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The healthcare workers are considered as a high-risk group for infection with SARS-CoV-2, so they were included in the first stage of the National Plan for Vaccination against COVID-19 in Colombia.An ongoing prospective cohort study to evaluate immune response to vaccination included 490 workers from health institutions in Bogotá, Colombia, vaccinated between March and June 2021 with BNT162b2 (Pfizer-BioNtech). Multiple samples were collected during a follow-up period of 6 months after immunization. We report cases of asymptomatic and symptomatic SARS-CoV-2 infections detected in this cohort. For each participant demographic data, vaccination dates, results for SARS-CoV-2 RT-PCR, and detection of antibody (IgG) tests during the follow-up period were collected.SARS-CoV-2 infection was detected in 38 (7.7 %) volunteers. Of these, 81.6% had a positive RT-PCR for SARS-CoV-2, and 18.4% were confirmed by detection of IgG anti-SARS-CoV-2 nucleoprotein; 76.3% of infections occurred after 7 days of second dose. A total of 57.9% of the cases were asymptomatic. No hospitalizations or deaths were registered. When infection occurred, 81.6% of infected participants had presence of IgG anti-S antibodies. In 12 samples in which genomic characterization was achieved, 83.4% corresponded to the variant Mu, 8.3% Gamma, and 8.3% Delta.All findings agree with other reports in different studies that show the benefit of COVID-19 vaccines, protecting specially against severe disease but not against infection or re-infection.

Resumen Introduccion La pandemia de COVID-19 ha ocasionado cerca de 25 millones de casos en el mundo Se ha descrito que los pacientes asintomaticos pueden ser fuentes de transmision Sin embargo, es dificil detectarlos y no es claro su papel en la dinamica de transmision del virus, lo que obstaculiza la implementacion de estrategias para la prevencion Objetivo Describir el comportamiento de la infeccion asintomatica por SARS-CoV-2 en una cohorte de trabajadores del Aeropuerto Internacional El Dorado "Luis Carlos Galan Sarmiento" de Bogota, Colombia Materiales y metodos Se diseno una cohorte prospectiva de trabajadores del Aeropuerto El Dorado El seguimiento se inicio en junio de 2020 con una encuesta a cada trabajador para caracterizar sus condiciones de salud y trabajo Cada 21 dias se tomo una muestra de hisopado nasofaringeo para detectar la presencia del SARS-CoV-2 mediante reaccion en cadena de la polimerasa con transcriptasa inversa (RT-PCR) Se analizo el comportamiento del umbral del ciclo (cycle threshold) de los genes ORFlab y N segun el dia de seguimiento Resultados En los primeros tres seguimientos de la cohorte se encontro una incidencia de la infeccion por SARS-CoV-2 del 16,51 % La proporcion de contactos positivos fue del 14,08 % La mediana del umbral del ciclo fue de 33,53 Conclusion Se determinaron las caracteristicas de la infeccion asintomatica por el SARS-CoV-2 en una cohorte de trabajadores La deteccion de infectados asintomaticos sigue siendo un reto para los sistemas de vigilancia epidemiologica Introduction: The 2019 coronavirus pandemic (COVID-19) has caused around 25 million cases worldwide Asymptomatic patients have been described as potential sources of transmission However, there are difficulties to detect them and to establish their role in the dynamics of virus transmission, which hinders the implementation of prevention strategies Objective: To describe the behavior of asymptomatic SARS-CoV-2 virus infection in a cohort of workers at the El Dorado "Luis Carlos Galan Sarmiento" International Airport in Bogota, Colombia Materials and methods: A prospective cohort of 212 workers from the El Dorado airport was designed The follow-up began in June, 2020 A survey was used to characterize health and work conditions Every 21 day, a nasopharyngeal swab was taken to identify the presence of SARS-CoV-2 using RT-PCR We analyzed the behavior of the cycle threshold (ORFlab and N genes) according to the day of follow-up Results: In the first three follow-ups of the cohort, we found an incidence of SARS-CoV-2 infection of 16 51% The proportion of positive contacts was 14 08% The median threshold for cycle threshold was 33 53 Conclusion: We characterized the asymptomatic SARS-CoV-2 infection in a cohort of workers The identification of asymptomatic infected persons continues to be a challenge for epidemiological surveillance systems

