Saturday, 30 August 2014

The fifth I give you...[UPDATED]

Senegal. 
According to it's Minister of Health, Awa Marie Coll Seck[1,2], a case of Ebola virus disease (EVD) has been imported from Guinea and it is confirmed by testing at the World Health Organization's collaboration Centre, the Pasteur Institute in Dakar.


Interesting that this occurred one week after Senegal closed its borders (again) with Guinea.[3,4] The infected 21-year old Guinean student travelled on 21-August to Dakar. On the 23rd he presented to a hospital but did not admit to being in contact with known EVD cases; Guinea issued an alert that a person with EVD contact has escaped surveillance 27-Aug; Senegal closed its borders around 22-August.[5,6,7,8].
[WHO Disease Outbreak News places his movements ahead of the closure of the border, arriving in Senegal 20-Aug [8]]

These borders are leaky and so the effect of "closure" essentially hinders aid, trade and economy (all very important to the region, especially right now) but very clearly does may not stop the spread of human hosts-as we have seen here


Humans are the variable in outbreaks. 


They behave differently each time. 


They respond differently each time. 


This is why no two outbreaks are identical. 


It's why you're a mug to assume this outbreak will be like the last outbreak.


While it looks like this is now a case study in why closing a border is ineffective, I maintain a position that border closures can't contain infectious disease. And please, do not point me to "temperature measurement" as a way to ensure capture of infected individuals. You could easily be harbouring an infection that does not yet express the symptom of fever. 

Click on image to enlarge. 
Graphic lifted from a great CNN video narrated by
Dr Sanjay Gupta. The video describes an example of
contact tracing and its importance to the fight
to contain EVD.[2] 

The contact tracing starts in Senegal now. A 42-day clock starts for the country and a signs and symptoms watch continues on all this case's contacts for 21-days.

References...
  1. http://in.reuters.com/article/2014/08/29/us-health-ebola-senegal-idINKBN0GT1CD20140829?feedType=RSS&feedName=health&utm_source=dlvr.it&utm_medium=twitter&dlvrit=309303
  2. http://edition.cnn.com/2014/08/29/health/ebola-outbreak-senegal/
  3. http://www.washingtonpost.com/news/world/wp/2014/08/29/the-ebola-virus-has-spread-to-senegal-as-the-deadliest-outbreak-in-history-gets-worse/
  4. http://www.washingtonpost.com/world/africa/alarm-grows-as-ebola-outbreak-spurs-more-flight-cancellations-border-closures/2014/08/25/87e6d020-2c66-11e4-994d-202962a9150c_story.html
  5. http://www.bbc.com/news/world-africa-28893835
  6. http://fox59.com/2014/08/22/senegal-closes-its-borders-with-guinea-over-ebola-fears/
  7. https://www.internationalsos.com/ebola/index.cfm?content_id=434&language_id=ENG



Thursday, 28 August 2014

MERS-CoV around the house-yes, it does transmit at home

Click on graph to enlarge.
Some Middle East respiratory syndrome coronavirus (MERS-CoV) questions remain stubbornly unanswered even after two and a half years.

Today comes a study from Prof Christian Drosten and colleagues, including Prof Ziad Memish, released by the New England Journal of Medicine.[1] This study takes a look at MERS-CoV infection among the contacts of MERS cases.

We already know that asymptomatic or "silent" MERS-CoV infections are not rare. At least 17% of detections of this virus have occurred in people with no overt signs or reported symptoms of disease. That's not to say that they didn't have a slightly raised temperature, headache, sniffle or something very mild that got overlooked or forgotten, but nothing noted or noteworthy. I'd love to see a study on asymptomatic MERS-CoV infected people that looked into fine detail signs and symptoms by the way-that might tell a nice little story about "silent" infections.

This new study looks at the contacts of infected cases from 26 different households, each with a single confirmed MERS-CoV infected case, with MERS. These households provided throat swabs from 280 contacts and antibody test results on at least 1 sample (only 44 permitted a second voluntary blood sample be taken-a shame) from the 280 contacts as well.

Some interesting findings included:

  • Median age of cases (65.4% male) was 55-years
  • Median age of contacts (52% male) was 29-years
  • Cases 7 household contacts (2.5%) were viral RNA-positive (RT-PCR) within 2-weeks of the index patient's illness onset. Similar to what PCR-based studies conducted previously have yielded.
  • 5 household contacts (1.7%) were considered antibody positive after a series of different tests were used. 3 were positive between 2-3 weeks after the index case's onset, and 1 each before or after that period. 
  • some indication that neutralizing antibodies against MERS-CoV might be low level and short lived in mild or asymptomatic infections and that previous antibody studies may have missed some cases if the took blood too long after a mild infection
Overall, 12 (4%) contacts acquired MERS-CoV infection from an index case, across 6 of 26 households (23.1%). 

Among others, one question I'd like answered is whether symptomatic cases being kept in home isolation, which was occurring during the Jeddah-2104 outbreak when they don't need hospital-based supportive care, is the best option for stopping transmission? We don't know whether mild or silent infections can transmit virus, which remains another important question. While 4% seems like a small proportion, it's big enough to perhaps explain some of the sporadic case occurrences. Also, we should be mindful that MERS-CoV infection is associated with the death of a third of the people it infects. I'd want to be pretty sure I wasn't letting a house-bound shedding mild/silent person spread MERS-CoV to a visiting old uncle with a co-morbidity.

