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Article ; Online: NIH HIV Reagent Program: A Valuable Resource for HIV Research.

Timani, Khalid / Rashid, Sujatha / Bradford, Rebecca / Leonelli, Joseph

2024 Volume 21, Issue 4, Page(s) 277–278

MeSH term(s)	Humans ; HIV Infections/diagnosis ; HIV Infections/prevention & control ; Biomedical Research ; National Institutes of Health (U.S.)
Language	English
Publishing date	2024-01-09
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2192348-6
ISSN	1873-4251 ; 1570-162X
ISSN (online)	1873-4251
ISSN	1570-162X
DOI	10.2174/1570162X2104231226194230
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Article ; Online: Development and validation of a rapid and easy-to-perform point-of-care lateral flow immunoassay (LFIA) for the detection of SARS-CoV-2 spike protein.

Mohammad, Shamim / Wang, Yuxia / Cordero, John / Watson, Christopher / Molestina, Robert / Rashid, Sujatha / Bradford, Rebecca

Frontiers in immunology

2023 Volume 14, Page(s) 1111644

Abstract: Development and validation of rapid and easy-to-perform diagnostics continue to be a high priority during the current COVID-19 pandemic. Although vaccines are now widely available, early detection and consistent transmission control provide ideal means ... ...

Abstract	Development and validation of rapid and easy-to-perform diagnostics continue to be a high priority during the current COVID-19 pandemic. Although vaccines are now widely available, early detection and consistent transmission control provide ideal means to mitigate the spread of SARS-CoV-2. Nucleic acid-based real-time PCR tests are widely acknowledged as the gold standard for reliable diagnosis of COVID-19 infection. These tests are based on detecting viable or nonviable viral nucleic acids. SARS-CoV-2 spike protein is an alternative and ideal target for SARS-CoV-2 diagnosis in the early phase of infection, but point-of-care kits to detect the SARS-CoV-2 spike protein are limited. Here we describe a rapid and convenient method based on Lateral Flow Immunoassay (LFIA) to detect SARS-CoV-2 spike proteins, including SARS-CoV-2 variants (A.23.1, B.1.1.1, 1.617.2, B.1.1.7, B.1.351, P.1, N501Y, R.1, P681H, P3, UK, and South African) within 5 to 10 minutes. We generated highly specific monoclonal antibodies (mAbs) against rationally designed SARS-CoV-2 spike protein. Matched pair mAbs were selected by epitope mapping and employed as antigen capture reagents by spotting onto a nitrocellulose membrane and as detector reagents by conjugation with colloidal gold nanoparticles. We evaluated the performance of the LFIA using recombinant spike proteins of SARS-CoV-2 and several SARS-CoV-2 variants. The specificity of the LFIA was assessed using heat-inactivated SARS-CoV-2 and related human coronaviruses (HCoV-OC43, HCoV-229E, HCoV-HKU1, and HCoV-NL63) and an FDA-approved respiratory pathogens (RP) panel. The assay exhibited 98% specificity and acceptable performance with respect to the minimum limit of detection (25 ng/test) in validation tests. This new LFIA provides improved performance for the early diagnosis of SARS-CoV-2, particularly for home monitoring and in situations with limited access to molecular methods.
MeSH term(s)	Humans ; SARS-CoV-2 ; COVID-19 ; Spike Glycoprotein, Coronavirus/analysis ; COVID-19 Testing ; Point-of-Care Systems ; Pandemics ; Gold ; Sensitivity and Specificity ; Metal Nanoparticles ; Immunoassay/methods
Chemical Substances	spike protein, SARS-CoV-2 ; Spike Glycoprotein, Coronavirus ; Gold (7440-57-5)
Language	English
Publishing date	2023-02-23
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2023.1111644
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Article ; Online: Dynamics of parasite growth in genetically diverse Plasmodium falciparum isolates.

