Showing posts with label camel. Show all posts
Showing posts with label camel. Show all posts

Saturday, 17 September 2016

MERS is a disease we spread...

There is little doubt now that Middle East respiratory syndrome  (MERS) disease outbreaks are triggered by sporadic zoonotic transmission of the MERS coronavirus (MERS-CoV) from an infected camel to a susceptible human. 

Little doubt to anyone who has followed the story of MERS at all, anyway.

But that's just the tip of the iceberg. 

The majority of human cases that have contributed to those steep rises in the cumulative MERS-CoV detection graph below are there because humans have infected other humans while in or associated with a healthcare facility. A telling picture when you consider that MERS-CoV is not a great transmitter. We've done much to make something from what should have been nothing.

Can we vaccinate against lapses in infection prevention and control?


Monday, 14 March 2016

Tread carefully when MERS-CoV stirs in hospitals as it can spiral out of control quickly..

In 2014 a stepwise increase in Middle East respiratory syndrome coronavirus (MERS-CoV) cases preceded the largest healthcare facility outbreak of MERS to date. 

If you look at the most recent daily Kingdom of Saudi Arabia (KSA) Ministry of Health report below,[1] you could be forgiven for thinking that there is currently a threatening rise in cases which could easily spiral out of control once again unless it is quickly stepped on.

Adding fuel to the fire is the fact that in Buraidah, in the province of Al Quassim , there has clearly been a healthcare-associated outbreak ticking over since November 2015 - patients, healthcare workers and relatively little camel contact make for a pretty clear picture.
When these fires are let smoulder in this way, they can quickly spread embers across the region and then cases fly out to other ports.
A week ago there were 8 cases reported in a day. That's far from the biggest reporting day we've seen in 3 MERS years (around 31 cases in a day n April '14), but it's still high. There have been 11 consecutive days with 2 -8 cases reported each day. The region in the map above has been the hotspot, but in the 12-March report there were 4 cases, each in a different city

There have also been an usually high number of camel mentions so far this MERS season. We do not usually see so many consecutive cases reported to have some form of camel contact. These are from cases across the KSA but also from United Arab Emirates- and Oman-acquired cases too. Is this because of a better understanding and acceptance of the role of camels in spreading MERS-CoV to humans, after research really hammered home the facts, or is it that more camels are infected, or there are more infected herds this season, are other animals becoming infected, or is it that, for some unknown reason, there is more contact between humans and infected camels/other animals this season?

There have been no viral gene or genome sequences from 2016 arriving on the interwebs yet, so we are left with a few of the old questions...again
  • is this all normal or is something different this time around?
  • has this season's MERS-CoV undergone a significant genetic change(s), affecting stability, tropism or transmission?
  • has infection control and prevention slipped again?
  • is there more contact with infected camels this year?
  • are increased camel descriptions an indication of better surveillance and questioning about camel contact?

Time to start watching and plotting MERS-CoV again.

References...

Saturday, 5 December 2015

The season of the MERS...is mainly whenever the infection control fails

I still only see a "seasonality" to MERS and human MERS-CoV detections that is made up of the times when hospital outbreaks spread cases due to missed opportunity to control and prevent infection wihtin their walls. In other words - no real season at all. 

MERS-CoV is an opportunistic virus - which includes making the most of the frequent opportunities we humans provide for it to spread.

Data from public sources up until December 3rd 2015.
Click on image to enlarge.

Any true seasonality is in that small percentage of cases that are the result of a primary, sporadic infection from an infected and infectious camel. Those cases may be related to times of camel calf weaning when young camels acquire their first infection, or it might just be whenever a particular herd has MERS-CoV raging though it.


Sunday, 22 November 2015

Updating the animal "to-do" list...

I have a couple of talks coming up, so I'm making graphics again. And I like to share those. 

This one is an update on some of the creatures that could also be considered suspects in the hunt for sources of MERS-CoV infection of humans.

Of course, camels are the ones we know to be a true risk for infection and there was that 1 bat that was positive for a very small diagnostic PCR product. Cattle contact was also recently listed, with little detail, as a significant risk factor among those acquiring MERS-CoV infection and we also know that cells from camels, horses, alpacas, cattle and goats can be infected and host genome or virus replication of MERS-CoV in the lab, or have the MERS-CoV cellular receptor, DPP4, on their surface.[1,2]

I heard that there will be more bat testing in the future, but we haven't read of any MERS-CoV targeted bat studies since 2013.

So here is the long laundry list of animal testing that needs more work - many of which have been tested in small numbers over limited time periods already - in a graphical form.

Click on image to enlarge.
You can also access this from Figshare.[3]
References...

  1. http://www.ncbi.nlm.nih.gov/pubmed/25656066
  2. http://wwwnc.cdc.gov/eid/article/22/1/15-1340_article
  3. http://figshare.com/articles/Creatures_of_interest_to_how_humans_acquire_a_MERS_CoV_infection/1609604

Thursday, 5 November 2015

Updating the very model of a modern mammal-camel....

The new findings from the case-control study out of the Kingdom of Saudi Arabia (and US CDC) deserve an update of my old model of how one might become infected with MERS-CoV after exposure to an infected camel.[1,2]

Some of the possible ways in which MERS-CoV may be spread from an infected
camel to a human in direct or close contact with the camel or with surfaces
onto which MERS-CoV-laden camel excretions or secretions have been deposited.
The major change is the removal of the ingestion options. As readers of this blog will know, I've never been a "believer" in that route of infection, and the new study would seem to support that gut feeling with some facts.

