Virus Diseases: May 2014

Saturday, May 31, 2014

The International Health Regulations (IHR) 2005...

I've heard a lot about the IHR but I have not read the entire document.

This post is just to note which States are considered to be a party to them and what they mean in general terms.

A blog-friendly reformatted excerpt from the Foreward (highlighting is mine)...

"The purpose and scope of the IHR (2005) are “to prevent, protect against, control and provide a public health response to the international spread of disease in ways that are commensurate with and restricted to public health risks, and which avoid unnecessary interference with international traffic and trade.” The IHR (2005) contain a range of innovations, including:

(a) a scope not limited to any specific disease or manner of transmission, but covering “illness or medical condition, irrespective of origin or source, that presents or could present significant harm to humans”;
(b) State Party obligations to develop certain minimum core public health capacities;
(c) obligations on States Parties to notify WHO of events that may constitute a public health emergency of international concern according to defined criteria;
(d) provisions authorizing WHO to take into consideration unofficial reports of public health events and to obtain verification from States Parties concerning such events;
(e) procedures for the determination by the Director-General of a “public health emergency of international concern” and issuance of corresponding temporary recommendations, after taking into account the views of an Emergency Committee;
(f) protection of the human rights of persons and travellers; and
(g) the establishment of National IHR Focal Points and WHO IHR Contact Points for urgent communications between States Parties and WHO."

This was taken from the PDF of the IHR2005 [1]

References...

International Health Regulations 2005
Second Edition
http://whqlibdoc.who.int/publications/2008/9789241580410_eng.pdf?ua=1

MERS-CoV detected in 21st country....no party ensues

Algeria has reported 2 cases of MERS-CoV infection among two men (66 and 59-years of age) returning from performing Umrah in the Kingdom of Saudi Arabia (KSA).[1,2]

No indication of any local transmission as yet. Seems the pilgrims arrived with signs and symptoms of disease so, as Crawford Kilian asks[6], just how carefully are authorities at KSA exit points examining departing people for signs of respiratory disease?

Click on image to enlarge.

While we await confirmation that all the laboratory "I"s have been dotted and "T"s crossed, I wonder if there was any camel/animal contact or if these men visited a hospital while there? If the answer to these questions is no, then we're left to suspect that there may be a lot more community transmission going on than we are getting wind of.

Daily total MERS-CoV detections have dropped to low levels and healthcare worker involvement no longer noted (i. because there are none or ii. because profession is no longer considered valid demographic detail for public consumption), so if not from animals or hospitals...then from where?

Less speculative is that we're also waiting on scrubbed detail from the WHO on hundreds of KSA cases, a Philippines case and detail about what is happening in Iran too. We've been waiting a while for some of that.

hat-tipping @crof, @Fla-Medic and @FluTrackers

References...

Snapdate MERS-CoV chart update

Just a quick look at some updated Middle East respiratory syndrome coronavirus (MERS-CoV) detection figures.

For 2-days this past week we had zero cases reported, but we still had a number of deaths. On the 27-May alone there were 5 deaths across 3 regions.

Weeklies chart.
Number of lab-confirmed cases on the left upright (y-axis), the cumulative weekly
average can be read from the right y-axis and the bottom (x-axis) lists data by week, usually week when signs & symptoms onset otherwise by hospitalisation date or
reporting if nothing else is available.
Click on image to enlarge.

The dailies chart shows that detections have reached zero. Been a while since that happened-earl April was the last time. This will possibly change as cases from coming days fall out with onset dates in this week.
Or perhaps there won't be any cases in the coming week. We can only hope.

Dailies chart.
Number of lab-confirmed detecteions on the left y-axis and the x-axis lists data by day,
usually day of when signs & symptoms onset otherwise by hospitalisation date or reporting
if nothing else is available.
Click on image to enlarge.

I haven't added a healthcare worker (HCW) to my line list for the past 63-detections. That's the longest period without an HCW in the history of MERS! Is that true or are those data now withheld form the Kingdom of Saudi Arabia's numbers? Don't know. But here's what it looks like as yet another healthcare-related outbreak subsides.

Cumulative number of lab-confirmed detections among HCWs on the left y-axis while the right y-axis shows the proportion of MERS-CoV detection who were HCWs that week. The x-axis lists data by week, usually day of when signs & symptoms onset otherwise by hospitalisation date or reporting if nothing else is available.
Click on image to enlarge.

Thursday, May 29, 2014

The MERS week in snapshots...