The COVID-19 pandemic caused by SARS-CoV-2 is a public health problem on a scale unprecedented in the last 100 years, as has been the response focused on the rapid genomic characterization of SARS-CoV-2 in virtually all regions of the planet. This pandemic emerged during the era of genomic epidemiology, a science fueled by continued advances in next-generation sequencing. Since its recent appearance, genomic epidemiology included the precise identification of new lineages or species of pathogens and the reconstruction of their genetic variability in real time, evidenced in past outbreaks of influenza H1N1, MERS, and SARS. However, the global and uncontrolled scale of this pandemic created a scenario where genomic epidemiology was put into practice en masse, from the rapid identification of SARS-CoV-2 to the registration of new lineages and their active surveillance throughout the world. Prior to the COVID-19 pandemic, the availability of genomic data on circulating pathogens in several Latin America and the Caribbean countries was scarce or nil. With the arrival of SARS-CoV-2, this scenario changed significantly, although the amount of available information remains scarce and, in countries such as Colombia, Brazil, Argentina, and Chile, the genomic information of SARS-CoV-2 was obtained mainly by research groups in genomic epidemiology rather than the product of a public health surveillance policy or program. This indicates the need to establish public health policies aimed at implementing genomic epidemiology as a tool to strengthen surveillance and early warning systems against threats to public health in the region.La pandemia de COVID-19 causada por el SARS-CoV-2 es un problema de salud pública sin precedentes en los últimos 100 años, así como la respuesta centrada en la caracterización genómica del SARS-CoV-2 prácticamente en todas las regiones del planeta. Esta pandemia surgió durante la era de la epidemiología genómica impulsada por los continuos avances en la secuenciación de próxima generación. Desde su reciente aparición, la epidemiología genómica permitió la identificación precisa de nuevos linajes o especies de agentes patógenos y la reconstrucción de su variabilidad genética en tiempo real, lo que se hizo evidente en los brotes de influenza H1N1, MERS y SARS. Sin embargo, la escala global y descontrolada de esta pandemia ha generado una situación que obligó a utilizar de forma masiva herramientas de la epidemiología genómica como la rápida identificación del SARS-CoV-2 y el registro de nuevos linajes y su vigilancia activa en todo el mundo. Antes de la pandemia de COVID-19 la disponibilidad e datos genómicos de agentes patógenos circulantes en varios países de Latinoamérica y el Caribe era escasa o nula. Con la llegada del SARS-CoV-2 dicha situación cambió significativamente, aunque la cantidad de información disponible sigue siendo escasa y, en países como Colombia, Brasil, Argentina y Chile, la información genómica del SARS-CoV-2 provino principalmente de grupos de investigación en epidemiología genómica más que como producto de una política o programa de vigilancia en salud pública.

Resumen Introduccion El nuevo coronavirus causante de un brote de enfermedad respiratoria aguda en China en diciembre de 2019 se identifico como SARS-CoV-2 La enfermedad, denominada COVID-19, fue declarada pandemia por la Organizacion Mundial de la Salud (OMS) El primer caso de COVID-19 en Colombia se reporto el 6 de marzo de 2020;en este estudio se caracterizo un aislamiento temprano del virus SARS-CoV-2 de una muestra recolectada en abril de 2020 Objetivos Describir y caracterizar una cepa temprana a partir de un aislamiento de SARS-CoV-2 durante la pandemia en Colombia Materiales y metodos Se obtuvo una muestra de un paciente con COVID-19 confirmada por qRT-PCR;la muestra fue inoculada en diferentes lineas celulares hasta la aparicion del efecto citopatico Para confirmar la presencia de SARS-CoV-2 en el cultivo, se utilizo la qRT-PCR a partir de los sobrenadantes, la inmunofluorescencia indirecta (IFI) en celulas Vero-E6, asi como microscopia electronica y secuenciacion de nueva generacion (next-generation sequencing) Resultados Se confirmo el aislamiento de SARS-CoV-2 en celulas Vero-E6 por la aparicion del efecto citopatico tres dias despues de la infeccion, asi como mediante la qRT-PCR y la IFI positiva con suero de paciente convaleciente positivo para SARS-CoV-2 Ademas, en las imagenes de microscopia electronica de trasmision y de barrido de celulas infectadas se observaron estructuras compatibles con viriones de SARS-CoV-2 Por ultimo, se obtuvo la secuencia completa del genoma, lo que permitio clasificar el aislamiento como linaje B 1 5 Conclusiones La evidencia presentada en este articulo permite confirmar el primer aislamiento de SARS-CoV-2 en Colombia Ademas, muestra que esta cepa se comporta en cultivo celular de manera similar a lo reportado en la literatura para otros aislamientos y que su composicion genetica esta acorde con la variante predominante en el mundo Finalmente, se resalta la importancia que tiene el aislamiento viral para la deteccion de anticuerpos, para la caracterizacion genotipica y fenotipica de la cepa y para probar compuestos con potencial antiviral Introduction: SARS-CoV-2 has been identified as the new coronavirus causing an outbreak of acute respiratory disease in China in December, 2019 This disease, currently named COVID-19, has been declared as a pandemic by the World Health Organization (WHO) The first case of COVID-19 in Colombia was reported on March 6, 2020 Here we characterize an early SARS-CoV-2 isolate from the pandemic recovered in April, 2020 Objective: To describe the isolation and characterization of an early SARS-CoV-2 isolate from the epidemic in Colombia Materials and methods: A nasopharyngeal specimen from a COVID-19 positive patient was inoculated on different cell lines To confirm the presence of SARS-CoV-2 on cultures we used qRT-PCR, indirect immunofluorescence assay, transmission and scanning electron microscopy, and next-generation sequencing Results: We determined the isolation of SARS-CoV-2 in Vero-E6 cells by the appearance of the cytopathic effect three days post-infection and confirmed it by the positive results in the qRT-PCR and the immunofluorescence with convalescent serum Transmission and scanning electron microscopy images obtained from infected cells showed the presence of structures compatible with SARS-CoV-2 Finally, a complete genome sequence obtained by next-generation sequencing allowed classifying the isolate as B 1 5 lineage Conclusion: The evidence presented in this article confirms the first isolation of SARS-CoV-2 in Colombia In addition, it shows that this strain behaves in cell culture in a similar way to that reported in the literature for other isolates and that its genetic composition is consistent with the predominant variant in the world Finally, points out the importance of viral isolation for the detection of neutralizing antibodies, for the genotypic and phenotypic characterization of the strain and for testing compounds with antiviral potential

