Friday 17 July 2015

Evidence that Reston ebolavirus resides in live bats in the Philippines...

Update #1 18JUN2015
Jayme and colleagues find some
"smoking bats"-possible bat reservoir
species for
Reston ebolavirus
in the Philippines.
In what I think is only the second example of this, a new collaborative study from Jayme and a team of eminent researchers in the Philippines, Australia, Vietnam and the United States, have reported the finding of Reston ebolavirus (RESTV) viral RNA and antibodies to viral infection in a range of different bat species....some more "smoking bats" - bats with more than just past evidence, sometimes considered vague and unreliable, of an ebolavirus being hosted by the animal.

The finding of RNA is not the same as actual infectious virus, but RNA is a very specific marker for the virus nonetheless. And the authors note that they didn't want to kill the bats so only a small volume of sample was available-not enough for culture.

Leroy and colleagues had previously reported finding Zaire ebolavirus RNA and antibodies against this species of virus in Hypsignathus monstrosus, Epomops franqueti and Myonycteris torquatebats, all fruit-eating megabats of the family Pteropodidae. These are considered to be important reservoir hosts, yet they do not show signs of disease.[2] 

According to one of the authors on the latest study, bats in the Philippines also seemed clinically well...

Locating the Philippine RESTV sequences
on the ebolavirus phylogenetic tree.
Jayme et al. Virology J. (2105) 12:107.[1]
Jayme's findings are important to the story of RESTV importations to animal facilities in the United States from the Philippines which occurred multiple times between 1989 to 1996. These fed into the dramatized retelling we know of as The Hot Zone. There were also signs of antibodies to the virus in humans working with infected non human primates in the Philippines in 1994, 1996 and 2008.

The amount of viral RNA in most of the bats was quite low - but was usually repeatably detectable. I'm a firm believer in PCR giving a specific signal when there is something specific present to detect (assuming it was done in a professional laboratory setting that reduces the risk of false positives-which it was in this instance). So low viral loads are not no viral loads.

RESTV RNA was repeatably found in oropharyngeal swabs taken from bats assigned to the following species:

...and in one sample from:
  • Chaerephon plicata (Wrinkle-lipped Free-tailed Bat; range; insectivorous bats)
What's particularly interesting to me is that some of these bat species are found in Australia. However, keep in mind that the range of some (?many) bats may be underestimated. The example here is using the IUCN Red List's described range for M. schreibersii-apparently it's a bat that inhabits an area around the Mediterranean.[4] Last I looked, the Philippines is a bit south of there. In the past, as Wikipedia lists, a much bigger range was ascribed to this bat, also including Australia,[5] Guinea, Liberia and Sierra Leone - among many others. Looks like there may be lots of work to do in the area of bat census.

Jayme and colleagues also sampled the blood of 61 flying foxes (of the fruit-eating bat family Pteropodidae) and antibodies were found by ELISA and Western blot in 3 Acerodon jubatus (giant golden crowned flying foxrange) bats and by ELISA alone in a Pteropus vampyrus (Large flying foxrange). If you trust the test, then this indicates past exposure.

Superman and the Joker know very well - Bats can be very tricky. But at least this finding helps to further address the Riddle(r) of the reservoir. Now, if only we could only nail down the specific culprit(s) in West Africa.

  1. Molecular evidence of Ebola Reston virus infection in Philippine bats
  2. Fruit bats as reservoirs of Ebola virus
  3. Many details about bats to be found at the excellent IUCN Red List
  4. Population Structure of a Cave-Dwelling Bat, Miniopterus schreibersii: Does It Reflect History and Social Organization?
  5. Seasonal movements of the Schreibers’ bat, Miniopterus schreibersii, in the northern Iberian Peninsula
  1. Added bat specie range data (and discussion) from IUCN Red List and Wikipedia.

Haemorrhagic fever viruses...

A viral haemorrhagic fever (VHF) is an umbrella description for severe illnesses, usually discussed in relation to human and non-human primates, which can be associated with bleeding - although not always or even most of the time. VHF diseases often have fever and can affect multiple organs and systems within the body.