MERS-CoV in the Netherlands...a detail analysis of cases

Red arrow indicates where Dutch
MERS-CoV case sequences sit.
Click on tree to enlarge

This comes from a shiny newly released Eurosurveillance report from Dutch researchers.

I've marked up my earlier tree to show where (based on partial 4,000nt fragment) the sequence from the Netherlands MERS-CoV positive cases (near identical) sits.

I've also charted Case 1's laboratory testing course, to show the variability of virus detection when a very thorough sampling and testing investigation is conducted.

Viral RNA remained detectable in the blood for all days tested demonstrating viraemia (well, RNAaemia technically) from day-4 onwards. Urine was not positive but a faecal sample was, on day-5. The latter has implication for infection control in hospital settings whereby flushing toilets creating aerosols could be another contributor to spread.

Reverse transcription real-time polymerase chain reaction (RT-rtPCR) results are shown as positive (tall bars), negative (stumpy bars) or not tested (empty space) plotted against day of sampling.
Click on image to enlarge.

This is, as far as I'm aware, is only the second time human faeces or urine have been found to contain signs of MERS-CoV.

A throat swab was positive early on and then again after a 2-day period of negativity. This points to the possibility of shedding for over a week, when associated with cough. But given that this case was part of a tour group and they didn't all become symptomatic, MERS-CoV still didn't spread efficiently or result in disease very often (if it did spread), for whatever reason(s). Antibody testing would be interesting here too.

It would also be very interesting to know whether virus was being shed during the initial diarrhoea in Case 1, which predated his return to the Netherlands by about 8-days, or whether that was unrelated to the MERS-CoV infection. Perhaps testing faeces for gastrointestinal viruses would be useful, or interesting, here.

Updated MERS-CoV full genome tree...

With thanks to @arambaut for some tips, and for tying my home computer up for 2-days running PHYML on the sequences (super-computer it ain't) - this is a slightly more robust tree of the MERS-CoV complete (or near-complete) genome nucleotide sequences published to date. This follows from my previous post and tree here.

Very little from 2014 despite the majority of MERS-CoV variants circulating then. But of course we have to wait because next generation sequencing is the main way we roll with MERS-CoV.

Alignment of 56 complete or near complete MERS-CoV genomes and an Egyptian divergent variant from a camel. Alignment made using Geneious v6.1.7. The PHYML v2.2.0 plug-in was added to make this tree, using 1000 bootstraps. Red stars indicate
virus which is reportedly from the same patient (seems doubtful). Vertical bars to the right indicate Clade A (dark blue) and B (pale blue). Sequences from the the 2013 Al-Ahsa hospital outbreak are boxed in pink; from the Jeddah 2014 hospital outbreak in blue; from the Hafr Al-Batin community cluster in green. Camel icons indicate genomes from camel variants for MERS-CoV. GenBank accession numbers are indicated at the end of each sequence name which also includes region of detection, host (human if not specified) and year of sample collection.
Click on image to enlarge.

The tree really highlights how remarkably interwoven the camel and human MERS-CoV genome sequences are; remembering that these 30,000nt genomes don't differ from each other by more than 1% at the nucleotide level.

Some new sequence analyses from the Netherlands cases should be coming out in the next issue of Eurosurveillance so get a tab ready and keep hitting refresh. Or, ya know, go get a life or something (I'm hitting refresh).

Wednesday, May 28, 2014

Updated MERS map moves stars around....

This new version adds a blue star to Iran, as it seems likely there has been some local transmission.

That star has been taken away from the USA (it's been a bad boy) since there has now been no sign of local transmission after the overnight retraction of the Illinois man's positive antibody test result.

Click on image to enlarge.

MERS-CoV did not just transmit via 2 meetings and a handshake...the retraction [UPDATED with CDC Press Release]

There must be a couple of internally relieved people around the US CDC today. Relieved. Why? Because they have got off their chest something they must have had a growing inkling about for at least a few days now. That being the news result that the Illinois 3rd US case was in fact not infected by MERS-CoV via a handshake and 2 meetings, 1 lasting 40min.

So that didn't happen.

And the implications for much simpler transmission of MERS-CoV did not result. And that all kinda makes more sense in the broader scheme of things MERS-related. This result always looked like an outlier.

Additional lab tests indicate IL resident wasn’t infected by IN MERS patient. No evidence of spread of #MERS in US.
— Dr. Tom Frieden (@DrFriedenCDC) May 28, 2014

Not a fun thing to have to report. Kudos to the team though for going back to correct an error. MERS reporting could definitely do with some more dynamic editing, and ownership, of it's mistakes.

