scholarly journals Evaluation of specimen types and saliva stabilization solutions for SARS-CoV-2 testing

2021 ◽  
Author(s):  
Sara B Griesemer ◽  
Greta Van Slyke ◽  
Dylan Ehrbar ◽  
Klemen Strle ◽  
Tugba Yildirim ◽  
...  
Keyword(s):  
New York ◽  
Room Temperature ◽  
Nasal Swab ◽  
Diagnostic Testing ◽  
New York State ◽  
Detection Sensitivity ◽  
Sample Type ◽  
Total N ◽  
Nasal Swabs ◽  
Alternative Specimen

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 4°C 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.

scholarly journals Evaluation of specimen types and saliva stabilization solutions for SARS-CoV-2 testing

2020 ◽  
Author(s):  
Sara B Griesemer ◽  
Greta Van Slyke ◽  
Dylan Ehrbar ◽  
Klemen Strle ◽  
Tugba Yildirim ◽  
...  
Keyword(s):  
New York ◽  
Room Temperature ◽  
Nasal Swab ◽  
Diagnostic Testing ◽  
New York State ◽  
Detection Sensitivity ◽  
Sample Type ◽  
Total N ◽  
Nasal Swabs ◽  
Alternative Specimen

AbstractIdentifying 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 4°C 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.

scholarly journals Performance of Abbott ID Now COVID-19 Rapid Nucleic Acid Amplification Test Using Nasopharyngeal Swabs Transported in Viral Transport Media and Dry Nasal Swabs in a New York City Academic Institution

2020 ◽  
Vol 58 (8) ◽  
Author(s):  
Atreyee Basu ◽  
Tatyana Zinger ◽  
Kenneth Inglima ◽  
Kar-mun Woo ◽  
Onome Atie ◽  
...  
Keyword(s):  
New York ◽  
The United States ◽  
Turnaround Time ◽  
Nucleic Acid Amplification ◽  
Molecular Diagnostic ◽  
Sample Type ◽  
Negative Results ◽  
Viral Transport ◽  
Recent Emergence ◽  
Nasal Swabs

ABSTRACT The recent emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has posed formidable challenges for clinical laboratories seeking reliable laboratory diagnostic confirmation. The swift advance of the crisis in the United States has led to Emergency Use Authorization (EUA) facilitating the availability of molecular diagnostic assays without the more rigorous examination to which tests are normally subjected prior to FDA approval. Our laboratory currently uses two real-time reverse transcription-PCR (RT-PCR) platforms, the Roche Cobas SARS-CoV2 and the Cepheid Xpert Xpress SARS-CoV-2. The two platforms demonstrate comparable performances; however, the run times for each assay are 3.5 h and 45 min, respectively. In search for a platform with a shorter turnaround time, we sought to evaluate the recently released Abbott ID Now COVID-19 assay, which is capable of producing positive results in as little as 5 min. We present here the results of comparisons between Abbott ID Now COVID-19 and Cepheid Xpert Xpress SARS-CoV-2 using nasopharyngeal swabs transported in viral transport media and comparisons between Abbott ID Now COVID-19 and Cepheid Xpert Xpress SARS-CoV-2 using nasopharyngeal swabs transported in viral transport media for Cepheid and dry nasal swabs for Abbott ID Now. Regardless of method of collection and sample type, Abbott ID Now COVID-19 had negative results in a third of the samples that tested positive by Cepheid Xpert Xpress when using nasopharyngeal swabs in viral transport media and 45% when using dry nasal swabs.

scholarly journals Detection of Infectious Tobamoviruses in Forest Soils

1998 ◽  
Vol 64 (4) ◽  
pp. 1430-1435 ◽  
Author(s):  
Ronald C. Fillhart ◽  
George D. Bachand ◽  
John D. Castello
Keyword(s):  
New York ◽  
Forest Soils ◽  
New York State ◽  
Soil Samples ◽  
Detection Sensitivity ◽  
Enzyme Linked Immunosorbent Assay ◽  
York State ◽  
Root Extracts ◽  
Bait Plants ◽  
Virus Content

