scholarly journals A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control

2021 ◽  
Author(s):  
Bryan Thornlow ◽  
Angie S. Hinrichs ◽  
Miten Jain ◽  
Namrita Dhillon ◽  
Scott La ◽  
...  
Keyword(s):  
Quality Control ◽  
Turnaround Time ◽  
Large Deletion ◽  
Health Concern ◽  
Viral Loads ◽  
Sequence Generation ◽  
Public Data ◽  
The Usa ◽  
Sequence Quality ◽  
Globally Distributed

AbstractWe report a SARS-CoV-2 lineage that shares N501Y, P681H, and other mutations with known variants of concern, such as B.1.1.7. This lineage, which we refer to as B.1.x (COG-UK sometimes references similar samples as B.1.324.1), is present in at least 20 states across the USA and in at least six countries. However, a large deletion causes the sequence to be automatically rejected from repositories, suggesting that the frequency of this new lineage is underestimated using public data. Recent dynamics based on 339 samples obtained in Santa Cruz County, CA, USA suggest that B.1.x may be increasing in frequency at a rate similar to that of B.1.1.7 in Southern California. At present the functional differences between this variant B.1.x and other circulating SARS-CoV-2 variants are unknown, and further studies on secondary attack rates, viral loads, immune evasion and/or disease severity are needed to determine if it poses a public health concern. Nonetheless, given what is known from well-studied circulating variants of concern, it seems unlikely that the lineage could pose larger concerns for human health than many already globally distributed lineages. Our work highlights a need for rapid turnaround time from sequence generation to submission and improved sequence quality control that removes submission bias. We identify promising paths toward this goal.

scholarly journals Quality control in scRNA-Seq can discriminate pacemaker cells: the mtRNA bias

2021 ◽  
Author(s):  
Anne-Marie Galow ◽  
Sophie Kussauer ◽  
Markus Wolfien ◽  
Ronald M. Brunner ◽  
Tom Goldammer ◽  
...  
Keyword(s):  
Quality Control ◽  
Cardiac Tissue ◽  
High Energy ◽  
Tissue Type ◽  
Pacemaker Cells ◽  
Data Set ◽  
Public Data ◽  
Standard Quality ◽  
Mitochondrial Transcripts

AbstractSingle-cell RNA-sequencing (scRNA-seq) provides high-resolution insights into complex tissues. Cardiac tissue, however, poses a major challenge due to the delicate isolation process and the large size of mature cardiomyocytes. Regardless of the experimental technique, captured cells are often impaired and some capture sites may contain multiple or no cells at all. All this refers to “low quality” potentially leading to data misinterpretation. Common standard quality control parameters involve the number of detected genes, transcripts per cell, and the fraction of transcripts from mitochondrial genes. While cutoffs for transcripts and genes per cell are usually user-defined for each experiment or individually calculated, a fixed threshold of 5% mitochondrial transcripts is standard and often set as default in scRNA-seq software. However, this parameter is highly dependent on the tissue type. In the heart, mitochondrial transcripts comprise almost 30% of total mRNA due to high energy demands. Here, we demonstrate that a 5%-threshold not only causes an unacceptable exclusion of cardiomyocytes but also introduces a bias that particularly discriminates pacemaker cells. This effect is apparent for our in vitro generated induced-sinoatrial-bodies (iSABs; highly enriched physiologically functional pacemaker cells), and also evident in a public data set of cells isolated from embryonal murine sinoatrial node tissue (Goodyer William et al. in Circ Res 125:379–397, 2019). Taken together, we recommend omitting this filtering parameter for scRNA-seq in cardiovascular applications whenever possible.

scholarly journals SHI7 Is a Self-Learning Pipeline for Multipurpose Short-Read DNA Quality Control

mSystems ◽  
2018 ◽  
Vol 3 (3) ◽  
Author(s):  
Gabriel A. Al-Ghalith ◽  
Benjamin Hillmann ◽  
Kaiwei Ang ◽  
Robin Shields-Cutler ◽  
Dan Knights
Keyword(s):  
Quality Control ◽  
Dna Sequences ◽  
Sequence Data ◽  
Background Knowledge ◽  
Sequencing Technology ◽  
Data Set ◽  
Short Read ◽  
Dna Quality ◽  
Public Data ◽  
User Friendly

