to discuss the emotional aspect of medicine was also included.


Overall, the program seems to emulate some educational aspects of a U.S. medical residency (although on a much smaller level), while providing extra support to pasantes who otherwise would have a very isolated and resource-restricted experience trying to care for the local community. Hearing pasantes talk about the various urgent cases that they have managed, you realize that with a few key resources and a good understanding of when to triage to a higher level of care, there is a lot that can be done in a very resource-limited setting. Some of those key resources include materials to start and maintain IVs, fluids, oxygen with nasal cannula, oral and nasal airways with ambu bag, suturing materials, local anesthetics, saline flushes, bandages, tourniquets, inhalers and nebulizers, steroids, antibiotics, anti-hypertensives, insulin, aspirin, and other key medications.

One thing that I will have to get used to in the coming weeks is the difficulty in obtaining laboratory work. In the U.S., when you start someone on anti-hypertensives, in particular on diuretics and ACE inhibitors, a basic chemistry panel is a must to ensure that our patients are not becoming hyper or hypokalemic. In the communities, however, the nearest lab may be over 2 hours away, a trip that many patients may not be able to afford or fit into their week. In the U.S., we order TSH screening tests like candy - if someone has constipation or fatigue or palpitations, failing to order a thyroid screening test would be neglect. However, in order to get a TSH in the communities, one not only has to travel to the hospital in Jaltenango, but one also has to pay an additional fee to the lab. For this reason, it is so important to be critical about what labs are actually likely to change management in a significant way. More on patient care in future posts, as I have yet to spend a significant amount of time in any one community.

Finally, one last observation that I have been struggling with is the fact that none of the pasantesare actually from Chiapas. The large majority of pasantes have graduated from one of the top Mexican medical universities, in particular from Instituto Tecnol�gico de Monterrey. On the one hand, CES is able to work with the best medical graduates to build their potential to function at a higher level and in that way bring up the overall quality of medical care in Mexico. These pasanteswill go on to complete residency programs in various specialties, some will pursue degrees in public health and look forward to a career in research and program development, others will remain as general practitioners and work to educate the upcoming classes of pasantesafter them. These individuals will be leaders within the Mexican medical system in the coming years. One day, CES can and should be run by Mexicans, who have a stake in improving their own health care system.


Nevertheless, Chiapas remains one of the poorest regions of Mexico, and the patients being seen in the community clinics are very different from the pasantes themselves. The difference in class and education and culture are marked. In some ways, the pasantes are almost as gringo as we are (of course, not really, but sort of). Some of them love camping and REI and American films as much as we do. Yet, the experience of serving these rural, impoverished communities must be striking and indeed quite impactful. In the U.S., programs like these (Teach for America, Americorps, National Health Service Corps) change the way individuals understand the inequalities in our society, and may help to change perspectives and policies down the road. Of course, what is ultimately needed is development of educational and employment opportunities and upward mobility for people in Chiapas. The goal is to have doctors from Chiapas who will stay in Chiapas and who understand better the needs of the community. What I have been told is that the universities in Chiapas are not good, and for this reason, CES has not had pasantes from Chiapas. However, how might the program change if these folks were sought out and recruited and mentored to their full potential? Certainly there would be challenges, but it would also bring a richness and perhaps greater accountability and responsiveness to community needs.


The CES Radio Show


Every Sunday morning, one of the CES supervising physicians H�ctor invites a guest speaker to a local radio station in Jaltenango (broadcast to many of the rural communities where CES works) to discuss a topic relevant to public health. Previous topics have included nutrition, alcoholism, diabetes, depression, antibiotic overuse, UTIs and others. This Sunday we talked about hypertension, and I was the �expert.� Some common myths that we covered included the idea that hypertension could be caused by a susto (a scare), an idea that many people in Guatemala also have regarding diabetes. Other myths included the fact that medicines for hypertension are caliente (hot), meaning that they interact with various vitamins and herbal remedies and may cause gastritis or other problems. Many people buy these medicines over the counter, sometimes without the evaluation and prescription of a doctor, and we had a caller who asked if I could prescribe something for her over the radio for her headaches that she felt could be caused by hypertension. (Of course I said no). Other people are prescribed anti-hypertensives, then stop taking them because they are told the medications interact with alcohol and they do not wish to abstain from alcohol. Others stop taking their meds when they start to feel better, not understanding that hypertension is a chronic disease. Still others spend their money buying medications from pharmacies in town, believing that the free medications offered at the community clinics must be worse because they are free. We addressed these concerns, while also discussing the enormous burden of hypertension in the world (9 million 400,000 people die from complications of hypertension every year) and in Mexico (according to a 2012 survey, 1 in 3 people live with hypertension, yet only half of them are aware of their diagnosis, and only half of those are controlled). Finally, we spent a good amount of time discussing dietary, exercise and other lifestyle changes to prevent and treat hypertension at the most basic level. We ended the radio show with one of my favorite songs by Marc Anthony  :)



