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1.
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
4.
Nature ; 599(7883): 108-113, 2021 11.
Article in English | MEDLINE | ID: covidwho-1434121

ABSTRACT

Throughout the coronavirus disease 2019 (COVID-19) pandemic, countries have relied on a variety of ad hoc border control protocols to allow for non-essential travel while safeguarding public health, from quarantining all travellers to restricting entry from select nations on the basis of population-level epidemiological metrics such as cases, deaths or testing positivity rates1,2. Here we report the design and performance of a reinforcement learning system, nicknamed Eva. In the summer of 2020, Eva was deployed across all Greek borders to limit the influx of asymptomatic travellers infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and to inform border policies through real-time estimates of COVID-19 prevalence. In contrast to country-wide protocols, Eva allocated Greece's limited testing resources on the basis of incoming travellers' demographic information and testing results from previous travellers. By comparing Eva's performance against modelled counterfactual scenarios, we show that Eva identified 1.85 times as many asymptomatic, infected travellers as random surveillance testing, with up to 2-4 times as many during peak travel, and 1.25-1.45 times as many asymptomatic, infected travellers as testing policies that utilize only epidemiological metrics. We demonstrate that this latter benefit arises, at least partially, because population-level epidemiological metrics had limited predictive value for the actual prevalence of SARS-CoV-2 among asymptomatic travellers and exhibited strong country-specific idiosyncrasies in the summer of 2020. Our results raise serious concerns on the effectiveness of country-agnostic internationally proposed border control policies3 that are based on population-level epidemiological metrics. Instead, our work represents a successful example of the potential of reinforcement learning and real-time data for safeguarding public health.


Subject(s)
COVID-19/diagnosis , COVID-19/prevention & control , Carrier State/diagnosis , Carrier State/prevention & control , Machine Learning , Travel Medicine , Travel , COVID-19/epidemiology , COVID-19/transmission , Carrier State/epidemiology , Carrier State/transmission , Greece , Humans , Prevalence , Public Health
6.
PLoS One ; 16(5): e0251123, 2021.
Article in English | MEDLINE | ID: covidwho-1388912

ABSTRACT

BACKGROUND: There is a lack of population level data on risk factors, incidence and impact of SARS-CoV-2 infection in pregnant women and their babies. The primary aim of this study was to describe the incidence, characteristics and outcomes of hospitalized pregnant women with symptomatic and asymptomatic SARS-CoV-2 in the UK compared to pregnant women without SARS-CoV-2. METHODS AND FINDINGS: We conducted a national, prospective cohort study of all hospitalized pregnant women with confirmed SARS-CoV-2 from 01/03/2020 to 31/08/2020 using the UK Obstetric Surveillance System. Incidence rates were estimated using national maternity data. Overall, 1148 hospitalized women had confirmed SARS-CoV-2 in pregnancy, 63% of which were symptomatic. The estimated incidence of hospitalization with symptomatic SARS-CoV-2 was 2.0 per 1000 maternities (95% CI 1.9-2.2) and for asymptomatic SARS-CoV-2 was 1.2 per 1000 maternities (95% CI 1.1-1.4). Compared to pregnant women without SARS-CoV-2, women hospitalized with symptomatic SARS-CoV-2 were more likely to be overweight or obese (adjusted OR 1.86, (95% CI 1.39-2.48) and aOR 2.07 (1.53-2.29)), to be of Black, Asian or Other minority ethnic group (aOR 6.24, (3.93-9.90), aOR 4.36, (3.19-5.95) and aOR 12.95, (4.93-34.01)), and to have a relevant medical comorbidity (aOR 1.83 (1.32-2.54)). Hospitalized pregnant women with symptomatic SARS-CoV-2 were more likely to be admitted to intensive care (aOR 57.67, (7.80-426.70)) but the absolute risk of poor outcomes was low. Cesarean births and neonatal unit admission were increased regardless of symptom status (symptomatic aOR 2.60, (1.97-3.42) and aOR 3.08, (1.99-4.77); asymptomatic aOR 2.02, (1.52-2.70) and aOR 1.84, (1.12-3.03)). The risks of stillbirth or neonatal death were not significantly increased, regardless of symptom status. CONCLUSIONS: We have identified factors that increase the risk of symptomatic and asymptomatic SARS-CoV-2 in pregnancy. Clinicians can be reassured that the majority of women do not experience severe complications of SARS-CoV-2 in pregnancy.