Nkhoma, Standwell C / Ahmed, Amel O A / Porier, Danielle / Rashid, Sujatha / Bradford, Rebecca / Molestina, Robert E / Stedman, Timothy T

Molecular and biochemical parasitology

2023 Volume 254, Page(s) 111552

Abstract: Multiple parasite lineages with different proliferation rates or fitness may coexist within a clinical malaria isolate, resulting in complex growth interactions and variations in phenotype. To elucidate the dynamics of parasite growth in multiclonal ... ...

Abstract	Multiple parasite lineages with different proliferation rates or fitness may coexist within a clinical malaria isolate, resulting in complex growth interactions and variations in phenotype. To elucidate the dynamics of parasite growth in multiclonal isolates, we measured growth rates (GRs) of three Plasmodium falciparum Cambodian isolates, including IPC_3445 (MRA-1236), IPC_5202 (MRA-1240), IPC_6403 (MRA-1285), and parasite lineages previously cloned from each of these isolates by limiting dilution. Following synchronization, in vitro cultures of each parasite line were maintained over four consecutive asexual cycles (192 h), with thin smears prepared at each 48-h cycle to estimate GR and fold change in parasitemia (FCP). Cell cycle time (CCT), the duration it takes for ring-stage parasites to develop into mature schizonts, was measured by monitoring the development of 0-3-h post-invasion rings for up to 52 h post-incubation. Laboratory lines 3D7 (MRA-102) and Dd2 (MRA-150) were used as controls. Significant differences in GR, FCP, and CCT were observed between parasite isolates and clonal lineages from each isolate. The parasite lines studied here have well-defined growth phenotypes and will facilitate basic malaria research and development of novel malaria interventions. These lines are available to malaria researchers through the MR4 collection of NIAID's BEI Resources Program.
MeSH term(s)	Animals ; Plasmodium falciparum/genetics ; Parasites ; Malaria, Falciparum/parasitology ; Malaria ; Phenotype
Language	English
Publishing date	2023-01-31
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	756166-0
ISSN	1872-9428 ; 0166-6851
ISSN (online)	1872-9428
ISSN	0166-6851
DOI	10.1016/j.molbiopara.2023.111552
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Article: The Use of Psychotropic Drug Therapy in Borderline Personality Disorder: a Case Report.

Bradford, Rebecca / Holt, Clare

Psychiatria Danubina

2015 Volume 27 Suppl 1, Page(s) S371–4

Abstract: It is estimated that around 75% of patients with Borderline Personality Disorder (BPD) are prescribed psychotropic medication during their treatment course, although this is not recommended as first line therapy. In the UK, there are no guidelines to ... ...

Abstract	It is estimated that around 75% of patients with Borderline Personality Disorder (BPD) are prescribed psychotropic medication during their treatment course, although this is not recommended as first line therapy. In the UK, there are no guidelines to advise which drug treatments to use in BPD, however, numerous, but mostly small scale studies, show evidence that different medications target specific core symptoms. We report a case of a 25 year old woman with BPD, who has received treatment with five different psychotropic medications. We go on to assess not only the efficacy of these treatments in this individual case, but also whether the use of these treatments is in line with best evidence according to currently available research.
MeSH term(s)	Adult ; Borderline Personality Disorder/diagnosis ; Borderline Personality Disorder/drug therapy ; Borderline Personality Disorder/psychology ; Combined Modality Therapy ; Drug Substitution ; Drug Therapy, Combination ; Female ; Humans ; Psychotropic Drugs/adverse effects ; Psychotropic Drugs/therapeutic use ; Treatment Outcome
Chemical Substances	Psychotropic Drugs
Language	English
Publishing date	2015-09
Publishing country	Croatia
Document type	Case Reports ; Journal Article
ZDB-ID	1067580-2
ISSN	0353-5053
ISSN	0353-5053
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Article: Propagation of SARS-CoV-2 in Calu-3 Cells to Eliminate Mutations in the Furin Cleavage Site of Spike

Baczenas, John James / Andersen, Hanne / Rashid, Sujatha / Yarmosh, David / Puthuveetil, Nikhita / Parker, Michael / Bradford, Rebecca / Florence, Clint / Stemple, Kimberly J. / Lewis, Mark G. / O’Connor, Shelby L.

