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Article ; Online: SARS-CoV-2 genotyping and sequencing following a simple and economical RNA extraction and storage protocol.

Hernandez, Sarah / Nguyen, Phuong-Vi / Azmain, Taz / Piantadosi, Anne / Waggoner, Jesse J

2023 Volume 18, Issue 1, Page(s) e0280577

Abstract: Since the beginning of the SARS-CoV-2 pandemic, supply chain shortages have caused major disruptions in sourcing the materials needed for laboratory-based molecular assays. With increasing demand for molecular testing, these disruptions have limited ... ...

Abstract	Since the beginning of the SARS-CoV-2 pandemic, supply chain shortages have caused major disruptions in sourcing the materials needed for laboratory-based molecular assays. With increasing demand for molecular testing, these disruptions have limited testing capacity and hindered efforts to mitigate spread of the virus and new variants. Here we evaluate an economical and reliable protocol for the extraction and short-term ambient temperature storage of SARS-CoV-2 RNA. Additional objectives of the study were to evaluate RNA from this protocol for 1) detection of single nucleotide polymorphisms (SNPs) in the spike gene and 2) whole genome sequencing of SARS-CoV-2. The RNAES protocol was evaluated with residual nasopharyngeal (NP) samples collected from Emory Healthcare and Emory Student Health services. All RNAES extractions were performed in duplicate and once with a commercial extraction robot for comparison. Following extraction, eluates were immediately tested by rRT-PCR. SARS-CoV-2 RNA was successfully detected in 56/60 (93.3%) RNAES replicates, and Ct values corresponded with comparator results. Upon testing in spike SNP assays, three genotypes were identified, and all variant calls were consistent with those previously obtained after commercial extraction. Additionally, the SARS-RNAES protocol yield eluate pure enough for downstream whole genome sequencing, and results were consistent with SARS-CoV-2 whole genome sequencing of eluates matched for Ct value. With reproducible results across a range of virus concentrations, the SARS-RNAES protocol could help increase SARS-CoV-2 diagnostic testing and monitoring for emerging variants in resource-constrained communities.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; COVID-19/diagnosis ; COVID-19 Testing ; RNA, Viral/genetics ; RNA, Viral/analysis ; Clinical Laboratory Techniques/methods ; Genotype
Chemical Substances	RNA, Viral
Language	English
Publishing date	2023-01-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0280577
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Effective Saccharification of Corn Stover Using Low-Liquid Aqueous Ammonia Pretreatment and Enzymatic Hydrolysis

Nguyen Phuong Vi Truong / Tae Hyun Kim

Molecules, Vol 23, Iss 5, p

2018 Volume 1050

Abstract: Low-liquid aqueous ammonia (LLAA) pretreatment using aqueous ammonia was investigated to enhance enzymatic saccharification of corn stover. In this method, ground corn stover was simply contacted with aqueous ammonia mist (ammoniation step), followed by ... ...

Abstract	Low-liquid aqueous ammonia (LLAA) pretreatment using aqueous ammonia was investigated to enhance enzymatic saccharification of corn stover. In this method, ground corn stover was simply contacted with aqueous ammonia mist (ammoniation step), followed by pretreatment at elevated temperature (90–150 °C) for an extended period (24–120 h) at different solid/liquid (S/L) ratios (0.29, 0.47 or 0.67), termed a pretreatment step. After that, excess (unreacted) ammonia was removed by evaporation, and the pretreated material was immediately saccharified by an enzyme without a washing step. The effects of key reaction parameters on both glucan digestibility and XMG digestibility were evaluated by analysis of variance (ANOVA). Under the best pretreatment conditions [S/L = 0.47, 0.16 (g NH3)/(g biomass), 90 °C, 24 h], LLAA pretreatment enhanced enzymatic digestibility from 23.1% for glucan and 11.3% for XMG (xylan + galactan + mannan) of untreated corn stover to 91.8% for glucan and 72.6% for XMG in pretreated solid.
Keywords	aqueous ammonia ; alkaline pretreatment ; enzymatic digestibility ; lignocellulosic biomass ; cellulosic sugar ; Organic chemistry ; QD241-441
Language	English
Publishing date	2018-05-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Effective Saccharification of Corn Stover Using Low-Liquid Aqueous Ammonia Pretreatment and Enzymatic Hydrolysis.

