scholarly journals San Diego county Nanopore SARS-Cov2 sequencing data shows metagenomic Prevotella, Haemophilus parainfluenzae, a lot of unknown species and chimeric reads

2020 ◽  
Author(s):  
Sandeep Chakraborty
Keyword(s):  
San Diego ◽  
Secondary Infection ◽  
Elongation Factor ◽  
Ground Glass Opacity ◽  
Ground Glass ◽  
Dominant Factor ◽  
Sequencing Data ◽  
Haemophilus Parainfluenzae ◽  
Unknown Species ◽  
Highly Correlated

Prevotella was definitely a dominant factor in the the SARS-Cov2 [1,2] patient [3], playing a key role in immune suppression [4]. The same immune suppressive proteins from the same bacteria (elongation factor Tu) was also observed in low amounts in two other patients [5].Prevotella is known to cause ground glass opacity [6] being used to identify SARS-Cov2 patients [7]. It is also known to increase IL-6 in plasma [8–10], which is correlated with severity/fatalities [11]. In 2003 SARS- Cov1 outbreak, secondary infection and IL-6 was highly correlated with hospitalization and deaths [12].Metagenomic presence - known bacteria, and many (10% of reads) unknown speciesHere, sequencing data (Accid:SRR11347377, Reads=2.64million, Nanopore) from San Diego show Prevotella, Haemophilus parainfluenzae (which can have the same ground glass in CT [13]) and other bacteria in small amounts (SI/bacteria.fa, N=23). More intriguingly, there are significant amount of reads with no known matches (SI/nomatches.fa, N=200K, about 10%).Chimeric reads (10% of reads) involving SARS-Cov2Like previous, data (N=3) showing SARS-Cov2 integration in bacteria [14], there are a significant percentage of chimeric reads (SI/integrated.fa, N=250K, ∼10%) having both SARS-Cov2 and something else (sometimes known bacterial reads). Is this sequencing artifact - or is the virus infecting both bacterial and human cells (which would be a first) [15]? It would explain the long incubations and false negatives.

scholarly journals Fetal hemoglobin that binds oxygen more strongly than adult hemoglobin saves children (and sickle-cell patients where it persists longer) from heme-binding (oxygen sequestering) proteins of anaerobic bacteria (Prevotella, et al) - thereby making SARS-Cov2 benign for them

2020 ◽  
Author(s):  
Sandeep Chakraborty
Keyword(s):  
Sickle Cell ◽  
Secondary Infection ◽  
Cardiac Injury ◽  
Anaerobic Bacteria ◽  
Fetal Hemoglobin ◽  
Ground Glass Opacity ◽  
Ground Glass ◽  
Heme Binding ◽  
Sequencing Data ◽  
Adult Hemoglobin

Here, I postulate (supported by sequencing data from patients) rationale behind two of the most critical (low SpO2 [1], need for ventilators) and baffling (doesnt effect children or malaria endemic regions [2]) effects observed in SARS-Cov2 [3–6]. In short, secondary infection with anaerobic bacteria [7–9] which express heme-expressing proteins, and can degrade and utilize hemoglobin as an effective heme source [10, 11] - causing oxygen levels (which binds to heme) to go down. Also, Prevotella is known to lower lymphocyte counts [12], increase IL-6 in plasma [13–15], cause ground glass opacity in lungs [16], and associated with cardiac injury [17] - all symptoms associated with Covid19.

scholarly journals Decreased IL-6 and NK Cells in Early-Stage Lung Adenocarcinoma Presenting as Ground-Glass Opacity

2021 ◽  
Vol 11 ◽  
Author(s):  
Pengfei Zhang ◽  
Boxue He ◽  
Qidong Cai ◽  
Guangxu Tu ◽  
Xiong Peng ◽  
...  
Keyword(s):  
Lung Adenocarcinoma ◽  
Nk Cells ◽  
Nk Cell ◽  
Early Stage ◽  
Ground Glass Opacity ◽  
Tumor Infiltrating Lymphocytes ◽  
Ground Glass ◽  
Normal Lung ◽  
Sequencing Data ◽  
Primary Lung Adenocarcinoma

BackgroundLung ground-glass opacities (GGOs) are an early manifestation of lung adenocarcinoma. It is of great value to study the changes in the immune microenvironment of GGO to elucidate the occurrence and evolution of early lung adenocarcinoma. Although the changes of IL-6 and NK cells in lung adenocarcinoma have caught global attention, we have little appreciation for how IL-6 and NK cells in the lung GGO affect the progression of early lung adenocarcinoma.MethodsWe analyzed the RNA sequencing data of surgical specimens from 21 patients with GGO-featured primary lung adenocarcinoma and verified the changes in the expression of IL-6 and other important immune molecules in the TCGA and GEO databases. Next, we used flow cytometry to detect the protein expression levels of important Th1/Th2 cytokines in GGO and normal lung tissues and the changes in the composition ratio of tumor infiltrating lymphocytes (TILs). Then, we analyzed the effect of IL-6 on NK cells through organoid culture and immunofluorescence. Finally, we explored the changes of related molecules and pathway might be involved.ResultsIL-6 may play an important role in the tumor microenvironment of early lung adenocarcinoma. Further research confirmed that the decrease of IL-6 in GGO tissue is consistent with the changes in NK cells, and there seems to be a correlation between these two phenomena.ConclusionThe IL-6 expression status and NK cell levels of early lung adenocarcinoma as GGO are significantly reduced, and the stimulation of IL-6 can up-regulate or activate NK cells in GGO, providing new insights into the diagnosis and pathogenesis of early lung cancer.

