The emergence of highly transmissible SARS-CoV-2 variants has led to surges in cases and the need for global genomic surveillance. While some variants rapidly spread worldwide, other variants only persist nationally. There is a need for more fine-scale analysis to understand transmission dynamics at a country scale. For instance, the Mu variant of interest, also known as lineage B.1.621, was first detected in Colombia and was responsible for a large local wave but only a few sporadic cases elsewhere. To provide a better understanding of the epidemiology of SARS-Cov-2 variants in Colombia, we used 14,049 complete SARS-CoV-2 genomes from the 32 states of Colombia, and performed Bayesian phylodynamic analyses to estimate the time of variants introduction, their respective effective reproductive number, and effective population size, and the impact of disease control measures. We detected a total of 188 SARS-CoV-2 Pango lineages circulating in Colombia since the start of the pandemic. We showed that the effective reproduction number oscillated drastically throughout the first two years of the pandemic, with Mu showing the highest transmissibility (Re and growth rate estimation). Our results reinforce that genomic surveillance programs are essential for countries to make evidence-driven interventions towards the emergence and circulation of novel SARS-CoV-2 variants.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are characterized by differences in transmissibility and response to therapeutics. Therefore, discriminating among them is vital for surveillance, infection prevention, and patient care. While whole viral genome sequencing (WGS) is the "gold standard" for variant identification, molecular variant panels have become increasingly available. Most, however, are based on limited targets and have not undergone comprehensive evaluation. We assessed the diagnostic performance of the highly multiplexed Agena MassARRAY(R) SARS-CoV-2 Variant Panel v3 to identify variants in a diverse set of 391 SARS-CoV-2 clinical RNA specimens collected across our health systems in New York City, USA as well as in Bogota, Colombia (September 2, 2020 - March 2, 2022). We demonstrate almost perfect levels of interrater agreement between this assay and WGS for 9 of 11 variant calls ({kappa} [≥] 0.856) and 25 of 30 targets ({kappa} [≥] 0.820) tested on the panel. The assay had a high diagnostic sensitivity ([≥]93.67%) for contemporary variants (e.g., Iota, Alpha, Delta, Omicron [BA.1 sublineage]) and a high diagnostic specificity for all 11 variants ([≥]96.15%) and all 30 targets ([≥]94.34%) tested. Moreover, we highlight distinct target patterns that can be utilized to identify variants not yet defined on the panel including the Omicron BA.2 and other sublineages. These findings exemplify the power of highly multiplexed diagnostic panels to accurately call variants and the potential for target result signatures to elucidate new ones. ImportanceThe continued circulation of SARS-CoV-2 amidst limited surveillance efforts and inconsistent vaccination of populations has resulted in emergence of variants that uniquely impact public health systems. Thus, in conjunction with functional and clinical studies, continuous detection and identification are quintessential to inform diagnostic and public health measures. Furthermore, until WGS becomes more accessible in the clinical microbiology laboratory, the ideal assay for identifying variants must be robust, provide high resolution, and be adaptable to the evolving nature of viruses like SARS-CoV-2. Here, we highlight the diagnostic capabilities of a highly multiplexed commercial assay to identify diverse SARS-CoV-2 lineages that circulated at over September 2, 2020 - March 2, 2022 among patients seeking care at our health systems. This assay demonstrates variant-specific signatures of nucleotide/amino acid polymorphisms and underscores its utility for detection of contemporary and emerging SARS-CoV-2 variants of concern.
AO_SCPLOWBSTRACTC_SCPLOWPersistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have been reported in immune-compromised individuals and people undergoing immune-modulatory treatments. Although intrahost evolution has been documented, to our knowledge, no direct evidence of subsequent transmission and stepwise adaptation is available. Here we describe sequential persistent SARS-CoV-2 infections in three individuals that led to the emergence, forward transmission, and continued evolution of a new Omicron sublineage, BA.1.23, over an eight-month period. The initially transmitted BA.1.23 variant encoded seven additional amino acid substitutions within the spike protein (E96D, R346T, L455W, K458M, A484V, H681R, A688V), and displayed substantial resistance to neutralization by sera from boosted and/or Omicron BA.1-infected study participants. Subsequent continued BA.1.23 replication resulted in additional substitutions in the spike protein (S254F, N448S, F456L, M458K, F981L, S982L) as well as in five other virus proteins. Our findings demonstrate that the Omicron BA.1 lineage can diverge further from its already exceptionally mutated genome during persistent infection in more than one host, and also document ongoing transmission of these novel variants. There is an urgent need to implement strategies to prevent prolonged SARS-CoV-2 replication and to limit the spread of newly emerging, neutralization-resistant variants in vulnerable patients.
