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INTRODUCTION: During the first months of the COVID-19 pandemic in Latin America, countries like Ecuador, Peru and Colombia experienced chaotic scenarios with public health systems collapsing and lack of testing capacity to control the spread of the virus. In main cities like Guayaquil in Ecuador, dramatic situations such as corpses in the streets were internationally broadcasted. METHODS: While the COVID-19 pandemic was devastating South America, SARS-CoV-2 transmission was successfully managed in the Galapagos Islands due to the implementation of a massive screening strategy including hospitalized and community-dwelling populations, and travel restrictions facilitated by its geographical location (972 km from the Ecuadorian continental territory). Floreana Island was one of the few locations in the world that remained COVID-19 free during 2020. RESULTS: In this study, we retrospectively analyzed the data related to SARS-CoV-2 massive testing campaigns from April to September 2020 in the Galapagos Islands, and found this territory to have the lowest positivity rate in South America (4.8-6.7%) and the highest testing ratio among Ecuadorian provinces (9.87% of the population, which is 2480 out of 25 124 inhabitants) during the first wave of the COVID-19 pandemic. CONCLUSION: This story of success was possible because of the interinstitutional collaboration between the regional government of Galapagos Islands (Consejo de Gobierno), the local authorities (Gobiernos Autonomos Descentralizados de Santa Cruz, San Cristobal and Isabela), the regional authorities from Ecuadorian Ministry of Health, the Agencia de Regulación y Control de la Bioseguridad y Cuarentena para Galápagos and Universidad de Las Américas.
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COVID-19 , SARS-CoV-2 , Humanos , Ecuador/epidemiología , COVID-19/epidemiología , Pandemias , Estudios Retrospectivos , América del SurRESUMEN
Canine Distemper Virus (CDV) is a highly contagious virus that can cross mammalian species barriers and has widespread impacts on both domestic animals and wildlife populations. This study describes a recent outbreak of CDV in the Galapagos Islands in 2019. A total number of 125 dogs with clinical signs compatible with CDV were included in this study. Nasal swabs were taken and analyzed by RT-qPCR for the detection of CDV, resulting in a positivity rate of 74.4% (IC95%, 66-81%). Among the CDV positive dogs, 82.2% presented with respiratory signs, 48.8% neurological signs, and 28.9% gastrointestinal signs. CDV has been previously reported in the domestic canine population of the Galapagos Islands in 2001 and 2004. The current study shows how CDV is still a threat for the endemic and endangered Galapagos sea lion, despite recent policies for dog population control and CDV vaccination.
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[This corrects the article DOI: 10.1016/j.onehlt.2020.100185.].
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More than one year since Coronavirus disease 2019 (COVID-19) pandemic outbreak, the gold standard technique for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection is still the RT-qPCR. This is a limitation to increase testing capacities, particularly at developing countries, as expensive reagents and equipment are required. We developed a two steps end point RT-PCR reaction with SARS-CoV-2 Nucleocapsid (N) gene and Ribonuclease P (RNase P) specific primers where viral amplicons were verified by agarose gel electrophoresis. We carried out a clinical performance and analytical sensitivity evaluation for this two-steps end point RT-PCR method with 242 nasopharyngeal samples using the CDC RT-qPCR protocol as a gold standard technique. With a specificity of 95.8%, a sensitivity of 95.1%, and a limit of detection of 20 viral RNA copies/uL, this two steps end point RT-PCR assay is an affordable and reliable method for SARS-CoV-2 detection. This protocol would allow to extend COVID-19 diagnosis to basic molecular biology laboratories with a potential positive impact in surveillance programs at developing countries.