BackgroundBy March 2022, around 34 million people in Colombia had received a complete scheme of vaccines against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) including, mRNA-based vaccines, viral vectored coronavirus vaccines, or the inactivated whole virus vaccine. However, as several SARS-CoV-2 variants of concern (VOC) and interest (VOI) co-circulate in the country, determining the resistance level to vaccine-elicited neutralizing antibodies (nAbs) is useful to improve the efficacy of COVID-19 vaccination programs.MethodsMicroneutralization assays with the most prevalent SARS-CoV-2 lineages in Colombia during 2020-2021 were performed using serum samples from immunologically naïve individuals between 9 and 13 weeks after receiving complete regimens of CoronaVac, BNT162b2, ChAdOx1, or Ad26.COV2.S. The mean neutralization titer (MN50) was calculated by the Reed–Muench method and used to determine differences in vaccine-elicited nAbs against the SARS-CoV-2 lineages B.1.111, P.1 (Gamma), B.1.621 (Mu), and AY.25.1 (Delta).ResultsThe most administered vaccines in the country, BNT162b2 and CoronaVac, elicited significantly different nAb responses against Mu, as the GMTs were 75.7 and 5.9-fold lower relative to the control lineage (B.1.111), while for Delta were 15.8 and 1.1-fold lower, respectively. In contrast, nAb responses against Mu and Delta were comparable between ChAd0×1-s and Ad26.COV2.S as the GMTs remained around 5 to 7-fold lower relative to B.1.111.ConclusionsThe emergence of SARS-CoV-2 variants in Colombia with a significant capacity to escape from vaccine-elicited nAbs indicates that a booster dose is highly recommended. Furthermore, other non-pharmacological measures should be retained in the vaccinated population.

Global surveillance programs for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are showing the emergence of variants with mutations in the spike protein. Genomic and laboratory surveillance are important to determine if these variants may be more infectious or less susceptible to antiviral treatments and vaccine-induced antibodies. Three of the most predominant SARS-CoV-2 variants in Colombia during the epidemiological peaks of 2021 were isolated: Mu, a variant of interest; Gamma, a variant of concern; B.1.111, which lacks genetic markers associated with greater virulence. Microneutralization assays were performed by incubating 120 mean tissue culture infectious doses (TCID50) of each SARS-CoV-2 isolate with five two-fold serial dilutions of sera from 31 BNT162b2-vaccinated volunteers. The mean neutralization titer (MN50) was calculated by the Reed–Muench method. At the end of August, Mu represented 49% of coronavirus disease 2019 (COVID-19) cases in Colombia, followed by 25% of Gamma. In contrast, B.1.111 became almost undetectable. The evaluation of neutralizing antibodies suggests that patients vaccinated with BNT162b2 generate neutralizing antibody titers against the Mu variant at significantly lower concentrations relative to B.1.111 and Gamma. This study shows the importance of continuing surveillance programs of emerging variants, as well as the need to evaluate the neutralizing antibody response induced by other vaccines.

SummaryBackgroundGlobal surveillance programs for the virus that causes COVID-19 are showing the emergence of variants with mutations in the Spike protein, including the Mu variant, recently declared a Variant of Interest (VOI) by the World Health Organization. Genomic and laboratory surveillance is important in these types of variants because they may be more infectious or less susceptible to antiviral treatments and vaccine-induced antibodies.ObjectivesTo evaluate the sensitivity of the Mu variant (B.1.621) to neutralizing antibodies induced by the BNT162b2 vaccine.Study designThree of the most predominant SARS-CoV-2 variants in Colombia during the epidemiological peaks of 2021 were isolated. Microneutralization assays were performed by incubating 120 TCDI50 of each SARS-CoV-2 isolate with five 2-fold serial dilutions of sera from 14 BNT162b2 vaccinated volunteers. The MN50 titer was calculated by the Reed-Muench formulaResultsThe three isolated variants were Mu, a Variant of Interest (VOI), Gamma, a variant of concern (VOC), and B.1.111 that lacks genetic markers associated with greater virulence. At the end of August, the Mu and Gamma variants were widely distributed in Colombia. Mu was predominant (49%), followed by Gamma (25%). In contrast, B.1.111 became almost undetectable. The evaluation of neutralizing antibodies suggests that patients vaccinated with BNT162-2 generate neutralizing antibody titers against the Mu variant at significantly lower concentrations relative to B.1.111 and Gamma.ConclusionsThis study shows the importance of continuing with surveillance programs of emerging variants as well as the need to evaluate the neutralizing antibody response induced by other vaccines circulating in the country against Mu and other variants with high epidemiological impact.HighlightsMu and Gamma variants represented 49% and 25% of cases in Colombia by August 2021.Increased proportion of SARS-COV-2 cases were mostly associated with Mu variant, despite being detected simultaneously with the VOC GammaThe Mu variant remarkably escapes from neutralizing antibodies elicited by the BNT162b2-vaccineLaboratory studies of neutralizing antibodies are useful to determine the efficacy of SARS-CoV-2 vaccines against VOC and VOI.