That said, for the life of me this morning, I cannot work out why the CDC announced part of the antibody (Ab) testing result without having put such an important preliminary piece of diagnostic information, with so many epidemiological implications, through an even more rigorous testing pipeline first. I had certainly assumed that had happened when I previously wrote in support of antibody-testing on the back of this result over a week ago...and made note that that hiccups in the Ab testing process could follow!

Let's look at what we know publicly about this test method. The CDC team have published 2 different papers [1,2] where they use an enzyme-linked immunosorbent assay (ELISA) first (the same one as used in the Illinois case I presume), then confirmed those results with either an imunofluorescence assay (IFA) or a virus neutralization (NT) test. The latter is the most specific method of showing that the MERS-CoV antibodies in a patients serum, if present, can block, or "neutralize", the ability of a virus to infect permissive cells in the lab. However, there has been a previously recorded issue with sera from SARS-CoV positive people cross-reacting in a MERS-CoV neutralization test. [3]

So the 2 papers have the following definitions relevant to antibody testing (my highlighting).

In the study of a possible MERS-CoV related stillbirth, the CDC team used the definition..

"MERS-CoV antibody positivity was defined as having positive a serologic result from the HKU5.2N Enzyme Immunoassay (EIA) and a correlated test-positive result from either the MERS-CoV Immuno-fluourescent assay (IFA) or MERS-CoV microneutralization titer assay (MNt) developed at CDC."[1]

*The HKY5.2N is a bat CoV antigenically related to MERS-CoV.

When they went back to the original Jordan cluster from 2012, the same definition was used..

"To maximize specificity, we defined MERS-CoV antibody positivity as subjects having correlated, positive laboratory results from the HKU5.2N screening ELISA as well as confirmed positive results by either the MERS-CoV immunofluorescence assay (IFA) or the MERS-CoV microneutralization assay (MNT)."[2]

What we know in the Illinois retraction story is that the IFA results did support the ELISA (less specific test) results (both were positive) before that result was announced.[4] They were clearly not supported by virus-specific MNT though. So the definitions above will need to be changed, perhaps to include all 3 results for a definitive answer or definitely have MNT in the tetsing mix somewhere. This has an impact on a result from the Jordan retrospective study[2] since 1 of those "positive" cases was defined using only ELISA and IFA-reactive without support from MNT (see Outbreak member 11; Table 1).[2]

Oh well. Just goes to show, no-one is perfect and everyone is subject to a little hysteria when the pressure is on.

I've gone back to strike-through the text relating to this retraction in my previous posts (might take me a little while to complete). I'm leaving the text in place as it was, but adding new comments in red. I've also deleted this line from my personal MERS-CoV line list.

While this sadly incident does nothing to help people trust antibody testing in the future, at least for MERS-CoV, the literature for MERS-CoV antibody testing contains good examples of well-validated assays that require and conduct multiple tests to yield robust results. I still think rigorously determined positive antibody test results should still be considered as valid indications of a MERS-CoV positive result. Clearly not in this instance because this seems to be a pipeline "in process".

References...

Stillbirth During Infection With Middle East Respiratory Syndrome Coronavirus
http://jid.oxfordjournals.org/content/early/2014/02/17/infdis.jiu068.full
Hospital-associated outbreak of Middle East Respiratory Syndrome Coronavirus: A serologic, epidemiologic, and clinical description
http://cid.oxfordjournals.org/content/early/2014/05/14/cid.ciu359.short
Cross-reactive antibodies in convalescent SARS patients' sera against the emerging novel human coronavirus EMC (2012) by both immunofluorescent and neutralizing antibody tests.
http://www.ncbi.nlm.nih.gov/pubmed/23583636
CDC concludes Indiana MERS patient did not spread virus to Illinois business associate
http://www.cdc.gov/media/releases/2014/p0528-mers.html

Monday, May 26, 2014

Iran reports 2 MERS-CoV cases: 20th country [UPDATED]

Click on map to enlarge.

Head of Communicable Disease Control (CDC) at the Iran Ministry of Health (MOH), Dr. Mohammad Mahdi Reports seem to indicate 2 sisters, one critically ill, have been confirmed as cases and 2 suspected cases, perhaps family members, are being observed/investigated for MERS-CoV.

I'll await the WHO report (which will hopefully appear soon) with more details but what we have so far suggests local spread, so the pink (unknown origin of case acquisition) will change to another colour of some sort, in the future.

The WHO were awaiting official notification from Iran's MOH about 10-hours ago.

