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This study investigates the intricate relationship between Venezuelan migration and urban growth in Colombia from 2018 to 2021. The study employs remote sensing data and social network metrics to uncover migration patterns and their impact on urban expansion. The methodology consists of three stages. Firstly, nighttime satellite imagery is used to analyze year-over-year urban growth in Colombia. Secondly, social network data estimates Venezuelan migration, overcoming challenges of underreporting and informal border crossings. Lastly, an econometric analysis explores the quantitative link between Venezuelan migration and urban growth, integrating socioeconomic variables to address endogeneity. The findings reveal the complex interplay of Venezuelan migration, socioeconomic factors, and urban growth. The study outlines remote sensing analysis, introducing the Anthropogenic Footprint Expansion Index (AFEI) to quantify urban growth. Facebook API data estimates migration trends and explores socioeconomic impacts on urban expansion. The analysis uncovers migration, poverty, aging, and urban population proportion as key factors affecting Colombia's urban landscape. Furthermore, the research underscores how Venezuelan migration affected short-term urban expansion pre- and post-COVID-19. Migration had a notable effect before the pandemic, but this influence waned afterward. The study highlights migration's short-term nature and emphasizes age demographics' role in medium-term dynamics. [ABSTRACT FROM AUTHOR]

Dengue has become one of the vector-borne diseases that affect humans worldwide. In Latin American countries, Colombia is historically one of the most affected by epidemics of this flavivirus. The underreporting of signs and symptoms of probable cases of dengue, the lack of characterization of the serotypes of the infection, and the few detailed studies of postmortem necropsies of patients are among other conditions that have delayed progress in the knowledge of the pathogenesis of the disease. This study presents the results of fragment sequencing assays on paraffin-embedded tissue samples from fatal DENV cases during the 2010 epidemic in Colombia. We found that the predominant serotype was DENV-2, with the Asian/American genotype of lineages 1 and 2. This work is one of the few reports of the circulating genotypes of dengue during the 2010 epidemic in Colombia, one of the most lethal dates in the country's history. [ABSTRACT FROM AUTHOR]

The family Tymoviridae comprises positive-sense RNA viruses, which mainly infect plants. Recently, a few Tymoviridae-like viruses have been found in mosquitoes, which feed on vertebrate sources. We describe a novel Tymoviridae-like virus, putatively named, Guachaca virus (GUAV), isolated from Culex pipiens and Culex quinquefasciatus species of mosquitoes and collected in the rural area of Santa Marta, Colombia. After a cytopathic effect was observed in C6/36 cells, RNA was extracted and processed through the NetoVIR next-generation sequencing protocol, and data were analyzed through the VirMAP pipeline. Molecular and phenotypic characterization of the GUAV was achieved using a 5′/3′ RACE, transmission electron microscopy, amplification in vertebrate cells, and phylogenetic analysis. A cytopathic effect was observed in C6/36 cells three days post-infection. The GUAV genome was successfully assembled, and its polyadenylated 3′ end was corroborated. GUAV shared only 54.9% amino acid identity with its closest relative, Ek Balam virus, and was grouped with the latter and other unclassified insect-associated tymoviruses in a phylogenetic analysis. GUAV is a new member of a family previously described as comprising plant-infecting viruses, which seem to infect and replicate in mosquitoes. The sugar- and blood-feeding behavior of the Culex spp., implies a sustained contact with plants and vertebrates and justifies further studies to unravel the ecological scenario for transmission. [ABSTRACT FROM AUTHOR]

