scholarly journals Assessing Multiplex Tiling PCR Sequencing Approaches for Detecting Genomic Variants of SARS-CoV-2 in Municipal Wastewater

mSystems ◽  
2021 ◽  
Author(s):  
Xuan Lin ◽  
Melissa Glier ◽  
Kevin Kuchinski ◽  
Tenysha Ross-Van Mierlo ◽  
David McVea ◽  
...  
Keyword(s):  
Municipal Wastewater ◽  
Population Sample ◽  
Great Promise ◽  
Clinical Patient ◽  
Genomic Variants ◽  
Sample Matrix ◽  
Patient Sample

Monitoring the genomic characteristics of the SARS-CoV-2 virus circulating in a population can shed important insights into epidemiological aspects of the COVID-19 outbreak. Sequencing every clinical patient sample in a highly populous area is a difficult feat, and thus sequencing SARS-CoV-2 RNA in municipal wastewater offers great promise to augment genomic surveillance by characterizing a pooled population sample matrix, particularly during an escalating outbreak.

scholarly journals Assessing multiplex tiling PCR sequencing approaches for detecting genomic variants of SARS-CoV-2 in municipal wastewater

2021 ◽  
Author(s):  
Xuan Lin ◽  
Melissa Glier ◽  
Kevin Kuchinski ◽  
Tenysha Ross-Van Mierlo ◽  
David McVea ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Municipal Wastewater ◽  
Rna Degradation ◽  
Geographic Region ◽  
Wastewater Sample ◽  
Municipal Wastewater Treatment ◽  
Primary Sludge ◽  
Genome Coverage ◽  
Genomic Variants ◽  
Influent Wastewater

Wastewater-based genomic surveillance of the SARS-CoV-2 virus shows promise to complement genomic epidemiology efforts. Multiplex tiled PCR is a desirable approach for targeted genome sequencing of SARS-CoV-2 in wastewater due to its low cost and rapid turnaround time. However, it is not clear how different multiplex tiled PCR primer schemes or wastewater sample matrices impact the resulting SARS-CoV-2 genome coverage. The objective of this work was to assess the performance of three different multiplex primer schemes, consisting of 150bp, 400bp, and 1200bp amplicons, as well as two wastewater sample matrices, influent wastewater and primary sludge, for targeted genome sequencing of SARS-CoV-2. Wastewater samples were collected weekly from five municipal wastewater treatment plants (WWTPs) in the Metro Vancouver region of British Columbia, Canada during a period of increased COVID-19 case counts from February to April, 2021. RNA extracted from clarified influent wastewater provided significantly higher genome coverage (breadth and median depth) than primary sludge samples across all primer schemes. Shorter amplicons appeared more resilient to sample RNA degradation, but were hindered by greater primer pool complexity in the 150bp scheme. The identified optimal primer scheme (400bp) and sample matrix (influent) was capable of detecting the emergence of mutations associated with genomic variants of concern, of which the daily wastewater load significantly correlated with clinical case counts. Taken together, these results provide guidance on best practices for implementing wastewater-based genomic surveillance, and demonstrate its ability to inform epidemiology efforts by detecting genomic variants of concern circulating within a geographic region.

scholarly journals Commutability Limitations Influence Quality Control Results with Different Reagent Lots

2011 ◽  
Vol 57 (1) ◽  
pp. 76-83 ◽  
Author(s):  
WGreg Miller ◽  
Aybala Erek ◽  
Tina D Cunningham ◽  
Olajumoke Oladipo ◽  
Mitchell G Scott ◽  
...  
Keyword(s):  
Quality Control ◽  
T Test ◽  
Good Laboratory Practice ◽  
Laboratory Practice ◽  
Clinical Patient ◽  
Patient Sample ◽  
Significant Difference ◽  
Good Laboratory ◽  
Sample Measurement

BACKGROUND Good laboratory practice includes verifying that each new lot of reagents is suitable for use before it is put into service. Noncommutability of quality control (QC) samples with clinical patient samples may preclude their use to verify consistency of results for patient samples between different reagent lots. METHODS Patient sample results and QC data were obtained from reagent lot change verification records for 18 QC materials, 661 reagent lot changes, 1483 reagent lot change–QC events, 82 analytes, and 7 instrument platforms. The significance of between-lot differences in the results for QC samples compared with those for patient samples was assessed by a modified 2-sample t test adjusted for heterogeneity of QC and patient sample measurement variances. RESULTS Overall, 40.9% of reagent lot change–QC events had a significant difference (P < 0.05) between results for QC samples compared with results for patient samples between 2 reagent lots. For QC results with differences <1.0 SD interval (83.1% of total), 37.7% were significantly different from the changes observed for patient samples. For QC results with differences ≥1.0 SD interval (16.9% of total), 57.0% were significantly different from those for patient samples. CONCLUSIONS Occurrence of noncommutable results for QC materials was frequent enough that the QC results could not be used to verify consistency of results for patient samples when changing lots of reagents.