@HelenBranswell Aware of reports on this, but have not receive official notification as per International Health Regulations (IHR)
— WHO (@WHO) May 26, 2014

A story from AFP [7] notes that the 2 sisters are being treated in the same hospital in Kerman, where they were believed to have acquired their infection from a pilgrim returning to Iran from Saudi Arabia. No mention of whether that pilgrim was tested and found to me MERS-CoV positive.

h/t to @Malaekeh and @HelenBranswell for alerting us to the CDC report.

Resources...

Crawford Kilian's post..
http://crofsblogs.typepad.com/h5n1/2014/05/iran-reports-first-mers-cases.html
MOH announcement..
http://www.behdasht.gov.ir/?siteid=1&fkeyid=&siteid=1&pageid=127&newsview=108713
FluTracker's thread..
http://www.flutrackers.com/forum/showthread.php?t=223788
Treyfish's post
http://swineflumagazine.blogspot.com.au/2014/05/iran-identification-of-novel-virus-2.html
Mike Coston's post..
http://afludiary.blogspot.com.au/2014/05/irans-moh-reports-2-mers-cases-testing.html
PressTV - English detail
http://www.presstv.ir/detail/2014/05/27/364327/iran-confirms-two-cases-of-mers/
AFP Report
http://www.interaksyon.com/article/87818/iran-reports-first-2-mers-cases

Camels and MERS: links to peer-reviewed scientific literature...[UPDATE #1]

Add caption
Camels at the centre, aerosol all around...

I thought this might be a useful page for anyone who would like to know just how much data has been generated that supports a link between camels and MERS-CoV, and studies that have shown near identical viral genomes from camels, and the humans in contact with them.

Its also worth nothing only 1 ~180nt PCR fragment from 1 bat in 1 study has had a MERS-CoV sequence detected in it and yet they are still considered the most likely ancestor of the MERS-CoV because bats seem to be the ancestral source of many CoVs.

No studies have found MERS-CoV or infection-blocking (neutralizing) antibodies to MERS-CoV in any non-human or non-dromedary camel animal despite investigation of:

horses
llamas
alpacas
bactrian camels
guanaco
goats
sheep
water buffalo
cows
birds
pigs
chickens

While rats and mice have not been tested in the wild, deliberately inoculated lab mice and Syrian hamsters do not support growth of MERS-CoV and 2 rat cell lines (Chan et al. J Infect Dis. 2013;207:p1743-52) did not support viral transcription or growth. Not the end of the small animal story of course and more testing of small animals is a good thing, but neither has the camel story been completed yet (finding infectious virus in milk, urine and meat and some air sampling and testing from around camels would be nice). However, the camel story does already have some very solid chapters suggesting humans could be coming into sporadic contact with the virus.

So a few quick thoughts to put camels in context with sporadic infections that are not traceable to contact with a known human case.

I don't think any scientist has ever suggested every camel is carrying/shedding MERS-CoV all the time. Nothing supports that.
Most MERS-CoV cases have been from spread between humans and most of those are now linked with hospital-based settings (thanks Jeddah outbreak!). Whether community spread is ongoing is completely unknown until someone tests the community, post-Jeddah outbreak, and not people linked to hospitalized confirmed cases (they only bias the results).
As we saw in 2nd and 3rd US MERS-CoV detections, 2 face-to-face business meetings, 1 with at least 40-min of face time, and a handshake, was sufficient to pass along MERS-CoV between humans when the index case was not all that ill.

~~I hope the R0 guys can build this sort of event into their predictive models and~~
~~I think this has real and major implications for what "contact" with a~~ camel ~~actually means. I have serious doubts that people who are RT-rtPCR positive and being interviewed and asked about their exposure to camels would think of~~ being near a camel ~~as contact with camels.~~ Is ~~that how they are being asked?~~
THIS RESULT WAS RETRACTED 28-May-2014 FOLLOWING A NEGATIVE NEUTRALIZING ANTIBODY TESTING.

Better understanding the proximity-possibility needs experimental testing but in the meantime it is also very important for those who are asking infected people about their animal exposures and contacts to understand that respiratory viruses don't just spread by physical contact. I am unaware of what is being asked and in how much detail - this may already be well understood.

If people being asked about past contact with camels are thinking "hey, yeah, I was walking between camel pens for 20 minutes, but no I didn't kiss one or lick its nose or feed it or anything touchy-feely" (I'm 100% certain those would be exactly the words in their heads) - then they may well say "no contact". To my mind, that level of proximity in that example, especially if 1 or 2 of those camels was symptomatic, would be contact.

