Andes virus — joint estimation of incubation, transmission timing, and R(t)

A Julia + Turing model for the Epuyén 2018–19 Andes hantavirus outbreak (Martínez et al. 2020, NEJM). From the line list given in the paper it jointly estimates the incubation period and the transmission timing of each secondary infection relative to its source's symptom onset, plus a time-varying reproduction number with offspring dispersion. Double interval censoring is handled by a continuous latent infection time for each case.

The generation interval (transmission timing plus the source's incubation period) and the serial interval (transmission timing plus the secondary's incubation period) are derived in post-processing from the fitted distributions. A per-pair constraint that the secondary's infection time is later than the source's keeps the generation interval positive at the latent level.

Headline results (Epuyén line list)

Incubation period (estimated)

Quantity	Posterior median (95% CrI)
Mean	22.5 d (20.3 – 25.3)
95th percentile	36.0 d (31.3 – 43.8)
99th percentile	44.7 d (37.5 – 57.6)

Transmission timing relative to source onset (estimated)

Negative values mean the secondary was infected before the source became symptomatic.

Quantity	Posterior median (95% CrI)
Mean	0.17 d (−0.17 – 0.49)
SD	0.61 d (0.46 – 0.83)
P(transmission is pre-symptomatic)	0.39 (0.20 – 0.61)
P(pre-symptomatic by more than 1 day)	0.03 (0.00 – 0.12)
P(pre-symptomatic by more than 2 days)	0.00 (0.00 – 0.01)

Generation interval / serial interval (derived from incubation and transmission timing)

Quantity	Posterior median (95% CrI)
Mean	22.7 d (20.4 – 25.5)
SD	7.3 d (5.6 – 10.3)

Offspring and time-varying reproduction number

Quantity	Posterior median (95% CrI)
Negative-Binomial offspring dispersion	0.33 (0.12 – 0.88)
R(t) — Nov 2018	1.32 (0.60 – 3.13)
R(t) — Dec 2018	0.51 (0.14 – 1.67)
R(t) — Jan 2019	0.40 (0.04 – 2.04)
R(t) — Feb 2019+	0.42 (0.02 – 2.99)

Repository layout

src/
  data.jl          — line list loading and bin definitions
  model.jl         — the joint Turing model (incubation, transmission timing, R(t))
  postprocess.jl   — diagnostics, summaries, CSV output
scripts/
  run.jl           — entry point
data/
  linelist.csv     — Epuyén outbreak line list (Martínez Table S2)
Project.toml       — Julia environment
LICENSE            — MIT

Data

The Epuyén line list (data/linelist.csv) is hand-encoded from Table S2 of the supplementary appendix of Martínez et al. 2020.

Running

julia --project=. -t auto scripts/run.jl

NUTS, 4 chains × 1000 samples. Takes a few minutes on a laptop. Posterior saved to output/posterior.csv.

Citing

If you use this code or the Epuyén line list encoding, please cite:

Martínez VP, Di Paola N, Alonso DO, et al. "Super-spreaders" and person-to-person transmission of Andes virus in Argentina. N Engl J Med 2020;383:2230–41. doi:10.1056/NEJMoa2009040

License

MIT (see LICENSE).