Leptospirosis: Morbidity, mortality, and spatial distribution of hospitalized cases in Ecuador. A nationwide study 2000-2020.

BACKGROUND: In Ecuador, leptospirosis surveillance involves a mandatory notification of all cases and a hospitalization for severe illness. Morbidity and mortality are, nevertheless, underestimated and contribute directly to the status of leptospirosis as a neglected disease. Leptospira spp. is zoonotic in Ecuador with established endemic transmission in the Tropics. Here, we review retrospective national data within the country to aid in control strategies. METHODOLOGY/PRINCIPAL FINDINGS: In a population-based nationwide study, we analysed morbidity, mortality, and spatial distribution on confirmed hospital-discharged leptospirosis cases from 2000-2020 from a publicly accesible National Database, including males and females of all ages. We computed data for the 24 provinces across the four-geoclimatic regions of Ecuador based on seasonal and monthly variations and calculated rates according to age and sex. The spatial distribution was estimated at the level of ecoregions, provinces, and cantons. A total of 2,584 hospitalizations were recorded over all three continental regions in 22 provinces, except Carchi province and the Galapagos Islands. The annual incidence varied from 0.27 to 2.45 cases per 100,000 inhabitants with ages ranging from 1 to 98 years-old and an overall male/female ratio of 1.92:1. Most hospitalizations and deaths occurred in males ages 25-34 years. We registered 79 fatalities (3.06%); the highest mortality rate was 0.05 per 100,000 inhabitants. More cases clustered in the tropical cantons of central and north of the Coast and in the southern Amazon when compared to the Andes. CONCLUSIONS AND SIGNIFICANCE: Our findings evidence leptospirosis endemicity and pinpoint the highest incidence within resource-poor tropical settings. The highest incidence occurred in males of adult age, with those also exhibiting the highest mortality. The national incidence rate was stable, but peaks occurred intermittently during the rainy seasons. Thus, strategies aimed at leptospirosis monitoring and control involving the application of preventive measures should consider this season and the aforementioned high-risk groups.

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.

Alternative RNA extraction-free techniques for the real-time RT-PCR detection of SARS-CoV-2 in nasopharyngeal swab and sputum samples.

Standard diagnoses of SARS-CoV-2 infections are done by RNA extraction and real-time RT-PCR (rRT-PCR). However, the need for RNA extraction complicates testing due to increased processing time, high cost, and limited availability of commercial kits. Therefore, alternative methods for rRT-PCR detection of SARS-CoV-2 without RNA extraction were investigated. Nasopharyngeal and sputum samples were used to compare the sensitivity of three techniques: Trizol RNA extraction, thermal shock, and the direct use of samples with an RNase inhibitor. Direct, extraction-free use of primary samples plus the RNase inhibitor produced diagnostic values of 100 % sensitivity and specificity compared to standard protocols, and these findings were validated in a second, independent laboratory.

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.

Analytical and Clinical Evaluation of Two RT-qPCR SARS-CoV-2 Diagnostic Tests with Emergency Use Authorization in Ecuador.

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.

Estudios sobre el virus del papiloma humano (VPH) en el Ecuador: parte I / Studies on human papillomavirus (HPV) in Ecuador: part I

Aprovechando la realización de las XL Jornadas Nacionales de Biología Espol en la ciudad de Guayaquil, se realizó una sesión dedicada a la epidemiología del virus de papiloma humano (VPH) y del cáncer cervical. Esta sesión tuvo la participación de varios investigadores provenientes de diferentes zonas del Ecuador. El presente artículo tiene como objeto presentar un resumen de estas charlas, junto a un análisis de la información mostrada además de una reflexión sobre las preguntas que quedan aún por responder en cuanto al perfil epidemiológico de esta patología en el país.

Taking advantage of the realization of theXL National Conference on Espol Biology in the city of Guayaquil, a session was held dedicated to the epidemiology of Human Papilloma Virus (HPV) and cervical cancer. This session was attended by several researchers from different areas of Ecuador. The object of this article is to present a summary of these talks, together with an analysis of the information shown in addition to a reflection on the questions still to be answered regarding the epidemiological profile of this pathology in the country.

Tercer molar superior retenido en seno maxilar. Presentación de un caso / Third Upper Molar Retained in Maxillary Sinus. Presentation of a Case

Se presentó una paciente de 38 años de edad, mestiza, la cual acudió a Consulta de Cirugía Maxilofacial del Hospital Lenin remitida del Servicio de Neurocirugía, que refirió ser objeto de varios estudios de cráneo (incluyendo TAC) por presentar cefaleas mantenidas de moderada a gran intensidad. Los resultados de los estudios fueron negativos. Refirió que recibió tratamiento farmacológico para aliviar los síntomas dolorosos, además, describió otros signos y síntomas como: caída del cabello, afectaciones visuales del lado derecho (visión borrosa, molestias), dolor facial difuso y edema en hemicara derecha. Al examen físico nada a señalar, con rayos x de senos paranasales se diagnosticó la presencia de un tercer molar incluido en seno maxilar derecho. La paciente fue llevada al salón de forma electiva y mediante la técnica de Caldwell-Lud fue extraído dicho molar. La paciente evolucionó de manera favorable.