As ever, the distinction between direct contact and being close enough to be exposed to droplets that are inhaled, has not been possible and wasn't attempted. The word "droplet" does not appear anywhere in the paper. In fact, animal contact and droplet-producing processes are all rolled together in the new study under the direct contact banner - so I have retained droplets among the possible risks shown in the figure.

References...

  1. http://virologydownunder.blogspot.com.au/2015/11/it-was-camel-in-library-with-mers-cov.html
  2. http://virologydownunder.blogspot.com.au/2014/05/camels-at-centre-aerosol-all-around.html

It was the camel, in the library, with the MERS-CoV...

In a paper out overnight, which is assigned to the January 1st 2016 edition of Emerging Infectious Diseases (why do you do this to us EID?!), Alraddadi and colleagues (overwhelmingly from the Kingdom of Saudi Arabia with help from the Centers for Disease Control and Prevention in the United States) have published Risk Factors for Primary Middle East Respiratory Syndrome Coronavirus Illness in Humans, Saudi Arabia, 2014

This is a long awaited case control study. Long awaited.


From [2]
It tells us that direct contact with dromedary camels (including the act of milking them) in Saudi Arabia, in the 2 weeks prior to symptoms ascribed to a confirmed MERS-CoV infection, is a significant risk factor for developing Middle East respiratory syndrome (MERS) disease. Cattle contact also fell out as a significant risk. 

However, cases were no more likely than controls to report exposure to bats, goats, horses, sheep or consumption of fruits, vegetables, or animal products, including uncooked meat, unpasteurized animal milk, or dromedary urine. 

The study also reminds us that the host factors of diabetes, heart diseases and smoking are associated with MERS (the disease, not how likely you are to get infected). If you do not have these then you may be more likely to have mild or asymptomatic outcomes if you were to be exposed and infected by MERS-CoV.

These are astounding findings that will take many by surprise and revolutionize out understanding of MERS (the disease) and MERS-CoV (the virus) throughout the Arabian Peninsula. 

Said no-one. Ever.



Ridiculous sarcasm aside though, much kudos to the Saudi research community! This case-control study, a long-awaited piece of work, was a camel that had to be broken by them for them, and now it has been. A win for science and for the region's science.

I hope the study helps to confirm the sizable pool of research that has come before.

But let's not lose sight of the camel in the room; most human cases of MERS come from other human infections closely associated with healthcare settings.

Defeating MERS and MERS-CoV requires battles on many fronts. As usual for any emerging viral disease. 

But then, it's a OneHealth kinda world.


References...
  1. http://wwwnc.cdc.gov/eid/article/22/1/15-1340_article
  2. http://virologydownunder.blogspot.com.au/2014/05/camels-at-centre-aerosol-all-around.html

Friday, 23 October 2015

Markets that deal in camels may help spread MERS-CoV variants..

This camel/MERS-CoV study from Farag and colleagues, serves as follow-up of sorts to my last post. The paper, which was published in July 2015's Infection, Ecology and Epidemiology, is entitled High proportion of MERS-CoV shedding dromedaries at slaughterhouse with a potential epidemiological link to human cases, Qatar 2014.[1]

The authors remind us in the background that the routes of direct or indirect zoonotic transmission are still unknown but that a "large proportion of MERS cases" are suspected to have resulted from zoonotic transmission.

105 dromedary camels (DCs) either from a market sale or directly from Qatar or the Kingdom of Saudi Arabia (KSA) were sampled in February (n=53) and March (n=52), 2014. Samples included nasal, oral, rectal and bronchial swabs and lymph nodes from animals grouped into age 3 groups: 0 to 6 months (n=41), 7 to 12 months (n=35) or greater than 12 months (n=29) of age. Testing for virus was by Corman et al's UpE and N gene real-time RT-PCRs.[2] Testing for antibodies was via the detection of a reaction to the MERS-CoV, severe acute respiratory syndrome (SARS)-CoV and human CoV (HCoV)-OC43 spike domain S1 antigen using the protein-microarray method described previously by this group.[4]

Findings...
  • 59% of DCs had at least one MERS-CoV RNA positive sample but no significant difference in viral load was apparent between sample types or ages
    • 61/101 (60.3%) of DC's nasal samples had RNA detected
    • 23/102 (22.5%) of DC's saliva samples had RNA detected
    • 15/103 (14.6%) of DC's rectal samples had RNA detected
    • 7/101 (6.9%) of DC's bronchial samples had RNA detected 
    • 5/53 (9.4%) of DC's lymph nodes had RNA detected
  • 5 different MERS-CoV variants (subtly different versions of MERS-CoV) were circulating in Qatar among the sampled animals at this time according to RT-PCR/sequencing method that targets a fragment of the S2 domain of the MERS-CoV Spike gene.[3]
  • 100/103 (97%) animals were reactive for IgG, and most of 53 animals tested, had antibodies capable of specifically neutralizing cellular infection by MERS-CoV as determined by a 90% plaque reduction neutralization test (PRNT90; [5])
  • Antibody levels and viral load did not correlate suggesting - based on this subset of the immune response - that reinfection may be possible since protection may be limited, as it is among humans with the 4 known HCoVs. The authors note that this may prove a challenge for any future DC vaccine which would need to produce a protective effect to meets its need
  • No age-specific differences were found in MERS-CoV RNA shedding - usually younger DCs are distinctly more likely to be shedding viral RNA than older DCs
Discussion...

