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Article ; Online: Assessment of Sample Pooling for Clinical SARS-CoV-2 Testing.

Griesemer, Sara B / Van Slyke, Greta / St George, Kirsten

2021 Volume 59, Issue 4

Abstract: Accommodating large increases in sample workloads has presented a major challenge to clinical laboratories during the coronavirus disease 2019 (COVID-19) pandemic. Despite the implementation of automated detection systems and previous efficiencies, ... ...

Abstract	Accommodating large increases in sample workloads has presented a major challenge to clinical laboratories during the coronavirus disease 2019 (COVID-19) pandemic. Despite the implementation of automated detection systems and previous efficiencies, including barcoding, electronic data transfer, and extensive robotics, capacities have struggled to meet the demand. Sample pooling has been suggested as an additional strategy to address this need. The greatest concern with this approach in clinical settings is the potential for reduced sensitivity, particularly detection failures with weakly positive samples. To investigate this possibility, detection rates in pooled samples were evaluated, with a focus on pools containing weakly positive specimens. Additionally, the frequencies of occurrence of weakly positive samples during the pandemic were reviewed. Weakly positive specimens, with threshold cycle (
MeSH term(s)	COVID-19 ; COVID-19 Testing ; Clinical Laboratory Techniques ; Humans ; Pandemics ; SARS-CoV-2 ; Specimen Handling
Language	English
Publishing date	2021-03-19
Publishing country	United States
Document type	Journal Article
ZDB-ID	390499-4
ISSN	1098-660X ; 0095-1137
ISSN (online)	1098-660X
ISSN	0095-1137
DOI	10.1128/JCM.01261-20
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Article ; Online: Vaccine Strain and Wild-Type Clades of Varicella-Zoster Virus in Central Nervous System and Non-CNS Disease, New York State, 2004-2019.

Bryant, Patrick / Yildirim, Tugba / Griesemer, Sara B / Shaw, Kara / Ehrbar, Dylan / St George, Kirsten

Journal of clinical microbiology

2022 Volume 60, Issue 4, Page(s) e0238121

Abstract: Since the introduction of the varicella-zoster virus (VZV) vaccine in the United States in 1995, there has been a dramatic decrease in both the number and severity of varicella cases. However, VZV surveillance data and information on the VZV clade ... ...

Abstract	Since the introduction of the varicella-zoster virus (VZV) vaccine in the United States in 1995, there has been a dramatic decrease in both the number and severity of varicella cases. However, VZV surveillance data and information on the VZV clade distribution in central nervous system (CNS) disease and non-CNS disease in New York State is not available. To investigate this, cerebrospinal fluid (CSF) samples from patients with encephalitis or meningitis and non-CSF samples from patients with non-CNS disease manifestations consistent with VZV, collected from 2004 to 2019, were tested with molecular VZV assays. A total of 341 CSF and 1,398 non-CSF samples that tested positive by a VZV-specific real-time PCR assay were further characterized as wild-type or vaccine strain by 3 biallelic real-time PCR assays targeting single nucleotide polymorphism (SNP) markers in open reading frame (ORF) 62. Genotyping was then performed on wild-type strains by conventional PCR and sequencing of 500-bp regions in ORFs 21, 22, and 50. Sequence analysis identified clades 1 to 5 in both sample types with a virtually identical clade distribution between CSF and non-CSF samples. In addition, 19 clade 6 and 13 clade 9 samples were detected in non-CSF samples after implementation of an expanded genotyping scheme, including ORF 29, 38, and 67. These clades were not detected in any CSF samples. Finally, a total of 28 vaccine strains were detected, 25 in the non-CSF samples and 3 in the CSF samples. All three cases of vaccine strain with CNS involvement experienced relatively minor symptoms of aseptic meningitis and fully recovered. These results support the evidence that while the VZV vaccine is capable of causing CNS disease, it is still a rare event and symptoms are typically less severe than those caused by wild-type infection.
MeSH term(s)	Central Nervous System ; DNA, Viral ; Encephalitis ; Herpes Zoster/epidemiology ; Herpesvirus 3, Human/genetics ; Humans ; New York/epidemiology ; Real-Time Polymerase Chain Reaction ; Vaccines
Chemical Substances	DNA, Viral ; Vaccines
Language	English
Publishing date	2022-03-24
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	390499-4
ISSN	1098-660X ; 0095-1137
ISSN (online)	1098-660X
ISSN	0095-1137
DOI	10.1128/jcm.02381-21
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Article ; Online: Assessment of sample pooling for clinical SARS-CoV-2 testing