Truong, Nguyen Phuong Vi / Kim, Tae Hyun

Molecules (Basel, Switzerland)

2018 Volume 23, Issue 5

Abstract	Low-liquid aqueous ammonia (LLAA) pretreatment using aqueous ammonia was investigated to enhance enzymatic saccharification of corn stover. In this method, ground corn stover was simply contacted with aqueous ammonia mist (ammoniation step), followed by pretreatment at elevated temperature (90⁻150 °C) for an extended period (24⁻120 h) at different solid/liquid (S/L) ratios (0.29, 0.47 or 0.67), termed a pretreatment step. After that, excess (unreacted) ammonia was removed by evaporation, and the pretreated material was immediately saccharified by an enzyme without a washing step. The effects of key reaction parameters on both glucan digestibility and XMG digestibility were evaluated by analysis of variance (ANOVA). Under the best pretreatment conditions [S/L = 0.47, 0.16 (g NH₃)/(g biomass), 90 °C, 24 h], LLAA pretreatment enhanced enzymatic digestibility from 23.1% for glucan and 11.3% for XMG (xylan + galactan + mannan) of untreated corn stover to 91.8% for glucan and 72.6% for XMG in pretreated solid.
MeSH term(s)	Ammonia/chemistry ; Glucans/chemistry ; Hydrolases/chemistry ; Zea mays/chemistry
Chemical Substances	Glucans ; Ammonia (7664-41-7) ; Hydrolases (EC 3.-)
Language	English
Publishing date	2018-05-01
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules23051050
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Article: SARS-CoV-2 molecular testing and whole genome sequencing following RNA recovery from used BinaxNOW COVID-19 Antigen Self Tests.

Nguyen, Phuong-Vi / Carmola, Ludy Registre / Wang, Ethan / Bassit, Leda / Rao, Anuradha / Greenleaf, Morgan / Sullivan, Julie A / Martin, Greg S / Lam, Wilbur A / Waggoner, Jesse J / Piantadosi, Anne

medRxiv : the preprint server for health sciences

2023

Abstract: Widespread use of over-the-counter rapid diagnostic tests for SARS-CoV-2 has led to a decrease in availability of clinical samples for viral genomic surveillance. As an alternative sample source, we evaluated RNA isolated from BinaxNOW swabs stored at ... ...

Abstract	Widespread use of over-the-counter rapid diagnostic tests for SARS-CoV-2 has led to a decrease in availability of clinical samples for viral genomic surveillance. As an alternative sample source, we evaluated RNA isolated from BinaxNOW swabs stored at ambient temperature for SARS-CoV-2 rRT-PCR and full viral genome sequencing. 81 of 103 samples (78.6%) yielded detectable RNA, and 46 of 57 samples (80.7 %) yielded complete genome sequences. Our results illustrate that SARS-CoV-2 RNA extracted from used Binax test swabs provides an important opportunity for improving SARS-CoV-2 genomic surveillance, evaluating transmission clusters, and monitoring within-patient evolution.
Language	English
Publishing date	2023-01-09
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.01.09.23284337
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Severe Acute Respiratory Syndrome Coronavirus 2 Evolution and Escape From Combination Monoclonal Antibody Treatment in a Person With HIV.

Khosravi, Dara / Soloff, Hannah / Langsjoen, Rose M / Bombin, Andrei / Kelley, Colleen F / Ray, Susan M / Gunthel, Clifford J / Zanoni, Brian C / Nguyen, Phuong-Vi / Waggoner, Jesse J / Wang, Yun F / Cantos, Valeria D / Piantadosi, Anne

Open forum infectious diseases

2023 Volume 10, Issue 2, Page(s) ofad054

Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) escape from combination monoclonal antibody treatment is rarely reported. We describe an immunocompromised individual with human immunodeficiency virus and persistent SARS-CoV-2 infection in ... ...

Abstract	Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) escape from combination monoclonal antibody treatment is rarely reported. We describe an immunocompromised individual with human immunodeficiency virus and persistent SARS-CoV-2 infection in whom substantial SARS-CoV-2 evolution occurred, including the emergence of 2 mutations associated with escape from the monoclonal antibody cocktail received.
Language	English
Publishing date	2023-02-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	2757767-3
ISSN	2328-8957
ISSN	2328-8957
DOI	10.1093/ofid/ofad054
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Article ; Online: SARS-CoV-2 molecular testing and whole genome sequencing following RNA recovery from used BinaxNOW COVID-19 antigen self tests.