ABSTRACT Our objectives were to evaluate elution and bait plant methods to detect infectious tobamoviruses in forest soils in New York State. Soils were collected from two forest sites: Whiteface Mountain (WF) and Heiberg Forest (HF). The effectiveness of four buffers to elute tomato mosaic tobamovirus (ToMV) from organic and mineral fractions of WF soil amended with ToMV was tested, and virus content was assessed by enzyme-linked immunosorbent assay (ELISA). The effectiveness ofChenopodium quinoa (Willd.) bait plants to detect the virus also was tested. Both methods then were utilized to detect tobamoviruses in 11 WF and 2 HF soil samples. A phosphate buffer (100 mM, pH 7.0) eluted more ToMV from soil than the other buffers tested. Mineral soil bound more virus than organic soil. Virus recoveries from virus-amended organic and mineral soils were 3 and 10%, respectively, and the detection sensitivity was 10 to 20 ng/g of soil. Roots of bait plants grown in all virus-amended soils tested positive by ELISA, and virus concentrations averaged 10 ng/g. Both ToMV and tobacco mosaic tobamovirus (TMV) were transmitted to C. quinoa by elution from one of two HF soil samples but not from the WF soil samples. A tobamovirus was detected by bait planting in 12 of 73 (16%) root extracts representing 5 of 13 soil samples (38%). Tobamovirus-like particles were seen by transmission electron microscopy in 6 of 12 infected root extracts. Tobamoviruses occur in forest soils in New York State. Abiotic soil transmission to trees may permit localized spread and persistence of these viruses in forest ecosystems.

scholarly journals Determinants of Severity in Cancer Patients with COVID-19 Illness

2020 ◽  
Author(s):  
Elizabeth V. Robilotti ◽  
N. Esther Babady ◽  
Peter A. Mead ◽  
Thierry Rolling ◽  
Rocio Perez-Johnston ◽  
...  
Keyword(s):  
New York ◽  
Checkpoint Inhibitors ◽  
Severe Disease ◽  
Diagnostic Testing ◽  
New York State ◽  
Respiratory Illness ◽  
Population Based ◽  
Major Surgery ◽  
Cancer Center ◽  
Patients With Cancer

New York State had 180,458 cases of SARS-CoV-2 and 9385 reported deaths as of April 10th, 2020. Patients with cancer comprised 8.4% of deceased individuals1. Population-based studies from China and Italy suggested a higher COVID-19 death rate in patients with cancer2,3, although there is a knowledge gap as to which aspects of cancer and its treatment confer risk of severe COVID-19 disease4. This information is critical to balance the competing safety considerations of reducing SARS-CoV-2 exposure and cancer treatment continuation. Since March 10th, 2020 Memorial Sloan Kettering Cancer Center (MSKCC) performed diagnostic testing for SARS-CoV-2 in symptomatic patients. Overall, 40% out of 423 patients with cancer were hospitalized for COVID-19 illness, 20% developed severe respiratory illness, including 9% that required mechanical ventilation, and 9% that died. On multivariate analysis, age ≥ 65 years and treatment with immune checkpoint inhibitors (ICI) within 90 days were predictors for hospitalization and severe disease, while receipt of chemotherapy within 30 days and major surgery were not. Overall, COVID-19 illness is associated with higher rates of hospitalization and severe outcomes in patients with cancer. Association between ICI and COVID-19 outcomes will need interrogation in tumor-specific cohorts.

Abstract P585: Age- and Sex-Specific Temporal Trends in the Incidence of Pediatric Stroke in New York State From 2006-2016

Stroke ◽  
2021 ◽  
Vol 52 (Suppl_1) ◽  
Author(s):  
Husitha R Vanguru ◽  
Nnabuchi Anikpezie ◽  
Karen C Albright ◽  
Julius G Latorre ◽  
Fadar O Otite
Keyword(s):  
New York ◽  
Census Data ◽  
Systems Of Care ◽  
New York State ◽  
Temporal Trends ◽  
Pediatric Stroke ◽  
Total N ◽  
Stroke Incidence ◽  
Over Time ◽  
Age And Sex

Objectives: 1. To estimate sex- and race-specific incidence of pediatric stroke by age group 2. To describe trends in pediatric stroke incidence in New York(NY) from 2006 to 2016 Methods: International Classification of Disease codes were used to retrospectively to identify all acute ischemic stroke (AIS), intracerebral hemorrhage (ICH), subarachnoid hemorrhage (SAH), and cerebral venous thrombosis (CVT) admissions in pediatric patients (0-19 years old [yo]) in the 2006-2016 NY State Inpatients Database (SID; total N=4,083). Incident counts were combined with annual US Census data to compute age- and sex-specific incidence. Joinpoint regression was used to evaluate trends in incidence over time. Results: Across the study period, 52% of all pediatric strokes were AIS, 23% ICH, 11% SAH, and 14% CVT. Total stroke incidence/100,000 population was 47.8 and the age-standardized incidence in >=1yo was 4.8. Incidence differed by age (1-4yo: 4.4, 5-9yo: 3.6, 10-14yo: 4.5, and 15-19yo: 6.7), but not by sex. Age-standardized incidence of strokes in >=1yo also differed by race (Blacks 5.9, Whites 4.0, Hispanics 3.3, Asians/Pacific Islanders 3.1). While there was no change in overall stroke, AIS, or SAH incidence, ICH (annualized percentage change [APC] 4.3%, 95%CI 1.7-6.9) and CVT (APC 4.1, 95%CI 1.22-6.25%) increased over time. When stratified by age, overall stroke incidence increased over time in 15-19 yo (APC 1.3%, 95%CI 0.27-2.35, p=0.019), but not in other age groups. Conclusion: We observed increasing incidence in pediatric ICH, CVT, and overall stroke in 15-19 yo in the state of NY. Pediatric stroke incidence in NY is disproportionately higher in blacks compared to other races. Further investigation is warranted to determine the association of these changes with risk factors, lifestyle and systems of care.

