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1.
PLoS One ; 16(12): e0261230, 2021.
Article in English | MEDLINE | ID: covidwho-1630984

ABSTRACT

The systematic screening of asymptomatic and pre-symptomatic individuals is a powerful tool for controlling community transmission of infectious disease on college campuses. Faced with a paucity of testing in the beginning of the COVID-19 pandemic, many universities developed molecular diagnostic laboratories focused on SARS-CoV-2 diagnostic testing on campus and in their broader communities. We established the UC Santa Cruz Molecular Diagnostic Lab in early April 2020 and began testing clinical samples just five weeks later. Using a clinically-validated laboratory developed test (LDT) that avoided supply chain constraints, an automated sample pooling and processing workflow, and a custom laboratory information management system (LIMS), we expanded testing from a handful of clinical samples per day to thousands per day with the testing capacity to screen our entire campus population twice per week. In this report we describe the technical, logistical, and regulatory processes that enabled our pop-up lab to scale testing and reporting capacity to thousands of tests per day.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , Clinical Laboratory Techniques/methods , Diagnostic Tests, Routine/methods , Mass Screening/methods , Pandemics/prevention & control , Diagnostic Screening Programs , Humans , Universities
2.
J Virol Methods ; 300: 114429, 2022 02.
Article in English | MEDLINE | ID: covidwho-1630206

ABSTRACT

The rapid spread of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has led the world to a pandemic. Therefore, rapid, sensitive, and reproducible diagnostic tests are essential to indicate which measures should be taken during pandemics. We retrospectively tested unextracted nasopharyngeal samples from consecutive patients with suspected SARS-CoV-2 infection (n = 334), and compared two different Ct cut-off values for interpretation of results using a modified Allplex protocol. Its performance was evaluated using the USA Centers for Disease Control and Prevention (CDC) as reference. The reduction on Ct cut-off to 35 increased the test NPA from 79.65 to 88.00 %, reducing the number of false positives, from 10.48 to 6.29 %, resulting in an almost perfect agreement between the Allplex and the CDC protocol (Cohen's Kappa coefficient = 0.830 ± 0.032). This study demonstrates that the Seegene Allplex™ 2019-nCoV protocol skipping the viral RNA extraction step using the Ct cut-off of 35 is a rapid and efficient method to detect SARS-CoV-2 in nasopharyngeal samples.


Subject(s)
COVID-19 , SARS-CoV-2 , Diagnostic Tests, Routine , Humans , Nasopharynx , RNA, Viral/genetics , Retrospective Studies , Sensitivity and Specificity
3.
Nat Commun ; 13(1): 236, 2022 01 11.
Article in English | MEDLINE | ID: covidwho-1621241

ABSTRACT

Healthcare facilities are vulnerable to SARS-CoV-2 introductions and subsequent nosocomial outbreaks. Antigen rapid diagnostic testing (Ag-RDT) is widely used for population screening, but its health and economic benefits as a reactive response to local surges in outbreak risk are unclear. We simulate SARS-CoV-2 transmission in a long-term care hospital with varying COVID-19 containment measures in place (social distancing, face masks, vaccination). Across scenarios, nosocomial incidence is reduced by up to 40-47% (range of means) with routine symptomatic RT-PCR testing, 59-63% with the addition of a timely round of Ag-RDT screening, and 69-75% with well-timed two-round screening. For the latter, a delay of 4-5 days between the two screening rounds is optimal for transmission prevention. Screening efficacy varies depending on test sensitivity, test type, subpopulations targeted, and community incidence. Efficiency, however, varies primarily depending on underlying outbreak risk, with health-economic benefits scaling by orders of magnitude depending on the COVID-19 containment measures in place.


