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Background: The COVID-19 pandemic poses a significant global health threat, characterized by high morbidity, severity, and the emergence of concerning variants. Latin America has been greatly affected, with high infection and mortality rates. Vaccination plays a crucial role in mitigating severe disease and controlling the pandemic. This study aims to assess the effectiveness of COVID-19 vaccines in preventing SARS-CoV-2 severe acute respiratory infections (SARI) in hospitalized vaccination target groups in Ecuador. Methods: This is a test-negative design study. We used data reported through sentinel surveillance of SARI between May 2021 and March 2022 in Ecuador. Patients with case criteria of SARI and hospitalized for a minimum of 24 hours were included in the study. Cases were defined as patients with SARI with a positive RT-qPCR test for SARS-CoV-2 and controls were those with a negative result. Information on vaccination status was obtained from the national vaccination registry, a valid dose of vaccination was considered when it was administered at least 14 days prior to symptom onset. Vaccine effectiveness (VE) (1-OR/OR) was calculated using a logistic regression. Results: A total of 1,277 patients were included in the analysis of VE. The adjusted vaccine effectiveness (aVE) in preventing hospitalization, adjusted for sex, age group, presence of one or more comorbidities, and period of the predominance of the omicron variant, was 44.5% for the partial primary schedule, 74.7% for the complete primary schedule, and 79.9% for the complete primary schedule plus booster doses. The aVE in avoiding ICU admissions was close to 80% with both the complete primary schedule and the booster doses, and in avoiding deaths, the aVE was 89% and 98%, respectively. Conclusions: In Ecuador, COVID-19 vaccination prevents hospitalizations, ICU admissions, and deaths. The effectiveness of the vaccines improves with more doses, offering increased protection across all age groups.
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Ecuador had substantial COVID-19-mortality during 2020 despite early implementation of non-pharmaceutical interventions (NPIs). Resource-limited settings like Ecuador have high proportions of informal labour which entail high human mobility, questioning efficacy of NPIs. We performed a retrospective observational study in Ecuador's national reference laboratory for viral respiratory infections during March 2020-February 2021 using stored respiratory specimens from 1950 patients, corresponding to 2.3% of all samples analysed within the Ecuadorian national surveillance system per week. During 2020, detection of SARS-CoV-2 (Pearson correlation; r = -0.74; p = 0.01) and other respiratory viruses (Pearson correlation; r = -0.68; p = 0.02) by real-time RT-PCR correlated negatively with NPIs stringency. Among respiratory viruses, adenoviruses (Fisher's exact-test; p = 0.026), parainfluenzaviruses (p = 0.04), enteroviruses (p < 0.0001) and metapneumoviruses (p < 0.0001) occurred significantly more frequently during months of absent or non-stringent NPIs (characterized by <55% stringency according to the Oxford stringency index data for Ecuador). Phylogenomic analyses of 632 newly characterized SARS-CoV-2 genomes revealed 100 near-parallel SARS-CoV-2 introductions during early 2020 in the absence of NPIs. NPI stringency correlated negatively with the number of circulating SARS-CoV-2 lineages during 2020 (r = -0.69; p = 0.02). Phylogeographic reconstructions showed differential SARS-CoV-2 dispersion patterns during 2020, with more short-distance transitions potentially associated with recreational activity during non-stringent NPIs. There were also fewer geographic transitions during strict NPIs (n = 450) than during non-stringent or absent NPIs (n = 580). Virological evidence supports that NPIs had an effect on virus spread and distribution in Ecuador, providing a template for future epidemics in resource-limited settings and contributing to a balanced assessment of societal costs entailed by strict NPIs.