Several SARS-CoV-2 variants of concern (VOC) and interest (VOI) co-circulate in Colombia, and determining the neutralizing antibody (nAb) responses is useful to improve the efficacy of COVID-19 vaccination programs. Thus, nAb responses against SARS-CoV-2 isolates from the lineages B.1.111, P.1 (Gamma), B.1.621 (Mu), AY.25.1 (Delta), and BA.1 (Omicron), were evaluated in serum samples from immunologically naïve individuals between 9 and 13 weeks after receiving complete regimens of CoronaVac, BNT162b2, ChAdOx1, or Ad26.COV2.S, using microneutralization assays. An overall reduction of the nAb responses against Mu, Delta, and Omicron, relative to B.1.111 and Gamma was observed in sera from vaccinated individuals with BNT162b2, ChAdOx1, and Ad26.COV2.S. The seropositivity rate elicited by all the vaccines against B.1.111 and Gamma was 100%, while for Mu, Delta, and Omicron ranged between 32 to 87%, 65 to 96%, and 41 to 96%, respectively, depending on the vaccine tested. The significant reductions in the nAb responses against the last three dominant SARS-CoV-2 lineages in Colombia indicate that booster doses should be administered following complete vaccination schemes to increase the nAb titers against emerging SARS-CoV-2 lineages. [ABSTRACT FROM AUTHOR]

Introduction: Monkeypox virus (MPXV) is an enveloped double-stranded DNA virus with a genome of approximately 197.209 bp. The current classification divides MPXV into three clades: Clade I (Central African or Congo Basin clade) and clades IIa and IIb (West African clades). Objective: To report the complete genome and phylogenetic analysis of a human monkeypox case detected in Colombia. Materials and methods: Exudate from vesicular lesions was obtained from a male patient with recent travel history to Spain. A direct genomic approach was implemented in which total DNA from the sample was purified through a column-based method, followed by sequencing on the Nanopore GridION. Reads were aligned against the MPXV reference genome using minimap2 v.2.24 and phylogenetic inference was performed using maximum likelihood estimation. Results: A total of 11.951 reads mapped directly to a reference genome with 96.8% of coverage (190.898 bp). Conclusion: Phylogenetic analysis of the MPXV circulating in Colombia demonstrated its close relationship to clade IIb responsible for the multi-country outbreak in 2022. [ABSTRACT FROM AUTHOR]

Background: Each year 3–6 million people develop life-threatening severe dengue (SD). Clinical warning signs for SD manifest late in the disease course and are nonspecific, leading to missed cases and excess hospital burden. Better SD prognostics are urgently needed. Methods: We integrated 11 public datasets profiling the blood transcriptome of 365 dengue patients of all ages and from seven countries, encompassing biological, clinical, and technical heterogeneity. We performed an iterative multi-cohort analysis to identify differentially expressed genes (DEGs) between non-severe patients and SD progressors. Using only these DEGs, we trained an XGBoost machine learning model on public data to predict progression to SD. All model parameters were "locked" prior to validation in an independent, prospectively enrolled cohort of 377 dengue patients in Colombia. We measured expression of the DEGs in whole blood samples collected upon presentation, prior to SD progression. We then compared the accuracy of the locked XGBoost model and clinical warning signs in predicting SD. Results: We identified eight SD-associated DEGs in the public datasets and built an 8-gene XGBoost model that accurately predicted SD progression in the independent validation cohort with 86.4% (95% CI 68.2–100) sensitivity and 79.7% (95% CI 75.5–83.9) specificity. Given the 5.8% proportion of SD cases in this cohort, the 8-gene model had a positive and negative predictive value (PPV and NPV) of 20.9% (95% CI 16.7–25.6) and 99.0% (95% CI 97.7–100.0), respectively. Compared to clinical warning signs at presentation, which had 77.3% (95% CI 58.3–94.1) sensitivity and 39.7% (95% CI 34.7–44.9) specificity, the 8-gene model led to an 80% reduction in the number needed to predict (NNP) from 25.4 to 5.0. Importantly, the 8-gene model accurately predicted subsequent SD in the first three days post-fever onset and up to three days prior to SD progression. Conclusions: The 8-gene XGBoost model, trained on heterogeneous public datasets, accurately predicted progression to SD in a large, independent, prospective cohort, including during the early febrile stage when SD prediction remains clinically difficult. The model has potential to be translated to a point-of-care prognostic assay to reduce dengue morbidity and mortality without overwhelming limited healthcare resources. [ABSTRACT FROM AUTHOR]