Subject(s)
COVID-19 Serological Testing/methods , COVID-19/diagnosis , COVID-19/epidemiology , Cross Infection/diagnosis , Cross Infection/epidemiology , Disease Outbreaks , SARS-CoV-2 , Antigens, Viral , COVID-19/prevention & control , COVID-19/transmission , Cost-Benefit Analysis , Cross Infection/prevention & control , Cross Infection/transmission , Diagnostic Tests, Routine , Epidemiological Monitoring , Hospitals , Humans , Risk Factors , Vaccination
4.
PLoS One ; 16(12): e0261778, 2021.
Article in English | MEDLINE | ID: covidwho-1613357

ABSTRACT

Many CRISPR/Cas platforms have been established for the detection of SARS-CoV-2. But the detection platform of the variants of SARS-CoV-2 is scarce because its specificity is very challenging to achieve for those with only one or a few nucleotide(s) differences. Here, we report for the first time that chimeric crRNA could be critical in enhancing the specificity of CRISPR-Cas12a detecting of N501Y, which is shared by Alpha, Beta, Gamma, and Mu variants of SARS-CoV-2 without compromising its sensitivity. This strategy could also be applied to detect other SARS-CoV-2 variants that differ only one or a few nucleotide(s) differences.


Subject(s)
COVID-19/diagnosis , Nucleic Acid Amplification Techniques/methods , SARS-CoV-2/genetics , COVID-19/genetics , CRISPR-Cas Systems/genetics , DNA Primers/genetics , Diagnostic Tests, Routine/methods , Humans , Mutation/genetics , RNA, Guide/genetics , RNA, Guide/metabolism , Sensitivity and Specificity
5.
ACS Appl Mater Interfaces ; 14(2): 2522-2533, 2022 Jan 19.
Article in English | MEDLINE | ID: covidwho-1606881

ABSTRACT

Electrochemical detection in complex biofluids is a long-standing challenge as electrode biofouling hampers its sensing performance and commercial translation. To overcome this drawback, pyrolyzed paper as porous electrode coupled with the drop casting of an off-the-shelf polysorbate, that is, Tween 20 (T20), is described here by taking advantage of the in situ formation of a hydrophilic nanocoating (2 nm layer of T20). The latter prevents biofouling while providing the capillarity of samples through paper pores, leveraging redox reactions across both only partially fouled and fresh electrodic surfaces with increasing detection areas. The nanometric thickness of this blocking layer is also essential by not significantly impairing the electron-transfer kinetics. These phenomena behave synergistically to enhance the sensibility that further increases over long-term exposures (4 h) in biological fluids. While the state-of-the-art antibiofouling strategies compromise the sensibility, this approach leads to peak currents that are up to 12.5-fold higher than the original currents after 1 h exposure to unprocessed human plasma. Label-free impedimetric immunoassays through modular bioconjugation by directly anchoring spike protein on gold nanoparticles are also allowed, as demonstrated for the COVID-19 screening of patient sera. The scalability and simplicity of the platform combined with its unique ability to operate in biofluids with enhanced sensibility provide the generation of promising biosensing technologies toward real-world applications in point-of-care diagnostics, mass testing, and in-home monitoring of chronic diseases.


Subject(s)
Antibodies, Viral/immunology , Biosensing Techniques/methods , COVID-19 Serological Testing/methods , Diagnostic Tests, Routine/methods , Recombinant Proteins/immunology , Spike Glycoprotein, Coronavirus/immunology , Early Diagnosis , Humans , Sensitivity and Specificity
6.
ACS Appl Mater Interfaces ; 14(2): 2501-2509, 2022 Jan 19.
Article in English | MEDLINE | ID: covidwho-1605760

