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Artikel ; Online: Enterovirus characterized from cerebrospinal fluid in a cohort from the Eastern United States.

Fall, Amary / Forman, Michael / Morris, C Paul / Gniazdowski, Victoria / Luo, Chun Huai / Hanlon, Ann / Miller, Heather / Bergman, Yehudit / Mostafa, Heba H

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

2023 Band 161, Seite(n) 105401

Abstract: Background: Enteroviruses (EVs) are predominant causes of a spectrum of neurological diseases. To better understand the origins of the outbreaks of disease associated with EV, it is essential to develop an efficient surveillance system that identifies ... ...

Abstract	Background: Enteroviruses (EVs) are predominant causes of a spectrum of neurological diseases. To better understand the origins of the outbreaks of disease associated with EV, it is essential to develop an efficient surveillance system that identifies the circulating EVs and correlate their genomic evolution with the disease presentations. Methods: The clinical presentations of patients with positive EV from cerebrospinal fluid (CSF) between 2014 and 2022, diagnosed at the Johns Hopkins Medical Microbiology Laboratory, were compared from year to year. EV typing and whole genome sequencing were performed and correlated to the spectrum of disease. Results: A total of 95 CSF specimens were positive for EV between 2014 and 2022. The percentage positivity ranged from the lowest of 1.1% in 2020 to the highest of 3.2% in 2015. The median ages declined from 22 years in 2014 to less than one year starting in 2016 to 34 in 2022. Typing using VP1 sequencing revealed that E30 and E6 were associated with meningitis in adults but coxsackieviruses (CVs-B3 and B5) were detected from pediatric patients with fever. Whole genome sequencing revealed multiple recombination events. In 2020, a recombinant CV-A9 was detected in a CSF sample associated with unusual presentation of sepsis, profound acute bilateral sensory neural hearing loss, and myofasciitis. Conclusions: EV genomic surveillance is needed for a better understanding of the genetic determinants of neurovirulence. Whole genome sequencing can reveal recombination events missed by traditional molecular surveillance methods.
Mesh-Begriff(e)	Adult ; Child ; Humans ; United States/epidemiology ; Infant ; Young Adult ; Enterovirus/genetics ; Phylogeny ; Enterovirus Infections/epidemiology ; Meningitis, Viral ; Sequence Analysis, DNA ; Cerebrospinal Fluid
Sprache	Englisch
Erscheinungsdatum	2023-02-13
Erscheinungsland	Netherlands
Dokumenttyp	Case Reports ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1446080-4
ISSN	1873-5967 ; 1386-6532
ISSN (online)	1873-5967
ISSN	1386-6532
DOI	10.1016/j.jcv.2023.105401
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Large Scale SARS-CoV-2 Molecular Testing and Genomic Surveillance Reveal Prolonged Infections, Protracted RNA shedding, and Viral Reinfections.

Morris, C Paul / Luo, Chun Huai / Sachithanandham, Jaiprasath / Li, Maggie / Schwartz, Matthew / Gaston, David C / Gniazdowski, Victoria / Giraldo-Castillo, Nicolas / Amadi, Adannaya / Norton, Julie M / Wright, William F / Klein, Eili Y / Pekosz, Andrew / Mostafa, Heba H

Frontiers in cellular and infection microbiology

2022 Band 12, Seite(n) 809407

Abstract: Large-scale SARS-CoV-2 molecular testing coupled with whole genome sequencing in the diagnostic laboratories is instrumental for real-time genomic surveillance. The extensive genomic, laboratory, and clinical data provide a valuable resource for ... ...

Abstract	Large-scale SARS-CoV-2 molecular testing coupled with whole genome sequencing in the diagnostic laboratories is instrumental for real-time genomic surveillance. The extensive genomic, laboratory, and clinical data provide a valuable resource for understanding cases of reinfection versus prolonged RNA shedding and protracted infections. In this study, data from a total of 22,292 clinical specimens, positive by SARS-CoV-2 molecular diagnosis at Johns Hopkins clinical virology laboratory between March 11
Mesh-Begriff(e)	COVID-19/diagnosis ; Genome, Viral/genetics ; Genomics ; Humans ; Molecular Diagnostic Techniques ; RNA, Viral/genetics ; Reinfection ; SARS-CoV-2/genetics
Chemische Substanzen	RNA, Viral
Sprache	Englisch
Erscheinungsdatum	2022-04-11
Erscheinungsland	Switzerland
Dokumenttyp	Journal Article ; Research Support, U.S. Gov't, P.H.S. ; Research Support, N.I.H., Extramural
ZDB-ID	2619676-1
ISSN	2235-2988 ; 2235-2988
ISSN (online)	2235-2988
ISSN	2235-2988
DOI	10.3389/fcimb.2022.809407
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Metagenomic Next-Generation Sequencing of Nasopharyngeal Specimens Collected from Confirmed and Suspect COVID-19 Patients.