Assessing multiplex tiling PCR sequencing approaches for detecting genomic variants of SARS-CoV-2 in municipal wastewater v1

2021 ◽  
Author(s):  
Xuan Lin ◽  
Melissa not provided Glier ◽  
Kevin Kuchinski ◽  
Tenysha Ross-Van Mierlo ◽  
David McVea ◽  
...  
Keyword(s):  
Municipal Wastewater ◽  
Amplicon Sequencing ◽  
Primary Sludge ◽  
Genomic Variants ◽  
Dna Library ◽  
Oxford Nanopore ◽  
Influent Wastewater

In this work, we aim to access the performance of three different multiplex primer schemes, i.e. Swift amplicon SARS-CoV-2 panel (150bp amplicons), ARTIC V3 panel (400bp amplicons), and SARS-CoV-2 midnight panel (1200bp amplicons), for metatranscriptomic sequencing of SARS-CoV-2 for influent wastewater and primary sludge. This protocol is adapted from the Swift amplicon™ SARS-COV-2 protocol (150bp amplicon), ARTIC V3 protocol (400bp amplicon), and "midnight" protocol (1200bp amplicon). Sequencing libraries are prepared with 1) Oxford Nanopore Ligation Sequencing Kit (SQK-LSK109) with Native Barcoding kit (EXP-NEB104 and EXP-NEB114), or 2) NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® with NEBNext® Multiplex Oligos for Illumina®. Links to the protocols are: Swift amplicon protocol (150bp): https://swiftbiosci.com/swift-amplicon-sars-cov-2-panel/ ARTIC V3 protocol (400bp): https://www.protocols.io/view/ncov-2019-sequencing-protocol-v3-locost-bh42j8ye?version_warning=no "midnight" protocol V4 (1200bp): dx.doi.org/10.17504/protocols.io.bh7hj9j6

scholarly journals Clinically Unreported Salmonellosis Outbreak Detected via Comparative Genomic Analysis of Municipal Wastewater Salmonella Isolates

2019 ◽  
Vol 85 (10) ◽  
Author(s):  
Sabrina Diemert ◽  
Tao Yan
Keyword(s):  
Public Health ◽  
Infectious Disease ◽  
Salmonella Enterica ◽  
Municipal Wastewater ◽  
Disease Outbreaks ◽  
Easy Access ◽  
Great Promise ◽  
Content Type ◽  
Health Clinics ◽  
Paratyphi B

ABSTRACT Municipal wastewater includes human waste that contains both commensal and pathogenic enteric microorganisms, and this collective community microbiome can be monitored for community diseases. In a previous study, we assessed the salmonellosis disease burden using municipal wastewater from Honolulu, Hawaii, which was monitored over a 54-week period. During that time, a strain of Salmonella enterica serovar Paratyphi B variant L(+) tartrate(+) (also known as Salmonella enterica serovar Paratyphi B variant Java) was identified; this strain was detected simultaneously with a clinically reported outbreak, and pulsed-field gel electrophoresis patterns were identical for clinical and municipal wastewater isolates. Months after the outbreak subsided, the same pulsotype was detected as the dominant pulsotype in municipal wastewater samples, with no corresponding clinical cases reported. Using genomic characterization (including core single-nucleotide polymorphism alignment, core genome multilocus sequence typing, and screening for virulence and antibiotic resistance genes), all S. Java municipal wastewater isolates were determined to be clonal, indicating a resurgence of the original outbreak strain. This demonstrates the feasibility and utility of municipal wastewater surveillance for determining enteric disease outbreaks that may be missed by traditional clinical surveillance methods. IMPORTANCE Underdetection of microbial infectious disease outbreaks in human communities carries enormous health costs and is an ongoing problem in public health monitoring (which relies almost exclusively on data from health clinics). Surveillance of municipal wastewater for community-level monitoring of infectious disease burdens has the potential to fill this information gap, due to its easy access to the mixed community microbiome. In the present study, the genomes of 21 S. Java isolates (collected from municipal wastewater in Honolulu) were analyzed; results showed that the same Salmonella strain that caused a known salmonellosis clinical outbreak in spring 2010 remerged as the most dominant strain in municipal wastewater in spring 2011, indicating a new outbreak that was not detected by health clinics. Our results show that wastewater monitoring holds great promise to inform the field of public health regarding outbreak status within communities.

Are HOLZ lines kinematic in off-zone-axis orientation?

