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Article: Laboratory Evaluation Links Some False-Positive COVID-19 Antigen Test Results Observed in a Field Study to a Specific Lot of Test Strips.

Carter, Alyssa M / Viloria Winnett, Alexander / Romano, Anna E / Akana, Reid / Shelby, Natasha / Ismagilov, Rustem F

2023 Volume 10, Issue 1, Page(s) ofac701

Abstract: During a household-transmission field study using COVID-19 antigen rapid diagnostic tests (Ag-RDT), a common test strip lot was identified among 3 participants with false-positive results. In blinded laboratory evaluation, this lot exhibited a ... ...

Abstract	During a household-transmission field study using COVID-19 antigen rapid diagnostic tests (Ag-RDT), a common test strip lot was identified among 3 participants with false-positive results. In blinded laboratory evaluation, this lot exhibited a significantly higher false-positive rate than other lots. Because a positive Ag-RDT result often prompts action, reducing lot-specific false positives can maintain confidence and actionability of true-positive Ag-RDT results.
Language	English
Publishing date	2023-01-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	2757767-3
ISSN	2328-8957
ISSN	2328-8957
DOI	10.1093/ofid/ofac701
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Despite Extensive Pollinator Sharing, Invasive Blackberry has Negligible Impacts on Reproductive Success of a Rare Native Wildflower

Shelby, Natasha / Peterson Merrill A

Northwest science. 2015 Jan., v. 89, no. 1

2015

Abstract: Plant invasions have the potential to disrupt community dynamics and impair essential ecosystem services, including the pollination of native flowers. Invaders most likely to invoke pollinator competition are characterized by conspicuous, resource-rich ... ...

Abstract	Plant invasions have the potential to disrupt community dynamics and impair essential ecosystem services, including the pollination of native flowers. Invaders most likely to invoke pollinator competition are characterized by conspicuous, resource-rich blooms and long flowering periods, while the natives most likely to be impacted are obligate out-crossers that are sensitive to disturbance or locally rare. We investigated the effects of a widespread showy invader of the Pacific Northwest, Rubus armeniacus (Himalayan blackberry), on an imperiled endemic wildflower, Sidalcea hendersonii. We observed pollinators, quantified pollen deposition and conducted pollen-supplementation experiments on S. hendersonii plants growing at three distances (1 m, 15 m and 50 m) from well-established blackberry patches in five adjacent field plots. Individual R. armeniacus flowers received more than three times as many total visits as S. hendersonii inflorescences; however, there was minimal overlap between the pollinator assemblages visiting the two species. R. armeniacus pollen was present on 67% of S. hendersonii stigmas; however, there was no significant relationship between distance and invasive pollen deposition or distance and natural seed set. Pollen-supplementation experiments revealed that S. hendersonii was moderately pollen-limited at all distances, and reproductive output was actually higher at the distance treatment closest to the invader, suggesting a positive proximity effect unrelated to pollination. Thus, although inconstant pollinator foraging and prodigious heterospecific pollen deposition suggest R. armeniacus influences pollinator interactions, it does not appear that the invader directly limits the reproductive success of S. hendersonii.
Keywords	blackberries ; ecological invasion ; ecosystem services ; flowers ; foraging ; pollen ; pollination ; pollinators ; reproductive performance ; reproductive success ; Rubus armeniacus ; seed set ; Sidalcea ; wild flowers
Language	English
Dates of publication	2015-01
Size	p. 47-57.
Publishing place	Washington State University Press
Document type	Article
ZDB-ID	953337-0
ISSN	0029-344X
ISSN	0029-344X
DOI	10.3955%2F046.089.0104
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Index cases first identified by nasal-swab rapid COVID-19 tests had more transmission to household contacts than cases identified by other test types.

