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1.
Proc Natl Acad Sci U S A ; 119(2)2022 01 11.
Article in English | MEDLINE | ID: covidwho-1602775

ABSTRACT

Pooled testing increases efficiency by grouping individual samples and testing the combined sample, such that many individuals can be cleared with one negative test. This short paper demonstrates that pooled testing is particularly advantageous in the setting of pandemics, given repeated testing, rapid spread, and uncertain risk. Repeated testing mechanically lowers the infection probability at the time of the next test by removing positives from the population. This effect alone means that increasing frequency by x times only increases expected tests by around [Formula: see text] However, this calculation omits a further benefit of frequent testing: Removing infections from the population lowers intragroup transmission, which lowers infection probability and generates further efficiency. For this reason, increasing testing frequency can paradoxically reduce total testing cost. Our calculations are based on the assumption that infection rates are known, but predicting these rates is challenging in a fast-moving pandemic. However, given that frequent testing naturally suppresses the mean and variance of infection rates, we show that our results are very robust to uncertainty and misprediction. Finally, we note that efficiency further increases given natural sampling pools (e.g., workplaces, classrooms) that induce correlated risk via local transmission. We conclude that frequent pooled testing using natural groupings is a cost-effective way to provide consistent testing of a population to suppress infection risk in a pandemic.


Subject(s)
Mass Screening/economics , Mass Screening/methods , COVID-19/diagnosis , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19 Testing , Cost-Benefit Analysis , Humans , Population Surveillance , Prevalence , SARS-CoV-2/isolation & purification , Uncertainty
2.
JAMA Netw Open ; 4(12): e2140602, 2021 12 01.
Article in English | MEDLINE | ID: covidwho-1597867

ABSTRACT

Importance: During the 2020-2021 academic year, many institutions of higher education reopened to residential students while pursuing strategies to mitigate the risk of SARS-CoV-2 transmission on campus. Reopening guidance emphasized polymerase chain reaction or antigen testing for residential students and social distancing measures to reduce the frequency of close interpersonal contact, and Connecticut colleges and universities used a variety of approaches to reopen campuses to residential students. Objective: To characterize institutional reopening strategies and COVID-19 outcomes in 18 residential college and university campuses across Connecticut. Design, Setting, and Participants: This retrospective cohort study used data on COVID-19 testing and cases and social contact from 18 college and university campuses in Connecticut that had residential students during the 2020-2021 academic year. Exposures: Tests for COVID-19 performed per week per residential student. Main Outcomes and Measures: Cases per week per residential student and mean (95% CI) social contact per week per residential student. Results: Between 235 and 4603 residential students attended the fall semester across each of 18 institutions of higher education in Connecticut, with fewer residential students at most institutions during the spring semester. In census block groups containing residence halls, the fall student move-in resulted in a 475% (95% CI, 373%-606%) increase in mean contact, and the spring move-in resulted in a 561% (95% CI, 441%-713%) increase in mean contact compared with the 7 weeks prior to move-in. The association between test frequency and case rate per residential student was complex; institutions that tested students infrequently detected few cases but failed to blunt transmission, whereas institutions that tested students more frequently detected more cases and prevented further spread. In fall 2020, each additional test per student per week was associated with a decrease of 0.0014 cases per student per week (95% CI, -0.0028 to -0.00001). Conclusions and Relevance: The findings of this cohort study suggest that, in the era of available vaccinations and highly transmissible SARS-CoV-2 variants, colleges and universities should continue to test residential students and use mitigation strategies to control on-campus COVID-19 cases.


Subject(s)
COVID-19 Testing/statistics & numerical data , COVID-19/epidemiology , COVID-19/transmission , Universities , Adolescent , COVID-19/diagnosis , Connecticut/epidemiology , Female , Housing , Humans , Male , Mass Screening/methods , Retrospective Studies , SARS-CoV-2 , Social Interaction , Young Adult
3.
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
4.
PLoS One ; 16(12): e0261921, 2021.
Article in English | MEDLINE | ID: covidwho-1581722