Subject(s)
COVID-19/epidemiology , Carrier State/epidemiology , Pregnancy Outcome , Adult , COVID-19/complications , COVID-19/diagnosis , COVID-19/virology , Carrier State/diagnosis , Carrier State/virology , Cesarean Section , Cohort Studies , Databases, Factual , Female , Humans , Incidence , Intensive Care Units , Minority Groups/statistics & numerical data , Obesity/complications , Odds Ratio , Pregnancy , Pregnant Women , Prospective Studies , SARS-CoV-2/isolation & purification , United Kingdom/epidemiology , Young Adult
7.
PLoS Med ; 18(8): e1003735, 2021 08.
Article in English | MEDLINE | ID: covidwho-1354750

ABSTRACT

BACKGROUND: SARS-CoV-2 antigen rapid diagnostic tests (Ag-RDTs) are increasingly being integrated in testing strategies around the world. Studies of the Ag-RDTs have shown variable performance. In this systematic review and meta-analysis, we assessed the clinical accuracy (sensitivity and specificity) of commercially available Ag-RDTs. METHODS AND FINDINGS: We registered the review on PROSPERO (registration number: CRD42020225140). We systematically searched multiple databases (PubMed, Web of Science Core Collection, medRvix, bioRvix, and FIND) for publications evaluating the accuracy of Ag-RDTs for SARS-CoV-2 up until 30 April 2021. Descriptive analyses of all studies were performed, and when more than 4 studies were available, a random-effects meta-analysis was used to estimate pooled sensitivity and specificity in comparison to reverse transcription polymerase chain reaction (RT-PCR) testing. We assessed heterogeneity by subgroup analyses, and rated study quality and risk of bias using the QUADAS-2 assessment tool. From a total of 14,254 articles, we included 133 analytical and clinical studies resulting in 214 clinical accuracy datasets with 112,323 samples. Across all meta-analyzed samples, the pooled Ag-RDT sensitivity and specificity were 71.2% (95% CI 68.2% to 74.0%) and 98.9% (95% CI 98.6% to 99.1%), respectively. Sensitivity increased to 76.3% (95% CI 73.1% to 79.2%) if analysis was restricted to studies that followed the Ag-RDT manufacturers' instructions. LumiraDx showed the highest sensitivity, with 88.2% (95% CI 59.0% to 97.5%). Of instrument-free Ag-RDTs, Standard Q nasal performed best, with 80.2% sensitivity (95% CI 70.3% to 87.4%). Across all Ag-RDTs, sensitivity was markedly better on samples with lower RT-PCR cycle threshold (Ct) values, i.e., <20 (96.5%, 95% CI 92.6% to 98.4%) and <25 (95.8%, 95% CI 92.3% to 97.8%), in comparison to those with Ct ≥ 25 (50.7%, 95% CI 35.6% to 65.8%) and ≥30 (20.9%, 95% CI 12.5% to 32.8%). Testing in the first week from symptom onset resulted in substantially higher sensitivity (83.8%, 95% CI 76.3% to 89.2%) compared to testing after 1 week (61.5%, 95% CI 52.2% to 70.0%). The best Ag-RDT sensitivity was found with anterior nasal sampling (75.5%, 95% CI 70.4% to 79.9%), in comparison to other sample types (e.g., nasopharyngeal, 71.6%, 95% CI 68.1% to 74.9%), although CIs were overlapping. Concerns of bias were raised across all datasets, and financial support from the manufacturer was reported in 24.1% of datasets. Our analysis was limited by the included studies' heterogeneity in design and reporting. CONCLUSIONS: In this study we found that Ag-RDTs detect the vast majority of SARS-CoV-2-infected persons within the first week of symptom onset and those with high viral load. Thus, they can have high utility for diagnostic purposes in the early phase of disease, making them a valuable tool to fight the spread of SARS-CoV-2. Standardization in conduct and reporting of clinical accuracy studies would improve comparability and use of data.