St. George, Kirsten / Griesemer, Sara B. / Van Slyke, Greta

bioRxiv

Abstract: Accommodating large increases in sample workloads has presented one of the biggest challenges to clinical laboratories during the COVID-19 pandemic. Despite the implementation of new automated detection systems, and previous efficiencies such as ... ...

Abstract	Accommodating large increases in sample workloads has presented one of the biggest challenges to clinical laboratories during the COVID-19 pandemic. Despite the implementation of new automated detection systems, and previous efficiencies such as barcoding, electronic data transfer and extensive robotics, throughput capacities have struggled to meet the demand. Sample pooling has been suggested as an additional strategy to further address this need. The greatest concern with this approach in a clinical setting is the potential for reduced sensitivity, particularly the risk of false negative results when weak positive samples are pooled. To investigate this possibility, detection rates in pooled samples were evaluated, with extensive assessment of pools containing weak positive specimens. Additionally, the frequency of occurrence of weak positive samples across ten weeks of the pandemic were reviewed. Weak positive specimens were detected in all five-sample pools but failed to be detected in four of the 24 nine-sample pools tested. Weak positive samples comprised an average 16.5% of the positive specimens tested during the pandemic thus far, slightly increasing in frequency during later weeks. Other aspects of the testing process should be considered, however, such as accessioning and reporting, which are not streamlined and may be complicated by pooling procedures. Therefore, the impact on the entire laboratory process needs to be carefully assessed prior to implementing such a strategy.
Keywords	covid19
Language	English
Publishing date	2020-05-27
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2020.05.26.118133
Database	COVID19

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Article ; Online: Assessment of sample pooling for clinical SARS-CoV-2 testing

Griesemer, Sara B / Van Slyke, Greta / St. George, Kirsten

bioRxiv

Abstract	Accommodating large increases in sample workloads has presented one of the biggest challenges to clinical laboratories during the COVID-19 pandemic. Despite the implementation of new automated detection systems, and previous efficiencies such as barcoding, electronic data transfer and extensive robotics, throughput capacities have struggled to meet the demand. Sample pooling has been suggested as an additional strategy to further address this need. The greatest concern with this approach in a clinical setting is the potential for reduced sensitivity, particularly the risk of false negative results when weak positive samples are pooled. To investigate this possibility, detection rates in pooled samples were evaluated, with extensive assessment of pools containing weak positive specimens. Additionally, the frequency of occurrence of weak positive samples across ten weeks of the pandemic were reviewed. Weak positive specimens were detected in all five-sample pools but failed to be detected in four of the 24 nine-sample pools tested. Weak positive samples comprised an average 16.5% of the positive specimens tested during the pandemic thus far, slightly increasing in frequency during later weeks. Other aspects of the testing process should be considered, however, such as accessioning and reporting, which are not streamlined and may be complicated by pooling procedures. Therefore, the impact on the entire laboratory process needs to be carefully assessed prior to implementing such a strategy.
Keywords	covid19
Publisher	BioRxiv; WHO
Document type	Article ; Online
DOI	10.1101/2020.05.26.118133
Database	COVID19

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Article ; Online: Delta-Omicron recombinant escapes therapeutic antibody neutralization.

iScience

2023 Volume 26, Issue 2, Page(s) 106075

Abstract: ... advantages of recombinant SARS-CoV-2 isolates over their parental lineages remain unknown. We identified ... between circulating SARS-CoV-2 variants as a functional mechanism of resistance to treatment and immune ...