ABSTRACT

Universal screening for suicidal ideation in primary care and mental health settings has become a key prevention tool in many healthcare systems, including the Veterans Healthcare Administration (VHA). In response to the coronavirus pandemic, healthcare providers faced a number of challenges, including how to quickly adapt screening practices. The objective of this analyses was to learn staff perspectives on how the pandemic impacted suicide risk screening in primary care and mental health settings. Forty semi-structured interviews were conducted with primary care and mental health staff between April-September 2020 across 12 VHA facilities. A multi-disciplinary team employed a qualitative thematic analysis using a hybrid inductive/deductive approach. Staff reported multiple concerns for patients during the crisis, especially regarding vulnerable populations at risk for social isolation. Lack of clear protocols at some sites on how to serve patients screening positive for suicidal ideation created confusion for staff and led some sites to temporarily stop screening. Sites had varying degrees of adaptability to virtual based care, with the biggest challenge being completion of warm hand-offs to mental health specialists. Unanticipated opportunities that emerged during this time included increased ability of patients and staff to conduct virtual care, which is expected to continue benefit post-pandemic.


Subject(s)
COVID-19/epidemiology , COVID-19/psychology , Health Personnel , Mass Screening/methods , Pandemics , SARS-CoV-2 , Suicidal Ideation , Veterans Health , Veterans/psychology , COVID-19/prevention & control , COVID-19/virology , Humans , Mental Health , Physical Distancing , Primary Health Care , Risk Assessment/methods , Telemedicine/methods
5.
J Cyst Fibros ; 20 Suppl 3: 31-38, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1587346

ABSTRACT

BACKGROUND: Depression and anxiety are two to four times more prevalent in people with CF (pwCF) than the general population. COVID-19 may exacerbate mental health challenges, increasing demand for psychological services, while decreasing their availability. We assessed the impact of the pandemic on depression and anxiety in pwCF, including how COVID-19 affected the frequency of mental health screening and the types of services provided. METHODS: A 38-item internet survey, completed in June 2020, assessed how COVID-19 affected: 1) the mental health clinician's role and screening processes; 2) barriers to screening and resource needs; 3) impact of COVID-19 on depression and anxiety, and 4) positive outcomes and confidence in sustaining mental health screening and treatment, including telehealth services, after the pandemic. RESULTS: Responses were obtained from 131 of the 289 US CF programs. Overall, 60% of programs (n=79) continued mental health screening and treatment, although less frequently; 50% provided individual tele-mental health interventions, and 9% provided telehealth group therapy. Clinically elevated depression symptoms (PHQ-9≥10; moderate to severe), were found in 12% of 785 pwCF, with 3.1% endorsing suicidal ideation. Similarly, elevated anxiety (moderate to severe; GAD-7≥10) was found in 13% of pwCF (n=779). CONCLUSIONS: The COVID-19 pandemic created an opportunity to implement innovative solutions to disruptions in mental health screening and treatment in CF programs. We found that pwCF had increased access to psychological interventions during the pandemic via telehealth, supporting the continued integration of tele-mental health screening and treatment into CF care.


Subject(s)
Anxiety , COVID-19 , Cystic Fibrosis , Depression , Mental Health , Psychosocial Intervention , Telemedicine , Anxiety/diagnosis , Anxiety/physiopathology , Anxiety/therapy , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19/psychology , Cystic Fibrosis/epidemiology , Cystic Fibrosis/psychology , Cystic Fibrosis/therapy , Delivery of Health Care/methods , Delivery of Health Care/trends , Depression/diagnosis , Depression/physiopathology , Depression/therapy , Health Services Accessibility/standards , Health Services Accessibility/statistics & numerical data , Humans , Mass Screening/methods , Needs Assessment , Psychosocial Intervention/methods , Psychosocial Intervention/trends , Psychosocial Support Systems , SARS-CoV-2 , Surveys and Questionnaires , Telemedicine/methods , Telemedicine/organization & administration , United States/epidemiology
7.
Ann Med ; 53(1): 337-344, 2021 12.
Article in English | MEDLINE | ID: covidwho-1575678

