Sunday, 31 August 2014

Ebola: Blood, sweat and tears...

This post follows up the recent one on convalescent semen being able to harbour infectious Ebola virus (EBOV; although I am not aware of any infection resulting from this route of transmission there has been at least one report for Marburg virus [4]).

I thought I'd give the same treatment to tears and sweat which are also fluids intermittently listed as possible sources of EBOV infection for humans. Some examples of the scientific literature which support the risk messaging, follow.


I think we are all pretty clear that the blood of an advanced case of Ebola virus disease (EVD) is heavily laden with virus and is the most serious of the risk factors for acquiring infection by an ebolavirus.

Viral loads (amount of virus in the sample) in blood can be above 106-108 plaque forming units or copies (pfu; a measure of infectious virus present using a lab test that measure the impact of virus on infected cells; copies measure viral genome and cannot prove infectious virus is present) per millilitre of blood in acute phase disease patients and non-human primates.[5,6]


There is not a lot on sweat containing signs of an ebolavirus.
  • Bausch and colleagues found no trace of EBOV in a single acute sweat sample.[1]
  • Jaax and colleagues found that in experimentally infected non-human primates (NHPs; rhesus macaques), that connective tissues next to hair follicles and sweat glands in the skin as well as the cells lining ducts of glands in the skin were sometimes positive for EBOV antigens (proteins).[2]
  • Davis and colleagues infected NHPs (African green monkeys) and found signs of EBOV antigens in the cells lining the sweat gland ducts and in cells in the connective tissues next to hair follicles, but no virus particles by electron microscopy.[3]
  • Zaki and colleagues found heavy signs of EBOV antigens (proteins) in the tissues around the sweat glands, but rarely also within sweat glands and ducts.[8] No virus particles were seen in the sweat glands or ducts when examined by electron microscopy.

There is also very little I have found on this one.

  • Bausch and colleagues found EBOV RNA in tears from 1 sample, but no infectious virus could be isolated.[1]
  • Jaax and colleagues found some signs of virus in macrophages in the ciliary body of the eye of experimentally infected NHPs
  • Bausch and colleagues found infectious EBOV in 1 of 12 acute saliva samples (from 10 patients; none from 4 convalescent samples) and EBOV RNA in 8 of 12 (67%) of acute samples (none from convalescent samples).[1] RT-PCR positivity was significantly associated with fatal outcome.
  • Formenty and colleagues found EBOV antigens and EBOV RNA in oral fluids from fatal cases and those who survived infection.[7]

Saturday, 30 August 2014

The fifth I give you...[UPDATED]

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.


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.

  2. If this is what MERS-CoV detections look like with more testing...what is the "normal" community level of virus?? [UPDATED]
  3. Guidelines for home isolation related to MERS Corona Virus infections | May 2014

Monday, 25 August 2014

The battle of Ebola gains a second front...the Democratic Republic of Congo (DRC; formerly Zaire) [UPDATE #3]

So there are three reasons for this post. 
  • It may be a little while before we get solid confirmed information from the DRC and I think maps are useful for those of us who are ignorant of where countries live! [See below for update from WHO]
  • 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]
An 24-Aug report quoted the Minister for Health, Felix Kabange Numbi.[2] This latest outbreak occurs in a country that was the site of the first (known) outbreak of a virus of species Zaire ebolavirus (called Ebola virus [1] or EBOV), and which has had six other battles with Ebola virus disease (EVD).

One of the two viruses was reported to have been genotyped as a member of the species Sudan ebolavirus (SUDV) and the second was a "mixed" infection of SUDV and an EBOV.[2] 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 noted 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. 

The latest updates define that the outbreak is solely due to viruses from the species Zaire ebolavirus.[7,8,9] The EBOV viral variants share 99% nucleotide identity with the Kikwit lineage of viruses from this same species (not "strain"). Put simply, this is the evidence needed to be able to state that the two concurrent EVD outbreaks (indicated in the map above as distinct events), are indeed due to genetically distinct viral variants of Zaire ebolavirus and are not related outbreaks. 

