Epidemiological Dynamics of SARS-CoV-2 Variants During Social Protests in Cali, Colombia.

Background: The third wave of the global health crisis attributed to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus reached Colombia in March 2021. Over the following 6 months, it was interpolated by manifestations of popular disapproval to the actual political regime-with multiple protests sprouting throughout the country. Large social gatherings seeded novel coronavirus disease 2019 (COVID-19) variants in big cities and propagated their facile spread, leading to increased rates of hospitalizations and deaths. Methods: In this article, we evaluate the effective reproduction number (Rt) dynamics of SARS-CoV-2 in Cali, Colombia, between 4 April 2021 and 31 July 2021 based on the analysis of 228 genomes. Results: Our results showed clear contrast in Rt values between the period of frequent protests (Rt > 1), and the preceding and following months (Rt < 1). Genomic analyses revealed 16 circulating SARS-CoV-2 lineages during the initial period-including variants of concern (VOCs) (Alpha, Gamma, and Delta) and variants of interest (VOIs) (Lambda and Mu). Furthermore, we noticed the Mu variant dominating the COVID-19 distribution schema as the months progressed. We identified four principal clusters through phylogenomic analyses-each one of potentially independent introduction to the city. Two of these were associated with the Mu variant, one associated with the Gamma variant, and one with the Lambda variant. Conclusion: Our results chronicle the impact of large group assemblies on the epidemiology of COVID-19 during this intersection of political turmoil and sanitary crisis in Cali, Colombia. We emphasize upon the effects of limited biosecurity strategies (which had characterized this time period), on the spread of highly virulent strains throughout Cali and greater Colombia.

Impact of SARS-CoV-2 Mu variant on vaccine effectiveness: A comparative genomics study at the peak of the third wave in Bogota, Colombia.

We assessed the circulation of severe acute respiratory syndrome coronavirus-2 variants amongst vaccinated military personnel in Bogotá, Colombia to evaluate the mutations of certain variants and their potential for breakthrough infection in vaccinated subjects. We observed that in vaccinated individuals the most frequent infecting lineage was Mu (B.1.621 and B.1.621.1). The above is possibly associated with specific mutations that confer it with vaccine-induced immune escape ability. Our findings highlight the importance of how genomic tracking coupled with epidemiological surveillance can assist in the study of novel emerging variants (e.g., Omicron) and their impact on vaccination efforts worldwide.

Epidemiological Indicators of SARS-CoV-2 (COVID-19) and Vaccination Effectiveness on the Report of Positive Cases in the Colombian Army.

The description of the epidemiological indicators of SARS-CoV-2 (COVID-19), such as the mortality rate (MR), the case fatality rate (CFR), and the attack rate (AR), as well as the geographical distribution and daily case reports, are used to evaluate the impact that this virus has had within the Colombian Army and its health system. As military forces around the world represent the force that defends sovereignty, independence, the integrity of the national territory, and the constitutional order, while maintaining migration controls in blocked border areas during this critical pandemic times, they must carry out strict epidemiological surveillance to control the situation among the servicemen. Up to date, the Colombian Army has faced a very high attack rate (AR = 8.55%) due, among others, to living conditions where active military personnel share bedrooms, bathrooms, and dining facilities, which facilitate the spread of the virus. However, being a mainly young and healthy population, the MR was 1.82 deaths/1,000 ha, while the CFR = 2.13% indexes consistently low if compared with those values reported for the national population. In addition, the effectiveness of vaccination is shown in daily cases of COVID-19, where, for the third peak, the active military population presented a decrease of positive patients compared to the dynamics of national transmission and the total population of the military forces (active, retired, and beneficiaries).

Phylogenomic Evidence of Reinfection and Persistence of SARS-CoV-2: First Report from Colombia.