Mostafa, Heba H / Fissel, John A / Fanelli, Brian / Bergman, Yehudit / Gniazdowski, Victoria / Dadlani, Manoj / Carroll, Karen C / Colwell, Rita R / Simner, Patricia J

mBio

2020 Band 11, Heft 6

Abstract: Metagenomic next-generation sequencing (mNGS) offers an agnostic approach for emerging pathogen detection directly from clinical specimens. In contrast to targeted methods, mNGS also provides valuable information on the composition of the microbiome and ... ...

Abstract	Metagenomic next-generation sequencing (mNGS) offers an agnostic approach for emerging pathogen detection directly from clinical specimens. In contrast to targeted methods, mNGS also provides valuable information on the composition of the microbiome and might uncover coinfections that may associate with disease progression and impact prognosis. To evaluate the use of mNGS for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and/or other infecting pathogens, we applied direct Oxford Nanopore long-read third-generation metatranscriptomic and metagenomic sequencing. Nasopharyngeal (NP) swab specimens from 50 patients under investigation for CoV disease 2019 (COVID-19) were sequenced, and the data were analyzed by the CosmosID bioinformatics platform. Further, we characterized coinfections and the microbiome associated with a four-point severity index. SARS-CoV-2 was identified in 77.5% (31/40) of samples positive by RT-PCR, correlating with lower cycle threshold (Ct) values and fewer days from symptom onset. At the time of sampling, possible bacterial or viral coinfections were detected in 12.5% of SARS-CoV-2-positive specimens. A decrease in microbial diversity was observed among COVID-19-confirmed patients (Shannon diversity index,
Mesh-Begriff(e)	Bacteria/classification ; COVID-19/microbiology ; COVID-19/virology ; Coinfection/microbiology ; Coinfection/virology ; Computational Biology ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; Metagenomics ; Microbiota ; Nasopharynx/virology ; RNA, Viral/genetics ; SARS-CoV-2/genetics ; Specimen Handling
Chemische Substanzen	RNA, Viral
Sprache	Englisch
Erscheinungsdatum	2020-11-20
Erscheinungsland	United States
Dokumenttyp	Journal Article
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mBio.01969-20
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Repeated Coronavirus Disease 2019 Molecular Testing: Correlation of Severe Acute Respiratory Syndrome Coronavirus 2 Culture With Molecular Assays and Cycle Thresholds.

Gniazdowski, Victoria / Paul Morris, C / Wohl, Shirlee / Mehoke, Thomas / Ramakrishnan, Srividya / Thielen, Peter / Powell, Harrison / Smith, Brendan / Armstrong, Derek T / Herrera, Monica / Reifsnyder, Carolyn / Sevdali, Maria / Carroll, Karen C / Pekosz, Andrew / Mostafa, Heba H

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

2020 Band 73, Heft 4, Seite(n) e860–e869

Abstract: Background: Repeated coronavirus disease 2019 (COVID-19) molecular testing can lead to positive test results after negative results and to multiple positive results over time. The association between positive test results and infectious virus is ... ...

Abstract	Background: Repeated coronavirus disease 2019 (COVID-19) molecular testing can lead to positive test results after negative results and to multiple positive results over time. The association between positive test results and infectious virus is important to quantify. Methods: A 2-month cohort of retrospective data and consecutively collected specimens from patients with COVID-19 or patients under investigation were used to understand the correlation between prolonged viral RNA positive test results, cycle threshold (Ct) values and growth of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in cell culture. Whole-genome sequencing was used to confirm virus genotype in patients with prolonged viral RNA detection. Droplet digital polymerase chain reaction was used to assess the rate of false-negative COVID-19 diagnostic test results. Results: In 2 months, 29 686 specimens were tested and 2194 patients underwent repeated testing. Virus recovery in cell culture was noted in specimens with a mean Ct value of 18.8 (3.4) for SARS-CoV-2 target genes. Prolonged viral RNA shedding was associated with positive virus growth in culture in specimens collected up to 21 days after the first positive result but mostly in individuals symptomatic at the time of sample collection. Whole-genome sequencing provided evidence the same virus was carried over time. Positive test results following negative results had Ct values >29.5 and were not associated with virus culture. Droplet digital polymerase chain reaction results were positive in 5.6% of negative specimens collected from patients with confirmed or clinically suspected COVID-19. Conclusions: Low Ct values in SARS-CoV-2 diagnostic tests were associated with virus growth in cell culture. Symptomatic patients with prolonged viral RNA shedding can also be infectious.
Mesh-Begriff(e)	COVID-19 ; Humans ; RNA, Viral/genetics ; Retrospective Studies ; SARS-CoV-2 ; Virus Shedding
Chemische Substanzen	RNA, Viral
Schlagwörter	covid19
Sprache	Englisch
Erscheinungsdatum	2020-10-24
Erscheinungsland	United States
Dokumenttyp	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1099781-7
ISSN	1537-6591 ; 1058-4838
ISSN (online)	1537-6591
ISSN	1058-4838
DOI	10.1093/cid/ciaa1616
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Genomic diversity of SARS-CoV-2 during early introduction into the Baltimore-Washington metropolitan area.

