Showing posts with label weekly cases. Show all posts
Showing posts with label weekly cases. Show all posts

Saturday, 3 January 2015

H7N9 outbreak #3 underway?

What better way to start 2015 than a snapdate!! For those who are new to them here on VDU, they were initiated here and defined here as snap updates - posts that don't have lots of detail and chat...although they almost always end up having lots of chat!

Figure 1. H7N9 cases by week of onset (or hospitalisation
or reporting dates of the preferred onset date was
not made public).
Click on image to enlarge.
This one is an update of the situation of one of the many avian influenza viruses ("bird flus" if you must) around again - avian influenza A(H7N9) virus, or just 'H7N9'.

In Figure 1, I've taken the huge liberty of adding in the start and end dates of the 3 outbreaks of H7N9 to date; and in doing so, I've said that China is in the early stages of one right now. I may well be wrong of course - this is a blog and these are my opinions - but it looks that way to me. 

Figure 2. China's northern laboratory network influenza
surveillance data up to Week 51 of 2014. [1].
Click on image to enlarge.
The case numbers for H7N9 in Figure 1 have been above zero for a little while and in particular November looked like a busy month (see weekly and monthly tallies here). Keep in mind that there is also a reporting lag - the time between date of onset (obtained from more detailed World Health Organization data) and the date the case was publicly reported (I rely on FluTrackers line list for these details). That delay can be a month or more on occasion; up to 38-days in late December. I suspect this is because China reports cases to the WHO in batches, something instigated toward the end of the 1st and 2nd outbreaks. So I suspect we will see more cases assigned to December, during reports that come out in January.

But it look like 'tis the season for influenza in humans in China (see figure 2 and the Chinese National Influenza Centre [2]) - and as some of us have discussed on Twitter, this is most probably due to the changes in weather (environmental conditions) which result in sustained viral survival on cough and sneeze-contaminated surfaces and in wet and dry propelled droplets and droplet nuclei; in both man and bird (see Hong Kong avian influenza detection report dates [3]). 

That sustained survival may well be all it takes for more of us to pick up an infectious viral dose.

Once the seasonal influenza viruses get a foothold in us, they spread well, causing disease in those who are susceptible and probably a bunch of unnoticed infections in those with previous exposure to that strain plus a healthy immune memory of that intrusion. By "seasonal influenza virus, I mean those that replicate in and circulate efficiently among humans, as opposed to the relatively inefficient avian subtypes.

So stay tuned to H7N9; it's not yet very good at spreading between humans but its established in birds and has been spilling over into humans since at least the beginning of 2013. We know how influenza can deal us a rough hand if the stars and its genetic segments align favourably (for it). Oh, and the continued reliance on fresh chicken obtained from and killed at live poultry markets. The majority of cases have very clearly had contact with poultry as defined by the WHO. 

References...

  1. http://www.cnic.org.cn/eng/show.php?contentid=738
  2. http://www.cnic.org.cn/eng/surveillance.php
  3. http://www.chp.gov.hk/files/pdf/global_statistics_avian_influenza_e.pdf

Wednesday, 16 July 2014

Middle East respiratory syndrome coronavirus (MERS-CoV) by week and month...

To follow up yesterday's daily numbers chart, here we have the number of MERS-CoV detections by week (Chart 1) and by month (Chart 2). 

Not a lot of change from my last posts of these 18-June and 23-June - we are currently in our 5th straight day without any new detections being reported - and prior to this drought, there had been very few other detections for a while so we can now very clearly see the Jeddah-2014 (Kingdom of Saudi Arabia) major hospital-base outbreak peak's beginning and end.

We're also in the second half of Ramadan, putting us past the maximum likely incubation period for those visitors to the holy places that may have acquired MERS-CoV infection at the beginning go the month. A pretty good indication that MERS-CoV is not spreading among the community. It is still strange to me that a region that was yielding sporadic cases up until very recently, is now not yielding any such cases. Perhaps it's the improvements initiated under Dr Fakeih's watch, or maybe the hot, dry weather? It could be that camel contacts are reduced or that festivals are not as frequent in the extreme heat.  It would be great to see some scientific literature emerge on the Jeddah-2104 outbreak, on seroprevalence, on camel testing, gene/genome sequencing, studies of other animals or transmission investigations. Things have been very quiet on the publication front for some time now and we still know very little detail about the largest flurry of (known) cases to have occurred since 2012.

We'll wait and watch and see, I suppose.

MERS-CoV detections, worldwide (but mostly in the Kingdom of Saudi Arabia), by week.
Click on chart to enlarge.


MERS-CoV detections, worldwide (but mostly in the Kingdom of Saudi Arabia), by month.
Note the yellow star which highlights a 10-fold higher scale for 2014 y-axis (left-hand side) than in the 2013 numbers. Even 2014's puny June surpassed any month in 2013.
Click on chart to enlarge.

Tuesday, 20 May 2014

MERS-CoV detections: The April wave recedes...

So welcome to the 114th Week of MERS-CoV among us. That week numbering may change shortly. Stay tuned if week numbering is your thing.