Copyright of Revista Razón Crítica is the property of La Fundacion Universidad de Bogota Jorge Tadeo Lozano and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

We assessed maternal and infant cytomegalovirus (CMV) infection in Colombia. Maternal serum was tested for CMV immunoglobulin G antibodies at a median of 10 (interquartile range: 8–12) weeks gestation (n = 1501). CMV DNA polymerase chain reaction was performed on infant urine to diagnose congenital (≤21 days of life) and postnatal (>21 days) infection. Maternal CMV seroprevalence was 98.1% (95% confidence interval [CI]: 97.5%–98.8%). Congenital CMV prevalence was 8.4 (95% CI: 3.9%–18.3%; 6/711) per 1000 live births. Among 472 infants without confirmed congenital CMV infection subsequently tested at age 6 months, 258 (54.7%, 95% CI: 50.2%–59.1%) had postnatal infection. Highlights: In this multi‐city study in Colombia, maternal CMV seroprevalence was 98.1%, the prevalence of congenital CMV infection was 8.4 per 1000 live births, and 54.7% of infants had postnatal infection by 6 months of age. [ABSTRACT FROM AUTHOR]

A few studies have carried out the taxonomic and molecular characterization of sylvatic mosquito species in Latin America, where some species have been incriminated as vectors for arboviruses and parasites transmission. The present study reports the molecular characterization of mosquito species in the Sierra Nevada de Santa Marta, a natural ecosystem in the Northern coast of Colombia. Manual capture methods were used to collect mosquitoes, and the specimens were identified via classical taxonomy. The COI marker was used for species confirmation, and phylogenetic analysis was performed using the neighborjoining method, with the Kimura-2-Parameters model. Aedes serratus, Psorophora ferox, Johnbelkinia ulopus, Sabethes chloropterus, Sabethes cyaneus, Wyeomyia aporonoma, Wyeomyia pseudopecten, Wyeomyia ulocoma and Wyeomyia luteoventralis were identified. We assessed the genetic variability of mosquitoes in this area and phylogenetic reconstructions allowed the identification at the species level. Classical and molecular taxonomy demonstrated to be useful and complementary when morphological characteristics are not well preserved, or the taxonomic group is not represented in public molecular databases. [ABSTRACT FROM AUTHOR]

Paracoccidioidomycosis (PCM) is a systemic granulomatous fungal infection caused by thermally dimorphic fungi of the genus Paracoccidioides. Endemic in Latin America, PCM presents with high incidence in Brazil, Colombia, and Venezuela, especially among rural workers. The main clinical types are acute/subacute (AF) form and chronic form (CF). Even after effective antifungal treatment, patients with CF usually present sequelae, such as pulmonary fibrosis. In general, pulmonary fibrosis is associated with dysregulation wound healing and abnormal fibroblast activation. Although fibrogenesis is recognized as an early process in PCM, its mechanisms remain unknown. In the current study, we addressed the role of Paracoccidioides spp. exoantigens in pulmonary fibroblast proliferation and responsiveness. Human pulmonary fibroblasts (MRC-5) and pulmonary fibroblasts isolated from BALB/c mice were cultivated with 2.5, 5, 10, 100, and 250 µg/ml of exoantigens produced from P. brasiliensis (Pb18 and Pb326) and P. lutzii (Pb01, Pb8334, and Pb66) isolates. Purified gp43, the immunodominant protein of P. brasiliensis exoantigens, was also evaluated at concentrations of 5 and 10 µg/ml. After 24 h, proliferation and production of cytokines and growth factors by pulmonary fibroblasts were evaluated. Each exoantigen concentration promoted a different level of interference of the pulmonary fibroblasts. In general, exoantigens induced significant proliferation of both murine and human pulmonary fibroblasts (p < 0.05). All concentrations of exoantigens promoted decreased levels of IL-6 (p < 0.05) and VEGF (p < 0.05) in murine fibroblasts. Interestingly, decreased levels of bFGF (p < 0.05) and increased levels of TGF-β1 (p < 0.05) and pro-collagen I (p < 0.05) were observed in human fibroblasts. The gp43 protein induced increased TGF-β1 production by human cells (p = 0.02). In conclusion, our findings showed for the first time that components of P. brasiliensis and P. lutzii interfered in fibrogenesis by directly acting on the biology of pulmonary fibroblasts. [ABSTRACT FROM AUTHOR]