On Government Programs

Later in the day, H�ctor took me on a jog through Jaltenango�s Ciudad Rural, a government program throughout Chiapas to build sustainable communities for low-income families. The community in Jaltenango was built after an earthquake destroyed the previous settlement, and is quite lovely. There are 600 brick homes with tile floors and enough space for a family, with a lawn in the front with space for a garden. There is a central garden where theoretically vegetables and fruits can be grown for local consumption (not sure whether this is currently in use, as it was too dark to see the gardens). There is a church. There is a central park/plaza for taking walks, sitting, jogging. There are streetlights powered by solar panels, which unfortunately cost too much to replace when they break (10,000 pesos), so at least half of the lights are out. Unfortunately, of the 600 homes, at least a third or more of the homes are currently unoccupied, as people have had to move out of the community to find work, as there are few job opportunities in the surrounding neighborhoods. Many of the residents work as mototaxistas, shuttling people around town in hybrid motocycle / taxis for 5 pesos (~33 cents) a ride. The homes were gifted to families, and thus are technically owned by the families that originally settled in the community. However, it seems there is some barrier to selling the homes if a family must move out, so the homes lie unused when a family can no longer support themselves on the meager job opportunities available in Jaltenango.

During our jog, H�ctor explained to me a bit about the Mexican public health care system, explaining concepts that had been brought up during the CES course for pasantes about biopoder(biopower, or the systems and hierarchies that affect people�s health on a broad institutional level). For example, all Mexican citizens have access to universal health care through Seguro Popular (the health safety net insurance for those who don�t qualify for other insurance programs through employment and income levels), with a list of at least 250 preventive and other medical conditions that are covered fully by the insurance. These include things like vaccines, diabetes and hypertension care, prenatal and postpartum care, and many common urgent care conditions like parasites, respiratory infections, ulcers, dengue, etc. The difficulty becomes when the government and their body of experts must decide which conditions are covered and which are not. Theoretically, the most cost effective interventions for common conditions are covered, while less cost effective interventions for rarer conditions are not. Through decisions like these, the government is able to maintain lower overall health care costs, with approximately 6% of the GDP dedicated to health expenses (compared to 17% in the U.S.). Nevertheless, it is difficult to place a cost on the value of a life and decide when it is not cost effective to try to save a life. Also, which conditions are covered may be influenced not only by objective measures, but likely also by politics and who is making the decisions.


A third program that is quite interesting and again partially problematic is the program now called Prospera, previously called Oportunidades.Effectively a welfare program, the payments are however tied to requirements such as attending prenatal appointments, following up with chronic disease care, ensuring that your children attend school, etc. Payments vary depending on income and family size, on the order of US$60-$100 monthly. The program becomes problematic when you think about the power that it gives to those supervising visits, who determine whether or not an individual has completed the requirements and thus qualifies for payment, and when thinking about the barriers to an individual or a family in fulfilling the requirements, and the fact that the most vulnerable individuals will have the most difficulty completing the requirements.

Publishing on 'ebola' is a booming pastime...

One of my jobs since October last year has been to keep up on the literature for Ebola virus and Ebola virus disease. 

At this stage I have a lot of reading to catch up on.


There were 1,858 publications during the 37 years including 1977 to 2013. In 2014 and 2015 (so far), there have been 1,485 publications. 

Click on image to enlarge.
According to a basic search of PubMed using the term 'ebola' - there have been over 1,500 publications - and those are the ones captured by PubMed - to be found using that search term.