We currently have a tally of 649 detections of MERS-CoV or viral antibodies in humans. I don't list camel numbers. My count says 192 fatalities among infected people, resulting in a proportion of fatal cases of 29.6%. That seems high. Because, until very recently, the Kingdom of Saudi Arabia's Ministry of Health did not regularly report deaths alongside their date of illness onset, it has been an interesting hobby to try and link them. The number is solid so along as the MOH has not been doubling up in the reporting or coming back later to re-report deaths. You'll be familiar with these issues if you follow me on Twitter.

I made a point of saying antibodies earlier because I am going to be including these sorts of laboratory data in my tally when produced by trustworthy laboratories who have described their methods and shown some validation data and an understanding of what the cross-reaction issues are when dealing with MERS-CoV serology. This will be despite the current WHO MERS case definition not allowing for inclusion of people who only have antibody but no virus or viral RNA detected in their samples. There may be some hiccups with MERS-CoV antibody testing along the way, but we need these data in humans and it's good to see the wheels rolling on this at last.
[One of those hiccups occurred 28-May-2014, when the test result from an Illinois man who had originally tested positive in an Ab test, was retracted.]

In my estimation though, serology (the testing of human sera for antibodies against a virus here, the main target being IgG which takes a couple of weeks to become detectable after infection) is a much more reliable way of defining an infection by MERS-CoV virus than by relying on patient recall bias of symptoms 2-weeks ago, or from directly observing signs and symptoms that are nondescript and difficult to distinguish, alone. The latter approach has been the mainstay of identifying cases of human infection for a very long time; still is. This approach is especially important during times of outbreak and pandemic when labs are swamped by testing requests and it must be assumed that cases are due to the bug of interest; if it looks like a camel, slobbers like a duck and walks like a duck, then it is a MERS-CoV infection yeah? No. If you can clinically characterise and laboratory test then you will more often know the virus the patient has/had than if you don't test. But I'm sure that's clear to everyone anyway.

For MERS, as for H1N1pdm09 influenza and perhaps SARS, finding a reliable pathognomonic set of signs or symptoms capable of reliably distinguishing a respiratory virus of interest from another virus capable of the same disease is not possible. These viruses cause a spectrum of illness. Testing is paramount if you want to know what's there and to address other aspects relevant to public health during an infectious disease cluster/outbreak/pandemic. There are a couple of issues here (at least!)...

From a patient management perspective, who really cares what is making my patient very ill anyway? It really doesn't matter right now if it's this respiratory virus or that one; there are few vaccines and I don't have an antiviral for most of them anyway. I and my healthcare team are already taking respiratory infection precautions and I just want to direct my supportive therapy and resources to the problems they have, right? I'll be (well...you, experienced medical types of which I am not one) doing that before many lab results show up anyway. 

From the perspective of interrupting and understanding viral transmission however, nondescript signs and symptoms are a nightmare. And in the early days of a new virus where we seem to know very little about what path(s) transmission is taking (and perhaps we're also learning some more about those possibilities in general), any infection by whatever method it is empirically determined should, I believe, be recorded as an infection in order to provide the biggest picture possible; a process we have seen unfolding in the United States with its 2 3 detections (1 locally transmitted) of MERS-CoV or its spiky little footprints.
THIS RESULT WAS RETRACTED 28-May-2014 FOLLOWING A NEGATIVE NEUTRALIZING ANTIBODY TESTING.

Given that many viruses cannot be distinguished by signs and symptoms alone, a clinical diagnosis to define a case is less reliable than any pathogen-specific laboratory test. I hope the WHO alters their case definition in the near future. Infectious disease is always teaching us - seems we learned a heap from SARS but even the relatively a few cases of MERS are presenting interesting issues and testing us in new ways. 
[While the US antibody-positive result above has since been retracted, I stand by these comments-Ab testing requires rigor, but that can be provided using several assays and applying a good understanding of Ab technologies and limitations to produce reliable results]

Anyhooooo...been stewing on that for a few days apparently. Let's move on and have a look at the 3 updated charts below. 

We are definitely through to the other side of the Jeddah outbreak (see weeklies chart). While cases do keep accruing each and every day (see dailies chart from 20-March), the downward trend of smaller numbers of illness onsets each day also continues. 

Weekly MERS-CoV detections.
Click to enlarge.

Daily MERS-CoV detections from 20-March.
Click to enlarge.

For perspective on the size and the influence of what 1 hospital cluster can turn into and how that can influence how a virus "looks", take a gander at the extent of the April outbreak. Case are still falling out into April as we get more data. If you look at the monthlies chart at the bottom, I've readjusted that y-axis scale again such that it's maximum value is now 10x higher (350 vs 35) than the scale used for 2012 or 2013's charts. May's tally is currently 4x greater than any month from 2012 or 2013. 

What does MERS-CoV hold for us in the coming months? 

Daily detections of MERS-CoV, 2012-current.
Click to enlarge. 

Monthly detection of MERS-CoV 2012-current.
Click to enlarge.


Monday, 5 May 2014

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.


Sunday, 4 May 2014

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.