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.

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.

No abstract

Information about factors potentially favoring the spread of SARS-CoV-2 in rural settings is limited. Following a case–control study design in a rural Ecuadorian village that was severely struck by the pandemic, SARS-CoV-2 RNA were detected by real-time PCR in swabs obtained from inner and upper walls in 24/48 randomly selected latrines from case-houses and in 12/48 flushing toilets from paired control-houses (P = 0.014; McNemar’s test). This association persisted in a conditional logistic regression model adjusted for relevant covariates (OR: 4.82; 95% CI: 1.38–16.8; P = 0.014). In addition, SARS-CoV-2–seropositive subjects were more often identified among those living in houses with a latrine (P = 0.002). Latrines have almost five times the odds of containing SARS-CoV-2 RNA than their paired flushing toilets. Latrines are reservoirs of SARS-CoV-2 RNA, and it cannot be ruled out that latrines could contribute to viral transmission in rural settings. Frequent disinfection of latrines should be recommended to reduce the likelihood of fecal contamination.

The Omicron variant of SARS-CoV-2 is the latest pandemic lineage causing COVID-19. Despite having a vaccination rate ≥85%, Ecuador recorded a high incidence of Omicron from December 2021 to March 2022. Since Omicron emerged, it has evolved into multiple sub-lineages with distinct prevalence in different regions. In this work, we use all Omicron sequences from Ecuador available at GISAID until March 2022 and the software Nextclade and Pangolin to identify which lineages circulate in this country. We detected 12 different sub-lineages (BA.1, BA.1.1, BA.1.1.1, BA.1.1.14, BA.1.1.2, BA.1.14, BA.1.15, BA.1.16, BA.1.17, BA.1.6, BA.2, BA.2.3), which have been reported in Africa, America, Europe, and Asia, suggesting multiple introduction events. Sub-lineages BA.1 and BA.1.1 were the most prevalent. Genomic surveillance must continue to evaluate the dynamics of current sub-lineages, the early introduction of new ones and vaccine efficacy against evolving SARS-CoV-2.