ABSTRACT

Rapid serology platforms are essential in disease pandemics for a variety of applications, including epidemiological surveillance, contact tracing, vaccination monitoring, and primary diagnosis in resource-limited areas. Laboratory-based enzyme-linked immunosorbent assay (ELISA) platforms are inherently multistep processes that require trained personnel and are of relatively limited throughput. As an alternative, agglutination-based systems have been developed; however, they rely on donor red blood cells and are not yet available for high-throughput screening. Column agglutination tests are a mainstay of pretransfusion blood typing and can be performed at a range of scales, ranging from manual through to fully automated testing. Here, we describe a column agglutination test using colored microbeads coated with recombinant SARS-CoV-2 spike protein that agglutinates when incubated with serum samples collected from patients recently infected with SARS-CoV-2. After confirming specific agglutination, we optimized centrifugal force and time to distinguish samples from uninfected vs SARS-CoV-2-infected individuals and then showed concordant results against ELISA for 22 clinical samples, and also a set of serial bleeds from one donor at days 6-10 postinfection. Our study demonstrates the use of a simple, scalable, and rapid diagnostic platform that can be tailored to detect antibodies raised against SARS-CoV-2 and can be easily integrated with established laboratory frameworks worldwide.


Subject(s)
Agglutination Tests/methods , Antibodies, Viral/immunology , COVID-19 Serological Testing/methods , Diagnostic Tests, Routine/methods , Recombinant Proteins/immunology , Spike Glycoprotein, Coronavirus/immunology , Early Diagnosis , Humans , Sensitivity and Specificity
8.
Medicine (Baltimore) ; 100(51): e28398, 2021 Dec 23.
Article in English | MEDLINE | ID: covidwho-1598050

ABSTRACT

ABSTRACT: Hospital-wide screenings for coronavirus disease (COVID-19) are important to identify healthcare workers at risk of exposure. However, the currently available diagnostic tests are expensive or only identify past infection. Therefore, this single-center observational study aimed to assess the positivity rate of hospital-wide antigen screening tests for COVID-19 and evaluate clinical factors associated with antigen positivity during a COVID-19 institutional outbreak in Sapporo, Japan.We analyzed the data of 1615 employees who underwent salivary or nasal swab antigen tests on November 18, 2020, to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Laboratory confirmation using reverse transcriptase polymerase chain reaction was performed for those with positive viral serology. The demographic characteristics, job titles, and risk of contact with COVID-19 patients were compared between employees with and without COVID-19.A total of 19 employees (1.2%) tested positive for the SARS-CoV-2 antigen. The positivity rate was high among rehabilitation therapists (2.1%) and employees in the low-risk contact group (6.1%). Although there was no association between the job titles and the seropositivity rate, those in the low-risk contact group had an increased risk of testing positive for the viral antigen (odds ratio, 8.67; 95% confidence interval, 3.30-22.8).The antigen positivity rate was low during the hospital outbreak, suggesting that risk assessment of exposure to COVID-19 patients may provide more useful information than using job titles to identify infected health care providers.


Subject(s)
COVID-19 , Health Personnel , Antigens, Viral/analysis , COVID-19/diagnosis , COVID-19 Testing , Diagnostic Tests, Routine , Hospitals , Humans , Japan/epidemiology , SARS-CoV-2 , Tertiary Care Centers
9.
J Am Dent Assoc ; 153(1): 14, 2022 01.
Article in English | MEDLINE | ID: covidwho-1597659
10.
Sci Rep ; 11(1): 24507, 2021 12 30.
Article in English | MEDLINE | ID: covidwho-1597358

ABSTRACT

Diagnostic tests that detect antibodies (AB) against SARS-CoV-2 for evaluation of seroprevalence and guidance of health care measures are important tools for managing the COVID-19 pandemic. Current tests have certain limitations with regard to turnaround time, costs and availability, particularly in point-of-care (POC) settings. We established a hemagglutination-based AB test that is based on bi-specific proteins which contain a dromedary-derived antibody (nanobody) binding red blood cells (RBD) and a SARS-CoV-2-derived antigen, such as the receptor-binding domain of the Spike protein (Spike-RBD). While the nanobody mediates swift binding to RBC, the antigen moiety directs instantaneous, visually apparent hemagglutination in the presence of SARS-CoV-2-specific AB generated in COVID-19 patients or vaccinated individuals. Method comparison studies with assays cleared by emergency use authorization demonstrate high specificity and sensitivity. To further increase objectivity of test interpretation, we developed an image analysis tool based on digital image acquisition (via a cell phone) and a machine learning algorithm based on defined sample-training and -validation datasets. Preliminary data, including a small clinical study, provides proof of principle for test performance in a POC setting. Together, the data support the interpretation that this AB test format, which we refer to as 'NanoSpot.ai', is suitable for POC testing, can be manufactured at very low costs and, based on its generic mode of action, can likely be adapted to a variety of other pathogens.


