Showing posts sorted by relevance for query upe. Sort by date Show all posts
Showing posts sorted by relevance for query upe. Sort by date Show all posts

Tuesday, 24 December 2013

Middle East respiratory syndrome coronavirus (MERS-CoV): camels, camels, camels!

Two studies in Eurosurveillance, an editorial note, A Lancet Infectious diseases report and a comment point 2 hairy toes toward camels as a harbour and source in some capacity, for MERS-CoV, or MERS-CoV-very-like, infections ticking over around the Arabian peninsula. All in the space of a week!

First up, Hemida and colleagues from Saudi Universities, China and the United States describe the search for neutralizing antibodies in animals in a 12-Dec Eurosurveillance article. Great to see Saudi Uni researchers involved. I've mentioned this virus neutralization assay and its intent before. This new study builds on that from Perera and colleagues who looked at camels and some other animals.

Some major findings from this study include:

  • Dromedary camels (n=310), sheep (n=100), goats (n=45), cattle (n=50) and chickens (n=240) from MERS-CoV hotspots in Saudi Arabia (Riyadh and Al Ahsa) were tested with the pseudoparticle neutralization (ppNT) test
  • 280 camel sera (90% of camel sera) were positive using the MERS-CoV ppNT test. No other animal sera reacted in this test
  • 96% of camels had MERS-CoV (or a close relative)-reactive antibodies by 1-year of age; two-thirds of camels that were younger than 1-year of age reacted, which suggests acquisition of these infections accrues rapidly during that 1st year, or maternal antibodies remain in the offspring
  • 54 randomly selected camel sera (18% of all camel sera) were diluted out and tested using ppNT and a standard MERS-CoV microneutralization test (MNT). High levels of calf antibody specific to BCoV did not block MERS-CoV infection nonetheless there were some similar titres to both viruses in some of the camel sera. A ≥4-fold higher amount of antibody reactivity towards 1 virus compared to the other defined which was the most likely virus reacting. It's possible (likely?) that camels have "seen" (been infected by) both viruses or similar viruses at some time. Some of the subset of camel sera had high levels of antibody only to MERS-CoV (or a close relative)
  • Cows did not have any sign of MERS-CoV-reacting antibodies in their sera; they did have BCoV reactivity though
  • It was not stated whether the camels were ill or healthy at sampling
So other animals were not neutralising-antibody positive but young Saudi camels, like Omani, Spanish [retired to the Canary islands] and Egyptian camels before them, had acquired and reacted to infection by MERS-CoV (or a close relative) according to these validated antibody-detection tests. Regular sampling of an animal cohort is one suggested future direction.

Secondly we have Reusken and colleagues from the Netherlands, Jordan and Germany look at animals from the first known site to harbour MERS-CoV infections in April 2012 at a hospital in Zarqa city in Jordan. This was published online 12-Dec in the same issue of Eurosurveillance. Just fyi, Prof Marion Koopmans is senior author on this study and on the study below.

Some of the key points include...
  • Sera from 3-14-month old dromedary camels (n=11), goats (n=150), sheep (n=126) and cows (n=91) were tested by an antibody microarray method, used previously by this group, and the results confirmed by identifying antibodies with the ability to neutralize MERS-CoV infection.
  • The lower levels of antibody than seen in an earlier study may reflect leftover maternal antibody protection, although the authors note than maternal camel antibodies wane within 2-months of birth and that adult camels had higher levels of antibodies
  • This study cited a reference noting that apart from cows, camels, goats and sheep are major sources of meat and milk in the region, ~1 sheep/pilgrim or ~1 camel/7 pilgrims is slaughtered in Saudi Arabia for the Hajj which equates to ~3,000,000 animals!
  • 11/11 camel and 6/126 sheep sera had antibodies that reacted with MERS-CoV but, in additional testing, the sheep sera were not able to neutralize infection by MERS-CoV
  • 23/91 cows and 128/150 goat sera reacted with the human CoV, OC43 (antigenically related to BCoV); no sera reacted with SARS-CoV
  • A broadly reactive CoV, or "pancoronavirus", PCR method was used to screen camel faeces; 3 BCoV sequences were obtained, but no sign of MERS-CoV RNA in the faeces hinting that there was not an active infection at the time of sampling. This last point assumes that MERS-CoV is excreted from the camel gut during/after an acute infection. The next study may not support that assumption.
  • It was not stated whether the camels were ill or healthy at sampling
Add young camels from Jordan to those from Saudi Arabia, Oman and retired Spaniard animals as possibly having been infected by MERS-CoV (or a...you know, similar thing) or at least having antibody acquired from their mothers. 11/11 POS may yield some more data to narrow down the age of acquisition; 3-months and seropositive could suggest MERS-CoV acquisition at or very close to birth, or simply remaining protective maternal antibody. Perhaps camel farms and farmers should be a next stop for detailed testing. 

