Malaria and dengue are vector-borne endemic diseases in the low-lying regions of Colombia. Outbreaks of both diseases appear during the occurrence of El Niño in the tropical Pacific. We present updated data confirming the relation, which are explained by the increase in temperature. Malaria shows an increasing trend, of which climate change cannot be disregarded. The migration of over 1?200?000 Venezuelans hiding away from the internal crisis has complicated the situation. Further research is needed to pinpoint the linkages between vector-borne diseases and climate variability, but also with current and future impacts of climate change, and alarming deforestation rates of Colombia. The public health system has been impacted by the COVID-19 pandemic, especially in the poorest and most vulnerable regions (Pacific coast, Amazon and Orinoco). This note constitutes a call to Colombia's public health system to maintain vector and water-borne diseases services, which cannot become neglected amid the COVID-19 pandemic.
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