A 38-year-old black, which came to Consultation of Maxillofacial Surgery at Lenin Hospital, from Neurosurgery Department was reported in this paper. The patient was referred to study due to be the subject of several studies of skull (including TAC) due to headaches maintained from moderate to high intensity. The results of the studies were negative. The patient received drug treatment to relieve the painful symptoms also described other signs and symptoms such as hair loss, visual detriment to the right side (blurred vision, discomfort), diffuse facial pain and swelling in right side of the face. Physical examination revealed nothing to indicate, with sinus x-rays the presence of a third molar in the right maxillary sinus was diagnosed. The patient was taken to the room and through elective Caldwell-Lud technique, the molar was extracted. The patient progressed favorably.

Tercer molar superior retenido en seno maxilar. Presentación de un caso / Third Upper Molar Retained in Maxillary Sinus. Presentation of a Case

Se presentó una paciente de 38 años de edad, mestiza, la cual acudió a Consulta de Cirugía Maxilofacial del Hospital Lenin remitida del Servicio de Neurocirugía, que refirió ser objeto de varios estudios de cráneo (incluyendo TAC) por presentar cefaleas mantenidas de moderada a gran intensidad. Los resultados de los estudios fueron negativos. Refirió que recibió tratamiento farmacológico para aliviar los síntomas dolorosos, además, describió otros signos y síntomas como: caída del cabello, afectaciones visuales del lado derecho (visión borrosa, molestias), dolor facial difuso y edema en hemicara derecha. Al examen físico nada a señalar, con rayos x de senos paranasales se diagnosticó la presencia de un tercer molar incluido en seno maxilar derecho. La paciente fue llevada al salón de forma electiva y mediante la técnica de Caldwell-Lud fue extraído dicho molar. La paciente evolucionó de manera favorable(AU)

A 38-year-old black, which came to Consultation of Maxillofacial Surgery at Lenin Hospital, from Neurosurgery Department was reported in this paper. The patient was referred to study due to be the subject of several studies of skull (including TAC) due to headaches maintained from moderate to high intensity. The results of the studies were negative. The patient received drug treatment to relieve the painful symptoms also described other signs and symptoms such as hair loss, visual detriment to the right side (blurred vision, discomfort), diffuse facial pain and swelling in right side of the face. Physical examination revealed nothing to indicate, with sinus x-rays the presence of a third molar in the right maxillary sinus was diagnosed. The patient was taken to the room and through elective Caldwell-Lud technique, the molar was extracted. The patient progressed favorably(AU)

Comparación de las técnicas in situ, in vitro y enzimática (celulasa) para estimar la digestibilidad de forrajes en ovinos / Comparison of the in situ, in vitro and enzimatic (cellulase) techniques for digestibility estimation of forages in sheep

Se comparó los resultados de las técnicas in vitro, in situ y enzimática (celulasa) para estimar la digestibilidad de forrajes de diferente calidad nutritiva en ovinos. Se colectó muestras de forraje de tres calidades: alta (rye grass de 2-4 semanas), media (rye grass de 8 semanas y heno de alfalfa) y baja (paja de avena). Las muestras fueron secadas, molidas y pasaron por tamiz de 1 mm para la técnica in vitro y celulasa y 3 mm para la técnica in situ. Se determinó la digestibilidad in vitro de la materia seca (DIVMS), digestibilidad in situ de la materia seca (DISMS) y digestibilidad a la celulasa de la materia seca (DCMS). Se emplearon tres ovinos con fístula ruminal y alimentados con maíz forrajero y heno de alfalfa. Se usó un diseño experimental con arreglo factorial de 4 x 3 (4 calidades de forraje y 3 técnicas). La DISMS fue superior (p<0.05) para los cuatro forrajes en estudio en relación a la DIVMS y la DCMS: 91.8 vs 73.9 y 76.5% para el forraje de alta calidad; 74.2 vs 71.6 y 70.9 para el rye grass de 8 semanas; 77.8 vs 68.9 y 68.0 para el heno de alfalfa y 34.7 vs 29.5 y 31.7 para la paja de avena. No se observó diferencias estadísticas entre la DIVMS y DCMS en los forrajes de mediana calidad. Los valores de DIVMS y DCMS sobreestimaron la cantidad de materia seca degradable en forrajes de alta calidad y subestimaron la cantidad de materia seca degradable en forrajes de mediana y baja calidad en relación a la DISMS en ovinos. Se concluye que existen diferencias entre las técnicas in situ, in vitro y celulasa para estimar la digestibilidad de la materia seca del forraje en ovinos y estas diferencias dependen de la calidad del forraje.