Anyway, do let me know if I've missed any papers below - or if new references come out.

Camels in the literature...

Reusken CB, Haagmans BL, Muller MA, Gutierrez C, Godeke GJ, Meyer B et al. Middle East respiratory syndrome coronavirus neutralising serum antibodies in dromedary camels: a comparative serological study. Lancet InfectDis 2013 October;13(10):859-66.
Perera RA, Wang P, Gomaa MR, El-Shesheny R, Kandeil A, Bagato O et al. Seroepidemiology for MERS coronavirus using microneutralisation and pseudoparticle virus neutralisation assays reveal a high prevalence of antibody in dromedary camels in Egypt, June 2013. Euro Surveill 2013;18(36):ii.
Hemida MG, Perera RA, Wang P, Alhammadi MA, Siu LY, Li M et al. Middle East Respiratory Syndrome (MERS) coronavirus seroprevalence in domestic livestock in Saudi Arabia, 2010 to 2013. Euro Surveill 2013;18(50):20659.
Reusken CB, Ababneh M, Raj VS, Meyer B, Eljarah A, Abutarbush S et al. Middle East Respiratory Syndrome coronavirus (MERS-CoV) serology in major livestock species in an affected region in Jordan, June to September 2013. EuroSurveill 2013;18(50):20662.
Haagmans BL, Al Dhahiry SH, Reusken CB, Raj VS, Galiano M, Myers R et al. Middle East respiratory syndrome coronavirus in dromedary camels: an outbreak investigation. Lancet Infect Dis 2014 February;14(2):140-5.
Alexandersen S, Kobinger GP, Soule G, Wernery U. Middle East respiratory syndrome coronavirus antibody reactors among camels in Dubai, United Arab Emirates, in 2005. Transbound Emerg Dis 2014 April;61(2):105-8.
Alagaili AN, Briese T, Mishra N, Kapoor V, Sameroff SC, Burbelo PD et al. Middle East respiratory syndrome coronavirus infection in dromedary camels in Saudi Arabia. MBio 2014;5(2):e00884-14.
Meyer B, Muller MA, Corman VM, Reusken CB, Ritz D, Godeke GJ et al. Antibodies against MERS coronavirus in dromedary camels, United Arab Emirates, 2003 and 2013. Emerg Infect Dis 2014 April;20(4):552-9.
Hemida MG, Chu DKW, Poon LLM, Perera RAPM, Alhammadi MA, Ng H-Y et al. MERS Coronavirus in dromedary camel herd, Saudi Arabia. Emerg Inf Dis2014;20(7).
Nowotny N, Kolodziejek J. Middle East respiratory syndrome coronavirus (MERS-CoV) in dromedary camels, Oman, 2013. Euro Surveill2014;19(16).
Raj VS, Farag EABA, Reusken CBEM, Lamers MM, Pas SD, Voermans J et al. Isolation of MERS Coronavirus form a Dromedary Camel, Qatar, 2014. EmergInf Dis 2014;20(8).
Corman VM, Jores J, Meyer B, Younan M, Liljander A, Said MY et al. Antibodies against MERS Coronavirus in Dromedary Camels,Kenya, 1992-2013. EmergInf Dis 2014;20(8).
Chu DKW, Poon LLM, Gomaa MR, Shehata MM, Perera RAPM, Zeid DA et al. MERS coronaviruses in dromedary camels, Egypt. Emerg Infect Dis 2014;20(6).

Camels and MERS: links to peer-reviewed scientific literature...[UPDATE #2]

Add caption
Camels at the centre, aerosol all around...

horses
llamas
alpacas
bactrian camels
guanaco
goats
sheep
water buffalo
cows
birds
pigs
chickens

I don't think any scientist has ever suggested every camel is carrying/shedding MERS-CoV all the time. Nothing supports that.
Most MERS-CoV cases have been from spread between humans and most of those are now linked with hospital-based settings (thanks Jeddah outbreak!). Whether community spread is ongoing is completely unknown until someone tests the community, post-Jeddah outbreak, and not people linked to hospitalized confirmed cases (they only bias the results).
As we saw in 2nd and 3rd US MERS-CoV detections, 2 face-to-face business meetings, 1 with at least 40-min of face time, and a handshake, was sufficient to pass along MERS-CoV between humans when the index case was not all that ill.

