H7N9: Source and origins identified

More of the H7N9 mystery has been solved (or almost solved) in an article published online in Nature today (Wed. Aug. 21, 2013). Let’s remember that H7N9 was first noted earlier this year in China; so far there have been >130 human cases reported, and 40 deaths, for a case fatality ratio of approx. 31%. The public health community–and I–have been concerned about this strain not because of the actual morbidity and mortality, but because of its potential for spread and increase.


Today’s article, published online in Nature (Lam, Wang, Shen et al, The genesis and source of the H7N9 influenza viruses causing human infections in China, doi:10.1038/nature12515) consists of a painstaking process of sampling from the environment as well as oropharyngeal and cloacal swabs from a variety of avian spp., including ducks, geese, and chickens. Phylogenies were then identified using quantitative reverse transciptase PCR (qRT-PCR). Based upon phylogenetic similarity, some of the article’s conclusions are:

1) Transfer of H7 viruses from domestic duck to chicken populations probably occurred at least twice in China;

2) Enzootic H9N2 viruses combined with the H7 viruses to produce H7N9, and a novel H7N7 virus that had not previously been identified. This was in chicken populations, and the novel virus has been shown, experimentally, to infect mammals.

3) Live poultry markets which are found widely in parts of China and other areas of Asia were implicated as potential foci of spread because of the presence of H7N9 in these markets. The authors caution that the H7N9 virus, and H7N7 viruses may be widespread in chickens, and therefore have the possibility of widespread species transfer to humans in these foci.


Echoing so many similar calls and observations, the authors warn that “Long-term influenza surveillance remains essential for early warning of novel reassortant viruses and interspecies transmission.”


This article is the latest of a series of articles on the molecular epidemiology of this novel virus. I argue that a big challenge is to combine two types of analysis: 1) molecular epidemiology identifying “clusters” of similar genomic configurations; and 2) geospatial analysis using GIS, spatial statistics, and spatial modeling, in combination with molecular epidemiology to understand patterns of spread of variants, and, indeed, to serve as early warning and surveillance instruments as new strains of flu and other viruses spread from localized foci, and threaten a more widespread population.

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H5N7: A problem in the making?

A new strain of avian influenza, H5N7, has been in the news recently, and every day brings with it reports of more cases and more deaths, principally in China. I am frequently asked: is this something to worry about?
It depends on the interpretation of the question. Any new strain of influenza is something for concern. Considering the mortality rates and the case fatality ratios of newly reassorted strains of influenza, we could see widespread and significant mortality and morbidity. At the same time, we must be circumspect before declaring a new strain as a potential public health emergency.

Much of the uncertainty comes from the fact that we do not know H5N7’s transmission dynamics: its R(0), or average number of people whom an infected individual infects. We do not know how virulent and pathogenic the strain is in even moderate numbers of people. In short, the basic characteristics of contagion and transmission are unknown. At this point, it is fairly certain that there is no human to human trnsmission. Were there human to human transmission, it might be time to be more concerned. Rather, H5N7 appears to be the product of genetic reassortment involving commercial and domestic fowl, and probably pigs as well. The same complex,, therefore, is probably involved here as it has been with many novel strains.
H5N7 does not appear to be completely new, although the media suggests, in many places, that it is. H5N7 was recognized in Italy in 2007.
So what are we to make out of what we see with H5N7? At this point, it bears watching through various surveillance tools available, including Flu View, WHO, CDC, ProMED, and others. I always have a great deal of respect for the destructive potential of influenza. However, during the same week that CDC has declared our period of seasonal flu transmission to be over, let’s just keep an eye on H5N7.

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Chronic pain as a public health problem

Some estimates suggest that 120 million Americans suffer from chronic pain. However, the issue is how to improve access to state of the art pain treatment. It is becoming clearer that treatments that are effective in acute pain, such as opioids, are far less effective in treating chronic pain. Chronic pain is fundamentally different than acute pain since chronic pain involves the remodeling of the brain and CNS. Acute pain is adaptive; chronic pain is usually maladaptive, and serves little physiologic purpose, yet its prevalence is so high.

In the last few years, it has become clear how little we know about public health approaches to chronic pain. Even the epidemiology and risk factors of chronic pain have received little attention–perhaps 10 or 15 people globally have published the major research in pain epidemiology. It is repeated again and again, now, that there is no proof that the use of opioids in chronic pain is appropriate. They may help some people adapt to chronic pain. The ultimate test is whether these individuals are more able to go about activities of daily living, and lives that *they* consider to be happy and productive.

Multiple disciplinary pain research teams have found in the last 50 years that graded exercise is very helpful in most chronic pain states–exercise that is appropriate for the particular individual. This includes both aerobic/cardio exercise, and appropriate muscle training, such as core muscle strengthening exercises. More recently, it has been shown that the use of imagery, relaxation techniques, and mindfulness meditation help to down regulate pain. Movement, exercise, imagery, and mindful breathing all have their places.

In addition, for many types of pain, antiepileptic medication such as gabapentin (Neurontin) and pregabalin (Lyrica, in the US) can help. Even earlier, it became clear that tricyclic antidepressants are helpful. More recently, some of the newer antidepressants, such as venlafaxine (Effexor) and duloxetine (Cymbalta) may be helpful.