Subject(s)
COVID-19 Serological Testing/methods , Age Factors , Antigens, Viral/analysis , COVID-19/diagnosis , COVID-19/etiology , COVID-19 Serological Testing/standards , Carrier State/diagnosis , Carrier State/virology , Humans , Nasopharynx/virology , Reagent Kits, Diagnostic , Reference Standards , SARS-CoV-2/immunology , Sensitivity and Specificity , Viral Load
8.
Sci Rep ; 11(1): 14232, 2021 07 09.
Article in English | MEDLINE | ID: covidwho-1303793

ABSTRACT

COVID-19 pandemic exerts a health care emergency around the world. The illness severity is heterogeneous. It is mostly unknown why some individuals who are positive for SARS-CoV-2 antibodies stay asymptomatic while others show moderate to severe disease symptoms. Reliable biomarkers for early detection of the disease are urgently needed to attenuate the virus's spread and help make early treatment decisions. Bioactive sphingolipids play a crucial role in the regulation of viral infections and pro-inflammatory responses involved in the severity of COVID-19. However, any roles of sphingolipids in COVID-19 development or detection remain unknown. In this study, lipidomics measurement of serum sphingolipids demonstrated that reduced sphingosine levels are highly associated with the development of symptomatic COVID-19 in the majority (99.24%) SARS-CoV-2-infected patients compared to asymptomatic counterparts. The majority of asymptomatic individuals (73%) exhibited increased acid ceramidase (AC) in their serum, measured by Western blotting, consistent with elevated sphingosine levels compared to SARS-CoV-2 antibody negative controls. AC protein was also reduced in almost all of the symptomatic patients' serum, linked to reduced sphingosine levels, measured in longitudinal acute or convalescent COVID-19 samples. Thus, reduced sphingosine levels provide a sensitive and selective serologic biomarker for the early identification of asymptomatic versus symptomatic COVID-19 patients.


Subject(s)
Acid Ceramidase/blood , COVID-19 , Carrier State , Lipid Metabolism , SARS-CoV-2/metabolism , Sphingolipids/blood , Sphingosine/blood , Adolescent , Adult , Aged , Aged, 80 and over , Biomarkers/blood , COVID-19/blood , COVID-19/diagnosis , Carrier State/blood , Carrier State/diagnosis , Female , Humans , Male , Middle Aged
9.
BMJ ; 374: n1637, 2021 07 06.
Article in English | MEDLINE | ID: covidwho-1299224