Ji, Jenny / Viloria Winnett, Alexander / Shelby, Natasha / Reyes, Jessica A / Schlenker, Noah W / Davich, Hannah / Caldera, Saharai / Tognazzini, Colten / Goh, Ying-Ying / Feaster, Matt / Ismagilov, Rustem F

PloS one

2023 Volume 18, Issue 10, Page(s) e0292389

Abstract: At-home rapid COVID-19 tests in the U.S. utilize nasal-swab specimens and require high viral loads to reliably give positive results. Longitudinal studies from the onset of infection have found infectious virus can present in oral specimens days before ... ...

Abstract	At-home rapid COVID-19 tests in the U.S. utilize nasal-swab specimens and require high viral loads to reliably give positive results. Longitudinal studies from the onset of infection have found infectious virus can present in oral specimens days before nasal. Detection and initiation of infection-control practices may therefore be delayed when nasal-swab rapid tests are used, resulting in greater transmission to contacts. We assessed whether index cases first identified by rapid nasal-swab COVID-19 tests had more transmission to household contacts than index cases who used other test types (tests with higher analytical sensitivity and/or non-nasal specimen types). In this observational cohort study, 370 individuals from 85 households with a recent COVID-19 case were screened at least daily by RT-qPCR on one or more self-collected upper-respiratory specimen types. A two-level random intercept model was used to assess the association between the infection outcome of household contacts and each covariable (household size, race/ethnicity, age, vaccination status, viral variant, infection-control practices, and whether a rapid nasal-swab test was used to initially identify the household index case). Transmission was quantified by adjusted secondary attack rates (aSAR) and adjusted odds ratios (aOR). An aSAR of 53.6% (95% CI 38.8-68.3%) was observed among households where the index case first tested positive by a rapid nasal-swab COVID-19 test, which was significantly higher than the aSAR for households where the index case utilized another test type (27.2% 95% CI 19.5-35.0%, P = 0.003 pairwise comparisons of predictive margins). We observed an aOR of 4.90 (95% CI 1.65-14.56) for transmission to household contacts when a nasal-swab rapid test was used to identify the index case, compared to other test types. Use of nasal-swab rapid COVID-19 tests for initial detection of infection and initiation of infection control may be less effective at limiting transmission to household contacts than other test types.
MeSH term(s)	Humans ; COVID-19/diagnosis ; COVID-19/epidemiology ; SARS-CoV-2 ; Family Characteristics ; Cohort Studies ; Nose
Language	English
Publishing date	2023-10-05
Publishing country	United States
Document type	Observational Study ; 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.0292389
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Daily SARS-CoV-2 Nasal Antigen Tests Miss Infected and Presumably Infectious People Due to Viral Load Differences among Specimen Types.

Viloria Winnett, Alexander / Akana, Reid / Shelby, Natasha / Davich, Hannah / Caldera, Saharai / Yamada, Taikun / Reyna, John Raymond B / Romano, Anna E / Carter, Alyssa M / Kim, Mi Kyung / Thomson, Matt / Tognazzini, Colten / Feaster, Matthew / Goh, Ying-Ying / Chew, Yap Ching / Ismagilov, Rustem F

Microbiology spectrum

2023 Volume 11, Issue 4, Page(s) e0129523

Abstract: In a recent household transmission study of SARS-CoV-2, we found extreme differences in SARS-CoV-2 viral loads among paired saliva, anterior nares swab (ANS), and oropharyngeal swab specimens collected from the same time point. We hypothesized these ... ...

Abstract	In a recent household transmission study of SARS-CoV-2, we found extreme differences in SARS-CoV-2 viral loads among paired saliva, anterior nares swab (ANS), and oropharyngeal swab specimens collected from the same time point. We hypothesized these differences may hinder low-analytical-sensitivity assays (including antigen rapid diagnostic tests [Ag-RDTs]) by using a single specimen type (e.g., ANS) from reliably detecting infected and infectious individuals. We evaluated daily at-home ANS Ag-RDTs (Quidel QuickVue) in a cross-sectional analysis of 228 individuals and a longitudinal analysis (throughout infection) of 17 individuals enrolled early in the course of infection. Ag-RDT results were compared to reverse transcription-quantitative PCR (RT-qPCR) results and high, presumably infectious viral loads (in each, or any, specimen type). The ANS Ag-RDT correctly detected only 44% of time points from infected individuals on cross-sectional analysis, and this population had an inferred limit of detection of 7.6 × 10
MeSH term(s)	Humans ; Cross-Sectional Studies ; Longitudinal Studies ; SARS-CoV-2 ; Viral Load ; COVID-19/diagnosis
Language	English
Publishing date	2023-06-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.01295-23
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Extreme differences in SARS-CoV-2 viral loads among respiratory specimen types during presumed pre-infectious and infectious periods.

