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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
3.
Ann Med ; 53(1): 151-159, 2021 12.
Article in English | MEDLINE | ID: covidwho-1574907

ABSTRACT

OBJECTIVE: To utilize publicly reported, state-level data to identify factors associated with the frequency of cases, tests, and mortality in the USA. MATERIALS AND METHODS: Retrospective study using publicly reported data collected included the number of COVID-19 cases, tests and mortality from March 14th through April 30th. Publicly available state-level data was collected which included: demographics comorbidities, state characteristics and environmental factors. Univariate and multivariate regression analyses were performed to identify the significantly associated factors with percent mortality, case and testing frequency. All analyses were state-level analyses and not patient-level analyses. RESULTS: A total of 1,090,500 COVID-19 cases were reported during the study period. The calculated case and testing frequency were 3332 and 19,193 per 1,000,000 patients. There were 63,642 deaths during this period which resulted in a mortality of 5.8%. Factors including to but not limited to population density (beta coefficient 7.5, p < .01), transportation volume (beta coefficient 0.1, p < .01), tourism index (beta coefficient -0.1, p = .02) and older age (beta coefficient 0.2, p = .01) are associated with case frequency and percent mortality. CONCLUSIONS: There were wide variations in testing and case frequencies of COVID-19 among different states in the US. States with higher population density had a higher case and testing rate. States with larger population of elderly and higher tourism had a higher mortality. Key messages There were wide variations in testing and case frequencies of COVID-19 among different states in the USA. States with higher population density had a higher case and testing rate. States with larger population of elderly and higher tourism had a higher mortality.


Subject(s)
Clinical Laboratory Techniques/statistics & numerical data , Coronavirus Infections/mortality , Pneumonia, Viral/mortality , COVID-19 , COVID-19 Testing , Comorbidity , Coronavirus Infections/diagnosis , Female , Healthcare Disparities , Humans , Male , Pandemics , Pneumonia, Viral/diagnosis , United States/epidemiology
4.
Ann Med ; 53(1): 34-42, 2021 12.
Article in English | MEDLINE | ID: covidwho-1574894

ABSTRACT

BACKGROUND: Studies have demonstrated the diagnostic efficiency of antibody testing in COVID-19 infection. There is limited data on the IgM/IgG changes in asymptomatic and discharged patients with reoccurring positive nucleic acid test (RPNAT). This study aims to investigate these IgM/IgG changes. METHODS: There were 111 patients with positive nucleic acid test (NAT) and 40 suspected patients enrolled in the study. The serum SARS-CoV-2 specific IgM/IgG antibody levels were retrospectively analysed with the disease progress in asymptomatic and RPNAT patients. RESULTS: The best overall performance was found by combining the IgM, IgG, and CT; 95.1% sensitivity and 75% specificity. This was tested in 111 RT-PCR positive cases. The median IgM and IgG levels were lower in the asymptomatic group compared to the symptomatic group (p < .01). Among 15 RPNAT cases, the IgM levels of the RPNAT group at the time of discharge (IgM2.79, IQR: 0.95-5.37) and retest (IgM 2.35, IQR: 0.88-8.65) were significantly higher than those of the non-reoccurring positive nucleic acid test group (Non-RPNAT) (IgM on discharge: 0.59, IQR: 0.33-1.22, IgG on retest: 0.92, IQR: 0.51-1.58). CONCLUSION: Serum SARS-CoV-2 specific IgM/IgG antibody levels remained at a low level during hospitalisation for asymptomatic patients. Elevated IgM levels may have implications in the identification of RPNAT patients before discharge. Key messages This study determined the IgM/IgG changes in asymptomatic and RPNAT patients. The rate of serum SARS-CoV-2 specific IgM/IgG antibody levels increase in the asymptomatic group was lower than in the symptomatic group during hospitalisation. The IgM level did not decrease significantly at discharge in the RPNAT patients, and was higher than that of the Non-RPNAT group on discharge. These results highlight the importance of timely monitoring of IgM levels to identify RPNAT patients before discharge.


