Nipah in Malaysia and Sinagapore, 1997-1999

These data describe incidence of human cases of Nipah virus encephalitis in Malaysia and Singapore from January 1997 through April 1999.

nipah_malaysia

Format

A data frame with 49 rows and 5 columns

date

Onset date (weekly)

perak

Number of cases (Perak State, Malaysia)

negeri_sembilan

Number of cases (Negeri Sembilan State, Malaysia)

selangor

Number of cases (Selangor State, Malaysia)

singapore

Number of cases (Singapore)

Nipah virus is a paramyxovirus that occurs in flying fox (fruit bat) populations throughout Asia. The data provided are from the first known emergence of Nipah virus into humans. During this outbreak, the virus was transmitted from bats to pigs, where it circulated in commercial pig farms, infecting mostly farm and abbatoir workers. The outbreak started in Perak State, later spreading to Negeri Sembilan and Seleangor through sale of infected pigs. There were also 11 cases reported among abbatoir workers in Singapor. The data, as published in Pulliam _et al_. (2011), include all 257 clinical cases recorded in humans from 1997-01-11 to 1999-04-14, when the outbreak ended following large-scale depopulation of pig farms. Human cases represent zoonotic infections, with little or no human-to-human transmission. Thus, the epidemic curve reflects transmission and spatial spread within pigs.

Source

Pulliam et al. (2011)

References

J.R.C. Pulliam, et al. 2011. Agricultural intensification, priming for persistence and the emergence of Nipah virus: a lethal bat-borne zoonosis. _Journal of the Royal Society Interface_, 9(66), 20110223. https://doi.org/10.1098/rsif.2011.0223

Author

Data from Funk et al. (2016), provided by Juliet Pulliam (github.com/jrcpulliam).

Examples

## show first few weeks of Dengue incidence
head(nipah_malaysia)
#> # A tibble: 6 × 5
#>   date       perak negeri_sembilan selangor singapore
#>   <date>     <int>           <int>    <int>     <int>
#> 1 1997-01-04     0               0        0         0
#> 2 1997-01-11     1               0        0         0
#> 3 1997-01-18     0               0        0         0
#> 4 1997-01-25     1               0        0         0
#> 5 1997-02-01     1               0        0         0
#> 6 1997-02-08     0               0        0         0

## convert data to incidence object and plot epicurve using the incidence package
library(incidence)
cases <- subset(nipah_malaysia, select = c("perak", "negeri_sembilan", "selangor",
 "singapore"))
i <- as.incidence(cases, dates = nipah_malaysia$date, interval = 7L)
plot(i)