Abstract	The emergence of recombinant viruses is a threat to public health, as recombination may integrate variant-specific features that together result in escape from treatment or immunity. The selective advantages of recombinant SARS-CoV-2 isolates over their parental lineages remain unknown. We identified a Delta-Omicron (AY.45-BA.1) recombinant in an immunosuppressed transplant recipient treated with monoclonal antibody Sotrovimab. The single recombination breakpoint is located in the spike N-terminal domain adjacent to the Sotrovimab binding site. While Delta and BA.1 are sensitive to Sotrovimab neutralization, the Delta-Omicron recombinant is highly resistant. To our knowledge, this is the first described instance of recombination between circulating SARS-CoV-2 variants as a functional mechanism of resistance to treatment and immune escape.
Language	English
Publishing date	2023-02-13
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2023.106075
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Evaluation of Specimen Types and Saliva Stabilization Solutions for SARS-CoV-2 Testing.

Griesemer, Sara B / Van Slyke, Greta / Ehrbar, Dylan / Strle, Klemen / Yildirim, Tugba / Centurioni, Dominick A / Walsh, Anne C / Chang, Andrew K / Waxman, Michael J / St George, Kirsten

Journal of clinical microbiology

2021 Volume 59, Issue 5

Abstract: Identifying SARS-CoV-2 infections through aggressive diagnostic testing remains critical ... the preferred sample type for SARS-CoV-2 detection, has become difficult due to the dramatic increase in testing ... collection. In this study, the detection sensitivity of SARS-CoV-2 in nasal swabs (NS) and saliva was ...

Abstract	Identifying SARS-CoV-2 infections through aggressive diagnostic testing remains critical to tracking and curbing the spread of the COVID-19 pandemic. Collection of nasopharyngeal swabs (NPS), the preferred sample type for SARS-CoV-2 detection, has become difficult due to the dramatic increase in testing and consequent supply strain. Therefore, alternative specimen types have been investigated that provide similar detection sensitivity with reduced health care exposure and the potential for self-collection. In this study, the detection sensitivity of SARS-CoV-2 in nasal swabs (NS) and saliva was compared to that of NPS using matched specimens from two outpatient cohorts in New York State (total
MeSH term(s)	COVID-19/diagnosis ; COVID-19 Testing ; Humans ; Nasopharynx/virology ; New York ; Pandemics ; SARS-CoV-2/isolation & purification ; Saliva/virology ; Sensitivity and Specificity ; Specimen Handling/methods ; Temperature
Language	English
Publishing date	2021-04-20
Publishing country	United States
Document type	Evaluation Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	390499-4
ISSN	1098-660X ; 0095-1137
ISSN (online)	1098-660X
ISSN	0095-1137
DOI	10.1128/JCM.01418-20
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Delta-Omicron recombinant escapes therapeutic antibody neutralization.

bioRxiv : the preprint server for biology

2022

Abstract: ... or immunity. The selective advantages of recombinant SARS-CoV-2 isolates over their parental lineages ... the : Results: A novel Delta-Omicron SARS-CoV-2 recombinant was identified in an unvaccinated, immunosuppressed ... without the RBD resistance mutation E340D.: Conclusions: Recombination between circulating SARS-CoV-2 variants ...

Abstract	Background: The emergence of recombinant viruses is a threat to public health. Recombination of viral variants may combine variant-specific features that together catalyze viral escape from treatment or immunity. The selective advantages of recombinant SARS-CoV-2 isolates over their parental lineages remain unknown. Methods: Multi-method amplicon and metagenomic sequencing of a clinical swab and the Results: A novel Delta-Omicron SARS-CoV-2 recombinant was identified in an unvaccinated, immunosuppressed kidney transplant recipient treated with monoclonal antibody Sotrovimab. The recombination breakpoint is located in the spike N-terminal domain, adjacent to the Sotrovimab quaternary binding site, and results in a 5'-Delta AY.45 and a 3'-Omicron BA.1 mosaic spike protein. Delta and BA.1 are sensitive to Sotrovimab neutralization, whereas the Delta-Omicron recombinant is highly resistant to Sotrovimab, both with and without the RBD resistance mutation E340D. Conclusions: Recombination between circulating SARS-CoV-2 variants can functionally contribute to immune escape. It is critical to validate phenotypes of mosaic viruses and monitor immunosuppressed COVID-19 patients treated with monoclonal antibodies for the selection of recombinant and immune escape variants. (Funded by NYU, the National Institutes of Health, and others).
Language	English
Publishing date	2022-08-16
Publishing country	United States
Document type	Preprint
DOI	10.1101/2022.04.06.487325
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Article ; Online: Mutagen resistance and mutation restriction of St. Louis encephalitis virus.