References
  1. http://www.nejm.org/doi/full/10.1056/NEJMoa1405858
  2. If this is what MERS-CoV detections look like with more testing...what is the "normal" community level of virus?? [UPDATED]
    http://virologydownunder.blogspot.com.au/2014/04/if-this-is-what-mers-cov-detections.html
  3. Guidelines for home isolation related to MERS Corona Virus infections | May 2014http://www.moh.gov.sa/en/Documents/3-Isolation.pdf

Monday, 25 August 2014

The battle of Ebola gains a second front...the Democratic Republic of Congo (DRC; formerly Zaire) [UPDATE #2]

So there are three reasons for this post. 
  • It may be a little while before we get solid confirmed information form the DRC and I think maps are useful for those of us who are ignorant of where countries live!
  • I'm looking for a quick post so I can move the previous post's grisly pictures down the page!
  • Mike Reid (see comments below; many thanks) brought to my attention that the range of the hammer-headed bat (Hypsignathus monstrosus; [5]) overlays the current ebolavirus outbreak areas strikingly well. I lifted that range graphic and (imperfectly, in pink) overlaid it onto my map - et voila!
Data for the hammer head bat's (Hypsignathus monstrosus) range come from The International Union for Conservation of Nature (IUCN) Red List of Threatened Species. I adapted the graphic for VDU from Wikipedia [3]
We don't know the details yet but early reports from a country that was the site of the first (known) outbreak of a virus (called Ebola virus [1] or EBOV) of species Zaire ebolavirus, suggest two confirmed cases.[2] 

One of the cases was reportedly genotyped as a member of the species Sudan ebolavirus (SUDV) and the second was a "mixed" infection of SUDV and an EBOV. A mixed natural infection of a human would be very...unheard of. Can't really say much more though, until we get this all clarified. A 26-Aug WHO-AFRO update notes that the index case, a woman from Ikanamongo village, died 11-Aug sometime after butchering a bush animal.[6] 24 suspected cases of haemorrhagic fever occurred between 28-Jul and 18-Aug.

This latest outbreak was previously and relatively quickly (perhaps a message in there for all of us) described by the World Health Organization as being due to gastroenteritis with haemorrhaging...

...but subsequently we learn today that...

The DRC outbreak seems to be a separate ebolavirus outbreak event to the one in West Africa. But one that shares at least one common potential animal vector. This is one of three bat species often pointed to as a possible natural host for ebolaviruses.

Since this is not the first time concurrent outbreaks of ebolaviruses have occurred, I was wondering about seasonal factors and whether they attract or affect bats. This new information adds another piece of information to current events.

References

Sunday, 24 August 2014

Fake/wrong Ebola virus disease images...

As if there isn't enough misery in the world that we need add false imagery to the mix.

Fake or hoax or just plain misunderstood images purporting to be from cases of Ebola virus disease are everywhere at the moment. The ones below are images I see regularly in the #ebola Twitter stream. 

I had once before found the real image of the first picture using a reveres image searhc on Tineye or Google's image search, but lost it until I recently downloaded my Twitter history and did a manual search for the words I thought I'd used. Bazinga! 

I'll add to this page as I find references for other fraudulent imagery. Feel free to send me other fake Ebola-related images (with the original source) and please use this page to throw at people using these images.

While I suspect much of this is just retweteed out of a lack of information, I'd ask that people check before they propagate this sort of stuff. It may dissuade others in the affected regions from seeking medical attention if they think they have been exposed because "If I don't look like that then I can't have an Ebola virus infection!"


NOT EBOLA VIRUS DISEASE
Figure 1. This is from a patient with which has haemorrhagic
bullae simulating purpura fulminans...whopping great blood
blisters and tissues that have been bled into. Image comes
from a case of leukaemia cutis published in the Indian Journal
of Dermatology, Venereology and Leprology in 2010 by
Misri and colleagues
.
Pubmed


NOT EBOLA VIRUS DISEASE
Figure 2. This is from a boy with smallpox disease. It can be found 

NOT EBOLA VIRUS DISEASE
Large hemorrhage on arm of dengue patient
Figure 3. This is bleeding under the skin in a patient with dengue
hemorrhagic fever. The image can be found on the National Institute
of Health's National Institute (NIH) of Allergy and Infectious
Diseases (NIAID) website
.
NOT EBOLA VIRUS DISEASE
Figure 4. This may be an allergic reaction, possibly 
to contact with poison ivy. I'm not as sure about the source
of this one. Some possible places include:
http://poison-ivy.org/
http://gloriousconfusion.squidoo.com/poisonous_plants_lily_of_valley_ivy_foxglove_digitalis
http://en.wikipedia.org/wiki/Contact_dermatitis
http://hardinmd.lib.uiowa.edu/dermnet/poisonivy1.html

UNSURE


Figure 5. I can only find ebolavirus-related results for this. 
If anyone can confirm or debunk it as being a valid EVD image, I'd 
be grateful if you could tell me.

Thursday, 21 August 2014

Ebola virus in semen is the real deal....

