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Why do people protest during public health crises? Bolivia is an important case of protest and noncompliance in the COVID-19 pandemic because the country has high poverty rates and few resources for public health yet fared better during the pandemic than its wealthier neighbors. Bolivia faced considerable challenges going into the pandemic: The Bolivian political crisis of 2019 spurred political polarization and elevated an interim government with low legitimacy. We argue that this polarization and the low levels of government legitimacy in many municipalities had detrimental effects on citizens’ willingness to comply when COVID-19 spread across the country and the national government issued strict quarantine orders. Using municipal-level data on COVID-19 cases, election returns, and protest, we show that Bolivians broke quarantine to protest in large numbers. In municipalities where the interim government enjoyed less support, protests were more likely. Furthermore, these municipalities relaxed COVID-19 restrictions more than others and saw spikes in cases and then deaths. However, most protests were for elections and against the interim government, and not against COVID-19 restrictions or policy. Our evidence sheds light on the local costs of low legitimacy in the context of a public health crisis, where citizen compliance is vital.