Outbreaks of VHFs are zoonotic (infection of humans after contact with an infected animal) and often irregular, reflecting sporadic transmission from an infected animal or insect host, spread between humans, or from an animal reservoir to other animal hosts.

As we learn more, it seems that the majority (?all) of viral infections result in outcomes that exist in a spectrum from severe to moderate to mild and even at times and perhaps controversially, asymptomatic infections (depending on what and how you measure and whether you look deeply enough and for long enough). Yet even though overt bleeding might not be obvious, there are frequently laboratory indications of clotting abnormalities in the blood of infected people-so the naming is still functional.[4] Bear in mind however, that "VHF" may not always be used to describe severe disease, but it will always be a term that pervades the historical literature.

VHF disease results mostly from infection by a number of viruses which have RNA genomes surrounded by a lipid envelope and which belong to a wide range of distinct viral families. Below I've listed some of these family names in italics (immediately adjacent to the filled bullet point) and under each family are some specific examples of viral species, also in italics (open bullet point):[3]
  • Arenaviridae including: 
    • Lassa mammarenavirus (disease: Lassa fever) 
    • Junín mammarenavirus (disease: Argentine haemorrhagic fever)
    • Machupo mammarenavirus (disease: Bolivian haemorrhagic fever)
  • Bunyaviridae including:
    • Crimean-Congo haemorrhagic fever virus 
    • Rift Valley fever virus (disease: Rift Valley fever)
    • Hantaan virus (diseases: hantavirus pulmonary syndrome [HPS], hantavirus haemorrhagic fever with renal syndrome [HFRS])
  • Filoviridae including: 
    • Zaire Ebolavirus (Ebola virus disease [EVD]) 
    • Marburg marburgvirus (Marburg virus disease)
  • Flaviviridae including: 
    • Yellow fever virus 
    • Dengue virus
    • Omsk hemorrhagic fever virus 
    • Kyasanur Forest disease virus
This blog has recently acquired quite a bit of knowledge about one of these VHF viruses - a variant of Zaire ebolavirus called Makona.You may have heard about what a single "sporadic" transmission is capable of in the right setting and circumstances.

Just like those all over the world who got caught out in different ways by the scale and ferocity of the EVD epidemic in West Africa last year and early this year, VDU knew little about the virus or the disease before March 2014. It took a lot of reading to get blog posts together in the early days and weeks. Over time VDU aims to learn more about the other viruses listed above so it can more effectively communicate about them...should the need arise; and that list is not exhaustive. As VDU learns, it will share that knowledge here. VDU isn't a textbook of course or is it a peer-reviewed source - its what's may be called community grey literature,[5,6] and there already many excellent resources for this knowledge. But as ever, I do this because it teaches me some new things as well as one or two of you - that makes it well worth my spare time and basically for purely selfish reasons! 

If you simply can't wait for more detail, you're now armed with a few go forth and learn more!


Monday 13 July 2015

MERS simmers down in South Korea...did we learn anything this time?

No new cases reported in 8 days and the most recent known date of illness onset now 10 days ago, are good indications that the Middle East respiratory syndrome coronavirus (MERS-CoV) hospital-driven outbreak in South Korea is pretty much over. At the least, it's contained. Finally.

Roughly speaking - based on the data from the South Korean Ministry of Health and Welfare, the World Health Organization and KBS news - there were four rounds of infection. In all, 186 cases of MERS have been reported, with 36 (19.4%) resulting in death up until the 13th July AEST:
MERS case spread among hospitals in South Korea
between the 11th May and the 19th June.
Cowling et al. Eurosurveillance Vol 20,
Issue 24, 25-JUN-2-15.
Click on image to enlarge.