The World Health Organization (WHO) Ebola virus disease factsheet notes that ebolaviruses may be transmitted via the semen of a male who is getting over an ebolavirus infection, for a period of 7-weeks (~49-days).[1] 

The European fact sheet for health professionals and a Public Health Agency of Canada Pathogen Safety Data Sheet both note the 7-week figure, the latter also adds a 61-day figure.[2,3] 

The United States Army Medical Research Institute of Infectious Diseases (USAMRIID) Medical Managements of Biological Casualties Handbook (7th edition) notes a 3-month (~80-days) period, during which one should probably avoid sexual relations so as not to deliver virus directly to a mucosal surface.[4]

Semen is therefore listed as one of the body fluids from which Ebola virus disease may be contracted. 

While convalescent patients seem to be discharged before 7-weeks have elapsed, I presume the men are made very aware of this risk. This was specifically noted in one of the studies below. [8] 

But I find it hard to just accept things. 

As a scientist I'm used to looking for the little bracketed or superscripted numbers or perhaps "(Scientist et al)", at the end of sentences. Then I can check out the information source for myself. So here, I thought I'd try and add those and pt it altogether in one place here - and you can do your own checking out if you feel the need. 

Here are the research papers I've found for EBOV so far (there are also Marburg virus studies) - by all means send me any others I've missed and I'll add them.

  • Bausch and colleagues [5] were able to isolate, in cell culture in the laboratory, infectious Ebola virus (EBOV) from the semen of 1 of 2 samples from a single recovering patient who had EVD. 
    • The samples was collected 40-days after disease onset; at 45-days he was no longer positive for EBOV
    • No acute phase (active infections) samples were tested.
    • 1 of 2 samples were also positive for EBOV RNA by RT-PCR (detecting a portion of the virus's RNA genome)
  • Rodriguez and colleagues [6] could isolate infectious EBOV from seminal fluid 82 days after disease (also RT-PCR positive then) and at 51-days after onset from a 27-year old male. 
    • EBOV RNA in 3 other convalescent cases (33, 29 and 25-years of age) at times ranging from 57 to 101-days after disease onset.
  • Rowe and colleagues [7] could detect EBOV RNA by RT-PCR from 4 convalescent cases (27, 25, 29 and 33-years of age) at times ranging from 47 to 91-days after disease onset 
    • No infectious virus could be isolated and no viral antigens were found
  • Emond and colleagues [8] were able to isolate infectious EBOV from seminal fluid collected 39 and 61 days after disease onset
    • No EBOV was isolated 76, 92 or 110-days later

So if you are a man who has been diagnosed with an Ebola virus infection and survived, please, seriously, take extra care to practice safe sex. Use a condom. Or, even safer, just wait.

References...

  1. http://www.who.int/mediacentre/factsheets/fs103/en/
  2. http://ecdc.europa.eu/en/healthtopics/ebola_marburg_fevers/factsheet-for-health-professionals/Pages/factsheet_health_professionals.aspx
  3. http://www.phac-aspc.gc.ca/lab-bio/res/psds-ftss/ebola-eng.php
  4. http://www.usamriid.army.mil/education/bluebookpdf/USAMRIID%20BlueBook%207th%20Edition%20-%20Sep%202011.pdf
  5. http://jid.oxfordjournals.org/content/196/Supplement_2/S142.full
  6. http://jid.oxfordjournals.org/content/179/Supplement_1/S170.long
  7. http://www.ncbi.nlm.nih.gov/pubmed/9988162
  8. http://www.ncbi.nlm.nih.gov/pubmed/890413

Tuesday, 19 August 2014

Protect the healthcare workers>>save lives>>stop Ebola virus disease

I live in Australia.

I have clean water on tap. Reliable electricity to burn. Internet access. A green garden. A lawn. A car. A very old cat who gets medical attention when he hiccups. A washing machine. A clothes drier. My kids have computer access. I have at least a dozen doctors within a 5min drive. 

I'm a virologist who has been through all levels of schooling available, then University, then went on to do a PhD. I'm privileged. I'm lucky. 

I want to help West Africa get its Ebola virus outbreak under control. I want to help support the healthcare workers (HCWs) that are far braver than I am. I want hem to live to fight another day in the mud, heat, fear and pressure. And to leave when the job is done and return to their lives as the heroes they are.

I don't know much of what is being done to help though. 

I don't know whether my own government is providing supplies in my name. I'd like them to be. I'd like philanthropists and industry and people who take my money to stop, and give some of it to help out. I'd particularly like those funds to be used right now to purchase, deliver, distribute and secure a steady stream of personal protective equipment (PPE) to all those well-trained HCW individuals and organizations battling to contain an acute, untreatable, easily spread, often fatal viral disease in countries with some of the poorest healthcare...In. The. World. I want them to have gloves, gowns, masks and goggles. I don't want them to have to re-use PPE and be infected in the process. I don't want them to be in fear of stopping a terrified potential patient from running away because they don't have the PPE to feel safe in just holding that person's arm and saying, "stay, we are here to help, if you leave we can't do that and you are more likely to die".

I don't feel guilty that I want this done for this disease now and not that disease all that time.

But what can I do?

