Effectiveness of COVID-19 vaccines in Ecuador: A test-negative design.

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.

Virological evidence of the impact of non-pharmaceutical interventions against COVID-19 in Ecuador, a resource-limited setting.

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.

Phylogenetic analysis reveals that the H5N1 avian influenza A outbreak in poultry in Ecuador in November 2022 is associated with the highly pathogenic clade 2.3.4.4b.

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.

Incidence and seasonality of respiratory viruses among medically attended children with acute respiratory infections in an Ecuador birth cohort, 2011-2014.

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.

First Report of SARS-CoV-2 Lineage B.1.1.7 (Alpha Variant) in Ecuador, January 2021.

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.

Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador.

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.

Analytical and clinical evaluation of a heat shock SARS-CoV-2 detection method without RNA extraction for N and E genes RT-qPCR.

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.

Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador.

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.

The epidemiology and severity of respiratory viral infections in a tropical country: Ecuador, 2009-2016.

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.

[Mutant alleles associated to chloroquine and sulfadoxine-pyrimethanime resistance in Plasmodium falciparum of the Ecuador-Peru and Ecuador-Colombia borders]. / Alelos mutantes asociados a la resistencia a cloroquina y sulfadoxina-pirimetamina en Plasmodium falciparum de las fronteras Ecuador-Perú y Ecuador-Colombia.

The frequency of mutations in pfCRT and DHFR/DHPS genes of Plasmodium falciparum associated with resistance to chloroquine and sulfadoxine-pyrimethamine was evaluated in 83 strains from the districts of Esmeralda and Machala, located on the borders of Ecuador-Peru and Ecuador-Colombia in 2002. Polymerase chain reaction (PCR), conventional and its variants, was used. Mutations in the pfCRT gene were found in more than 90% of the samples from Esmeralda and Machala. For the DHFR gene, 90% of the strains were mutant samples from Esmeralda, 3 were double mutations and 1 was a triple mutation. In Machala, 25% were simple mutant forms and 75% mixed mutant forms (wild forms/mutant). In conclusion, resistance to chloroquine has been fixed in strains carrying K76T pfCRT mutation, whereas genetic imprinting for resistance to pyrimethamine is evolving, particularly in the district of Esmeralda.

Alelos mutantes asociados a la resistencia a cloroquina y sulfadoxina-pirimetamina en Plasmodium falciparum de las fronteras Ecuador-Perú y Ecuador-Colombia / Mutant alleles associated to chloroquine and sulfadoxine-pyrimethanime resistance in Plasmodium falciparum of the Ecuador-Peru and Ecuador-Colombia borders

Se evaluó la frecuencia de mutaciones en los genes pfCRT y DHFR/DHPS del Plasmodium falciparum asociados a la resistencia a cloroquina y sulfadoxina-pirimetamina en 83 cepas provenientes de los distritos Esmeralda y Machala ubicados en las fronteras entre Ecuador-Perú y Ecuador-Colombia durante el año 2002. Se empleó la reacción en cadena de polimerasa (PCR) convencional y sus variantes. El gen pfCRT presentó más de 90% de muestras mutantes en Esmeralda y Machala. Para el gen DHFR, el 90% de las cepas fueron muestras mutantes en Esmeralda, tres fueron mutaciones dobles y una triple; en Machala se encontró 25% de formas mutantes simples y 75% de formas mixtas (formas silvestres/mutantes). En conclusión, la resistencia a cloroquina se ha fijado en las cepas portadoras de la mutación K76T pfCRT, mientras que la impronta genética a la resistencia a pirimetamina está en evolución, principalmente en el distrito de Esmeralda.

The frequency of mutations in pfCRT and DHFR/DHPS genes of Plasmodium falciparum associated with resistance to chloroquine and sulfadoxine-pyrimethamine was evaluated in 83 strains from the districts of Esmeralda and Machala, located on the borders of Ecuador-Peru and Ecuador-Colombia in 2002. Polymerase chain reaction (PCR), conventional and its variants, was used. Mutations in the pfCRT gene were found in more than 90% of the samples from Esmeralda and Machala. For the DHFR gene, 90% of the strains were mutant samples from Esmeralda, 3 were double mutations and 1 was a triple mutation. In Machala, 25% were simple mutant forms and 75% mixed mutant forms (wild forms/mutant). In conclusion, resistance to chloroquine has been fixed in strains carrying K76T pfCRT mutation, whereas genetic imprinting for resistance to pyrimethamine is evolving, particularly in the district of Esmeralda.

Evidence of diversification of dengue virus type 3 genotype III in the South American region.

In order to gain insight into the genetic variability of dengue virus type 3 (DENV-3) genotype III isolated in the Latin American region, phylogenetic analysis were carried out using envelope (E) gene sequences from 57 DENV-3 genotype III strains isolated in 11 Latin American countries. At least six different genotype III clades were observed. Amino acids substitutions were found in domain III E protein neutralization epitopes and in surface-exposed domain II and III E protein amino acid sequences.

Modeling gene sequence changes over time in type 3 dengue viruses from Ecuador.

Dengue virus (DENV) is a member of the genus Flavivirus of the family Flaviviridae. DENV-3 re-emerged in Central America in 1994, and continues to expand into the South American region. Little is known about the evolutionary rates, viral spread and population dynamics of this genotype in the Latin American region. In order to gain insight into these matters, we used a Bayesian Markov chain Monte Carlo (MCMC) approach, to analyze envelope (E) gene sequences of the DENV-3 genotype III of strains included in a monophyletic cluster composed by Ecuadorian as well as strains from Cuba, Puerto Rico and Peru. The results of these studies revealed that the expansion population growth model was the best fit to the data. The most common recent ancestor (MRCA) was placed around 1989, in agreement with the first reports of the emergence of this new DENV-3 type. A mean rate 1.033 x 10(-3) nucleotide substitution per site per year was obtained. This rate is comparatively higher than the ones obtained for DENV-2 and DENV-4 in the same region. Faster population growth and greater population dispersal may have contributed to the vigorous initial transmission dynamics of this genotype in the Latin American region.

Phylogenetic analysis of the NS5 gene of dengue viruses isolated in Ecuador.

Dengue virus (DENV) is a member of the genus Flavivirus of the family Flaviviridae. DENV causes a wide range of diseases in humans, from the acute febrile illness dengue fever (DF) to life-threatening dengue hemorrhagic fever/dengue shock syndrome (DHF/DSS). There is not knowledge of the genetic relations among DENV circulating in Ecuador. Given the emerging behaviour of DENV, a single tube RT-PCR assay using a pair of consensus primers to target the NS5 coding region has been recently validated for rapid detection of flaviviruses. In order to gain insight into the degree of genetic variation of DENV strains isolated in Ecuador, DENV NS5 sequences from 23 patients were obtained by direct sequencing of PCR fragments using the mentioned one step RT-PCR assay. Phylogenetic analysis carried out using the 23 Ecuadorian DENV NS5 sequences, as well as 56 comparable sequences from DENV strains isolated elsewhere, revealed a close genetic relation among Ecuadorian strains and DENV isolates of Caribbean origin. The use of partial NS5 gene sequences may represent a useful alternative for a rapid phylogenetic analysis of DENV outbreaks.