PNAS nexus

2023 Volume 2, Issue 3, Page(s) pgad033

Abstract: SARS-CoV-2 viral-load measurements from a single-specimen type are used to establish diagnostic strategies, interpret clinical-trial results for vaccines and therapeutics, model viral transmission, and understand virus-host interactions. However, ... ...

Abstract	SARS-CoV-2 viral-load measurements from a single-specimen type are used to establish diagnostic strategies, interpret clinical-trial results for vaccines and therapeutics, model viral transmission, and understand virus-host interactions. However, measurements from a single-specimen type are implicitly assumed to be representative of other specimen types. We quantified viral-load timecourses from individuals who began daily self-sampling of saliva, anterior-nares (nasal), and oropharyngeal (throat) swabs before or at the incidence of infection with the Omicron variant. Viral loads in different specimen types from the same person at the same timepoint exhibited extreme differences, up to 10
Language	English
Publishing date	2023-03-14
Publishing country	England
Document type	Journal Article
ISSN	2752-6542
ISSN (online)	2752-6542
DOI	10.1093/pnasnexus/pgad033
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The ratio between SARS-CoV-2 RNA viral load and culturable viral titer differs depending on stage of infection

Porter, Michael K. / Viloria Winnett, Alexander / Hao, Linhui / Shelby, Natasha / Reyes, Jessica A. / Schlenker, Noah W. / Romano, Anna E. / Tognazzini, Colton / Feaster, Matthew / Goh, Ying-Ying / Gale, Michael / Ismagilov, Rustem F.

medRxiv

Abstract: Analysis of incident, longitudinal RNA viral loads in saliva and nasal swabs and culturable viral titers in nasal swabs collected twice-daily by a tricenarian male infected with SARS-CoV-2 revealed the ratio between viral load and viral titer can be five ...

Abstract	Analysis of incident, longitudinal RNA viral loads in saliva and nasal swabs and culturable viral titers in nasal swabs collected twice-daily by a tricenarian male infected with SARS-CoV-2 revealed the ratio between viral load and viral titer can be five orders of magnitude higher during early infection than late infection.
Keywords	covid19
Language	English
Publishing date	2023-07-12
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2023.07.06.23292300
Database	COVID19

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Article ; Online: Index Cases First Identified by Nasal-Swab Rapid COVID-19 Tests Had More Transmission to Household Contacts Than Cases Identified by Other Test Types

Ji, Jenny / Viloria Winnett, Alexander / Shelby, Natasha / Reyes, Jessica A. / Schlenker, Noah W. / Davich, Hannah / Caldera, Saharai / Tognazzini, Colten / Goh, Ying-Ying / Feaster, Matthew / Ismagilov, Rustem F.

medRxiv

Abstract: Importance: At-home rapid COVID-19 tests utilize nasal-swab specimens and require high viral loads to reliably give positive results. Longitudinal studies from the onset of infection have found infectious virus can present in oral specimens days before ... ...