I donate some of my money. I do this every year anyway but I'm donating some more now because there are some worthwhile organizations that I trust to help West Africa, now. I don't send myself into debt. But I give a chunk now. I gave a chunk last week. I'll give another chunk soon. Some of this will be in my name, some in my wife's and some in my kid's name. Some might be a present for someone else. If we all did that, we could help. But we shouldn't just give it to organizations or individuals who have no plan or skills to use it. Or to those who will spend it on salaries and overheads.

So I give my donations to these organizations now:
  • Médecins Sans Frontières (MSF)
    They are meticulous, fastidious and well trained so they don't needlessly risk themselves. They are on the front lines everywhere. They have been all over this outbreak from early one. They warned us.
    http://www.msf.org/
  • Direct Relief
    They can (and have) mobilize the PPE I want delivered. They have contacts with others in industry. They are a nexus for getting this done.
    http://www.directrelief.org/
  • International Federation of Red Cross and Red Crescent SocietiesThey are one the ground helping keep locals informed about Ebola virus
    http://www.ifrc.org/
Some organizations I have not donated to yet, but like the look of...


Some other recipients for your chunks could be in these lists...
I am also making others aware of these organizations so they can add their chunks in if, and as, they see fit. You can do that too. 

If you have a favourite company, try contacting them. If you have a favourite movie, hit up the actors, producers, directors. Try anything. Spend an hour tomorrow looking up some people and sending them an email or a Tweet to ask them to help provide the fuel needed by the people who know how to get this done.

Be part of helping out. 

Sunday, 17 August 2014

Ebola, pigs, primates and people

This is a companion piece to my collaborative article, Ebola virus may be spread by droplets, but not by an airborne route: what that means, posted a couple of days ago. I suggest you read the both together.

In this post, I'd like to make sure we all understand that an airborne route of Ebola virus infection has been used to deliberately infect non-human primates (NHPs). It is possible and it can be done. Okay? I'm not covering up any secret knowledge or trying to conceal facts that only we few evil-society-of-science types know. I don't secretly work for an agency aiming to delude you dear readers into feeling falsely safe about the risks associated with being near an Ebola virus infected person (which most reading this will likely never be). Frankly, I'm learning this as I go.

Don't expect perfection from risk mitigation advice.

Like all things that involve biology, there are hardly ever clear-cut lines and yes or  no definitions and explanations. Sometimes that's because things vary...because biology! Sometimes that's because we haven't yet done enough science to know those answers. I'm not an expert on ebolaviruses nor on Ebola virus disease (EVD) - but in my time learning about the viruses and the disease, its clear that this is (yet another) area that is lacking in all sorts of information. So risks are judged using what we do know and can support and verify, with softer language used when decision makers don't know for certain; less so when they think they do. 

When that message of risk gets passed to the public, it is important to be accurate, clear, concise but not to over-simplify things because that may degrade trust in the body(s) sending the message if things change later. That's a very tough balance when dealing with biological risks.

So having said that, let's talk pigs.

Pigs are not primates.

In ebolaville - the virtual world created by social and mainstream media stories and discussion about ebolaviruses - a lot of people have been throwing the 2012 pig to macaque study (8) around as an argument for why we should admit that ebolaviruses spread by an airborne route and run for the hills. This is why that is not a good comparison:
  • Pigs have a different disease and replication process to humans. 
    • Pigs tend to have much more virus growing in their lungs.(12) 
    • Pigs tend to cough and sneeze and generally propel more of said pathogen from their lungs.(11) 
  • Pigs may eject more infectious viruses in their droplets than do primates
If we look at the study of disease occurrence and spread in previous outbreaks, that epidemiology does not suggest an airborne spread - the numbers and nature of human-to-human spread don;t show it as any sort of major contributor to spread. Might it be a minor contributor? Possibly. We don;t know either way with 100% surety. But we do  know some other things. One of these is that it takes very little virus to infect pigs and NHPs. If there are not obvious signs of an airborne spread in humans, we just not have detected it yet or, it may have a biological basis. It is possible that the infectious dose (amount of virus needed to get a foothold and start an infection) may be much higher for humans; infected and severely ill human cases may not breathe out infectious virus or ebolaviruses may not survive for long in the aerosols expired by humans,(19) even if they can survive on hard surfaces or in generated aerosols under laboratory conditions.(20)

Non-human primates can be infected with ebolaviruses via a lab-made aerosol with lots of lab virus at lab temperatures and lab humidity and other lab conditions in a lab.

You get that this is done in a lab? Cool.

It apparently does not take much virus to infect a human via an aerosol according to the Public Health Agency of Canada's (PHAC) Pathogen Safety Data Sheet (PSDS) on ebolavirus.(1) Only 1-10 infectious organisms (see above). But one problem with that PSDS is that it cites only 1 paper to support that range. Ref 21 from the PSDS is entitled Clinical recognition and management of patients exposed to biological warfare agents.(2) It is 1997 review that does not specify if this range is specific to any 1 or more of the ebolaviruses, just "viral hemorrhagic fevers". The PSDS seems to rely on that 1 line. In that reference, there are no further links to studies that define this range for humans, ebolaviruses or an Ebola virus (EBOV) of the species Zaire ebolavirus. I've sent a couple of emails in the past week, seeking further clarification from ebolavirus experts, but have yet to hear anything back.