In an Editorial note, the Eurosurveillance Editors note that these data do not define the primary source for human acquisition is still unclear.

Thirdly we have Haagmans and colleagues from the Netherlands, Qatar and the United Kingdom describing the study of the Qatari farm camels and temporally related human infection, from which MERS-CoV was detected back in late November. This article was published online by the Lancet Infectious Diseases (17-Dec).

Some key findings here include...


  • The article's introduction suggests that the genetic diversity of human MERS-CoV viruses determined to date is the result of multiple zoonotic acquisitions 
  • This study started with a 61-year-old Qatari male (61M; FT#144) farm owner who had not travelled outside Qatar and his 23-year-old male (23M; FT#150) employee
  • 61M was RT-PCR POS (upE assay) on a sputum sample (collected Oct-13) and 23M on a throat swab (collected Oct-17) and subgenomic (ORF1b and nucleocapsid [N]) sequencing at the Public Health England confirmed the detection to be MERS-CoV
  • MERS-CoV genomic sequences from the 2 human cases were placed on GenBank and called Qatar_3_2013 [61M] and Qatar_4_2013 [23M] as were camel sequences from the subsequent experiments
  • Sera, rectal swabs and flocked nasal swabs were collected from all of the farm's 14 camels as well as 5 stool samples from 3 cages, by a team wearing personal protective equipment. Samples were shipped to the Netherlands for upE, N and ORF1a RT-PCR testing
  • Vero and Huh-7 cells were inoculated with swabs that had been added to viral transport medium onsite. A single culture from Camel#7 was upE RT-PCR positive at day-4 after inoculation but no culture yielded infectious virus
  • 5/14 camel nose swabs were MERS-CoV PCR positive using upE, N and ORF1a assays
  • Sequencing of a fragment of Spike gene yielded 100% identity with other Saudi MERS-CoV sequences; sequence only differing by 1 base from the original isolate, MERS-CoV/EMC.
  • All camel sera were antibody positive using an immunofluorescence test on MERS-CoV/EMC-infected cells
  • There was no "direction" to the acquisition of MERS-CoV. Whether the camels infected the humans or the humans infected the camels could not be determined from this outbreak
  • The authors conclude that detailed cases histories are important to identify animal exposures. These might not otherwise be though important in a cursory question and answer of a patient, their family or contacts
This study adds very important data that indicate a recent or resolving MERS-CoV infection in camels. No positivity was found from gastrointestinal samples. Despite no isolation of infectious MERS-CoV, the detection of RNA is an acceptable surrogate for the presence of "live" virus in an animal or person (even if it could not propagate in vitro). So the camel story has some very important new chapters added in this series of studies.

In a Comment in LID, Ferguson and Verkhove note how the One health concept is exemplified by not only this publication; as it has been by the entire MERS-CoV story. The comment also notes the need for much more study, passive and active surveillance of human and animal disease/movements and better and faster reporting to link these, or any other, animals back to the cases that are spread across a very broad geographic region. They hold Haagmans and colleagues' article up as an example of how to get more answers and prevent sustained MERS-CoV transmission among humans from developing in the future.

Tracing and testing camels imported into the region from Africa for use as food may also open a new front to identify the transmission potential of MERS-CoV (or a similar beastie) in camel infections. Testing of pneumonia causes at these other sites both for virus and antibodies against virus is probably also warranted. 

As usual, new data bring new questions and so many papers in only a week makes for lots of questions. 

Wednesday, 18 September 2013

MERS-CoV WHO testing guidelines: September update

The World Health Organization has updates its laboratory testing guidelines. They can be accessed here.