BackgroundHealthcare workers are at increased risk of infection due to occupational exposure to SARS-CoV-2-infected patients. The objective of this study was to determine the seroprevalence of SARS-CoV-2 in healthcare workers in Colombia.MethodsThis study is a cross-sectional study focused on estimating the seroprevalence of SARS-CoV-2 antibodies in healthcare workers from 65 hospitals in 10 cities in Colombia during the second semester of 2020. The seroprevalence was determined using an automated immunoassay (Abbott SARS-CoV-2 CLIA IgG). The study included a survey to establish the sociodemographic variables and the risk of infection. A multivariate model was used to evaluate the association between the results of seroprevalence and risk factors.ResultsThe global seroprevalence of antibodies against SARS-CoV-2 was 35% (95% Bayesian CI 33% to 37%). All the personnel reported the use of protective equipment. General services personnel and nurses presented the highest ratios of seroprevalence among the healthcare workers. Low socioeconomic strata have shown a strong association with seropositivity.ConclusionThis study estimates the prevalence of SARS-CoV-2 infection among healthcare workers. Even though all the personnel reported the use of protective equipment, the seroprevalence in the general services personnel and nurses was high. Also, a significant difference by cities was observed.

The E484K mutation at the SARS-CoV-2 Spike protein emerged independently in different variants around the world, probably as part of the ongoing adaptation of the virus to the human host, and has been widely associated with immune escape from neutralizing antibodies generated during previous infection or vaccination. In this work, the B.1+L249S+E484K lineage was isolated along with A.1, B.1.420 and B.1.111 SARS-CoV-2 lineages without the E484K mutation and the neutralizing titer of convalescent sera was compared using microneutralization assays. While no significant differences in the neutralizing antibody titers were found between A1 and B lineages without the E484K mutation, the neutralizing titers against B.1+L249S+E484K were 1.5, 1.9, 2.1, and 1.3-fold lower than against A.1, B.1.420, B.1.111-I, and B.1.111-II, respectively. However, molecular epidemiological data indicate that there is no increase in the transmissibility rate associated with this new lineage. Hence, although the evidence provided in this study support a Variant of Interest Status (VOI) for the B1+L249S+E484K lineage, enhanced laboratory characterization of this particular lineage and other emerging lineages with the E484K mutation should be carried out in individuals with immunity acquired by natural infection and vaccination. This study accentuated the capability of new variants with the E484K mutation to be resistant to neutralization by humoral immunity, and therefore the need to intensify surveillance programs.HIGHLIGHT⍰The E484K mutation in B.1+L249S+E484K appears not to affect the viral titer⍰Sensitivity of lineages without E484K mutation to neutralizing antibodies did not change⍰B.1+L249S+E484K lineage shows a reduction in its neutralizing capacity

Project Vigilancia de Embarazadas con Zika (VEZ), an intensified surveillance of pregnant women with symptoms of the Zika virus disease (ZVD) in Colombia, aimed to evaluate the relationship between symptoms of ZVD during pregnancy and adverse pregnancy, birth, and infant outcomes and early childhood neurodevelopmental outcomes. During May–November 2016, pregnant women in three Colombian cities who were reported with symptoms of ZVD to the national surveillance system, or with symptoms of ZVD visiting participating clinics, were enrolled in Project VEZ. Data from maternal and pediatric (up to two years of age) medical records were abstracted. Available maternal specimens were tested for the presence of the Zika virus ribonucleic acid and/or anti-Zika virus immunoglobulin antibodies. Of 1213 enrolled pregnant women with symptoms of ZVD, 1180 had a known pregnancy outcome. Results of the Zika virus laboratory testing were available for 569 (48.2%) pregnancies with a known pregnancy outcome though testing timing varied and was often distal to the timing of symptoms; 254 (21.5% of the whole cohort; 44.6% of those with testing results) were confirmed or presumptive positive for the Zika virus infection. Of pregnancies with a known outcome, 50 (4.2%) fetuses/infants had Zika-associated brain or eye defects, which included microcephaly at birth. Early childhood adverse neurodevelopmental outcomes were more common among those with Zika-associated birth defects than among those without and more common among those with laboratory evidence of a Zika virus infection compared with the full cohort. The proportion of fetuses/infants with any Zika-associated brain or eye defect was consistent with the proportion seen in other studies. Enhancements to Colombia’s existing national surveillance enabled the assessment of adverse outcomes associated with ZVD in pregnancy.

Objective To determine the spatial distribution of the risk of Zika virus disease in each region of Colombia during the 2015–2016 epidemic. Methods An ecological study was designed to estimate the risks for each Colombian region using first‐order neighbors, covariate effects, and three adjacent periods of time (beginning, development, and end of the epidemic) to analyze the spatial distribution of the disease based on a Bayesian hierarchical model. Results Spatial distribution of the estimated risks of Zika virus disease showed that it increased in a strip that crosses the central area of the country from west to east. Analysis of the three time periods showed greater risk of the disease in the central and southern zones—Arauca and Santander—where the increase in risk was four times higher during the peak phase compared with the initial phase of the outbreak. Conclusion In the identified high‐risk areas, integrated surveillance systems for Zika virus disease and its complications must be strengthened to provide up‐to‐date and accurate epidemiological information. This information would allow those involved in policy and decision making to identify new outbreaks and risk clusters, enabling more focused and accurate measures to target at‐risk populations., The spatial distribution of the estimated risk of Zika virus disease in Colombia was four times higher during the epidemic phase of the outbreak.