Abstract	Importance: At-home rapid COVID-19 tests utilize nasal-swab specimens and require high viral loads to reliably give positive results. Longitudinal studies from the onset of infection have found infectious virus can present in oral specimens days before nasal. Detection and initiation of infection-control practices may therefore be delayed when nasal-swab rapid tests are used, resulting in greater exposure and transmission to contacts. Objective: We assessed whether index cases first identified by rapid nasal-swab COVID-19 tests had more transmission to household contacts than index cases who used other test types (tests with higher analytical sensitivity but longer turnaround times, and/or that utilize non-nasal specimen types). Design: In this observational cohort study, members of households with a recent COVID-19 case were screened for infection at least daily by RT-qPCR on one or more self-collected upper-respiratory specimen types. Participants reported demographic/medical information (including COVID-19 testing), symptom and exposure information, and household infection-control practices. A two-level random intercept model was used to assess the association between the infection outcome of household contacts and each covariable (household size, race/ethnicity, age, vaccination status, viral variant, infection-control practices, and whether a rapid nasal-swab test was used to initially identify the household index case). Setting: Southern California, September 2020-June 2021 and November 2021-March 2022. Participants: Cohort of 370 individuals from 85 households. Main Outcome(s) and Measure(s): Transmission was quantified by adjusted secondary attack rates (aSAR) and adjusted odds ratios (aOR). Results: An aSAR of 53.6% (95%CI 38.8-68.3%) was observed among households where the index case first tested positive by a rapid nasal-swab COVID-19 test, which was significantly higher than the aSAR for households where the index case utilized another test type (27.2% [19.5-35.0%], P=0.003 pairwise comparisons of predictive margins). We observed an aOR of 4.90 (95%CI 1.65-14.56) for transmission to household contacts when a nasal-swab rapid test was used to identify the index case, compared to other test types. Conclusions and Relevance: Use of nasal-swab rapid COVID-19 tests for initial detection of infection and initiation of infection control may not limit transmission as well as other test types.
Keywords	covid19
Language	English
Publishing date	2023-03-10
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2023.03.09.23286855
Database	COVID19

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Article ; Online: Morning SARS-CoV-2 Testing Yields Better Detection of Infection Due to Higher Viral Loads in Saliva and Nasal Swabs upon Waking.

Viloria Winnett, Alexander / Porter, Michael K / Romano, Anna E / Savela, Emily S / Akana, Reid / Shelby, Natasha / Reyes, Jessica A / Schlenker, Noah W / Cooper, Matthew M / Carter, Alyssa M / Ji, Jenny / Barlow, Jacob T / Tognazzini, Colten / Feaster, Matthew / Goh, Ying-Ying / Ismagilov, Rustem F

Microbiology spectrum

2022 Volume 10, Issue 6, Page(s) e0387322

Abstract: Optimizing specimen collection methods to achieve the most reliable SARS-CoV-2 detection for a given diagnostic sensitivity would improve testing and minimize COVID-19 outbreaks. From September 2020 to April 2021, we performed a household-transmission ... ...

Abstract	Optimizing specimen collection methods to achieve the most reliable SARS-CoV-2 detection for a given diagnostic sensitivity would improve testing and minimize COVID-19 outbreaks. From September 2020 to April 2021, we performed a household-transmission study in which participants self-collected specimens every morning and evening throughout acute SARS-CoV-2 infection. Seventy mildly symptomatic participants collected saliva, and of those, 29 also collected nasal swab specimens. Viral load was quantified in 1,194 saliva and 661 nasal swab specimens using a high-analytical-sensitivity reverse transcription-quantitative PCR (RT-qPCR) assay. Viral loads in both saliva and nasal swab specimens were significantly higher in morning-collected specimens than in evening-collected specimens after symptom onset. This aspect of the biology of SARS-CoV-2 infection has implications for diagnostic testing. We infer that morning collection would have resulted in significantly improved detection and that this advantage would be most pronounced for tests with low to moderate analytical sensitivity. Collecting specimens for COVID-19 testing in the morning offers a simple and low-cost improvement to clinical diagnostic sensitivity of low- to moderate-analytical-sensitivity tests.
MeSH term(s)	Humans ; SARS-CoV-2 ; COVID-19/diagnosis ; COVID-19 Testing ; Saliva ; Clinical Laboratory Techniques/methods ; Viral Load ; Specimen Handling/methods
Language	English
Publishing date	2022-10-26
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.03873-22
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: SARS-CoV-2 Viral Load in Saliva Rises Gradually and to Moderate Levels in Some Humans.

