Multi-Organ Systems Involvement in COVID-19 is Associated With a Worse Prognosis.

Background: Coronavirus disease 2019 (COVID-19) has multiple organ system involvement but the association of organ system involvement with disease prognosis has not been reported. We study the association of organ systems involved with in-hospital mortality and hospital length of stay (LOS) in COVID-19. Methods: Retrospective study of 808 consecutive patients with confirmed-laboratory diagnosis of COVID-19 in a New York hospital from March 1-May 15, 2020. Results: Increased number of organs systems involved was associated with increased odds for in-hospital mortality (odds ratio [OR]: 1.36, 95% confidence interval [CI]: 1.11-1.66, p < 0.01) and increased LOS (B = 0.02, SE = 0.01, p < 0.05). Increased platelet count was associated with decreased odds for mortality (OR: 0.996, 95% CI: 0.994-0.998, p < 0.001). Increased white blood cell count was associated with increased odds for mortality (OR: 14.00, 95% CI: 3.41-57.38, p < 0.001). Increased creatinine and glucose were each associated with increased LOS (B = 0.11, SE = 0.04, p < 0.01, and B = 0.12, SE = 0.05, p < 0.05, respectively). Increased odds for mortality were also found in high FiO2 oxygen requirement (OR: 11.63, 95% CI: 3.90-34.75, p < 0.001) and invasive mechanical ventilation (OR: 109.93, 95% CI: 29.44-410.45, p < 0.001). Conclusion: Multiple organ systems involvement in COVID-19 is associated with worse prognosis. Clinical/laboratory values corresponding to each organ system may be used as prognostic tools in clinical settings to tailor treatments for COVID-19 patients.

Dengue Burden and Factors Influencing Severity in Honduras: A Descriptive and Analytical Study.

BACKGROUND: Dengue is a disease that accounts for a major morbidity and mortality in Honduras. METHODS: This descriptive study used an analytical component based on the data from the National Virology Laboratory between 2016-2022. Ordinal logistic regression was used to identify the factors associated with the classification of dengue without warning signs (DWOS), dengue with warning signs (DWS), and severe dengue (SD). RESULTS: Overall, 14,687 dengue cases were included; 50.1% had DWOS, 36.5% had DWS, and 13.4% had SD. Patients that were more associated with a higher probability of DWS and SD were patients in the age groups 1-4 years (DWS OR 1.61; 95%CI:1.33-1.94), (SD OR 1.52; 95% CI:1.26-1.84), 5-9 years (DWS OR 2.01; 95% CI:1.68-2.40), (SD OR 2.00; 95% CI:1.67-2.40), and 10-19 years (DWS OR 1.55; 95% CI:1.30-1.85) (SD OR 1.57; 95% CI:1.31-1.88). The departments that were associated with a higher probability of DWS and SD were La Paz (OR 6.35; 95% CI:3.53-11.42), (OR 10.94; 95% CI:5.96-20.08), Copán (OR 6.94; 95% CI:5.05-9.53) (OR 7.33; 95% CI: 5.35-10.03), Valle (OR 5.22; 95% CI:1.25-21.82) (OR 10.71; 95% CI:2.21-51.88). CONCLUSIONS: During the study period, dengue presented endemic behavior, with peaks consistent with the last two epidemics in Honduras in 2015 and 2019. The main factors associated with dengue severity were age< 19 years, male sex, and being from La Paz, Copán, or Valle.

Dengue Burden and Factors Influencing Severity in Honduras: A Descriptive and Analytical Study

ABSTRACT Background: Dengue is a disease that accounts for a major morbidity and mortality in Honduras. Methods: This descriptive study used an analytical component based on the data from the National Virology Laboratory between 2016-2022. Ordinal logistic regression was used to identify the factors associated with the classification of dengue without warning signs (DWOS), dengue with warning signs (DWS), and severe dengue (SD). Results: Overall, 14,687 dengue cases were included; 50.1% had DWOS, 36.5% had DWS, and 13.4% had SD. Patients that were more associated with a higher probability of DWS and SD were patients in the age groups 1-4 years (DWS OR 1.61; 95%CI:1.33-1.94), (SD OR 1.52; 95% CI:1.26-1.84), 5-9 years (DWS OR 2.01; 95% CI:1.68-2.40), (SD OR 2.00; 95% CI:1.67-2.40), and 10-19 years (DWS OR 1.55; 95% CI:1.30-1.85) (SD OR 1.57; 95% CI:1.31-1.88). The departments that were associated with a higher probability of DWS and SD were La Paz (OR 6.35; 95% CI:3.53-11.42), (OR 10.94; 95% CI:5.96-20.08), Copán (OR 6.94; 95% CI:5.05-9.53) (OR 7.33; 95% CI: 5.35-10.03), Valle (OR 5.22; 95% CI:1.25-21.82) (OR 10.71; 95% CI:2.21-51.88). Conclusions: During the study period, dengue presented endemic behavior, with peaks consistent with the last two epidemics in Honduras in 2015 and 2019. The main factors associated with dengue severity were age< 19 years, male sex, and being from La Paz, Copán, or Valle.

