Friday, 25 April 2014

MERS-CoV partial spike gene sequences do not implicate viral change in April's Jeddah human case cluster

Stars highlight difference in scale at left-hand side,
 (x-axis) numbers. Seasons based on info [2]
Click on image to enlarge.
With a new article at ScienceInsider written by Kai Kupferschmidt (@kakape on Twitter)[1], it seems that the idea of a Spring start to human detections of MERS-CoV in Saudi Arabia is gaining some support from other scientists.

Springing into action...

The "pattern" of MERS-CoV detection seen in the chart still need some fleshing out wit more time. They might be heavily and unrealistically biased by the enormous number of recent hospital detections. However, it's worth noting that in April 2013, it was the Al-Ahsa cluster that added to detection numbers. In April 2014 it is the Jeddah outbreak started with a hospital cluster. What's that about? I say "detection" rather than cases so we don't get bogged down in whether they were ill or not at the time of sampling. In fact the pattern seems to be one that begins with a hospital cluster. 

I've tried to track down when Spring is in this region, and the chart - a rework of one I've been showing for a while now - overlays the seasons of interest.[2]
CC BY 2.0
Camels have a very long gestational period, up to 15-mths, which makes it difficult to know when a 1-2-year old camel, the ones most likely to acquire MERS-CoV and to shed virus, are around and mixing with humans. Jennifer Yang reported that most camel births occur between Nov and Jan and so their birthdays would fall on...well you can do the maths.

NOTE: The fatal case numbers in the past month, as with most data in the past month, are lacking detail which means I cannot plot them. Pleeease post scrubbed data from all April and late March detections soon WHO.

A pattern of animal to human to hospital to human..?

So could how about this summary of MERS-CoV movement among animals and people?

Young camels become infected within a year or so of birth > virus spreads to humans in contact with camels, a rare few of whom become ill > seriously ill cases shed virus and infect other humans in a healthcare setting > humans spread to other humans, severe illness showing up mostly in those who are already diseased due to something else (e.g. diabetes or cardiac issues)

Hospitals are an obvious starting point for this human-to-human spread to occur because of increased level of close contact and the concentration of already ill people.

But my question today is, as spread of MERS-CoV among humans has likely been occurring since at least 2012 (I suspect earlier), why such a big spike in detections in Jeddah now? Also, lest we forget, among that temporally-linked large cluster of paramedics in Abu Dhabi (being able to link that to Jeddah would answer an important question for me).

Part of the spike gene sequenced but not a sign of viral change...

We learned today, at very long last (I know it's been less than a month but these clusters seem to have been going on for years!), that a part of the MERS-CoV genome from 30/31 samples from Jeddah have been able to be amplified by Christian Drosten's group in Germany (collaborating with Dr Memish and the Kingdom of Saudi Arabia's Ministry of Health) using a separate assay that that used in screening (a safe assumption as spike is not a diagnostic screening target recommended by the WHO). That means that laboratory contamination is a less likely cause of case climb. It doesn't exclude it though. We call this a possible "false positive". It can be due to a reverse-transcription polymerase chain reaction (RT-PCR) being accidentally contaminated ;by some DNA from a previous test and showing up as positive result, when in fact there was no MERS-CoV RNA in that person. Contamination can also occur at the purification step, when (viral) RNA is extracted from the patient material and DNA (or RNA from another high viral load specimen) again contaminates the process. The latter will always be positive while the former may appear virus-positive in 1 reaction run and negative in another.

Sample selection for sequencing...

We don't know how the 31 samples tested by Drosten's lab were selected for packaging and transport to Germany. It is possible that only repeatedly positive samples were sent.

Schematic of a coronavirus virion.
Click to enlarge
In Kupferschmidt's article, Drosten informs us that there is nothing different or distinctive about the 2014 MERS-CoV partial spike gene sequences he's generated thus far when compared to sequences from previously sequenced MERS-CoV genomes in 2012 and 2013. This is not the end of that story though as we are not yet sure which part of the spike was sequenced and still have a lot of the genome to see before we can feel assured that the virus has not changed. We also don't know if sample selection has occurred from cases during the beginning, middle and later stages of the Jeddah cluster and thus whether these new sequence data accurately represent all the viruses circulating among detected in the Jeddah outbreak. But this is a good start.

Severe acute respiratory syndrome (SARS) and spike..

The ~4,000nt, region of the MERS-CoV genome 
that encodes the ~1,300aa spike gene is highlighted in 
pink. Schematic derived from the EMC-2012 variant 
sequence of MERS-CoV.
Click to enlarge.
With the SARS-CoV, evolutionary changes in the spike gene (especially between amino acids 75-1025 or nucleotides 224-3075) could be used retrospectively as a marker of the virus adapting though time,[5] perhaps towards a better transmitting variant among humans. Along with ORF1a, these two regions showed changes suggestive of adaptation from animal to human.[5] I'm not sure that we've seen that with the human/camel genomes sequenced to date have we? Does this reflect that the virus has already "settled in" to humans? Or does it mean that the spike region is just less informative for MERS-CoV than it was for SARS-CoV? To answer that we'd need older camel MERS-CoV sequence. With the new data we have for MERS-CoV, we begin to wonder whether we can exclude viral change. Hopefully that information will be forthcoming when compete genomes are sequenced and when we know more about which "part of the spike gene" was sequenced. Those details will probably be delivered via a rapid scientific publication.

So, a day full of new data and a mad day on Twitter. 

Thanks to @nika7k, @yasnot and @AB_Algaissi for very helpful Twitter exchanges on this topic this morning.

  1. Soaring MERS Cases Cause Pandemic Jitters, but Causes Are Unclear
  3. Tracking MERS-CoV through time: a spikey problem
  4. Saudi Geography and Climate
  5. Molecular evolution of the SARS coronavirus during the course of the SARS epidemic in China
  6. Camels likely source of deadly coronavirus, study shows