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

A Julia + Turing model fitted to the Epuyén 2018–19 Andes hantavirus outbreak (Martínez et al. 2020, NEJM).

Four quantities are estimated jointly from the line list: the incubation period, the transmission timing of each secondary infection relative to its source's symptom onset, a weekly time-varying reproduction number, and offspring dispersion. Exposure and onset dates are interval-censored. Each case is given a continuous latent infection time and a continuous latent onset time, each sampled within its recorded window. Generation interval and serial interval are derived from the fitted distributions in post-processing.

Pages

• Model — priors, data augmentation, GI / SI derivation.

• Limitations — known caveats around exposure encoding, late R(t) bins, dispersion identifiability, and right-truncation.

• Analysis walkthrough — runs the full analysis end to end.

• API Reference — exported functions.

Citing

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

The reporting follows:

Charniga K, et al. Best practices for estimating and reporting epidemiological delay distributions of infectious diseases. 2024. arXiv:2405.08841