Copyright of Biomédica: Revista del Instituto Nacional de Salud is the property of Instituto Nacional de Salud of Colombia and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Biomédica: Revista del Instituto Nacional de Salud is the property of Instituto Nacional de Salud of Colombia and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

We assessed the relative influence of ecoregional features in explaining diatom distribution in the Orinoco river basin. Ecoregions in the Colombian Orinoco can be seen as imprints of the evolutionary history of the basin, for their current biodiversity and physiographic features are the result of the geological and climatic shifts that have occurred since the Tertiary. Thus, they represent an ideal testing ground for studying the interplay between ecological and evolutionary processes shaping diversity patterns of microorganisms, such as diatoms, in the present day. To study this interplay, we compared diatom community composition variance within and among seven ecoregions and assessed the explanatory power of environmental, spatial and historical drivers. This was done by a combination of correlation analyses, multivariate methods and constrained ordinations. We also deconstructed the whole community data set into ecological guilds (low‐ and high‐profile, and motile) to explore their individual response to the contemporary and historical drivers. Taken together, these analyses indicated that contemporary constraints to species occurrence and dispersal, as well as the legacies of historical events, can provide an explanation for the contemporary distribution of diatoms in the Colombian Orinoco. Specifically, we provided evidence showing that both historical legacies and contemporary environmental conditions (temperature, pH, and phosphorus concentration) are interacting to determine diatoms' distribution. Our results suggest the need to consider ecoregional gradients for unraveling the mechanisms shaping tropical diversity as well as for designing conservation plans. [ABSTRACT FROM AUTHOR]

In March 2015, a patient in Colombia with HIV/AIDS was hospitalized for disseminated ulcers after milking cows that had vesicular lesions on their udders. Vaccinia virus was detected, and the case met criteria for progressive vaccinia acquired by zoonotic transmission. Adherence to an optimized antiretroviral regimen resulted in recovery. [ABSTRACT FROM AUTHOR]