SummaryThe genetic diversity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has the potential to impact the virus transmissibility and the escape from natural infection- or vaccine-elicited neutralizing antibodies. Here, representative samples from circulating SARS-CoV-2 in Colombia between January and April 2021, were processed for genome sequencing and lineage determination following the nanopore amplicon ARTIC network protocol and PANGOLIN pipeline. This strategy allowed us to identify the emergence of the B.1.621 lineage, considered a variant of interest (VOI) with the accumulation of several substitutions affecting the Spike protein, including the amino acid changes T95I, Y144T, Y145S and the insertion 146N in the N-terminal domain, R346K, E484K and N501Y in the Receptor-binding Domain (RBD) and P681H1 in the S1/S2 cleavage site of the Spike protein. The rapid increase in frequency and fixation in a relatively short time in Magdalena, Atlántico, Bolivar, Bogotá D.C, and Santander that were near the theoretical herd immunity suggests an epidemiologic impact. Further studies will be required to assess the biological and epidemiologic roles of the substitution pattern found in the B.1.621 lineage.HighlightsMonitoring the emergence of new variants of SARS-CoV-2 in real time is a worldwide priority.Emerging variants of SARS-CoV-2 may have high impact biological implications for public healthThe SARS-CoV-2 B.1.621 variant of interest was characterized by several substitutions: T95I, Y144T, Y145S, ins146N, R346K, E484K, N501Y and P681H in spike protein.

Summary: Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to cause very high morbidity and mortality throughout Latin American countries. However, few population-based seroprevalence surveys have been conducted to quantify attack rates and characterize drivers of transmission. Methods: We conducted a population-based cross-sectional study to assess the seroprevalence of antibodies against SARS-CoV-2 in ten cities in Colombia between September and December 2020. The study involved multi-stage cluster sampling at each city. Participants provided a serum sample and answered a demographic and risk factor questionnaire. Prior infection by SARS-CoV-2 was ascertained using the ''SARS-CoV-2 Total (COV2T) Advia Centaur - Siemens'' chemiluminescence assay. Findings: A total of 17863 participants from 7320 households participated in the study. Seroprevalence varied substantially between cities, ranging from 26% (95%CI 23–29 %) in Medellín to 68% (95%CI 62–74 %) in Guapi. There were no differences in seroprevalence by sex, but seropositivity was higher in certain ethnic groups. There was substantial heterogeneity in seroprevalence within cities, driven to a large extent by a strong association between socioeconomic stratum and seropositivity. Interpretation: Colombia has been one of the Latin American countries most affected by the COVID-19 pandemic. This study documented very high attack rates in several Colombian cities by the end of 2020 and identified key drivers of heterogeneities including ethnicity and socioeconomic stratum. Few studies of seroprevalence of SARS-CoV-2 have been conducted in Latin America, and therefore this study contributes to the fundamental understanding of the pandemic in the region. Funding: The study was sponsored by, Ministerio de Ciencia y Tecnología e Innovación –CT361/2020, Ministerio de Salud y Protección Social, Fundación Universitaria del Norte, Imperial College of London, Universidad Nacional de Colombia (Sede Medellín), Universidad de Córdoba, California University, Unidad Nacional de Gestión del Riesgo, Centro de Atención y Diagnóstico de Enfermedades Infecciosas -CDI-, Centro Internacional de Entrenamiento e Investigaciones Médicas -CIDEIM-, Departamento Administrativo Nacional de Estadística - DANE, Fondo Nacional de Turismo -FONTUR-, Secretarías de Salud Departamentales, Distritales y Municipales and Instituto Nacional de Salud.

Background Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) is an emerging viral pandemic disease. In the last 6 months, SARS-CoV-2 has caused millions of reported cases and hundreds of thousands of deaths. As other world regions, South America has not contained the pandemic’s advance since it lacks the hospital and economic capacities. Public health implications of transmission, while the asymptomatic/presymptomatic infection is a critical concern at the current pandemic. Objective Describe the socio-demographic, clinical, and viral features of a cohort of SARS-CoV-2 infected individuals from the Colombian Caribbean. Methods Six hundred eighty-six clinical samples of suspected SARS-CoV-2 infection cases and contacts individuals from several hospital centers in the department of Córdoba, Colombia, were received at our laboratory between April 9th and May 16th, 2020. RNA was extracted using lysis buffers and spin columns. The samples were tested for SARS-CoV-2 by reverse transcription real-time polymerase chain reaction (RT-qPCR) using commercially available multiplex real-time PCR assay for simultaneous detection of 3 target genes of SARS-CoV-2 (Allplex™, 2019-nCoV assay, Korea). Viral copies quantification was done using a standard curve constructed from seriated dilutions of a SARS-CoV-2 positive control. Statics descriptive methods were used. Results Thirty-five nasopharyngeal samples were positive for SARS-CoV-2 infection; the average age was 43 (range, 1–95 years). Seventeen of 35 (49%) of the patients showed symptoms. Most of them had a cough, fever, and odynophagia; three of the patients reported having arthralgia. Only two patients required hospitalization. None of the patients had known co-morbidities. RT-qPCR results show that two of the symptomatic patients had significantly higher RNA copies than the rest. Eighteen of 35 (51%) individuals were asymptomatic, and the average age was 30 (range, 6–61 years). Four asymptomatic individuals showed a higher copy than some symptomatic patients; nonetheless, the average of RNA copies 8.26 × 1010 was lower than the symptomatic. Conclusions This study shows that asymptomatic patients may develop infections with a high number of RNA copies. Since a considerable percentage of infections may be asymptomatic/presymptomatic, enhanced testing approaches may be needed to detect these persons. Due the occurrence of a large proportion of infections being a result from transmission originated in asymptomatic/presymptomatic individuals, public health interventions in Colombia should be based on two steps: a massive molecular screening, and viral load quantification. Finally, a remarkable issue in our study is the average age of symptomatic and asymptomatic groups (43 and 30 respectively) which may be important because of the economic impact that has been caused by the coronavirus pandemic and may be probably the cause of the reduced lethality observed in the country and the department at the time of this study.

