Snapdate: MERS-CoV detections near 500...

MERS-CoV detection by day; Jeddah outbreak.
Click on image to enlarge.

Welcome to the beginning of MERS-CoV's 112th week (2.15 years). We sit at 497 cases (probably over 500 if the United Arab Emirates would confirm their cases with some extra data that made them more identifiable and "real". For now, I'm not including them after the recent issue around theUAE12. For now my count says at 497 with ~131 deaths (26.3%).

Judging by tonight's announcement of only 3 cases (only 1 with an onset date which was 24-Apr), let's hope this is the week where the Jeddah outbreak gets put to bed.

MERS-CoV detection by week 2012-present.
Click on image to enlarge.

Also, make this the week that the Kingdom of Saudi Arabia's(KSA) Ministry of Health adds some consistency to its releases. They've been doing a 100% improved job in the past weeks, adding much more detail, but it needs to be the same detail for every case, every day. And the listing of deaths and recovered cases is also great; but is currently not able to be linked to the original announcements so we don't know where they these people were from, comorbidities, HCWs etc as there are often 2 or more people from the same region with the same age. A date of affliction is needed to permit the linkage between original announcement and death/recovery. Just 1 more variable guys. Pleeease.

Nonetheless the dailies seem to be slowing, although the cumulative average still strolls upwards but in a linear, not exponential manner.

We stay tuned.

Ebola virus disease (EVD) West Africa update for 02-May, WHO-AFRO update...

Click on image to enlarge.

Thankfully the latest World Health Organisation update includes figures for Liberia. The last West Africa update did not, so I didn't post a chart.

Summary..

Total suspected/probable/confirmed cases: 244
Total suspected/probable/confirmed deaths: 162 (66.4%)
Total lab confirmations: 133 (54.5% of 227)

These figures are very important for two reasons...

Firstly they show a drop in suspect/probable cases after data scrubbing by the Liberian Ministry of Health and Social Welfare. This reinforces that the outbreak is being well controlled.;The date of isolation of the most recent confirmed cases is 30-April from Conakry and Guekedou (Guinea).

Secondly there has been a concomitant rise in the proportion of fatal cases of EVD due toZaire ebolavirus (see the percentages above the orange line in the chart). This is not because the numbers have jumped, it's because the denominator has shrunk for the relevant calculation:

No. EVD fatalities/No. total susp/prob/conf cases.

We've known this rise in proportion was coming because it was highly likely that case numbers would change as the dust settles and the susp/prob EVD patient numbers get discarded because they are found to be infected by something else; clinically similar disease, but not because of infection with Zaire ebolavirus. I've written about it previously if you'd like some background.

With the use of more antibody testing, the numbers will continue to change, as they always do in outbreaks.

This will be my last update on this outbreak linked to the WHO-AFRO announcements unless anything major happens.

A reminder - the chart above is made for general interest. It may be that I have misinterpreted the language in the report (sometimes a little tricky to wade through these reports) but the trends should still be informative even if a number or data point is out of place.


Sources...

1. http://www.who.int/csr/don/don_updates/en/
2. http://reliefweb.int/report/liberia/unicef-liberia-ebola-virus-disease-sitrep-20-2-may-2014
3. http://virologydownunder.blogspot.com.au/2014/04/ebola-virus-disease-and-lab-testing.html

MERS-CoV by month, now with added camels and hospital outbreaks...

Weekly case tallies for 20012-4 (blue-surviving 
and fatal cases; red-fatal cases). Also indicated 
are the season in which camels give birth (I've
noted "birthdays" because it seems to be 1-year
old or older camels that are usually positive for
MERS-CoV. Past and future Hajj pilgrimage 
dates are also shown as is 1 of several
large camel events in the KSA.
Click on image to enlarge.

While the World Health Organization is yet to produce confirmed case data for the majority of the MERS-CoV outbreaks' biggest month, some of those data and extra information are being provided by the Kingdom of Saudi Arabia Ministry of Health v2.0. 

And it's very welcome and much appreciated. There still remain some vagaries and data gaps that make consistency an issue. But further information is not forthcoming so let look at some charts of what we have. 