Viruses. 2021 Dec. 04, v. 13, no. 12

2021

Abstract: SARS-CoV-2 pathogenesis, vaccine, and therapeutic studies rely on the use of animals challenged with highly pathogenic virus stocks produced in cell cultures. Ideally, these virus stocks should be genetically and functionally similar to the original ... ...

Abstract	SARS-CoV-2 pathogenesis, vaccine, and therapeutic studies rely on the use of animals challenged with highly pathogenic virus stocks produced in cell cultures. Ideally, these virus stocks should be genetically and functionally similar to the original clinical isolate, retaining wild-type properties to be reliably used in animal model studies. It is well-established that SARS-CoV-2 isolates serially passaged on Vero cell lines accumulate mutations and deletions in the furin cleavage site; however, these can be eliminated when passaged on Calu-3 lung epithelial cell lines, as presented in this study. As numerous stocks of SARS-CoV-2 variants of concern are being grown in cell cultures with the intent for use in animal models, it is essential that propagation methods generate virus stocks that are pathogenic in vivo. Here, we found that the propagation of a B.1.351 SARS-CoV-2 stock on Calu-3 cells eliminated viruses that previously accumulated mutations in the furin cleavage site. Notably, there were alternative variants that accumulated at the same nucleotide positions in virus populations grown on Calu-3 cells at multiple independent facilities. When a Calu-3-derived B.1.351 virus stock was used to infect hamsters, the virus remained pathogenic and the Calu-3-specific variants persisted in the population. These results suggest that Calu-3-derived virus stocks are pathogenic but care should still be taken to evaluate virus stocks for newly arising mutations during propagation.
Keywords	Severe acute respiratory syndrome coronavirus 2 ; animal models ; epithelial cells ; lungs ; pathogenesis ; therapeutics ; vaccines ; virulent strains ; viruses
Language	English
Dates of publication	2021-1204
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2516098-9
ISSN	1999-4915
ISSN	1999-4915
DOI	10.3390/v13122434
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows.

Connor, Ryan / Shakya, Migun / Yarmosh, David A / Maier, Wolfgang / Martin, Ross / Bradford, Rebecca / Brister, J Rodney / Chain, Patrick S G / Copeland, Courtney A / di Iulio, Julia / Hu, Bin / Ebert, Philip / Gunti, Jonathan / Jin, Yumi / Katz, Kenneth S / Kochergin, Andrey / LaRosa, Tré / Li, Jiani / Li, Po-E /

Lo, Chien-Chi / Rashid, Sujatha / Maiorova, Evguenia S / Xiao, Chunlin / Zalunin, Vadim / Purcell, Lisa / Pruitt, Kim D

Viruses

2024 Volume 16, Issue 3

Abstract: Genomic sequencing of clinical samples to identify emerging variants of SARS-CoV-2 has been a key public health tool for curbing the spread of the virus. As a result, an unprecedented number of SARS-CoV-2 genomes were sequenced during the COVID-19 ... ...

Abstract	Genomic sequencing of clinical samples to identify emerging variants of SARS-CoV-2 has been a key public health tool for curbing the spread of the virus. As a result, an unprecedented number of SARS-CoV-2 genomes were sequenced during the COVID-19 pandemic, which allowed for rapid identification of genetic variants, enabling the timely design and testing of therapies and deployment of new vaccine formulations to combat the new variants. However, despite the technological advances of deep sequencing, the analysis of the raw sequence data generated globally is neither standardized nor consistent, leading to vastly disparate sequences that may impact identification of variants. Here, we show that for both Illumina and Oxford Nanopore sequencing platforms, downstream bioinformatic protocols used by industry, government, and academic groups resulted in different virus sequences from same sample. These bioinformatic workflows produced consensus genomes with differences in single nucleotide polymorphisms, inclusion and exclusion of insertions, and/or deletions, despite using the same raw sequence as input datasets. Here, we compared and characterized such discrepancies and propose a specific suite of parameters and protocols that should be adopted across the field. Consistent results from bioinformatic workflows are fundamental to SARS-CoV-2 and future pathogen surveillance efforts, including pandemic preparation, to allow for a data-driven and timely public health response.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; COVID-19/epidemiology ; Pandemics ; Workflow ; Computational Biology
Language	English
Publishing date	2024-03-11
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v16030430
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Article ; Online: Propagation of SARS-CoV-2 in Calu-3 Cells to Eliminate Mutations in the Furin Cleavage Site of Spike.