BackgroundSaliva is an optimal specimen for detection of viruses that cause upper respiratory infections including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) due to its cost-effectiveness and non-invasive collection. However, together with intrinsic enzymes and oral microbiota, childrens unique dietary habits may introduce substances that interfere with diagnostic testing. MethodsTo determine whether childrens dietary choices impact SARS-CoV-2 detection in saliva, we performed a diagnostic study that simulates testing of real-life specimens provided from healthy children (n=5) who self-collected saliva at home before and at 0, 20, and 60 minutes after eating from 20 foods they selected. Each of seventy-two specimens was split into two volumes and spiked with SARS-CoV-2-negative or -positive standards prior to side-by-side testing by reverse-transcription polymerase chain reaction matrix-assisted laser desorption ionization time-of-flight (RT-PCR/MALDI-TOF) assay. ResultsDetection of internal extraction control and SARS-CoV-2 nucleic acids was reduced in replicates of saliva collected at 0 minutes after eating 11 of 20 foods. Interference resolved at 20 and 60 minutes after eating all foods except hot dog in one participant. This represented a significant improvement in detection of nucleic acids compared to saliva collected at 0 minutes after eating (P=0.0005). ConclusionsWe demonstrate successful detection of viral nucleic acids in saliva self-collected by children before and after eating a variety of foods. Fasting is not required before saliva collection for SARS-CoV-2 testing by RT-PCR/MALDI-TOF, but waiting 20 minutes after eating is sufficient for accurate testing. These findings should be considered for SARS-CoV-2 testing and broader viral diagnostics in saliva specimens.
As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to circulate, multiple variants of concern (VOC) have emerged. New variants pose challenges for diagnostic platforms since sequence diversity can alter primer/probe binding sites (PBS), causing false-negative results. The Agena MassARRAY(R) SARS-CoV-2 Panel utilizes reverse-transcription polymerase chain reaction and mass-spectrometry to detect five multiplex targets across N and ORF1ab genes. Herein, we utilize a dataset of 256 SARS-CoV-2-positive specimens collected between April 11, 2021-August 28, 2021 to evaluate target performance with paired sequencing data. During this timeframe, two targets in the N gene (N2, N3) were subject to the greatest sequence diversity. In specimens with N3 dropout, 69% harbored the Alpha-specific A28095U polymorphism that introduces a 3-mismatch to the N3 forward PBS and increases risk of target dropout relative to specimens with 28095A (relative risk (RR): 20.02; p<0.0001; 95% Confidence Interval (CI): 11.36-35.72). Furthermore, among specimens with N2 dropout, 90% harbored the Delta-specific G28916U polymorphism that creates a 3-mismatch to the N2 probe PBS and increases target dropout risk (RR: 11.92; p<0.0001; 95% CI: 8.17-14.06). These findings highlight the robust capability of Agena MassARRAY(R) SARS-CoV-2 Panel target results to reveal circulating virus diversity and underscore the power of multi-target design to capture VOC.
The COVID-19 pandemic sparked rapid development of SARS-CoV-2 diagnostics. However, emerging variants pose the risk for target dropout and false-negative results secondary to primer/probe binding site (PBS) mismatches. The Agena MassARRAY(R) SARS-CoV-2 Panel combines RT-PCR and MALDI-TOF mass-spectrometry to probe for five targets across N and ORF1ab genes, which provides a robust platform to accommodate PBS mismatches in divergent viruses. Herein, we utilize a deidentified dataset of 1,262 SARS-CoV-2-positive specimens from Mount Sinai Health System (New York City) from December 2020 through April 2021 to evaluate target results and corresponding sequencing data. Overall, the level of PBS mismatches was greater in specimens with target dropout. Of specimens with N3 target dropout, 57% harbored an A28095T substitution that is highly-specific for the alpha (B.1.1.7) variant of concern. These data highlight the benefit of redundancy in target design and the potential for target performance to illuminate the dynamics of circulating SARS-CoV-2 variants.