~~I hope the R0 guys can build this sort of event into their predictive models and~~
~~I think this has real and major implications for what "contact" with a~~ camel ~~actually means. I have serious doubts that people who are RT-rtPCR positive and being interviewed and asked about their exposure to camels would think of~~ being near a camel ~~as contact with camels.~~ Is ~~that how they are being asked?~~
THIS RESULT WAS RETRACTED 28-May-2014 FOLLOWING A NEGATIVE NEUTRALIZING ANTIBODY TESTING.

Reusken CB, Haagmans BL, Muller MA, Gutierrez C, Godeke GJ, Meyer B et al. Middle East respiratory syndrome coronavirus neutralising serum antibodies in dromedary camels: a comparative serological study. Lancet InfectDis 2013 October;13(10):859-66.
Perera RA, Wang P, Gomaa MR, El-Shesheny R, Kandeil A, Bagato O et al. Seroepidemiology for MERS coronavirus using microneutralisation and pseudoparticle virus neutralisation assays reveal a high prevalence of antibody in dromedary camels in Egypt, June 2013. Euro Surveill 2013;18(36):ii.
Hemida MG, Perera RA, Wang P, Alhammadi MA, Siu LY, Li M et al. Middle East Respiratory Syndrome (MERS) coronavirus seroprevalence in domestic livestock in Saudi Arabia, 2010 to 2013. Euro Surveill 2013;18(50):20659.
Reusken CB, Ababneh M, Raj VS, Meyer B, Eljarah A, Abutarbush S et al. Middle East Respiratory Syndrome coronavirus (MERS-CoV) serology in major livestock species in an affected region in Jordan, June to September 2013. EuroSurveill 2013;18(50):20662.
Haagmans BL, Al Dhahiry SH, Reusken CB, Raj VS, Galiano M, Myers R et al. Middle East respiratory syndrome coronavirus in dromedary camels: an outbreak investigation. Lancet Infect Dis 2014 February;14(2):140-5.
Alexandersen S, Kobinger GP, Soule G, Wernery U. Middle East respiratory syndrome coronavirus antibody reactors among camels in Dubai, United Arab Emirates, in 2005. Transbound Emerg Dis 2014 April;61(2):105-8.
Alagaili AN, Briese T, Mishra N, Kapoor V, Sameroff SC, Burbelo PD et al. Middle East respiratory syndrome coronavirus infection in dromedary camels in Saudi Arabia. MBio 2014;5(2):e00884-14.
Meyer B, Muller MA, Corman VM, Reusken CB, Ritz D, Godeke GJ et al. Antibodies against MERS coronavirus in dromedary camels, United Arab Emirates, 2003 and 2013. Emerg Infect Dis 2014 April;20(4):552-9.
Hemida MG, Chu DKW, Poon LLM, Perera RAPM, Alhammadi MA, Ng H-Y et al. MERS Coronavirus in dromedary camel herd, Saudi Arabia. Emerg Inf Dis2014;20(7).
Nowotny N, Kolodziejek J. Middle East respiratory syndrome coronavirus (MERS-CoV) in dromedary camels, Oman, 2013. Euro Surveill2014;19(16).
Raj VS, Farag EABA, Reusken CBEM, Lamers MM, Pas SD, Voermans J et al. Isolation of MERS Coronavirus form a Dromedary Camel, Qatar, 2014. Emerg Inf Dis 2014;20(8).
Corman VM, Jores J, Meyer B, Younan M, Liljander A, Said MY et al. Antibodies against MERS Coronavirus in Dromedary Camels,Kenya, 1992-2013. EmergInf Dis 2014;20(8).
Chu DKW, Poon LLM, Gomaa MR, Shehata MM, Perera RAPM, Zeid DA et al. MERS coronaviruses in dromedary camels, Egypt. Emerg Infect Dis 2014;20(6).
Ziad A. Memish, Matthew Cotten, Benjamin Meyer, Simon J. Watson, Abdullah J. Alsahafi, Abdullah A. Al Rabeeah, Victor Max Corman, Andrea Sieberg, Hatem Q. Makhdoom, Abdullah Assiri, Malaki Al Masri, Souhaib Aldabbagh, Berend-Jan Bosch, Martin Beer, Marcel A. Müller, Paul Kellam, and Christian Drosten. Human Infection with MERS Coronavirus after Exposure to Infected Camels, Saudi Arabia, 2013. Emerg Inf Dis 20(6) (online May 16).
Esam I. Azhar, Ph.D., Sherif A. El-Kafrawy, Ph.D., Suha A. Farraj, M.Sc., Ahmed M. Hassan, M.Sc., Muneera S. Al-Saeed, B.Sc.,Anwar M. Hashem, Ph.D., and Tariq A. Madani, M.D. Evidence for Camel-to-Human Transmission of MERS Coronavirus

NEJM June 4.
NB. This study is the same human case and camel herd tested in #14. Sampling times differ subtly.