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COVID-19 , Humanos , Adenoviridae/genética , COVID-19/epidemiología , COVID-19/prevención & control , Ecuador/epidemiología , Configuración de Recursos Limitados , SARS-CoV-2/genética , Estudios RetrospectivosRESUMEN
The ongoing H5N1 outbreak in the Americas caused by clade 2.3.4.4 is causing unprecedented impact in poultry and wild birds. In November 2022, a highly pathogenic avian influenza A outbreak was declared in poultry in Ecuador, affecting more than 1.1 million heads of poultry in two farms by February 2023. Phylogenetic analysis shows that the virus clade is 2.3.4.4b, and to the best of our knowledge, this is the first scientific publication reporting this clade in South America.
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Subtipo H5N1 del Virus de la Influenza A , Gripe Aviar , Humanos , Animales , Gripe Aviar/epidemiología , Aves de Corral , Filogenia , Subtipo H5N1 del Virus de la Influenza A/genética , Ecuador/epidemiología , Brotes de EnfermedadesAsunto(s)
Virus de la Influenza A , Gripe Humana , Animales , Humanos , Pandemias , América del Sur , FilogeniaRESUMEN
To study the spatial and temporal patterns of Influenza A virus (IAV) is essential for an efficient control of the disease caused by IAV and efficient vaccination programs. However, spatiotemporal patterns of spread as well as genetic lineage circulation of IAV on a countrywide scale have not been clearly determined for many tropical regions of the world. In order to gain insight into these matters, the spatial and temporal patterns of IAV in six different geographic regions of Ecuador, from 2011 to 2021, were determined and the timing and magnitude of IAV outbreaks in these localities investigated. The results of these studies revealed that although Ecuador is a South American country situated in the Equator line, its IAV epidemiology resembles that of temperate Northern Hemisphere countries. Phylogenetic analysis of H1N1pdm09 and H3N2 IAV strains isolated in five different localities of Ecuador revealed that provinces in the south of this country have the largest effective population size by comparison with provinces in the north, suggesting that the southern provinces may be acting as a source of IAV. Co-circulation of different H1N1pdm09 and H3N2 genetic lineages was observed in different geographic regions of Ecuador.
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Virus de la Influenza A , Gripe Humana , Humanos , Virus de la Influenza A/genética , Filogenia , Subtipo H3N2 del Virus de la Influenza A/genética , Ecuador/epidemiología , Estaciones del Año , Gripe Humana/epidemiologíaAsunto(s)
COVID-19 , SARS-CoV-2 , Humanos , Prueba de COVID-19 , América Latina , España , Ecuador/epidemiología , Carga ViralRESUMEN
BACKGROUND: Ecuador annually has handwashing and respiratory hygiene campaigns and seasonal influenza vaccination to prevent respiratory virus illnesses but has yet to quantify disease burden and determine epidemic timing. METHODS: To identify respiratory virus burden and assess months with epidemic activity, we followed a birth cohort in northwest Ecuador during 2011-2014. Mothers brought children to the study clinic for routine checkups at ages 1, 2, 3, 5, and 8 years or if children experienced any acute respiratory illness symptoms (e.g., cough, fever, or difficulty breathing); clinical care was provided free of charge. Those with medically attended acute respiratory infections (MAARIs) were tested for common respiratory viruses via real-time reverse-transcription polymerase chain reaction (rRT-PCR). RESULTS: In 2011, 2376 children aged 1-4 years (median 35 months) were enrolled in the respiratory cohort and monitored for 7017.5 child-years (cy). The incidence of respiratory syncytial virus (RSV) was 23.9 (95% CI 17.3-30.5), influenza 10.6 (2.4-18.8), adenoviruses 6.7 (4.6-28.0), parainfluenzas 5.0 (2.3-10.5), and rhinoviruses, bocaviruses, human metapneumoviruses, seasonal coronaviruses, and enteroviruses <3/100 cy among children aged 12-23 months and declined with age. Most (75%) influenza detections occurred April-September. CONCLUSION: Cohort children frequently had MAARIs, and while the incidence decreased rapidly among older children, more than one in five children aged 12-23 months tested positive for RSV, and one in 10 tested positive for influenza. Our findings suggest this substantial burden of influenza occurred more commonly during the winter Southern Hemisphere influenza season.