For now, we can see in the daily graph, 4-days into May, that cases are still being announced but at what looks like a slower rate. We are seeing cases reported with a lag of approximately a week from when they became ill/were hospitalised (when those dates are present).

A plot of cases per day. Many (?most) are based on dates of reporting although
more dates of illness onset have emerged lately and I am working through them. This means that the specific peaks may chop and change a little as dates are assigned. Nonetheless, the trend seems to be one of decreasing numbers per day and
the cumulative average may be suggesting a peaked for this KSA outbreak.
Click on image to enlarge.

MERS-CoV snapdate: detections by most likely region of acquisition...

Click on image to enalerge.

Just a quick check. 

Yup. 

MERS-CoV detections still rising in a linear and steep manner.

But we are nearly at the end of Week 111, and it has so far yielded (dates still to be finalised and largely based on dates reported) 42 detections compared to Week 110's 102 MERS-CoV detections. Things may well have started to slow down.

MERS in the USA....

The source of all exported MERS-CoV positive people lies within the Arabian peninsula. Very limited local spread has occurred within 3 non-peninsula countries.
Click on image to enlarge.

The Middle East respiratory syndrome coronavirus (MERS-CoV) made its way to another country yesterday; the United States of America (USA).

MERS-CoV in the KSA during April.
Filled red circles mark towns and cities for general interest.
The darker sandy coloured areas indicate KSA Regions
(also Egypt and the United Arab EMirates) where
MERS-CoV detections have been located recently.
Click on image to enlarge.

This is not a big surprise and it's not the end of days, but dude...it lit up Twitter and had reporters high-five'ing like nothing the 460 cases before it, mostly around the Arabian peninsula, managed to achieve. But then MERS-CoV detections have only been accruing for 111 weeks. 

These things can take time to warm up.

The USA case was in a healthcare worker (HCW) travelling back from the Kingdom of Saudi Arabia (KSA).

What else do we know?

• FluTrackers #456
• The HCW who was working in Riyadh, KSA, travelled back from there to Chicago in the USA via a transfer at Heathrow airport in the United Kingdom, 24-Apr.
• Illness became more noticeable 27-Apr (coughing, shortness of breath and fever), and the person was hospitalized 28-Apr in Indiana.
  Was less noticeable illness present first? We know little about what the earliest inklings that someone has a MERS-CoV passenger feel/look/sound like.
• Age and sex of the patient have not been officially released.
  I should stop complaining about that from the KSA Ministry of Health data. Still important to know it, but if its not provided by one high income economy, why expect it to be provided by any other?
• The laboratory confirmation was made 2-May (~4-days)

Because the person wasn't coughing, sneezing or noticeably wheezing on the planes, it will be unlikely that any virus was propelled towards, or impacted upon surfaces shared by, people nearby. We will of course be watching as the USA health professionals track, observe and hopefully swab and test at least some of the contacts from the planes and post-transit spaces. These people can tell us a lot about what the virus is doing among people not defined as "close" contacts; a kind of live experiment to check if MERS-CoV transmits any differently now than it did the last time it got loose from the Arabian peninsula. On those recent occasions neither Greece, Malaysia nor the Philippines saw any additions to the transmission chain.

I can remember when MERS and H7N9 cases were so rare I used to do a work up like this on each announcement. Ahh the good old (slow) days.

Sources...

1. http://www.cdc.gov/media/releases/2014/p0502-US-MERS.html
2. http://www.in.gov/activecalendar/EventList.aspx?fromdate=5/1/2014&todate=5/31/2014&display=Month&type=public&eventidn=169819&view=EventDetails&information_id=200566&print=print

MERS-CoV detected in asymptomatic people....

Maia Majumder has put by recent charting and charting efforts to shame. She is all over the latest Middle East respiratory syndrome coronavirus (MERS-CoV) numbers. So if you're not following her on Twitter or watching her charts on piktochart or her blog, Mens et Manus, then you may be missing the latest numbers as well as some interesting ideas and chats and some self-described wild guesses (one other letter to the acronym which I won't spell out here).

Maia has been covering some subsets of the MERS-CoV positive population of the Arabian peninsula of late; particularly to do with healthcare workers (which I also like to cover), those with comorbidities and those with no disease at all (asymptomatics) who are still in some way positive (PCR or antibody) for the MERS-CoV.