The objective of the study was to compare the efficiency of the in situ, in vitro and enzymatic (cellulose) techniques in estimating the digestibility of forage with different nutritional quality in sheep. Samples of three qualities of forage were collected: high (rye grass of 2-4 weeks), medium (rye grass of 8 weeks and alfalfa hay), and low (oat straw). The samples were dried, grounded and passed through 1 mm sieve for the in vitro and cellulose technique and 3 mm sieve for the in situ technique. The in vitro digestibility of dry matter (IVDDM), in situ digestibility of dry matter (ISDDM), and cellulose digestibility of dry matter (CDDM) were determined. Three adult rams with ruminal fistula and fed with a diet based on alfalfa hay and corn stalk. A complete randomized 4 x 3 experimental design (4 quality forages and 3 techniques) was used. The ISDDM was higher (p<0.05) in all forages as compared to IVDDM and CDDM: 91.8 vs 73.9 and 76.5% for high quality forage, 74.2 vs 71.6 and 70.9 for ray grass of 8 weeks and 77.8 vs 68.9 and 68.0 for alfalfa hay, and 34.7 vs 29.5 and 31.7 for low quality forage. None differences were observed between IVDDM and CDDM in forages of medium quality. IVDDM and CDDM values overestimated the quantity of degradable dry matter in high quality forages and underestimated it in medium and low quality forages in relation to ISDDM. It is concluded that there are differences between the in situ, in vitro and cellulose techniques when estimating the digestibility of dry matter forage in sheep, and these difference depend upon the quality of the forage.

Estudio comparativo de las técnicas de digestibilidad in vitro, in situ y enzimática con forrajes de diferente calidad nutritiva en alpacas / Comparative study of techniques of in vitro digestibility, in situ and different enzymatic forage nutritional quality in alpacas

The objective of the present study was to evaluate the in vitro, in situ and cellulose techniques to estimate the digestibility of different nutritional quality forages in alpacas. Samples of forages of three different qualities were used: high (Rye grass of four weeks), medium (Rye grass of eight weeks) and low (oat straw). The samples were dried and ground trough a 1-mm screen for the in vitro and cellulose techniques and in 3-mm screen for the in situ technique. The in vitro (IVDDM), in situ (ISDDM) and cellulose (CDDM) digestibity of dry matter were determined. Three male alpacas, ruminal cannulated, and fed with cornstalk and alfalfa hay were used. A completely randomized design with three treatments (techniques) for each quality of forage and three repetitions per treatment was used. The ISDDM was lower (p0.05). The IVDDM and CDDM techniques overestimated the degradable dry matter in high quality forages and underestimated the degradable dry matter in medium and low quality forages, in relation to the ISDDM in alpacas. It was concluded that there are differences between the in vitro, in situ and cellulose techniques for the estimation of the dry matter digestibility of forages. Moreover, the in vitro and cellulose techniques were inappropriate for the evaluation of forages in alpacas in comparison to the in situ technique.

Se evaluaron las técnicas de digestibilidad in vitro, in situ y celulasa para estimar la digestibilidad de forrajes de diferente calidad nutritiva en alpacas. Se colectaron muestras de forraje de tres calidades: alta (rye grass de 4 semanas), media (rye grass de 8 semanas) y baja (paja de avena). Las muestras fueron secadas, molidas y pasaron por tamiz y 1 mm para la técnica in vitro y celulasa, y de 3 mm para la técnica in situ. Se determinó la digestibilidad in vitro (DIVMS), in situ (DISMS) y a la celulada (DCMS) de la materia seca. Se usaron 3 alpacas machos con fistula ruminal y alimentadas con maíz forrajero y heno de alfalfa. Se utilizó un diseño irrestricto al azar con tres tratamientos (técnicas) para las calidades de forraje y tres repeticiones por tratamiento. En caso de existir diferencia estadística significativa (p0.05) entre la DIVMS y DCMS en las tres calidades de forrajes. Los valores de DIVMS y DCMS sobrestimaron la cantidad de materia seca degradable en forrajes de alta calidad y subestimaron la cantidad de materia seca degradable en forrajes de mediana y baja calidad en relación a la DISMS en alpacas. Se concluye que existen diferencias entre las técnicas in situ, in vitro y celulasa para estimar la digestibilidad de la materia seca del forraje en alpacas, y estas diferencias dependen de la calidad del forraje; y que las técnicas in vitro y celulasa fueron inadecuadas para evaluar los forrajes en alpacas en relación a la técnica in situ.