For more on naming ebolaviruses - check out my earlier post "Behind the naming of ebolaviruses".[10]

This latest outbreak was previously and relatively quickly (too 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 outbreaks share at least one common potential animal vector range. 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 the puzzle.


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!"

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

Figure 2. This is from a boy with smallpox disease. It can be found 

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
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:


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.... [UPDATED]

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 sample 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 onset from a 27-year old male (also RT-PCR positive then). A sample at 51-days after onset was RT-PCR positive, but did not yield infectious virus.
    • EBOV RNA , but not virus, 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], who examined the same patients, detected EBOV RNA by RT-PCR from 4 convalescent cases (27, 25, 29 and 33-years of age as above) 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.


Tuesday, 19 August 2014

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

Updated 061014
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 givers and 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 doing more than paying for others to fight this epidemic. 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 the other times.

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.
  • 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.
  • International Federation of Red Cross and Red Crescent Societies.They are one the ground helping keep locals informed about Ebola virus
  • United Nations International Children's Emergency Fund (UNICEF)
    Always finding way to help children. There is a growing orphaned population in West Africa.
  • United Nations Foundation Ebola Response Fund
    The UN created this fund as way to allow individuals, corporations and civil society organizations to directly support UN entities in their efforts to respond to the Ebola virus disease outbreak.
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
. 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.[21] Not only was there no disease in the inoculated animals 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.


Friday, 15 August 2014

Wednesday, 13 August 2014

Behind the naming of ebolaviruses... [UPDATE 2]

This post has been moved to the new Virology Down Under platform on Wordpress.

You can get to this specific post by clicking on the link below...

Please adjust your bookmarks.

Apologies for any inconvenience.

Sunday, 10 August 2014

How to read a VDU graph...

I'm a pretty simple guy. So the stuff that I put onto Virology Down Under's (VDU) blog is usually something I think can be understood by you - my yard stick is that if I can understand it, then I think you can. Sometimes it can get pretty technical though and with things always done in a rush, I don't stop and explain as much as I could. Which is why I value feedback. And I've had some good stuff from @DeclanButlerNat, @JorgeCastillaE and @Moro_Cedric this week. 

Different levels of experience read this blog and my posts on Twitter, so sometimes I direct my graphs towards them. But I do understand that we scientists can be easily carried away by our interests and forget that we're quite used to interpreting our own presentation styles in a certain and speedy way. We've had lots of experience doing it that way. I can change a tyre (as I was reminded a couple of nights ago, at midnight) but I couldn't fix my engine.

At the heart of reading a graph is this fact: you have to look at the axes to understand what the lines or bars or areas mean. Once you know the style, you can understand it at a glance - but first time, examine it with care. If it's one of mine, feel free to ask me what I'm trying to show if it is not immediately obvious. I very well may have failed to make it clear.

So this is a little overview of how to read some of the graphs which I use to communicate what I consider to be otherwise yawn-inducing tables of numbers about viral infection and disease numbers.

A picture is worth a thousand words..

This is a good thing because with my lack of typing skills, if I had to type 1,000 word all the time, that would be at least 200 typos. Graphs plot those tabular numbers in a more colourful and visual way. Once you know how to read a graph, they can become powerful and quick ways to get a quick update on the state of play. On VDU the game seems to be about outbreak data. That's just the way things have evolved for me since I first blogged on 28-March 2013. This includes graphing the number of people with disease (cases), changes in the number of cases, numbers that are suspected versus the number that are actually laboratory confirmed (my currency), dates of onset illness (favoured piece of data and the hardest to come by publicly), the numbers who die, the proportion (%) of all cases/detections who die, dates when disease was reported, sex, age and all of that can be plotted on graphs by day, week, month or year.

Interpreting a basic graph on VDU...