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Prueba de Ácido Nucleico para COVID-19/métodos , COVID-19/diagnóstico , SARS-CoV-2/genética , COVID-19/genética , Prueba de Ácido Nucleico para COVID-19/economía , Prueba de COVID-19/métodos , Proteínas de la Nucleocápside de Coronavirus/genética , Cartilla de ADN , Electroforesis en Gel de Agar/métodos , Humanos , Laboratorios , Nasofaringe/virología , ARN Viral/genética , Ribonucleasa P/genética , Ribonucleasa P/metabolismo , SARS-CoV-2/patogenicidad , Sensibilidad y EspecificidadRESUMEN
BACKGROUND: Several RT-qPCR kits are available for SARS-CoV-2 diagnosis, some of them with Emergency Use Authorization (EUA) by FDA, but most of them lacking of proper evaluation studies due to covid19 emergency. OBJECTIVE: We evaluated Viasure RT-qPCR kit (CerTest Biotec, Spain) for SARS-CoV-2 diagnosis using FDA EUA 2019-nCoV CDC kit (IDT, USA) as a gold standard. RESULTS: Although we found the lack of RNA quality control probe as the main limitation for the Viasure kit, the sensitivity was 91.9% and the specificity was 100%. The limit of detection (LOD) was 2000 copies/mL and 1000 copies/mL for Viasure and IDT kits, respectively. CONCLUSIONS: Viasure RT-qPCR kit is a reliable tool for SARS-CoV-2 diagnosis but improvement of an alternative RT-qPCR reaction for RNA extraction quality control as RNaseP is recommended.
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Prueba de COVID-19/métodos , COVID-19/diagnóstico , Juego de Reactivos para Diagnóstico , Reacción en Cadena en Tiempo Real de la Polimerasa/métodos , SARS-CoV-2 , COVID-19/virología , Humanos , Límite de Detección , Carga ViralRESUMEN
The COVID-19 pandemic has spread worldwide since the outbreak in Wuhan (China) in December 2019, currently infecting over 25 million people and causing more than 800.000 deaths. In Ecuador, up to the 30th of August 2020, overall 113.648 confirmed cases and 6.555 deaths have been declared. Besides overloading of hospital, capacity for molecular diagnosis of SARS-CoV-2 by the Ministry of Public Health was quickly overwhelmed. In this context, emergency authorization for SARS-CoV-2 RT-qPCR diagnosis was granted to other institutions, like the "Agencia de Regulación y Control para la Bioseguridad y Cuarentena de Galápagos" (ABG), that implemented "LabGal" with support of One Health Research Group from "Universidad de Las Américas" (UDLA). The previous experience of ABG and the One Health Research Group in conducting massive surveillance of zoonotic diseases on livestock was crucial to the success on the control of COVID-19 outbreak at Galapagos Islands by the end of May 2020, when Latin American countries were leading the spread of the pandemic.
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BACKGROUND: The CDC protocol for SARS-CoV2 RT-PCR diagnosis (2019-nCoV CDC kit) is considered a gold standard worldwide; based on three different FAM probes (N1 and N2 for viral detection; RP for RNA extraction quality control), three reactions per sample are needed for SARS-CoV-2 diagnosis. RESULTS: We herein describe a sample pooling protocol: pooling 3 RNA extractions into a single PCR reaction; we tested this protocol with 114 specimens grouped in 38 pools and found no significant differences for N1 and N2 Ct values between pool and single sample PCR reaction. CONCLUSION: This pool of three protocol has a sensitivity of 100 % compared to the standard single sample protocol. For a typical 96-well plate, this pool assay allows 96 samples processing, speeding up diagnosis and reducing cost while maintaining clinical performance, particularly useful for SARS-CoV-2 diagnosis at developing countries.
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Prueba de Ácido Nucleico para COVID-19 , COVID-19/diagnóstico , SARS-CoV-2/aislamiento & purificación , Manejo de Especímenes/métodos , Prueba de Ácido Nucleico para COVID-19/economía , Pruebas Diagnósticas de Rutina , Humanos , Nasofaringe/virología , ARN Viral/genética , Juego de Reactivos para Diagnóstico , Reacción en Cadena en Tiempo Real de la Polimerasa , SARS-CoV-2/genética , Sensibilidad y Especificidad , Manejo de Especímenes/normas , Factores de TiempoRESUMEN
CDC and WHO guidelines for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnosis only recommend synthetic fiber swabs for nasopharyngeal (NP) sampling. We show that cotton-tipped plastic swabs do not inhibit PCR and have equivalent performance to rayon swabs. Cotton-tipped plastic swabs are massively produced worldwide and would prevent swab supply shortages under the current high SARS-CoV-2 testing demands, particularly in developing countries.