Subject(s)
Antibodies, Viral/blood , Betacoronavirus/isolation & purification , Coronavirus Infections/immunology , Immunoglobulin G/blood , Immunoglobulin M/blood , Pneumonia, Viral/immunology , COVID-19 , COVID-19 Testing , Case-Control Studies , Clinical Laboratory Techniques , Coronavirus Infections/diagnosis , Female , Humans , Immunoenzyme Techniques/methods , Male , Pandemics , Retrospective Studies , SARS-CoV-2
5.
J Nanobiotechnology ; 19(1): 348, 2021 Oct 30.
Article in English | MEDLINE | ID: covidwho-1555350

ABSTRACT

Viral infections are the most common among diseases that globally require around 60 percent of medical care. However, in the heat of the pandemic, there was a lack of medical equipment and inpatient facilities to provide all patients with viral infections. The detection of viral infections is possible in three general ways such as (i) direct virus detection, which is performed immediately 1-3 days after the infection, (ii) determination of antibodies against some virus proteins mainly observed during/after virus incubation period, (iii) detection of virus-induced disease when specific tissue changes in the organism. This review surveys some global pandemics from 1889 to 2020, virus types, which induced these pandemics, and symptoms of some viral diseases. Non-analytical methods such as radiology and microscopy also are overviewed. This review overlooks molecular analysis methods such as nucleic acid amplification, antibody-antigen complex determination, CRISPR-Cas system-based viral genome determination methods. Methods widely used in the certificated diagnostic laboratory for SARS-CoV-2, Influenza A, B, C, HIV, and other viruses during a viral pandemic are outlined. A comprehensive overview of molecular analytical methods has shown that the assay's sensitivity, accuracy, and suitability for virus detection depends on the choice of the number of regions in the viral open reading frame (ORF) genome sequence and the validity of the selected analytical method.


Subject(s)
Clinical Laboratory Techniques , Virus Diseases/diagnosis , Viruses/isolation & purification , Biosensing Techniques , COVID-19/diagnosis , COVID-19/epidemiology , Humans , Nucleic Acid Amplification Techniques , Pandemics , SARS-CoV-2/genetics , SARS-CoV-2/immunology , SARS-CoV-2/isolation & purification , Viral Proteins/genetics , Viral Proteins/immunology , Virus Diseases/epidemiology , Viruses/classification , Viruses/genetics , Viruses/immunology
6.
Infect Control Hosp Epidemiol ; 42(10): 1257-1259, 2021 10.
Article in English | MEDLINE | ID: covidwho-1541092

ABSTRACT

We performed a prospective study of 501 patients, regardless of symptoms, admitted to the hospital, to estimate the predictive value of a negative nasopharyngeal swab for severe acute respiratory coronavirus virus 2 (SARS-CoV-2). At a positivity rate of 10.2%, the estimated negative predictive value (NPV) was 97.2% and the NPV rose as prevalence decreased during the study.


Subject(s)
COVID-19 , Clinical Laboratory Techniques , Hospitalization , Humans , Prospective Studies , SARS-CoV-2
8.
Evid Based Dent ; 21(3): 82-83, 2020 09.
Article in English | MEDLINE | ID: covidwho-1526069

ABSTRACT

Basic health and infection control measures are the main methods of protection against COVID-19. Patients are well informed about how practitioners should be conducting themselves, however, they may lose trust in clinicians who fail to demonstrate, and promote those same basic prevention measures. The broader COVID-19 strategy has included the rapid development and deployment of swabs and antibody tests. Flaws in testing fail to offer assurances due to false negatives while even true positives cannot guarantee future immunity as there is uncertainty regarding long-term antibody response. An understanding of human factors and an appreciation of the limitations of available tests could offer healthcare staff mechanisms to encourage safety.


Subject(s)
Betacoronavirus , Clinical Laboratory Techniques , Coronavirus Infections , Pandemics , Pneumonia, Viral/epidemiology , Antibody Formation , COVID-19 , COVID-19 Testing , Coronavirus Infections/diagnosis , Humans , SARS-CoV-2
10.
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
11.
Clin Microbiol Rev ; 34(3)2021 06 16.
Article in English | MEDLINE | ID: covidwho-1501522

ABSTRACT

Public health laboratories (PHLs) continue to face internal and external challenges to their abilities to provide successful, timely responses to public health crises and emerging threats. These laboratories are mandated to maintain the health of their communities by identifying, diagnosing, and warning constituents of potential and real health emergencies. Due to the changing characteristics of public health threats and their cross-jurisdictional nature, laboratories are facing increased pressure to ensure that they respond in a consistent and coordinated manner. Here, the Association of Public Health Laboratories (APHL) Emerging Leader Program Cohort 11 members have compiled stories from subject matter experts (SMEs) at PHLs with direct involvement in crises to determine the characteristics of a successful response. Experts examined a diverse selection of emerging threats from across PHLs, including infectious diseases, opioids, natural disasters, and government shutdowns. While no public health crisis will be identical to another, overarching themes were consistent across subjects. Experiences from SMEs that could improve future responses to emerging threats are highlighted.