Aim: To identify and characterize the distribution of invertebrate taxa in the Orinoco basin and how their distribution affects the metacommunity structure along the river network. Location: Meta and Guaviare sub‐basins, Orinoco basin, Colombia, South America. Methods: We characterized the invertebrate communities and environmental characteristics of 25 streams from six ecoregions in the Orinoco basin. The ecoregions present different historical evolution, altitude, slope, climate and vegetation features. We used multiplicative diversity partitioning to compare the contributions of riffle (α and β1), stream (β2) and ecoregional (β3) scales to the overall gamma diversity of the basin. We also applied the Elements of Metacommunity Structure framework to delineate metacommunity types and a distance‐based redundancy analysis to assess the relative relevance of environmental, spatial and ecoregional drivers in species compositions of invertebrate communities. Results: Streams showed significant differences in community composition among the ecoregions. Several discrete pools of invertebrate taxa occurred in the basin that largely matched the distribution of the ecoregions. Consequently, the metacommunity in the basin resembled a Clementsian idealized structure. The species composition of invertebrate communities was mostly explained by ecoregion type and its interaction with the local environment, particularly its physiographic features. Main conclusions: Historical and evolutionary processes have resulted in species pools differing between the ecoregions of the Orinoco basin. At the basin scale, the metacommunity structure seems to be constrained by ecoregional features rather than by spatial structure or the local environment. Hence, using the basin as a unit for biodiversity conservation and river management would not adequately reflect the diversity and distribution patterns in highly heterogeneous basins such as the Orinoco basin. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Copyright of Revista de la Academia Colombiana de Ciencias Exactas, Físicas y Naturales is the property of Academia Colombiana de Ciencias Exactas, Fisicas y Naturales and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Few studies have explored the ecology and interrelationship with other organisms of the many endangered freshwater turtle species inhabiting the Neotropical region. The focus of the current study was to shed light on the relationship between Neotropical turtle carapaces and primary producers, insofar as the surface of former constitutes a suitable substrate for the colonization and establishment of the latter. The under-explored relationship between turtle carapaces and the diatom assemblages inhabiting them was investigated and characterized in terms of taxonomic and biological traits (bio-volume, life-form, and attachment). The carapaces of seven native turtle species were surveyed. Among these carapaces, a total of 45 diatom taxa were found, and diatom taxa varied among turtle species. Podocnemis vogli and Podocnemis expansa supported more diverse diatom assemblages than Podocnemis lewyana, Rhinoclemmys diademata, and Rhinoclemmys melanosterna, which were dominated by Navicula spp. Analysis, further showed that carapace size did not explain differences in diatom diversity. However, a trait-based analysis suggests that both carapace roughness and an assemblage's successional stage might explain the differences in assemblage composition. Because turtles can serve as dispersal vectors, characterizing their epibiont diatom assemblages may contribute to our understanding of diatom distribution on larger scales, as well as, give us some clues as to the auto-ecology of turtles that help us to effectively determine conservation areas for these endangered species. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Guatavita Lake is a small, sheltered tropical high mountain lake located in the Colombian Andes, with a closed watershed and a maximum depth of 25 m. It is the freshwater source for human consumption in nearby small towns, as well as being a site of cultural value for the country, as it was a sacred place to indigenous peoples until about five centuries ago. As the structure and function of this aquatic ecosystem is poorly understood, this study provides initial knowledge on its phytoplankton biomass dynamics, which should be useful in designing efficient management plans with environmental baseline information for similar lakes elsewhere. Physical and chemical data, and photosynthetic pigment concentrations, were measured for the period November 1999–November 2000 at the central vertical axis of Guatavita Lake. The vertical profile of the chlorophyll- a concentration was closely related to the dissolved inorganic nitrogen concentrations and the thermal stratification characteristics. The maximum chlorophyll- a concentration in the metalimnion was recorded for the thermal stratification period (November 1999–June 2000). Deepening of the maximum chlorophyll- a concentration began in February, continuing to June, when it reached its lowest value at the 15 m depth. The phytoplankton biomass values showed an increment within the entire water column at the beginning of the mixing period (July). The relation between the metalimnetic peak of chlorophyll- a and the dissolved inorganic nitrogen concentration suggests the growth of the phytoplankton community is limited mainly by the availability of nitrogen. [ABSTRACT FROM AUTHOR]

Introduction: Since the emergence of the new virus SARS-CoV-2, multiple lineages have appeared. The virus's genetic diversity has the potential to impact its transmissibility and evade natural infection- or vaccine-elicited neutralizing antibodies. It is necessary then to monitor the different variants and/or set of mutations and to track their diffusion throughout the world as they play a crucial role in controlling the pandemic. Assays other than next-generation sequencing (NGS) can be used as screening tests to track these variants. Objective: To evaluate different real-time RT-PCR protocols for the molecular detection of SARS-CoV-2 variants of concern (VOC) and variants of interest (VOI). Materials and methods: Nasopharyngeal samples were used for RNA extraction; 5 µL of the extracted RNA underwent real-time RT-PCR targeting the virus gene E. We used gene RNAse P as an internal control. On average, 20 positive specimens were further analyzed with six different commercial and in-house protocols for the detection of SARS-CoV-2 VOC and VOI following manufacturers' instructions. All the samples were characterized by NGS using the amplicon sequencing protocol v3 (https://www. protocols.io/view/ncov-2019-sequencing-protocol-v3-locost-bh42j8ye). The assembly of raw data was performed by following the pipeline described in the Oxford Nanopore Technologies platform (https://artic.network/ncov-2019/ncov2019-bioinformatics-sop. html) and the lineages were assigned by using the pangolin software. Results: We found that most of the molecular targets present in these variants were detected by the assays. On average, 81% of the samples were detected correctly as VOC and VOI with a maximum and minimum sensitivity of 100% and 60%, respectively. The protocol proposed by Vogels, et al. allowed the screening of different circulating VOC and VOI in the country. Conclusion: Our results showed that qRT-PCR protocols for detecting mutations of concern or interest in SARS-CoV-2 variants are useful as a screening method to prioritize samples before whole-genome sequencing. We recommend the use of this approach for the early detection of VOC and VOI in Colombia. [ABSTRACT FROM AUTHOR]

