Transmission tree of the highly pathogenic avian influenza (H5N1) epidemic in Israel, 2015
© The Author(s) 2016
Received: 12 April 2016
Accepted: 14 September 2016
Published: 4 November 2016
The transmission tree of the Israeli 2015 epidemic of highly pathogenic avian influenza (H5N1) was modelled by combining the spatio-temporal distribution of the outbreaks and the genetic distance between virus isolates. The most likely successions of transmission events were determined and transmission parameters were estimated. It was found that the median infectious pressure exerted at 1 km was 1.59 times (95% CI 1.04, 6.01) and 3.54 times (95% CI 1.09, 131.75) higher than that exerted at 2 and 5 km, respectively, and that three farms were responsible for all seven transmission events.
Introduction, methods and results
In mid-January 2015, the Israel’s national reference laboratory for avian influenza (Kimron Institute), confirmed the presence of highly pathogenic avian influenza (H5N1) virus in an extensive turkey farm. In an attempt to control the spread of the virus, human and poultry movements were restricted and culling, cleaning and disinfection were implemented in the infected farm and its vicinity. Within the next 4 weeks, the virus was isolated in seven other farms, mainly turkey farms, all located within 25 km from the first case. The objectives of this study were to estimate relevant transmission parameters and to reconstruct the most likely sequence of transmission events by combining the spatio-temporal distribution of the outbreaks and the genetic distance between the virus isolates.
The data used in this study relate to the eight cases of highly pathogenic avian influenza (H5N1) that were reported in Israel in January and February 2015. For all infected farms, the location, the date when increased mortality was reported, the date when samples were taken for laboratory confirmation and the date when cleaning and disinfection ended were recorded. Actual dates of infection were unknown and were therefore treated as model parameters to be estimated . In each infected farm, a single virus strain was isolated and its full hemagglutinin gene was sequenced . Assuming that the isolated strains were representative of the pool of viruses in the farms where they had been sampled, the genetic distance between virus isolates was determined.
The modelling approach used in this study combines epidemiologic and genetic data to infer possible transmission trees. It has already been used to model the spread of several animal pathogens, including highly pathogenic avian influenza virus [1, 3] and foot-and-mouth disease virus . This approach assumes that all cases were reported and that there was only one virus introduction in the study area: except for the index case that had been infected by an unknown source, all successive cases were infected by one of the seven other infected farms through an unknown route.
To reconstruct the transmission tree, it was hypothesised that the likelihood that farm A infected farm B increased if A was still infectious when B became infected, if A and B were geographically close to each other, if the genetic sequence taken from A was similar to that from B and if there was no other farm that could have infected B.
Summary of the posterior distributions of the parameters
Median (95% credible interval)
Shape parameter of the spatial kernel
1.12 (0.11, 3.46)
Probability of mutation
1.06e−3 (0.55e−3, 1.82e−3)
Effective reproduction number of farm 1
2.00 (2.00, 2.00)
Effective reproduction number of farm 2
Effective reproduction number of farm 3
2.92 (1.27, 3.48)
Effective reproduction number of farm 4
Effective reproduction number of farm 5
Effective reproduction number of farm 6
2.08 (1.52, 3.73)
Effective reproduction number of farm 7
At the time each farm (except the index case) was likely to become infected (i.e. between 4 and 8 days before reporting) there was at least one farm that was still infectious (already infected but not yet cleaned and disinfected) within a radius of 20 km. Therefore, the spatio-temporal distribution of the eight outbreaks does not show evidence that some outbreaks remained undetected or that there was more than one virus introduction. However, whilst six of the seven strains isolated amongst the secondary cases had two or less than two nucleotides of difference relative to at least one previously isolated strain, the strain isolated in farm 4 differed from all other previously isolated strains by at least six nucleotides. Possible reasons for this include (1) a sudden burst in mutations on farm 4, (2) the transmission of a very different subvariant from the farm that infected farm 4, (3) the presence of undetected infected farms that infected farm 4 or (4) a secondary introduction to farm 4. Further phylogenetic analyses would be required to assess the likelihood of a separate introduction , although these will be challenging to apply to the current dataset due to the small number of farms infected.
The strains sequenced on farms 4 and 7 displayed the same point mutation (position 132, see Additional file 1). Given that this mutation was not found in strains isolated from any other farms, it is unlikely to have occurred independently on both farms. This pattern may reflect infection from a common source: strains isolated on farms 4 and 7 might have both originated from a variant that appeared—but was not isolated—on farm 3 (Figure 1). Alternatively, this may also suggest a transmission event, not captured in the modelled transmission tree, between these two farms. Such a transmission event might have been direct between these two farms or mediated by unreported cases elsewhere. It is worth noting that the number of mutations between strains isolated in different farms had a strong influence on the estimated likelihood of the transmission events. Indeed, each additional mutation decreased the likelihood of the transmission event by a factor equal to the odds of the mutation rate, estimated here at 944 (95% CI 549, 1827). Consequently, to ensure meaningful inference, it is crucial to appreciate the genetic diversity of a strain within a farm by sequencing several strains from the same infected farm , and to integrate this information into the transmission tree modelling. Until then, such analyses should be interpreted cautiously .
Whilst most of the likely transmission events identified using the transmission tree modelling were consistent with outbreak investigations, the former approach cannot incorporate as many sources of information as the latter to make informed decisions and is therefore more limited when it comes to unexpected transmission events, particularly with small datasets. A continuation of this work could be to incorporate the prior knowledge on transmission events generated from the outbreak investigations into the Bayesian parameter estimation procedures to estimate integrated measures of transmission probabilities.
Transmission tree modelling provided a consistent statistical framework to investigate the 2015 Israeli HPAI (H5N1) epidemic. By combining spatial, temporal and genetic data, it was possible to estimate transmission parameters and reconstruct the sequence of the most likely transmission events under a set of assumptions. We suggest that such a statistical approach should be used in real time to gain additional insights into the evolution of an epidemic. We further note that sequencing several strains isolated in each infected farm will allow better capturing genetic diversity and aid in calibrating and validating such models.
The authors declare they have no competing interests.
TV conceived the study, designed and performed the computational experiments, interpreted the results and wrote the manuscript; GF conceived the study, designed the computational experiments, interpreted the results and reviewed the manuscript; RJFY designed the computational experiments and reviewed the manuscript; MPM processed the data, interpreted the results and reviewed the manuscript; RK, IS, AL and SP processed the data and reviewed the manuscript; DUP coordinated the project, interpreted the results and reviewed the manuscript. All authors read and approved the final manuscript.
This work was carried out with the financial support of the Israeli Ministry of Agriculture and Rural Development.
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