1993 ◽  
Vol 51 ◽  
pp. 692-693
Author(s):  
J. M. Zuo ◽  
A. L. Weickenmeier ◽  
R. Holmestad ◽  
J. C. H. Spence
Keyword(s):  
Structure Determination ◽  
Standard Procedure ◽  
High Order ◽  
Zone Axis ◽  
Great Promise ◽  
Line Position ◽  
Measured Intensity ◽  
Constant Intensity ◽  
Axis Orientation ◽  
Diffraction Condition

The application of high order reflections in a weak diffraction condition off the zone axis center, including those in high order laue zones (HOLZ), holds great promise for structure determination using convergent beam electron diffraction (CBED). It is believed that in this case the intensities of high order reflections are kinematic or two-beam like. Hence, the measured intensity can be related to the structure factor amplitude. Then the standard procedure of structure determination in crystallography may be used for solving unknown structures. The dynamic effect on HOLZ line position and intensity in a strongly diffracting zone axis is well known. In a weak diffraction condition, the HOLZ line position may be approximated by the kinematic position, however, it is not clear whether this is also true for HOLZ intensities. The HOLZ lines, as they appear in CBED patterns, do show strong intensity variations along the line especially near the crossing of two lines, rather than constant intensity along the Bragg condition as predicted by kinematic or two beam theory.

Development of the UHV-STM

1990 ◽  
Vol 48 (1) ◽  
pp. 322-323
Author(s):  
M. Iwatsuki ◽  
S. Kitamura ◽  
A. Mogami
Keyword(s):  
Surface Science ◽  
Real Space ◽  
Atomic Scale ◽  
Scanning Tunneling ◽  
Great Promise ◽  
Force Microscopy ◽  
Atomic Force ◽  
Stm Image ◽  
Surface Construction ◽  
Very High

Since Binnig, Rohrer and associates observed real-space topographic images of Si(111)-7×7 and invented the scanning tunneling microscope (STM),1) the STM has been accepted as a powerful surface science instrument.Recently, many application areas for the STM have been opened up, such as atomic force microscopy (AFM), magnetic force microscopy (MFM) and others. So, the STM technology holds a great promise for the future.The great advantages of the STM are its high spatial resolution in the lateral and vertical directions on the atomic scale. However, the STM has difficulty in identifying atomic images in a desired area because it uses piezoelectric (PZT) elements as a scanner.On the other hand, the demand to observe specimens under UHV condition has grown, along with the advent of the STM technology. The requirment of UHV-STM is especially very high in to study of surface construction of semiconductors and superconducting materials on the atomic scale. In order to improve the STM image quality by keeping the specimen and tip surfaces clean, we have built a new UHV-STM (JSTM-4000XV) system which is provided with other surface analysis capability.

Behavioral Genetics: Concepts for Research and Practice in Language Development and Disorders

1995 ◽  
Vol 38 (5) ◽  
pp. 1126-1142 ◽  
Author(s):  
Jeffrey W. Gilger
Keyword(s):  
Language Development ◽  
Behavioral Genetics ◽  
State Of The Art ◽  
Genetic Research ◽  
Great Promise ◽  
Behavioral Genetic ◽  
Fine Grained ◽  
Future Goals ◽  
Current State ◽  
Research Designs

This paper is an introduction to behavioral genetics for researchers and practioners in language development and disorders. The specific aims are to illustrate some essential concepts and to show how behavioral genetic research can be applied to the language sciences. Past genetic research on language-related traits has tended to focus on simple etiology (i.e., the heritability or familiality of language skills). The current state of the art, however, suggests that great promise lies in addressing more complex questions through behavioral genetic paradigms. In terms of future goals it is suggested that: (a) more behavioral genetic work of all types should be done—including replications and expansions of preliminary studies already in print; (b) work should focus on fine-grained, theory-based phenotypes with research designs that can address complex questions in language development; and (c) work in this area should utilize a variety of samples and methods (e.g., twin and family samples, heritability and segregation analyses, linkage and association tests, etc.).

Personality Measurement and Profile in a European Sample of Civil Airline Pilots

2019 ◽  
Vol 35 (6) ◽  
pp. 791-800 ◽  
Author(s):  
Karina Mesarosova ◽  
Alex B. Siegling ◽  
Rachel A. Plouffe ◽  
Donald H. Saklofske ◽  
Martin M. Smith ◽  
...  
Keyword(s):  
Structural Equation ◽  
Structural Model ◽  
Population Sample ◽  
Civil Aviation ◽  
Equation Modeling ◽  
Personality Profile ◽  
Working Population ◽  
Internal Reliability ◽  
Airline Pilots ◽  
Pilot Sample

Abstract. The study examined the psychometric properties of the Revised NEO Personality Inventory (NEO PI-R, UK edition) in a large European sample of civil airline pilots. The NEO PI-R is a comprehensive and robust measure of personality that has been validated across cultures and contexts. Furthermore, the personality profile of the pilot sample was examined and compared to a normative sample representing the UK working population. Data from 591 pilots (95.1% male) were collected. Analyses include the internal reliability and factorial validity (precisely, Exploratory Structural Equation Modeling) to examine the measurement equivalence of the NEO PI-R with reference to UK norms ( N = 1,301). Internal reliability estimates of the NEO PI-R scores were good at the domain level, but generally weak at the facet level. The structural model in the pilot sample was congruent with the general working population sample. Furthermore, there was convincing evidence for a distinct personality profile of civil pilots, although the stability of this profile will require further validation. The NEO PI-R’s validity in the assessment of general personality in civil airline pilots is discussed, along with implications of the results for the utility of personality assessment in civil aviation contexts.

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