Background: The COVID-19 pandemic has caused societal disruption globally, and South America has been hit harder than other lower-income regions. This study modeled the effects of six weather variables on district-level SARS-CoV-2 reproduction numbers (Rt) in three contiguous countries of tropical Andean South America (Colombia, Ecuador, and Peru), adjusting for environmental, policy, healthcare infrastructural and other factors. Methods: Daily time-series data on SARS-CoV-2 infections were sourced from the health authorities of the three countries at the smallest available administrative level. Rt values were calculated and merged by date and unit ID with variables from a unified COVID-19 dataset and other publicly available sources for May–December, 2020. Generalized additive models were fitted. Findings: Relative humidity and solar radiation were inversely associated with SARS-CoV-2 Rt. Days with radiation above 1000 kJ/m2 saw a 1.3% reduction in Rt, and those with humidity above 50% recorded a 0.9% reduction in Rt. Transmission was highest in densely populated districts, and lowest in districts with poor healthcare access and on days with lowest population mobility. Wind speed, temperature, region, aggregate government policy response, and population age structure had little impact. The fully adjusted model explained 4.3% of Rt variance. Interpretation: Dry atmospheric conditions of low humidity increase district-level SARS-CoV-2 reproduction numbers, while higher levels of solar radiation decrease district-level SARS-CoV-2 reproduction numbers — effects that are comparable in magnitude to population factors like lockdown compliance. Weather monitoring could be incorporated into disease surveillance and early warning systems in conjunction with more established risk indicators and surveillance measures.
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