BackgroundIn Bogota by August 1st, more than 27,000 COVID-19 deaths have been reported, while complete and partial vaccination coverage reached 30% and 37%, respectively. Although reported cases are decreasing, the potential impact of new variants is uncertain. MethodsWe used an agent-based model of COVID-19 calibrated to local data. Variants and vaccination strategies were included. We estimated the impact of vaccination and modelled scenarios of early and delayed introduction of the delta variant, along with changes in mobility, social contact, and vaccine uptake over the next months. FindingsBy mid-July, vaccination may have prevented 17,800 (95% CrI: 16,000 - 19,000) deaths in Bogota. We found that delta could lead to a fourth wave of magnitude and timing dependent on social mixing, vaccination strategy, and delta dominance. In scenarios of early dominance of delta by mid-July, age prioritization and maintaining the interval between doses were important factors to avert deaths. However, if delta dominance occurred after mid-September, age prioritization would be less relevant, and the magnitude of a four wave would be smaller. In all scenarios, higher social mixing increased the magnitude of the fourth wave. Increasing vaccination rates from 50,000/day to 100,000/day reduced the impact of a fourth wave due to delta. InterpretationThe magnitude and timing of a potential fourth wave in Bogota caused by delta would depend on social mixing and the timing of dominance. Rapidly increasing vaccination coverage with non-delayed second doses could reduce the burden of a new wave. FundingNSF RAPID DEB 2027718. HERMES 50419. Medical Research Council. MR/R024855/1 Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSThe impact of vaccination strategies in the context of emerging SARS-CoV-2 variants and increasing social mixing in Colombia had not been previously evaluated through mathematical modelling. We searched PubMed for modelling studies using the terms "COVID-19 vaccine AND model AND variant AND Colombia" or "SARS-CoV-2 AND vaccine AND model AND variant AND Colombia" (From 2021/1/1 to 2021/07/31). We did not find studies addressing this question. However, we found a model describing the evolution of the epidemic in the country during the first year, and research on the emergence of alpha, gamma, and B.1.621 variants in Colombia. We extended a previous version of our SARS-CoV-2 agent-based model for Bogota to include the potential effect of vaccination and variants. This model simulates transmission of SARS-CoV-2 based on daily activity patterns of a synthetic population, representing demographic and geographic characteristics of the total population of the city. Added value of this studyFirst, our study provides a preliminary estimate of the impact of the vaccination program in Bogota in terms of the number of deaths prevented. The second major finding is the indication that due to the introduction of the delta variant in the city, and based on the current knowledge of its biology, there is a risk of a fourth epidemic wave, whose time of occurrence and magnitude would depend mainly on three factors: when delta becomes dominant, the intensity of social contact, and vaccination roll-out strategy and coverage. Implications of all the available evidenceWe estimate that by mid-July, vaccination may have already prevented 17,800 (95% CrI: 16,000 - 19,000) deaths in Bogota. The delta variant could become dominant and lead to a fourth wave later in the year, but its timing will depend on the date of introduction, social mixing patterns, and vaccination strategy. In all scenarios, higher social mixing is associated with a fourth wave of considerable magnitude. If an early delta introduction occurred (dominance by mid-July), a new wave may occur in August/September and in such case, age prioritization of vaccination and maintaining the 21-day interval between doses of the Pfizer-BioNTech BNT162b2 are more important. However, if introduction occurred one or two months later (with dominance by mid-August/September) a fourth wave would be of smaller magnitude, the age-prioritization is less relevant, but maintaining the dose scheme without postponement is more important. In all scenarios we found that increasing the vaccination rate from the current average of 50,000/day to 100,000/day reduces the impact of a potential fourth wave due to the delta variant. Our study indicates that given the possibility of a fourth wave in the city, it is necessary to continue maintaining adherence to non-pharmacological interventions, such as the use of face masks and physical distancing, to be cautious with the intensification of social activities, and that it is essential to increase the current pace of vaccinations to rapidly reach high vaccination coverage in the population of the city.
