ABSTRACT Introduction: Rodents are potential transmitters of Leptospira spp. In the municipality of Villavicencio, Colombia, leptospirosis is a disease that, although notifiable, is still underreported. In this region, rodent species that can host pathogenic leptospira remain unknown. Objective: To detect the presence of Leptospira spp. through molecular analysis in rodents (Rodentia) from peri-urban and rural areas belonging to the municipality of Villavicencio in Colombia. Methods: Peri-urban and rural areas of the townships belonging to Villavicencio municipality were selected for sampling. These areas presented similar ecological conditions: they were near water bodies and peridomiciliary areas, and some of them included fields of agricultural crops. Rodents´ kidneys were removed and frozen in liquid nitrogen. DNA was extracted using a commercial kit and subsequently amplified through conventional polymerase chain reaction. Results: The rodent species collected were: Rattus rattus, Mus musculus, Zygodontomys brevicauda, Oligoryzomys sp, Hylaeamys (formerly Oryzomys) and Proechimys cf. oconnelli. Leptospira DNA was amplified in six rodents and the purified amplicons were sent to Macrogen Inc. (Seoul, Korea) for sequencing. The alignment analysis of the sequenced products demonstrated 98.64% of coverage and identity with Leptospira interrogans. Conclusions: This is the first study carried out on wild and synanthropic rodents in the municipality of Villavicencio. The incidence of leptospirosis raises the alarm due to the important role of these small mammals in the transmission of this zoonosis, which is considered the second cause, after dengue, of undifferentiated febrile illness in Villavicencio.

RESUMEN Introducción: Los roedores son potenciales transmisores de Leptospira spp. En el municipio de Villavicencio, Colombia, la leptospirosis es una enfermedad que, aunque debe notificarse obligatoriamente, sigue subreportada. En esta región, algunas especies de roedores pueden ser reservorios de leptospiras patógenas, situación que se desconoce. Objetivo: Detectar la presencia de Leptospira spp. a través del análisis molecular en roedores (Rodentia) de áreas periurbanas y rurales del municipio de Villavicencio, Colombia. Métodos: Para el trampeo se seleccionaron áreas periurbanas y rurales de las veredas pertenecientes al municipio de Villavicencio. Las áreas escogidas presentaban condiciones ecológicas similares: cerca de cuerpos de agua y áreas peridomiciliarias; algunas de ellas localizadas en campos de cultivos de la agricultura. Se extirparon los riñones de los roedores y se conservaron en nitrógeno líquido. Se extrajo el ADN usando un estuche comercial y posteriormente se amplificó mediante reacción en cadena de la polimerasa convencional. Resultados: Las especies de roedores colectadas fueron: Rattus rattus, Mus musculus, Zygodontomys brevicauda, Oligoryzomys sp., Hylaeamys (ahora Oryzomys) y Proechimys oconnelli. El ADN de leptospira se amplificó en seis roedores y los amplicones purificados se enviaron a Macrogen Inc. (Seoul, Korea) para secuenciación. El análisis de alineamiento de los productos secuenciados demostró un 98,64 % de cobertura e identidad con Leptospira interrogans. Conclusiones: Este es el primer estudio llevado a cabo en roedores silvestres y sinantrópicos en el municipio de Villavicencio. La incidencia de la leptospirosis genera una alarma con respecto a la importancia del papel de esos pequeños mamíferos en la transmisión de esta zoonosis, la cual es la segunda causa de los síndromes febriles indiferenciados en Villavicencio, después del dengue.

BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a virus of zoonotic origin that can bind to ACE2 receptors on the cells of many wild and domestic mammals. Studies have shown that the virus can circulate among animals mutate, lead to animal-to-human zoonotic jump, and further onward spread between humans. Infection in pets is unusual, and there are few human-to-pet transmission reports worldwide. OBJECTIVE To describe the SARS-CoV-2 infection in a domestic animal in Córdoba, Colombian Caribbean region. METHODS A cross-sectional molecular surveillance study was carried out, oral and rectal swabs were taken from cats and dogs living with people diagnosed with coronavirus disease 2019 (COVID-19). RESULTS SARS-CoV-2 was found in a cat living with a person with COVID-19. Genome sequencing showed that the B.1.111 lineage caused the infection in the cat. The owner’s sample could not be sequenced. The lineage is predominant in Colombia, and this variant is characterised by the presence of the D614D and Q57H mutation. CONCLUSION The present work is the first report of an infected cat with SARS-CoV-2 with whole-genome sequencing in Colombia. It highlights the importance of detecting SARS-CoV-2 mutations that could promote the transmissibility of this new coronavirus. There is still a significant information gap on human-to-cat-to-human infection; we encourage self-isolation measures between COVID-19 patients and companion animals. The findings of this study give a preliminary view of the current panorama of SARS-CoV-2 infection in animals in Colombia.

Resumen Se formulan recomendaciones de un grupo de consenso de expertos sobre los criterios para evaluar el desempeño diagnóstico (tamaño y selección de muestras para sensibilidad y especificidad analíticas, criterios para establecer límites de detección, criterios para establecer el estándar de oro para las serologías) que deberían ser tenidos en cuenta al evaluar y validar las pruebas diagnósticas para SARS CoV-2. Con el propósito de asegurar la calidad de las pruebas serológicas a utilizar en el país, se recomienda la participación en un programa de control de calidad externo, que garantice la idoneidad y desempeño en la realización de las pruebas diagnósticas serológicas y moleculares durante esta pandemia, ya que su uso tiene profundas implicaciones para las medidas de intervención clínicas individuales y de seguimiento y control en salud pública.

Abstract We formulate recommendations from a consensus working group on the criteria to evaluate the diagnostic performance (size and criteria of selection of samples to determine sensitivity, analytical specificity, criteria for limit of detection, criteria for gold standard to evaluate serological assays) that should be taken into account during the evaluation and validation/verification of diagnostic tests for SARS CoV-2 infection. A national external quality control program should be established to guarantee the suitability and performance of these diagnostic serological and molecular tests during this pandemic, that will have deep implications for decisions on clinical and public health.

Abstract INTRODUCTION: In Colombia, there is insufficient epidemiological surveillance of zoonotic hemorrhagic viruses. METHODS: We performed a sero-epidemiological study in indigenous populations of Wayuü, Kankuamos, and Tuchin communities using Maciel hantavirus and Junin arenavirus antigens for IgG detection by ELISA. RESULTS IgG antibodies to hantavirus and arenavirus were found in 5/506 (1%) and 2/506 (0.4%) serum samples, respectively. CONCLUSIONS: Arenavirus and hantavirus circulate in indigenous populations from the Colombian Caribbean region, and the results indicate that the indigenous populations are exposed to these zoonotic agents, with unknown consequences on their health, despite low seroprevalence.

ABSTRACT Introduction: Rickettsia is a genus of Gram-negative obligate intracellular bacteria that cause several epidemics around the world and are transmitted mainly by ticks, fleas, lice and mites. Rickettsiosis is a re-emergent infectious disease without epidemiological surveillance in Colombia. Until few years ago, Rickettsia rickettsi was the only tick-borne Rickettsioses in America; however, new species are being described, and although their pathogenicity has not been confirmed, they should be considered as potential pathogens. Objective: The aim of this study was to determine the presence of rickettsial agents in ticks in the state of Meta, Colombia. Material and Methods: A descriptive cross-sectional study was conducted; ticks were collected and, after their taxonomic identification, gltA,ompAand ompB genes were amplified and sequenced. Results: A total of 169 pools were obtained to which PCR were carried out, of which 2 PCR were amplified for the gltA, ompA and ompB genes. Conclusions: These results demonstrate the presence of Rickettsia spp in ticks in the State of Meta.