The continuing evolution of SARS-CoV-2 and the emergence of novel variants have raised concerns about possible reinfection events and potential changes in the coronavirus disease 2019 (COVID-19) transmission dynamics. Utilizing Oxford Nanopore technologies, we sequenced paired samples of three patients with positive RT-PCR results in a 1-2-month window period, and subsequent phylogenetics and genetic polymorphism analysis of these genomes was performed. Herein, we report, for the first time, genomic evidence of one case of reinfection in Colombia, exhibiting different SARS-CoV-2 lineage classifications between samples (B.1 and B.1.1.269). Furthermore, we report two cases of possible viral persistence, highlighting the importance of deepening our understanding on the evolutionary intra-host traits of this virus throughout different timeframes of disease progression. These results emphasize the relevance of genomic surveillance as a tool for understanding SARS-CoV-2 infection dynamics, and how this may translate effectively to future control and mitigations efforts, such as the national vaccination program.

Distribution, treatment outcome and genetic diversity of Leishmania species in military personnel from Colombia with cutaneous leishmaniasis.

BACKGROUND: Leishmaniasis is one of the most important infectious diseases affecting the Colombian National Army due to the high number of reported cases and exposure throughout military operations in endemic areas. The main aim of this study was to estimate the geographical distribution along with the genetic diversity and treatment outcome of Leishmania species in Colombian military personnel. METHODS: Skin lesion samples by smear and aspirate were collected in 136 patients having parasitological cutaneous leishmaniasis (CL) diagnosis. DNA was extracted, the nuclear marker heat shock protein 70 (HSP70) was amplified by PCR and sequenced. Leishmania species were identified by BLASTn. The geo-spatial distribution of the identified parasites was determined according to the possible site of infection. Gene tree was constructed by maximum likelihood (ML), diversity indices (π, h) were estimated and haplotype network was constructed under the Templeton-Crandall-Sing algorithm in order to determine the geographic relationships of the genetic variants of Leishmania species circulating in Colombian military population. RESULTS: The species were identified in 77.94% of the samples, with a predominance of L. braziliensis (65.09%), followed by L. panamensis (31.13%), L. naiffi by the first time reported in Colombia in two patients (1.89%) as well as L. lindenbergi in a single patient (0.945%) with possible infection in the municipality of Miraflores, Guaviare and L. infantum in a single patient (0.945%) notified with CL in the municipality of Tumaco, Nariño. The phylogenetic analysis was consistent according to bootstrap, showing four strongly differentiated clades. CONCLUSIONS: The geo-spatial distribution suggested that L. braziliensis has a greater abundance, while L. panamensis has a greater dispersion. The phylogenetic relationships of Leishmania species in Colombian military personnel was estimated with the confirmation of two new species circulating without prior report in the country and a species with no background for CL in the Colombian army. A substantial genetic diversity of Leishmania braziliensis was defined. This study contributes through the understanding of the molecular epidemiology to the CL transmission in Colombia.

Prevalence of Trypanosoma cruzi infection in active military population of The Colombian National Army gathered in five departments.

BACKGROUND: The National Army of Colombia is present in all of the national territory, focused in sylvatic zones where they are exposed continually to potential risk of transmission of Trypanosoma cruzi, the etiological agent of the Chagas disease. People of this study were active personal that were born and lived during their first years in endemic areas of transmission through domiciled vectors as Rhodnius prolixus. AIM: The main aim of this study was to estimate the prevalence of Chagas disease in the active military population of the National Army, gathered in five departments. METHODS: An observational and descriptive study with cross-sectional analysis was carried out. Blood sample each patient in order to apply serological diagnosis by two different Enzyme Linked ImmunoSorbent Assay tests, following the algorithm of National Institute of Health, Colombia. In cases of serum results with inconsistencies, a Hemagglutination Inhibition test and Indirect Immunofluorescence assay test were performed to solve inconclusiveness. Positive samples by two different tests were considered seropositive. Additionally, to each positive sample by at least one serological test, we did extraction of DNA for molecular diagnosis. RESULTS: 295 serums were analyzed and two of them were positive in order to get a prevalence of 0.68%. Two samples analyzed by molecular diagnosis were negative. CONCLUSION: The prevalence was < 1% It is probable the infection in the seropositive individuals occurred before enlisting in the military service due to origin locations with transmission such as Casanare and Boyacá. These findings allow defining the prevention and control programs of chronic cases and reduction in the disease burden.