ABSTRACT

BACKGROUND: To minimise the risk of COVID-19 transmission, an ambulant screening protocol for COVID-19 in patients before admission to the hospital was implemented, combining the SARS CoV-2 reverse-transcriptase polymerase chain reaction (RT-PCR) on a nasopharyngeal swab, a chest computed tomography (CT) and assessment of clinical symptoms. The aim of this study was to evaluatethe diagnostic yield and the proportionality of this pre-procedural screeningprotocol. METHODS: In this mono-centre, prospective, cross-sectional study, all patients admitted to the hospital between 22nd April 2020 until 14th May 2020 for semi-urgent surgery, haematological or oncological treatment, or electrophysiological investigationunderwent a COVID-19 screening 2 days before their procedure. At a 2-week follow-up, the presence of clinical symptoms was evaluated by telephone as a post-hoc evaluation of the screening approach.Combined positive RT-PCR assay and/or positive chest CT was used as gold standard. Post-procedural outcomes of all patients diagnosed positive for COVID-19 were assessed. RESULTS: In total,528 patients were included of which 20 (3.8%) were diagnosed as COVID-19 positive and 508 (96.2%) as COVID-19 negative. 11 (55.0%) of COVID-19 positive patients had only a positive RT-PCR assay, 3 (15.0%) had only a positive chest CT and 6 (30%) had both a positive RT-PCR assay and chest CT. 10 out of 20 (50.0%) COVID-19 positive patients reported no single clinical symptom at the screening. At 2 week follow-up, 50% of these patients were still asymptomatic. 37.5% of all COVID-19 negative patients were symptomatic at screening. In the COVID-19 negative group without symptoms at screening, 78 (29.3%) patients developed clinical symptoms at a 2-week follow-up. CONCLUSION: This study suggests that routine chest CT and assessment of self-reported symptoms have limited value in the preprocedural COVID-19 screening due to low sensitivity and/or specificity.


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , Mass Screening/methods , Patient Admission , Adult , Aged , COVID-19/epidemiology , Cross-Sectional Studies , Female , Follow-Up Studies , Humans , Male , Middle Aged , Prospective Studies , Reverse Transcriptase Polymerase Chain Reaction , Sensitivity and Specificity , Tomography, X-Ray Computed
8.
BMC Med Genomics ; 14(Suppl 6): 289, 2021 12 14.
Article in English | MEDLINE | ID: covidwho-1571758

ABSTRACT

BACKGROUND: Virus screening and viral genome reconstruction are urgent and crucial for the rapid identification of viral pathogens, i.e., tracing the source and understanding the pathogenesis when a viral outbreak occurs. Next-generation sequencing (NGS) provides an efficient and unbiased way to identify viral pathogens in host-associated and environmental samples without prior knowledge. Despite the availability of software, data analysis still requires human operations. A mature pipeline is urgently needed when thousands of viral pathogen and viral genome reconstruction samples need to be rapidly identified. RESULTS: In this paper, we present a rapid and accurate workflow to screen metagenomics sequencing data for viral pathogens and other compositions, as well as enable a reference-based assembler to reconstruct viral genomes. Moreover, we tested our workflow on several metagenomics datasets, including a SARS-CoV-2 patient sample with NGS data, pangolins tissues with NGS data, Middle East Respiratory Syndrome (MERS)-infected cells with NGS data, etc. Our workflow demonstrated high accuracy and efficiency when identifying target viruses from large scale NGS metagenomics data. Our workflow was flexible when working with a broad range of NGS datasets from small (kb) to large (100 Gb). This took from a few minutes to a few hours to complete each task. At the same time, our workflow automatically generates reports that incorporate visualized feedback (e.g., metagenomics data quality statistics, host and viral sequence compositions, details about each of the identified viral pathogens and their coverages, and reassembled viral pathogen sequences based on their closest references). CONCLUSIONS: Overall, our system enabled the rapid screening and identification of viral pathogens from metagenomics data, providing an important piece to support viral pathogen research during a pandemic. The visualized report contains information from raw sequence quality to a reconstructed viral sequence, which allows non-professional people to screen their samples for viruses by themselves (Additional file 1).


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , Computational Biology/methods , Genome, Viral , Genomics , Metagenomics , SARS-CoV-2/genetics , Algorithms , Animals , Automation , Coronavirus Infections/genetics , High-Throughput Nucleotide Sequencing , Humans , Mass Screening/methods , Pandemics , Pangolins , Reference Values , Software , Transcriptome , Workflow
9.
JAMA Netw Open ; 4(12): e2137189, 2021 12 01.
Article in English | MEDLINE | ID: covidwho-1567892