In a laboratory experiment reported in 1995, transmission of an EBOV from one set NHPs infected by injection, to another set  resulted in 2 of 3 NHPs (1 with a heavy load of virus in the lung) becoming infected and that seemed to have occurred through some kind of airborne route as the 2 groups of animals were separated by 3m and care was taken to avoid creating bigger droplets and splashes during cage cleaning.(15) While the authors noted that fomites (contaminated objects and surfaces) or contact droplet transmission of virus was unlikely, the exact mode of transmission to the second group of NHPs could not be determined. In a follow-up study, the authors were able to prove that conjunctival and oral exposure to an EBOV could indeed result in infection in NHPs.(18) Thus we have plenty of reason for the use of masks, goggles and face shields that are already part of the recommended personal protective equipment (PPE) items for dealing with infected humans.

However, there are a number of issues related to forced aerosol infection of NHPs, many of which can be found in a massive and detailed 2008 review by Dr. Jens Kuhn.(3) These include:
  • Often unrealistically high viral loads - the exact amount of infectious virus humans are exposed to during outbreaks has not been defined.
  • Temperature and humidity conditions that were unlikely to reflect conditions during outbreaks in Africa - but may reflect conditions in hospitals.
  • An initially lung-focussed pattern of viral replication (7) results from direct aerosol delivery of virus to NHP airways which seems different to infection of humans via the more frequent natural direct contact route. Systemic spread to multiple organs then follows via infected dendritic cells and macrophages and blood monocytes.
  • Different routes of virus acquisition can lead to different incubation periods.
  • Different virus isolates, sources and preparations may affect the course of infection and disease
  • Because of the small and enclosed space and air throughput in head-only chambers, droplets rather than droplet nuclei may be the vehicle carrying infectious virus. This is important because, as you can read in the companion piece, droplet nuclei are the component of a lingering "airborne route" of acquisition and if NHPs are in fact infected by the droplets, that may be more indicative of direct fluid contact than true airborne travel.
A head-only inhalation chamber of the sort used in NHP
aerosol inoculation studies. Biaera Technologies.
Image from http://www.biaera.com/our-technology/peripheral-
aerosol-instruments/head-only-chamber/
. See also (17)

Click on image to enlarge.
Some NHP studies that have successfully caused initial respiratory infection using an airborne route to infect NHPs under controlled experimental conditions include the following:
  • 1,000 plaque forming units (PFU; a measure of how much virus is in a preparation using cell culture methods in the lab) of either a Kikwit EBOV isolate or a Boniface isolate of Sudan virus (SUDV; species Sudan ebolavirus) isolate were delivered using a Collison nebulizer (producing small droplets) after intramuscular immunization with a recombinant adenovirus vaccine.(5) 
  • 1,000 PFU of a Kikwit EBOV isolate was delivered with a Collision nebulizer via a head-only aerosol chamber, after intramuscular immunization with a recombinant vesicular stomatitis virus (VSV) vaccine.(6)
  • 743-274,000 PFU of a Kikwit EBOV isolate was delivered to with a Collision nebulizer via a head-only aerosol chamber, to examine aerosol-related pathology.(7)
  • ~50 or ~500 PFU of a Boniface SUDV isolate were delivered to 3 different NHP species using a Collison nebulizer via a head-only chamber to compare species-specific effects.(14) 
  • 0.8-128 PFU of a Kikwit EBOV isolate was delivered to 3 different NHP species using a Collision nebulizer via a head-only aerosol chamber, to examine disease course between species.(9)
  • ~300-50,000 PFU of an EBOV isolate was delivered to with a Collision nebulizer (0.8-1.2um droplets) via a head-only aerosol chamber, to examine aerosol-related pathology.(16)
Are primates humans?

Judging by the effort we put into getting rid of our fur compared to an NHP, I'd say we're not! 

But on the topic of EVD, some NHPs that we infect with an ebolavirus, show very similar disease signs, symptoms and disease progression to those of EVD in humans; especially rhesus macaques [Macaca mulatta] although oneo f the studies above showed that 3 different NHP species were not that different in the way they responded to infection (rhesus macaques as well as cynomolgous macaques [Macaca fascicularis] and African green monkeys [Chlorocebus aethiops]).(9) 

Rhesus macaques become febrile, anorexic, lethargic, viraemic, develop a rash and sometimes develop diarrhoea and melena (gastrointestinal bleeding).(3)

But no animal model seems to completely capture other components of human disease which have historically included conjunctivitis, diarrhoea and vomiting and coughing up blood. Vomiting up blood and having bleeding gums occurs more often in fatal cases than in survivors.(3) 

Bleeding only occurred in 41% of 103 observed human patients during the 1995 Kikwit outbreak of an EBOV.(3)

So the answer is, primates are not humans when it comes to EVD, but they are pretty close. Yet within that "pretty close" lies an immeasurable amount of variation that may mislead when trying to map the course of NHP disease onto that of humans.

Where does that leave us?

I admit to being very uneasy saying that there is no risk at all of an airborne route of ebolavirus infection. Clearly it can be forced to happen, but we have no evidence that it has ever happened in humans in an outbreak. But let's put that into context. An absence of evidence is not evidence of absence. Outbreaks of ebolaviruses are not particularly conducive to large careful research projects measuring infectious droplet nuclei around critically ill people, especially when the occur in exotic locations in someone else's back yard.

