Development and Optimization of a Multiplex Real-Time RT-PCR to Detect SARS-CoV-2 in Human Samples.

PCR and its variants (RT-PCR and qRT-PCR) are valuable and innovative molecular techniques for studying nucleic acids. qPCR has proven to be highly sensitive, efficient, and reproducible, generating reliable results that are easy to analyze. During the COVID-19 pandemic, qPCR became the gold standard technique for detecting the SARS-CoV-2 virus that allowed to confirm the infection event, and those asymptomatic ones, and thus save millions of lives. In-house multiplex qPCR tests were developed worldwide to detect different viral targets and ensure results, follow the infections, and favor the containment of a pandemic. Here, we present the detailed fundamentals of the qPCR technique based on fluorogenic probes and processes to develop and optimize a successful multiplex RT-qPCR test for detecting SARS-CoV-2 that could be used to diagnose COVID-19 accurately.

Field validation of the performance of paper-based tests for the detection of the Zika and chikungunya viruses in serum samples.

In low-resource settings, resilience to infectious disease outbreaks can be hindered by limited access to diagnostic tests. Here we report the results of double-blinded studies of the performance of paper-based diagnostic tests for the Zika and chikungunya viruses in a field setting in Latin America. The tests involved a cell-free expression system relying on isothermal amplification and toehold-switch reactions, a purpose-built portable reader and onboard software for computer vision-enabled image analysis. In patients suspected of infection, the accuracies and sensitivities of the tests for the Zika and chikungunya viruses were, respectively, 98.5% (95% confidence interval, 96.2-99.6%, 268 serum samples) and 98.5% (95% confidence interval, 91.7-100%, 65 serum samples) and approximately 2 aM and 5 fM (both concentrations are within clinically relevant ranges). The analytical specificities and sensitivities of the tests for cultured samples of the viruses were equivalent to those of the real-time quantitative PCR. Cell-free synthetic biology tools and companion hardware can provide de-centralized, high-capacity and low-cost diagnostics for use in low-resource settings.

A Case Series of Severe Dengue with Neurological Presentation in Children from a Colombian Hyperendemic Area.

Dengue transmission is sustained in Colombia with increasing prevalence mainly in children. This work aimed to describe a case series of children diagnosed with dengue presenting neurological disease in Huila Province of Colombia. Eleven pediatric febrile patients confirmed for dengue disease and presenting neurological signs were studied in the University Hospital of Neiva, Huila Province. Clinical and laboratory findings, CSF cytochemical analysis, neurology images, and serology and molecular studies were performed. Viral RNA was detected in all patients' sera by RT-PCR. Nine out of 11 were primary infections. Tonic-clonic seizures (73%), consciousness alterations (27%), irritability (27%), and ataxia (18%) were the most frequent neurological signs. None of the patients had plasma leakage, hypovolemic shock, or liver disease, confirming the encephalitis diagnosis. Diagnostic images did not show abnormal findings, but neither bacterial nor fungal infections were detected in CSF analysis. All patients survived without sequelae except for one patient that presented ataxia for months. In conclusion, we described a group of children with neurological signs during severe dengue disease as the main finding, indicating the importance to including dengue as a differential diagnosis in neurological patients from endemic areas.

Prevalence of dengue antibodies in healthy children and adults in different Colombian endemic areas.

OBJECTIVES: Colombia is a dengue hyperendemic country; however, the prevalence of antibodies against dengue in the general population including the inhabitants of rural areas is unknown. This study aimed to determine the prevalence of dengue IgM and IgG antibodies in healthy children and adults in urban and rural areas of seven different endemic regions in Colombia between 2013 and 2015. DESIGN OR METHOD: Blood samples from healthy volunteers (1,318) were processed by serology (by indirect IgG and capture IgM and IgG ELISA) and molecular tests to detect viral RNA and circulating serotypes. RESULTS: The seroprevalence of IgG for dengue were 85% in children and over 90% for adults. In addition to the high IgM positive rate (14.9%) and secondary recent infection marker rate (capture IgG, 16%), 8.4% of the healthy volunteers were positive for dengue virus (DENV) RNA. CONCLUSION: This study confirmed the broad and permanent circulation of DENV in Colombia and the high rates of infection and reinfection suffered by its inhabitants. This information can be used by the health authorities to strengthen vector control and vaccine policies and review the algorithms of diagnosis and disease management in children and adults.

