Metadata for Dengue in San Juan, Puerto Rico - 1990/1991 to 2008/2009 Seasons

The dataset contains weekly dengue data for the San Juan-Carolina-Caguas Metropolitan Statistical Area. The dataset includes the following variables:

season: the transmission season;
season_week: week of the season (not the calendar year - the season starts following the week with historically lowest dengue cases over the years 1990-2009);
week_start_date: date of the first day of the week;
denv1_cases: number of laboratory confirmed cases with DENV1;
denv2_cases: number of laboratory confirmed cases with DENV2;
denv3_cases: number of laboratory confirmed cases with DENV3;
denv4_cases: number of laboratory confirmed cases with DENV4;
other_positive_cases: laboratory-positive cases without serotype identified (these include acute IgM positive and IgM conversions);
additional_cases: at times not all specimens submitted were tested due to overload of the capacity for testing or incomplete case information. For those weeks, the number of additional laboratory-positive cases among those not tested was estimated by multiplying the number of untested cases by the rate of laboratory-positive cases amongst those that were tested;
total_cases: the sum of all cases (denv1-4_cases + other_positive_cases + additional_cases), the target time series for forecasting.

Over time, the sensitivity of testing increased, particularly in 2005 when PCR was implemented for routine diagnostics, in 2007 when improved IgM testing was implemented, and in 2009 when a more sensitive PCR assay was adopted. Details are presented in Sharp et al. 2010.

Sharp TM, Hunsperger E, Santiago GA, Muñoz-Jordan JL, Santiago LM, Rivera A, et al. (2013) Virus-Specific Differences in Rates of Disease during the 2010 Dengue Epidemic in Puerto Rico. PLoS Negl Trop Dis 7(4): e2159. doi:10.1371/journal.pntd.0002159

San Juan-Carolina-Caguas Metropolitan Statistical Area including the municipalities of Aguas Buenas, Aibonito, Barceloneta, Barranquitas, Bayamón, Caguas, Canóvanas, Carolina, Cataño, Cayey, Ceiba, Ciales, Cidra, Comerío, Corozal, Dorado, Fajardo, Florida, Guaynabo, Gurabo, Humacao, Juncos, Las Piedras, Loíza, Luquillo, Manatí, Maunabo, Morovis, Naguabo, Naranjito, Orocovis, Río Grande, San Juan, San Lorenzo, Toa Alta, Toa Baja, Trujillo Alto, Vega Alta, Vega Baja, and Yabucoa.