Cryoablation for pulmonary vein isolation in atrial fibrillation has been considered a relative contraindication in the presence of a septal occluder device. We describe the successful conduct of this technique with a multimodality imaging approach.
The coronavirus disease 2019 (COVID-19) pandemic has accelerated the need for rapid implementation of diagnostic assays for detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in respiratory specimens. While multiple molecular methods utilize nasopharyngeal specimens, supply chain constraints and need for easier and safer specimen collection warrant alternative specimen types, particularly saliva. Although saliva has been found to be a comparable clinical matrix for detection of SARS-CoV-2, evaluations of diagnostic and analytic performance across platforms for this specimen type are limited. Here, we compared two methods for SARS-CoV-2 detection in saliva: the Roche cobas(R) 6800/8800 SARS-CoV-2 real-time RT-PCR Test and the Agena Biosciences MassARRAY(R) SARS-CoV-2 Panel/MassARRAY(R) System. Overall, both systems had high agreement with one another, and both demonstrated high diagnostic sensitivity and specificity when compared to matched patient upper respiratory specimens. We also evaluated the analytical sensitivity of each platform and determined the limit of detection of the Roche assay was four times lower than that of Agena for saliva specimens (390.6 v. 1,562.5 copies/mL). Furthermore, across individual target components of each assay, T2 and N2 targets had the lowest limits of detection for each platform, respectively. Together, we demonstrate that saliva represents an appropriate specimen for SARS-CoV-2 detection in two technologies that have high agreement and differ in analytical sensitivities overall and across individual component targets. The addition of saliva as an acceptable specimen and understanding the sensitivity for testing on these platforms can further inform public health measures for screening and detection to combat the COVID-19 pandemic.
IntroductionVenezuela and Colombia both adopted measures of containment early in response to the COVID-19 pandemic. However, Venezuelas ongoing humanitarian crisis has decimated its health care system, and forced millions of Venezuelans to flee through its porous border with Colombia. The extensive shared border, and illegal cross-border transit through improvised trails between the two countries are major challenges for public health authorities. We report the first SARS-CoV-2 genomes from Venezuela, and present a snapshot of the SARS-CoV-2 epidemiologic landscape in the Colombian-Venezuelan border region. MethodsWe sequenced and assembled viral genomes from total RNA extracted from nasopharyngeal (NP) clinical specimens using a custom reference-based analysis pipeline. Three assemblies obtained were subjected to typing using the Phylogenetic Assignment of Named Global Outbreak LINeages Pangolin tool. A total of 376 publicly available SARS-CoV-2 genomes from South America were obtained from the GISAID database to perform comparative genomic analyses. Additionally, the Wuhan-1 strain was used as reference. ResultsWe found that two of the SARS-CoV-2 genomes from Venezuela belonged to the B1 lineage, and the third to the B.1.13 lineage. We observed a point mutation in the Spike protein gene (D614G substitution), previously reported to be associated with increased infectivity, in all three Venezuelan genomes. An additional three mutations (R203K/G204R substitution) were present in the nucleocapsid (N) gene of one Venezuelan genome. ConclusionsGenomic sequencing demonstrates similarity between SARS-CoV-2 lineages from Venezuela and viruses collected from patients in bordering areas in Colombia and from Brazil, consistent with cross-border transit despite administrative measures including lockdowns. The presence of mutations associated with increased infectivity in the 3 Venezuelan genomes we report and Colombian SARS-CoV-2 genomes from neighboring borders areas may pose additional challenges for control of SARS-CoV-2 spread in the complex epidemiological landscape in Latin American countries. Public health authorities should carefully follow the progress of the pandemic and its impact on displaced populations within the region.