The authors noted here that discrepancies do exist between their study and those of some others - specifically, that others have not found viral RNA in faeces - but those studies also tested fewer animals. It is important, when percentages are not high, to test enough animals to see the full extent of MERS-CoV shedding and potential transmission routes.

DCs from different regions within Qatar and outside Qatar, may be shedding MERS-CoV while in DC markets and holding pens, sometimes for weeks, awaiting slaughter. 

Camel markets are thus a likely high risk area for acquiring a MERS-CoV infection - and multiple variants can be circulating here. 

In previous Qatari investigations, human cases have been linked with visits to the areas studied here and have also included DC slaughterer cases, supporting the notion that humans with DC exposures (presumably when they are infected with MERS-CoV) are at risk of becoming infected themselves. 

Yet this study did not manage to capture the process of transmission in action. It is that process that holds such importance for this chapter on MERS-CoV and especially for those who disbelieve the role of DCs in human MERS cases. 

In the next post, we will re-visit a study that did seem to capture DC>human infection.

References...
  1. High proportion of MERS-CoV shedding dromedaries at slaughterhouse with a potential epidemiological link to human cases, Qatar 2014.
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4505336/
  2. http://www.ncbi.nlm.nih.gov/pubmed/23041020 
  3. http://www.ncbi.nlm.nih.gov/pubmed/25728084
  4. http://virologydownunder.blogspot.com.au/2015/10/if-you-are-often-in-contact-with-camels.html
  5. http://www.thelancet.com/journals/laninf/article/PIIS1473-3099(13)70164-6/abstract

Tuesday, 20 October 2015

If you are often in contact with camels are you more likely to acquire MERS-CoV? [spoiler: yep]

This dromedary camel (DC)/Middle East respiratory syndrome (MERS) themed post is a quick review of a paper from 2015 by Reusken and a team of absolute champions in this space. 

It, as many have been, was published in the Emerging Infectious Disease journal, listed in its August issue (but online earlier) and entitled, Occupational Exposure to Dromedaries and Risk for MERS-CoV Infection, Qatar, 2013–2014.[1]

The study examined 498 sera from humans in Qatar split into different exposures types. Included were European (the Netherlands and Germany) human sera for use as controls - collected from a part of the world where there was not expected to have been any MERS-coronavirus (CoV) exposure and so no antibodies were expect to be present; a test for the tests.

As an aside, we've seen some great informative MERS-CoV/camel studies come out of Qatar. I love watching good collaborations pay dividends.

The 498 sera breakdown as follows:
  • 294 from those with daily DC exposure
    • Cohort A: 109 camel (A1; n=5) and sheep (A2; n=104) slaughterers
    • Cohort B: 8 central animal market (CAM) workers
    • Cohort C: 22 healthy males living & working at Al Shahaniya barn complex adjacent to DC race track
    • Cohort D: 155 healthy males living & working at DC farm
  • 204 from those without camel contact
    • Cohort E: 56 samples from construction workers
    • Cohort F: 10 people living in a complex with 200 sheep barns
    • Cohort G: 138 specificity testing samples (66 from the Netherlands and Germany who had recent CoV infection (G1) and 72 from the Netherlands obtained for Bordetella pertussis infection testing (G2)
The antibody testing regimen relied on a multi-tier approach (the best ones do, until we're sure that any single assay can cope with all the variables):
  • Tier 1: IgG antibodies were sought using the MERS-CoV, severe acute respiratory syndrome (SARS)-CoV, human CoV (HCoV)-OC43 spike domain S1 antigen protein-microarray method used previously by this group [2]
    • 20/294 samples (6.8%) reacted (had IgG antibody in them) - none were from controls sera or from those without DC contact
    • 4/22 Cohort C, 8/155 Cohort D, 3/104 Cohort A2 and 4/5 Cohort A1 samples were reactive
    • All samples from A1, A2, B, C, D, E, F and G1 showed responses to HCoV-OC43 S1
    • None of 498 sera reacted to SARS-CoV S1
  • Tier 2: A 90% plaque reduction neutralization test (PRNT90 [4]) was used to show whether antibodies in samples could specifically stop MERS-CoV from infecting cells after sera and virus were co-incubated ahead of infection of a cell line
    • the 20 IgG reactive samples from Cohort A to D were tested and 10 were able to neutralize infection
    • 34/35 samples from those with camel contact (Cohorts A1, B and C) that were IgG non-reactive, also had no neutralizing antibody
  • "Tier 3": Use of a whole MERS-CoV immunofluorescence assay (IFA). However, the results from testing 8 reactive samples (5 of which were positive by IFA) were not included
This paper has a nice central finding which goes something like: if you don't have contact with camels, you don't get infected by MERS-CoV. If you do regularly have contact with camels - you are much more likely to get infected as determined by you having developed antibodies to that virus; you were infected but you fought off the infection. A similar finding came out of the larger serosurvey from the Kingdom of Saudi Arabia.[3] 

I do wonder about the reactive sheep slaughterers though (Cohort A2) - where did those infections come from?  