Griesemer, Sara B / Kramer, Laura D / Van Slyke, Greta A / Pata, Janice D / Gohara, David W / Cameron, Craig E / Ciota, Alexander T

The Journal of general virology

2017 Volume 98, Issue 2, Page(s) 201–211

Abstract: The error rate of the RNA-dependent RNA polymerase (RdRp) of RNA viruses is important in maintaining genetic diversity for viral adaptation and fitness. Numerous studies have shown that mutagen-resistant RNA virus variants display amino acid mutations in ...

Abstract	The error rate of the RNA-dependent RNA polymerase (RdRp) of RNA viruses is important in maintaining genetic diversity for viral adaptation and fitness. Numerous studies have shown that mutagen-resistant RNA virus variants display amino acid mutations in the RdRp and other replicase subunits, which in turn exhibit an altered fidelity phenotype affecting viral fitness, adaptability and pathogenicity. St. Louis encephalitis virus (SLEV), like its close relative West Nile virus, is a mosquito-borne flavivirus that has the ability to cause neuroinvasive disease in humans. Here, we describe the successful generation of multiple ribavirin-resistant populations containing a shared amino acid mutation in the SLEV RdRp (E416K). These E416K mutants also displayed resistance to the antiviral T-1106, an RNA mutagen similar to ribavirin. Structural modelling of the E416K polymerase mutation indicated its location in the pinky finger domain of the RdRp, distant from the active site. Deep sequencing of the E416K mutant revealed lower genetic diversity than wild-type SLEV after growth in both vertebrate and invertebrate cells. Phenotypic characterization showed that E416K mutants displayed similar or increased replication in mammalian cells, as well as modest attenuation in mosquito cells, consistent with previous work with West Nile virus high-fidelity variants. In addition, attenuation was limited to mosquito cells with a functional RNA interference response, suggesting an impaired capacity to escape RNA interference could contribute to attenuation of high-fidelity variants. Our results provide increased evidence that RNA mutagen resistance arises through modulation of the RdRp and give further insight into the consequences of altered fidelity of flaviviruses.
MeSH term(s)	Amino Acid Substitution ; Antiviral Agents/pharmacology ; Drug Resistance, Viral/genetics ; Encephalitis Virus, St. Louis/drug effects ; Encephalitis Virus, St. Louis/enzymology ; Encephalitis Virus, St. Louis/genetics ; Encephalitis, St. Louis/virology ; Glutamic Acid/genetics ; HeLa Cells ; Humans ; Lysine/genetics ; Models, Molecular ; Mutagens/pharmacology ; Mutation ; Nucleosides/pharmacology ; Protein Domains ; Pyrazines/pharmacology ; RNA Replicase/chemistry ; RNA Replicase/genetics ; Ribavirin/pharmacology ; Viral Nonstructural Proteins/chemistry ; Viral Nonstructural Proteins/genetics
Chemical Substances	Antiviral Agents ; Mutagens ; NS5 protein, flavivirus ; Nucleosides ; Pyrazines ; T 1106 ; Viral Nonstructural Proteins ; Glutamic Acid (3KX376GY7L) ; Ribavirin (49717AWG6K) ; RNA Replicase (EC 2.7.7.48) ; Lysine (K3Z4F929H6)
Keywords	covid19
Language	English
Publishing date	2017-03-10
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	219316-4
ISSN	1465-2099 ; 0022-1317
ISSN (online)	1465-2099
ISSN	0022-1317
DOI	10.1099/jgv.0.000682
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Article ; Online: Mutagen resistance and mutation restriction of St. Louis encephalitis virus.