Winnett, Alexander / Cooper, Matthew M / Shelby, Natasha / Romano, Anna E / Reyes, Jessica A / Ji, Jenny / Porter, Michael K / Savela, Emily S / Barlow, Jacob T / Akana, Reid / Tognazzini, Colten / Feaster, Matthew / Goh, Ying-Ying / Ismagilov, Rustem F

medRxiv : the preprint server for health sciences

2020

Abstract: Transmission of SARS-CoV-2 in community settings often occurs before symptom onset, therefore testing strategies that can reliably detect people in the early phase of infection are urgently needed. Early detection of SARS-CoV-2 infection is especially ... ...

Abstract	Transmission of SARS-CoV-2 in community settings often occurs before symptom onset, therefore testing strategies that can reliably detect people in the early phase of infection are urgently needed. Early detection of SARS-CoV-2 infection is especially critical to protect vulnerable populations who require frequent interactions with caretakers. Rapid COVID-19 tests have been proposed as an attractive strategy for surveillance, however a limitation of most rapid tests is their low sensitivity. Low-sensitivity tests are comparable to high sensitivity tests in detecting early infections when two assumptions are met: (1) viral load rises quickly (within hours) after infection and (2) viral load reaches and sustains high levels (>10
Language	English
Publishing date	2020-12-11
Publishing country	United States
Document type	Preprint
DOI	10.1101/2020.12.09.20239467
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Quantitative SARS-CoV-2 viral-load curves in paired saliva and nasal swabs inform appropriate respiratory sampling site and analytical test sensitivity required for earliest viral detection.

Savela, Emily S / Winnett, Alexander / Romano, Anna E / Porter, Michael K / Shelby, Natasha / Akana, Reid / Ji, Jenny / Cooper, Matthew M / Schlenker, Noah W / Reyes, Jessica A / Carter, Alyssa M / Barlow, Jacob T / Tognazzini, Colten / Feaster, Matthew / Goh, Ying-Ying / Ismagilov, Rustem F

medRxiv : the preprint server for health sciences

2021

Abstract: Early detection of SARS-CoV-2 infection is critical to reduce asymptomatic and pre-symptomatic transmission, curb the spread of variants by travelers, and maximize treatment efficacy. Low-sensitivity nasal-swab testing (antigen and some nucleic-acid- ... ...

Abstract	Early detection of SARS-CoV-2 infection is critical to reduce asymptomatic and pre-symptomatic transmission, curb the spread of variants by travelers, and maximize treatment efficacy. Low-sensitivity nasal-swab testing (antigen and some nucleic-acid-amplification tests) is commonly used for surveillance and symptomatic testing, but the ability of low-sensitivity nasal-swab tests to detect the earliest stages of infection has not been established. In this case-ascertained study, initially-SARS-CoV-2-negative household contacts of individuals diagnosed with COVID-19 prospectively self-collected paired anterior-nares nasal-swab and saliva samples twice daily for viral-load quantification by high-sensitivity RT-qPCR and digital-RT-PCR assays. We captured viral-load profiles from the incidence of infection for seven individuals and compared diagnostic sensitivities between respiratory sites. Among unvaccinated persons, high-sensitivity saliva testing detected infection up to 4.5 days before viral loads in nasal swabs reached the limit of detection of low-sensitivity nasal-swab tests. For most participants, nasal swabs reached higher peak viral loads than saliva, but were undetectable or at lower loads during the first few days of infection. High-sensitivity saliva testing was most reliable for earliest detection. Our study illustrates the value of acquiring early (within hours after a negative high-sensitivity test) viral-load profiles to guide the appropriate analytical sensitivity and respiratory site for detecting earliest infections. Such data are challenging to acquire but critical to design optimal testing strategies in the current pandemic and will be required for responding to future viral pandemics. As new variants and viruses emerge, up-to-date data on viral kinetics are necessary to adjust testing strategies for reliable early detection of infections.
Language	English
Publishing date	2021-08-26
Publishing country	United States
Document type	Preprint
DOI	10.1101/2021.04.02.21254771
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