The authors also addressed why other serologic studies of humans with occupational exposures have not found reactive sera-those studies hardly ever documented infected camels at the workplaces and there may not have been any (for some significant period of time presumably). More infected camels may be associated with more human infections. No surprise. The authors had found, outside this publication, that 60% of camels at the CAM and slaughterhouse were shedding MERS-CoV. This discrepancy has been a question of mine for a long while - and I like this answer.

Interestingly, the participants with antibodies don't recall being seriously sick. So you may get infected and just think you have the flu, or a cold, or nothing at all. This result may further confuse camel-deniers who do not have any background in the wide spectrum of outcomes one can expect after infection by any virus. Nonetheless, such apparently unnoticeable infections add more weight to the story that the current proportion of fatal cases is an exaggeration. So we learned yesterday that MERS (the disease) is rare, that camel contact makes up only a proportion of the likely sources of infection and now we see that you may not even get sick if you do get infected. A few things to digest there.

Also very interesting to me is that the neutralizing antibody titres were lower than had been found elsewhere. The authors suggest this may be due to these infections producing only mild disease. Without a prospective study though, it's very hard to be sure about the true disease severity - recall bias can be a pest. This is an area that needs a more focussed study; do our antibody tools detect mild and asymptomatic cases as reliably as severe MERS cases, for how long and in all cases of infection?

Its feels like its getting pretty hard to mount any realistic case for why we should ignore the role of camels in infecting us with MERS-CoV - even if they do so rarely, and perhaps often without serious complications.

References...
  1. http://wwwnc.cdc.gov/eid/article/21/8/15-0481_article
  2. http://virologydownunder.blogspot.com.au/2015/10/kenyan-camel-coronaviruses.html
  3. http://www.thelancet.com/journals/laninf/article/PIIS1473-3099(15)70090-3/abstract
  4. http://www.thelancet.com/journals/laninf/article/PIIS1473-3099(13)70164-6/abstract

Monday, 19 October 2015

Can MERS-CoV be found in the upper and lower respiratory tract of infected camels? You bet your single hump it can!

Today's review is of a paper listed as published in Emerging Infectious Diseases in July 2015, authored by Khalafalla and colleagues from King Faisal University in the Kingdom of Saudi Arabia and from the CDC in the United States of America.[1]

Al Omran City (also Al Umran) city is located 
just adjacent to Al Hofuf on this map.
The introduction tells us that bats "seem to be the reservoir host" but are not the likely ongoing source of human Middle East respiratory syndrome (MERS) cases in the KSA. An assumption based on the finding of 1 small yet diagnostic MERS-CoV sequence in 1 bat from 1,003 samples, once.[5,6] It also reminds us that up to this point in time, camels were mostly sampled from the nose and eye during MERS-CoV investigations. We still didn't know whether other parts of the camel respiratory tract could test positive for MERS coronavirus (MERS-CoV). This is important knowledge as it pertains to virus transmission from camel-to-camel and camel-to-human.

This study focused on the dromedary camel (DC; Camelus dromedarius) collected samples
from around the Al-Ahsa area. These comprised two sample populations collected during a year (April 2013-May 2014):
  1. Tissue from at least lung lobe of camels slaughtered at the Al Omran Abattoir, Al Omran City. Animals were kept in groups of 10-15 for up to 4 days in stock markets prior to slaughter
    ..8 batches of samples were collected (a batch every 1-2 months) from 91 carcasses in total
    ..28 young animals (<4 years of age) and 63 adult animals (4 or more years old) were sampled
  2. Over the same period, age-matched nasal swab samples were collected from Al Omran abattoir, Al Ahsa livestock market and the King Faisal University veterinary hospital
    ..96 animals were swabbed; 36 young animals and 60 adults
    ..only 2/94 animals were visibly unwell - the 2 had nasal and lacrimal discharge
Samples were tested by a pancoronavirus conventional RT-PCR assay [4] as well as two real-time RT-PCR assays [2,3] No culture of virus was attempted so we must extrapolate from the RT-PCR findings to assume a positive finding of MERS-CoV RNA represents replicating virus-at some point during the infection anyway (a safe assumption).

The findings...
  • 84 of 187 DCs (44.9%) tested positive, most often during the cooler months (NOV2013-JAN2014) and more often from young camels than adults
  • 59 of 91 (61.5%) DC carcasses had MERS-CoV RNA detected
  • 28 of 86 (29.2%) nasal swabs were positive
  • 4 samples yielded a spike gene sequence-these differed from each other but clustered with other human and camel MERS-CoV spike gene sequence
The authors are clearly not exuberant that their findings have shed much new light on the camel>human debate and call for longitudinal studies to better understand how MERS-CoV spreads among DCs. A good suggestion indeed. 

Nonetheless, this study adds pieces to the story; DCs appear to be infected throughout their respiratory tract, not just at the openings usually swabbed. And if the seasonality of MERS-CoV in DCs hinted at by this study at this locale, does not overlap perfectly with human cases at the same time and place, that is most likely because camel>human infections are very rare. Also this mismatch is likely because most human infections are not due to camel/human interactions, but are acquired from human-to-human infections, thanks to errors in the management of a sick index case. That case's uncontrolled infection is what usually results in many other patients, healthcare workers and visitors becoming infected. 

That's the camel in the room that seems to be overlooked so frequently. 

Another thing that seem lost in translation - MERS itself is a relatively rare human disease and when you consider that camel>human transmission is only a fraction of that.... 

