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Online Discussion: Tracking new emerging diseases and the next pandemic

Analyzed sequences

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    Posted: June 11 2013 at 4:22pm
The graphs are greek to me but the text below is very interesting.

Submitted by Andrew Rambaut on Mon, 2013-06-10 20:10

MERS-Coronavirus Molecular Epidemiology and Genetic Analysis

This is an update of an older analysis based on 5 sequences.

We now have 9 complete genome sequences:

4 sequences from the Al-Hasa hospital outbreak have now been isolated and deposited in GenBank by Cotten,M., Watson,S.J., Palser,A.L., Gall,A., Kellam,P., Zumla,A., Memish,Z.A  and the Kingdom of Saudi Arabia, Ministry of Health, Riyadh 11176, Kingdom of Saudi Arabia. The genbank links are: KF186564-KF186567.

As these are a tightly epidemiologically-linked I have taken the most recent of these (Al-Hasa 1, collected on 2013-05-09) to add to the genetic analysis.

NameLocationAccessionSourceDate of collection
KSA/EMCKSAJX869059Patient 32012-06-13
Qatar/UK England1QatarKC667074.1Patient 42012-09-12
England2KSA?HPA WebsitePatient 102013-2-10
Jordan-N3JordanKC776174Patient 1between 2012-04-09 and 2012-04-19
Munich/Abu_DhabiAbu DhabiInstitute of Virology WebsitePatient 172013-03-22
Al-Hasa 1KSAKF186567Unknown2013-05-09

When did these strains share a common ancestor?

With sequences sampled from different times, we can attempt to estimate the rate of evolution. To do this we estimated a maximum likelihood tree under the GTR + gamma model of substitution using PhyML. This is the unrooted maximum likelihood topology with estimated branch lengths:

MERS-CoV.codons.9.phyml.BS1000.tree.png

A maximum likelihood tree estimated using PhyML and the GTR + G model. Branch lengths are in substitutions per site. The tree is arbitrarily rooted midway between the most distant sequences. Numbers below-left of the nodes are bootstrap percentages of 1000 replicates.

A rate of evolution for these sequences can be estimated using root-to-tip regression using our software Path-O-Gen. Here only one Al-Hasa sequence is used as these are strongly linked epidemiologically and cannot be considered independent points. This plots genetic distance from the root of the tree against the time of isolation of each virus:

MERS-CoV.6.Phyml.path.png

The root-to-tip regression of genetic distances against time of isolation using the maximum likelihood tree above. The position of the root of the tree was found to maximize the correlation of this plot.

The estimate of the rate of evolution is given by the slope of the line and the time of the most recent common ancestor by the x-intercept:

Rate:1.48x10-3 subst/site/year
tMRCA:2011.48

This would result in the common ancestor of all sampled viruses being in the in the middle of 2011. This rate of evolution is similar to rates of epidemic influenza A and at least one estimate of the rate of SARS-CoV evolution in humans. The residuals from the link give some indication of the stochasticity of the molecular evolutionary process. 

What is the nearest non-human host relative?

The closest non-human sequence to both the human cases is a short fragment from a CoV isolated from a pipistrelle bat in the Netherlands collected in 2008. The fragment consists 332 nucleotides of pp1b located at nucleotide 15033 in the human CoV genomes. There are 41 differences between the human cases and the bat sequence giving a divergence of 0.123 subst/site which, at the same rate as above (about 1.5x10-3 subst/site/year), corresponds to an MRCA existing about 40 years ago. With the previous rate of 4.4x10-3 this would be over 150 years. So this fragment can tell us little about the possible location and species of the reservoir host for the human cases.

Interpretation

Based on the above results and the restricted geographical range of the known cases, it seems unlikely that this virus has been circulating entirely in humans since these sequences shared a common ancestor. Although it is certain that the virus can spread from human to human (familial cases are noted and the large hospital-associated cluster at Al-Hasa, KSA), a single introduction into humans and subsequent epidemic would be unlikely to have remained restricted to the Ariabian Peninsula (the UK case from January was a transitory visitor to Saudi Arabia).