ABSTRACT

Importance: COVID-19 posed an unprecedented threat to residential colleges in the fall of 2020. While there were mathematical models of COVID-19 transmission, there were no established or tested protocols of COVID-19 testing or mitigation for school administrators to follow. Objective: To investigate the association of a multifaceted COVID-19 mitigation strategy using social, behavioral, and educational interventions and a program of frequent testing with prevalence of disease spread. Design, Setting, and Participants: This cohort study was conducted as a retrospective review of COVID-19 positivity from August 16, 2020, to April 30, 2021, at Delaware State University, a publicly funded historically Black university. Participants included all students, faculty, and staff members with a campus presence. Positivity rates after use of mitigation strategies and testing on campus were compared with those of the surrounding community. Data were analyzed from July through September 2021. Exposures: Mitigation strategies included education and outreach about social distancing, masking, and handwashing, and a COVID-19 testing plan consisted of twice-weekly polymerase chain reaction (PCR) screening using anterior nasal samples (fall and early spring semester) and then saliva-based samples (middle to late spring semester). Main Outcomes and Measures: Cumulative tests, infections, daily quarantine, and isolation residence hall occupancy were measured, and comparisons were made with statewide COVID-19 positivity rates. Results: The campus cohort included 2320 individuals (1575 resident students, 415 nonresident students, and 330 faculty or staff members). There were 1488 (64.1%) women and 832 (35.9%) men; mean (SD) age was 27.5 (12.9) years. During the fall semester, 36 500 COVID-19 PCR tests were performed. Weekly positivity rates ranged from 0 of 372 tests to 16 of 869 tests (1.8%) (mean [SD] positivity rate, 0.5% [0.5%]; 168 positive results and 36 312 negative results). During the same period, statewide positivity ranged from 589 of 25 120 tests (2.3%) to 5405 of 54 596 tests (9.9%) (mean [SD] positivity rate, 4.8% [2.6%]). In the spring semester, 39 045 PCR tests were performed. Weekly positivity rates ranged from 4 of 2028 tests (0.2%) to 36 of 900 tests (4.0%) (mean [SD] positivity rate, 0.8% [0.9%]; 267 positive results and 38 767 negative results). During the same period, statewide positivity ranged from 1336 of 37 254 tests (3.6%) to 3630 of 42 458 tests (8.5%) (mean [SD] positivity rate, 5.1% [1.3%]). Compared with statewide rates, campus positivity rates were mean (SD) 4.4 (2.6) percentage points lower during the fall semester (P < .001) and mean (SD) 5.6 (1.6) percentage points lower during the spring semester (P < .001). Total daily quarantine and isolation residence hall occupancy ranged from 0 to 43 students in the fall and 1 to 47 students during the spring. Conclusions and Relevance: This study found that the combination of campuswide mitigation policies and twice-weekly COVID-19 PCR screening was associated with a significant decrease in COVID-19 positivity at a residential historically Black university campus compared with the surrounding community. Given the socioeconomic demographics of many students at historically Black colleges and universities, keeping these resident campuses open is critical not only to ensure access to educational resources, but also to provide housing and food security.


Subject(s)
COVID-19 Testing , COVID-19/prevention & control , Communicable Disease Control/methods , Health Education , Mass Screening/methods , Students , Universities , Adolescent , Adult , COVID-19/diagnosis , COVID-19/epidemiology , COVID-19/transmission , Delaware/epidemiology , Female , Housing , Humans , Male , Polymerase Chain Reaction , Prevalence , Residence Characteristics , Retrospective Studies , SARS-CoV-2 , Young Adult
10.
J Med Virol ; 93(12): 6837-6840, 2021 12.
Article in English | MEDLINE | ID: covidwho-1544319