Hans Rosling, a micro-outbreak of Ebola in Liberia and trust issues in Guinea...

As is always the case, Prof Rosling can be seen in front of an audience here, providing a beautifully articulated example of how trust in the Ebola virus disease (EVD) treatment centre/unit plays such a pivotal role in (a) the containment of EVD, even witting a family and its contacts, and (b), the likelihood of survival of EVD patients.

Frame taken from a BBC News video which was being hosted in
an African Geographic Magazine story here. Red dots are survivors,
black dots are deaths
Click on image to enlarge.
In this example, which you can listen to in its entirety here, as time went on, trust grew and this fewer transmission occurred and more f those infected, survived.

This would seem to be a great example of what is lacking in Guinea - trust - a lack of trust that others are be able to stop the spread of virus and to save the lives of those infected. Thus people are not presenting for help at all and still being managed in the community - possibly infecting others - or else they are not presenting early enough, before the disease has done too much damage to the person. Trust and communication is increasingly seen as being as important to the successful reduction of cases in Liberia and Sierra Leone as the building of treatment centres - the two must co-occur.

Trust comes from understanding, and that is heavily influenced by communication. Communication of accurate information, of clear and digestible information. Communication to the right people using the moist effective channels is also essential.

It still feels like communication, or at least accurate and successful communication accessing the key important and influential people, may be the weakest part of the response in Guinea. It seems to have been better implemented in Liberia and Sierra Leone - or maybe just better received. Is it a groundwork thing? Difference in the way science is presented in different countries? I know far too little to guess further.

There continue to be more security incidents and other types of refusal to cooperate in Guinea compared to the other two countries afflicted with the Makona variant of Ebola virus. These incidents are a marker of a community that does not believe or trust those claiming to be here to help. And that's a problem for stopping the constant rivulet of EVD cases in Guinea; a rivulet that never became the river of hundreds of EVD cases per week seen in Liberia or Sierra Leone, but was still a flow that seeded infection across the region and the world. A case anywhere is a threat everywhere, to paraphrase others.


Location of laboratories in Guinea, Liberia, and Sierra Leone
 Location of laboratories in Guinea,
Liberia, and Sierra Leone.
From WHO SitRep 01APR2015.
But there may be other issues to consider and question. 

There are fewer treatment centres and laboratories in Guinea than in Liberia or Sierra Leone - strange given that Guinea is larger and that it still has a geographically widespread distribution of cases. 

While it has lately been noted that new cases in Guinea could be adding to the tally more simply because of success in reaching more remote areas, this seems only to add support to the need for better communication and to provide more of a presence in these remote areas. Hopefully, now that this happening through the efforts of the US CDC and others, we will soon see the pay off as a reduction of EVD cases. But the rainy season is near and travel will be made into a muddy mess by that. Time has never been on the side of those trying to stop this epidemic.

DNA structure... a primer

A DNA Down Under post
For an organism, or a virus, to grow or replicate, it must make new pieces of itself and assemble those pieces into something functional.

Simple pieces or units can form larger and larger structures. In humans this process starts with proteins then moves on to form cells, then tissues, then organs and eventually whole bodies. 

In viruses the process of assembly is much shorter and less complex than in humans, with proteins assembled into a relatively simple final product, a virion or single virus particle.

So what tells the machinery of an organism to make proteins? Basically, the information is stored by a blueprint or template which is made of deoxyribonucleic acid, or DNA. DNA forms the basis of the genes of an organism or virus. But, even though DNA code has all the information needed to make proteins, it needs to be "decoded" into something that enzymes can recognise. In humans, this process is carried out by the ribonucleic acid, or RNA. RNA is a middle-man or mediator for the early steps required to produce an organism - be it a human, or quite often, a virus. RNA is also needed as a template to make more copies of the DNA. So you can see that there are two processes going on - making proteins from the DNA, and making new DNA copies from the original DNA.

Nucleobases.
What I've just described is a general, pretty simplistic plan. There are exceptions to these rules and a big one is found among viruses. Some viruses don't have genes made of DNA, they are made of RNA instead. Some viruses have thus developed special ways and workarounds to make proteins and copies of their genes. More on that later.