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , Hemorrhagic Fever, Ebola/diagnosis , Measles/diagnosis , Opioid-Related Disorders/diagnosis , Public Health/methods , COVID-19/epidemiology , Clinical Laboratory Techniques , Hemorrhagic Fever, Ebola/epidemiology , Humans , Laboratories , Measles/epidemiology , Opioid-Related Disorders/epidemiology
12.
Clin Infect Dis ; 73(9): e2901-e2907, 2021 11 02.
Article in English | MEDLINE | ID: covidwho-1500984

ABSTRACT

BACKGROUND: With the limited availability of testing for the presence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus and concerns surrounding the accuracy of existing methods, other means of identifying patients are urgently needed. Previous studies showing a correlation between certain laboratory tests and diagnosis suggest an alternative method based on an ensemble of tests. METHODS: We have trained a machine learning model to analyze the correlation between SARS-CoV-2 test results and 20 routine laboratory tests collected within a 2-day period around the SARS-CoV-2 test date. We used the model to compare SARS-CoV-2 positive and negative patients. RESULTS: In a cohort of 75 991 veteran inpatients and outpatients who tested for SARS-CoV-2 in the months of March through July 2020, 7335 of whom were positive by reverse transcription polymerase chain reaction (RT-PCR) or antigen testing, and who had at least 15 of 20 lab results within the window period, our model predicted the results of the SARS-CoV-2 test with a specificity of 86.8%, a sensitivity of 82.4%, and an overall accuracy of 86.4% (with a 95% confidence interval of [86.0%, 86.9%]). CONCLUSIONS: Although molecular-based and antibody tests remain the reference standard method for confirming a SARS-CoV-2 diagnosis, their clinical sensitivity is not well known. The model described herein may provide a complementary method of determining SARS-CoV-2 infection status, based on a fully independent set of indicators, that can help confirm results from other tests as well as identify positive cases missed by molecular testing.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19 Testing , Clinical Laboratory Techniques , Humans , Laboratories , Sensitivity and Specificity
14.
J Appl Lab Med ; 6(6): 1452-1462, 2021 Nov 01.
Article in English | MEDLINE | ID: covidwho-1493847

ABSTRACT

BACKGROUND: The detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in patient samples is of critical importance in the management of patients and monitoring transmission in the population. However, data on the analytical performance characteristics for detection of SARS-CoV-2 in clinical specimens between individual targets within the same platform, and among different analytical platforms, are limited. METHODS: Here we evaluated the performance of 6 different sample-to-answer SARS-CoV-2 detection methods-Roche cobas 6800, Cepheid GeneXpert, Diasorin Simplexa, Luminex Aries emergency use authorization (EUA), Luminex Aries research use only (RUO), and bioMérieux BioFire-in clinical specimens with a range of viral loads. RESULTS: The positive percentage agreement between the Roche cobas 6800 and GeneXpert was 100%, Diasorin 95%, Aries EUA 74%, Aries RUO 83%, and BioFire 97%. Notably, in samples with cycle threshold (Ct) values below 30 for the E gene on the Roche cobas 6800 platform, we found 100% positive agreement among all platforms. Given these results, we examined the distribution of over 10 000 Ct values of all positive specimens from individuals at our institution on the Roche cobas platform. Nearly 60% of specimens from asymptomatic individuals had a PCR Ct value >30 as measured using the cobas 6800 assay E gene. CONCLUSIONS: Our results demonstrate performance characteristics between different platforms by Ct value and provide data regarding the distribution of viral RNA present in positive specimens.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19 Testing , Clinical Laboratory Techniques , Humans , Sensitivity and Specificity
15.
J Immunol Methods ; 499: 113174, 2021 12.
Article in English | MEDLINE | ID: covidwho-1487843

ABSTRACT

INTRODUCTION: As in other viral infections, anti-nuclear antibodies (ANAs) are observed in SARS-CoV-2 infection. We investigated the presence of autoantibodies in acute COVID-19 and the association with early laboratory findings. MATERIALS AND METHODS: We examined 50 sera (>18 years, 25 Female) from patients with acute COVID-19. ANAs (HEp-20-10 liver biochip), anti-neutrophil cytoplasmic antibody (ANCA, Europlus Granulocyte Mosaic 32) and anti-double stranded DNA were investigated with product of Euroimmune AG (Luebeck, Germany) by indirect immunofluorescence (IIF) method. Also, antibody against cyclic citrullinated peptide (anti-CCP) was examined by a chemiluminisens assay (Euroimmun AG, Luebeck, Germany). Samples from 50 blood bank donors collected before the COVID-19 pandemic were used as controls. RESULTS: The IIF-ANA test was positive in 18% (N = 9/50) of the patients. The median time of sample collection was 7 days (range: 1-28 days) after diagnosis. ANA was positive in only one (2%) control sample. Five (55.5%) patients were ANA positive with a strong titer (3+). There was no relationship between antibody titration and time of sample collection (p = 0,55). Anti-CCP was detected in a nucleolar (3+) positive patient (2%). ANA was detected in 14.28% (N = 1/7, rods-rings (±), p = 0,78) of patients in the intensive care unit(ICU). Patients treated in the clinic have more and higher titers of ANA, mostly in nucleolar patterns, than ICU patients. CONCLUSIONS: The variety of antibodies detected in acute COVID-19 and the uncertainty of how long they persist can lead to confusion, especially in the diagnosis of systemic autoimmune rheumatic diseases for IIF-ANA testing in immunology laboratories. Improvements in cell lines and methods will facilitate the diagnostic process.