Nguyen, Phuong-Vi / Carmola, Ludy Registre / Wang, Ethan / Bassit, Leda / Rao, Anuradha / Greenleaf, Morgan / Sullivan, Julie A / Martin, Greg S / Lam, Wilbur A / Waggoner, Jesse J / Piantadosi, Anne

Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology

2023 Volume 162, Page(s) 105426

Abstract	Widespread use of over-the-counter rapid diagnostic tests for SARS-CoV-2 has led to a decrease in availability of clinical samples for viral genomic surveillance. As an alternative sample source, we evaluated RNA isolated from BinaxNOW swabs stored at ambient temperature for SARS-CoV-2 rRT-PCR and full viral genome sequencing. 81 of 103 samples (78.6%) yielded detectable RNA, and 46 of 57 samples (80.7 %) yielded complete genome sequences. Our results illustrate that SARS-CoV-2 RNA extracted from used Binax test swabs provides an important opportunity for improving SARS-CoV-2 genomic surveillance, evaluating transmission clusters, and monitoring within-patient evolution.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; COVID-19/diagnosis ; RNA, Viral/genetics ; RNA, Viral/analysis ; Molecular Diagnostic Techniques ; Whole Genome Sequencing/methods
Chemical Substances	RNA, Viral
Language	English
Publishing date	2023-03-24
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1446080-4
ISSN	1873-5967 ; 1386-6532
ISSN (online)	1873-5967
ISSN	1386-6532
DOI	10.1016/j.jcv.2023.105426
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Article: Subgenomic RNA Abundance Relative to Total Viral RNA Among Severe Acute Respiratory Syndrome Coronavirus 2 Variants.

Su, Maxwell / Ping, Sara / Nguyen, Phuong-Vi / Rojas, Alejandra / Hussaini, Laila / Carmola, Ludy Registre / Taz, Azmain / Sullivan, Julie / Martin, Greg S / Piantadosi, Anne / Martinez, Magaly / Lam, Wilbur A / Anderson, Evan J / Waggoner, Jesse J

Open forum infectious diseases

2022 Volume 9, Issue 11, Page(s) ofac619

Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) subgenomic RNA (sgRNA) may indicate actively replicating virus, but sgRNA abundance has not been systematically compared between SARS-CoV-2 variants. sgRNA was quantified in 169 clinical ... ...

Abstract	Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) subgenomic RNA (sgRNA) may indicate actively replicating virus, but sgRNA abundance has not been systematically compared between SARS-CoV-2 variants. sgRNA was quantified in 169 clinical samples by real-time reverse-transcription polymerase chain reaction, demonstrating similar relative abundance among known variants. Thus, sgRNA detection can identify individuals with active viral replication regardless of variant.
Language	English
Publishing date	2022-11-10
Publishing country	United States
Document type	Journal Article
ZDB-ID	2757767-3
ISSN	2328-8957
ISSN	2328-8957
DOI	10.1093/ofid/ofac619
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Article ; Online: SARS-CoV-2 molecular testing and whole genome sequencing following RNA recovery from used BinaxNOW COVID-19 Antigen Self Tests

Nguyen, Phuong-Vi / Carmola, Ludy Registre / Wang, Ethan / Bassit, Leda / Rao, Anuradha / Greenleaf, Morgan / Sullivan, Julie A / Martin, Greg / Lam, Wilbur / Waggoner, Jesse / Piantadosi, Anne

medRxiv

Abstract	Widespread use of over-the-counter rapid diagnostic tests for SARS-CoV-2 has led to a decrease in availability of clinical samples for viral genomic surveillance. As an alternative sample source, we evaluated RNA isolated from BinaxNOW swabs stored at ambient temperature for SARS-CoV-2 rRT-PCR and full viral genome sequencing. 81 of 103 samples (78.6%) yielded detectable RNA, and 46 of 57 samples (80.7 %) yielded complete genome sequences. Our results illustrate that SARS-CoV-2 RNA extracted from used Binax test swabs provides an important opportunity for improving SARS-CoV-2 genomic surveillance, evaluating transmission clusters, and monitoring within-patient evolution.
Keywords	covid19
Language	English
Publishing date	2023-01-09
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2023.01.09.23284337
Database	COVID19

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Article: Investigation of Blood Plasma Viral Nucleocapsid Antigen as a Marker of Active Severe Acute Respiratory Syndrome Coronavirus 2 Omicron Variant Infection.

Damhorst, Gregory L / Schoof, Nils / Nguyen, Phuong-Vi / Verkerke, Hans / Wilber, Eli / McLendon, Kaleb / O'Sick, William / Baugh, Tyler / Cheedarla, Suneethamma / Cheedarla, Narayanaiah / Stittleburg, Victoria / Fitts, Eric C / Neja, Margaret A / Babiker, Ahmed / Piantadosi, Anne / Roback, John D / Waggoner, Jesse J / Mavigner, Maud / Lam, Wilbur A

Open forum infectious diseases

2023 Volume 10, Issue 5, Page(s) ofad226

Abstract: Background: Nasopharyngeal qualitative reverse-transcription polymerase chain reaction (RT-PCR) is the gold standard for diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, but it is not practical or sufficient in every ... ...