DNA was discovered in 1869 by Friedrich Miescher, a Swiss physician. He found an acidic substance in the nuclei of cells in pus that he named nuclein. 

It was not until 1878 that the German chemist Albrecht Kossel purified the protein away from these nucleic acids, and also later identified its nucleobases (see above) - or component parts.

A pentose sugar (middle) attached
to a monophosphate group (left) 

and the site where a purine or 
pyrimidine nucleobase attaches (right). 
Nucleoside=sugar + base;
Nucleotide=sugar + base 

phosphate group
In 1919 the Lithuanian-American chemist Phoebus Levene identified that units of DNA (a nitrogenous base, a sugar and a phosphate; right) associated into chains. In 1937 these structures were first revealed through X-Ray diffraction thanks to English physicist and molecular biologist, William Astbury. In 1952 Dr Rosalind Franklin captured images of the patterns DNA crystals made when scattering X-Rays. In 1953 American molecular biologist James Watson and English molecular biologist Francis Crick proposed the double-helix model of DNA structure, based on an X-ray diffraction image.

Nucleic acid is one of several macromolecules (big molecules) found in the body (others include proteins and carbohydrates) which are formed by lots of individual molecules (nucleotides) strung together to form a polynucleotide. Each nucleotide consists of a sugar, a nitrogen base and a phosphate group. In RNA the sugar is called ribose (how the name ribonucleic acid comes about), and in DNA it is called deoxyribose which means that it is missing ("deoxy") a carbon atom compared to a ribose sugar.

The combination of a sugar with a any one of five different nitrogen bases creates a nucleoside. The five bases are divided into two categories based on the structure of their molecules; purines have two ring structures (adenine and guanine) while pyrimidines have one (thymine, cytosine and uracil). Adenine, guanine, thymine and cytosine are found in DNA whereas RNA replaces thymine with uracil.

If a phosphate molecule is added to a nucleoside it becomes known as a nucleotide. Nucleotides with a ribose sugar are therefore ribonucleotides, and nucleotides with a deoxyribose sugar are deoxyrobonucleotides. Each nucleotide's name can be shortened to a single letter, A for adenine, C for cytosine, G for guanine, T for thymine and U for uracil.

The chemical bond that links one nucleotide to another is formed between the phosphate group of one nucleotide and the sugar group of the next nucleotide via an ester bond between a carbon atom and an oxygen atom. Two things remain the same no matter how many nucleotides are added to the growing polynucleotide chain; one end of the chain has a free phosphate group and the other end has a free hydroxyl (-OH) group. These ends are called 5' ("five prime") and 3' ("three prime") respectively (there's no Optimus prime).



This naming system comes from the way we present a sugar structure when we draw it on paper. We start at the "top, right-hand" carbon and count in a clock-wise manner. The phosphate group of the previous nucleotide is linked to carbon number 5, and the phosphate group of the next nucleotide is linked to carbon number 3. The naming system, 5' to 3' is used to describe the order of the nucleotides in the DNA strand. Think of the system as being similar to the way European people are taught to read and write - from the left side of a page to right side.


Rhinoviruses (RVs)...a primer

Schematic of a human rhinovirus (RV) genome. (+)ssRNA genome.
Based on GenBank accession no. NC_001490 for HRV-C3 (f.QPM).
Use images freely but please cite www.newsmedicalnet.blogspot.com.au 
and Dr. Ian M Mackay as their source.
Click on image to enlarge
More than 100 serologically distinct types (serotypes), and another 50 or more genotypically defined and distinct types (genotypes) of human rhinovirus (RV; Greek rhin = nose) exist within the genus Enterovirus. Along with other members of the family Picornaviridae, the RVs are unenveloped viruses with a positive sense, single-stranded RNA genome that is preceded by a genome-linked protein (5' VPg) and terminated with a poly(A) tract (3').

Other genera within the family include Aphthovirus, Aquamavirus, Avihepatovirus, Cardiovirus, Cosavirus, Dicipivirus, Enterovirus, Erbovirus, Hepatovirus, Kobuvirus, Megrivirus, Parechovirus, Salivirus, Sapelovirus, Senecavirus, Teschovirus and Tremovirus.

HRV discovery...

