Epidemiological and ecological determinants of Zika virus transmission in an urban setting
- University of Oxford, United Kingdom
- FIOCRUZ, Brazil
- UMI 233, INSERM U1175 and Institut de Biologie Computationnelle, LIRMM, Université de Montpellier, France
- Universidade Estadual de Feira de Santana, Brazil
- University of Exeter, United Kingdom
Figures
Figure 1
Zika virus epidemics in Feira de Santana and Brazil (2015–2016).
(A) Comparison of weekly notified Zika cases (full red line) with monthly Microcephaly cases (blue bars) in Feira de Santana (FSA), overimposed with total Zika cases at the level of the country (BR, …
Figure 2 with 3 supplements
Eco-epidemiological factors and model fit to notified cases.
(A) Zika case data (black) and daily climatic series for rainfall (gold), humidity (blue) and mean temperature (green) for Feira de Santana (FSA). Climate data available as Dataset 1. (B) Resulting …
Figure 2—figure supplement 1
Relationship between temperature and egg hatching success.
Empirical data on Aedes aegypti’s and albopictus’s egg hatching success (in the model ) is taken from (Dickerson, 2007). Data includes measurements of hatching for 5 different temperatures above …
Figure 2—figure supplement 2
Prior selection and sensitivity.
(A1) Priors for the linear coefficients (scaling factor for effect of temperature on mosquito incubation period - EIP) and (scaling factor for effect of temperature on mosquito mortality - …
Figure 2—figure supplement 3
Eco-epidemiological factors and model fit to notified cases.
(A) Daily climatic series for rainfall (black), humidity (orange) and mean temperature (purple) for Feira de Santana (FSA). (B) Estimated vector lifespan (green), extrinsic incubation period (EIP, …
Figure 3 with 2 supplements
Estimated epidemiological and ecological parameters.
MCMC posterior distributions, based on model fitting to notified case data between 2015–2017 and obtained from sampling 1 million MCMC steps after burn-in. (A) Posterior of the introduction date …
Figure 3—figure supplement 1
Sensitivity output for MCMC chains.
(A) The last 1.5 million states of a 5 million run were sampled (25,000 samples), and the correlation of the states was calculated between the chains of particular parameters (windows of 50 samples …
Figure 3—figure supplement 2
Eco-epidemiological factors and model fit to notified cases when using 2 observation rates.
(A) Resulting Bayesian MCMC fit to weekly (black line: data, purple line: model fit) and cumulative incidence (black line: data, grey line: model fit). The grey area highlights the period before the …
Figure 4
Projected Zika virus dynamics and transmission potential.
(A) Fitted and projected epidemic attack rate (% population infected, or herd-immunity, green), basic reproduction number (, red) and effective reproduction number (, blue).(B) Colourmap showing …
Figure 5
Sensitivity to reporting and microcephaly risk in Feira de Santana (FSA).
(A) The observation rate (OR) can be expressed as the product of the proportion of cases that are symptomatic (0.18 [Duffy et al., 2009]), with the proportion of symptomatic that seek medical …
Tables
Table 1
Model climate-dependent parameters.
https://doi.org/10.7554/eLife.29820.003| Notation | Description |
|---|---|
| transition rate from aquatic to adult mosquito life-stages | |
| mortality rate of aquatic mosquito life-stage | |
| mortality rate of adult mosquito life-stage | |
| (human) intrinsic oviposition rate of adult mosquito life-stage | |
| (vector) extrinsic incubation period of adult mosquito life-stage | |
| vector-to-human probability of transmission per infectious bite | |
| egg hatching success | |
| adult vector biting rate |
Table 2
Model constant parameters.
https://doi.org/10.7554/eLife.29820.004| Notation | Value | Description | References |
|---|---|---|---|
| 0.25 per day | mosquito biting rate | [ 76, 88 ] | |
| 0.5 | proportion of females (sex ratio) | [ 52, 59 ] | |
| 0.5 | human-to-vector probability of transmission per infectious bite | – | |
| 75 years | human mean lifespan | [ 83 ] |
Table 3
Literature-based reports on key ZIKV epidemiological and entomological parameters.
https://doi.org/10.7554/eLife.29820.010| Parameter/Function | Values and ranges reported | References |
|---|---|---|
| Intrinsic incubation period | 6.5, 5.9 days | [ 34, 50 ] |
| Human infectious period | 4.7, 9.9 days | [ 34, 50 ] |
| Extrinsic incubation period | 8.2, , days | [ 34, 51, 84 ] |
| Attack rates | 74, 50, 73, 94, 52% | [ 17, 26, 47, 28 ] |
| 3.2, 2.5, 4.8, 2.05, 2.6–4.8, 4.3–5.8, 1.8–2.0 | [ 17, 37, 38, 47, 64 ] | |
| Observation rate | 0.024, 0.06, 0.03, 0.11 | [ 17, 37, 47 ] |
Table 4
Model estimated parameters.
https://doi.org/10.7554/eLife.29820.011| Notation | Description | Ranges / priors |
|---|---|---|
| time point of first case (in a human) | (, ) | |
| aquatic carrying capacity | (0, ) | |
| linear factor for mosquito mortality | (0, ) | |
| linear factor for extrinsic incubation period | (0, ) | |
| non-linear factor for effects of humidity and rainfall | (0, ) | |
| human infectious period | (0, 15) | |
| human (intrinsic) incubation period | (0, 15) | |
| observation rate | (0, 1) |
Additional files
-
Source data 1
Dataset 1.
Climate time series for Feira de Santana (2013–2017), including daily temperature, humidity and rainfall (FSA_climate_series.xls).
- https://doi.org/10.7554/eLife.29820.017
-
Source data 2
Dataset 2.
Age-related data for Feira de Santana (2015), including case counts per age, total population numbers and gender ratios (FSA_age_data.xls).
- https://doi.org/10.7554/eLife.29820.018
-
Source data 3
Dataset 3.
Total weekly notified cases in Feira de Santana (2015–2017) (FSA_incidence_series.xls).
- https://doi.org/10.7554/eLife.29820.019
-
Source data 4
Dataset 4.
Total notified cases of Microcephaly in Feira de Santana (2015–2017), including confirmed and suspected/not confirmed (FSA_Microcephaly_series.xls).
- https://doi.org/10.7554/eLife.29820.020
-
Supplementary file 1
Sample model deterministic solutions for incidence (Incidence_detsolution.csv).
- https://doi.org/10.7554/eLife.29820.021
-
Supplementary file 2
Sample model deterministic solutions for R0 (R0_detsolution.csv).
- https://doi.org/10.7554/eLife.29820.022
-
Supplementary file 3
Sample model deterministic solutions for Re (Re_detsolution.csv).
- https://doi.org/10.7554/eLife.29820.023
-
Supplementary file 4
Sample model stochastic solutions for incidence (Incidence_stosolution.csv).
- https://doi.org/10.7554/eLife.29820.024
-
Supplementary file 5
Sample model stochastic solutions for R0 (R0_stosolution.csv).
- https://doi.org/10.7554/eLife.29820.025
-
Supplementary file 6
Sample model stochastic solutions for Re (Re_stosolution.csv).
- https://doi.org/10.7554/eLife.29820.026
-
Transparent reporting form
- https://doi.org/10.7554/eLife.29820.027