Although Aelurostrongylus abstrusus infections in domestic cats (Felis silvestris catus) have sporadically been reported in Colombia, there is still no data available on epidemiology nor on the biology of this neglected lungworm parasite. Thus, this epidemiological study aimed to evaluate the occurrence of patent A. abstrusus infections in domestic cats from the Colombian Federal State of Antioquia. In total, 473 fecal samples of indoor/outdoor domestic cats were collected and analyzed thereafter by the Baermann funnel migration technique for the presence of A. abstrusus first stage larvae 1 (L1). The occurrence of A. abstrusus was confirmed in 0.4% (2/473) of investigated cats. Due to the presence of patent A. abstrusus infections in investigated cats, it is unfailing to include this lungworm within differential diagnoses of feline pulmonary disorders. Despite the fact that the Baermann funnel technique is currently the cheapest and the gold standard diagnostic tool for feline aelurostrongylosis, this technique is still unknown by Colombian veterinary surgeons and rarely utilized in small animal veterinary clinics. The current survey intends to generate awareness on this neglected parasitosis and to be considered as a baseline study for future surveys monitoring feline aelurostrongylosis not only in domestic/stray cats but also in endemic wild felid species of Colombia. [ABSTRACT FROM AUTHOR]

Background: Providencia rettgeri is a nosocomial pathogen associated with urinary tract infections and related to Healthcare-Associated Infection (HAI). In recent years isolates producing New Delhi Metallo-β-lactamase (NDM) and other β-lactamases have been reported that reduce the efficiency of clinical antimicrobial treatments. In this study, we analyzed antibiotic resistance, the presence of resistance genes and the clonal relationship of two P. rettgeri isolates obtained from male patients admitted to the same hospital in Bogotá – Colombia, 2015. Results: Antibiotic susceptibility profile evaluated by the Kirby-Bauer method revealed that both isolates were resistant to third-generation carbapenems and cephalosporins. Whole-genome sequencing (Illumina HiSeq) followed by SPAdes assembling, Prokka annotation in combination with an in-house Python program and resistance gene detection by ResFinder identified the same six β-lactamase genes in both isolates: blaNDM-1, blaVIM-2, blaCTX-M-15, blaOXA-10, blaCMY-2 and blaTEM-1. Additionally, various resistance genes associated with antibiotic target alteration (arnA, PmrE, PmrF, LpxA, LpxC, gyrB, folP, murA, rpoB, rpsL, tet34) were found and four efflux pumps (RosAB, EmrD, mdtH and cmlA). The additional resistance to gentamicin in one of the two isolates could be explained by a detected SNP in CpxA (Cys191Arg) which is involved in the stress response of the bacterial envelope. Genome BLAST comparison using CGView, the ANI value (99.99%) and the pangenome (using Roary) phylogenetic tree (same clade, small distance) showed high similarity between the isolates. The rMLST analysis indicated that both isolates were typed as rST-61,696, same as the RB151 isolate previously isolated in Bucaramanga, Colombia, 2013, and the FDAARGOS_330 isolate isolated in the USA, 2015. Conclusions: We report the coexistence of the carbapenemase genes blaNDM-1, and blaVIM-2, together with the β-lactamase genes blaCTX-M-15, blaOXA-10, blaCMY-2 and blaTEM-1, in P. rettgeri isolates from two patients in Colombia. Whole-genome sequence analysis indicated a circulation of P. rettgeri rST-61,696 strains in America that needs to be investigated further. [ABSTRACT FROM AUTHOR]