scholarly journals Multilocus phylogenies reveal three new truffle-like taxa and the traces of interspecific hybridization in Octaviania (Boletaceae, Boletales)

IMA Fungus ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Takamichi Orihara ◽  
Rosanne Healy ◽  
Adriana Corrales ◽  
Matthew E. Smith
Keyword(s):  
Rna Polymerase Ii ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Gene Tree ◽  
Phylogenetic Network ◽  
Elongation Factor ◽  
Morphological Observation ◽  
Tree Comparison ◽  
Unknown Species ◽  
The Usa

ABSTRACTAmong many convergently evolved sequestrate fungal genera in Boletaceae (Boletales, Basidiomycota), the genus Octaviania is the most diverse. We recently collected many specimens of Octaviania subg. Octaviania, including several undescribed taxa, from Japan and the Americas. Here we describe two new species in subgenus Octaviania, O. tenuipes and O. tomentosa, from temperate to subtropical evergreen Fagaceae forests in Japan based on morphological observation and robust multilocus phylogenetic analyses (nrDNA ITS and partial large subunit [LSU], translation elongation factor 1-α gene [TEF1] and the largest subunit of RNA polymerase II gene [RPB1]). Based on specimens from the Americas as well as studies of the holotype, we also taxonomically re-evaluate O. asterosperma var. potteri. Our analysis suggests that O. asterosperma var. potteri is a distinct taxon within the subgenus Octaviania so we recognize this as O. potteri stat. nov. We unexpectedly collected O. potteri specimens from geographically widespread sites in the USA, Japan and Colombia. This is the first verified report of Octaviania from the South American continent. Our molecular analyses also revealed that the RPB1 sequence of one O. tenuipes specimen was identical to that of a closely related species, O. japonimontana, and that one O. potteri specimen from Minnesota had an RPB1 sequence of an unknown species of O. subg. Octaviania. Additionally, one O. japonimontana specimen had an unusually divergent TEF1 sequence. Gene-tree comparison and phylogenetic network analysis of the multilocus dataset suggest that these heterogenous sequences are most likely the result of previous inter- and intra-specific hybridization. We hypothesize that frequent hybridization events in Octaviania may have promoted the high genetic and species diversity found within the genus.

P45.01 Lung Cancer Probability and Clinical Outcomes of Baseline and New Ground-Glass Opacity Nodules Detected on Low-Dose CT Screening

2021 ◽  
Vol 16 (3) ◽  
pp. S486-S487
Author(s):  
Y.W. Kim ◽  
B.S. Kwon ◽  
S.Y. Lim ◽  
Y.J. Lee ◽  
J.S. Park ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Clinical Outcomes ◽  
Low Dose ◽  
Ground Glass Opacity ◽  
Ground Glass ◽  
Ct Screening ◽  
Low Dose Ct

scholarly journals Correlation between CT findings and outcomes in 46 patients with coronavirus disease 2019

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Qiang Lei ◽  
Guangming Li ◽  
Xiaofen Ma ◽  
Junzhang Tian ◽  
Yun fan Wu ◽  
...  
Keyword(s):  
Ground Glass Opacity ◽  
Ground Glass ◽  
Short Term ◽  
Lung Lobe ◽  
Reactive Protein ◽  
Ct Findings ◽  
Short Term Mortality ◽  
Recovery Group ◽  
Diffuse Distribution ◽  
Death Group

AbstractThe aim of this study was to analyze initial chest computed tomography (CT) findings in COVID-19 pneumonia and identify features associated with poor prognosis. Patients with RT-PCR-confirmed COVID-19 infection were assigned to recovery group if they made a full recovery and to death group if they died within 2 months of hospitalization. Chest CT examinations for ground-glass opacity, crazy-paving pattern, consolidation, and fibrosis were scored by two reviewers. The total CT score comprised the sum of lung involvement (5 lobes, scores 1–5 for each lobe, range; 0, none; 25, maximum). 40 patients who recovered from COVID-19 and six patients who died were enrolled. The initial chest CTs showed 27 (58.7%) patients had ground-glass opacity, 19 (41.3%) had ground glass and consolidation, and 35 (76.1%) patients had crazy-paving pattern. None of the patients who died had fibrosis in contrast to six (15%) patients who recovered from COVID-19. Most patients had subpleural lesions (89.0%) as well as bilateral (87.0%) and lower (93.0%) lung lobe involvement. Diffuse lesions were present in four (67%) patients who succumbed to coronavirus but only one (2.5%) patient who recovered (p < 0.001). In the death group of patients, the total CT score was higher than that of the recovery group (p = 0.005). Patients in the death group had lower lymphocyte count and higher C-reactive protein than those in the recovery group (p = 0.011 and p = 0.041, respectively). A high CT score and diffuse distribution of lung lesions in COVID-19 are indicative of disease severity and short-term mortality.

scholarly journals Efficacy of an Augmented Reality Navigation System (SIRIO) for Percutaneous Computed Tomographic-Guided Pulmonary Ground-Glass Opacity Biopsies

2020 ◽  
Author(s):  
Faiella Eliodoro ◽  
Pacella Giuseppina ◽  
Altomare Carlo ◽  
Andresciani Flavio ◽  
Zobel Beomonte Bruno ◽  
...  
Keyword(s):  
Augmented Reality ◽  
Navigation System ◽  
Ground Glass Opacity ◽  
Ground Glass ◽  
Computed Tomographic
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