Subject(s)
Antibodies, Viral/blood , COVID-19 Serological Testing/methods , Diagnostic Tests, Routine/methods , Hemagglutination Tests/methods , Point-of-Care Testing , Spike Glycoprotein, Coronavirus/immunology , Humans , Proof of Concept Study
11.
PLoS One ; 16(12): e0261956, 2021.
Article in English | MEDLINE | ID: covidwho-1597233

ABSTRACT

A direct, real-time reverse transcriptase PCR test on pooled saliva was validated in 2,786 participants against oropharyngeal swabs. Among asymptomatic/pre-symptomatic participants, the test was found to be in 99.21% agreement and 45% more sensitive than contemporaneous oropharyngeal swabs. The test was then used for surveillance testing on 44,242 saliva samples from asymptomatic participants. Those whose saliva showed evidence of SARS-CoV-2 within 50 cycles of amplification were referred for confirmatory testing, with 87% of those tested by nasal swab within 72 hours receiving a positive diagnostic result on Abbott ID NOW or real-time PCR platforms. Median Ct values on the saliva PCR for those with a positive and negative confirmatory tests was 30.67 and 35.92 respectively, however, binary logistic regression analysis of the saliva Ct values indicates that Ct thresholds as high as 47 may be useful in a surveillance setting. Overall, data indicate that direct RT-PCR testing of pooled saliva samples is an effective method of SARS-CoV-2 surveillance.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , Carrier State/diagnosis , Diagnostic Tests, Routine/methods , Real-Time Polymerase Chain Reaction/methods , Saliva/virology , Humans , Sensitivity and Specificity
12.
Diagn Microbiol Infect Dis ; 102(2): 115591, 2022 Feb.
Article in English | MEDLINE | ID: covidwho-1596631

ABSTRACT

Testing for SARS-CoV-2 in resource-poor settings remains a considerable challenge. Gold standard nucleic acid tests are expensive and depend on availability of expensive equipment and highly trained laboratory staff. More affordable and easier rapid antigen tests are an attractive alternative. This study assessed field performance of such a test in western Kenya. We conducted a prospective multi-facility field evaluation study of NowCheck COVID-19 Ag-RDT compared to gold standard PCR. Two pairs of oropharyngeal and nasopharyngeal swabs were collected for comparative analysis. With 997 enrolled participants the Ag-RDT had a sensitivity 71.5% (63.2-78.6) and specificity of 97.5% (96.2-98.5) at cycle threshold value <40. Highest sensitivity of 87.7% (77.2-94.5) was observed in samples with cycle threshold values ≤30. NowCheck COVID-19 Ag-RDT performed well at multiple healthcare facilities in an African field setting. Operational specificity and sensitivity were close to WHO-recommended thresholds.


Subject(s)
Antigens, Viral/analysis , COVID-19 Serological Testing/methods , COVID-19/diagnosis , Nasopharynx/virology , Oropharynx/virology , SARS-CoV-2/immunology , Adult , Child , Cross-Sectional Studies , Developing Countries , Diagnostic Tests, Routine , Female , Humans , Kenya , Male , Middle Aged , Point-of-Care Testing , Prospective Studies , Sensitivity and Specificity
13.
Sci Rep ; 11(1): 24503, 2021 12 30.
Article in English | MEDLINE | ID: covidwho-1596506