ABSTRACT Next-generation sequencing technology is of great importance for many biological disciplines; however, due to technical and biological limitations, the short DNA sequences produced by modern sequencers require numerous quality control (QC) measures to reduce errors, remove technical contaminants, or merge paired-end reads together into longer or higher-quality contigs. Many tools for each step exist, but choosing the appropriate methods and usage parameters can be challenging because the parameterization of each step depends on the particularities of the sequencing technology used, the type of samples being analyzed, and the stochasticity of the instrumentation and sample preparation. Furthermore, end users may not know all of the relevant information about how their data were generated, such as the expected overlap for paired-end sequences or type of adaptors used to make informed choices. This increasing complexity and nuance demand a pipeline that combines existing steps together in a user-friendly way and, when possible, learns reasonable quality parameters from the data automatically. We propose a user-friendly quality control pipeline called SHI7 (canonically pronounced “shizen”), which aims to simplify quality control of short-read data for the end user by predicting presence and/or type of common sequencing adaptors, what quality scores to trim, whether the data set is shotgun or amplicon sequencing, whether reads are paired end or single end, and whether pairs are stitchable, including the expected amount of pair overlap. We hope that SHI7 will make it easier for all researchers, expert and novice alike, to follow reasonable practices for short-read data quality control. IMPORTANCE Quality control of high-throughput DNA sequencing data is an important but sometimes laborious task requiring background knowledge of the sequencing protocol used (such as adaptor type, sequencing technology, insert size/stitchability, paired-endedness, etc.). Quality control protocols typically require applying this background knowledge to selecting and executing numerous quality control steps with the appropriate parameters, which is especially difficult when working with public data or data from collaborators who use different protocols. We have created a streamlined quality control pipeline intended to substantially simplify the process of DNA quality control from raw machine output files to actionable sequence data. In contrast to other methods, our proposed pipeline is easy to install and use and attempts to learn the necessary parameters from the data automatically with a single command.

scholarly journals Baylisascaris procyonis roundworm infection patterns in raccoons (Procyon lotor) from Missouri and Arkansas, USA

2017 ◽  
Vol 54 (2) ◽  
pp. 113-118 ◽  
Author(s):  
H. S. Al-Warid ◽  
A. V. Belsare ◽  
K. Straka ◽  
M. E. Gompper
Keyword(s):  
Procyon Lotor ◽  
Missouri River ◽  
Geographic Range ◽  
Health Concern ◽  
Mean Intensity ◽  
Baylisascaris Procyonis ◽  
Wildlife Species ◽  
The Usa ◽  
Paratenic Hosts ◽  
North And South

Summary Baylisascaris procyonis is a helminth parasite of raccoons Procyon lotor and represents a health concern in paratenic hosts, including humans and diverse domestic and wildlife species. In North America the helminth is expanding its geographic range. To better understand patterns of infection in the Ozark region of the USA, raccoons (n = 61) were collected in 2013-2014 from five counties in Missouri and Arkansas, USA and necropsied. We documented B. procyonis in all surveyed locations. The overall prevalence of B. procyonis was 44.3 % (95 % CI = 31.9 - 57.4) and was significantly higher in females than males. There were also significant differences in prevalence among raccoons sampled north and south of the Missouri River. Mean intensity was 9.9 (CI = 5.44 - 17.22), and parasites were highly aggregated among hosts such that approximately 20 % of hosts harbor 90 % of parasites. These levels of parasitism indicate that B. procyonis is common in the region and its impacts on paratenic hosts could be qualitatively similar to effects observed in other localities.

Plasmid-mediated colistin resistance in animals: current status and future directions

2017 ◽  
Vol 18 (2) ◽  
pp. 136-152 ◽  
Author(s):  
Jian Sun ◽  
Ximin Zeng ◽  
Xing-Ping Li ◽  
Xiao-Ping Liao ◽  
Ya-Hong Liu ◽  
...  
Keyword(s):  
Production Systems ◽  
Multidrug Resistant ◽  
Animal Production ◽  
Health Concern ◽  
Current Status ◽  
Peptide Antibiotic ◽  
Colistin Resistance ◽  
Significant Public Health ◽  
The Usa ◽  
Food Animals

AbstractColistin, a peptide antibiotic belonging to the polymyxin family, is one of the last effective drugs for the treatment of multidrug resistant Gram-negative infections. Recent discovery of a novel mobile colistin resistance gene,mcr-1, from people and food animals has caused a significant public health concern and drawn worldwide attention. Extensive usage of colistin in food animals has been proposed as a major driving force for the emergence and transmission ofmcr-1; thus, there is a worldwide trend to limit colistin usage in animal production. However, despite lack of colistin usage in food animals in the USA,mcr-1-positiveEscherichia coliisolates were still isolated from swine. In this paper, we provided an overview of colistin usage and epidemiology ofmcr-1in food animals, and summarized the current status of mechanistic and evolutionary studies of the plasmid-mediated colistin resistance. Based on published information, we further discussed several non-colistin usage risk factors that may contribute to the persistence, transmission, and emergence of colistin resistance in an animal production system. Filling the knowledge gaps identified in this review is critical for risk assessment and risk management of colistin resistance, which will facilitate proactive and effective strategies to mitigate colistin resistance in future animal production systems.

scholarly journals Comparative Analysis of Energy Consumption between Green Building Certified and Non-Certified Buildings in Korea

Energies ◽  
2020 ◽  
Vol 13 (5) ◽  
pp. 1049 ◽  
Author(s):  
Sangtae No ◽  
Chungyeon Won
Keyword(s):  
Energy Consumption ◽  
Energy Use ◽  
Residential Buildings ◽  
Green Building ◽  
Seed Certification ◽  
Portal Site ◽  
Energy Evaluation ◽  
Public Data ◽  
The Usa ◽  
Energy Use Intensity