Click on image to enlarge.
The first rhinovirus to be isolated in cell culture was at the Common Cold Unit (Salisbury, UK).[4] By 1967, 55 serologically distinct (sero)types had been recognized. In 2006 the first report[3] defining a distinct genetic grouping of RV types not previously recognized by Mackay and colleagues contributed to the addition of 50 more distinct types assigned to a new species, RV-C. In 2014, a number of additional RV genomes, as well as known ones, were sequenced and published.[7,8,9]

HRV taxonomy: a tale of types and variants...

Predictive capsid model of a rhinovirus C virion (RV-C3, f.QPM).
3D rendering of predicted RV-C3 capsid providing imagery
similar to that obtained by cryo-electron microscopy
reconstruction at 10 � resolution.
doi:10.1371/journal.pone.0001847.g005 [10]  
    
RV genotypes and serotypes are most simply referred to as "types". Keep in mind that individual types are still written as �HRV-blahblah� whereas the species shorthand or conversationally written form has dropped the �H� to leave �RV�. The 2 best RV schemes for genetically defining an RV type versus a variant of an RV type (the same RV type, but detected in another patient - very little genetic distance separates one RV variant from another in any region of the genome), have been described by Prof Peter Simmonds and colleagues.[5,6] For the latest naming development check the Picornavirus Study Group�s websites.[1,2]

HRVs and pneumonia...

Pneumonia is a disease that of the young and the elderly in particular. It is responsible for millions of deaths each year and is associated with viral and/or bacterial infections. Pneumonia requires an X-Ray confirmation of inflammatory infiltration of the lung tissue. Community-acquired pneumonia (CAP) in children is frequent in developing countries. CAP can also make existing chronic medical conditions worse and takes advantage of the ageing immune system.

HRVs play some role in the development of bacterial pneumonia, but the extent is likely to be underestimated. Determining the cause of pneumonia is made difficult by the low frequency of sampling the lower respiratory tract, by studies that are  conducted over short periods of time and by the complexity of the viral and bacterial mix involved. Quick and  easy sampling of the upper airways is ideal for routine sampling of patients. This convenience and reduced risk  associated with some sampling methods (needle aspirates for example) sampling of the lower respiratory tract  means that often, detection of putative viral or bacterial pathogens in the upper airways is assumed to be related  to LRT disease, especially in children under the age of 5 years. Studies of pneumonia studies are also  complicated by the infrequent inclusion of a control patient group and by the fact that sputum is not produced  from the healthy lower airway. 

Before PCR methods, respiratory syncytial virus (RSV) and then RVs were described as the major viral  contributors to CAP (between 1 and 2 thirds of cases). In the golden PCR age, RVs are increasingly the major  viral group detected from both upper and lower respiratory tract (sputum) specimens from children with CAP.  These findings are supported even when studies span more than a 12-month period, which should encompass  change in the prevalence of seasonal viruses. 

Viruses, including RVs, are thought to pave the way for bacterial super-infection in some direct or indirect way.  There are data from laboratory research studies which support this as well as clinical data finding a high proportion of  RV and bacterial co-detections. Despite considerable comment in the literature, rhinoviruses are in fact less likely to be co-detected with another virus, than are many other viruses.[11]
References... 
  1. Nick Knowles, Chair of the Picornavirus Study Group's excellent Picornaviridae website 
  2. The official Picornaviridae Study Group website 
  3. KE Arden et al. Frequent detection of human rhinoviruses, paramyxoviruses, coronaviruses, and bocavirus during acute respiratory tract infections. J Med Virol.  2006. 78(9):1232-40 
  4. IM Mackay, Human rhinoviruses: The cold wars resume. J Clin Virol. 2008. 42:297-320 
  5. P Simmonds and colleagues. Proposals for the classification of human rhinovirus species C into genotypically assigned types. J Gen Virol. 2010. 91(Pt 10):2409- 19
  6. CL McIntyre and colleagues. Proposals for the classification of human rhinovirus species A, B and C into genotypically assigned types. J Gen Virol. 2013  94(Pt8):1791-806
  7. Liggett and colleagues. Genome sequences of rhinovirus C isolates from Wisconsin pediatric respiratory studies. Genome Announc. 2014 2(2) e00203-14
  8. Liggett and colleagues. Genome sequences of rhinovirus B isolates from Wisconsin pediatric respiratory studies. Genome Announc. 2014 2(2) e00202-14
  9. Liggett and colleagues. Genome sequences of rhinovirus A isolates from Wisconsin pediatric respiratory studies. Genome Announc. 2014 2(2) e00200-14
  10. McErlean and colleagues. Distinguishing molecular features and clinical characteristics of a putative new rhinovirus species, human rhinovirus C (HRV C). PLoS  One. 2008 3(4):e1847
  11. Greer and colleagues. Do rhinoviruses reduce the probability of viral co-detection during acute respiratory tract infections? J Clin Virol. 2009 45(1):10-5