Plastome phylogenomics reveals an early Pliocene North- and Central America colonization by long-distance dispersal from South America of a highly diverse bromeliad lineage.

Understanding the spatial and temporal frameworks of species diversification is fundamental in evolutionary biology. Assessing the geographic origin and dispersal history of highly diverse lineages of rapid diversification can be hindered by the lack of appropriately sampled, resolved, and strongly supported phylogenetic contexts. The use of currently available cost-efficient sequencing strategies allows for the generation of a substantial amount of sequence data for dense taxonomic samplings, which together with well-curated geographic information and biogeographic models allow us to formally test the mode and tempo of dispersal events occurring in quick succession. Here, we assess the spatial and temporal frameworks for the origin and dispersal history of the expanded clade K, a highly diverse Tillandsia subgenus Tillandsia (Bromeliaceae, Poales) lineage hypothesized to have undergone a rapid radiation across the Neotropics. We assembled full plastomes from Hyb-Seq data for a dense taxon sampling of the expanded clade K plus a careful selection of outgroup species and used them to estimate a time- calibrated phylogenetic framework. This dated phylogenetic hypothesis was then used to perform biogeographic model tests and ancestral area reconstructions based on a comprehensive compilation of geographic information. The expanded clade K colonized North and Central America, specifically the Mexican transition zone and the Mesoamerican dominion, by long-distance dispersal from South America at least 4.86 Mya, when most of the Mexican highlands were already formed. Several dispersal events occurred subsequently northward to the southern Nearctic region, eastward to the Caribbean, and southward to the Pacific dominion during the last 2.8 Mya, a period characterized by pronounced climate fluctuations, derived from glacial-interglacial climate oscillations, and substantial volcanic activity, mainly in the Trans-Mexican Volcanic Belt. Our taxon sampling design allowed us to calibrate for the first time several nodes, not only within the expanded clade K focal group but also in other Tillandsioideae lineages. We expect that this dated phylogenetic framework will facilitate future macroevolutionary studies and provide reference age estimates to perform secondary calibrations for other Tillandsioideae lineages.

New plastome structural rearrangements discovered in core Tillandsioideae (Bromeliaceae) support recently adopted taxonomy.

Full plastome sequences for land plants have become readily accessible thanks to the development of Next Generation Sequencing (NGS) techniques and powerful bioinformatic tools. Despite this vast amount of genomic data, some lineages remain understudied. Full plastome sequences from the highly diverse (>1,500 spp.) subfamily Tillandsioideae (Bromeliaceae, Poales) have been published for only three (i.e., Guzmania, Tillandsia, and Vriesea) out of 22 currently recognized genera. Here, we focus on core Tillandsioideae, a clade within subfamily Tillandsioideae, and explore the contribution of individual plastid markers and data categories to inform deep divergences of a plastome phylogeny. We generated 37 high quality plastome assemblies and performed a comparative analysis in terms of plastome structure, size, gene content and order, GC content, as well as number and type of repeat motifs. Using the obtained phylogenetic context, we reconstructed the evolution of these plastome attributes and assessed if significant shifts on the evolutionary traits' rates have occurred in the evolution of the core Tillandsioideae. Our results agree with previously published phylogenetic hypotheses based on plastid data, providing stronger statistical support for some recalcitrant nodes. However, phylogenetic discordance with previously published nuclear marker-based hypotheses was found. Several plastid markers that have been consistently used to address phylogenetic relationships within Tillandsioideae were highly informative for the retrieved plastome phylogeny and further loci are here identified as promising additional markers for future studies. New lineage-specific plastome rearrangements were found to support recently adopted taxonomic groups, including large inversions, as well as expansions and contractions of the inverted repeats. Evolutionary trait rate shifts associated with changes in size and GC content of the plastome regions were found across the phylogeny of core Tillandsioideae.