A more likely interpretation of the data would be multiple zoonotic transmissions from an animal reservoir. If the reservoir has a high contact rate with humans (e.g., a domesticated or farmed animal) then multiple small chains of human transmission could be hypothesized allowing for contact with the cases that have been described so far. It is also clear that a group is developing of the more recently isolated viruses (consisting of Qatar/England1, Munich/AbuDhabi, England2 and the Al-Hasa sequences). It is possibly more plausible that this represents an emerging cluster of human-circulating cases with a common ancestor in the second half of 2012. A recent paper in the Lancet has suggested the virus has a incubation period of up to 12 days. In the time between 2012.6 (the TMRCA of this clade) and 2013.35 (the time of the most recent sample) there is time for a minimum of 22 incubations. At any significant growth rate (R0>>1) this would result in a large number of infections. In this scenario, the recorded cases represent a small fraction of the total number of cases with a bias towards severe cases and traced contacts. However, if this were the case then it would be likely to have spread more widely globally with occasional severe cases croping up to indicate this. With an R0 < 1 then it is possible to get chains of transmission without going to high total numbers of cases but these will generally die out. How long (in terms of the number of infections) these chains will be before they stochastically die out will depend on the value of R0. 

Once again, sequence data from more individual cases and potentially some consideration of the spatial pattern of these may be able to tell us more about the likely number of zoonotic events and degree of human circulation.

Deeper virus origins

Whilst the (relatively) close phylogenetic relationship of the human virus to bat coronavirus may indicate bats as an ultimate source of this virus, it seems unlikely that bats are the immediate contact for the human cases as human bat contacts are relatively low frequency. Speculatively, it would be plausible that the virus crossed from bats to a domesticated or agricultural animal which then spread widely within the last few years in the Arabian Peninsula. Further surveillance of both bats and other potential reservoirs will undoubtedly be ongoing and the epidemiology of this virus will become more clear.

 




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Post Options Post Options   Thanks (0) Thanks(0)   Quote debbiencusa Quote  Post ReplyReply Direct Link To This Post Posted: June 11 2013 at 5:42pm
Super find. Thank you for a remarkable job you do. Based on what I know about Arab habits, when they speak of domesticated animals, from what I have been told by Arab people from several middle eastern countries the idea of allowing dogs in doors to live with humans is typically not done. I know that Egypt is symbolic with cats, I have no idea whether they dwell with them. I think some study into animal history in regions where the virus is prominent may be in order. It could be a insect that is both biting bats and then farm animals or people also. I have know they have fleas, I have no clue what other insects there are capable of disease spread, anyone else??
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Post Options Post Options   Thanks (0) Thanks(0)   Quote nc_girl Quote  Post ReplyReply Direct Link To This Post Posted: June 12 2013 at 9:31am
Well, I dated an Arab for almost 3 yrs from Qatar in the 80s and can tell you that 1) they don't like dogs, 2) they do like cats and 3) the most common indoor pet for them to own is a bird.  He bought an african Grey parrott and loved it until it kept biting him because he was afraid of it.  He talked alot about one day getting a hawk or other prey bird when he got back home and had his own house.

Just my two cents!

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Post Options Post Options   Thanks (0) Thanks(0)   Quote jacksdad Quote  Post ReplyReply Direct Link To This Post Posted: June 12 2013 at 12:26pm
So this thing is evolving as fast as epidemic influenza A? That's not good
"Buy it cheap. Stack it deep"
"Any community that fails to prepare, with the expectation that the federal government will come to the rescue, will be tragically wrong." Michael Leavitt, HHS Secretary.
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Post Options Post Options   Thanks (0) Thanks(0)   Quote debbiencusa Quote  Post ReplyReply Direct Link To This Post Posted: June 12 2013 at 2:53pm
NC girl, That helps a lot, I have suspected a cat link,  also in China they eat cats. Cats eat birds, cats also go after bats (mice with wings). Cats mingle and can pass disease easy amongst each other. One cat with Pan lukapenia can wipe out a animal shelters entire cat population in days. That could explain why some family members get the disease others do not, ones who interact with the cats catch it, ones who do not , do not. Even if it does not apply with Mers it is good info to know.  Thanks.
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