The graph below (Graph 1) comes from following Middle East respiratory syndrome (MERS) public data. It shows the key parts of the structure of the graphs - the axes (the horizontal and vertical lines that are the key to reading the plotted numbers) and the axes.

  • A basic graph has a bottom horizontal line called the x-axis and it has a vertical line on the side called the y-axis. These are used to tell you what the numbers plotted on the graph mean; they are a key to the placement of each point on a graph, according to at least 2 different values.
  • Each point on a graph represents a coordinate. Its made up of an x-axis values (abscissa) and a y-axis value (ordinate). For example we plot 50 cases reported on Thursday or 50 on the y-axis and Thursday one the x-axis (x,y)
  • The points that we plot as pairs of x and y data can be joined up and shown as a line (the area underneath the line can also be coloured in which looks like a mountain that may have peaks and troughs) or they can be plotted as bars. There are other ways too - but I keep it simple. Joining up these dots is not always accurate - we may have no idea what is really happening to the numbers between any 2 points, in that case a bar graph may be more realistic as it shows the numbers at a distinct point in time. Sometimes bar graphs don't work from a formatting perspective (eg bars get so skinny you can't see them). Other times, joining the dots reveals the trends (the general direction that events are heading even if we don't know the values). Trends are useful in infectious disease as they show what has happened and what the latest data mean in the context of what has come before - so not too unrealistic. Some of this is about being accurate while not being too overly obsessive.

The particular example graph I've included below (Graph 1)  is a little trickier than some because it has 2 y-axes (vertical lines) - a primary (left-hand side) and a secondary (right-hand side). Some of the numbers are plotted against the primary y-axis (left vertical line) and some against the secondary y-axis (the right hand vertical line). This lets me "double-dip" on shared x-axis numbers, in this case, dates. I'm graphing the course of 2 different things (number of actual cases by day of illness onset) and the number of reported detected by date. These are 2 different things that have dates in common. 

This graph lets us compare, using the same x-axis, what the MERS case numbers look like when they are plotted by the day the people were reported to have become ill compared to the date of public reporting of the cases. There are differences that become more clear when you can run the 2 lines on the same graph, that may be a bit harder to see when they are plotted on 2 separate graphs. This graph highlights that when cases become ill and when they are reported are different things. It also shows that there were a bunch of cases (113) reported in 1 day that have never been given dates of illness onset (or hospitalization or the date they were each reported to the Ministry of Health). It also makes use of the 2 y-axes to have different scales. The primary or left-hand y-axis goes up to 35 while the secondary or right-hand y-axis maxes out at 120. If the same axis values were used, the illness onset cases would mostly be hard to see.

Graph 1. The basics of a graph.
What about cumulative graphs? What are they and how do I interpret those?

The next graph is made to show cases piling up over time (Graph 2). This is the graph that sparked this blog. It plots numbers as a line graph but instead of showing the value at that timepoint (day, week, month, year), it adds the new number to sum of all the previous numbers. It is plotting a cumulative tally, so it will always be a hill with an upwards (left-to-right, bottom to top) slope except when there are no new cases to add, when the curve becomes parallel to the x-axis - a flat line. How steep that line is can tells us how rapidly cases are piling up. That can also be fudged if you present the chart with a very short or long x-axis.