Sunday, May 25, 2014

Jeddah changed the MERS-CoV age:sex landscape...

Note. Not every death or case is listed.
See bottom-left corner for breakdown.
Click on charts to enlarge.

I've broken down the age and sex in these charts.

As usual, it's mostly about males and older people until we get to the Jeddah outbreak.

In the top pair of charts (note the different scale used here compared to that used in the charts below) we see the breakdown for all MERS-CoV detections to date on the left and the fatal cases from among those on the right.
An apple in terms of people shapes.

In the middle pair of charts we look at all cases form 2012 up until the day before the Jeddah outbreak. The total case pyramid shows an older age bulge but the deaths look very similar to those for all fatal outcomes. M:F is similar to the total case charts above.

In the bottom pair of charts we're looking at what happened from the beginning of the Jeddah outbreak until now. We see a marked change in distribution with many more younger adults being positive for MERS-CoV. We also see a major shift towards more females than we'd seen beforehand. All the result of more widespread testing and a greater healthcare worker contribution I presume. Strangely though, given the younger adult demographic here, we see no accompanying jump in numbers of children. Are they not subject to testing? Are the younger adults often foreign workers who do not have children/children with them with them? There is no reason for children to test any less frequently MERS-CoV-positive and they are also just as likely as healthy adults to get mild or asymptomatic disease (as far as we know). If positive, children will have an important potential role in the MERS-CoV transmission story, especially when visiting elderly relatives.

The recent Al Qunfudhah teacher who is MERS-CoV just reinforces that children are shaping up to be a strange data gap. Yeah. I know. Another one.

MERS-CoV cluster in Al Qunfudhah...

5 cases in 4 days from a city we haven't seen prior MERS-CoV detection in (as far as I can tell) = a cluster.

The south western coastal city of the Kingdom of Saudi Arabia (KSA) is home to ~200,000 people[1].

While the cases have been asymptomatic when reported, the first, a 65-year old male (65M; was isolated at home [2]), came into contact with another case (see below) while at a government hospital. Which case that was and at what hospital, is unclear.

But there are other worrying issues here:

This city is in Makkah region, home to the 2 holiest Mosques and not a site in which anyone wants to see active spread of this virus again as we get closer to the Hajj; we don't want to see it spread anywhere at all of course.
FluTrackers has a thread on this (when don't they!?; my thanks to Sharon Sanders for pointing me to it) from 21-May and at least one of the 5 cases seems to be a teacher at a school in Al Quoz, 25 km south of Al Qunfudhah. No school-children have been reported positive to date though. The 4 cases after 65M were aged 25, 28, 25 and 45 - could some be teachers or are they all family of 65M? Family accompanied 65M to visit a relative in a Jeddah hospital (presumably the contact for 65M?). We no longer get any information from the KSA's Ministry of Health (MOH) about occupation, so one is left to guess...as usual. There seems to be mention of symptoms among some of these cases?
Could healthcare workers in Al Qunfudhah be among these younger asymptomatic (presumable) contacts of 65M?

This city may be seen written as Al Qunfudah, Qunfudah, Qunfutha, Kunfuda, Gonfodah or Gonfothah. I was helped out on the naming of this city recently - my thanks to @AmboceptorBlog

@MackayIM Arabic only has 3 vowels- usually translated A/I/U (each has short&long forms) This also depends on dialect. Short U -> O in Egypt
— Amboceptor (@AmboceptorBlog) May 22, 2014

Sources...

Saturday, May 24, 2014

MERS-CoV among healthcare workers: no longer identified or the end of a hospital cluster?

Just looking at @maiamajumder's vast array of MERS-related charts on Twitter and had a thought.

She and I and others have been wondering for a while if perhaps the Kingdom of Saudi Arabia's (KSA) Ministry of Health (MOH) reporting has decided to simply no longer identify healthcare workers (HCWs) as such. That would not be the strangest thing to occur with these data, believe me (deaths that have been "previously reported" that actually haven't, people who were discharged from hospital who were previously not described as being hospitalised, and of course, some instances of HCWs in KSA being identified as MERS-CoV positive by their country of origin and not by the KSA MOH). Perhaps not identifying HCWs is a way of attempting to stop pointing to what was a huge problem in infection prevention and control just last month?

But perhaps that is not entirely what is happening.