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Gripe Humana , Infecciones por Virus Sincitial Respiratorio , Virus Sincitial Respiratorio Humano , Infecciones del Sistema Respiratorio , Virus , Cohorte de Nacimiento , Niño , Preescolar , Ecuador/epidemiología , Humanos , Incidencia , Lactante , Gripe Humana/epidemiología , Infecciones por Virus Sincitial Respiratorio/epidemiología , Estaciones del Año , Virus/genéticaRESUMEN
On January 5 2021, Ecuadorian COVID-19 genomic surveillance program detected a suspicious case of the B.1.1.7 lineage (alpha variant) of SARS-CoV-2 in Los Rios province, later confirmed by genome sequencing. The patient travelled from the UK by the end of December 2020. By contact tracing, several new cases were detected confirming B.1.1.7 transmission and spreading in Ecuador.
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Characterisation of severe acute respiratory syndrome coronavirus-2 (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 coronavirus-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, with differential degrees of persistence and national dissemination.
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BACKGROUND: The COVID-19 pandemic has caused significant supply shortages worldwide for SARS-CoV-2 molecular diagnosis, like RNA extraction kits. OBJECTIVE: The aim of our study was to evaluate the clinical performance and analytical sensitivity of a simple SARS-CoV-2 diagnosis protocol based on heat shock without RNA extraction using both "CDC" (N gene) and "Charite" (E gene) RT-qPCR protocols. RESULTS: 1,036 nasopharyngeal samples, 543 of them SARS-CoV-2 positive, were analyzed. The heat shock method correctly identified 68.8% (232/337) and 89.4% (202/226) of SARS-CoV-2 positive samples for N gene and E gene, respectively. Analytical sensitivity was assessed for heat shock method using the CDC RT-qPCR protocol, obtaining sensitivity values of 98.6%, 93.3% and 84.8% for limit of detection of 100.000, 50.000 and 20.000 viral RNA copies/mL of sample. CONCLUSIONS: Our findings show that a simple heat shock SARS-CoV-2 RT-qPCR diagnosis method without RNA extraction is a reliable alternative for potentially infectious SARS-CoV-2 positive patients at the time of testing. This affordable protocol can help overcome the cost and supply shortages for SARS-CoV-2 diagnosis, especially in developing countries. In Ecuador, it has been used already by laboratories in the public health system for more than 100.000 specimens.
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COVID-19 , SARS-CoV-2 , Prueba de COVID-19 , Respuesta al Choque Térmico , Humanos , Pandemias , ARN Viral/genética , Reacción en Cadena en Tiempo Real de la Polimerasa , Sensibilidad y EspecificidadRESUMEN
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 generate and analyse 160 whole genome sequences sampled from all provinces of Ecuador in 2020. Molecular clock and phylgeographic 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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Dozens of RT-qPCR kits are available in the market for SARS-CoV-2 diagnosis, some of them with Emergency Use Authorization (EUA) by the Food and Drug Administration (FDA) or at least by a responsible agency of their country of origin, but many of them lack proper evaluation studies because of COVID-19 pandemic emergency. We evaluated the clinical performance of two commercially available kits in South America, the 2019-nCoV kit (Da An Gene, Guangzhou, China) and GenomeCoV19 kit (ABM, Richmond, Canada), for RT-qPCR SARS-CoV-2 diagnosis using the FDA EUA 2019-nCoV CDC kit (IDT, Coralville, IA) as gold standard. We found striking differences among clinical performance and analytical sensitivity in both kits; whereas the 2019-nCoV kit (Da An Gene) has a limit of detection of 2,000 copies/mL and 100% of sensitivity, the GenomeCoV19 kit (ABM) has a poor sensitivity of 75% and a limit of detection estimated to be over 8.000 copies/mL. The GenomeCoV19 kit (ABM) lacks clinical use authorization in Canada; however, the 2019-nCoV kit (Da An Gene) is authorized by the Chinese CDC. Our results support that only SARS-CoV-2 diagnosis kits with clinical use authorization from their country of origin should be exported to developing countries lacking proper evaluation agencies to avoid a deep impact of the COVID-19 pandemic due to unreliable diagnosis.