Some seem to think that lots of infected camels must equate to lots of infected humans if this crazy theory about camels being the source of human cases is to be believed. Sorry. Not the case (unless reported contacts are much more frequent than we are being told). 

There are definitely human MERS-CoV infections who only had DC, not infected human, exposures. Unarguably we do need to do better to try and catch transmission 'in the act' and show how it happened in order to dot the 'i' and cross the 't'. The same also applies to a lot of zoonoses. Until those breakthroughs though - we have a lot of data which can be used to better protect people from getting infected by MERS-CoV. 

Seems pretty dumb to wait on more convenient data while people still get infected, become sick and often die.
On balance, separating camels from humans, being better protected when in contact with camels, and improving infection prevention and control in hospitals may even obviate the need for vaccination. Gasp.

References...
  1. MERS-CoV in Upper Respiratory Tract and Lungs of Dromedary Camels, Saudi Arabia, 2013–2014Abdelmalik I. Khalafalla, Xiaoyan Lu, Abdullah I.A. Al-Mubarak, Abdul Hafeed S. Dalab, Khalid A.S. Al-Busadah, and Dean D. Erdman
    http://wwwnc.cdc.gov/eid/article/21/7/15-0070_article
  2. http://www.ncbi.nlm.nih.gov/pubmed/23041020
  3. http://www.ncbi.nlm.nih.gov/pubmed/24153118
  4.  http://www.ncbi.nlm.nih.gov/pubmed/19057882
  5. http://wwwnc.cdc.gov/eid/article/19/11/pdfs/13-1172.pdf
  6. http://virologydownunder.blogspot.com.au/2013/08/mers-cov-genetic-sequences-found-in.html

Saturday, 17 October 2015

Kenyan camel coronaviruses...

Two studies have now found antibodies from Middle East respiratory syndrome coronavirus (MERS-CoV)-like coronaviruses in dromedary camels (DCs). The "like" bit reflects that unless we have some sequence, we can't say for certain that the virus that infected those camels in the past, causing them to respond with these antibodies, was a MERS-CoV variant. The virus(es) may have been a different camel CoV that just so happens to share some antigens and is detected by MERS-CoV-"specific" antibody detection tests. The old story of "we don't know what we don't know" can perhaps be extended here to "we can't validate a test against viruses we haven't found yet". Or that may just be too nerdy.

Anyhoo, we have two papers to look at here. 

Antibodies against MERS coronavirus in dromedary camels, Kenya, 1992-2013

This paper went into the August edition of Emerging Infectious Diseases, authored by Corman and team (online much earlier but no way to track that thanks to no date of ePub ahead of print - loud sigh!) from Germany, Kenya, the Netherlands and Sweden.[1]

The introduction sets the scene for a paper seeking to know about where the MERS-CoV we know and love today, may have come from to be so common amongst camels. We suspect that this could be from another animal in its current form, or by recombination and mutation from a different ancestral form that has yet to be discovered in an animal (or human). This study seeks out MERS-CoV or a MERS-CoV like virus, or an ancestor, from camels in Kenya using their blood to look for footprints of previous infection - in this case, antibodies.

774 DC blood and stored sera collected from three regions of Kenya between 1992 and 2013 were subjected to a multi-step testing process:
  1. All samples, diluted 1:100, were screened using MERS-CoV spike protein subunit 1–based ELISA (rELISA; described before at [2])
    .228 of 774 (29%) were positive
  2. The 228, diluted 1:40, were next examined using a recombinant immunofluorescence assay using Vero cells expressing MERS-CoV spike protein (rIFA; described before at [3]
    .213 of 228 (93%; 28% of the 774) were still positive in the second tier of testing
  3. The third tier of testing of samples diluted between 1:80 and 1:800 used a highly specific MERS-CoV microneutralization assay (MNT assay; also previously described in [3])
    .119 of 213 (56%; 15% of the 774) had titres (dilutable levels) greater than or equal to 1:80 and 14 had titres above 800
    .Some counties of Kenya had 60-100% of samples test positive 
Figure 1. From Corman et al, Emerg Infect
Dis. 2014 Vol 20, No 8. 1319:1322.[1]
Click on image to enlarge.
North-eastern and northern regions generally had higher titres (Fig.1).These are regions closer to other countries with known antibody-positive camels (Egypt, Sudan, Somalia and Ethiopia). Further, nomadic camels from the East had higher antibody titres than those farmed in the north-west of the Rift Valley. Nomadic camels are taken across borders for trade.[2] DCs that had been kept isolated since 1998 were negative signs of past MERS-CoV virus. 

Adults had higher antibody levels than juveniles - presumably because infections happen when the DCs are young, producing the antibodies we detect in adult DCs.

Figure 2. Quote from [1]
Click on image to enlarge.
Camel density was also important. More camels were antibody positive in areas with higher densities of camels - also presumably because virus can spread better from one infected DC to others when more DC contacts are around. Similar story for humans, a contributing factor for those super-spreading conditions. The authors also made a comment that is very important to the answer the question of why human cases have not been found in areas with animal infections (see Figure 2).

Moving on to the next publication from Kenya.

Serological Evidence of MERS-CoV Antibodies in Dromedary Camels (Camelus dromedaries) in Laikipia County, Kenya

This one just came out on PLOS|ONE authored by Deem and colleagues from the United Stets of America, Kenya, New Zealand and the Netherlands.[4]

The introduction also reminds us that understanding MERS-CoV in camels in countries with herds, can help us assess and manage the risk for humans in those countries. In this case, Kenya has over 3 million DCs and mean and milk is worth $USD 11 million a year. These figures that may help you understand why DC interests don't want to have a significant human pathogen harboured by their animals.