scholarly journals Performance of Saliva, Oropharyngeal Swabs, and Nasal Swabs for SARS-CoV-2 Molecular Detection: A Systematic Review and Meta-analysis

2020 ◽  
Author(s):  
Rose A. Lee ◽  
Joshua C. Herigon ◽  
Andrea Benedetti ◽  
Nira R. Pollock ◽  
Claudia M. Denkinger
Keyword(s):  
Meta Analysis ◽  
Diagnostic Testing ◽  
Rna Extraction ◽  
High Sensitivity ◽  
Nucleic Acid Amplification ◽  
Sample Collection ◽  
Specimen Collection ◽  
Nasal Swabs ◽  
The Impact ◽  
Alternative Specimen

ABSTRACTBackgroundNasopharyngeal (NP) swabs are considered the highest-yield sample for diagnostic testing for respiratory viruses, including SARS-CoV-2. The need to increase capacity for SARS-CoV-2 testing in a variety of settings, combined with shortages of sample collection supplies, have motivated a search for alternative sample types with high sensitivity. We systematically reviewed the literature to understand the performance of alternative sample types compared to NP swabs.MethodsWe systematically searched PubMed, Google Scholar, medRxiv, and bioRxiv (last retrieval October 1st, 2020) for comparative studies of alternative specimen types [saliva, oropharyngeal (OP), and nasal (NS) swabs] versus NP swabs for SARS-CoV-2 diagnosis using nucleic acid amplification testing (NAAT). A logistic-normal random-effects meta-analysis was performed to calculate % positive alternative-specimen, % positive NP, and % dual positives overall and in sub-groups. The QUADAS 2 tool was used to assess bias.ResultsFrom 1,253 unique citations, we identified 25 saliva, 11 NS, 6 OP, and 4 OP/NS studies meeting inclusion criteria. Three specimen types captured lower % positives [NS (0.82, 95% CI: 0.73-0.90), OP (0.84, 95% CI: 0.57-1.0), saliva (0.88, 95% CI: 0.81 – 0.93)] than NP swabs, while combined OP/NS matched NP performance (0.97, 95% CI: 0.90-1.0). Absence of RNA extraction (saliva) and utilization of a more sensitive NAAT (NS) substantially decreased alternative-specimen yield.ConclusionsNP swabs remain the gold standard for diagnosis of SARS-CoV-2, although alternative specimens are promising. Much remains unknown about the impact of variations in specimen collection, processing protocols, and population (pediatric vs. adult, late vs. early in disease course) and head-to head studies of sampling strategies are urgently needed.

scholarly journals Performance of Saliva, Oropharyngeal Swabs, and Nasal Swabs for SARS-CoV-2 Molecular Detection: A Systematic Review and Meta-analysis

2021 ◽  
Author(s):  
Rose A. Lee ◽  
Joshua C. Herigon ◽  
Andrea Benedetti ◽  
Nira R. Pollock ◽  
Claudia M. Denkinger
Keyword(s):  
Meta Analysis ◽  
Diagnostic Testing ◽  
Rna Extraction ◽  
High Sensitivity ◽  
Nucleic Acid Amplification ◽  
Sample Collection ◽  
Specimen Collection ◽  
Nasal Swabs ◽  
The Impact ◽  
Alternative Specimen