Some key points:

  • Lower respiratory tract samples are recommended since there are data to support higher viral loads (better detectability using PCR) from these samples
  • The upE real-time reverse transcriptase polymerase chain reaction (RT-rtPCR) assay of Corman et al is considered highly sensitive and is recommended for screening
  • The ORF1a screening assay is of equal sensitivity and the ORF1b slightly less sensitive than upE
  • RdRp and N gene assay are suitable for genotyping
  • Antibody testing assays are described and some seem to be very sensitive. none have been validated against a large panel of known MERS-CoV POS sera and result interpretation is still without consensus
  • Laboratories should notify their local public health authorities as soon as they receive a specimen for MERS-CoV testing and all results should also be passed along to these authorities.
  • Member States are asked to immediately notify WHO of initially POS laboratory results even before confirmatory testing is complete.
Pretty clear and straightforward really.

17 new MERS-CoV sequences bind perfectly to frontline screening PCR assay for MERS...

Click to enlarge. The primers/probe are depicted as grey boxes.
If mismatches existed they would show up as horizontal black
lines within the grey box. No mismatches are evident.
The GenBank accession numbers are
shown on the left of this alignment of 17 MERS-CoV
sequences.
Only 17 of the 45 sequences seem to include the region covered by the upE laboratory assay I just posted about in the WHO laboratory testing update but of those, the forward and reverse oligonucleotide primers and the probe all bind without any mismatch.

While that may sound like an obvious statement considering that these viruses were probably detected using that assay it isn't.

The new MERS-CoV sequences were determined using using unbiased 2nd generation high-throughput sequencing technologies that did not rely on these primers to generate them. So we are now able to check and see if there are any nucleotide changes at the target sites for the primers and probe, that would reduce the efficiency the assay.

There are no such oligonucleotide mismatches between primer and viral genes among those 17 sequences, which is good news for that assay's continued usefulness.

Built to last eh?

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

Monday, 2 November 2015

MERS in bats..what have we actually found so far?

Only 1 MERS-CoV sequence. In 1 bat.

That's the short answer.

Researchers found a Middle East respiratory syndrome (MERS) coronavirus (CoV) sequence in a bat. They've found lots of other coronavirus sequences in bats before and after that. Heaps of them. But from different CoVs. I'm not even sure how many dromedary camels (DCs) have tested positive for viral RNA or MERS-CoV-specific (as far as we know) antibodies.

One bat.

I'm deviating from the camel literature reviews for this post to go back to the paper that describes that one sequence found in that one bat. I had asked for a little more info on the paper from the authors but they are busy and I have little patience so I'll update this post if that information comes my way. Worthy of note is that some of the specifics about which CoV came from what sample and whether that was from a live bat or old dried faecal pellets can be a bit hard to decipher.

Oh, and I have posted on this paper before by the way:
  1. MERS-CoV genetic sequences found in Taphozous perforatus bat.(22AUG2013; [6])
  2. Taphozous perforatus - The Egyptian Tomb Bat.(22AUG2013; [4])
  3. MERS-CoVs: South African bats vs Saudi Arabian bats.(23AUG2013; [3])
  4. T.perforatus MERS-CoV strain sequence, and others, online...(26AUG2013; [7])
  5. A model of MERS-CoV acquisition (ver1).(30AUG2013; [7])
  6. Is there a better smoking bat or camel?(01SEPT2013; [5])
On to this post. The paper in question comes from Professors Memish, Lipkin and crew. Good pedigree. Sadly, not an ongoing collaboration.[1] The paper, in Emerging Infectious Diseases' November 2013 edition was entitled Middle East Respiratory Syndrome Coronavirus in Bats, Saudi Arabia.