RESUMEN Introducción: Las Rickettsias son un género de bacterias Gram negativas intracelulares obligadas causantes de muchas epidemias en el mundo y son transmitidas principalmente por garrapatas, pulgas, piojos y ácaros. Las rickettsiosis son enfermedades infecciosas reemergentes sin vigilancia epidemiológica en Colombia. Hasta hace pocos años Rickettsia rickettsi era la única Rickettsia transmitida por garrapatas presente en América; sin embargo, nuevas especies están siendo descritas, y aunque su patogenicidad no ha sido confirmada pueden ser consideradas patógenos potenciales. Objetivo: Determinar la presencia de rickettsias en garrapatas del departamento del Meta, Colombia. Material y Métodos: Se realizó un estudio descriptivo de corte transversal, fueron colectadas garrapatas y después de su identificación taxonómica, los genes gltA, ompA y ompB fueron amplificados y secuenciados. Resultados: Se obtuvieron un total de 169 grupos a los que se les realizó PCR de los cuales 2 grupos amplificaron para los genes gltA, ompA y ompB. Conclusiones: Los resultados demuestran la presencia de Rickettsia spp en garrapatas del departamento del Meta.

Resumen Objetivo. El objetivo de este estudio fue proporcionar evidencia molecular de infección por C. burnetii en ovinos y caprinos de algunos rebaños de Valledupar, Cesar, Colombia. Materiales y métodos. Quince rebaños de ovinos y caprinos fueron seleccionados a conveniencia para investigar la infección por C. burnetii, durante marzo y abril de 2013. En este estudio se incluyeron 328 caprinos y 66 ovinos de 15 rebaños. La leche procedente de ovinos y muestras de moco vaginal de caprinos fueron analizados mediante PCR (Reacción en Cadena de Polimerasa) para la detección de ADN del gen transposasa (IS1111) de C. burnetii. Resultados. Se encontró ADN de C. burnetii en 6% (4/66) de leche de oveja y 0,6% (2/328) de moco vaginal de cabras. El 13% (2/15) de los rebaños tenían al menos un animal infectado. Discusión. Nuestros hallazgos sugieren la circulación de C. burnetii en ovinos y caprinos de algunos rebaños de Valledupar, Colombia, y destaca la posibilidad de ocurrencia de infecciones en humanos y animales. Conclusiones. La detección de C. burnetii en la leche de oveja podría representar un factor de riesgo para la salud pública de las personas que consumen con frecuencia leche cruda, quesos o personas que trabajan en la agricultura y manipulación de ganado. Otros estudios son necesarios para evaluar otras rutas como la mordedura de la garrapata, las heces, la leche de las cabras y el moco vaginal de las ovejas de esta región de Colombia.

Abstract Objective. The aim of this study was to provide molecular evidence of C. burnetii in sheep and goats from some herds of Valledupar, Cesar, Colombia. Materials and methods. Fifteen herds of sheep and goats were chosen by convenience to investigate the infection by C. burnetii, during March and April of 2013. 328 female goats and 66 sheep from 15 herds were included in this study. Milk from ewes and vaginal mucus samples from goats were analyzed by Polymerase Chain Reaction for DNA detection of transposase gene (IS1111) of C. burnetii. Results. DNA of C. burnetii in 6% (4/66) of sheep’s milk and 0.6% (2/328) vaginal mucus from goats was found. 13% (2/15) of the herds had at least one infected animal. Discussion. Our findings suggest the circulation of C. burnetii in sheep and goats from some herds of Valledupar, Colombia, and it highlights the possibility of occurrence of infections in humans and animals. Conclusions. The detection of C. burnetii in sheep milk could represent a public health risk factor for people who consuming raw milk, cheeses or people associated to agriculture and livestock handling. Further studies are necessary to evaluate other routes such as tick’s bite, feces, milk from goats and vaginal mucus from sheep of this region of Colombia.

Abstract The last past two decades, there has been a tremendous expansion in the discovery and description of novel insect- specific viruses (ISVs). This has corresponded with progresses in metagenomic analyses for virus revealing and the increasing attention in insect microbiomes. Plentiful of the new ISVs seem to be members of the family Flaviviridae, genus Flavivirus, and are usual in insect populations in wildlife, with a global geographic circulation.