Development of a Digital Droplet Polymerase Chain Reaction (ddPCR) assay to detect Leishmania DNA in samples from Cutaneous Leishmaniasis patients.

AIM: Here, we evaluate the ddPCR platform using an evaluated qPCR-based diagnostic assay for the detection of Leishmania infection in Cutaneous Leishmaniasis patients. METHODS: A standard curve of cultured Leishmania parasite material and clinical samples of CL patients were tested with ddPCR to determine the analytical and diagnostic performance. RESULTS: The limit of detection of the assay on the ddPCR platform was much higher than the published limit of detection of the same assay on the qPCR platform (100 vs 1 parasites/mL, respectively). CONCLUSION: While the performance of this assay in ddPCR format was acceptable for research purposes, it is not sufficient for clinical diagnostic purposes. The assay is more suited to the qPCR platform.

Spatial distribution, Leishmania species and clinical traits of Cutaneous Leishmaniasis cases in the Colombian army.

In Colombia, the cutaneous leishmaniasis (CL) is the most common manifestation across the army personnel. Hence, it is mandatory to determine the species associated with the disease as well as the association with the clinical traits. A total of 273 samples of male patients with CL were included in the study and clinical data of the patients was studied. PCR and sequencing analyses (Cytb and HSP70 genes) were performed to identify the species and the intra-specific genetic variability. A georeferenced database was constructed to identify the spatial distribution of Leishmania species isolated. The identification of five species of Leishmania that circulate in the areas where army personnel are deployed is described. Predominant infecting Leishmania species corresponds to L. braziliensis (61.1%), followed by Leishmania panamensis (33.5%), with a high distribution of both species at geographical and municipal level. The species L. guyanensis, L. mexicana and L. lainsoni were also detected at lower frequency. We also showed the identification of different genotypes within L. braziliensis and L. panamensis. In conclusion, we identified the Leishmania species circulating in the areas where Colombian army personnel are deployed, as well as the high intra-specific genetic variability of L. braziliensis and L. panamensis and how these genotypes are distributed at the geographic level.

[Do some conditions contribute to the reemergence of the Venezuelan equine encephalitis virus in the Colombian Alta Guajira?]. / ¿Existen condiciones que favorecen la reaparición del virus de la encefalitis equina venezolana en la Alta Guajira colombiana?

INTRODUCTION: In the last 18 years, epizootics of Venezuelan equine encephalitis have not occurred in places with historic epidemic register (1925-1995) in the Guajira Peninsula, Colombia. OBJECTIVE: To assess if the Guajira Peninsula, Colombia, still maintains the epidemiological conditions for Venezuelan equine encephalitis virus reemergence. MATERIALS AND METHODS: Research was carried out in places affected by the 1995 epidemic. We evaluated: 1) abundance and seasonal variation of vector mosquito populations; 2) availability of mammals that are potential amplifiers of the virus, and 3) knowledge among the community about the disease and its vectors. RESULTS: Most of the 16 mosquito species were found during the rainy season. Aedes taeniorhynchus and Psorophora confinnis showed direct relation with rainfall and temperature. In contrast, the dominant species, Deinocerites atlanticus , was always present in the collections, regardless of climatic conditions. No IgG antibodies were found in humans younger than 17 years old, goats or bovine sera. One third of those interviewed remembered the last epidemic and had basic understanding of the disease. Only 20% of the families were owners of equines, and 8% was informed of the importance of equine vaccination. CONCLUSIONS: Some epidemiological conditions that eventually could help epizootic Venezuelan equine encephalitis virus reemergence are maintained. However, an abrupt decrease in the number of susceptible equines was found in the area. Apparently, this new condition has not allowed the virus reemergence and is the biggest observed change.