This study is based in Laikipia County, almost in the centre of Kenya (Fig 1), which has a growing camel population. 

335 camels were sample from 9 easily accessed herds.

  1. All samples, diluted 1:20, were screened using a MERS-CoV, severe acute respiratory syndrome (SARS)-CoV, human CoV (HCoV)-OC43 spike domain S1 antigen protein-microarray method used previously by this group [5,6,7,8,9]
    _46.9% of DCs were seropositive (had antibodies) including at least 1 animal per herd
    _60.8% of adult DCs were seropositive and 21.3% of the juvenile animals
    _bovine CoV (tested for by including the HCoV-OC43 antigens) seroprevalence was high, as it often is in DCs
    _this study did not see a significant difference in seroprevalence between nomadic herds or those managed in more commercial ways and no differences between different degrees of herd isolation
Figure 3. Quote from [4]
Click on image to enlarge.
The authors concluded that these herds were being exposed to MERS-CoV (or a similar virus) on an ongoing basis, even though they were not near borders and at lower densities that the more northern sites reported by the Corman et al. study above. They did not feel these disparities were due to diagnostic differences and that the DC densities in Lakipia County were sufficient to maintain virus circulation. 

The conclusion noted the need to get sequence from this virus or these viruses n order to see whether they are the MERS-CoV we know, a different clade of MERS-CoV variants or another virus entirely. That sort of information can't be gleaned from antibody studies and so RT-PCR methods are needed.

The report wrapped up with a comment about a lack of reporting of human cases (Fig.3).


Clearly, camels are commonly infected by MERS-CoV or a close relative in parts of Africa and the Arabian Peninsula which receives camel imports from Africa. 

Also very clearly, DCs survive the experience apparently fine and unharmed lending more support for MERS-CoV in DCs being just a "camel cold". The camels do not need to be culled the way we do to other ill virus-infected animals (I'm looking at you chooks with high pathogenicity influenza A(H5N1) virus..or other flu viruses). We just need to remove camels from humans - or better manage the interactions we have to have. It's not rocket science but it will take thoughtful, considered and collaborative discussions.

References...
  1. Antibodies against MERS coronavirus in dromedary camels, Kenya, 1992-2013
    Corman VM, Jores J, Meyer B, Younan M, Liljander A, Said MY, Gluecks I, Lattwein E, Bosch BJ, Drexler JF, Bornstein S, Drosten C, Müller MA.
    http://www.ncbi.nlm.nih.gov/pubmed/25075637
  2. http://wwwnc.cdc.gov/eid/article/20/6/14-0402_article
  3. http://wwwnc.cdc.gov/eid/article/20/4/13-1746_article
  4. Serological Evidence of MERS-CoV Antibodies in Dromedary Camels (Camelus dromedaries) in Laikipia County, Kenya
    Sharon L. Deem , Eric M. Fèvre, Margaret Kinnaird, A. Springer Browne, Dishon Muloi, Gert-Jan Godeke, Marion Koopmans, Chantal B. Reusken
    http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0140125
  5. http://virologydownunder.blogspot.com.au/2013/08/camels-carry-signs-of-coronavirus.html
  6. http://virologydownunder.blogspot.com.au/2013/12/middle-east-respiratory-syndrome.html
  7. http://virologydownunder.blogspot.com.au/2014/01/antibodies-in-10-year-old-uae-camel.html
  8. http://www.thelancet.com/journals/laninf/article/PIIS1473-3099(13)70164-6/abstract
  9. http://wwwnc.cdc.gov/eid/article/20/8/14-0590_article



Thursday, 15 October 2015

MERS and the media in Saudi Arabia - a match that fuels confusion....

I'm interrupting my reviews on MERS and camels to briefly critique a recent media article published in the Arab News, Wednesday 14th of October. This was also on camels, but a view into the other side of this story.

The title of the article: ‘No conclusive proof’ camels spread MERS: Expert.[1]

There are two trains of thought here - and perhaps I have not clarified them so far. The first train doesn't believe that camels have a role in human cases of MERS-I disagree completely with the sentiment here. The second train of thought wants more testing of more and different animal species. I agree with this wholeheartedly. And those who can do this should be getting on with the job of doing it or organising those who can do it instead of wishing the data we absolutely do have, were different.

Let's keep in mind that seeking out other sources is a research endeavour. You cannot write public health messaging around things for which you have absolutely no supporting evidence. You can't protect your population, especially those most at risk, if you don't have proof to support how they are at risk. Looking after the public's health requires data. Research gets those data. Support the research. Look at those data instead of ignoring them because they scare you, point a finger at your favourite animal or conjure fears of an animal-driven negative economic impact. 

Distancing humans from infected camel vectors is a here and now action. It is not the result of a future research study. Finding ways to act on the data may have an impact on cases. 

Rather than guess at what people's concerns are - let's have a read of some key sections of this article, and comment as we go.

"There is no conclusive evidence that shows camels are responsible for the spread of the deadly Middle East Respiratory Syndrome coronavirus (MERS-CoV), according to research conducted by a Saudi expert at King Saud University in Riyadh."