Perhaps there is another reason and there may be some precedent to support it; HCW numbers have in fact realistically decreased because they are no longer being infected as often. Why not? Perhaps because April's Jeddah hospital-based MERS-CoV outbreak is under control. Have a look at the chart below. Some things to note afterwards:

Click on image to enlarge

HCW numbers have stopped accumulating so rapidly. That mirrors total MERS-CoV detections of course. See some recent posts on the now receding wave of April's MERS surge here and here.
The precedent I mentioned? When the Al-Ahsa hospital-related outbreak stopped in May 2013, so did the number of HCW positives/week dropped away.
There have clearly been a bunch of other HCW peaks which may also have been related to hospital-clusters that were not so obviously publicised (I'll have a loo over this some time in the future). Those spikes of HCW infections have narrower bases and higher peaks than does the Jeddah outbreak, so perhaps that can be used as an indication of them being short-lived clusters that were better controlled than Jeddah. Not rocket science I guess and probably stating the obvious to the experts out there.
Infections in HCWs serve, as we already know, as a kind of sentinel system for identifying a spike in overall cases since more severe disease shows its face in hospitals and most likely represents the presence of other cases out in the community. His statement is much more believable now that we ;can look back and know that milder signs and symptoms of disease, or none at all, do not infrequently follow MERS-CoV infection).

I hope that our original hypotheses - that the KSA MOH has quashed identifying HCWs - was wrong. Heading towards Hajj-2014, it would be best to be polishing the very tarnished reputation of of the KSA MOH on matters ;of communication, not further damaging it.

Thursday, May 22, 2014

The impact of cell culture on virus as highlighted by deep sequencing..[UPDATED]

Alignment of complete or near complete MERS-CoV
genomes made using Geneious v6.1.7.
The Neighbor-Joining tree was made using MEGA with
1000 bootstraps. Red stars indicate virus from same patient.
Vertical bars to the right indicate Clade A (dark blue)
and B (pale blue). Sequences from the the 2013 Al-Ahsa
hospital outbreak are boxed in pink. GenBank
accession numbers are indicated at the end of
each sequence name which also includes region
of detection, host and date of sample collection.
Click on image to enlarge.

Just a quick post to note the difference that "passage" in cell culture (isolation of an infectious virus using lab cells inoculated with the original virus-positive patient material, some of which is taken off and added to a new flask of cells and this process repeated as needed) can do to the virus as it changes to grow most effectively in the new environment...this is akin to the adaptive changes seen when a virus first jumps to a an entirely different species.

Apparently the 2 starred (red stars in the figure) virus genomes are from the same 60-year old male patient [1,2,3; ] but the original variant, EMC/2012, was sequenced from material after 6 rounds of cell culture [3] while the Bisha_1 variant was not [1]; it was subjected to deep sequencing directly after nucleic acid preparation using an original respiratory sample aliquot (nasopharyngeal swab)[1].

Given that cell culture passage seems to be related to the positioning of EMC/2012 in Clade A versus Bisha_1 in Clade B (indicated by a pale blue line), does this mean there is no Clade A (dark blue vertical bar) and that it's just an artefact??

Probably not. Why? Because the Jordan-N3/2012 virus that is also found in Clade A and it also originates from a human specimen collected in 2012. It is listed as having been sequenced from a bronchial sample. There is no mention of cell culture on its GenBank record - which does not mean there was no culture. But when that sample was passaged through culture and sequenced (N3/2012 MG167; sequence not shown in this tree) it remained 99.95% identical to the original sequence; just 2 nucleotide differences out of 30,028nt. 1 difference in the spike gene and 1 Open Reading Frame 1a). These are unlikely to be enough to switch its clade but I'm realigning with this sequence included just to be sure about that!

I thought that was kinda interesting.

NB. There may be some concern over the specimen labelling used to identify samples for sequencing of EMC/2012 or Bisha_1. I'm attempting to sort our by following this up with the lead author.[1]

Reference...

Transmission and evolution of the Middle East respiratory syndrome coronavirus in Saudi Arabia: a descriptive genomic study. Cotten et al. Lancet 2012;382:1993-2002
60-year old man from Bisha who died in a Jeddah hospital (EMC/2012 variant)
Isolation of a Novel Coronavirus from a Man with Pneumonia in Saudi Arabia. Zaki et al. N Engl J Med 2012; 367:1814-1820
Genomic workup on EMC/2012
Genomic Characterization of a Newly Discovered Coronavirus Associated with Acute Respiratory Distress Syndrome in Humans. van Boheemen. mBio 2002; 3(6): e00473-12

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