Clinical characterization of hospitalized COVID-19 patients during the second wave of pandemic in the district of Rohrbach, Upper Austria

AbstractWide-scale SARS-CoV-2 genome sequencing is critical to tracking viral evolution during the ongoing pandemic. We develop the software tool, Variant Database (VDB), for quickly examining the changing landscape of spike mutations. Using VDB, we detect an emerging lineage of SARS-CoV-2 in the New York region that shares mutations with previously reported variants. The most common sets of spike mutations in this lineage (now designated as B.1.526) are L5F, T95I, D253G, E484K or S477N, D614G, and A701V. This lineage was first sequenced in late November 2020. Phylodynamic inference confirmed the rapid growth of the B.1.526 lineage. In concert with other variants, like B.1.1.7, the rise of B.1.526 appears to have extended the duration of the second wave of COVID-19 cases in NYC in early 2021. Pseudovirus neutralization experiments demonstrated that B.1.526 spike mutations adversely affect the neutralization titer of convalescent and vaccinee plasma, supporting the public health relevance of this lineage.

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Characterization of the early development of specific hypaxial muscles from the ventrolateral myotome

Development ◽

10.1242/dev.126.19.4305 ◽

1999 ◽

Vol 126 (19) ◽

pp. 4305-4315 ◽

Cited By ~ 10

Author(s):

Y. Cinnamon ◽

N. Kahane ◽

C. Kalcheim

Keyword(s):

Confocal Microscopy ◽

Early Development ◽

Early Generation ◽

Intercostal Muscles ◽

Fundamental Component ◽

Vital Dyes ◽

First Time ◽

Second Wave ◽

Longitudinal Cell

We have previously found that the myotome is formed by a first wave of pioneer cells generated along the medial epithelial somite and a second wave emanating from the dorsomedial lip (DML), rostral and caudal edges of the dermomyotome (Kahane, N., Cinnamon, Y. and Kalcheim, C. (1998a) Mech. Dev. 74, 59–73; Kahane, N., Cinnamon, Y. and Kalcheim, C. (1998b) Development 125, 4259–4271). In this study, we have addressed the development and precise fate of the ventrolateral lip (VLL) in non-limb regions of the axis. To this end, fluorescent vital dyes were iontophoretically injected in the center of the VLL and the translocation of labeled cells was followed by confocal microscopy. VLL-derived cells colonized the ventrolateral portion of the myotome. This occurred following an early longitudinal cell translocation along the medial boundary until reaching the rostral or caudal dermomyotome lips from which fibers emerged into the myotome. Thus, the behavior of VLL cells parallels that of their DML counterparts which colonize the opposite, dorsomedial portion of the myotome. To precisely understand the way the myotome expands, we addressed the early generation of hypaxial intercostal muscles. We found that intercostal muscles were formed by VLL-derived fibers that intermingled with fibers emerging from the ventrolateral aspect of both rostral and caudal edges of the dermomyotome. Notably, hypaxial intercostal muscles also contained pioneer myofibers (first wave) showing for the first time that lateral myotome-derived muscles contain a fundamental component of fibers generated in the medial domain of the somite. In addition, we show that during myotome growth and evolution into muscle, second-wave myofibers progressively intercalate between the pioneer fibers, suggesting a constant mode of myotomal expansion in its dorsomedial to ventrolateral extent. This further suggests that specific hypaxial muscles develop following a consistent ventral expansion of a ‘compound myotome’ into the somatopleure.

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Unsupervised delineation of landfill geometries based on geophysical imaging results

10.5194/egusphere-egu2020-8578 ◽

2020 ◽

Author(s):

Matthias Steiner ◽

Werner Chwatal ◽

Andreas Freudenthaler ◽

Adrian Flores Orozco

Keyword(s):