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Prueba de Ácido Nucleico para COVID-19/métodos , COVID-19/diagnóstico , Juego de Reactivos para Diagnóstico , SARS-CoV-2/genética , Ecuador/epidemiología , Humanos , Sensibilidad y EspecificidadRESUMEN
BACKGROUND: Respiratory viral infections (RVI) are a leading cause of mortality worldwide. We compared the epidemiology and severity of RVI in Ecuador during 2009-2016. METHODS: Respiratory specimens collected within the national surveillance system were tested for influenza viruses, respiratory syncytial virus (RSV), adenovirus, parainfluenza virus, and human metapneumovirus. Overall and virus-specific positive detection rate (PDR) were calculated and compared the timing of epidemics caused by the different viruses. Logistic regression models were used to compare the age distribution and risk of death across respiratory viruses. RESULTS: A total of 41,172 specimens were analyzed: influenza (PDR=14.3%) and respiratory syncytial virus (RSV) (PDR=9.5%) were the most frequently detected viruses. Influenza epidemics typically peaked in December-January and RSV epidemics in March; seasonality was less evident for the other viruses. Compared to adults, children were more frequently infected with RSV, adenovirus, parainfluenza, and influenza B, while the elderly were less frequently infected with influenza A(H1N1)p. The age-adjusted risk of death was highest for A(H1N1)p (odds ratio [OR] 1.73, 95% confidence intervals [CI] 1.38-2.17), and lowest for RSV (OR 0.75, 95%CI 0.57-0.98). CONCLUSIONS: Whilst influenza and RSV were the most frequently detected pathogens, the risk of death differed by RVI, being highest for pandemic influenza and lowest for RSV.
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Infecciones del Sistema Respiratorio/epidemiología , Adolescente , Adulto , Factores de Edad , Anciano , Niño , Preescolar , Ecuador/epidemiología , Femenino , Humanos , Lactante , Recién Nacido , Subtipo H1N1 del Virus de la Influenza A/aislamiento & purificación , Masculino , Metapneumovirus/aislamiento & purificación , Persona de Mediana Edad , Vigilancia de la Población , Virus Sincitial Respiratorio Humano/aislamiento & purificación , Infecciones del Sistema Respiratorio/patología , Infecciones del Sistema Respiratorio/virología , Estudios Retrospectivos , Factores de Riesgo , Estaciones del Año , Índice de Severidad de la Enfermedad , Clima Tropical , Adulto JovenRESUMEN
BACKGROUND: Influenza-associated illness results in increased morbidity and mortality in the Americas. These effects can be mitigated with an appropriately chosen and timed influenza vaccination campaign. To provide guidance in choosing the most suitable vaccine formulation and timing of administration, it is necessary to understand the timing of influenza seasonal epidemics. OBJECTIVES: Our main objective was to determine whether influenza occurs in seasonal patterns in the American tropics and when these patterns occurred. METHODS: Publicly available, monthly seasonal influenza data from the Pan American Health Organization and WHO, from countries in the American tropics, were obtained during 2002-2008 and 2011-2014 (excluding unseasonal pandemic activity during 2009-2010). For each country, we calculated the monthly proportion of samples that tested positive for influenza. We applied the monthly proportion data to a logistic regression model for each country. RESULTS: We analyzed 2002-2008 and 2011-2014 influenza surveillance data from the American tropics and identified 13 (81%) of 16 countries with influenza epidemics that, on average, started during May and lasted 4 months. CONCLUSIONS: The majority of countries in the American tropics have seasonal epidemics that start in May. Officials in these countries should consider the impact of vaccinating persons during April with the Southern Hemisphere formulation.