¿Existen condiciones que favorecen la reaparición del virus de la encefalitis equina venezolana en la Alta Guajira colombiana? / Do some conditions contribute to the reemergence of the Venezuelan equine encephalitis virus in the Colombian Alta Guajira?

Introducción. En los últimos 18 años, no se han vuelto a registrar epizootias de encefalitis equina venezolana en áreas con antecedentes históricos de epidemia (1925-1995) en la península de La Guajira. Objetivo. Establecer si en la Alta Guajira colombiana se mantienen las condiciones que favorecen la reaparición de las cepas epizoóticas del virus de la encefalitis equina venezolana. Materiales y métodos. La investigación se realizó en las localidades afectadas por la epidemia de 1995, y se evaluaron los siguientes aspectos: 1) abundancia y variación estacional de las poblaciones de los mosquitos vectores; 2) disponibilidad de mamíferos sensibles amplificadores del virus, y 3) conocimiento de los habitantes sobre la enfermedad y sus vectores. Resultados. La mayoría de las especies de mosquitos, incluidas las de los vectores, se encontraron durante la estación lluviosa. Aedes taeniorhynchus y Psorophora confinnis presentaron relación con la precipitación y la temperatura. Deinocerites atlanticus estuvo siempre presente, independientemente de las condiciones climáticas. No se encontraron anticuerpos de tipo IgG en los sueros de humanos menores de 17 años, tampoco en los de los animales caprinos y bovinos analizados. En la encuesta sobre conocimientos, se detectó que la tercera parte de los encuestados recordaba la última epidemia y tenía conocimientos básicos sobre la enfermedad. Solamente 20 % de las familias poseía équidos y el 8 % estaba informado sobre la necesidad de vacunarlos. Conclusiones. Se mantienen algunas condiciones epidemiológicas que eventualmente podrían favorecer la reaparición del virus, pero el número de equinos en riesgo es escaso, lo cual constituye el cambio más notable y lo que, aparentemente, ha impedido la reaparición del virus.

Introduction: In the last 18 years, epizootics of Venezuelan equine encephalitis have not occurred in places with historic epidemic register (1925-1995) in the Guajira Peninsula, Colombia. Objective: To assess if the Guajira Peninsula, Colombia, still maintains the epidemiological conditions for Venezuelan equine encephalitis virus reemergence. Materials and methods: Research was carried out in places affected by the 1995 epidemic. We evaluated: 1) abundance and seasonal variation of vector mosquito populations; 2) availability of mammals that are potential amplifiers of the virus, and 3) knowledge among the community about the disease and its vectors. Results: Most of the 16 mosquito species were found during the rainy season. Aedes taeniorhynchus and Psorophora confinnis showed direct relation with rainfall and temperature. In contrast, the dominant species, Deinocerites atlanticus , was always present in the collections, regardless of climatic conditions. No IgG antibodies were found in humans younger than 17 years old, goats or bovine sera. One third of those interviewed remembered the last epidemic and had basic understanding of the disease. Only 20% of the families were owners of equines, and 8% was informed of the importance of equine vaccination. Conclusions: Some epidemiological conditions that eventually could help epizootic Venezuelan equine encephalitis virus reemergence are maintained. However, an abrupt decrease in the number of susceptible equines was found in the area. Apparently, this new condition has not allowed the virus reemergence and is the biggest observed change.

Validation of a Poisson-distributed limiting dilution assay (LDA) for a rapid and accurate resolution of multiclonal infections in natural Trypanosoma cruzi populations.