ABSTRACT

It is partially unknown whether the immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection persists with time. To address this issue, we detected the presence of SARS-CoV-2 antibodies in different groups of individuals previously diagnosed with COVID-19 disease (group 1 and 2), or potentially exposed to SARS-CoV-2 infection (group 3 and 4), and in a representative group of individuals with limited environmental exposure to the virus due to lockdown restrictions (group 5). The primary outcome was specific anti-SARS-CoV-2 antibodies in the different groups assessed by qualitative and quantitative analysis at baseline, 3 and 6 months follow-up. The seroconversion rate at baseline test was 95% in group 1, 61% in group 2, 40% in group 3, 17% in group 4 and 3% in group 5. Multivariate logistic regression analysis revealed male gender, close COVID-19 contact and presence of COVID-19 related symptoms strongly associated with serological positivity. The percentage of positive individuals as assessed by the qualitative and quantitative tests was superimposable. At the quantitative test, the median level of SARS-CoV-2 antibody levels measured in positive cases retested at 6-months increased significantly from baseline. The study indicates that assessing antibody response to SARS-CoV-2 through qualitative and quantitative testing is a reliable disease surveillance tool.


Subject(s)
COVID-19 , Diagnostic Tests, Routine/methods , Occupational Exposure/statistics & numerical data , Pandemics , Antibodies, Viral/blood , COVID-19/epidemiology , COVID-19/immunology , Female , Humans , Male , Middle Aged , Risk Factors
14.
PLoS One ; 16(12): e0262159, 2021.
Article in English | MEDLINE | ID: covidwho-1596328

ABSTRACT

INTRODUCTION: GENECUBE® is a rapid molecular identification system, and previous studies demonstrated that GENECUBE® HQ SARS-CoV-2 showed excellent analytical performance for the detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) with nasopharyngeal samples. However, other respiratory samples have not been evaluated. METHODS: This prospective comparison between GENECUBE® HQ SARS-CoV-2 and reference real-time reverse transcriptase polymerase chain reaction (RT-PCR) was performed for the detection of SARS-CoV-2 using anterior nasal samples and saliva samples. Additionally, we evaluated a new rapid examination protocol using GENECUBE® HQ SARS-CoV-2 for the detection of SARS-CoV-2 with saliva samples. For the rapid protocol, in the preparation of saliva samples, purification and extraction processes were adjusted, and the total process time was shortened to approximately 35 minutes. RESULTS: For 359 anterior nasal samples, the total-, positive-, and negative concordance of the two assays was 99.7% (358/359), 98.1% (51/52), and 100% (307/307), respectively. For saliva samples, the total-, positive-, and negative concordance of the two assays was 99.6% (239/240), 100% (56/56), and 99.5% (183/184), respectively. With the new protocol, total-, positive-, and negative concordance of the two assays was 98.8% (237/240), 100% (56/56), and 98.4% (181/184), respectively. In all discordance cases, SARS-CoV-2 was detected by additional molecular examinations. CONCLUSION: GENECUBE® HQ SARS-CoV-2 provided high analytical performance for the detection of SARS-CoV-2 in anterior nasal samples and saliva samples.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , Diagnostic Tests, Routine/methods , Nasopharynx/virology , Pandemics , Saliva/virology , Humans , Prospective Studies
15.
PLoS One ; 16(12): e0261931, 2021.
Article in English | MEDLINE | ID: covidwho-1594058

