Description of the interdisciplinary studies combining phylodynamics and mathematical modelling or integrating epidemiological and genetic data.
Supplementary Table 4 is also available in Excel format here.
| Phylodynamics category | Model description | Software | Genetic sequences | Sequence length (pb) | Data source | Parameters inferred | Model category | Original model reference | Spatially explicit | Inference method | Dog population structure | Quantitative results | Outcome in sensitivity analysis | Key parameters in sensitivity analysis | Optimal control strategy | Reference |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Bayesian discrete phylogeography | Asymmetric DTA + BSSVS | BEAST 1 | N, P, intergenic G-L (n = 250) | 3080 | Passive | Markov jumps, migration rates, reward-associated distances, spread-associated landscape features, tMRCA | Spatial spread along phylogenetic trees | YES | Simulation | Spatial distribution of cases | NA | Talbi et al., 2010 | ||||
| Bayesian phylodynamics | Exponential growth coalescent | BEAST 1 | intergenic G-L (n = 176) | 760 | Passive | tMRCA | Directed Acyclic Graph | Morelli et al., 2012 | YES | MCMC | Distance between direct and indirect cases, number of cases, incubation period, infectious period, strength of exogeneous and individual sources, | NA | Mollentze et al., 2014 | |||
| Bayesian discrete phylogeography | Symmetric DTA + BSSVS | BEAST 1 | G, P (n = 39) | 2463 | Passive | Migration rates, tMRCA | Deterministic compartmental |
Hampson et al., 2007 Kitala et al., 2002 Panjeti and Real, 2011 |
NO | Simulation | Time to detection | Time to detection | Reporting rate | NA | Tohma et al., 2016 | |
| Bayesian continuous phylogeography | Relaxed random walk (lognormal prior) | BEAST 1 | N, P, M, G, intergenic G-L (n = 88) | 5061 | Passive | Nucleotide substitution rate, number of introductions, tMRCA, velocity | Re | NO | particle MCMC | Number and rate of introductions, outbreak periodicity, Re | Temporal variation of Re | Robust to detection probability | NA | Bourhy et al., 2016 | ||
| Bayesian phylodynamics | Birth-Death | BEAST 2 | N (n = 29) | 1350 | Passive | Re |
Deterministic compartmental Stochastic compartmental |
Zinsstag et al., 2009 | NO | Least-square fitting |
Vaccination rate, dog-to-dog transmission rate, dog-to-human transmission rate, R0 |
Rabies dynamics | Robust to detection probability | NA | Zinsstag et al., 2017 | |
| N, P, M, G, intergenic G-L (n = 151) | 5061 | Passive | Graph model | YES | Graph pruning and intersection | R, rate of importation, rate of unobserved importation | Clusters and R | Reporting rate, graph pruning cutoff | NA | Cori et al., 2018 | ||||||
|
Bayesian discrete phylogeography Bayesian continuous phylogeography |
DTAa GLM on the effective population sizes Relaxed random walk (lognormal prior) |
BEAST 1 |
N (n = 543) G (n = 491) |
1350 1575 |
Passive | tMRCA, velocity, diffusion coefficients, velocity-associated landscape features | Deterministic compartmental |
Anderson et al., 1981 Hampson et al., 2007 Zinsstag et al., 2009 |
NO | MCMC | Carrying capacity, dog- to-dog transmission rate, dog-to-human transmission rate, R0 | Rabies dynamics | Transmission rates, initial conditions | NA | Tian et al., 2018 | |
| Note: | ||||||||||||||||
| Abbreviations: BSSVS, Bayesian Stochastic Search Variable Selection; DTA, Discrete Trait Analysis; GLM, Generalized Linear Model; MCMC, Markov Chain Monte Carlo; R0, basic reproduction ratio; Re, effective reproduction ratio; tMRCA, time to the Most Recent Common Ancestor | ||||||||||||||||
| a Symmetry not indicated |