Trypanosoma cruzi is the causative agent of American trypanosomiasis, a complex zoonotic disease that affects more than 10million people in the Americas. Strains of this parasite possess a significant amount of genetic variability and hence can be divided into at least six discrete typing units (DTUs). The life cycle of this protist suggests that multiclonal infections may emerge due to the likelihood of contact of triatomine insects with more than 100 mammal species. To date, there have been a few studies on but no consensus regarding standardised methodologies to identify multiclonal infections caused by this parasite. Hence, the aim of this study was to develop and validate a limiting dilution assay (LDA) to identify multiclonal infections in T. cruzi populations by comparing the feasibility and reliability of this method with the widely applied solid phase blood agar (SPBA) methodology. We cloned reference strains belonging to three independent genotypes (TcI, TcII, and TcIV) and mixed infections (TcI+TcII) using LDA and SPBA; the comparison was conducted by calculating the feasibility and reliability of the methods employed. Additionally, we implemented LDA in strains recently isolated from Homo sapiens, Rhodnius prolixus, Triatoma venosa, Panstrongylus geniculatus, Tamandua tetradactyla, Rattus rattus, Didelphis marsupialis and Dasypus novemcinctus, with the aim of resolving multiclonal infections using molecular characterization employing SL-IR (spliced leader intergenic region of mini-exon gene), the 24Sα rDNA gene and microsatellite loci. The results reported herein demonstrate that LDA is an optimal methodology to distinguish T. cruzi subpopulations based on microsatellite markers by showing the absence of multiple peaks within a single locus. Conversely, SPBA showed patterns of multiple peaks within a single locus suggesting multiclonal events. The biological consequences of these results and the debate between multiclonality and aneuploidy are discussed.

Natural and emergent Trypanosoma cruzi I genotypes revealed by mitochondrial (Cytb) and nuclear (SSU rDNA) genetic markers.

Chagas disease is a tropical and systemic disease caused by the parasite Trypanosoma cruzi. This parasite has been divided into six Discrete Typing Units (DTU's) due to its high genetic diversity. T. cruzi I (TcI) is the most prevalent DTU in Colombia and recently associated to cardiomyopathies. The aim of this study was to unravel the genetic variability among a set of 70 cell-single TcI clones from different geographical regions and hosts using the sequences of Cytb and SSU rDNA. The results showed two genotypes associated to transmission cycles of Chagas disease in Colombia and supports the previous descriptions using SL-IR. Phylogenetic networks were developed detecting recombination events within TcI. We also tested the phylogenetic relationships beneath TcI clones and TcIII/TcIV sequences observing the high relatedness of TcI clones from sylvatic cycle with TcIII/TcIV. We corroborate the high genetic diversity displayed by TcI, the plausible recombination within this DTU supporting the previous model of genetic exchange proposed in T. cruzi populations. We conclude inquiring the need to pursue new studies to elucidate the genetic structure of TcI across Chagas disease endemic countries.

Multilocus PCR-RFLP profiling in Trypanosoma cruzi I highlights an intraspecific genetic variation pattern.

Chagas disease represents a serious problem in public health. This zoonotic pathology is caused by the kinetoplastid Trypanosoma cruzi which displays a high genetic diversity falling into six Discrete Typing Units (TcI-TcVI). In Colombia, the prevalent DTU is TcI with findings of TcII, TcIII and TcIV in low proportions. The aim of this work was to observe the genetic variability within TcI using a multilocus PCR-RFLP strategy. We analyzed 70 single-celled clones from triatomines, reservoirs and humans that were amplified and restricted via ten PCR-RFLPs targets across TcI genome, the restriction fragments were used to construct phylograms according to calculated genetic distances. We obtained five polymorphic targets (1f8, HSP60, HSP70, SAPA and H1) and the consensus tree constructed according to these regions allowed us to observe two well-defined groups with close association to the transmission cycles (domestic/peridomestic and sylvatic) of Chagas disease in Colombia. Our findings allowed us to corroborate the previous reported genotypes based on the intergenic region of mini-exon gene. More studies examining the genetic diversity among T. cruzi I populations must be conducted in order to obtain a better understanding in regions where this DTU is endemic.