Subject(s)
Antibodies, Antinuclear/analysis , COVID-19/diagnosis , Clinical Laboratory Techniques , Fluorescent Antibody Technique, Indirect , Acute Disease , Adult , Aged , Aged, 80 and over , Antibodies, Antinuclear/immunology , COVID-19/immunology , Female , Humans , Male , Middle Aged , Pandemics , Young Adult
16.
BMC Infect Dis ; 21(1): 1114, 2021 Oct 29.
Article in English | MEDLINE | ID: covidwho-1486556

ABSTRACT

BACKGROUND: COVID-19 disease has had a profound impact worldwide since it was discovered in Wuhan, China, in December 2019. Laboratory testing is crucial to prompt identification of positive cases, initiation of treatment and management strategies. However, medical scientists are vulnerable to infection due to the risk of exposure in the laboratory and the community. This study sought to determine the awareness of laboratory safety measures, assess the personal efforts of medical scientists in creating a safe laboratory environment for testing and examine the laboratory safety enabling factors. METHODS: The data used for the study were generated among medical scientists in Nigeria through an internet-broadcasted questionnaire and were analyzed using IBM SPSS Statistics (version 25). RESULTS: The majority of the respondents had a high awareness of laboratory safety measures (60.3%) and demonstrated good personal efforts in creating a safe laboratory testing environment (63%). The level of awareness of laboratory safety measures was significantly associated with respondents' level of education (χ2 = 6.143; p = 0.046) and influences respondents' efforts in creating a safe laboratory testing environment (p = 0.007). However, just a few respondents could convincingly attest to the availability of adequate and appropriate PPE with proper utilization training (45.1%), adequate rest and other welfare packages (45.8%) as well as access to appropriate Biological Safety Cabinets (BSCs) and other essential equipment in their laboratories (48.8%). Furthermore, a significant association existed between the availability of laboratory safety enabling factors and respondents' efforts in creating a safe environment for testing with the p-value ranging between < 0.0001 and 0.003. CONCLUSION: This study revealed that despite the high awareness of safety measures and good personal efforts of the study participants in creating a safe laboratory-testing environment, there was poor availability of safety facilities, equipment, support and welfare packages required to enhance their safety. It is, therefore, crucial to provide necessary laboratory biosafety equipment and PPE in order not to compromise medical scientists' safety as they perform their duties in COVID-19 pandemic response.


Subject(s)
COVID-19 , Pandemics , Clinical Laboratory Techniques , Containment of Biohazards , Humans , SARS-CoV-2
17.
Bratisl Lek Listy ; 122(11): 763-770, 2021.
Article in English | MEDLINE | ID: covidwho-1485294

ABSTRACT

AIMS: This review is focused on the laboratory diagnoses of the coronavirus disease 2019 (COVID-19) by recognizing the antigen of the causative agent SARS-CoV-2 virus. Various antigen tests are available in this moment and these tests are being further developed in order to reach a better diagnostic value. The issue is reviewed in a complex view. METHODS: In this work, a complex survey of the current literature was made. The relevant and recent papers related to antigen tests of COVID-19 are discussed and cited. Basic specifications of the antigen tests and competitive methods were also scrutinized in the current literature. RESULTS: The survey of the current literature (years 2019 ‒ 2021) was made and diagnostic methods like lateral flow tests (lateral flow immunochromatographic assay) and various types of biosensors were specified as tools for COVID-19 diagnosis and their application to be used as a point-of-care test is considered. CONCLUSIONS: Small hand-held assays applicable in the point-of-care conditions for diagnosis of COVID-19 by analysis of SARS-CoV-2 antigen are the means of a growing interest and these means undergo a significant development leading to the improvements of their specifications and applicability to the current praxis. Merit of the assays is discussed in this paper (Tab. 3, Fig. 2, Ref. 109).


Subject(s)
COVID-19 , Antibodies, Viral , COVID-19 Testing , Clinical Laboratory Techniques , Humans , Point-of-Care Systems , SARS-CoV-2 , Sensitivity and Specificity
18.
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
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