Renal Manifestations and their Association with Mortality and Length of Stay in COVID-19 Patients at a Safety-net Hospital.

Background: Renal involvement in COVID-19 leads to severe disease and higher mortality. We study renal parameters in COVID-19 patients and their association with mortality and length of stay in hospital. Methods: A retrospective study (n=340) of confirmed COVID-19 patients with renal involvement determined by the presence of acute kidney injury. Multivariate analyses of logistic regression for mortality and linear regression for length of stay (LOS) adjusted for relevant demographic, comorbidity, disease severity, and treatment covariates. Results: Mortality was 54.4% and mean LOS was 12.9 days. For mortality, creatinine peak (OR:35.27, 95% CI:2.81, 442.06, p<0.01) and persistent renal involvement at discharge (OR:4.47, 95% CI:1.99,10.06, p<0.001) were each significantly associated with increased odds for mortality. Increased blood urea nitrogen peak (OR:0.98, 95%CI:0.97,0.996, p<0.05) was significantly associated with decreased odds for mortality. For LOS, increased blood urea nitrogen peak (B:0.001, SE:<0.001, p<0.01), renal replacement therapy (B:0.19, SE:0.06, p<0.01), and increased days to acute kidney injury (B:0.19, SE:0.05, p<0.001) were each significantly associated with increased length of stay. Conclusion: Our study emphasizes the importance in identifying renal involvement parameters in COVID-19 patients. These parameters are associated with LOS and mortality, and may assist clinicians to prognosticate COVID-19 patients with renal involvement.

Respiratory involvement parameters in hospitalized COVID-19 patients and their association with mortality and length of stay.

Introduction/Background: Patients with Coronavirus Disease 2019 (COVID-19) present with a spectrum of respiratory symptoms. There are no studies describing respiratory system involvement adjusted for other organ systems, oxygen saturation nadir, hospitalization days until respiratory involvement, proportion of days of respiratory system involvement, and persistent respiratory involvement at discharge in COVID-19 patients. We studied these parameters in COVID-19 patients that received respiratory therapy interventions and their association with mortality and length of stay (LOS). Methods: A single-center cross-sectional retrospective study of 738 COVID-19 patients with respiratory involvement at a hospital in the New York metropolitan area. Results: COVID-19 patients with respiratory involvement had increased mortality with oxygen requirement of FiO2 >55% (OR:39.02, 95% CI:1.59-960.51, P < 0.05) and mechanical ventilation (OR:236.64, 95% CI:8.24-6798.93, P < 0.01). Respiratory system involvement adjusted for other organ system involvement was associated with increased mortality (OR:1.60, 95% CI:1.20, 2.14, P < 0.01) and LOS (B = 0.02, SE = 0.01, P < 0.01). Oxygen saturation nadir of 70%-89% was significantly associated with increased LOS (B = 0.07, SE = 0.03, P < 0.05), whereas oxygen saturation nadir of <70% was associated with increased mortality (OR:12.95, 95% CI:2.72-61.61, P < 0.01). An increased proportion of days in hospital with respiratory system involvement was associated with decreased mortality (OR:0.004, 95% CI:<0.001-0.06, P < 0.001) and increased LOS (B = 0.90, SE = 0.07, P < 0.001). Respiratory involvement on days 4-7 was associated with decreased mortality (OR:0.02, 95% CI:<0.003-0.17, P < 0.001), and respiratory involvement on day >1 was associated with increased LOS. Respiratory involvement persistent at discharge was associated with increased mortality (OR:56.82, 95%CI:18.51-174.43, P < 0.001). Conclusions: Among all respiratory parameters, high oxygen requirements and low oxygen saturation nadir are the most predictive of COVID-19 prognosis.

Glucose dysregulation and its association with COVID-19 mortality and hospital length of stay.