Evaluación de la variabilidad genética e aislamientos colombianos de Trypanosoma cruzi mediante marcadores microsatélites / Genetic variability evaluation of Trypanosoma cruzi Colombian isolates based on microsatellite DNA markers

Introducción. La enfermedad de Chagas, cuyo agente causal es Trypanosoma cruzi, constituye una antropozoonosis ampliamente distribuida en América Latina. Los estudios moleculares y los perfiles genéticos han demostrado que el parásito presenta una gran variabilidad y han permitido la clasificación de T. cruzi en seis unidades discretas de tipificación (I-VI), de las cuales, TcII a TcVI han sido ampliamente caracterizadas por distintos marcadores moleculares. Objetivo. Evaluar la variabilidad genética de TcI, mediante el uso de marcadores de microsatélites. Materiales y métodos. Se evaluaron siete microsatélites en quince aislamientos colombianos obtenidos mediante PCR a partir de reservorios, vectores y humanos, y se analizaron en un gel para desnaturalizar de poliacrilamida de un secuenciador láser fluorescente automático (ALF). Los datos se analizaron en un software para análisis de genética de poblaciones (Arlequin® 3.1 y Microsat®). Resultados. Los resultados demostraron variabilidad dentro de TcI al obtener 24 alelos, de los cuales, 12 se reportan por primera vez. Aunque se encontraron genotipos asociados a la infección humana y al ciclo selvático de transmisión, ningún locus permitió comprobar la presencia de los genotipos previamente reportados. Los parámetros de heterocigocidad observada y esperada, permitieron determinar la presencia de dos poblaciones (aislamientos domésticos y selváticos); asimismo, el desequilibrio de ligamento facilitó la creación de dos mapas físicos para los loci analizados. Conclusiones. Se corrobora la gran variabilidad genética presente en TcI, lo que sugiere un patrón de variación intraespecífica en Colombia.

Introduction: Chagas disease which is caused by the protozoan Trypanosoma cruzi, is a major public health problem in Latin American countries with a different distribution of the parasite across the continent in which nearly 15 million people are infected and 28 million are at risk. Genetic profiling of T. cruzi has shown great diversity and variability of the parasite allowing its classification into six discrete typing units (DTUs I-VI) in which TcII to TcVI are well characterized by different molecular markers. However, the presence of four subgroups according to the transmission cycle has only been reported in DTU T. cruzi I. Objective: To evaluate the genetic variability evidenced within TCI by the use of microsatellite markers. Materials and methods: Seven microsatellite loci were tested in fifteen Colombian isolates from vectors, reservoirs, and humans by means of PCR and automatic laser fluorescent sequencer (ALF). Data were analyzed using a population genetic data analysis software (Arlequin® 3.1 and Microsat®). Results: Variability among the isolates was demonstrated with 24 alleles, from which twelve had never been reported before. However, none of the microsatellite loci were able to support the idea of genotypes within TcI strains. The parameters of expected and observed heterozygocity allowed us to determine presence of two populations (domestic and sylvatic isolates); likewise, the linkage disequilibrium helped with the construction of two physical maps for the loci analyzed. Conclusions: We corroborated the high genetic variability displayed by TcI populations suggesting a pattern of intraspecific variation in Colombia.

Phylogenetic reconstruction based on Cytochrome b (Cytb) gene sequences reveals distinct genotypes within Colombian Trypanosoma cruzi I populations.

Chagas disease caused by Trypanosoma cruzi comprises an important problem of public health in the Americas. This parasite has been recently divided into six Discrete Typing Units (DTUs) due to its high genetic diversity. We sequenced the Cytochorme b (Cytb) gene of 70 T. cruzi I Colombian clones finding four genotypes related to transmission cycles of Chagas disease in Colombia and also to specific hosts of T. cruzi. The genotypes herein described based on Cytb gene sequences are in accordance with those found using the mini-exon gene and reveals once again the enormous genetic diversity at sub-DTU level evidenced in T. cruzi I.