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1.
PLoS One ; 16(12): e0261230, 2021.
Article in English | MEDLINE | ID: covidwho-1581758

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 Comput Assist Tomogr ; 44(5): 627-632, 2020.
Article in English | MEDLINE | ID: covidwho-1501243

ABSTRACT

OBJECTIVE: To determine the predictive computed tomography (CT) and clinical features for diagnosis of COVID-19 pneumonia. METHODS: The CT and clinical data including were analyzed using univariate analysis and multinomial logistic regression, followed by receiver operating characteristic curve analysis. RESULTS: The factors including size of ground grass opacity (GGO), GGO with reticular and/or interlobular septal thickening, vascular enlargement, "tree-in-bud" opacity, centrilobular nodules, and stuffy or runny nose were associated with the 2 groups of viral pneumonia, as determined by univariate analysis (P < 0.05). Only GGO with reticular and/or interlobular septal thickening, centrilobular nodules, and stuffy or runny nose remained independent risk factors in multinomial logistic regression analysis. Receiver operating characteristic curve analysis showed that the area under curve of the obtained logistic regression model was 0.893. CONCLUSION: Computed tomography and clinical features including GGO with reticular and/or interlobular septal thickening, absence of centrilobular nodules, and absence of stuffy or runny nose are potential patients with COVID-19 pneumonia.


Subject(s)
Betacoronavirus , Clinical Laboratory Techniques/methods , Coronavirus Infections/diagnosis , Lung/diagnostic imaging , Pneumonia, Viral/diagnosis , Tomography, X-Ray Computed/methods , Adult , COVID-19 , COVID-19 Testing , Diagnosis, Differential , Female , Humans , Male , Middle Aged , Pandemics , Predictive Value of Tests , Reproducibility of Results , Retrospective Studies , SARS-CoV-2
3.
Hong Kong Med J ; 26(3): 176-183, 2020 06.
Article in English | MEDLINE | ID: covidwho-1468777

ABSTRACT

INTRODUCTION: This study evaluated the preparedness of family doctors during the early phase of the coronavirus disease 2019 (COVID-19) outbreak in Hong Kong. METHODS: All members of the Hong Kong College of Family Physicians were invited to participate in a cross-sectional online survey using a 20-item questionnaire to collect information on practice preparedness for the COVID-19 outbreak through an email followed by a reminder SMS message between 31 January 2020 and 3 February 2020. RESULTS: Of 1589 family doctors invited, 491 (31%) participated in the survey, including 242 (49%) from private sector. In all, 98% surveyed doctors continued to provide clinical services during the survey period, but reduced clinic service demands were observed in 45% private practices and 24% public clinics. Almost all wore masks during consultation and washed hands between or before patient contact. Significantly more private than public doctors (80% vs 26%, P<0.001) experienced difficulties in stocking personal protective equipment (PPE); more public doctors used guidelines to manage suspected patients. The main concern of the respondents was PPE shortage. Respondents appealed for effective public health interventions including border control, quarantine measures, designated clinic setup, and public education. CONCLUSION: Family doctors from public and private sectors demonstrated preparedness to serve the community from the early phase of the COVID-19 outbreak with heightened infection control measures and use of guidelines. However, there is a need for support from local health authorities to secure PPE supply and institute public health interventions.


Subject(s)
Coronavirus Infections/epidemiology , Coronavirus Infections/prevention & control , Disease Outbreaks/prevention & control , Family Practice/organization & administration , Health Care Surveys/methods , Pandemics/prevention & control , Pneumonia, Viral/epidemiology , Pneumonia, Viral/prevention & control , Surveys and Questionnaires , COVID-19 , COVID-19 Testing , Clinical Laboratory Techniques/methods , Clinical Laboratory Techniques/statistics & numerical data , Communicable Disease Control/methods , Coronavirus Infections/diagnosis , Disease Outbreaks/statistics & numerical data , Female , Hong Kong/epidemiology , Humans , Male , Outcome Assessment, Health Care , Physicians, Family/statistics & numerical data
10.
Sci Rep ; 11(1): 18955, 2021 09 23.
Article in English | MEDLINE | ID: covidwho-1437688