  • This is plain wrong. There is considerable body of peer reviewed scientific literature providing evidence both for spread among camels and between camels and humans, even data strongly suggesting that direction (camel>human). A review I co-authored last year goes into a lot of that detail - it has a huge table on the camel related literature.[2]

“All the studies published in scientific journals do not at this stage show that the blood samples taken from camels have the virus present."

  • This is an English language article so I am going to take that at face value. Virus in the blood, or viraemia, is not considered a major concern for spread human or camel MERS-CoV infection - the real and larger concern is virus, in high amounts, that is regularly identified in the nose of infected camels. This is quote is not evidence of an expert comment.

"The reality is that more than 80 percent of the tested samples prove that camels’ blood carry protective antibodies against the virus,” he said."
  • Again, this comment highlights a lack of expertise in virology or immunology. Fields important for this discussion. The camels have antibodies because they have been previously infected. Research has found that camels seem capable of being reinfected - infected again even when they already have antibody from a previous infection. These camel antibodies may not be protective. Cell mediated immunity (h/t @MarionKoopmans) may be an important study subject here to better understand what happens in camels.

"He said some studies have found that 5 to 6 percent of shepherds and persons dealing with camels carry antibodies against MERS, and do not have the virus itself."
  • This is where a science reporter would have been really helpful to Arab News. Shepherds (camel herders?) don't have the virus by the time they develop antibodies because, like many viruses, MERS-CoV causes a short-lived, or acute, infection in humans and camels. Those few percent of shepherds with antibodies were previously infected and the virus was subsequently cleared by their immune system, usually near to or before those antibodies develop.

“In our previous studies we found out that Heavy Chain Antibodies are present in the blood of camels and are carried out with its milk. This research was published in the Journal of Proteomics. This in itself proves that immunity is transferred from camels to humans,” he said."
  • This does no such thing at all. This shows that antibodies are in camel blood and milk - if indeed that was what was found. What are the previous studies that showed these antibodies were ingested by humans and survived the digestive tract to remain effective against MERS-CoV? There are none that I have read but I'd be interested in seeing them.

Science tests and measures, it calculates and concludes. Very little of that process is evident here, but a sense of the confusion around this topic is. These stories should be great starting points for the Saudi Ministry of Health to work up local, relevant and specific answers, (more) factsheets or Ministry-involved media interviews and internet posts to help educate those with concerns about there camels. Listen, communicate, take feedback, re-tune, communicate, listen....

References...

  1. ‘No conclusive proof’ camels spread MERS: Expert
    http://www.arabnews.com/featured/news/820181
  2. Middle East respiratory syndrome: An emerging coronavirus infection tracked by the crowd.
    http://www.ncbi.nlm.nih.gov/pubmed/25656066

Wednesday, 14 October 2015

MERS-CoV on the farm...

I'm going to spend a few posts catching up on some excellent papers showing the role of camels in harbouring and transmitting the Middle East respiratory syndrome coronavirus (MERS-CoV). There also seems to be some confusion remaining about what we know, what we don't know, and also how bats fit in to the picture. I'll finish the next few posts with a summary.

Please do check out my previous listing of the literature around MERS-CoV and camels.[1]

I'll republish an updated literature list in the summary post as well.

First up, an article from the scientific literature which was published by Hemida et al. in the July 2014 edition of Emerging Infectious Diseases, but would have gone online much earlier (CDC don't list that date for some reason I cannot fathom).[2]

This authors first remind us that MERS-CoV RNA has been detected in humans and dromedary camels (DCs) before and that DC infection has been shown to precede human infection in one study (well, two but they both analyse the same camels and humans).[3]

This study collected and froze nasal, oral or rectal swabs and blood samples from DCs on 2 farms in Al-Ahsa in the Kingdom of Saudi Arabia (KSA). The authors then looked for MERS-CoV RNA and antibodies.
  • Farm A:
    • 70 DCs
      • 4: 1 month of age
      • 8: approximately 1 year of age
      • 58: adults
    • Sampled 5 times between NOV2013 & FEB2014
    • Herd never grazed in the desert (so wasn't exposed to other camels)
    • November 30th 2013 results
      • 10 DCs were MERS-CoV RNA positive; 8 of 9 DCs that had both nasal and faecal samples tested were only positive in the nasal swab, 1 DC only in the faecal swab
    • December 2013 results
      • No positive DCs December 4th; the following resulted from December 30th
      • 7 of 8 calves and 2 of 3 adults
      • 12 adults with sera collected before this testing were seropositive - this include 2 that were MERS-CoV RNA positive suggesting DCs can be reinfected
      • 2 seronegative 1-year old calves had the highest nasal loads of MERS-CoV RNA suggesting maternal antibody may not be protective
      • 4 DCs had the equivalent of a human cold - cough, sneeze, discharge, elevated temperature and were off their food
    • February 14th 2014 results
      • No MERS-CoV RNA was detected in DCs
    • All 3 MERS-CoV RNA-positive DC calves who had sera collected on December 30th and February 14th, were MERS-CoV RNA negative in the February sample (thus an acute not chronic infection in camels) and all had a four-fold or great rise in antibody titer
  • Farm B:
    • 20 DCs
      • 3: calves
      • 17: adults
    • Sampled once, FEB-2014
    • Herd sometimes grazed in the desert
    • No MERS-CoV RNA was detected in DCs
Samples were tested by 2 MERS-CoV specific real-time RT-PCRs and a broadly reactive coronavirus conventional RT-PCR. MERS-CoV positive samples were re-extracted (nucleic acids were purified from another aliquot of the original sample) and re-tested to confirm.