Background: Nasopharyngeal (NP) swabs are considered the highest-yield sample for diagnostic testing for respiratory viruses, including SARS-CoV-2. The need to increase capacity for SARS-CoV-2 testing in a variety of settings, combined with shortages of sample collection supplies, have motivated a search for alternative sample types with high sensitivity. We systematically reviewed the literature to understand the performance of alternative sample types compared to NP swabs. Methods: We systematically searched PubMed, Google Scholar, medRxiv, and bioRxiv (last retrieval October 1st, 2020) for comparative studies of alternative specimen types [saliva, oropharyngeal (OP), and nasal (NS) swabs] versus NP swabs for SARS-CoV-2 diagnosis using nucleic acid amplification testing (NAAT). A logistic-normal random-effects meta-analysis was performed to calculate % positive alternative-specimen, % positive NP, and % dual positives overall and in sub-groups. The QUADAS 2 tool was used to assess bias. Results: From 1,253 unique citations, we identified 25 saliva, 11 NS, 6 OP, and 4 OP/NS studies meeting inclusion criteria. Three specimen types captured lower % positives [NS (82%, 95% CI: 73-90%), OP (84%, 95% CI: 57-100%), saliva (88%, 95% CI: 81 – 93%)] than NP swabs, while combined OP/NS matched NP performance (97%, 95% CI: 90-100%). Absence of RNA extraction (saliva) and utilization of a more sensitive NAAT (NS) substantially decreased alternative-specimen yield. Conclusions: NP swabs remain the gold standard for diagnosis of SARS-CoV-2, although alternative specimens are promising. Much remains unknown about the impact of variations in specimen collection, processing protocols, and population (pediatric vs. adult, late vs. early in disease course) and head-to head studies of sampling strategies are urgently needed.

scholarly journals Performance of Abbott ID NOW COVID-19 rapid nucleic acid amplification test in nasopharyngeal swabs transported in viral media and dry nasal swabs, in a New York City academic institution

2020 ◽  
Author(s):  
Atreyee Basu ◽  
Tatyana Zinger ◽  
Kenneth Inglima ◽  
Kar-mun Woo ◽  
Onome Atie ◽  
...  
Keyword(s):  
New York ◽  
The United States ◽  
Turnaround Time ◽  
Nucleic Acid Amplification ◽  
Molecular Diagnostic ◽  
Sample Type ◽  
Negative Results ◽  
Viral Transport ◽  
Recent Emergence ◽  
Nasal Swabs

AbstractThe recent emergence of the SARS-CoV-2 pandemic has posed formidable challenges for clinical laboratories seeking reliable laboratory diagnostic confirmation. The swift advance of the crisis in the United States has led to Emergency Use Authorization (EUA) facilitating the availability of molecular diagnostic assays without the more rigorous examination to which tests are normally subjected prior to FDA approval. Our laboratory currently uses two real time RT-PCR platforms, the Roche Cobas SARS-CoV2 and the Cepheid Xpert Xpress SARS-CoV-2. Both platforms demonstrate comparable performance; however, the run times for each assay are 3.5 hours and 45 minutes, respectively. In search for a platform with shorter turnaround time, we sought to evaluate the recently released Abbott ID NOW COVID-19 assay which is capable of producing positive results in as little as 5 minutes. We present here the results of comparisons between Abbott ID NOW COVID-19 and Cepheid Xpert Xpress SARS-CoV-2 using nasopharyngeal swabs transported in viral transport media and comparisons between Abbott ID NOW COVID-19 and Cepheid Xpert Xpress SARS-CoV-2 using nasopharyngeal swabs transported in viral transport media for Cepheid and dry nasal swabs for Abbott ID NOW. Regardless of method of collection and sample type, Abbott ID NOW COVID-19 had negative results in a third of the samples that tested positive by Cepheid Xpert Xpress when using nasopharyngeal swabs in viral transport media and 45% when using dry nasal swabs.

Cultural Competence Needed to Distinguish Disorder from Difference: Beyond Kumbaya

2015 ◽  
Vol 22 (2) ◽  
pp. 64-76 ◽  
Author(s):  
Catherine J. Crowley ◽  
Kristin Guest ◽  
Kenay Sudler
Keyword(s):  
New York ◽  
New York City ◽  
Public Schools ◽  
Cultural Competence ◽  
York City ◽  
Cultural Sensitivity ◽  
Graduate Program ◽  
Language Disorder ◽  
New York State ◽  
Deep Understanding

What does it mean to have true cultural competence as an speech-language pathologist (SLP)? In some areas of practice it may be enough to develop a perspective that values the expectations and identity of our clients and see them as partners in the therapeutic process. But when clinicians are asked to distinguish a language difference from a language disorder, cultural sensitivity is not enough. Rather, in these cases, cultural competence requires knowledge and skills in gathering data about a student's cultural and linguistic background and analyzing the student's language samples from that perspective. This article describes one American Speech-Language-Hearing Association (ASHA)-accredited graduate program in speech-language pathology and its approach to putting students on the path to becoming culturally competent SLPs, including challenges faced along the way. At Teachers College, Columbia University (TC) the program infuses knowledge of bilingualism and multiculturalism throughout the curriculum and offers bilingual students the opportunity to receive New York State certification as bilingual clinicians. Graduate students must demonstrate a deep understanding of the grammar of Standard American English and other varieties of English particularly those spoken in and around New York City. Two recent graduates of this graduate program contribute their perspectives on continuing to develop cultural competence while working with diverse students in New York City public schools.

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