JCI insight

2021 Band 6, Heft 6

Abstract: The early COVID-19 pandemic was characterized by rapid global spread. In Maryland and Washington, DC, United States, more than 2500 cases were reported within 3 weeks of the first COVID-19 detection in March 2020. We aimed to use genomic sequencing to ... ...

Abstract	The early COVID-19 pandemic was characterized by rapid global spread. In Maryland and Washington, DC, United States, more than 2500 cases were reported within 3 weeks of the first COVID-19 detection in March 2020. We aimed to use genomic sequencing to understand the initial spread of SARS-CoV-2 - the virus that causes COVID-19 - in the region. We analyzed 620 samples collected from the Johns Hopkins Health System during March 11-31, 2020, comprising 28.6% of the total cases in Maryland and Washington, DC. From these samples, we generated 114 complete viral genomes. Analysis of these genomes alongside a subsampling of over 1000 previously published sequences showed that the diversity in this region rivaled global SARS-CoV-2 genetic diversity at that time and that the sequences belong to all of the major globally circulating lineages, suggesting multiple introductions into the region. We also analyzed these regional SARS-CoV-2 genomes alongside detailed clinical metadata and found that clinically severe cases had viral genomes belonging to all major viral lineages. We conclude that efforts to control local spread of the virus were likely confounded by the number of introductions into the region early in the epidemic and the interconnectedness of the region as a whole.
Mesh-Begriff(e)	Adolescent ; Adult ; Aged ; Aged, 80 and over ; Baltimore ; Base Sequence ; COVID-19/epidemiology ; COVID-19/transmission ; COVID-19/virology ; Child ; Disease Outbreaks ; Disease Transmission, Infectious ; District of Columbia ; Female ; Genome, Viral ; Genomics/methods ; Global Health ; Humans ; Male ; Middle Aged ; Pandemics ; Phylogeny ; SARS-CoV-2/genetics ; Young Adult
Sprache	Englisch
Erscheinungsdatum	2021-03-22
Erscheinungsland	United States
Dokumenttyp	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	2379-3708
ISSN (online)	2379-3708
DOI	10.1172/jci.insight.144350
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel: Repeat COVID-19 Molecular Testing: Correlation of SARS-CoV-2 Culture with Molecular Assays and Cycle Thresholds

Gniazdowski, Victoria / Morris, C Paul / Wohl, Shirlee / Mehoke, Thomas / Ramakrishnan, Srividya / Thielen, Peter / Powell, Harrison / Smith, Brendan / Armstrong, Derek T / Herrera, Monica / Reifsnyder, Carolyn / Sevdali, Maria / Carroll, Karen C / Pekosz, Andrew / Mostafa, Heba H

Clin. infect. dis

Abstract: BACKGROUND: Repeat COVID-19 molecular testing can lead to positive test results after negative tests and to multiple positive test results over time. The association between positive tests and infectious virus is important to quantify. METHODS: A two ... ...