So have I deserted by position from yesterday's post stating no airborne role for ebolavirus transmission between humans? No, not at all. What we know is that the overwhelming majority of human EVD cases acquire their infection during the time they are in direct contact with the fluids of a very ill EVD case; be that through physical contact or wet droplet spray impact. Beyond that fact, it may just be a discussion based on academic musings and hand-waving. But it is a discussion we should be having a little more I feel. A back-and-forth rather than messages with guarantees and statements dealing in black and white absolutes. I'm not sure the public believe in or feel safer with such absolutes today. We're all a bit too cynical for that.

If infection can happen between primates via the air, it is a very, very inefficient process as a study of 78 people from 27 households with EVD cases during the 1995 Kikwit  revealed.(10) Those 78 household members had no physical contact with the cases, and they did not get sick. Others who had physical contact, got EVD. 

In a recent study by the authors of the 2012 pig/macaque study we started this post with, infected NHPs did not pass EBOV to uninfected NHPs only 30cm away. Not only was there no disease but no antibodies were detectable in the uninfected NHPs 4-weeks later. There had been no infection at all.

While at some point we'll need to be more sure of all this for humans than we are now, we can say that pigs aren't primates and airborne route has not been shown to be a risk for human acquisition of an EBOV.

References..
  1. http://www.phac-aspc.gc.ca/lab-bio/res/psds-ftss/ebola-eng.php#note21
  2. http://www.ncbi.nlm.nih.gov/pubmed/9244332
  3. http://www.ncbi.nlm.nih.gov/pubmed/18637412
  4. http://www.ncbi.nlm.nih.gov/pubmed/9988155
  5. http://www.ncbi.nlm.nih.gov/pubmed/20181765
  6. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3398796/pdf/nihms390624.pdf
  7. http://vet.sagepub.com/content/50/3/514.long
  8. http://www.nature.com/srep/2012/121115/srep00811/full/srep00811.html
  9. http://www.ncbi.nlm.nih.gov/pubmed/21651988
  10. http://jid.oxfordjournals.org/content/179/Supplement_1/S87.long
  11. https://www.sciencenews.org/article/airborne-transmission-ebola-unlikely-monkey-study-shows
  12. http://www.vox.com/2014/8/10/5980553/ebola-outbreak-virus-aerosol-airborne-pigs-monkeys/in/5712456
  13. http://www.nature.com/srep/2014/140725/srep05824/full/srep05824.html
  14. http://www.ncbi.nlm.nih.gov/pubmed/23202456
  15. http://www.ncbi.nlm.nih.gov/pubmed/8551825
  16. http://www.ncbi.nlm.nih.gov/pubmed/7547435
  17. http://www.mdpi.com/1999-4915/4/8/1305/htm
  18. http://www.ncbi.nlm.nih.gov/pubmed/8712894
  19. http://www.ncbi.nlm.nih.gov/pubmed/15588056
  20. http://www.ncbi.nlm.nih.gov/pubmed/20553340

Friday, 15 August 2014

Ebola virus may be spread by droplets, but not by an airborne route: what that means

An article collaboratively written by (alphabetically)..

Dr. Katherine Arden
A postdoctoral researcher with interests in the detection, culture, characterization and epidemiology of respiratory viruses.
Dr Graham Johnson
A post-doctoral scientist with extensive experience investigating respiratory bioaerosol production and transport during breathing, speech and coughing and determining the physical characteristics of these aerosols.
Dr. Luke Knibbs
A Lecturer in Environmental Health at the University of Queensland. He is interested in airborne pathogen transmission and holds an NHMRC Early Career Fellowship in this area.
A. Prof Ian Mackay
A virologist with interest in everything viral but especially respiratory, gastrointestinal and central nervous system viruses of humans.



________________________

The flight of the aerosol
Understanding what we mean when we discuss airborne virus infection risk

A variant Ebola virus belonging to Zaire ebolavirus (EBOV) is active in four West African countries right now. Much is being said and written about it, and much of that revolves around our movie-influenced idea of an easily spread, airborne horror virus. Many people worry about their risks of catching EBOV, particularly since it hopped on a plane to Nigeria. However, all evidence suggests that this variant is not airborne. The most frequent routes to acquire an EBOV infection involve direct contact with the blood, vomit, sweat or stool of a person with advanced Ebola virus disease (EVD). But what is direct contact? What is an “airborne” route? For that matter what is an aerosol and what role do aerosols play in spreading EVD? How is an aerosol different from a droplet spray? Can droplets carry EBOV through the air?

Direct contact includes physical touch but also contact with infectious droplets; the contact is directly from one human to the next, rather than indirectly via an intermediate object or a lingering cloud of infectious particles. You cannot catch EVD by an airborne route, but you may from droplet sprays. Wait, what?? This is where a simple definition becomes really important.