  • In the case of the Zaire ebolavirus outbreak in West Africa, we have the unusual ability to compare numbers from multiple countries at the same time, and use the same x-axis. Here, we show the date when the World Health Organization's Disease Outbreak News update was released. Sadly for us graph addicts, this doesn't include any illness onset dates, but the WHO do have those data and plot it themselves here (1).
  • A steep slope indicates a rapid rise in cases and this results from a lot of new cases being added in a short period of time.
  • A near flat or horizontal slope to the line shows that there are not many new cases being added. 
  • In this graph we also show multiple lines plotted using the primary (left) x-axis to present how much and at what rate the total suspect, probable and laboratory confirmed case numbers are piling up (pink) as well as how the deaths from among that number are changing (blue line) and how many of the cases are being laboratory confirmed (green line) as due to the virus suspected of being the cause. This last one is important as it gives a glimpse of how the laboratory network is coping, perhaps how specimen access is going and how much faith to put in the other two totals. Why are we worried about the result totals? Because many other things can look like Ebola virus disease (EVD) early on, and even later in the disease course. A laboratory test is the only way to be certain that the patient had that virus.
  • Nigeria's numbers look to be rising alarmingly fast. Relative to each other they are, but compared to the dozens of new EVD cases being added between reports in other countries, it is still a small (although still very bad for Nigeria!) increase. This highlights that care is needed when reading charts. Perhaps also an understanding that between different outbreaks, the rate of new cases being added is disease specific. Lots of influenzavirus detections during flu season is what we expect, any ebolavirus cases are not what we expect nor what we want to see. Context. A hard thing to account for and probably a matter of experience.
Graph 2. The cumulative case graph. Adding new numbers to the sum of all the numbers that came before. 
Click on image to enlarge.

Graph 3. Changing the scale. Raising the primary y-axis (left) scale to 750, the level of the other country graphs, makes Nigeria's case numbers look tiny. But it underestimates the impact of the localised spread of Zaire ebolavirus in an are that was not part of the outbreak until a case flew in and spread it. Changing the scale is not just whimsical decision making, it can highlight the importance of events that may otherwise go unnoticed.
Click on image to enlarge.

Take care when interpreting a graph - look at the axes and also use your noodle

Finally, I'm going to look at the way in which I present the numbers I plot on a graph. I'm using the cumulative case chart for Liberia as my example (Graph 4 collection). Its the same one used in Graph 3 - the only thing different is that I've dragged the x-axis to the left (shrunk) or to the right (stretched) to see what that does. 
  • The line plots look more or less steep when you shrink or stretch the x-axis, respectively. But the numbers have not changed. Possibly, our interpretation of them has, as a result of seeing the slope change. Remember though, check the axes. If you look at the x-axis, the shrunken version shows that those cases have climbed over a longer period than the slope suggests. Always check the denominator (the y of x/y) when you think about slope. Equally, the flatter curves of the stretched out x-axis, at the bottom of the Graph 4 collection, have to be looked at in context with time. The dates have been dragged out to what may be an unreasonable length, which makes the slopes look less; but they are still steeper in July than they were in April. Look around the graph for comparison. 
  • As I said above, the current multi-country outbreak lets us compare and so we can see that some areas are adding new cases very rapidly between each report (Liberia and Sierra Leone) while others (Guinea) are not adding as many as quickly. Nigeria looks to have jumped quickly but that is also because of the altered scale (discussed above) 
  • On VDU I get around this by also adding charts that plot total numbers per day or week or month or year. This shows a more discrete series of data that grow or shrink as the outbreak peaks or resolves. The 2 peaks of influenza A(H7N9) virus outbreaks illustrate this nicely - especially when combined with a cumulative case chart (Graph 5)!
  • There is no real right or wrong here (although there are pixel width constraints)- but don't let your perceptions fool you when looking at someone's graphs for the first time. Take some time to really look at the graphs.
Graph 4 collection. Stretching the x-axis can seem like stretching the truth. But carefully read the axes. Some experience is needed here and ultimately you are at the mercy of the person presenting the data.
Click on image to enlarge.

Graph 5. Influenza A(H7N9) virus outbreak in China during 2013 and 2014. Plotting the numbers discretely (by week) clearly shows the two outbreak peaks (darker blue lines joining the data point dots) and gives valuable context to the cumulative graph in the background (pale blue mountain). This is probably my favourite style of disease numbers graph.
Click on image to enlarge.
I hope that has helped make sense of my graphs, and perhaps those of others too. I'm always on Twitter so hit me up with questions about this or requests for more posts like this, or to tell me whether it was helpful.