Conventional (Sanger) full genome sequencing was also conducted generating 3 genomes from Farm A, KFU-HKU 13, KFU-HKU 19Dam (faecal swab) and KFU-HKU 1. These were identical in sequence across the full 30,100 nucleotide genome and across the spike gene of 4 more viruses.

Virus isolation using the Vero E6 cell line was successful from 2 nasal swabs and 1 faecal swab - all with high amounts of viral RNA (culture is nowhere near as sensitive as PCR-based detection methods) - collected on December 30, 2013.
  • A genome sequence from the faecal swab and the 2nd passage of culture isolate from the same faecal swab were directly compared - 3 nucleotide changes were identified, 2 of which led to an amino acid change (spike and membrane proteins)
So we learned from this study that DC MERS-CoV (genetically near identical to virus found in humans) doesn't mutate within a given DC herd (genetically stable in DCs), but does change a little upon cell culture in the laboratory. That change is not unexpected as cell lines in a flask are not camel/human cells in a complex microenvironment in the body. It's also not the first time such mutation has been seen.

We can also see that not all farms in a region of KSA have MERS-CoV when one does but that infections spreads within and around the herd - not persisting once it has moved through. However this herd and others in the region is one from which DCs can be moved to the via Buraidah in the KSA to the United Arab Emirates. Imports and exports and movement to shows and festivals being a problem when your animal is carrying an infectious agent - just as it is when an infected human hops on a plane and travels to Nigeria, or South Korea or the United States...or anywhere. We saw that adult DCs could probably be reinfected despite a pre-existing antibody response. But we learned nothing about the cell-mediated immune response - a gap in our knowledge that extends to the human immune response to MERS-CoV infection also.

While the peak of infection at Farm A occurred in late December in this study, only a limited time periods was sampled and too few farms to know if this is the pattern throughout the Arabian Peninsula, or just chance in Al Ahsa in 2013/2014. But there is another study that has looked a little longer and I'll review that soon. 

Sadly, there were no human farmers involved. The study would have been made more valuable if it had also followed any and all humans in contact with these camels over this period as well. More examples of camel-to-human infection would be great to have since there are still those who don't "believe" camels play a role in MERS. Of course, it's not belief that's needed, it's the willingness to sit down and listen to the scientific facts we have at hand. And that comes down to finding a way to pitch the facts in a way that works for each type of audience.

References...
  1. http://virologydownunder.blogspot.com.au/2014/05/camels-and-mers-links-to-peer-reviewed_27.html
  2. MERS Coronavirus in Dromedary Camel Herd, Saudi Arabia
    Hemida MG, Chu DK, Poon LL, Perera RA, Alhammadi MA, Ng HY, Siu LY, Guan Y, Alnaeem A, Peiris M.
    Emerg Infect Dis. 2014 Jul;20(7):1231-4
    http://www.ncbi.nlm.nih.gov/pubmed/24964193
  3. http://virologydownunder.blogspot.com.au/2014/06/1-of-these-papers-is-pretty-much.html

Friday, 18 September 2015

MERS by month, camel and mass gathering...

I haven't updated this figure in a long while but recently had the chance to add some new camel calving season data [1] and another festival to my earlier lists [2-4] - the Um Ragaiba festival.[6] 

The Um Ragaiba festival is purportedly the largest of the human|camel gatherings, located north of Riyadh and near Buraidah and Hafr Al-Batin - interestingly, are all sites of infamy among the tales told in MERSville.[5]

MERS-CoV detection in humans by month. Also showing spring and
summer seasons in the Kingdom of Saudi Arabia and some key
camel and festival dates.
Click on image to enlarge
The latest version of this figure highlights a few things to me:
  1. I don't see a seasonality here which is not surprising. Most human cases are due to human error creating the circumstances by which health care related outbreaks take off. These happen at different times. It is hard to remove that very loud noise and see if a seasonality remains. A seasonality that is presumably due to times when there are more active camel infections increasing the risk of human infections through proximity and direct contact with infected hosts
  2. The Kingdom of Saudi Arabia has at last taken the threat posed by MERS-CoV infected camels seriously. In 2015, two big festivals which had camel involvement, Janadriyah and Um Ragaiba were not held. Take note China and avian influenza
  3. The bulk of human cases occur within a timeframe bracketed by camel calving season - so, keeping in mind what I said above, rather than season, perhaps we can agree that the period in which higher numbers of MERS-CoV cases occur, seems to be in the Arabian Peninsula's spring and summer - even if that outbreak is in South Korea! When virus activity rises at the source, so does the risk of death and significant economic and social impact beyond the borders of that source

Reference...

  1. http://www.ncbi.nlm.nih.gov/pubmed/26256102
  2. http://virologydownunder.blogspot.com.au/2014/01/a-date-with-middle-east-respiratory.html
  3. http://virologydownunder.blogspot.com.au/2014/04/an-update-on-april-outbreak-of-mers-cov.html
  4. http://virologydownunder.blogspot.com.au/2013/09/can-mers-cov-seasonality-tell-us.html
  5. https://www.saudiaramcoworld.com/issue/200803/heads.high.htm
  6. http://www.ncbi.nlm.nih.gov/pubmed/25714162