BACKGROUND AND AIMS: We investigate the impact of blood glucose on mortality and hospital length of stay (HLOS) among COVID-19 patients. METHODS: Retrospective study of 456 patients with confirmed COVID-19 and glycemic dysregulation in the New York City area. RESULTS: We found that impaired glucose adjusted for other organs systems involved (OR:1.87; 95% CI:1.36-2.57, p < 0.001), increased glucose nadir (OR:34.28; 95% CI:3.97-296.05, p < 0.01) and abnormal blood glucose levels at discharge (OR:5.07; 95% CI:2.31-11.14, p < 0.001) were each significantly associated with increased odds for mortality. New or higher from baseline insulin requirement during hospitalization (OR:0.34; 95% CI:0.15-0.78; p < 0.05) was significantly associated with decreased odds for mortality. Increased glucose peak (B = 0.001, SE=<0.001, p < 0.001), new or higher from baseline insulin requirement during hospitalization (B = 0.11, SE = 0.03, p < 0.001), and increased days to dysglycemia (B = 0.15, SE = 0.04, p < 0.001) were each significantly associated with increased HLOS. Increased glucose nadir (B = -0.67, SE = 0.07, p < 0.001), insulin intravenous drip (B = -0.10, SE = 0.05, p < 0.05), and increased proportion days endocrine system involved (B = -0.25, SE = 0.06, p < 0.001) were each significantly associated with decreased HLOS. CONCLUSION: Glucose dysregulation adversely affects mortality and HLOS in COVID-19. These data can help clinicians to guide patient treatment and management in COVID-19 patients.

Hematologic Involvement as a Predictor of Mortality in COVID-19 Patients in a Safety Net Hospital.

INTRODUCTION: COVID-19 affects the hematologic system. This article evaluated the impact of hematologic involvement of different blood cell line parameters of white blood cells including absolute neutrophil count (ANC), hemoglobin, and platelets in COVID-19 patients and their association with hospital mortality and length of stay (LOS). METHODS: This was a retrospective study of 475 patients with confirmed positive COVID-19 infection and hematologic abnormalities in the metropolitan New York City area. RESULTS: Elevated absolute neutrophil count (OR: 1.20; 95% CI: 1.02-1.42; p < 0.05) increased days of hematologic involvement (OR: 4.44; 95% CI: 1.42-13.90; p < 0.05), and persistence of hematologic involvement at discharge (OR: 2.87; 95% CI: 1.20-6.90; p < 0.05) was associated with higher mortality. Higher hemoglobin at admission (OR: 0.77; 95% CI:0.60-0.98; p < 0.001) and platelets peak (OR: 0.995; 95% CI: 0.992-0.997; p < 0.001) were associated with decreased mortality. Patients with higher white blood cell peak (B = 0.46; SE = 0.07; p < 0.001) and higher hemoglobin at admission (B = 0.05; SE = 0.01; p < 0.001) were associated with higher LOS. Those with higher hemoglobin nadir (B = -0.06; SE = 0.01; p < 0.001), higher platelets nadir (B = -0.001; SE = < 0.001; p < 0.001), and hematologic involvement at discharge or death (B = -0.06; SE = 0.03; p < 0.05) were associated with lower LOS. CONCLUSIONS: These findings can be used by clinicians to better risk-stratify patients with hematologic involvement in COVID-19 and tailor therapies potentially to improve patient outcomes.

MELD-Na score, Acute Physiologic and Chronic Health Evaluation II score, and SOFA score and their association with mortality in critically ill COVID-19 patients with liver injury: A retrospective single-center study.

Background: The Acute Physiologic and Chronic Health Evaluation II (APACHE-II), Sequential Organ Failure Assessment (SOFA), and Model for End-Stage Liver Disease modified for Sodium concentration (MELD-Na) scores are validated to predict disease mortality. We studied the prognostic utility of these scoring systems in critically ill coronavirus disease 2019 (COVID-19) patients with liver injury. Methods: This was a retrospective study of 291 confirmed COVID-19 and liver injury patients requiring intensive care unit level of care. These patients required supplemental oxygen requirement with fraction of inspired oxygen >55% and/or the use of vasopressor. MELD-Na, SOFA, and APACHE-II scores were adjusted. Outcomes were mortality and length of stay (LOS). Results: SOFA (odds ratio: 0.78, 95% confidence interval: 0.63-0.98, P < 0.05) was associated with decreased odds for mortality. APACHE-II and MELD-Na were not associated with mortality or LOS. Conclusions: We suggest that the novel nature of COVID-19 necessitates new scoring systems to predict outcomes in critically ill COVID-19 patients with liver injury.