Abstract	BACKGROUND: Repeat COVID-19 molecular testing can lead to positive test results after negative tests and to multiple positive test results over time. The association between positive tests and infectious virus is important to quantify. METHODS: A two months cohort of retrospective data and consecutively collected specimens from COVID-19 patients or patients under investigation were used to understand the correlation between prolonged viral RNA positive test results, cycle threshold (Ct) values and growth of SARS-CoV-2 in cell culture. Whole genome sequencing was used to confirm virus genotype in patients with prolonged viral RNA detection. Droplet digital PCR (ddPCR) was used to assess the rate of false negative COVID-19 diagnostic tests. RESULTS: In two months, 29,686 specimens were tested and 2,194 patients received repeated testing. Virus recovery in cell culture was noted in specimens with SARS-CoV-2 target genes' Ct value average of 18.8 ± 3.4. Prolonged viral RNA shedding was associated with positive virus growth in culture in specimens collected up to 20 days after the first positive result but mostly in individuals symptomatic at time of sample collection. Whole genome sequencing provided evidence the same virus was carried over time. Positive tests following negative tests had Ct values higher than 29.5 and were not associated with virus culture. ddPCR was positive in 5.6% of negative specimens collected from COVID-19 confirmed or clinically suspected patients. CONCLUSIONS: Low Ct values in SARS-CoV-2 diagnostic tests were associated with virus growth in cell culture. Symptomatic patients with prolonged viral RNA shedding can also be infectious.
Schlagwörter	covid19
Verlag	WHO
Dokumenttyp	Artikel
Anmerkung	WHO #Covidence: #892076
Datenquelle	COVID19

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Artikel ; Online: Repeat COVID-19 Molecular Testing

Clinical Infectious Diseases ; ISSN 1058-4838 1537-6591

Correlation of SARS-CoV-2 Culture with Molecular Assays and Cycle Thresholds

2020

Abstract: Abstract Background Repeat COVID-19 molecular testing can lead to positive test results after negative tests and to multiple positive test results over time. The association between positive tests and infectious virus is important to quantify. Methods A ... ...

Abstract	Abstract Background Repeat COVID-19 molecular testing can lead to positive test results after negative tests and to multiple positive test results over time. The association between positive tests and infectious virus is important to quantify. Methods A two months cohort of retrospective data and consecutively collected specimens from COVID-19 patients or patients under investigation were used to understand the correlation between prolonged viral RNA positive test results, cycle threshold (Ct) values and growth of SARS-CoV-2 in cell culture. Whole genome sequencing was used to confirm virus genotype in patients with prolonged viral RNA detection. Droplet digital PCR (ddPCR) was used to assess the rate of false negative COVID-19 diagnostic tests. Results In two months, 29,686 specimens were tested and 2,194 patients received repeated testing. Virus recovery in cell culture was noted in specimens with SARS-CoV-2 target genes’ Ct value average of 18.8 ± 3.4. Prolonged viral RNA shedding was associated with positive virus growth in culture in specimens collected up to 20 days after the first positive result but mostly in individuals symptomatic at time of sample collection. Whole genome sequencing provided evidence the same virus was carried over time. Positive tests following negative tests had Ct values higher than 29.5 and were not associated with virus culture. ddPCR was positive in 5.6% of negative specimens collected from COVID-19 confirmed or clinically suspected patients. Conclusions Low Ct values in SARS-CoV-2 diagnostic tests were associated with virus growth in cell culture. Symptomatic patients with prolonged viral RNA shedding can also be infectious.
Schlagwörter	Microbiology (medical) ; Infectious Diseases ; covid19
Sprache	Englisch
Verlag	Oxford University Press (OUP)
Erscheinungsland	uk
Dokumenttyp	Artikel ; Online
DOI	10.1093/cid/ciaa1616
Datenquelle	BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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Artikel: Genomic Diversity of SARS-CoV-2 During Early Introduction into the United States National Capital Region.

medRxiv : the preprint server for health sciences

2020

Abstract: Background: The early COVID-19 pandemic has been characterized by rapid global spread. In the United States National Capital Region, over 2,000 cases were reported within three weeks of its first detection in March 2020. We aimed to use genomic ... ...

Abstract	Background: The early COVID-19 pandemic has been characterized by rapid global spread. In the United States National Capital Region, over 2,000 cases were reported within three weeks of its first detection in March 2020. We aimed to use genomic sequencing to understand the initial spread of SARS-CoV-2, the virus that causes COVID-19, in the region. By correlating genetic information to disease phenotype, we also aimed to gain insight into any correlation between viral genotype and case severity or transmissibility. Methods: We performed whole genome sequencing of clinical SARS-CoV-2 samples collected in March 2020 by the Johns Hopkins Health System. We analyzed these regional SARS-CoV-2 genomes alongside detailed clinical metadata and the global phylogeny to understand early establishment of the virus within the region. Results: We analyzed 620 samples from the Johns Hopkins Health System collected between March 11-31, 2020, comprising 37.3% of the total cases in Maryland during this period. We selected 143 of these samples for sequencing, generating 114 complete viral genomes. These genomes belong to all five major Nextstrain-defined clades, suggesting multiple introductions into the region and underscoring the diversity of the regional epidemic. We also found that clinically severe cases had genomes belonging to all of these clades. Conclusions: We established a pipeline for SARS-CoV-2 sequencing within the Johns Hopkins Health system, which enabled us to capture the significant viral diversity present in the region as early as March 2020. Efforts to control local spread of the virus were likely confounded by the number of introductions into the region early in the epidemic and interconnectedness of the region as a whole.
Schlagwörter	covid19
Sprache	Englisch
Erscheinungsdatum	2020-08-23
Erscheinungsland	United States
Dokumenttyp	Preprint
DOI	10.1101/2020.08.13.20174136
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Repeat COVID-19 Molecular Testing: Correlation with Recovery of Infectious Virus, Molecular Assay Cycle Thresholds, and Analytical Sensitivity