ABSTRACT

BACKGROUND: Gargle samples have been proposed as a noninvasive method for detection of SARS-CoV-2 RNA. The clinical performance of gargle specimens diluted in Cobas® PCR Media and in Cobas® Omni Lysis Reagent was compared to oropharyngeal/nasopharyngeal swab (ONPS) for the detection of SARS-CoV-2 RNA. STUDY DESIGN: Participants were recruited prospectively in two COVID-19 screening clinics. In addition to the ONPS, participants gargled with 5 ml of natural spring water split in the laboratory as follows: 1 ml was added to 4.3 ml of polymerase chain reaction (PCR) media and 400 µl was added to 200 µl of lysis buffer. Testing was performed with the Cobas® SARS-CoV-2 test on the Cobas® 6800 or 8800 platforms. RESULTS: Overall, 134/647 (20.7%) participants were considered infected because the ONPS or at least one gargle test was positive. ONPS had, respectively, a sensitivity of 96.3% (95% confidence interval [CI]: 91.3-98.5); both gargle processing methods were slightly less but equally sensitive (90.3% [95% CI: 83.9-94.3]). When ONPS and gargle specimens were both positive, the mean cycle threshold (Ct ) was significantly higher for gargles, suggesting lower viral loads. CONCLUSION: Gargle specimens directly added in PCR Media provide a similar clinical sensitivity to chemical lysis, both having a slightly, not significantly, lower sensitivity to ONPS.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , COVID-19/virology , Nasopharynx/virology , Oropharynx/virology , SARS-CoV-2/genetics , Diagnostic Tests, Routine/methods , Humans , Mass Screening/methods , Prospective Studies , RNA, Viral/genetics , Saliva/virology , Specimen Handling/methods , Viral Load/genetics
11.
J Med Virol ; 93(12): 6544-6550, 2021 12.
Article in English | MEDLINE | ID: covidwho-1544302

ABSTRACT

We developed a rapid and simple magnetic chemiluminescence enzyme immunoassay on the Real Express-6 analyzer, which could simultaneously detect immunoglobulin G and immunoglobulin M antibodies against SARS-CoV-2 virus in human blood within 18 min, and which could be used to detect clinical studies to verify its clinical efficacy. We selected blood samples from 185 COVID-19 patients confirmed by polymerase chain reaction and 271 negative patients to determine the clinical detection sensitivity, specificity, stability, and precision of this method. Meanwhile, we also surveyed the dynamic variance of viral antibodies during SARS-CoV-2 infection. This rapid immunoassay test has huge potential benefits for rapid screening of SARS-CoV-2 infection and may help clinical drug and vaccine development.


Subject(s)
Antibodies, Viral/blood , COVID-19 Serological Testing/methods , COVID-19/diagnosis , Immunoglobulin G/blood , Immunoglobulin M/blood , SARS-CoV-2/immunology , Adolescent , Adult , Aged , Aged, 80 and over , Cross Reactions/immunology , Early Diagnosis , Female , Humans , Immunoassay/methods , Luminescent Measurements , Male , Mass Screening/methods , Middle Aged , Polymerase Chain Reaction , Sensitivity and Specificity , Young Adult
12.
J Med Virol ; 93(12): 6778-6781, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1544295

ABSTRACT

A high-throughput, fully automated antigen detection test for SARS-CoV-2 is a viable alternative to reverse-transcription polymerase chain reaction (RT-qPCR) for mass screening during outbreaks. In this study, we compared RT-qPCR for viral load and the VITROS® SARS-CoV-2 Antigen Test with reference to the results of the LUMIPULSE® SARS-CoV-2 Ag Test. Of 128 nasopharyngeal swab specimens taken from patients suspected of being infected with SARS-CoV-2, 49 were positive and 79 were negative according to RT-qPCR. Consistent dose-dependent detection with VITROS® assay was successfully achieved when using nasopharyngeal swab specimens with Ct values of 32.0 or lesser, whereas the CLEIA-based LUMIPULSE® assay was able to detect lower viral loads compared with the VITROS® assay. Our results show that the performance of the VITROS® assay was satisfactory for the diagnosis of contagious COVID-19 patients in the clinical setting. Highlights The performance of the VITROS® SARS-CoV-2 Antigen Test was sufficient for the diagnosis of contagious COVID-19. This test showed high sensitivity and specificity in the detection of SARS-CoV-2 in samples with a Ct value of 32 or less.


Subject(s)
COVID-19 Serological Testing/methods , COVID-19 Testing/methods , COVID-19/diagnosis , COVID-19/immunology , Immunoenzyme Techniques/methods , Immunologic Tests/methods , SARS-CoV-2/immunology , Antigens, Viral/genetics , Antigens, Viral/immunology , COVID-19/virology , Humans , Mass Screening/methods , Nasopharynx/immunology , Nasopharynx/virology , RNA, Viral/genetics , RNA, Viral/immunology , Real-Time Polymerase Chain Reaction/methods , SARS-CoV-2/genetics , Sensitivity and Specificity , Viral Load/genetics , Viral Load/immunology
13.
Pediatrics ; 148(1)2021 07.
Article in English | MEDLINE | ID: covidwho-1533449