The samples were tested by eight different PCR methods:
  1. A nested pan-CoV reverse-transcription polymerase chain reaction (RT-PCR; "pan"meaning an assay that theoretically detects all known and perhaps as-yet-undiscovered CoVs; assay called 'PLQ') targeting the RNA dependent RNA polymerase (RdRp)
  2. A nested pan-CoV RT-PCR assay (called WT-CoV) targeting RdRp region
  3. A semi-nested MERS-CoV RT-PCR assay (called EMC-SeqRdRp) targeting RdRp region
  4. A semi-nested MERS-CoV RT-PCR assay (called EMC-SeqN) targeting the nucleocapsid (N) region
  5. A nested pan-CoV RT-PCR assay (called NM-CoV) targeting the helicase region
  6. A nested MERS RT-PCR assay (called NM-HCOV) targeting RdRp region
  7. A semi-nested MERS RT-PCR assay (called NM-NSeq) targeting the N region
  8. A real-time RT-PCR (RT-rtPCR) assay (called upE [7]) targeting upstream of the E region
  9. An RT-rtPCR assay (called ORF1b) targeting the ORF 1b region.[7]
Samples included those from a known number of bats (some with multiple samples taken) and also samples of opportunity - bat faecal pellets that could not be matched to a bat so bat numbers could not be estimated. Samples were collected in two rounds (whether a MERS-CoV sequence or any other fragment of CoV RNA genome was identified, is indicated within brackets):
  1. The first in October 2012, shortly after the first human MERS case was identified in Bisha (the MERS-CoV variant represented by Human betacoronavirus 2c EMC/2012, complete genome, on GenBank as JX869059 [8]; 96 bats) 
    • 314 samples from which 8 (2.5% of samples; from 8 distinct bats I think) were positive for a CoV, 1 of which was MERS-CoV
    • 96 bats were tested encompassing 7 species...
      • Rhinopoma hardwickii (CoVs detected)
      • Rhinopoma microphyllum
      • Taphozous perforatus (MERS-CoV & other CoVs detected)
      • Pipistrellus kuhlii (CoVs detected)
      • Eptesicus bottae
      • Eidolon helvum (CoVs detected)
      • Rosettus aegyptiacus
      • From 29 T.perforatus bats in Bisha ruins...
        • 29 yielded throat swabs
        • 25 yielded faecal pellets (2 CoV positives; 1 yielded  a MERS-CoV sequence)
        • 8 yielded urine samples
        • 22 yielded sera
        • 10 yielded roost faeces samples (1 CoV positive)
      • From 25 E.helvum bats in Bisha town centre
        • 25 yielded throat swabs
        • 25 yielded faecal pellets (5 CoV positives)
        • 13 yielded urine samples
        • 19 yielded sera
      • From 3 R.aegypticus bats in Bisha town centre
        • 3 yielded throat swabs
        • 3 yielded faecal pellets
        • 1 yielded urine sample
        • 2 yielded sera
      • From 36 R.hardwickii bats in Naqi and Old Naqi
        • 36 yielded throat swabs
        • 35 yielded faecal pellets
        • 4 yielded urine samples
        • 15 yielded roost faeces samples
      • From 1 R.microphyllum bat in Old Naqi
        • 1 yielded a throat swab
        • 1 yielded a faecal pellet
      • From 1 E.bottae bat in Bisha ruins
        • 1 yielded throat swab
        • 1 yielded faecal pellets
        • 1 yielded urine sample
        • 32 yielded roost faces samples
      • From 1 P.kuhlii bat in Bisha ruins
        • 1 yielded throat swab
        • 1 yielded faecal pellets
  2. The second in April  2013 (mostly faecal pellets and samples; 14  bats)
    • 689 samples, 219 (31.8% of samples) positive for a CoV
    • 14 bats and a lot of faeces not associated with bats, were tested..
      • From R.hardwickii bats in Greater Bisha area
        • 209 yielded roost faeces samples (93 CoV positives)
      • From T.perforatus bats in Bisha ruins
        • 203 yielded roost faeces samples
      • From 9 P.kuhlii bats in Greater Unaizah area
        • 9 yielded throat swabs
      • From 5 P.kuhlii bats in Greater Riyadh area
        • 5 yielded throat swabs
      • Also from P.kuhlii bats in Greater Unaizah area
        • 263 yielded roost faeces samples (126 CoV positives)
So in total, 1,003 samples were tested and 1 MERS-CoV hit was returned while 226 other coronaviruses were confirmed by sequencing. The authors attribute the big difference between finding 8 CoVs in the October 2012 bat sampling (2.5% of samples) and 219 in the April 2013 sampling (31.8% of samples) to a cold chain failure after the arrival of samples back to the United States for testing. There were also fewer roost faeces samples in the October 2012 vs. April 2013 batch (52 vs. 472). No April 2013 T.perforatus bats, from which the October 2012 MERS-CoV sequence was obtained, yielded any CoV sequences. 

