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

Wednesday, 7 September 2016

MERS-CoV: alpacapalooza...

In the search for the animals that may be another reservoir for, or just support infection by, Middle East respiratory syndrome coronavirus (MERS-CoV), a few studies have looked at furry little alpacas (Vicugna pacos). 

We already know from Eckerle and colleagues' work that cells derived from alpacas have the required receptor molecule used by MERS-COV (
DPP4) and that they can support replication of MERS-CoV in the lab,[1] But are cells in flasks different from furry animals in the wild?

Three articles came out in the June 2016 issue of Emerging Infectious Diseases looking at alpacas and MERS-CoV. There's no way to tell who submitted when in this journal (ongoing grr).

Colorado State University team sought an easier - but still relevant - animal model than camels to work with.[2] They infected 3 (called A1, A2 and A3) alpacas with 107 plaque forming units (PFU; a cell-specific measure of the amount of infectious virus in a diluted sample) of the HCoV-EMC/2012 variant of MERS-CoV via 3ml of diluted virus per nostril. 3 days later, they housed 3 more uninfected alpacas (A4-A6) with the infected ones.  

After 70 days, A1-A6 were infected again ("challenged"), in the same way. Three other alpacas were infected the same way but euthanized 5 days after infection and their tissues collected for analysis. Nasal swabs were collected before infection and then daily from all living animals for 5 days post-infection and on day 10. A4-A6 were also swabbed 3 times per week to day 19. This could all have been a bit more clearly demonstrated using a timeline by the way.

None of the infected animals had a fever or observable nasal discharge and their appetites and activity remained constant; they didn't seem to be affected by infection with MERS-CoV. Infectious MERS-CoV was shed by A1-A3 to day 5 and transmission occurred to the A4-A6 arrivals:

  • A4 was found to shed virus for 1 day, 
  • A5 shed no virus and 
  • A6 shed across 8 days. 
Lots of variation even in a controlled environment like this.

When furries A1-A6 were challenged with a fresh infection, A1-A3 developed antibodies which protected them from infection (because no virus was shed). A4-A6 shed a little infectious virus for at most 2 days. A4-A6 also developed neutralizing antibodies but took longer than A1-A3 to do so. 

A wild transmission occurred from inoculated A1-A3 to naive A4-A6. This was a lower dose than the original inoculum, and seemed to elicit a milder antibody response in animals A4-A6 as well. 

Virus was found in the nose, larynx and trachea of A7-A9 but not the lungs.



The Australian/Singapore team sought an animal model of MERS with a better temperament and more manageable size than the camel.[3] 

Under biosafety level 3 conditions, they used a camel MERS-CoV variant (Al-Hasa_KFU-HKU13/2013) and exposed each alpaca to 106 50% tissue culture infectious doses (TCID50; another cell-specific measure of infectious virus quantity), monitored for 21 days then challenged as described above.

Blood as well as nasal, oral, rectal and urogenital swabs were collected over time and tested by sensitive RT-PCR, culture and for the presence of neutralizing antibodies.


The furries once again did not develop a fever (animal No.2 had a raised temperature though) or a respiratory illness.
Not a great model of disease, perhaps good for transmission?

Infectious virus was isolated from oral upper and deep nasal swabs but not from urogenital or rectal swabs. RNA detection by RT-PCR followed this same pattern. After challenge and in the presence of antibodies which had appeared from day 10-12, viral RNA could not be detected anywhere in any animal.

Neutralizing antibody did not appear until 21 days in animal No. 1, 10 days in No. 2 and still hadn't appeared at day 35 in No. 3. But, it was apparently unnecessary for protection from reinfection in this study of alpacas.


These 2 studies used 106-107 cell-specific quantities of MERS-CoV to infect the alpacas, but, when sought, less was produced by the newly infected animals - except in one of the Australian/Singapore animals where the peak of 106 TCID50 detected equalled the input dose. This finding suggests the laboratory inoculum may not be relatable to real-world amounts of virus produced by an infected animal source. It may however, just be how much is needed to get a model system infected.

The authors all agreed that alpacas could be a good model for MERS-CoV in camels and that animal infections supported the finding of the initial alpaca cell culture work. But that culture link is not quite so straightforward.

Deliberately infected goats, sheep and horses (using the HCoV-EMC/2012 variant of MERS-CoV) - also animals whose cells had supported MERS-CoV in the laboratory - showed little or no sign of viral replication and the animals mostly remained healthy (some nasal discharge was seen from 2 of 4 horses).[5]

Despite some signs of neutralizing antibody developing in goats and a sheep, the same Colorado team were not convinced that any of these animals would be likely hosts for MERS-CoV in the wild.


Cells in a flask are not always the most realistic model for animal transmission I guess.


The final alpaca article was from a Qatar/Netherlands team who tested alpacas in a region of Qatar where MERS-CoV is found to be enzootic among camels (spreading naturally among the animals).[4] 

Hobby alpaca and camel herds were the subjects of this study. They had been kept about 200m apart in the same farm and cared for by the same animal workers.

Blood samples were tested from 15 alpacas and 10 dromedary camels; nasal swabs were also collected from the 10 camels. Nasal, rectal and oral samples were only collected from a subset of the alpacas for antibody testing and sensitive RT-PCR.

MERS-CoV neutralizing antibody was present in 15 of 15 alpacas and 9 of the 10 camels according to a 90% plaque-reduction neutralization test. This indicated past natural infections had occurred.

Antibodies were also detected that suggested past infection by dromedary betacoronaviruses and camelid alphacoronaviruses but this was not unusual nor unexpected.

No swabs were positive by RT-PCR indicating that no animals were infected at the time of sampling. The authors did not know when, how or how often MERS-CoV may have naturally infected the alpacas.



So we can add alpacas to camels on the short list of animals that can host MERS-CoV infection.

References...
  1. Replicative Capacity of MERS Coronavirus in Livestock Cell Lines
    https://wwwnc.cdc.gov/eid/article/20/2/pdfs/13-1182.pdf
  2. Infection, Replication, and Transmission of Middle East Respiratory Syndrome Coronavirus in Alpacas
    http://wwwnc.cdc.gov/eid/article/22/6/pdfs/16-0192.pdf
  3. Experimental Infection and Response to Rechallenge of Alpacas with Middle East Respiratory Syndrome Coronavirus
    http://wwwnc.cdc.gov/eid/article/22/6/pdfs/16-0007.pdf
  4. MERS-CoV Infection of Alpaca in a Region Where MERS-CoV is Endemic
    http://wwwnc.cdc.gov/eid/article/22/6/pdfs/15-2113.pdf
  5. Inoculation of Goats, Sheep, and Horses with MERS-CoV Does Not Result in Productive Viral Shedding
    http://www.mdpi.com/1999-4915/8/8/230

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

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