ABSTRACT

BACKGROUND AND OBJECTIVES: Depression is common, and suicide rates are increasing. Adolescent depression screening might miss those with unidentified suicide risk. Our primary objective in this study was to compare the magnitude of positive screen results across different approaches. METHODS: From June 2019 to October 2020, 803 mostly Medicaid-enrolled adolescents aged ≥12 years with no recent history of depression or self-harm were screened with the Patient Health Questionnaire-9 Modified for Adolescents (PHQ-9A) and the Ask Suicide-Screening Questions (ASQ) across 12 primary care practices. Two PHQ-9A screening strategies were evaluated: screening for any type of depression or other mental illness (positive on any item) or screening for major depressive disorder (MDD) (total score ≥10). RESULTS: Overall, 56.4% of patients screened positive for any type of depression, 24.7% screened positive for MDD, and 21.1% screened positive for suicide risk. Regardless of PHQ-9A screening strategy, the ASQ identified additional subjects (eg, 2.2% additional cases compared with screening for any type of depression or other mental illness and 8.3% additional cases compared with screening positive for MDD). Of those with ≥6 month follow-up, 22.9% screened positive for any type of depression (n = 205), 35.6% screened positive for MDD (n = 90), and 42.7% with a positive ASQ result (n = 75) had a depression or self-harm diagnosis or an antidepressant prescription. CONCLUSIONS: Suicide risk screening identifies cases not identified by depression screening. In this study, we underscore opportunities and challenges in primary care related to the high prevalence of depression and suicide risk. Research is needed regarding optimal screening strategies and to help clinicians manage the expected number of screening-identified adolescents.


Subject(s)
Depression/epidemiology , Mass Screening/methods , Primary Health Care/methods , Suicide/statistics & numerical data , Adolescent , Antidepressive Agents/therapeutic use , COVID-19/epidemiology , COVID-19/psychology , Child , Depression/diagnosis , Depression/drug therapy , Depressive Disorder, Major/diagnosis , Depressive Disorder, Major/drug therapy , Depressive Disorder, Major/epidemiology , Female , Humans , Loneliness , Male , Mental Disorders/diagnosis , Mental Disorders/epidemiology , Pandemics , Risk Factors , SARS-CoV-2 , Social Isolation , Suicide/prevention & control , Young Adult
14.
Sci Rep ; 11(1): 21650, 2021 11 04.
Article in English | MEDLINE | ID: covidwho-1504883

ABSTRACT

The SARS-CoV2 has now spread worldwide causing over four million deaths. Testing strategies are highly variable between countries and their impact on mortality is a major issue. Retrospective multicenter study with a prospective database on all inpatients throughout mainland France. Using fixed effects models, we exploit policy discontinuities at region borders in France to estimate the effect of testing on the case fatality rate. In France, testing policies are determined at a regional level, generating exogenous variation in testing rates between departments on each side of a region border. We compared all contiguous department pairs located on the opposite sides of a region border. The increase of one percentage point in the test rate is associated with a decrease of 0.0015 percentage point in the death rate, that is, for each additional 2000 tests, we could observe three fewer deaths. Our study suggests that COVID-19 population testing could have a significant impact on the mortality rate which should be considered in decision-making. As concern grows over the current second wave of COVID-19, our findings support the implementation of large-scale screening strategies in such epidemic contexts.


Subject(s)
COVID-19 Testing/trends , COVID-19/diagnosis , COVID-19/mortality , France/epidemiology , Humans , Mass Screening/methods , Mass Screening/trends , Mortality/trends , Retrospective Studies , SARS-CoV-2/pathogenicity
15.
PLoS One ; 16(11): e0258700, 2021.
Article in English | MEDLINE | ID: covidwho-1504697

ABSTRACT

Protecting healthcare professionals is crucial in maintaining a functioning healthcare system. The risk of infection and optimal preventive strategies for healthcare workers during the COVID-19 pandemic remain poorly understood. Here we report the results of a cohort study that included pre- and asymptomatic healthcare workers. A weekly testing regime has been performed in this cohort since the beginning of the COVID-19 pandemic to identify infected healthcare workers. Based on these observations we have developed a mathematical model of SARS-CoV-2 transmission that integrates the sources of infection from inside and outside the hospital. The data were used to study how regular testing and a desynchronisation protocol are effective in preventing transmission of COVID-19 infection at work, and compared both strategies in terms of workforce availability and cost-effectiveness. We showed that case incidence among healthcare workers is higher than would be explained solely by community infection. Furthermore, while testing and desynchronisation protocols are both effective in preventing nosocomial transmission, regular testing maintains work productivity with implementation costs.