ABSTRACT

OBJECTIVE: To assess the performance of the SARS-CoV-2 antigen rapid lateral flow test (LFT) versus polymerase chain reaction testing in the asymptomatic general population attending testing centres. DESIGN: Observational cohort study. SETTING: Community LFT pilot at covid-19 testing sites in Liverpool, UK. PARTICIPANTS: 5869 asymptomatic adults (≥18 years) voluntarily attending one of 48 testing sites during 6-29 November 2020. INTERVENTIONS: Participants were tested using both an Innova LFT and a quantitative reverse-transcriptase polymerase chain reaction (RT-qPCR) test based on supervised self-administered swabbing at testing sites. MAIN OUTCOME MEASURES: Sensitivity, specificity, and predictive values of LFT compared with RT-qPCR in an epidemic steady state of covid-19 among adults with no classic symptoms of the disease. RESULTS: Of 5869 test results, 22 (0.4%) LFT results and 343 (5.8%) RT-qPCR results were void (that is, when the control line fails to appear within 30 minutes). Excluding the void results, the LFT versus RT-qPCR showed a sensitivity of 40.0% (95% confidence interval 28.5% to 52.4%; 28/70), specificity of 99.9% (99.8% to 99.99%; 5431/5434), positive predictive value of 90.3% (74.2% to 98.0%; 28/31), and negative predictive value of 99.2% (99.0% to 99.4%; 5431/5473). When the void samples were assumed to be negative, a sensitivity was observed for LFT of 37.8% (26.8% to 49.9%; 28/74), specificity of 99.6% (99.4% to 99.8%; 5431/5452), positive predictive value of 84.8% (68.1% to 94.9%; 28/33), and negative predictive value of 93.4% (92.7% to 94.0%; 5431/5814). The sensitivity in participants with an RT-qPCR cycle threshold (Ct) of <18.3 (approximate viral loads >106 RNA copies/mL) was 90.9% (58.7% to 99.8%; 10/11), a Ct of <24.4 (>104 RNA copies/mL) was 69.4% (51.9% to 83.7%; 25/36), and a Ct of >24.4 (<104 RNA copies/mL) was 9.7% (1.9% to 23.7%; 3/34). LFT is likely to detect at least three fifths and at most 998 in every 1000 people with a positive RT-qPCR test result with high viral load. CONCLUSIONS: The Innova LFT can be useful for identifying infections among adults who report no symptoms of covid-19, particularly those with high viral load who are more likely to infect others. The number of asymptomatic adults with lower Ct (indicating higher viral load) missed by LFT, although small, should be considered when using single LFT in high consequence settings. Clear and accurate communication with the public about how to interpret test results is important, given the chance of missing some cases, even at high viral loads. Further research is needed to understand how infectiousness is reflected in the viral antigen shedding detected by LFT versus the viral loads approximated by RT-qPCR.


Subject(s)
COVID-19 Nucleic Acid Testing , COVID-19 Serological Testing , COVID-19/diagnosis , Carrier State/diagnosis , Carrier State/virology , Adult , COVID-19/complications , Cohort Studies , Female , Humans , Male , Pilot Projects , Predictive Value of Tests , ROC Curve , Reverse Transcriptase Polymerase Chain Reaction , United Kingdom
10.
N Engl J Med ; 385(4): 320-329, 2021 07 22.
Article in English | MEDLINE | ID: covidwho-1287848

ABSTRACT

BACKGROUND: Information is limited regarding the effectiveness of the two-dose messenger RNA (mRNA) vaccines BNT162b2 (Pfizer-BioNTech) and mRNA-1273 (Moderna) in preventing infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and in attenuating coronavirus disease 2019 (Covid-19) when administered in real-world conditions. METHODS: We conducted a prospective cohort study involving 3975 health care personnel, first responders, and other essential and frontline workers. From December 14, 2020, to April 10, 2021, the participants completed weekly SARS-CoV-2 testing by providing mid-turbinate nasal swabs for qualitative and quantitative reverse-transcriptase-polymerase-chain-reaction (RT-PCR) analysis. The formula for calculating vaccine effectiveness was 100% × (1 - hazard ratio for SARS-CoV-2 infection in vaccinated vs. unvaccinated participants), with adjustments for the propensity to be vaccinated, study site, occupation, and local viral circulation. RESULTS: SARS-CoV-2 was detected in 204 participants (5%), of whom 5 were fully vaccinated (≥14 days after dose 2), 11 partially vaccinated (≥14 days after dose 1 and <14 days after dose 2), and 156 unvaccinated; the 32 participants with indeterminate vaccination status (<14 days after dose 1) were excluded. Adjusted vaccine effectiveness was 91% (95% confidence interval [CI], 76 to 97) with full vaccination and 81% (95% CI, 64 to 90) with partial vaccination. Among participants with SARS-CoV-2 infection, the mean viral RNA load was 40% lower (95% CI, 16 to 57) in partially or fully vaccinated participants than in unvaccinated participants. In addition, the risk of febrile symptoms was 58% lower (relative risk, 0.42; 95% CI, 0.18 to 0.98) and the duration of illness was shorter, with 2.3 fewer days spent sick in bed (95% CI, 0.8 to 3.7). CONCLUSIONS: Authorized mRNA vaccines were highly effective among working-age adults in preventing SARS-CoV-2 infection when administered in real-world conditions, and the vaccines attenuated the viral RNA load, risk of febrile symptoms, and duration of illness among those who had breakthrough infection despite vaccination. (Funded by the National Center for Immunization and Respiratory Diseases and the Centers for Disease Control and Prevention.).