Baczenas, John James / Andersen, Hanne / Rashid, Sujatha / Yarmosh, David / Puthuveetil, Nikhita / Parker, Michael / Bradford, Rebecca / Florence, Clint / Stemple, Kimberly J / Lewis, Mark G / O'Connor, Shelby L

Viruses

2021 Volume 13, Issue 12

Abstract	SARS-CoV-2 pathogenesis, vaccine, and therapeutic studies rely on the use of animals challenged with highly pathogenic virus stocks produced in cell cultures. Ideally, these virus stocks should be genetically and functionally similar to the original clinical isolate, retaining wild-type properties to be reliably used in animal model studies. It is well-established that SARS-CoV-2 isolates serially passaged on Vero cell lines accumulate mutations and deletions in the furin cleavage site; however, these can be eliminated when passaged on Calu-3 lung epithelial cell lines, as presented in this study. As numerous stocks of SARS-CoV-2 variants of concern are being grown in cell cultures with the intent for use in animal models, it is essential that propagation methods generate virus stocks that are pathogenic in vivo. Here, we found that the propagation of a B.1.351 SARS-CoV-2 stock on Calu-3 cells eliminated viruses that previously accumulated mutations in the furin cleavage site. Notably, there were alternative variants that accumulated at the same nucleotide positions in virus populations grown on Calu-3 cells at multiple independent facilities. When a Calu-3-derived B.1.351 virus stock was used to infect hamsters, the virus remained pathogenic and the Calu-3-specific variants persisted in the population. These results suggest that Calu-3-derived virus stocks are pathogenic but care should still be taken to evaluate virus stocks for newly arising mutations during propagation.
MeSH term(s)	Animals ; COVID-19/virology ; Cell Line, Tumor ; Chlorocebus aethiops ; Cricetinae ; Furin/metabolism ; Humans ; Mutation ; SARS-CoV-2/genetics ; SARS-CoV-2/growth & development ; SARS-CoV-2/pathogenicity ; Serial Passage/methods ; Spike Glycoprotein, Coronavirus/genetics ; Vero Cells
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Furin (EC 3.4.21.75)
Language	English
Publishing date	2021-12-04
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v13122434
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Article ; Online: Bacterial-Fungal Interactions Including Quorum Sensing, Between 2 Opportunistic Pathogens, Resulting in Post-Traumatic Sepsis in a Child Presenting With a Closed Femoral Fracture.

Bradford, Rebecca / O'Loughlin, Kate / Munro, Alice / Jani, Bhavdeep R / Singham, Surendra / Cansick, Janette

The Pediatric infectious disease journal

2016 Volume 35, Issue 12, Page(s) 1360–1362

Abstract: Pseudomonas aeruginosa and Candida albicans (are opportunistic pathogens that cause systemic infections in immune-suppressed patients. They show important bacterial-fungal interactions including quorum sensing. This involves cell signaling to communicate ...