Dengue is hyperendemic in Colombia, where a cyclic behavior of serotype replacement leading to periodic epidemics has been observed for decades. This level of endemicity favors accumulation of dengue virus genetic diversity and could be linked to disease outcome. To assess the genetic diversity of dengue virus type 2 in Colombia, we sequenced the envelope gene of 24 virus isolates from acute cases of dengue or severe dengue fever during the period 2013–2016. The phylogenetic analysis revealed the circulation of the Asian-American genotype of dengue virus type 2 in Colombia during that period, the intra-genotype variability leading to divergence in two recently circulating lineages with differential geographic distribution, as well as the presence of nonsynonymous substitutions accompanying their emergence and diversification. [ABSTRACT FROM AUTHOR]

• The Mu and Gamma variants dominated the third epidemic peak of SARS-CoV-2 in Colombia. • Worse COVID-19 outcomes are associated with the male sex, older age, and chronic obstructive pulmonary disease, among others. • Dominant variants impact public health, independent of variants of interest/concern status. The higher number of cases and deaths caused by COVID-19 in Colombia occurred during the third epidemic peak, where the Mu variant was associated with 50% of the cases. To evaluate the association between the clinical outcome of COVID-19 with health conditions and SARS-CoV-2 lineages. In this study, clinical metadata and SARS-CoV-2 lineages from 535 patients with different degrees of COVID-19 severity were obtained after the SARS-CoV-2 genomic surveillance in Colombia. Then, the associations between these variables were determined using a multidimensional unfolding analysis. Asymptomatic, symptomatic, severe, and deceased outcomes represented 15.2%, 29.7%, 7.3%, and 47.8% of the cases, respectively. Males tend to develop more serious COVID-19, and severe or fatal outcomes were typically observed in patients aged >60 years with comorbidities, including chronic obstructive pulmonary disease, heart disease, kidney disease, obesity, asthma, and smoking history. The SARS-CoV-2 Mu and Gamma variants dominated the third epidemic peak and accounted for most fatal cases with odd ratio values of 128.2 (CI 53.0-310.1) and 18.6 (CI 8.294-41.917). This study shows the high impact of SARS-CoV-2 lineages with higher prevalence on public health and the importance of monitoring COVID-19 risk factors to control the associated mortality. [ABSTRACT FROM AUTHOR]

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. • 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. • Genomic data of circulating SARS-CoV-2 allow the refinement of molecular protocols for COVID-19 diagnosis [ABSTRACT FROM AUTHOR]

Bluetongue virus (BTV) group antibodies are widely distributed in Costa Rica and Northern Colombia; prevalence is highest at lowest altitudes. Clinical evidence of bluetongue (BT) infection in cattle is not seen. Evidence exists of the circulation of BTV serotypes 6 and 14 in Costa Rica and BTV serotype 12, 14 and 17 in Northern Colombia in the period 1981-1983. Culicoides insignis is implicated as a probable vector in Colombia.

Recent evidence of bluetongue (BT) virus infection of livestock in scattered localities in the neotropics prompted a serologic survey of cattle in Colombia and Costa Rica. In Costa Rica 48.1% of 1435 bovine animals had BT virus antibody in the agar gel precipitation test (AGPT). In Colombia 51.8% of 635 cattle were AGPT-positive for BT virus. Antibody prevalence ranged from over 50% in the lowlands to 0% in Costa Rica and 19% in Colombian cattle above 2000 m altitude. Neutralization tests indicated that Costa Rican cattle had been exposed to BT virus types 6, 12, 14 and 17.