ABSTRACT

The world is facing an exceptional pandemic caused by SARS-CoV-2. To allow the diagnosis of COVID-19 infections, several assays based on the real-time PCR technique have been proposed. The requests for diagnosis are such that it was immediately clear that the choice of the most suitable method for each microbiology laboratory had to be based, on the one hand, on the availability of materials, and on the other hand, on the personnel and training priorities for this activity. Unfortunately, due to high demand, the shortage of commercial diagnostic kits has also become a major problem. To overcome these critical issues, we have developed a new qualitative RT-PCR probe. Our system detects three genes-RNA-dependent RNA polymerase (RdRp), envelope (E) and nucleocapsid (N)-and uses the ß-actin gene as an endogenous internal control. The results from our assay are in complete agreement with the results obtained using a commercially available kit, except for two samples that did not pass the endogenous internal control. The coincidence rate was 0.96. The LoD of our assay was 140 cp/reaction for N and 14 cp/reaction for RdRp and E. Our kit was designed to be open, either for the nucleic acid extraction step or for the RT-PCR assay, and to be carried out on several instruments. Therefore, it is free from the industrial production logics of closed systems, and conversely, it is hypothetically available for distribution in large quantities to any microbiological laboratory. The kit is currently distributed worldwide (called MOLgen-COVID-19; Adaltis). A new version of the kit for detecting the S gene is also available.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , SARS-CoV-2/genetics , COVID-19/genetics , COVID-19 Testing/methods , Clinical Laboratory Techniques/methods , Coronavirus Envelope Proteins/genetics , Coronavirus Nucleocapsid Proteins/genetics , Coronavirus RNA-Dependent RNA Polymerase/genetics , Humans , Pandemics , Phosphoproteins/genetics , Qualitative Research , RNA, Viral/genetics , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/pathogenicity , Sensitivity and Specificity
15.
Jpn J Infect Dis ; 74(4): 325-332, 2021 Jul 21.
Article in English | MEDLINE | ID: covidwho-1380108

ABSTRACT

Studies describing reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay-based infection control strategies (LAMP-based ICSs) for coronavirus disease 2019 (COVID-19) are limited. We reviewed the medical records of cases in which RT-LAMP was performed. Standard ICSs and LAMP-based ICSs were implemented during the study period. The strategies were intended to impose longer periods of infection control precautions (ICPs) for specific patients, such as those with a history of exposure to COVID-19 patients and/or bilateral ground glass opacities (bGGO) on chest computed tomography (CT). Of 212 patients, which included 13 confirmed COVID-19 patients in the diagnostic cohort, exposure to COVID-19 patients (P <0.0001) and chest CT bGGO (P = 0.0022) were identified as significant predictors of COVID-19. In the 173 hospitalized patients in which the results of the first RT-LAMP were negative, the duration of ICPs was significantly longer in patients with exposure to COVID-19 and/or a high clinical index of suspicion and patients with bGGO than in the remaining patients (P = 0.00046 and P = 0.0067, respectively). Additionally, no confirmed COVID-19 cases indicating nosocomial spread occurred during the study period. Establishing a comprehensive system that combines rational LAMP-based ICSs with standard ICSs might be useful for preventing nosocomial spread.


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , COVID-19/virology , Infection Control/methods , Reverse Transcription/genetics , SARS-CoV-2/genetics , Adult , Clinical Laboratory Techniques/methods , Female , Hospitals , Humans , Male , Molecular Diagnostic Techniques/methods , Nucleic Acid Amplification Techniques/methods , RNA, Viral/genetics , Sensitivity and Specificity , Tokyo , Young Adult
16.
Int J Mol Sci ; 22(16)2021 Aug 13.
Article in English | MEDLINE | ID: covidwho-1354988