Abstract	Pseudomonas aeruginosa and Candida albicans (are opportunistic pathogens that cause systemic infections in immune-suppressed patients. They show important bacterial-fungal interactions including quorum sensing. This involves cell signaling to communicate between the cells of their own colony and the cells of rival microbes or the host. It is thought that this phenomenon is vital in the potential competition and virulence of the organisms. We report a case of a previously healthy 2-year-old boy, where an accidental injury had been sustained resulting in a closed fracture of femur. He subsequently developed sepsis related to co-infection by C. albicans and P. aeruginosa. Trauma may result in a transient immune-suppression and predispose to sepsis caused by opportunistic microorganisms. They can engage in bacterial-fungal interaction. Clinicians should consider invasive co-infection when initial cultures show evidence for only 1 pathogen.
MeSH term(s)	Candida albicans ; Candidemia ; Child, Preschool ; Coinfection/microbiology ; Femoral Fractures/complications ; Humans ; Male ; Microbial Interactions ; Opportunistic Infections ; Pseudomonas Infections ; Pseudomonas aeruginosa ; Quorum Sensing ; Sepsis/microbiology
Language	English
Publishing date	2016-12
Publishing country	United States
Document type	Case Reports ; Journal Article
ZDB-ID	392481-6
ISSN	1532-0987 ; 0891-3668
ISSN (online)	1532-0987
ISSN	0891-3668
DOI	10.1097/INF.0000000000001337
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Article: A Rare Deletion in SARS-CoV-2 ORF6 Dramatically Alters the Predicted Three-Dimensional Structure of the Resultant Protein.

Riojas, Marco A / Frank, Andrew M / Puthuveetil, Nikhita P / Flores, Beth / Parker, Michael / King, Stephen P / Peiris, Malik / Chu, Daniel K W / Benton, Briana / Bradford, Rebecca / Hazbón, Manzour Hernando / Rashid, Sujatha

bioRxiv : the preprint server for biology

2020

Abstract: The function of the SARS-CoV-2 accessory protein p6, encoded by ORF6, is not fully known. Based upon its similarity to p6 from SARS-CoV, it may play a similar role, namely as an antagonist of type I interferon (IFN) signaling. Here we report the ... ...

Abstract	The function of the SARS-CoV-2 accessory protein p6, encoded by ORF6, is not fully known. Based upon its similarity to p6 from SARS-CoV, it may play a similar role, namely as an antagonist of type I interferon (IFN) signaling. Here we report the sequencing of a SARS-CoV-2 strain passaged six times after original isolation from a clinical patient in Hong Kong. The genome sequence shows a 27 nt in-frame deletion (Δ27,264-27,290) within ORF6, predicted to result in a 9 aa deletion ( ΔFKVSIWNLD ) from the central portion of p6. This deletion is predicted to result in a dramatic alteration in the three-dimensional structure of the resultant protein (p6
Keywords	covid19
Language	English
Publishing date	2020-06-10
Publishing country	United States
Document type	Preprint
DOI	10.1101/2020.06.09.134460
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Article ; Online: A cautionary perspective regarding the isolation and serial propagation of SARS-CoV-2 in Vero cells.

Funnell, Simon G P / Afrough, Babak / Baczenas, John James / Berry, Neil / Bewley, Kevin R / Bradford, Rebecca / Florence, Clint / Duff, Yann Le / Lewis, Mark / Moriarty, Ryan V / Connor, Shelby L O / Osman, Karen L / Pullan, Steven / Rashid, Sujatha / Richards, Kevin S / Stemple, Kimberly J / Knezevic, Ivana

NPJ vaccines

2021 Volume 6, Issue 1, Page(s) 83

Abstract: An array of SARS-CoV-2 virus variants have been isolated, propagated and used in in vitro assays, in vivo animal studies and human clinical trials. Observations of working stocks of SARS-CoV-2 suggest that sequential propagation in Vero cells leads to ... ...

Abstract	An array of SARS-CoV-2 virus variants have been isolated, propagated and used in in vitro assays, in vivo animal studies and human clinical trials. Observations of working stocks of SARS-CoV-2 suggest that sequential propagation in Vero cells leads to critical changes in the region of the furin cleavage site, which significantly reduce the value of the working stock for critical research studies. Serially propagating SARS-CoV-2 in Vero E6 cells leads to rapid increases in genetic variants while propagation in other cell lines (e.g. Vero/hSLAM) appears to mitigate this risk thereby improving the overall genetic stability of working stocks. From these observations, investigators are urged to monitor genetic variants carefully when propagating SARS-CoV-2 in Vero cells.
Language	English
Publishing date	2021-06-17
Publishing country	England
Document type	Journal Article
ISSN	2059-0105
ISSN (online)	2059-0105
DOI	10.1038/s41541-021-00346-z
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