And what of that 1 MERS-CoV sequence? We don't know precisely which of the 8 PCR assays amplified it though (probably #3 or #6 above). We do know it's very short and that it could not be confirmed by other PCR assays. 

We know that to date there is no other bat CoV, anywhere, that has a sequence that is 100% identical to a MERS-CoV variant's sequence, except for the T.perfortaus faecal pellet sequence; not Neoromicia/PML-PHE1/RSA/2011 (but close), not Bat HKU4, Bat HKU5, Bat HKU9, and not Bat HKU10...just human and camel MERS-CoV variants. 

But it is of interest that two of these camel variants are called NRCE-HKU205 and NRCE-HKU270 from camels in Egypt. The sequence of these MERS-CoV variants in other places across the genome is relatively different from the majority of MERS-CoV variants from humans and camels. This may provide support for the existence of other different MERS-CoV variants out there, that look like the MERS-CoV we know in small parts of their genomes, but are otherwise quite distinct. And perhaps they reside in other camels outside the Arabian peninsula, or in bats. 

The T.perforatus faecal pellet sequence is a diagnostic sequence as far as we know. It most likely came from a MERS-CoV virus or a variant or ancestor we have not yet met. Or...a contaminant from someone or something else with a MERS-CoV infection of course. 

So, to all the people who continue to insist that bats are a current player in human cases of MERS, I suggest you organize some funding and do some collaborative bat testing because so far there is very limited evidence of there being a bat host for MERS-CoV. 

Just 1 MERS-CoV sequence. 

From 1 bat.

References...
  1. http://virologydownunder.blogspot.com.au/2014/02/coming-back-to-merserable-data.html
  2. Middle East Respiratory Syndrome Coronavirus in Bats, Saudi Arabia
    Memish ZA, Mishra N, Olival KJ, Fagbo SF, Kapoor V, Epstein JH, Alhakeem R, Durosinloun A, Al Asmari M, Islam A, Kapoor A, Briese T, Daszak P, Al Rabeeah AA, Lipkin WI.
    http://dx.doi.org/10.3201/eid1911.131172
  3. http://virologydownunder.blogspot.com.au/2013/08/mers-covs-south-african-bats-vs-saudi.html
  4. http://virologydownunder.blogspot.com.au/2013/08/taphozous-perforatus-egyptian-tomb-bat.html
  5. http://virologydownunder.blogspot.com.au/2013/09/is-there-better-smoking-bat-or-camel.html
  6. http://virologydownunder.blogspot.com.au/2013/08/mers-cov-genetic-sequences-found-in.html
  7. http://virologydownunder.blogspot.com.au/2013/06/new-mers-cov-genomes-dont-impact-on.html
  8. http://www.ncbi.nlm.nih.gov/nuccore/JX869059

Thursday, 12 June 2014

MERS-CoV in the blood....

The Middle East respiratory syndrome coronavirus (MERS-CoV) is, at its core, a respiratory virus. Well, as far as we know it is anyway. But, like other respiratory viruses (see an earlier post on rhinoviruses), MERS-CoV can be detected in the blood....a so-called "viraemia". In some cases this is identified in other virus infections in parallel with the viral load being generally high, perhaps indicating that virus is replicating beyond the body's ability to contain and control it at the site of initial replication. 

Perhaps, and MERS-CoV may be a good example of this, so-called extra-respiratory spread of a respiratory virus occurs when it has a penchant for blood vessel cells (they present its receptor in their surface, or have something in their cellular machinery that aids virus replication) or some other ability to specifically get beyond the respiratory tract. 

However it occurs, the result is a much wider spread of the virus around the body; blood being something that is widely traveled! We already know that MERS-CoV has a love for growing in kidney cells so extra-respiratory spread may create a perfect storm for delivering this little bomb to a site where it can create even more havoc than in our airways. If those kidneys are already a bit bashed about, say by diabetes, then the blast radius is perhaps increased that much more.

A new paper just out in Emerging Infectious Diseases [1] is the latest to highlight viraemia, or pedantically because its viral RNA in the blood, RNAemia and its role in detection of MERS-CoV.

A lower respiratory tract (LRT) sample (bronchoalveolar lavage; BAL) was collected from a 66-year old man (66M) who returned to Tunisia after after a 5-week visit (20-March to 28-April) with his daughter in Qatar, interspersed with a pilgrimage to Mecca (Makkah; 27-March to 04-April) in the Kingdom of Saudi Arabia (KSA). 