ABSTRACT

The reverse transcription quantitative polymerase chain reaction (RT-qPCR) is an established tool for the diagnosis of RNA pathogens. Its potential for automation has caused it to be used as a presence/absence diagnostic tool even when RNA quantification is not required. This technology has been pushed to the forefront of public awareness by the COVID-19 pandemic, as its global application has enabled rapid and analytically sensitive mass testing, with the first assays targeting three viral genes published within days of the publication of the SARS-CoV-2 genomic sequence. One of those, targeting the RNA-dependent RNA polymerase gene, has been heavily criticised for supposed scientific flaws at the molecular and methodological level, and this criticism has been extrapolated to doubts about the validity of RT-qPCR for COVID-19 testing in general. We have analysed this assay in detail, and our findings reveal some limitations but also highlight the robustness of the RT-qPCR methodology for SARS-CoV-2 detection. Nevertheless, whilst our data show that some errors can be tolerated, it is always prudent to confirm that the primer and probe sequences complement their intended target, since, when errors do occur, they may result in a reduction in the analytical sensitivity. However, in this case, it is unlikely that a mismatch will result in poor specificity or a significant number of false-positive SARS-CoV-2 diagnoses, especially as this is routinely checked by diagnostic laboratories as part of their quality assurance.


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , Molecular Diagnostic Techniques/methods , Real-Time Polymerase Chain Reaction/methods , SARS-CoV-2/isolation & purification , COVID-19/epidemiology , COVID-19/virology , Clinical Laboratory Techniques/methods , Humans , Pandemics , RNA, Viral/genetics , RNA-Dependent RNA Polymerase , SARS-CoV-2/genetics , Sensitivity and Specificity , Temperature
17.
Microbiol Spectr ; 9(1): e0031221, 2021 09 03.
Article in English | MEDLINE | ID: covidwho-1352539

ABSTRACT

Pooled testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection is instrumental for increasing test capacity while decreasing test cost. Pooled testing programs permit sustainable, long-term surveillance measures, which are essential for the early detection of virus resurgence in communities or the emergence of variants of concern. While numerous pooled approaches have been proposed to increase test capacity, uptake by laboratories has been limited. On 9 December 2020, we invited 362 U.S. laboratories that inquired about the Yale School of Public Health SalivaDirect test to participate in a survey to evaluate testing constraints and pooling strategies for SARS-CoV-2 testing. The survey was distributed using Qualtrics, and three reminders were sent. The survey closed on 21 January 2021. Of 93 responses received (25.7% response rate), 90 were from Clinical Laboratory Improvement Amendments (CLIA)-certified laboratories conducting SARS-CoV-2 testing. The remaining three were excluded from the analyses. Responses indicated that the major barriers to the uptake of pooled testing in the United States may not simply be the number of tests a laboratory can process per day, but rather the lack of clear protocols and adequate resources; laboratories are working with fixed physical and human capital constraints. Importantly, laboratories across the country are heterogeneous in infrastructure and workflow. The need for SARS-CoV-2 testing will remain for years to come. Testing programs can be maintained through pooled PCR testing strategies, and while statisticians, operations researchers, and others with expertise in sampling design have important value to add, laboratories require support on how to transition from traditional diagnostic testing to pooled surveillance. IMPORTANCE While numerous pooled SARS-CoV-2 testing approaches have been described in an effort to increase testing capacity and decrease test prices, uptake by laboratories has been limited. Responses to our survey of United States-based laboratories highlight the importance of consulting end-users-those that solutions are being designed for-so challenges can be addressed in a manner tailored to meet the specific needs out in the field. It may be surprising to those designing pooled testing strategies to learn that laboratories view pooling as more time-consuming than testing samples individually, and therefore that it is thought to create delays in test reporting.


Subject(s)
COVID-19 Testing/methods , COVID-19 Testing/statistics & numerical data , COVID-19/diagnosis , COVID-19 Testing/standards , Clinical Laboratory Techniques/methods , Diagnostic Tests, Routine , Humans , Laboratories/statistics & numerical data , RNA, Viral , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Specimen Handling , Time , United States
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