Since its emergence in Wuhan (China) on December 2019 the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has rapidly spread worldwide. After its arrival in South America in February 2020 the virus has expanded throughout the region infecting over 900,000 individuals with approximately 41,000 reported deaths to date. In response to the rapidly growing number of cases, a number of different primer-probe sets have been developed. However, despite being highly specific most of these primer-probe sets are known to exhibit variable sensitivity. Currently, there are more than 700 SARS-CoV2 whole genome sequences deposited in databases from Brazil, Chile, Ecuador, Colombia, Uruguay, Peru and Argentina. To test how regional viral diversity may impact oligo binding sites and affect test performance, we reviewed all available primer-probe sets targeting the E, N and RdRp genes against available South American SARS-CoV-2 genomes checking for nucleotide variations in annealing sites. Results from this in silico analysis showed no nucleotide variations on the E-gene target region, in contrast to the N and RdRp genes which showed massive nucleotide variations within oligo binding sites. In lines with previous data, our results suggest that E-gene stands as the most conserved and reliable target when considering single-gene target testing for molecular diagnosis of SARS-CoV-2 in South America.
ObjectiveAsymptomatic carriers (AC) of the new Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) represent an important source of spread for Coronavirus Disease 2019 (COVID-19). Early diagnosis of these cases is a powerful tool to control the pandemic. Our objective was to characterize patients with AC status and identify associated sociodemographic factors. MethodsUsing a cross-sectional design and the national database of daily occurrence of COVID-19, we characterized both socially and demographically all ACs. Additional Correspondence Analysis and Logistic Regression Model were performed to identify characteristics associated with AC state (OR, 95% CI). Results2338 ACs (11.8%; 95% CI, 11.3-12.2%) were identified, mainly in epidemiological week 18 [EW] (3.98; 3.24-4.90). Age [≤] 39 years (1.56; 1.42-1.72). Male sex (1.39; 1.26-1.53), cases imported from Argentina, Spain, Peru, Brazil, Costa Rica or Mexico (3.37; 1.47-7.71) and autochthonous cases (4.35; 2.12-8.93) increased the risk of identifying AC. We also identified groups of departments with moderate (3.68; 3.13-4.33) and strong (8.31; 6.10-7.46) association with AC. DiscussionSociodemographic characteristics strongly associated with AC were identified, which may explain its epidemiological relevance and usefulness to optimize mass screening strategies and prevent person-to-person transmission.
We performed phylogenomic analysis of severe acute respiratory syndrome coronavirus-2 (SARS-CoV2) from 88 infected individuals across different regions of Colombia. Eleven different lineages were detected, suggesting multiple introduction events. Pangolin lineages B.1 and B.1.5 were the most frequent, with B.1 being associated with prior travel to high-risk areas. Article Summary LineWe sequenced 88 genomes of SARS-CoV2 from Colombia finding 11 lineages and eight different introduction events
La cetoacidosis diabética y el estado hiperglicémico hiperosmolar son las dos complicaciones metabólicas más graves de la diabetes. Estas enfermedades aparecen tantoen los pacientes con diabetes tipo 1 como en la tipo 2 y ocurren durante estrés catabólico o enfermedades agudas severas. La tasa de mortalidad en pacientes con cetoacidosis diabética es del 5 por ciento mientras que la tasa de mortalidad del estado hiperglicémico hiperosmolar es de aproximadamente el 11 por ciento. como prioridad en todo paciente que ingresa al servicio de urgencias se tendrá en cuenta el ABC en la evaluación inicial con medidas de soporte, monitorización y acceso venoso. Las metas terapéuticas en la cetoacidosis diabética se dirigen hacia la corrección de la deshidratación para mejorar el volumen circulante, la administración adecuada de insulina y el reemplazo de potasio. La administración de bicarbonato, fosfato, magnesio u otras terapias puede ser ventajosa en algunos pacientes, pero no se deben considerar como la primera línea de manejo. Luego de la estabilización del paciente es muy importante el tratamiento basado en la educación para reconocer oportunamente una descompensación,tratando de llevar siempre al paciente a una prevención de eventos posteriores.
Diabetic Ketoacidosis/diagnosis , Diabetic Ketoacidosis/physiopathology , Diabetic Ketoacidosis/therapy