Coronavirus disease (COVID-19) in Colombia was first diagnosed in a traveler arriving from Italy on February 26, 2020. However, limited data are available on the origins and number of introductions of COVID-19 into the country. We sequenced the causative agent of COVID-19, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), from 43 clinical samples we collected, along with another 79 genome sequences available from Colombia. We investigated the emergence and importation routes for SARS-CoV-2 into Colombia by using epidemiologic, historical air travel, and phylogenetic observations. Our study provides evidence of multiple introductions, mostly from Europe, and documents >12 lineages. Phylogenetic findings validate the lineage diversity, support multiple importation events, and demonstrate the evolutionary relationship of epidemiologically linked transmission chains. Our results reconstruct the early evolutionary history of SARS-CoV-2 in Colombia and highlight the advantages of genome sequencing to complement COVID-19 outbreak investigations.

BackgroundCOVID-19 pandemic caused by infection with the betacoronavirus SARS-CoV-2 is the greatest public health defiant on a global scale in the last 100 years. Governments and health Institutes face challenges during the pandemic, related to the diagnosis, mitigation, treatment, and timely detection after the epidemic peak for the prevention of new infections and the evaluation of the real impact of the COVID-19 disease in different geographic areas. To develop a valuable tool to study the seroprevalence of SARS-CoV-2 infection in Colombia, an “in-house” ELISA was achieved for the detection of IgG anti-SARS-CoV-2 antibodies in serum.MethodsThe test was standardized using an antigenic epitope “Pool” of the synthetic peptide as antigen derived from antigenic regions of the spike, nucleocapsid, envelope, and membrane structural proteins, which were designed, based on the genomic information of SARS-CoV-2 circulating in Colombia. In the ELISA standardization process, 94 positive sera were used, including sera from asymptomatic and symptomatic patients (mild and severe) and 123 negative sera, including pre-pandemic historical negatives originating from patients living in arbovirus endemic areas or patients with a history of respiratory diseases and sera from patients with a negative rRT-PCR test for SARS-CoV-2.ResultsThe in-house peptide ELIPSE-COL test showed promising performance, being able to detect reactivity in sera from asymptomatic and symptomatic patients. The sensitivity and specificity of the assay were 91.4% and 83.7% respectively.ConclusionELIPSE-COL assay was developed as an ELISA test using synthetic peptides for the study of the seroprevalence of SARS-CoV-2 infection in Colombia.SUMMARY BOXDetection of IgG anti-SARS-CoV-2 antibodies is required for the evaluation of the pandemic impact and vaccination strategies.ELIPSE-COL is an in-house test based on synthetic peptides as antigen derived from antigenic regions of the spike, nucleocapsid, envelope, and membrane structural proteins.The sensitivity and specificity of the assay were 91.4% and 83.7% respectively suggesting a promising performance.ELIPSE-COL test is a valuable tool for the study of seroprevalence in Colombia.

COVID-19, a global pandemic causing to date more than 50 million cases and more than a million deaths, has to be controlled. SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) was identified as the causative agent. Controversy about this virus origin and infectious mechanism for adapting to humans remains a matter for discussion. Among all strategies for obtaining safe and potent vaccines, approaches based on attenuated-killed virus and non-replicating RNA viral vectors are demonstrating promising results. However, specificity of viral components targeted by human antibodies so far has not been demonstrated. A consistent strategy for obtaining functional-active antigens from SARS-CoV-2 specific ligands lead us to propose and test a number of synthetic components. From hundreds of starting sequences only fifteen fulfilled the design requirements and were produced as monomer and polymer forms and immuno-chemically tested. The design was based on worldwide representative reported virus genomes. A bioinformatics scheme by conventional methods and knowledge on MHC-I and II antigen processing mechanisms and HLA haplotype-restriction was performed including sensitive and resistant human populations to virus infection. Covid-19 patients’ sera reactivity for synthetic SARS-CoV-2-designed components have proven a high recognition of specific molecules, as well as some evidence for a long-lasting humoral immune response.

Acute Respiratory Infections are among the leading causes of death globally, particularly in developing countries, and are highly correlated with the quality of health and surveillance systems and effective early interventions in high-risk age groups. According to the World Health Organization, about four million people die each year from mostly preventable respiratory tract infections, making it a public health concern. The official declaration of a pandemic in March 2020 due to the Sars-CoV-2 virus coincided with the influenza season in Colombia and with environmental alerts about low air quality that increase its incidence. The objective of this document is the application of a flexible model for the identification of the pattern and monitoring of ARI morbility for Colombia by age group that shows atypical patterns in the reported series for 5 departments and that coincide with the decisions implemented to contain the COVID-19.