Subject(s)
COVID-19 Vaccines , COVID-19/prevention & control , Viral Load , Adolescent , Adult , COVID-19/diagnosis , COVID-19/virology , COVID-19 Nucleic Acid Testing , COVID-19 Vaccines/immunology , Carrier State/diagnosis , Carrier State/prevention & control , Emergency Responders , Female , Health Personnel , Humans , Male , Middle Aged , Patient Acuity , Prospective Studies , SARS-CoV-2/isolation & purification , Treatment Outcome , Young Adult
11.
Rev Esp Anestesiol Reanim (Engl Ed) ; 68(6): 346-352, 2021.
Article in English | MEDLINE | ID: covidwho-1263366

ABSTRACT

INTRODUCTION: Due to its high transmissibility, measures aimed at reducing the spread of SARS CoV2 have become mandatory. Different organizations have recommended performing polymerase chain reaction tests (PCR) as part of the preoperative screening of surgical patients. We aimed to determine the performance of PCR testing to detect asymptomatic carriers. METHODS: Observational study carried out at a tertiary care center. We compared the results of preoperative real-time reverse-transcription-PCR test (RT-PCR) performed on a cohort of patients pending surgery with the results we would have expected assuming the epidemiological data released by government offices. RESULTS: We registered no positives in the 2,722 preoperative RT-PCR tests performed in our health care area between epidemiological Weeks 18 to 21, meaning a cumulative incidence trending to zero. Assuming public epidemiological data, the probabilistic projection of potential asymptomatic individuals ranged from 0.27 × 10e-4 (according to official data of new cases diagnosed by PCR) to 4.69 × 10e-4 if we assumed cases confirmed by IgG test in our province. Assuming a RT-PCR sensitivity of 95%, to obtain a positive result we should perform 38,461 and 2,028 tests respectively. CONCLUSIONS: In scenarios of very low prevalence and despite high sensitivity scores, indiscriminate preoperative RT-PCR screening is of a questionable effectiveness for detecting asymptomatic carriers. Our findings evidence the difficulty of establishing reliable predictive models for the episodic and rapidly evolving incidence of infections such as has characterized the SARS CoV2 pandemic.


Subject(s)
COVID-19 Nucleic Acid Testing , COVID-19/diagnosis , Carrier State/diagnosis , Pandemics , Preoperative Care , SARS-CoV-2 , COVID-19/epidemiology , COVID-19 Nucleic Acid Testing/statistics & numerical data , Carrier State/epidemiology , Humans , Incidence , Prevalence , Retrospective Studies , Spain/epidemiology
12.
Proc Natl Acad Sci U S A ; 118(21)2021 05 25.
Article in English | MEDLINE | ID: covidwho-1223146

ABSTRACT

We analyze data from the fall 2020 pandemic response efforts at the University of Colorado Boulder, where more than 72,500 saliva samples were tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using qRT-PCR. All samples were collected from individuals who reported no symptoms associated with COVID-19 on the day of collection. From these, 1,405 positive cases were identified. The distribution of viral loads within these asymptomatic individuals was indistinguishable from what has been previously observed in symptomatic individuals. Regardless of symptomatic status, ∼50% of individuals who test positive for SARS-CoV-2 seem to be in noninfectious phases of the disease, based on having low viral loads in a range from which live virus has rarely been isolated. We find that, at any given time, just 2% of individuals carry 90% of the virions circulating within communities, serving as viral "supercarriers" and possibly also superspreaders.