Abstract	Background: Nasopharyngeal qualitative reverse-transcription polymerase chain reaction (RT-PCR) is the gold standard for diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, but it is not practical or sufficient in every clinical scenario due to its inability to distinguish active from resolved infection. Alternative or adjunct testing may be needed to guide isolation precautions and treatment in patients admitted to the hospital. Methods: We performed a single-center, retrospective analysis of residual clinical specimens and medical record data to examine blood plasma nucleocapsid antigen as a candidate biomarker of active SARS-CoV-2. Adult patients admitted to the hospital or presenting to the emergency department with SARS-CoV-2 ribonucleic acid (RNA) detected by RT-PCR from a nasopharyngeal swab specimen were included. Both nasopharyngeal swab and a paired whole blood sample were required to be available for analysis. Results: Fifty-four patients were included. Eight patients had positive nasopharyngeal swab virus cultures, 7 of whom (87.5%) had concurrent antigenemia. Nineteen (79.2%) of 24 patients with detectable subgenomic RNA and 20 (80.0%) of 25 patients with N2 RT-PCR cycle threshold ≤ 33 had antigenemia. Conclusions: Most individuals with active SARS-CoV-2 infection are likely to have concurrent antigenemia, but there may be some individuals with active infection in whom antigenemia is not detectable. The potential for high sensitivity and convenience of a blood test prompts interest in further investigation as a screening tool to reduce reliance on nasopharyngeal swab sampling and as an adjunct diagnostic test to aid in clinical decision making during the period after acute coronavirus disease 2019.
Language	English
Publishing date	2023-05-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	2757767-3
ISSN	2328-8957
ISSN	2328-8957
DOI	10.1093/ofid/ofad226
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: SARS-CoV-2 Variants in Paraguay: Detection and Surveillance with an Economical and Scalable Molecular Protocol.

Martinez, Magaly / Nguyen, Phuong-Vi / Su, Maxwell / Cardozo, Fátima / Valenzuela, Adriana / Franco, Laura / Galeano, María Eugenia / Rojas, Leticia Elizabeth / Díaz Acosta, Chyntia Carolina / Fernández, Jonás / Ortiz, Joel / Del Puerto, Florencia / Mendoza, Laura / Nara, Eva / Rojas, Alejandra / Waggoner, Jesse J

Viruses

2022 Volume 14, Issue 5

Abstract: SARS-CoV-2 variant detection relies on resource-intensive whole-genome sequencing methods. We sought to develop a scalable protocol for variant detection and surveillance in Paraguay, pairing rRT-PCR for spike mutations with Nanopore sequencing. A total ... ...

Abstract	SARS-CoV-2 variant detection relies on resource-intensive whole-genome sequencing methods. We sought to develop a scalable protocol for variant detection and surveillance in Paraguay, pairing rRT-PCR for spike mutations with Nanopore sequencing. A total of 201 acute-phase nasopharyngeal samples were included. Samples were positive for the SARS-CoV-2 N2 target and tested with the Spike SNP assay to detect mutations associated with the following variants: alpha (501Y), beta/gamma (417variant/484K/501Y), delta (452R/478K), and lambda (452Q/490S). Spike SNP calls were confirmed using amplicon (Sanger) sequencing and whole-genome (Nanopore) sequencing on a subset of samples with confirmed variant lineages. Samples had a mean N2 Ct of 20.8 (SD 5.6); 198/201 samples (98.5%) tested positive in the Spike SNP assay. The most common genotype was 417variant/484K/501Y, detected in 102/198 samples (51.5%), which was consistent with the P.1 lineage (gamma variant) in Paraguay. No mutations (K417 only) were found in 64/198 (32.3%), and K417/484K was identified in 22/198 (11.1%), consistent with P.2 (zeta). Seven samples (3.5%) tested positive for 452R without 478K, and one sample with genotype K417/501Y was confirmed as B.1.1.7 (alpha). The results were confirmed using Sanger sequencing in 181/181 samples, and variant calls were consistent with Nanopore sequencing in 29/29 samples. The Spike SNP assay could improve population-level surveillance for mutations associated with SARS-CoV-2 variants and inform the judicious use of sequencing resources.
MeSH term(s)	COVID-19/diagnosis ; COVID-19/epidemiology ; Humans ; Paraguay/epidemiology ; SARS-CoV-2/genetics
Language	English
Publishing date	2022-04-22
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v14050873
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