Background. Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) is an emerging viral pandemic disease. In the last six months, SARS-CoV-2 has caused millions of reported cases and hundreds of thousands of deaths. As other world regions, nowadays, South America has not contained the pandemic's advance since it lacks the hospital and economic capacities. Public health implications of transmission, while the asymptomatic infection is a critical concern at the current pandemic.Objective: Describe the socio-demographic, clinical, and viral kinetics features of a cohort of SARS-CoV-2 infected individuals from the Colombian Caribbean. Methods: Six hundred eighty-six clinical samples of suspected SARS-CoV-2 infection cases and contacts individuals from several hospital centers in the department of Córdoba, Colombia, were received at our laboratory between April 9th and May 16th, 2020. RNA was extracted using lysis buffers and spin columns. The samples were tested for SARS-CoV-2 by RT-qPCR (Reverse transcription real-time polymerase chain reaction) using commercially available multiplex real-time PCR assay for simultaneous detection of 3 target genes of SARS-CoV-2 (AllplexTM, 2019-nCoV assay, Korea). Viral copies quantification was done using a standard curve constructed from seriated dilutions of a SARS-CoV-2 positive control. Statics descriptive methods were used. Results: Thirty-five nasopharyngeal samples were positive for SARS-CoV-2 infection; the average age was 43 (range, 1-95 years). Seventeen of 35 (49%) of the patients showed symptoms. Most of them had a cough, fever, and odynophagia; three of the patients reported having arthralgia. Only two patients required hospitalization. None of the patients had known co-morbidities. RT-qPCR results show that two of the symptomatic patients had significantly higher RNA copies than the rest. Eighteen of 35 (51%) individuals were asymptomatic, and the average age was 30 (range, 6-61 years). Four asymptomatic individuals showed a higher copy than some symptomatic patients; nonetheless, the average of RNA copies 8.26 x10+10 was lower than the symptomatic.Conclusions: the population studied was young, with an average of 43 years in symptomatic and 30 years of asymptomatic; this is important because of the high impact in the economy. Because a large proportion of infections may result from transmission from asymptomatic or pre-symptomatic persons, the usefulness of public health interventions in Colombian provinces should be based on molecular screening in a vast conglomerate population and quantify the viral load.

Coronavirus disease 2019 (COVID-19) was first diagnosed in Colombia from a traveler arriving from Italy on February 26, 2020. To date, available data on the origins and number or introductions of SARS-CoV-2 into the country are limited. Here, we sequenced SARS-CoV-2 from 43 clinical samples and—together with other 73 genomes sequences available from the country—we investigated the emergence and the routes of importation of COVID-19 into Colombia using epidemiological, historical air travel and phylogenetic observations. Our study provided evidence of multiple introductions, mostly from Europe, with at least 12 lineages being documented. Phylogenetic findings validated the lineage diversity, supported multiple importation events and the evolutionary relationship of epidemiologically-linked transmission chains. Our results reconstruct the early evolutionary history of SARS-CoV-2 in Colombia and highlight the advantages of genome sequencing to complement COVID-19 outbreak investigation.

Summary The COVID-19 pandemic caused by SARS-CoV-2 is a public health problem unprecedented in the recent history of humanity. Different in-house real-time RT-PCR (rRT-PCR) methods for SARS-CoV-2 diagnosis and the appearance of genomes with mutations in primer regions have been reported. Hence, whole-genome data from locally-circulating SARS-CoV-2 strains contribute to the knowledge of its global variability and the development and fine tuning of diagnostic protocols. To describe the genetic variability of Colombian SARS-CoV-2 genomes in hybridization regions of oligonucleotides of the main in-house methods for SARS-CoV-2 detection, RNA samples with confirmed SARS-CoV-2 molecular diagnosis were processed through next-generation sequencing. Primers/probes sequences from 13 target regions for SARS-CoV-2 detection suggested by 7 institutions and consolidated by WHO during the early stage of the pandemic were aligned with Muscle tool to assess the genetic variability potentially affecting their performance. Finally, the corresponding codon positions at the 3′ end of each primer, the open reading frame inspection was identified for each gene/protein product. Complete SARS-CoV-2 genomes were obtained from 30 COVID-19 cases, representative of the current epidemiology in the country. Mismatches between at least one Colombian sequence and five oligonucleotides targeting the RdRP and N genes were observed. The 3′ end of 4 primers aligned to the third codon position, showed high risk of nucleotide substitution and potential mismatches at this critical position. Genetic variability was detected in Colombian SARS-CoV-2 sequences in some of the primer/probe regions for in-house rRT-PCR diagnostic tests available at WHO COVID-19 technical guidelines; its impact on the performance and rates of false-negative results should be experimentally evaluated. The genomic surveillance of SARS-CoV-2 is highly recommended for the early identification of mutations in critical regions and to issue recommendations on specific diagnostic tests to ensure the coverage of locally-circulating genetic variants., Highlights • Colombian SARS-CoV-2 sequences displayed genetic variability in some target regions used for COVID-19 diagnosis. • Mismatches in critical primer regions could impact their performance and the rate of false-negative results.

