Background: Chikungunya (CHIKV) and Zika (ZIKV) significantly affected Latin America in the period 2015–2017. Most studies were reported from urban areas of Brazil and Colombia. In this paper we estimate Incidence rates for CHIKV and ZIKV in Caqueta, the Amazonian gateway area of Colombia, from 2015 to 2018. Methods: Using surveillance data of CHIKV and ZIKV in Caqueta, Colombia, incidence rates were estimated (cases/100,000 population). Sixteen geographical information systems (GIS)-based municipal maps were developed. GIS software used was Kosmo 3.0®. Results: From 1st of January 2015 to the 24th of November 2018, 825 cases of CHIK and 1079 of ZIKV were reported, yielding cumulated incidence rates of 169.42 and 221.59 cases/100,000 population respectively. In 2016, 48.7% of the CHIKV cases (402) and 96.6% of the ZIKV cases (1042) were reported. The highest number of both arboviral diseases occurred at Florencia (capital department city), 225 cases for CHIKV (127.17 cases/100,000 pop.) and 611 for ZIKV (345.34 cases/100,000 pop.). Discussion: The temporo-spatial distribution of CHIKV and ZIKV infections in Caquetá reflected the pattern of concurrent epidemics, especially in 2016. Studies using GIS-linked maps are necessary to attain accurate epidemiological analyses for public health decisions. That is also useful for an epidemiologically based assessment of traveler risks when visiting specific areas in destination countries.
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