ABSTRACT

BACKGROUND: Understanding the actual prevalence of COVID-19 transmission in the community is vital for strategic responses to the pandemic. This study aims to estimate the actual infection of COVID-19 through a seroprevalence survey and to predict infection fatality rate (IFR) in Tanjung Priok, the hardest-hit sub-district by the COVID-19 in Jakarta, Indonesia. METHODS: We conducted a venous blood sampling (phlebotomy) to 3,196 individuals in Tanjung Priok between Nov 23, 2020, and Feb 19, 2021 to detect their antibodies against SARS-CoV-2. Using an enumerator-administered questionnaire, we collected data on the respondents' demographic characteristics, COVID-19 test history, COVID-19 symptoms in the last 14 days, comorbidities, and protective behaviours during the last month. We employed descriptive analysis to estimate the seroprevalence and IFR. FINDINGS: The prevalence of Antibody against SARS-CoV-2 was 28.52% (95% CI 25.44-31.81%), with the result being higher in females than males (OR 1.20; 95% CI 1.02-1.42). By the end of the data collection (February 9, 2021), the cumulative cases of COVID-19 in Tanjung Priok were reported to be experienced by 9,861 people (2.4%). Those aged 45-65 were more likely to be seropositive than 15-19 years old (OR 1.42; 95% CI 1.05-1.92). Nearly one third (31%) of the subjects who developed at least one COVID-19 symptom in the last 14 days of the data collection were seropositive. The estimated IFR was 0.08% (95% CI 0.07-0.09), with a higher figure recorded in males (0.09; 95% CI 0.08-0.10) than females (0.07; 95% CI 0.06-0.08), and oldest age group (45-65) (0.21; 95% CI 0.18-0.23) than other younger groups. CONCLUSION: An under-reporting issue was found between the estimated COVID-19 seroprevalence and the reported cumulative cases in Tanjung Priok. More efforts are required to amplify epidemiological surveillance by the provincial and local governments.


Subject(s)
COVID-19/epidemiology , SARS-CoV-2/immunology , Seroepidemiologic Studies , Adolescent , Adult , Aged , Aged, 80 and over , Antibodies, Viral/analysis , Antibodies, Viral/blood , COVID-19/immunology , Child , Diagnostic Tests, Routine/methods , Female , Humans , Indonesia/epidemiology , Male , Middle Aged , Pandemics , SARS-CoV-2/pathogenicity
16.
Int J Infect Dis ; 115: 239-244, 2022 Feb.
Article in English | MEDLINE | ID: covidwho-1587627

ABSTRACT

BACKGROUND: In Yemen, initial surveillance of coronavirus disease 2019 (COVID-19) focused primarily on patients with symptoms or severe disease. The full spectrum of the disease remains unclear. To the best of the authors' knowledge, this is the first seroprevalence study performed in Yemen. METHODS: This cross-sectional investigation included 2001 participants from all age groups from four districts in Aden, southern Yemen. A multi-stage sampling method was used. Data were collected using a well-structured questionnaire, and blood samples were taken. Healgen COVID-19 IgG/IgM Rapid Diagnostic Test (RDT) Cassettes were used in all participants. All positive RDTs and 14% of negative RDTs underwent enzyme-linked immunosorbent assay (ELISA) testing (WANTAI SARS-CoV-2 Ab ELISA Kit) for confirmation. RESULTS: In total, 549 of 2001 participants were RDT positive and confirmed by ELISA, giving a prevalence of COVID-19 of 27.4%. The prevalence of immunoglobulin G was 25%. The prevalence of asymptomatic COVID-19 in the entire study group was 7.9%. The highest prevalence was observed in Al-Mansurah district (33.4%). Regarding sociodemographic factors, the prevalence of COVID-19 was significantly higher among females, housewives and subjects with a history of contact with a COVID-19 patient: 32%, 31% and 39%, respectively. CONCLUSION: This study found high prevalence of COVID-19 in the study population. Household transmission was common.


Subject(s)
COVID-19 , SARS-CoV-2 , Antibodies, Viral , Cross-Sectional Studies , Diagnostic Tests, Routine , Female , Humans , Immunoglobulin M , Seroepidemiologic Studies , Yemen/epidemiology
19.
Lancet Infect Dis ; 22(1): 17-18, 2022 01.
Article in English | MEDLINE | ID: covidwho-1586202
20.
Lancet Infect Dis ; 22(1): 16, 2022 01.
Article in English | MEDLINE | ID: covidwho-1586199
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