Airborne, aerosols, droplets, nuclei and confusion

Whether propelled by sneezing, coughing, talking, splashing, flushing or some other process, aerosols (an over-arching term) include a range of particle sizes. Those droplets larger than 5-10 millionths of a meter (a micron [µm]; about 1/10 the width of a human hair), fall to the ground within seconds or impact on another surface, without evaporating (see Figure). The smaller droplets that remain suspended in the air evaporate very quickly (< 1/10 sec in dry air), leaving behind particles consisting of proteins, salts and other things left after the water is removed, including suspended viruses and bacteria. These leftovers, which may be more like a gel, depending on the humidity, are called droplet nuclei. They can remain airborne for hours and, if unimpeded, travel wherever the wind blows them. Coughs, sneezes and toilet flushes generate both droplets and droplet nuclei. Droplets smaller than 5-10µm almost always dry fast enough to form droplet nuclei without falling to the ground, and it is usual for scientists to refer to these as being in the airborne size range. It is only the droplet nuclei that are capable of riding the air currents through a hospital, shopping centre or office building.

The droplet nuclei and the air that surrounds them are correctly referred to as an aerosol, but so are lots of other things and this is where confusion grows. The term aerosol is used to refer to any collection of particles suspended in air, and particle sizes vary enormously. Spray paint from a can is produced in droplets a few hundred microns in diameter so as to quickly coat the intended surface rather than undesirably linger in the air. A can of fly spray on the other hand produces smaller droplets, because that aerosol should stay suspended for long enough to make contact with insects. ‘Aerosol’ is a confusing term, and its varied usage does not help when discussing risk of EBOV infection.

The simplest definition for public understanding of infection risk is to use “airborne” to refer only to the droplet nuclei component.(4) 
  
Figure 1. A representation of how different viruses may be propelled on their journey to cause disease in humans. Recommended droplet precautions for dealing with cases of EVD include the use of gloves, impermeable gowns, protective goggles or face shield and a face mask.(5,6)
Image updated 26-August.



For EBOV at least, airborne droplet nuclei are apparently not infectious to primates. Why that is so is not known, but perhaps it is because this virus does not survive being dried down, or that primates don’t produce enough virus in what is coughed out to make infectious droplet nuclei.

How the science helps and also hinders understanding.

The scientific literature has a number of very specific examples where droplet nuclei have been used to infect non-human primates with ebolaviruses in order to study the effectiveness of vaccines or antivirals.(1,7,8) These infections are under idealised laboratory conditions, often with what we think are unrealistically high levels of virus. Although airborne infection can be made to occur in a lab, there is no evidence for airborne droplet nuclei spreading EBOV from person-to-person or between non-human primates whether inside or outside the lab.

Protection and clarification.

Included in guidelines issued by the WHO (7) and CDC (5) is the need for droplet precautions (Figure). This is very important for healthcare workers, family and other caregivers who stay close and are frequently exposed for lengthy periods of time with severely ill, highly virulent cases of EVD. These cases may actively propel infectious droplets containing vomit and blood across the short distances separating them from caregivers. But this is a form of direct transmission, and is not airborne transmission.

Messaging the masses.

Leaving aside other issues around acquiring a rare disease like Ebola when outside of the current outbreak region, the case definitions and risk assessments have raised confusion. There are questions around how otherwise apparently well-protected healthcare workers in West Africa are acquiring an EBOV. For a virus described as spreading only through direct contact, recommendations for the use of masks, implying airborne spread to many, fuel such questions.  In fact, face protection is recommended to prevent infectious droplets landing on vulnerable membranes (mouth and eyes).

It’s important to pass a message that is correct, but also to ensure distrust does not result from a public reading apparently contradictory literature. Such distrust and real concern have been rampant among a hyperactive #ebola social media. Simple, clear phrases like “ebolaviruses cannot be caught from around a corner” (h/t @Epidemino), may help uncomplicate the communication lines. And it works on Twitter.

References
  1. http://www.ncbi.nlm.nih.gov/pubmed/21651988
  2. WHO page
    http://www.phac-aspc.gc.ca/lab-bio/res/psds-ftss/ebola-eng.php#note21
  3. http://www.who.int/csr/resources/publications/WHO_CDS_EPR_2007_6c.pdf?ua=1
  4. http://www.cdc.gov/vhf/ebola/hcp/infection-prevention-and-control-recommendations.html
  5. http://www.who.int/csr/resources/who-ipc-guidance-ebolafinal-09082014.pdf?ua=1
  6. http://www.ncbi.nlm.nih.gov/pubmed/24462697
  7. http://www.ncbi.nlm.nih.gov/pubmed/20181765

Wednesday, 13 August 2014

Behind the naming of ebolaviruses...

Just don't call me a taxi
Virus taxonomy is the classification of viruses into groups based on similarities. 

Today classification is supported by viral gene and genome sequence information.

The International Committee on Taxonomy of Viruses (ICTV) takes care of the official virus taxonomy. It has a pretty friendly website with a good search engine and the latest (2013 at writing) virus taxonomy can be found here. [1]

So what does it, and its tome, Virus Taxonomy, Ninth Report of the International Committee on Taxonomy of Viruses [2], have to say about ebolaviruses? Well, not as much as you might like, if you want to be able to name them, talk conversationally about them and discuss the issues around the disease resulting from infection by most of them. Sure, you can just call it all "Ebola" (which is a river in Africa by the way) and be done with it, but you'd be wrong. And some smart alec will correct you for sure. Here is where the ICTV Filoviridae Study Group fills in a lot of blanks.

One thing to get on top of first up. When talking or writing about these    looking little pathogens, we can just call lump them together under the conversational term "ebolaviruses" thus..."Hey Jeanette, did you hear about the latest ebolavirus infection numbers over the weekend?" is a question that could refer to any of the 5 very different viruses.