Geophysical Methods ◽

Subjective Perception ◽

Random Walker ◽

Upper Austria ◽

Base Points ◽

Imaging Results ◽

Refraction Seismic ◽

High Gradients ◽

Geophysical Imaging

<p> Environmental aspects and the growing interest in the economical exploitation of landfills urges the need for cost-efficient workflows providing information with high spatial resolution. Especially for landfill mining, a detailed characterization of the landfill geometry and the waste composition is critical to assess the economic potential. Geophysical methods have proven to fulfill these requirements since they permit to collect data in a quasi-continuous manner. However, the subjective perception of the geophysical imaging results might bias the interpretation, e.g. the characterization of the landfill boundaries and the estimation of waste volumes. To overcome such shortcomings, we present here an unsupervised method for the post-processing of geophysical imaging to identify subsurface interfaces associated to e.g. landfill geometries, waste variation etc. Our methodology is applicable for results obtained with a single method, or the combination of different geophysical methods, e.g. refraction seismic tomography (RST), electrical resistivity tomography (ERT) or induced polarization (IP). Assuming strong contrasts in the retrieved physical properties associated to interfaces, our method computes the magnitude of the gradient vector for each point in the resolved model. In the next step, a random walker algorithm converts the gradient magnitude image into a binary image permitting to obtain the contours of subsurface regions characterized by high gradients. Originating from the centroid for such a region further base points are determined and used in the final step to compute shape and location of the corresponding interface. To demonstrate the applicability of our method we present here results obtained for a landfill located in Upper Austria, where RST, ERT and IP data were collected along several transects. Our results demonstrate that the method proposed here has the potential to enhance geophysical investigations of landfills by permitting an improved interpretation of the imaging results, as required, for instance to estimate waste volume.</p>

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Characterization of Elastomers and Elastomeric Composites Using Ultrasound

MRS Proceedings ◽

10.1557/proc-733-t6.11 ◽

2002 ◽

Vol 733 ◽

Author(s):

Subash Jayaraman ◽

Jonathan Dick ◽

Timothy Craychee ◽

Jikai Du ◽

Bernhard Tittmann

Keyword(s):

Wave Amplitude ◽

Contact Method ◽

Wave Velocities ◽

Ultrasonic Techniques ◽

Second Wave ◽

Non Destructive ◽

Sample Set ◽

Elastomeric Composites ◽

Polymer Type

AbstractThe knowledge of elastic properties of the various types of rubber is significant for many commercial and academic applications. A sample set consisting of generic elastomeric compounds was studied using non-destructive non-contact ultrasonic techniques. The longitudinal sound wave velocities in the sample and wave amplitude attenuation in the sample were measured using the Second Wave Inc. Non-Contact Analyzer 1000 (NCA1000). The Contact method was then used to corroborate the results obtained. A rule-of-mixture model was used to compare the velocity values obtained by the non-contact technique. The preliminary results suggest that the differences in attenuation are driven by polymer type and also to a lesser extent by the loading level of carbon black fillers.

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The First Molecular Characterization of Serbian SARS-CoV-2 Isolates From a Unique Early Second Wave in Europe

Frontiers in Microbiology ◽

10.3389/fmicb.2021.691154 ◽

2021 ◽

Vol 12 ◽

Author(s):

Danijela Miljanovic ◽

Ognjen Milicevic ◽

Ana Loncar ◽

Dzihan Abazovic ◽

Dragana Despot ◽

...

Keyword(s):

Functional Characterization ◽

Early Summer ◽

Future Research ◽

Viral Genomes ◽

Rare Mutations ◽

Second Wave ◽

Genome Variants ◽

Local Transmission

March 6, 2020 is considered as the official date of the beginning of the COVID-19 epidemic in Serbia. In late spring and early summer 2020, Europe recorded a decline in the rate of SARS-CoV-2 infection and subsiding of the first wave. This trend lasted until the fall, when the second wave of the epidemic began to appear. Unlike the rest of Europe, Serbia was hit by the second wave of the epidemic a few months earlier. Already in June 2020, newly confirmed cases had risen exponentially. As the COVID-19 pandemic is the first pandemic in which there has been instant sharing of genomic information on isolates around the world, the aim of this study was to analyze whole SARS-CoV-2 viral genomes from Serbia, to identify circulating variants/clade/lineages, and to explore site-specific mutational patterns in the unique early second wave of the European epidemic. This analysis of Serbian isolates represents the first publication from Balkan countries, which demonstrates the importance of specificities of local transmission especially when preventive measures differ among countries. One hundred forty-eight different genome variants among 41 Serbian isolates were detected in this study. One unique and seven extremely rare mutations were identified, with locally specific continuous dominance of the 20D clade. At the same time, amino acid substitutions of newly identified variants of concern were found in our isolates from October 2020. Future research should be focused on functional characterization of novel mutations in order to understand the exact role of these variations.