Subject(s)
COVID-19/virology , Carrier State/virology , SARS-CoV-2 , Asymptomatic Infections/epidemiology , COVID-19/diagnosis , COVID-19/epidemiology , COVID-19/transmission , Carrier State/diagnosis , Carrier State/epidemiology , Carrier State/transmission , Colorado/epidemiology , Hospitalization/statistics & numerical data , Humans , Mass Screening/statistics & numerical data , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Saliva/virology , Universities , Viral Load , Virion
13.
Viruses ; 13(5)2021 04 30.
Article in English | MEDLINE | ID: covidwho-1217119

ABSTRACT

It is unclear whether universal PCR screening for SARS-CoV-2 in asymptomatic individuals prior to admission is useful. From April to December 2020, the positive rate of universal pre-admission screening was 0.005% (4/76,521) in a tertiary care hospital in Korea. The positive rates were not different between the periods (period 1 (daily new patients of <1 per million inhabitants) vs. period 2 (1-8.3 per million inhabitants) vs. period 3 (10.3 to 20 per million inhabitants); P = 0.45). Universal pre-admission screening for SARS-CoV-2 had a lower positive rate than that of symptom-based screening (0.005% vs. 0.049% (53/109,257), p < 0.001). In addition, seven patients with negative pre-admission test results had subsequent positive PCR during hospitalization, and four patients had secondary transmission. Universal pre-admission PCR screening may not be practical in settings of low prevalence of COVID-19, and negative PCR results at admission should not serve as a basis for underestimating the risk of nosocomial spread from asymptomatic patients.


Subject(s)
Asymptomatic Diseases/epidemiology , COVID-19 Nucleic Acid Testing/methods , COVID-19 , Carrier State , Nasopharynx/virology , SARS-CoV-2/isolation & purification , COVID-19/diagnosis , COVID-19/epidemiology , Carrier State/diagnosis , Carrier State/epidemiology , Humans , Prevalence , Republic of Korea/epidemiology , Tertiary Care Centers
14.
PLoS Biol ; 19(4): e3001216, 2021 04.
Article in English | MEDLINE | ID: covidwho-1207620

ABSTRACT

Lateral flow devices (LFDs) are quickly being implemented for use in large-scale population surveillance programs for SARS-CoV-2 infection in the United Kingdom. These programs have been piloted in city-wide screening in the city of Liverpool and are now being rolled out to support care home visits and the return home of University students for the Christmas break. Here, we present data on the performance of LFDs to test almost 8,000 students at the University of Birmingham between December 2 and December 9, 2020. The performance is validated against almost 800 samples using PCR performed in the University Pillar 2 testing lab and theoretically validated on thousands of Pillar 2 PCR testing results performed on low-prevalence care home testing samples. Our data show that LFDs do not detect infections presenting with PCR Ct values over 29 to 30 as determined using the Thermo Fisher TaqPath asssay. This may be of particular importance in detecting individuals that are either at the early, or late stages of infection, and reinforces the need for frequent, recurrent testing.


Subject(s)
COVID-19 Serological Testing , COVID-19/diagnosis , Carrier State/diagnosis , SARS-CoV-2/isolation & purification , COVID-19/epidemiology , COVID-19 Nucleic Acid Testing , Carrier State/epidemiology , Humans , Immunoassay , Mass Screening , Prevalence , SARS-CoV-2/genetics , SARS-CoV-2/immunology , Sensitivity and Specificity , United Kingdom/epidemiology , Universities
15.
J Med Virol ; 93(3): 1828-1831, 2021 03.
Article in English | MEDLINE | ID: covidwho-1196520

ABSTRACT

To gain knowledge about the role of young children attending daycare in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic, a random sample of children (n = 84) aged between 6 and 30 months attending daycare in Belgium was studied shortly after the start of the epidemic (February 29th) and before the lockdown (March 18th) by performing in-house SARS-CoV-2 real-time polymerase chain reaction. No asymptomatic carriage of SARS-CoV-2 was detected, whereas common cold symptoms were common (51.2%). Our study shows that in Belgium, there was no sign of early introduction into daycare centers at the moment children being not yet isolated at home, although the virus was clearly circulating. It is clear that more evidence is needed to understand the actual role of young children in the transmission of SARS-CoV-2 and their infection risk when attending daycare.