So, let's try and make that tearoom conversation a little more accurate.

The very dry detailed stuff down to the level of a species.

The italicization and the capitalization below are really important to taxonomy guys - so, ya know, care

Also, the ICTV reminds us that the name of the species is not the name of a virus - they are 2 different things. The species is a broad term for all the measurably different viruses out in the wild, that it contains. Here, species is to viruses what Mitsubishi Sigma is to identifying my old car. A virus name,

e.g. Ebola virus (see below), is like identifying my car as "a silver 1988 Mitsubishi Sigma". 

What if we used taxonomy on cars? A different way to explain how to name ebolaviruses.
Click to enlarge


The viruses we are talking about here belong to the order Mononegavirales, family Filoviridae, genus Ebolavirus. 

There are 5 species within the genus. The species names are in italics below. Underneath is the name of the virus (the virus belongs to the species container) and its abbreviation. The viruses in bold have caused outbreaks of human disease.
  • Taï Forest ebolavirus
    • Taï Forest virus (TAFV)
  • Reston ebolavirus
    • Reston virus (RESTV)
  • Sudan ebolavirus
    • Sudan virus (SUDV)
  • Zaire ebolavirus
    • Ebola virus (EBOV)
  • Bundibugyo ebolavirus
    • Bundibugyo virus (BDBV)

But what should I call the latest ebolavirus strain, variant, genotype, subtype, serotype, isolate thingy?

In the case of the current outbreak, that latest virus is an Ebola virus (EBOV), which we can now say belongs to the species Zaire ebolavirus (a Mitsubishi Sigma). 

But back to the car analogy. The silver 1989 Mitsubishi Sigma name is still not enough to tell it apart from any other silver Mitsubishi Sigma parked at the same shopping centre. How do you choose yours in a way that won't get you arrested for breaking into someone else's car? They both look like silver Mitsubishi Sigmas. But the silver Mitsubishi Sigma with license plate ABC 321 is yours and your alone, and that code differentiates your car from any other anywhere in the world.

We know from genome sequencing studies that the virus circulating in Guinea is an EBOV (a silver Mitsubishi Sigma) and is not identical to the one in (what was called) Zaire in 1976 (this silver Mitsubishi Sigma car has a different license plate). They couldn't be the same physical virus anyway, because each person hosts millions and millions of virions, each cell has a varied population of viruses in it, and each virion has a relatively short life. 

There is no universal definition for classification of viruses below the level of a species. But there are lots of terms that are used - most are listed in the heading to this section. In filovirus-land, the Study Group has sought to impart some order upon the chaos [3]. 

A virus strain needs to have 1 or more observable, genetically stable and unique differences compared to other viruses in the same species. For instance, one might cause a disease that is different from the one we know. So apart from a different license plate, it might also have an Awesome Mix #1 CD in the tray. 

variant has some genetic sequence or other differences that may result in a slightly different observable change. As far as we can tell from the >100 near-complete genome sequences online now, the West African EBOV is a variant and not a strain of Zaire ebolavirus. For example, these from Guinea and Sierra Leone (ManoRiver variants from samples collected in June 2014)


A virus isolate is a virus sample resulting from growing or culturing it in cells or tissues. Variants can therefore be represented by isolates. These isolates can be identical or slightly different (your neighbour could order the exact same car as you did-but he would still have a different license plate and no bobble-heads and fluffy dice).

The naming schemes do go into further detail, but you can read that in [3].

The disease.

The disease caused by EBOV, SUDV, TAFV and BDBV is called Ebola virus disease (EVD). Frankly, that is a tough one to explain after all of the above. It reads as though we are talking about just 1 virus causing disease (EBOV). But not so. Viruses from 4 species cause EVD - EBOV, SUDV, TAFV and BDBV. Diseases are named by World Health Organization's International Classification of Diseases (ICD) site, (4) and the name of this disease goes back many years and has not been updated yet. The disease has been called Ebola haemorrhagic fever, but is not now. And to continue from the taxonomy above, EVD is caused by a virus that can be ascribed to a species. In West Africa right now, EVD is due to infection by an Ebola virus variant classified in the species  Zaire ebolavirus.

Navigating a tree in the ebolavirus jungle.

Lastly, I've cobbled together a tree of genomes from each of the 5 ebolavirus species. It may help. Or not.


A phylogenetic tree of some genome sequences of the 5 species of ebolavirus, each indicated with a specific coloured dot.


References...
  1. ICTV Virus Taxonomy: 2013 Release
    http://www.ictvonline.org/virusTaxonomy.asp
  2. Ebola virus disease World Helath Organization fact sheet
    http://www.who.int/mediacentre/factsheets/fs103/en/
  3. Virus nomenclature below the species level: a standardized nomenclature for natural variants of viruses assigned to the family Filoviridae.Arch Virol (2013) 158:301–311.
    http://download.springer.com/static/pdf/619/art%253A10.1007%252Fs00705-012-1454-0.pdf?auth66=1408093824_af9d701ab93574066469a6f6745c11d7&ext=.pdf
  4. International Classification of Diseases (ICD)
    http://www.who.int/classifications/icd/en/