  • the 1st round was the person who flew into South Korea after visiting all over the Arabian Peninsula - he became ill on the 11th of May.[1,2]
  • the 2nd round included approximately 45 cases.[3] This group started becoming ill on the 19th of May, continuing until the 4th of June.[5]
  • the 3rd round included approximately 108 cases.[3] These people started showing signs and symptoms of disease between the 27th of May and the 13th of June.[5] 
  • the 4th round included approximately 22 cases.[3] This group became ill between the 5th of June and the 2nd of July.[5]
We've learned a few things (perhaps "relearned"?) and had a few things reinforced (even more) during this latest successful test of our healthcare systems ability to defend against a case becoming an outbreak...successful from the coronavirus' point of view that is. 

For example we saw that..
MERS-CoV detections, deaths, sex and age distribution in
the South Korean hospital outbreak.
From my MERS-CoV in South Korea page.
Click on image to enlarge
  1. MERS-CoV doesn't spread efficiently between humans - over 16,100 contacts did not develop MERS.[6] 186 did.
    While there were probably more infections among contacts (and future studies from South Korea will hopefully investigate and answer this), disease did not develop among many of those exposed to infected people.
  2. Closing schools, wearing masks in public, putting thermal imaging cameras in office buildings and quarantining zoo camels when not a single case has been acquired without link to a hospital was an exercise in failed communication between government and public.
    There was no indication that any of these costly, high profile measures prevented any transmission. There was also no point to them, precisely because transmission outside the hospital setting did not occur.[3]
    We have to learn to talk more, more often, and more clearly to our populations about the realistic risks of a new and scary virus when it shows up on our shores. We need to build trust here. Trust and respect takes time to build. In these outbreaks, we're always forced to rush because we seem incapable of investing in this before an event. Gods forbid we'd teach these concepts at school. We need to make a bigger deal about educating and informing our public about virus transmission. That is best done if the materials and the processes to roll the messages out to the public are already in place
  3. Holding back information that you have already collected doesn't build confidence in you.
    Whether that is not releasing the name of a hospital or the detailed data about deidentified cases, or presenting a list without discussion, engagement or correction when necessary 
  4. Hospitals are great places to spread infections, if infection control is not constantly running.
    Viruses aren't big on forgiving. Neither are zombies. The undead really suck that way. But the truth may well be that hospitals need to be on guard, cleaning surfaces and in PPE 24 hours  day, 7 days a week if they are dealing with cases of infectious disease that can be expelled from a human in the form of coughing, sneezing, bleeding or vomiting. Judging whether to use "standard precautions", "droplet precautions" or "airborne precautions" at some point after a coughing and sneezing patient has been sitting in the waiting area for hours, is going to be too little too late to stop new healthcare worker infections
  5. Allowing the public - that is, the otherwise healthy - to co-care for patients within hospitals and to sleep in rooms or wards with infected people expelling virus (as per #4) - is a bad idea if trying to contain an acute viral infection
  6. People with other underlying diseases get more seriously sick after MERS-CoV infection.
    Adult health in richer nations is not in a good way. When a wimpy spreader like MERS-CoV comes to town, it may do little damage to the young and otherwise healthy population, but we are not all healthy. 
We all have a role to play in protecting those among us who will suffer more greatly from an otherwise simple acute viral infection by even a rare and obscure camel-cold virus. Whether that is getting a vaccine to prevent us from becoming a hijacked virus production facility, being mindful of others when we cough and sneeze, or seeking out information from trustworthy sources to learn about the realistic threats from a new (or old) virus when it comes to town, we can all make some difference here. 

At some point, one of these viruses may well be better at hopping between us and may cause severe disease not just in those who have an existing ailment. If that day comes, we have proven yet again, that no facet of our response will be up to the task of halting its spread. 

We're not ready.  

But hey - that virus' arrival is probably many, many cycles of leadership change, war, and petty bickering away yet. We'll be ready by then. Right?


Ebola virus disease, getting ahead of communication needs and WHO

Sunday 5 July 2015

Editor's Note #23: Tweepidemiology#2..

Thought it was time to update the "Tweepidemiology" graph I first posted back in September of 2014.

The Ebola virus disease epidemic of 2014 certainly drive the biggest of my Tweepidemics.