Click on image to enlarge.

So I've created a new chart for the asymptomatic detection of MERS-CoV. And it's interesting.

We can see more cases per week (blue line) being reported recently, and this naturally fuels a steep (but linear) climb in the cumulative tally (orange line) of asymptomatic detections. These are largely related to the Jeddah healthcare outbreak.

What's particularly interesting to me is what we see when we look at the proportions of cases each week that are described in the public domain as being asymptomatic.

Thanks again to Maia for a chat about the following definitions. Week #105 of the MERS epidemic contains the 1st case with "Jeddah" i its notes and an illness onset date of 22-Mar. Thus, we define the Jeddah outbreak (for now) as starting in the week beginning 17-Mar. We have seen 13-50% of cases in 5 of those past 7 weeks being described as asymptomatic (grey bars; this week not yet being complete).

Can this information be used to support thoughts that the virus and/or the way it is spreading, has changed? 
No. 
Why? 
Because this jump is not so different from the higher weekly proportions we saw in Sept-2013 and Dec-2013 (well before Jeddah). Oh, and because so far, there is no sign in the 3 complete genomes or 30 partial spike gene sequences that the Jeddah viruses are anything special. In saying that, keep in mind that we don't know how many cases are part of/linked to the "Jeddah outbreak". We do know of 245 distinct viral detections (31 fatal cases) made among humans since 22-Mar and so perhaps 3 genomes is not yet sufficiently representative for us to say there have been no viral changes at all, yet - if we even know what those changes will look like for the MERS-CoV.

As it stands, we are not seeing a disproportionate increase in MERS-CoV-positive people without signs or symptoms of disease. And that is good to know. It would also be good to know if asymptomatic people can shed MERS-CoV. The obvious answer is, no they cannot, because how would the virus get out of them? No coughing or sneezing means no easy way to excrete a respiratory virus. Perhaps there are short periods of signs that just get missed/forgotten/not reported? We do still need to test human urine, faeces, blood and saliva for infectious virus (virus that can be grown, not only identified by detection of its possibly non-replicating or contaminating nucleic acids). But I suspect that is all still a ways down the track.

So, as ever, we keep watching to see what the next few weeks bring to the knowledge base of MERS and the MERS-CoV...as we've been doing for over 110 weeks now.

What. The. Heck?

This is presented without comment...

@sheeraf @DJSiri @philipgeany @onlyonewowwow @DMashak @MackayIM Amazing how a PhD in PHILOSOPHY makes one an expert in microbiology
— Thea Goodman (@TheaGood) April 30, 2014

@MackayIM @philipgeany @sheeraf @DJSiri @onlyonewowwow @DMashak I suggest you read up on the new viruses but I see your forte is PHILOSOPHY
— Thea Goodman (@TheaGood) April 30, 2014

@TheaGood @sheeraf @DJSiri @philipgeany @DMashak @MackayIM PHD's are invariably arrogant know-alls, who live in vacuums,& just regurgitate -
— Wow (@onlyonewowwow) May 1, 2014

@TheaGood @sheeraf @DJSiri @philipgeany @DMashak @MackayIM someone else's discoveries ! VERY,VERY few have ever had an original thought !
— Wow (@onlyonewowwow) May 1, 2014

@TheaGood @sheeraf @DJSiri @philipgeany @DMashak @MackayIM And their worst & most destructive trait, is that they maintain the status quo !
— Wow (@onlyonewowwow) May 1, 2014

@TheaGood @sheeraf @DJSiri @philipgeany @DMashak @MackayIM PHD's are the modern day #Pharisees ! Just look at all the PHD's getting it

— Wow (@onlyonewowwow) May 1, 2014

@TheaGood @sheeraf @DJSiri @philipgeany @DMashak @MackayIM wrong, wrong & totally missing the obvious re economy, blinded by their one-trick
— Wow (@onlyonewowwow) May 1, 2014

@TheaGood @sheeraf @DJSiri @philipgeany @DMashak @MackayIM repetition, ala religious brainwashing, of Keynesian voodoo !
— Wow (@onlyonewowwow) May 1, 2014