Subject(s)
Asymptomatic Infections , COVID-19 Testing/methods , COVID-19/diagnosis , COVID-19/economics , Health Personnel , SARS-CoV-2 , Algorithms , Cost-Benefit Analysis , Cross Infection , Data Collection , Delivery of Health Care , Hospitals , Humans , Mass Screening/methods , Models, Theoretical , Occupational Exposure , Pandemics , Risk , Stochastic Processes , Switzerland/epidemiology
16.
Cardiovasc Diabetol ; 20(1): 218, 2021 11 06.
Article in English | MEDLINE | ID: covidwho-1503722

ABSTRACT

Type 2 diabetes is one of the most relevant risk factors for heart failure, the prevalence of which is increasing worldwide. The aim of the review is to highlight the current perspectives of the pathophysiology of heart failure as it pertains to type 2 diabetes. This review summarizes the proposed mechanistic bases, explaining the myocardial damage induced by diabetes-related stressors and other risk factors, i.e., cardiomyopathy in type 2 diabetes. We highlight the complex pathology of individuals with type 2 diabetes, including the relationship with chronic kidney disease, metabolic alterations, and heart failure. We also discuss the current criteria used for heart failure diagnosis and the gold standard screening tools for individuals with type 2 diabetes. Currently approved pharmacological therapies with primary use in type 2 diabetes and heart failure, and the treatment-guiding role of NT-proBNP are also presented. Finally, the influence of the presence of type 2 diabetes as well as heart failure on COVID-19 severity is briefly discussed.


Subject(s)
COVID-19/epidemiology , Diabetes Mellitus, Type 2/epidemiology , Disease Management , Heart Failure/epidemiology , Mass Screening/methods , Biomarkers/blood , COVID-19/blood , COVID-19/diagnosis , Diabetes Mellitus, Type 2/blood , Diabetes Mellitus, Type 2/diagnosis , Glycated Hemoglobin A/metabolism , Heart Failure/blood , Heart Failure/diagnosis , Humans , Mass Screening/trends , Natriuretic Peptide, Brain/blood , Peptide Fragments/blood , Prognosis
18.
Sci Rep ; 11(1): 21385, 2021 11 01.
Article in English | MEDLINE | ID: covidwho-1493218

ABSTRACT

Shortages of reverse transcriptase (RT)-polymerase chain reaction (PCR) reagents and related equipment during the COVID-19 pandemic have demonstrated the need for alternative, high-throughput methods for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)-mass screening in clinical diagnostic laboratories. A robust, SARS-CoV-2 RT-loop-mediated isothermal amplification (RT-LAMP) assay with high-throughput and short turnaround times in a clinical laboratory setting was established and compared to two conventional RT-PCR protocols using 323 samples of individuals with suspected SARS-CoV-2 infection. Limit of detection (LoD) and reproducibility of the isolation-free SARS-CoV-2 RT-LAMP test were determined. An almost perfect agreement (Cohen's kappa > 0.8) between the novel test and two classical RT-PCR protocols with no systematic difference (McNemar's test, P > 0.05) was observed. Sensitivity and specificity were in the range of 89.5 to 100% and 96.2 to 100% dependent on the reaction condition and the RT-PCR method used as reference. The isolation-free RT-LAMP assay showed high reproducibility (Tt intra-run coefficient of variation [CV] = 0.4%, Tt inter-run CV = 2.1%) with a LoD of 95 SARS-CoV-2 genome copies per reaction. The established SARS-CoV-2 RT-LAMP assay is a flexible and efficient alternative to conventional RT-PCR protocols, suitable for SARS-CoV-2 mass screening using existing laboratory infrastructure in clinical diagnostic laboratories.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , COVID-19/epidemiology , Molecular Diagnostic Techniques/methods , Nucleic Acid Amplification Techniques/methods , Pandemics , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/genetics , COVID-19/virology , Genome, Viral , Humans , Infection Control/methods , Limit of Detection , Mass Screening/methods , RNA, Viral/genetics , RNA, Viral/isolation & purification , RNA-Directed DNA Polymerase/genetics , Reproducibility of Results , Reverse Transcription/genetics , Sensitivity and Specificity
19.
Molecules ; 26(21)2021 Oct 31.
Article in English | MEDLINE | ID: covidwho-1488680