Background Colombia was the second most affected country during the American Zika virus (ZIKV) epidemic, with over 109,000 reported cases. Despite the scale of the outbreak, limited genomic sequence data were available from Colombia. We sought to sequence additional samples and use genomic epidemiology to describe ZIKV dynamics in Colombia. Methods We sequenced ZIKV genomes directly from clinical diagnostic specimens and infected Aedes aegypti samples selected to cover the temporal and geographic breadth of the Colombian outbreak. We performed phylogeographic analysis of these genomes, along with other publicly-available ZIKV genomes from the Americas, to estimate the frequency and timing of ZIKV introductions to Colombia. Results We attempted PCR amplification on 184 samples; 19 samples amplified sufficiently to perform sequencing. Of these, 8 samples yielded sequences with at least 50% coverage. Our phylogeographic reconstruction indicates two separate introductions of ZIKV to Colombia, one of which was previously unrecognized. We find that ZIKV was first introduced to Colombia in February 2015 (95%CI: Jan 2015 – Apr 2015), corresponding to 5 to 8 months of cryptic ZIKV transmission prior to confirmation in September 2015. Despite the presence of multiple introductions, we find that the majority of Colombian ZIKV diversity descends from a single introduction. We find evidence for movement of ZIKV from Colombia into bordering countries, including Peru, Ecuador, Panama, and Venezuela. Conclusions Similarly to genomic epidemiological studies of ZIKV dynamics in other countries, we find that ZIKV circulated cryptically in Colombia. More accurately dating when ZIKV was circulating refines our definition of the population at risk. Additionally, our finding that the majority of ZIKV transmission within Colombia was attributable to transmission between individuals, rather than repeated travel-related importations, indicates that improved detection and control might have succeeded in limiting the scale of the outbreak within Colombia.

Our objective was to determine the frequency of zika (ZIKV), chikungunya (CHIKV) and dengue (DENV) virus coinfection and describe the mortality cases that occurred during the epidemiologic surveillance of the ZIKV epidemic in Colombia. We analysed all cases of suspected ZIKV infection that were reported to the National Institute of Health (October 2015–December 2016). DENV, CHIKV and ZIKV RNA were detected in serum or tissue samples using polymerase chain reaction assay. Medical records of the fatal cases were reviewed. We identified that 23 871 samples were processed. The frequency of viral agents was 439 (1.84%) for DENV, 257 (1.07%) for CHIKV and 10118 (42.38%) for ZIKV. Thirty-four (0.14%) cases of coinfection were identified. The CHIKV–ZIKV coinfection was present in 28 cases (82.3%), DENV–CHIKV in three (8.8%) and DENV–ZIKV in three (8.8%). Seven (20.6%) coinfection cases were fatal (two DENV–CHIKV cases and five CHIKV–ZIKV cases). Two cases were foetal deaths and the others were related to neurological syndrome and sepsis. In conclusion, the frequency of arbovirus coinfection during epidemic of ZIKV was low, and CHIKV–ZIKV coinfection was the most common. Mortality was high among coinfection patients. The role of each virus in the mortality cases of coinfection warrants further studies.

Chikungunya alphavirus has caused large epidemics worldwide and leads to acute incapacitating polyarthralgia. The inflammatory reaction over several days will drive robust innate and humoral responses essential to control the infection. Critically, fatal cases and mother-to-child transmission have also been described. Chikungunya can give rise to chronic musculoskeletal diseases, which can last for months to years, particularly in elderly individuals, and occasionally leads to seronegative rheumatoid arthritis-like pathologies. Histopathological studies of patient biopsy specimens and animal models have revealed that chikungunya virus can hide in tissue sanctuaries, and ongoing research should help to decipher the inflammatory mechanisms of tissue injuries.

Objective. To determine the prevalence of Helicobacter pylori resistance to and the possible mutations that generate this worldwide resistance. Materials and methods. A systematic search for literature was performed in the databases Medline, Science Direct (Elsevier), Ovid, PubMed, Lilacsand MedicLatina using relevant key words. Data extraction was independent and checklists were prepared to assess the methodologicalquality of the studies. Analysis of information was done with RevMan 5®. Results. We found Helicobacter pylori resistance prevalence rates of 1% for North America, 8% for Central and South America, 5% for Asia, and 2% for Europe. The mutation associated to this resistance is in the 16S rDNA gene at nucleotide position 967TTC to AGA965 responsible of high resistance to tetracycline. Conclusions. Antibiotic resistance is one of the causes most associated to treatment failure in the eradication of Helicobacter pylori, as well as poor adherence to treatment and indiscriminate use of antibiotics. We also evidenced that the rate of tetracycline resistance is higher whenit is used in a second treatment scheme. The distribution of resistance is variable in different areas and it is important to know these resistances to avoid treatment failures.Key words: Helicobacter pylori, tetracycline, resistance, mutation, treatment, epidemiology, 16S rRNA.

A b s t r a c t !e clinical outcome of Helicobacter pylori infection has been particularly associated with virulence genotypes. !ese genotypes are useful as molecular markers in the identification of patients that are infected and at high risk for developing more severe gastric pathologies. Our main objective was to determine the prevalence of virulence genotypes cag A, vac A, ice A and bab A2 of H.pylori , in patients with functional dyspepsia who are infected with the bacteria. H. pylori genotypes bab A2 and cag A as well as vac A and ice A allelic variants were identified by PCR in 122 isolates resulting from 79 patients with functional dyspepsia. A high prevalence of genes cag A+ (71%), vac As1am1 (34%), bab A2 (57%) and ice A1 (87%) was found. !e most frequent combined genotype found were cag A+/vac As1am1/ bab A2+/ice A1 and cag A–/ vac As1am1/ bab A2+/ice A1, regardless of any family history of gastric cancer or MALT lymphoma. !e very virulent genotype cag A+/vac As1am1/ bab A2+/ice A1 prevailed in the studied patients with functional dyspepsia. Our results provide information about the prevalence of four of the more important virulent factors and constitute new evidence on the prevalence of the most virulent H. pylori genotype in patients with functional dyspepsia.