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Not a white girl and speaking English with slang: Negotiating Hmong American identities in Minneapolis-St. Paul, Minnesota, USA

Multilingua ◽

10.1515/multi-2019-0082 ◽

2020 ◽

Vol 0 (0) ◽

Author(s):

Rika Ito

Keyword(s):

Local Community ◽

American English ◽

Vowel Production ◽

White Girl ◽

Local Setting ◽

White Majority ◽

Hmong Americans ◽

Hmong American ◽

Second Wave

AbstractThis paper analyzes metalinguistic comments of two young Hmong Americans in the Minneapolis-St Paul area regarding their identity negotiation using tactics of intersubjectivity (Bucholtz & Hall 2004a, 2004b, 2005), the notion of brought-along identity (Williams 2008) and Zhang's (2017) sociohistorical perspectives in analyzing linguistic variation. Two Hmong American individuals were selected from over 60 Hmong American interviewees because their vowel production is nearly identical to each other and that of the local white youth. Although their almost identical vowel production is viewed as their acculturation to the local white majority norm in the first- and second-wave variationist sociolinguistic perspective (Eckert 2012), their speech's characterization reveals a range of potential meanings (Eckert 2008) to index nuanced and unique positions in their local community. The young woman is ambivalent about her speech being characterized as “not having an accent” and claims that she is “not a white girl”. The teenage boy discusses his speech as “Hmonglish” and “English with slang” but carefully distances himself from quintessential African American English. While their characterization of their speech is distinct from each other, their tactics are strikingly similar. Through highlighting and downplaying differences and similarities to a locally salient way of speaking that indexes whiteness or blackness, the two Hmong Americans carve out their own complex identities of race, ethnicity, gender, and class in a local setting.

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Presence of gustatory and olfactory dysfunction in the time of the COVID-19 pandemic

BMC Infectious Diseases ◽

10.1186/s12879-021-06294-2 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Alexander Kusnik ◽

Christel Weiss ◽

Melanie Neubauer ◽

Bianca Huber ◽

Marlis Gerigk ◽

...

Keyword(s):

Regional Differences ◽

Clinical Characteristics ◽

Olfactory Dysfunction ◽

Symptom Duration ◽

The Novel ◽

Binary Outcome ◽

Detailed Characterization ◽

Populations At Risk ◽

Second Wave

Abstract Background The unexpected outbreak of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused more than 49 million cases and an estimated 2,000,000 associated deaths worldwide. In Germany, there are currently more than 2,000,000 laboratory-confirmed coronavirus disease 2019 (COVID-19) cases including 51,800 deaths. However, regional differences also became apparent and with the second wave of infections, the detailed characterization of COVID-19 patients is crucial to early diagnosis and disruption of chains of infections. Methods Handing out detailed questionnaires to all individuals tested for COVID-19, we evaluated the clinical characteristics of negative and positive tested individuals. Expression of symptoms, symptom duration and association between predictor variables (i.e. age, gender) and a binary outcome (olfactory and gustatory dysfunction) were assessed. Results Overall, the most common symptoms among individuals who tested positive for SARS-CoV-2 were fatigue, headache, and cough. Olfactory and gustatory dysfunction were also reported by many SARS-CoV-2 negative individuals, more than 20% of SARS-CoV-2 negative tested individuals in our study reported olfactory and gustatory dysfunction. Independent of SARS-CoV-2 status, more females displayed symptoms of gustatory (29.8%, p = 0.0041) and olfactory dysfunction (22.9%, p = 0.0174) compared to men. Conclusions Bringing early SARS-CoV-2 tests to the populations at risk must be a main focus for the upcoming months. The reliability of olfactory and gustatory dysfunction in COVID-19 negative tested individuals requires deeper investigation in the future.

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Emergence of Novel SARS-CoV-2 variants in India: second wave

The Journal of Infection in Developing Countries ◽

10.3855/jidc.15484 ◽

2021 ◽

Vol 15 (11) ◽

pp. 1578-1583

Author(s):

Rama Adiga ◽

Varun Nayak

Keyword(s):