Followers of my @MackayIM Twitter account (and this blog which gets
promoted through it) since I started tweeting.
This shows the cumulative rise, and pause, of followers and the relationship between the rate of that rise and some active periods of infectious disease outbreaks..
Click on the graph to enlarge

This will be something I check back in on from time to time. Interesting stuff. 

As above but zoomed in to show the dip in followers of the @MackayIM Twitter account.
Click on the graph to enlarge.
Something else this little analysis showed me was still interesting, but very disappointing. That thing was one of the biggest losses of followers and slowest periods of follower gains that my Twitter account has had in its 2 years. 

This dip happened immediately after I changed the background on my avatar to reflect my support for the US Supreme Court's legalisation of same sex marriage. I kept that background for a week. I haven't been able to find anything else to attribute to the dip - I haven't been any more annoying or rude than I usually am! I don't blog to gain followers per se but followers are very helpful because they help spread sometimes useful information further than it might otherwise reach. Also, because you're mostly a likable bunch of course! In the scheme of things it was a blip - and there is always a turnover of newcomers and "newleavers" and the latter generally increases in proportion to a decrease in my level of engagement. It just strikes me as sad that people feel so much dislike or annoyance that they need to respond by leaving the table in disgust or annoyance like a child who doesn't get what they want.

Data. So many things to learn from them.

Saturday 4 July 2015

Editor's Rant: Communicating the data and about the data...

It is pretty damn hard work trying to get hold of data on virus outbreaks around the world. 

When it is, it may be available in unfriendly formats. It may not be made public at all. When it is available, it is often slow to appear or it may have random reporting gaps, or be partially incomplete. The style of the released data can change overnight as well, sometimes going from detail to summary.

So why bother about trying to get hold of these numbers at all? It's not like I work in the field. Well, that is a question I'm increasingly asking myself of late too. My personal reason has been because I think there need to be more voices in the vacuum between the numbers being reported and the often dry public health reports. I think scientists, even if they are not lifetime experts on a given virus or outbreak, still have much to offer when they come out from behind their manuscripts and apply their skills to interpreting what's happening. Well, many do anyway. And they should do it more. Now, perhaps more than ever, science needs steer away from its cold, dense and boring niche writing to a chattier, more helpful and community-based style of engagement. It astonishes me how often the public's interpretation of outbreak numbers must come from the media or from hobbyists, or even professionals who work in other areas and give of their own time to help explain something to us in their personal time. Helpful and engaging information and better access should come from the source of the data.

So it becomes really annoying (you would have to know me quite well to know how many times I just rewrote those words) when data are given out for public use that are a total mess...and there is not one tiny mote of explanation for it. I called it appalling on Twitter tonight. And at other times there are no explanations for why there are gaps, why data are delayed, why the format may have changed today compared to last week, why a line list is missing a case, using a new and totally independent numbering scheme or suddenly reshuffled, why there is no news about a new outbreak. No word. No contact. No-one taking the lead. No...communication.

I have met a lot of people since I have been blogging who, in various ways, have put in their own personal time to help out bigPublicHealth, to help take up the slack in communicating to the media and to the public. It is hard to quantify the impact of that combined help-but I can assure you that it reaches far and wide and is not insignificant. One would think that it should be easier to provide this help when one is willing to make use of their own time and use their own resources, or that those people should be shown enough respect to be able to simply find and apply reliable raw data so they can help out. But one would be an idiot. I very clearly remember a time when I could send a public Tweet to WHO's Head of Public Relations, Gregory Haertl, and get an informed reply. Those days have passed. I remember there being an #AskEbola channel on Twitter that gave answers. That engagement is just not there anymore. I'm sure its funding and resources and blah blah...but not as sure as I could be if that were spoken about in public. Communication. Someone needs to step up on this. As the quotes above allude to, 2015 is not 2014. And one of those differences is that everyone wants timely and comprehensive information they can rely on during times of outbreak. This hasn't been discusses enough but it should be.

Friday 3 July 2015

Ebola virus: wild and domestic animals, plants and insects...

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