Although interest in and the importance of green building certification have increased, it is difficult to determine how much less energy the buildings actually consume after obtaining sustainability related certification, such as LEED in the USA, and G-SEED in Korea. Focusing on building energy evaluation, we compared and analyzed the energy evaluation items of LEED and G-SEED. In addition, from the Korean public data portal site, this study investigated the annual site energy consumption (electricity and gas) per floor area of non-residential buildings that obtained G-SEED certification in Korea. The energy consumption of non-certified general buildings was compared with the energy consumption of certified buildings. As a result of examining 84 samples of this study, non-residential buildings with G-SEED certification showed energy use intensity that was at least (35.5 to 48.9)% lower than that of uncertified buildings.

Use of the internet and self-collected samples as a sexually transmissible infection intervention in rural Illinois communities

Sexual Health ◽  
2011 ◽  
Vol 8 (1) ◽  
pp. 79 ◽  
Author(s):  
Wiley D. Jenkins ◽  
Charlie Rabins ◽  
Mathilda Barnes ◽  
Patricia Agreda ◽  
Charlotte Gaydos
Keyword(s):  
At Risk ◽  
Rural Areas ◽  
Cost Effective ◽  
Initial Study ◽  
Health Concern ◽  
The Usa ◽  
Use Of The Internet ◽  
Central Illinois ◽  
Sexually Transmissible Infection ◽  
Transmissible Infection

Background: In the USA, reported cases of chlamydia (Chlamydia trachomatis) continue to rise despite substantial funding for screening. National gonorrhoea (Neisseria gonorrhoeae) rates have remained relatively stable, with clusters associated with metropolitan areas. Rural areas are no exception, as every county in Illinois reported cases of chlamydia in 2007. Morbidity associated with infection remains a public health concern, with costs of $US2.5+ billion annually. Novel screening interventions must be examined for their ability to reach those at risk who are missed by traditional methods. Methods: The website Iwantthekit.org was modified to allow residents from 25 contiguous counties in Central Illinois to request a self-collected sample kit. Returned kits were tested for chlamydia and gonorrhoea. The initial study period was 12 months. Results: During the study period, 343 kits were requested from 20 counties and 39.9% were satisfactorily returned for analysis. Positivity rates for chlamydia and gonorrhoea were 5.8% and 1.2%, respectively, for females and 1.9% and 0% for males. Males comprised 37.7% of all internet samples (compared with 23.4% for traditional screening venues) and 40.4% of all internet samples submitted by whites (compared with only 17.2% of traditional screening). Conclusions: The female positivity rate was comparable to those seen in other screening venues and the method successfully engaged at-risk males. Overall, participation was low and the costs associated with the program outweighed the averted costs associated with the few cases identified. While this methodology resulted in sample requests from a wide area, it must be utilised by more individuals to become cost-effective.

scholarly journals Leptospira in breast tissue and milk of urban Norway rats (Rattus norvegicus)

2016 ◽  
Vol 144 (11) ◽  
pp. 2420-2429 ◽  
Author(s):  
D. DE OLIVEIRA ◽  
C. P. FIGUEIRA ◽  
L. ZHAN ◽  
A. C. PERTILE ◽  
G. G. PEDRA ◽  
...  
Keyword(s):  
Rattus Norvegicus ◽  
Breast Tissue ◽  
Developed Countries ◽  
Immunofluorescence Assay ◽  
Health Concern ◽  
Tissue Samples ◽  
Norway Rat ◽  
First Time ◽  
Globally Distributed ◽  
Norway Rats

SUMMARYLeptospirosis is a zoonosis caused by bacteria of the genus Leptospira. The disease is globally distributed and a major public health concern. The Norway rat (Rattus norvegicus) is the main reservoir of the pathogen in urban slums of developing and developed countries. The potential routes of intra-specific leptospire transmission in rats are largely unknown. Herein, we identified pathogenic Leptospira spp. in breast tissue and milk of naturally infected rats. We examined kidney, breast tissue and milk from 24 lactating rats for the presence of leptospires using immunofluorescence, immunohistochemistry, polymerase chain reaction (PCR) and scanning electronic microscopy. All 24 rats had evidence for Leptospira in the kidneys, indicating chronic carriage. The majority of kidney-positive rats had detectable leptospires in milk (18, 75%) and breast tissue (16, 67%), as evidenced by immunofluorescence assay and immunohistochemistry. Four (17%) milk samples and two (8%) breast tissue samples were positive by quantitative real-time PCR. Scanning electron microscopy confirmed the presence of leptospires in breast tissue. No major pathological changes in breast tissue were found. This study, for the first time, identified leptospires in the milk and breast tissue of wild Norway rats, suggesting the possibility of milk-borne transmission of leptospirosis to neonates.

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