Aislamiento de citomegalovirus humano a partir de fluidos corporales / Isolation of the human cytomegalovirus from bodily fluids

ABSTRACT In vitro studies on the pathogenesis of the human cytomegalovirus (HCMV) are conducted regularly using laboratory adapted strains that lose some characteristics during the adaptation process. Since HCMV is excreted from bodily fluids during infection or reactivation, this work aimed to isolate and culture HCMV from the MRC-5 human cells found in the urine, bronchoalveolar lavage, saliva, and plasma samples of pediatric patients with probable or confirmed infection. The samples were inoculated on cell cultures either for 14 days or until a cytopathic effect (CPE) of 80 % was observed. The cell lysates and supernatants were used to perform successive viral passages. Besides HCMV, the herpes simplex virus was detected from all the saliva samples. Inoculation of the HCMV positive sera induced cell clustering and immediate monolayer damage that restricted their use. One sample of bronchoalveolar lavage induced a CPE after inoculation like that of the HCMV reference strains (Towne and Merlin), which was consequently propagated and titrated. A second viral isolate derived from the urine sample of a patient with congenital infection did not demonstrate a CPE, although presence of the virus had been confirmed using PCR. The viral isolates were examined and found to be negative for adenoviruses or enteroviruses. Despite the evident difficulty encountered for the isolation and harvesting of the HCMV, this work shows that it was possible to obtain a low passage viral strain using a modified shell vial method and inoculation protocol with extended follow-up and confirmation.

RESUMEN Estudios in vitro de la patogénesis del citomegalovirus humano (HCMV) se hace empleando cepas adaptadas de laboratorio que han perdido algunas de sus características durante ese proceso. En vista que el HCMV se excreta en distintos fluidos corporales, dependiendo de la condición clínica del paciente, en este trabajo se propuso aislar y propagar HCMV en fibroblastos MRC-5 usando muestras de orina, lavado broncoalveolar, saliva y plasma de pacientes pediátricos. Estas muestras fueron inoculadas sobre los cultivos celulares por 14 días o hasta alcanzar un efecto citopático en el 80 % de la monocapa. El lisado celular y el sobrenadante del aislamiento se usaron para hacer pasajes virales sucesivos. Además de HCMV, el virus de herpes simple se aisló en todas las muestras de saliva. Con el empleo de los sueros positivos para HCMV se observó la formación de agregados y daño inmediato en la monocapa que impidieron su uso. Una muestra de lavado broncoalveolar indujo ECP desde la inoculación, similar al control positivo para HCMV (cepas Towne y Merlin), por lo que fue propagada y se tituló. Un segundo aislamiento viral obtenido de la orina de un paciente con infección congénita no produjo ECP a pesar de ser confirmado por PCR. En los aislamientos llevados hasta el pasaje 1, se descartó la presencia de enterovirus y adenovirus. A pesar de la evidente dificultad para aislar y propagar el HCMV, fue posible obtener un aislamiento usando un protocolo de Shell vial e inoculación modificado, y con un seguimiento prolongado del proceso.

Dengue Virus Infection of Blood-Brain Barrier Cells: Consequences of Severe Disease.

More than 500 million people worldwide are infected each year by any of the four-dengue virus (DENV) serotypes. The clinical spectrum caused during these infections is wide and some patients may develop neurological alterations during or after the infection, which could be explained by the cryptic neurotropic and neurovirulent features of flaviviruses like DENV. Using in vivo and in vitro models, researchers have demonstrated that DENV can affect the cells from the blood-brain barrier (BBB) in several ways, which could result in brain tissue damage, neuronal loss, glial activation, tissue inflammation and hemorrhages. The latter suggests that BBB may be compromised during infection; however, it is not clear whether the damage is due to the infection per se or to the local and/or systemic inflammatory response established or activated by the BBB cells. Similarly, the kinetics and cascade of events that trigger tissue damage, and the cells that initiate it, are unknown. This review presents evidence of the BBB cell infection with DENV and the response established toward it by these cells; it also describes the consequences of this response on the nervous tissue, compares these evidence with the one reported with neurotropic viruses of the Flaviviridae family, and shows the complexity and unpredictability of dengue and the neurological alterations induced by it. Clinical evidence and in vitro and in vivo models suggest that this virus uses the bloodstream to enter nerve tissue where it infects the different cells of the neurovascular unit. Each of the cell populations respond individually and collectively and control infection and inflammation, in other cases this response exacerbates the damage leaving irreversible sequelae or causing death. This information will allow us to understand more about the complex disease known as dengue, and its impact on a specialized and delicate tissue like is the nervous tissue.