ABSTRACT

Early diagnosis with rapid detection of the virus plays a key role in preventing the spread of infection and in treating patients effectively. In order to address the need for a straightforward detection of SARS-CoV-2 infection and assessment of viral spread, we developed rapid, sensitive, extraction-free one-step reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and reverse transcription loop-mediated isothermal amplification (RT-LAMP) tests for detecting SARS-CoV-2 in saliva. We analyzed over 700 matched pairs of saliva and nasopharyngeal swab (NSB) specimens from asymptomatic and symptomatic individuals. Saliva, as either an oral cavity swab or passive drool, was collected in an RNA stabilization buffer. The stabilized saliva specimens were heat-treated and directly analyzed without RNA extraction. The diagnostic sensitivity of saliva-based RT-qPCR was at least 95% in individuals with subclinical infection and outperformed RT-LAMP, which had at least 70% sensitivity when compared to NSBs analyzed with a clinical RT-qPCR test. The diagnostic sensitivity for passive drool saliva was higher than that of oral cavity swab specimens (95% and 87%, respectively). A rapid, sensitive one-step extraction-free RT-qPCR test for detecting SARS-CoV-2 in passive drool saliva is operationally simple and can be easily implemented using existing testing sites, thus allowing high-throughput, rapid, and repeated testing of large populations. Furthermore, saliva testing is adequate to detect individuals in an asymptomatic screening program and can help improve voluntary screening compliance for those individuals averse to various forms of nasal collections.


Subject(s)
COVID-19/diagnosis , COVID-19/genetics , Reverse Transcriptase Polymerase Chain Reaction/methods , COVID-19 Testing/methods , Humans , Mass Screening/methods , Nucleic Acid Amplification Techniques/methods , RNA/isolation & purification , RNA, Viral/genetics , SARS-CoV-2/genetics , SARS-CoV-2/pathogenicity , Saliva/chemistry , Sensitivity and Specificity , Specimen Handling/methods
20.
Viruses ; 13(10)2021 10 14.
Article in English | MEDLINE | ID: covidwho-1470995

ABSTRACT

The gold standard for diagnosis of SARS-CoV-2 infection has been nucleic acid amplification tests (NAAT). However, rapid antigen detection kits (Ag-RDTs), may offer advantages over NAAT in mass screening, generating results in minutes, both as laboratory-based test or point-of-care (POC) use for clinicians, at a lower cost. We assessed two different POC Ag-RDTs in mass screening versus NAAT for SARS-CoV-2 in a cohort of pediatric patients admitted to the Pediatric Emergency Unit of IRCCS-Polyclinic of Sant'Orsola, Bologna (from November 2020 to April 2021). All patients were screened with nasopharyngeal swabs for the detection of SARS-CoV-2-RNA and for antigen tests. Results were obtained from 1146 patients. The COVID-19 Ag FIA kit showed a baseline sensitivity of 53.8% (CI 35.4-71.4%), baseline specificity 99.7% (CI 98.4-100%) and overall accuracy of 80% (95% CI 0.68-0.91); the AFIAS COVID-19 Ag kit, baseline sensitivity of 86.4% (CI 75.0-93.9%), baseline specificity 98.3% (CI 97.1-99.1%) and overall accuracy of 95.3% (95% CI 0.92-0.99). In both tests, some samples showed very low viral load and negative Ag-RDT. This disagreement may reflect the positive inability of Ag-RDTs of detecting antigen in late phase of infection. Among all cases with positive molecular test and negative antigen test, none showed viral loads > 106 copies/mL. Finally, we found one false Ag-RDTs negative result (low cycle thresholds; 9 × 105 copies/mL). Our results suggest that both Ag-RDTs showed good performances in detection of high viral load samples, making it a feasible and effective tool for mass screening in actively infected children.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19 Serological Testing/methods , COVID-19/diagnosis , Viral Load/methods , Antigens, Viral/analysis , Child , Child, Preschool , Female , Humans , Male , Mass Screening/methods , RNA, Viral/analysis , SARS-CoV-2/genetics , SARS-CoV-2/immunology , Sensitivity and Specificity
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