The weakening pulse of the Ebola monster...

As of this post, some of the most comprehensive publicly available data on an emerging virus is coming out of the Kingdom of Saudi Arabia in relation to the Middle East respiratory syndrome coronavirus (MERS-CoV). Yeah-that's what I said. Even with all the issues I complain about, its more detailed than for other current outbreaks. 

In 2015, China became a major disappointment in its poor publication of data for the avian influenza A(H7N9) virus's 3rd outbreak - choosing to release bulk updates and little to no detail on who, where or when. 

The continuing avian influenza A(H5N1) virus outbreak in Egypt is also a mystery to all but a very few. Something that is a concern I think, for a much larger number.

Data from the Ebola virus hotzone countries in western Africa has also had many ups and downs. This is not at all surprising given the conditions, the extent of mobile communications, the history of the region, the political and social issues, the poor health infrastructure and the speed with which Ebola virus disease (EVD) spread through Guinea, Liberia and Sierra Leone in 2014. Many different patterns have emerged over the past year among these numbers. 

One pattern is the "heartbeat" of EVD cases - the difference in number between update and summary tallies - seen when plotting the data reported by the World Health Organization.


Click on image to enlarge.
The peaks (Wednesdays and Mondays) and troughs in this chart both hide and reveal all sorts of tales. Principal among these is that the pulse is slowing. The life of the EVD epidemic monster is steadily draining away as the courageous aid workers in western Africa, those from within and from outside each afflicted nation, track the monster to its every hideout and starve it of its avenues for escape and further spread. 

It is perhaps the slowest and most painstaking of the phases of this epidemic, but the process still moves forward towards the goal of zero cases and the complete eradication of these particular variants of Zaire ebolavirus, from the planet.

Where did the MERS-CoV comorbidity and animal contact fields go...? [UPDATED]

Is this the work of the US CDC and other visitors helping the Kingdom of Saudi Arabia (KSA) Ministry of Health (MOH) resolve their Middle East respiratory syndrome coronavirus (MERS-CoV) problem? Is it an arbitrary reporting change by the Command and Control Center (CCC)? Is it someone forgetting to unhide the relevant columns in their spreadsheet?
Changes to the KSA MOH MERS-CoV public 
reporting detail after 17-March-2015.
1. The MERS-CoV graph changed scale and caught up.
2. Three fields disappeared: pre-existing disease, 
animal exposure and contact with a known cases 
within a hospital setting
3. The promise of weekly updates was dangled-
without reference to a host site.
Click on image to enlarge.

I don't know why, but since 17th March, the KSA MOH MERS-CoV reports have stopped posting information about whether each newly announced MERS case had a comorbidity and whether they had animal contact. Granted, the last field was almost always "No" or "Under Investigation" - and thus of little use (we rely almost exclusively on the World Health Organization reports to provide useful animal data) - but I wonder why the MOH has chosen to stop posting even the heading this month? 

The much more epidemiologically significant description of whether the case was an "expat" or a "Saudi" citizen remains - whew! 

And the MOH has continued to do away with all of that pesky detail that might allow an observer to link a death to a previously announced case. Thank goodness we don't have that clutter to deal with - or the details from the found113 which I presume are now completely lost in the sands of time. 

I guess the removal of these latest 2 data fields is just all part of providing the world with more of that full transparency and up-to-date information about this emerging pathogen - like the MOH "News" page - all the latest info you could want from August and earlier is to be found there. 

Oh well, at least you can get the latest from the weekly updates...if Google Translate's efforts can be understood.

It really isn't as hard as it is being made to look to get the reporting aspects right.

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