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Betacoronavirus/aislamiento & purificación , Técnicas de Laboratorio Clínico/instrumentación , Infecciones por Coronavirus/diagnóstico , Equipo para Diagnóstico/provisión & distribución , Equipos Desechables/provisión & distribución , Neumonía Viral/diagnóstico , Reacción en Cadena en Tiempo Real de la Polimerasa/instrumentación , Betacoronavirus/genética , COVID-19 , Prueba de COVID-19 , Celulosa/provisión & distribución , Técnicas de Laboratorio Clínico/métodos , Infecciones por Coronavirus/virología , Fibra de Algodón/provisión & distribución , Humanos , Nasofaringe , Pandemias , Plásticos/provisión & distribución , Neumonía Viral/virología , ARN Viral/análisis , Reacción en Cadena en Tiempo Real de la Polimerasa/métodos , SARS-CoV-2 , Manejo de Especímenes/instrumentación , Manejo de Especímenes/métodosRESUMEN
BACKGROUND: Several qPCR kits are available for SARS-CoV-2 diagnosis, mostly lacking of evaluation due to covid19 emergency. OBJECTIVE: We evaluated nCoV-QS (MiCo BioMed) kit using CDC kit as gold standard. RESULTS: We found limitations for nCoV-QS: 1) lower sensitivity 2) lack of RNA quality control probe. CONCLUSIONS: Validation studies should be implemented for any SARS-CoV-2 RT-qPCR commercial kit to prevent unreliable diagnosis.
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Betacoronavirus/aislamiento & purificación , Infecciones por Coronavirus/diagnóstico , Neumonía Viral/diagnóstico , Reacción en Cadena en Tiempo Real de la Polimerasa/métodos , Betacoronavirus/genética , COVID-19 , Infecciones por Coronavirus/virología , Humanos , Nasofaringe/virología , Pandemias , Neumonía Viral/virología , Juego de Reactivos para Diagnóstico , SARS-CoV-2 , Sensibilidad y EspecificidadRESUMEN
Vector-borne diseases result in significant morbidity and mortality in domestic dogs in tropical and subtropical regions and also pose a potential threat to wildlife species and humans. Ehrlichia canis, the causative agent of canine monocytic ehrlichiosis (CME), has a high reported seroprevalence in dogs on Santa Cruz in the Galápagos Islands, Ecuador. Veterinary diagnostic and treatment resources are often scarce and clinical follow-up is lacking in the Galápagos. This study evaluated 58 dogs presenting to the Darwin Animal Doctors clinic in the city of Puerto Ayora on Santa Cruz Island during August of 2018. The seroprevalence of E. canis/Ehrlichia ewingii (48.3%), Anaplasma phagocytophilum/Anaplasma platys (12.1%), and Borrelia burgdorferi (0%), as well as the proportion of dogs actively infected with E. canis (12.1%) and E. ewingii (0%), are reported. Active infection was defined as the identification of antigen by PCR. Dogs with a packed cell volume (PCV) ≤ 30% had a 10-fold risk of active infection with E. canis compared to dogs with a PCV ≥ 31% (p = .0124). A PCV cutoff of 30% may be a useful screening tool for active E. canis infection in regions with high Ehrlichia seroprevalence, in the absence of other apparent causes of anemia. Dirofilaria immitis antigen was present in 6.9% of examined dogs, with the highest prevalence in the barrio Las Ninfas. PCR and Sanger sequencing were used to provide the first molecular identification of D. immitis in the Galápagos. This study updates the seropositivity and prevalence data of these canine vector-borne pathogens and highlights the need for continued surveillance in the region.