66M arrived back in Tunisia 28-April with an acute respiratory illness which progressed and from which the LRT sample was collected. A subsequent X-Ray identified cellular infiltrates in his lungs. His 30-year old daughter (30F) stayed in Qatar. His 34-year old son (34M), a nurse, cared for him both at home and later in the intensive care unit as his disease progressed, eventually ending in his death from multi-organ failure. He was buried 13-May and his daughter returned from Qatar for the funeral. 66M's LRT sample was not positive for MERS-CoV and he had no other respiratory viruses (not detected using PCR testing which may have been more appropriate). His daughter and son were positive for MERS-CoV so 66M was described as a "probable" case (travel, signs & symptoms, and at least subsequent contact with MERS-CoV cases). The incubation period for his illness placed 66M in Qatar at the likely time of acquisition of virus and his son was likely to have acquired his infection from his father in Tunisia. The daughter may have acquired the virus from her father while he was in Qatar or from a related source in Qatar (but seems to have been a Qatar-related acquisition of some sort). 66M's wife, 2 other well children and his son's wife were not MERS-CoV positive 5-weeks later (but then they were unlikely to have tested positive so far out from the event). 

Afterwards the US CDC tested a serum sample (tested 5-August-2013, blood taken 9-May-2013) by reverse transcription real-time polymerase chain reaction (RT-rtPCR), and it was positive. Thus - the cluster is resolved. Got a better appreciation for the amount of work that goes into tracking this stuff down in detail?

But this was not the first time a MERS-CoV diagnosis was obtained retrospectively, or as part of a study, using RT-PCR (conventional or real-time) on serum (cell free blood) rather than a respiratory tract sample. Yet remember that the presence of viral genome (or bits thereof) identified by RT-PCR does not guarantee that infectious virus was in the blood, only that viral RNA could be detected there.
  • Case No. 1 from the original hospital cluster of MERS cases in Al-Zarqa, Jordan in March-May 2012, was identified thanks to retrospective RT-rtPCR (CDC version) on a convalescent serum sample.[2] 
  • The 2 French MERS cases (1 imported, 1 locally acquired from contact) had RNA in their blood (UpE RT-rtPCR); the patient who died was positive for at least 4-weeks while the surviving patient cleared viral RNA in the 1st week after symptom onset.[3] 
  • Two cases imported into the Netherlands from the KSA were found to have viral RNA in their blood for days; Case #1 from day-0 after diagnosis until at least day-9 and Case #2 from day-1 until at least day-5.[4] In this study viraemia outlasted virus detectability in the faeces but was detected for as long as virus in throat swabs of Case #1. RNA was not detected in the urine.[4]
Serum may be a useful sample, not just to determine whether antibodies to MERS-CoV develop(ed), but to help detect MERS-CoV RNA, as a surrogate for infectious virus, when a respiratory sample is not available. 

The finding of MERS-CoV RNA in the blood so frequently, among those studies that have looked, may also indicate it is a useful marker of disease severity as seen in the French cases. Serum is already a sample recommended for collection for antibody studies.[5] Let's see if these papers can trigger a little more looking back at those samples, which are hopefully stored in freezers somewhere. 

Anything that helps nail down "probable" cases and better define the pathogenesis of MERS-CoV is a good thing. 

Some typos & grammar corrected 05MAR2015

References.... 

  1. Family Cluster of Middle East Respiratory Syndrome Coronavirus Infections, Tunisia, 2013 http://wwwnc.cdc.gov/eid/article/20/9/14-0378_article.htm
  2. Novel coronavirus infections in Jordan, April 2012: epidemiological findings from a retrospective investigation
    http://applications.emro.who.int/emhj/v19/Supp1/EMHJ_2013_19_Supp1_S12_S18.pdf
  3. Distinct Immune Response in Two MERS-CoV-Infected Patients: Can We Go from Bench to Bedside?
    http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0088716
  4. Middle East respiratory syndrome coronavirus (MERS-CoV) infections in two returning travellers in the Netherlands, May 2014
    http://www.eurosurveillance.org/images/dynamic/EE/V19N21/art20817.pdf
  5. http://who.int/csr/disease/coronavirus_infections/MERS_Lab_recos_16_Sept_2013.pdf?ua=1