Indian Subcontinent ◽

Asian Countries ◽

Sample Collection ◽

High Coverage ◽

Time Period ◽

Indian State ◽

Rapid Pace ◽

Global Initiative ◽

Second Wave

Introduction: Globally South-East Asia reported 40% of SARS-CoV-2 infected cases in the fourth week of April 2021. It continued to show an increase with India accounting for 50% of cases worldwide and 30% of global deaths. Genomic surveillance should continue at a rapid pace because of the continuously evolving nature of the virus. The time period of sample collection from the Global Initiative on Sharing All Influenza Data database was concurrent with the surge in new cases seen in the Indian subcontinent. Methodology: 7,415 sequences were downloaded from Global Initiative on Sharing All Influenza Data between January and April 2021; out of which 4,411 were high coverage genome sequences and were considered for analysis. Phylogenetic analysis were carried out using Nextstrain. Results: 21A or B.1.617 or delta was the most prevalent lineage in India accounting for 67.7% of the genomes. Next important clades were 20A, 20B and 20I accounting for 23.6%, 11.8% and 12.1% respectively collected between January 2021 and April 2021. The remaining sequences were assigned to clade 20H, 20J, 20D, 20C, 20G,20E,19A and 19B.The spike mutation frequencies of L452R, E484Q and P681R in Indian state of Maharashtra were 62.4%, 66.5% and 61.5% respectively. Two unique N-terminal domain deletion of spike protein were found at position 67 and 68. Conclusions: The phylogenomics of the delta variant or 21A emerged in neighboring Asian countries of Thailand, Bangladesh, Indonesia and Japan. We analyzed the SARS-CoV-2 genomes from India for mutation characterization of the spike glycoprotein and the nucleocapsid protein.

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Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil

10.1101/2020.12.23.20248598 ◽

2020 ◽

Author(s):

Carolina M Voloch ◽

Ronaldo da Silva F ◽

Luiz G P de Almeida ◽

Cynthia C Cardoso ◽

Otavio J. Brustolini ◽

...

Keyword(s):

Rio De Janeiro ◽

Neutralizing Antibodies ◽

Health Management ◽

The State ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Viral Genomes ◽

Genomic Characterization ◽

Second Wave

AbstractIn this study, we report the sequencing of 180 new viral genomes obtained from different municipalities of the state of Rio de Janeiro from April to December 2020. We identified a novel lineage of SARS-CoV-2, originated from B.1.1.28, distinguished by five single-nucleotide variants (SNVs): C100U, C28253U, G28628U, G28975U, and C29754U. The SNV G23012A (E484K), in the receptor-binding domain of Spike protein, was widely spread across the samples. This mutation was previously associated with escape from neutralizing antibodies against SARS-CoV-2. This novel lineage emerged in late July being first detected by us in late October and still mainly restricted to the capital of the state. However, as observed for other strains it can be rapidly spread in the state. The significant increase in the frequency of this lineage raises concerns about public health management and continuous need for genomic surveillance during the second wave of infections.Article Summary LineWe identified a novel circulating lineage of SARS-CoV-2 in the state of Rio de Janeiro Brazil originated from B.1.1.28 lineage.

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Strains, functions and dynamics in the expanded Human Microbiome Project

Nature ◽

10.1038/nature23889 ◽

2017 ◽

Vol 550 (7674) ◽

pp. 61-66 ◽

Cited By ~ 411

Author(s):

Jason Lloyd-Price ◽

Anup Mahurkar ◽

Gholamali Rahnavard ◽

Jonathan Crabtree ◽

Joshua Orvis ◽

...

Keyword(s):

Human Microbiome ◽

Human Microbiome Project ◽

Temporal Analysis ◽

National Institutes Of Health ◽

Strain Identification ◽

Multiple Time ◽

Functional Profiling ◽

Multiple Time Points ◽

Second Wave

Abstract The characterization of baseline microbial and functional diversity in the human microbiome has enabled studies of microbiome-related disease, diversity, biogeography, and molecular function. The National Institutes of Health Human Microbiome Project has provided one of the broadest such characterizations so far. Here we introduce a second wave of data from the study, comprising 1,631 new metagenomes (2,355 total) targeting diverse body sites with multiple time points in 265 individuals. We applied updated profiling and assembly methods to provide new characterizations of microbiome personalization. Strain identification revealed subspecies clades specific to body sites; it also quantified species with phylogenetic diversity under-represented in isolate genomes. Body-wide functional profiling classified pathways into universal, human-enriched, and body site-enriched subsets. Finally, temporal analysis decomposed microbial variation into rapidly variable, moderately variable, and stable subsets. This study furthers our knowledge of baseline human microbial diversity and enables an understanding of personalized microbiome function and dynamics.

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