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Background Coronavirus disease 2019 (COVID-19) has become a global pandemic with serious consequences that have led to the implementation of unprecedented social isolation measures. At the early stages of the pandemic, Ecuador was one of the most affected countries in Latin America. The objective of this study was to assess the levels of depression, anxiety and stress in the Ecuadorian general population during the social isolation period due to COVID-19. Methods A web-based survey consisting of 31 short-answer and multiple-choice questions was administered to the general population from April 22–May 3, 2020. Mental health status was assessed through the Depression, Anxiety and Stress Scale-21 Items (DASS-21) questionnaire. Ordinal logistic analyses were used to identify potential risk factors associated with the severity of mental health issues. Results A total of 626 individuals were included. Most of them were females (60.5%), and their mean age was 29.6 ± 11.7 years. Approximately 17.7% of the respondents had moderate to very severe levels of depression, 30.7% had similar levels of anxiety, and 14.2% experienced stress. Female sex, younger age, student status, and having a relative diagnosed with COVID-19 were associated with significantly higher levels of depression, anxiety and stress. Ordinal regression models showed that being a student was a risk factor for having more severe levels of depression (OR = 3.67; 95% CI = 2.56–5.26, p: 0.0001), anxiety (OR= 1.86; 95% CI= 1.35–2.55, p: 0.0001), and stress (OR = 2.17; 95% CI= 1.47–3.19, p: 0.0001). Having a relative with COVID-19 was also found to be a risk factor only for depression (OR= 1.70; 95% CI= 1.03–2.80, p: 0.036) and anxiety (OR = 2.17; 95% CI= 1.35–3.47, p: 0.001). Additionally, male sex,  older age, and having more children were found to be protective factors for the three conditions. Conclusions Our findings suggest that social isolation due to the COVID-19 outbreak has impacted the mental health of the general population in Ecuador. We identified potential risk and protective factors that could serve as a foundation from which to develop psychological strategies to safeguard the mental health of our population during the current pandemic.

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Characterisation of SARS-CoV-2 genetic diversity through space and time can reveal trends in virus importation and domestic circulation, and permit the exploration of questions regarding the early transmission dynamics. Here we present a detailed description of SARS-CoV-2 genomic epidemiology in Ecuador, one of the hardest hit countries during the early stages of the COVID-19 pandemic. We generated and analysed 160 whole genome sequences sampled from all provinces of Ecuador in 2020. Molecular clock and phylogeographic analysis of these sequences in the context of global SARS-CoV-2 diversity enable us to identify and characterise individual transmission lineages within Ecuador, explore their spatiotemporal distributions, and consider their introduction and domestic circulation. Our results reveal a pattern of multiple international importations across the country, with apparent differences between key provinces. Transmission lineages were mostly introduced before the implementation of non-pharmaceutical interventions (NPIs), with differential degrees of persistence and national dissemination.

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