Griesemer, Sara B / Kramer, Laura D / Van Slyke, Greta A / Pata, Janice D / Gohara, David D / Cameron, Craig E / Ciota, Alexander T

The Journal of general virology

2016

Abstract	The error rate of the RNA-dependent RNA polymerase (RdRp) of RNA viruses is important in maintaining genetic diversity for viral adaptation and fitness. Numerous studies have shown that mutagen-resistant RNA virus variants display amino acid mutations in the RdRp and other replicase subunits, which in turn exhibit an altered fidelity phenotype affecting viral fitness, adaptability, and pathogenicity. St. Louis encephalitis virus (SLEV), like its close relative West Nile virus (WNV), is a mosquito-borne flavivirus which has the ability to cause neuroinvasive disease in humans. Here, we describe the successful generation of multiple ribavirin-resistant populations containing a shared amino acid mutation in the SLEV RdRp (E416K). These E416K mutants also displayed resistance to the antiviral T-1106, an RNA mutagen similar to ribavirin. Structural modeling of the E416K polymerase mutation indicate its location in the pinky finger domain of the RdRp, distant from the active site. Deep-sequencing of the E416K mutant revealed lower genetic diversity than wildtype SLEV after growth in both vertebrate and invertebrate cells. Phenotypic characterization showed E416K mutants displayed similar or increased replication in mammalian cells, as well as modest attenuation in mosquito cells, consistent with previous work with WNV high-fidelity variants. In addition, attenuation was limited to mosquito cells with a functional RNA interference (RNAi) response, suggesting an impaired capacity to escape RNAi could contribute to attenuation of high-fidelity variants. Our results provide increased evidence that RNA mutagen resistance arises through modulation of the RdRp and gives further insight into the consequences of altered fidelity of flaviviruses.
Keywords	covid19
Language	English
Publishing date	2016-12-12
Publishing country	England
Document type	Journal Article
ZDB-ID	219316-4
ISSN	1465-2099 ; 0022-1317
ISSN (online)	1465-2099
ISSN	0022-1317
DOI	10.1099/jgv.0.000682
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Zs.A 610: Show issues

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Article ; Online: Evaluation of specimen types and saliva stabilization solutions for SARS-CoV-2 testing

Griesemer, Sara B / Van Slyke, Greta / Ehrbar, Dylan / Strle, Klemen / Yildirim, Tugba / Centurioni, Dominick A / Walsh, Anne C / Chang, Andrew K / Waxman, Michael J / St. George, Kirsten

medRxiv

Abstract: Identifying SARS-CoV-2 infections through aggressive diagnostic testing remains critical ... the preferred sample type for SARS-CoV-2 detection, has become difficult due to the dramatic increase in testing ... In this study, the detection sensitivity of SARS-CoV-2 in nasal swabs (NS) and saliva was compared ...

Abstract	Identifying SARS-CoV-2 infections through aggressive diagnostic testing remains critical in tracking and curbing the spread of the COVID-19 pandemic. Collection of nasopharyngeal swabs (NPS), the preferred sample type for SARS-CoV-2 detection, has become difficult due to the dramatic increase in testing and consequential supply strain. Therefore, alternative specimen types have been investigated, that provide similar detection sensitivity with reduced health care exposure and potential for self-collection. In this study, the detection sensitivity of SARS-CoV-2 in nasal swabs (NS) and saliva was compared to that of NPS, using matched specimens from two outpatient cohorts in New York State (total n = 463). The first cohort showed only a 5.4% positivity but the second cohort (n=227) had a positivity rate of 41%, with sensitivity in NPS, NS and saliva of 97.9%, 87.1%, and 87.1%, respectively. Whether the reduced sensitivity of NS or saliva is acceptable must be assessed in the settings where they are used. However, we sought to improve on it by validating a method to mix the two sample types, as the combination of nasal swab and saliva resulted in 94.6% SARS-CoV-2 detection sensitivity. Spiking experiments showed that combining them did not adversely affect the detection sensitivity in either. Virus stability in saliva was also investigated, with and without the addition of commercially available stabilizing solutions. The virus was stable in saliva at both 4C and room temperature for up to 7 days. The addition of stabilizing solutions did not enhance stability and in some situations reduced detectable virus levels.
Keywords	covid19
Language	English
Publishing date	2020-06-18
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2020.06.16.20133041
Database	COVID19

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