Gniazdowski, Victoria / Morris, C. Paul / Wohl, Shirlee / Mehoke, Thomas / Ramakrishnan, Srividya / Thielen, Peter / Powell, Harrison / Smith, Brendan D / Armstrong, Derek T / Herrera, Monica / Reifsnyder, Carolyn / Sevdali, Maria / Carroll, Karen C / Pekosz, Andrew / Mostafa, Heba H

medRxiv

Abstract: Repeat molecular testing for SARS-CoV-2 may result in scenarios including multiple positive results, positive test results after negative tests, and repeated false negative results in symptomatic individuals. Consecutively collected specimens from a ... ...

Abstract	Repeat molecular testing for SARS-CoV-2 may result in scenarios including multiple positive results, positive test results after negative tests, and repeated false negative results in symptomatic individuals. Consecutively collected specimens from a retrospective cohort of COVID-19 patients at the Johns Hopkins Hospital were assessed for RNA and infectious virus shedding. Whole genome sequencing confirmed the virus genotype in patients with prolonged viral RNA shedding and droplet digital PCR (ddPCR) was used to assess the rate of false negative standard of care PCR results. Recovery of infectious virus was associated with Ct values of 18.8 ± 3.4. Prolonged viral RNA shedding was associated with recovery of infectious virus in specimens collected up to 20 days after the first positive result in patients who were symptomatic at the time of specimen collection. The use of Ct values and clinical symptoms provides a more accurate assessment of the potential for infectious virus shedding.
Schlagwörter	covid19
Sprache	Englisch
Erscheinungsdatum	2020-08-06
Verlag	Cold Spring Harbor Laboratory Press
Dokumenttyp	Artikel ; Online
DOI	10.1101/2020.08.05.20168963
Datenquelle	COVID19

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Artikel ; Online: Genomic Diversity of SARS-CoV-2 During Early Introduction into the United States National Capital Region

medRxiv

Abstract	Background: The early COVID-19 pandemic has been characterized by rapid global spread. In the United States National Capital Region, over 2,000 cases were reported within three weeks of its first detection in March 2020. We aimed to use genomic sequencing to understand the initial spread of SARS-CoV-2, the virus that causes COVID-19, in the region. By correlating genetic information to disease phenotype, we also aimed to gain insight into any correlation between viral genotype and case severity or transmissibility. Methods: We performed whole genome sequencing of clinical SARS-CoV-2 samples collected in March 2020 by the Johns Hopkins Health System, building on methods developed by the ARTIC network. We analyzed these regional SARS-CoV-2 genomes alongside detailed clinical metadata and the global phylogeny to understand early establishment of the virus within the region. Results: We analyzed 620 samples from the Johns Hopkins Health System collected between March 11-31, 2020, comprising 37.3% of the total cases in Maryland during this period. We selected 143 of these samples for sequencing, generating 114 complete viral genomes. These genomes belonged to all five major Nextstrain-defined clades, suggesting multiple introductions into the region and underscoring the diversity of the regional epidemic. We also found that clinically severe cases had genomes belonging to all of these clades. Conclusions: We established a pipeline for SARS-CoV-2 sequencing within the Johns Hopkins Health system, which enabled us to capture the significant viral diversity present in the region as early as March 2020. Efforts to control local spread of the virus were likely confounded by the number of introductions into the region early in the epidemic and interconnectedness of the region as a whole.
Schlagwörter	covid19
Sprache	Englisch
Erscheinungsdatum	2020-08-15
Verlag	Cold Spring Harbor Laboratory Press
Dokumenttyp	Artikel ; Online
DOI	10.1101/2020.08.13.20174136
Datenquelle	COVID19

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