Medical intervention aside, might more walkable cities help in the treatment and even prevention of pain? Research has shown that walkable neighborhoods are associated with lower rates of obesity, and possibly lower rates of obesity-related disease, such as diabetes, and cardiovascular disease. Might these walkable neighborhoods–areas with sidewalks, good lighting, and parks, to name a few characteristics–help to prevent and treat chronic pain? A testable hypothesis is that such neighborhoods are associated with lower chronic pain prevalence, after adjusting for confounders and effect modifiers.

The fact that there is no central pain registry, and that it is nearly impossible to get geographically specific data from some of the national health survey data, such as the National Health Interview Survey, hinders pain research. Basically, it is necessary to collect primary data to address these questions, which poses logistical and financial difficulties.

The fact that chronic pain is viewed as a symptom rather than as a set of pathological conditions in themselves may hinder research. This is because most research is disease oriented rather than symptom oriented. For example, most departments of epidemiology have cancer epidemiologists, cardiovascular epidemiologists, neuroepidemiologists, and, going back to the origins of the field, infectious disease epidemiologists. Though there have been several books published on the epidemiology of pain, I know of no epidemiology departments that have pain epidemiologists (maybe I am the only one).

This poses a more fundamental question: is chronic pain a symptom or a disease? A disease in itself that hinders function and happiness. Pain researchers have begun to view chronic pain as a disease. I prefer to consider it as a phenomenon: it just *is*, but chronic pain hinders happiness and harms public health.

If one third of a population (such as in the US) reports that they have chronic pain, we are dealing with one of the most prevalent public health problems. It is time to increase funding for and research on chronic pain. It is time to address chronic pain as perhaps the most prevalent public health issues. And, once there is more understanding and more appreciation of chronic pain, it will be time to address it definitively from a public policy perspective.

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Flu season 2012-2013 could be bad

The CDC influenza surveillance system indicates that seasonal flu (H3N2) has gotten off to an earlier start than usual, and the attack rates are higher than usual. Collaborating labs are reporting steadily increasing numbers of isolates. There is only one reported case of a novel virus, indicating that genetic shift has not occurred. The ILI (influenza like illness) surveillance system indicates very high activity in Texas and in some of the southeastern states. See:


for CDC’s “Fluview”. 

The actual trends have been presaged by similar increases in search term inquiries in Google Flu Trends, which has been shown to predict actual flu activity–and precede surveillance data by weeks.

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Medical geography: a better name needed

The traditional “medical geography” has been replaced in discussions in the field of geography by “health geography.” Neither describe the field adequately. To me, the importance of medical geography is one of perspective and of methodology: a view of health and disease from the perspective of spatial patterns, and of human-environment relationships. “Medical” refers more to diagnosis and treatment. “Health geography” connotes, to me, a de-emphasis of disease, while most research in epidemiology and related areas deals with disease. “Disease geography” de-emphasizes health. So “epidemiologic geography”? “Geography of health and disease”? Please leave suggestions or comments.

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New SARS-like virus identified

I am back again after a long interval during which I had spine surgery. It was my first experience with an operation. I have seen over 500 of them from the OR side for a project on anesthesia and pain, but had yet to experience anesthesia myself. It was very interesting, really. A very smooth induction, and a very smooth emergence without nausea and vomiting–both pretty common post-anesthesia, but less so with some of the agents that are now being used. It is ironic that in the midst of a long standing project and interest in pain, I had the “privilege” of experience both. I find that most of my ideas come from experience.

My first seminar of the year on medical geography begins today, and I am excited to meet the new graduate students (17)

The subject of today’s posting is the new SARS-like coronavirus that has been identified in two patients: one in Saudi Arabia who died, and another in the UK. It is difficult to ascertain what the significance of this newly identified virus is. Are these patients just two of many who have contracted the virus, and it was not identified previously? Are these isolated cases? Is this the beginning of an epidemic? Only time will tell.

The rapid identification of the virus demonstrates the importance of new technologies for identifying the genomes of viruses and other pathogens. Identifying genotype can now occur quickly using DNA/RNA amplification techniques, and this allows placement of the virus on a phylogenetic tree, which is a statistical and graphical technique for ascertaining similarities between viruses.
See the following website for an excellent glossary:

This virus is not *SARS*. There are many coronaviruses, with renewed interest since the SARS outbreak. Some of these can cause respiratory symptoms, and others gastrointestinal symptoms.

Only time will tell whether this particular virus will be consequential for human health. It is impossible to tell from only two cases.

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Are social determinants of health actually determinants?

There has obviously been a tremendous proliferation of research on what has long been labeled “social determinants of health.” The wording, however, is unfortunate. “Determinants” suggests determinism–a mechanistic set of influences that do not allow for the possible, for the stochastic, for the undetermined. The problem with “social determinants of health” is that it is too–deterministic. This is an irony. We cannot treat social factors such as locus of control, inequality, and structural violence as though they are deterministic variables in simple Newtonian mechanics. The irony is great. I now use “social influences on health” as a simple substitute. We need new words. Language can determine how we think.

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