Subject(s)
COVID-19/epidemiology , Carrier State/diagnosis , Carrier State/virology , Child Day Care Centers/statistics & numerical data , Belgium/epidemiology , Child, Preschool , Humans , Infant , Real-Time Polymerase Chain Reaction/methods , SARS-CoV-2/genetics
16.
Epidemiol Infect ; 149: e91, 2021 04 14.
Article in English | MEDLINE | ID: covidwho-1182770

ABSTRACT

An outbreak of SARS-CoV2 infection in a Barcelona prison was studied. One hundred and forty-eight inmates and 36 prison staff were evaluated by rt-PCR, and 24.1% (40 prisoners, two health workers and four non-health workers) tested positive. In all, 94.8% of cases were asymptomatic. The inmates were isolated in prison module 4, which was converted into an emergency COVID unit. There were no deaths. Generalised screening and the isolation and evaluation of the people infected were key measures. Symptom-based surveillance must be supplemented by rapid contact-based monitoring in order to avoid asymptomatic spread among prisoners and the community at large.


Subject(s)
COVID-19/epidemiology , Carrier State/epidemiology , Infection Control , Prisons , Public Health , Quarantine , Adult , Aged , COVID-19/diagnosis , COVID-19/prevention & control , COVID-19 Nucleic Acid Testing , Carrier State/diagnosis , Carrier State/prevention & control , Disease Outbreaks , Health Personnel , Hospitalization , Humans , Male , Middle Aged , Prisoners , SARS-CoV-2 , Severity of Illness Index , Spain/epidemiology , Young Adult
17.
Respiration ; 100(6): 510-514, 2021.
Article in English | MEDLINE | ID: covidwho-1158153

ABSTRACT

BACKGROUND: The coronavirus disease 2019 (COVID-19) pandemic has drastically affected hospital and operating room (OR) workflow around the world as well as trainee education. Many institutions have instituted mandatory preoperative SARS-CoV-2 PCR nasopharyngeal swab (NS) testing in patients who are low risk for COVID-19 prior to elective cases. This method, however, is challenging as the sensitivity, specificity, and overall reliability of testing remains unclear. OBJECTIVES: The objective of this study was to assess the concordance of a negative NS in low risk preoperative patients with lower airway bronchoalveolar lavage (BAL) specimens obtained from the same patients. METHODS: We prospectively sent intraoperative lower airway BAL samples collected within 48 h of a negative mandatory preoperative NS for SARS-CoV-2 PCR testing. All adult patients undergoing a scheduled bronchoscopic procedure for any reason were enrolled, including elective and nonelective cases. RESULTS: One-hundred eighty-nine patients were included. All BAL specimens were negative for SARS-CoV-2 indicative of 100% concordance between testing modalities. CONCLUSIONS: These results are promising and suggest that preoperative nasopharyngeal SARS-CoV-2 testing provides adequate screening to rule out active COVID-19 infection prior to OR cases in a population characterized as low risk by negative symptom screening. This information can be used for both pre-procedural screening and when reintroducing trainees into the workforce.


Subject(s)
Bronchoalveolar Lavage Fluid , COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , Carrier State/diagnosis , Nasopharynx , Adult , Aged , Aged, 80 and over , Bronchoalveolar Lavage , Bronchoscopy , Female , Humans , Male , Mass Screening , Middle Aged , Preoperative Care , Prospective Studies , Risk , Sensitivity and Specificity , Young Adult
18.
Elife ; 102021 03 29.
Article in English | MEDLINE | ID: covidwho-1156211

ABSTRACT

Here, we develop a simple molecular test for SARS-CoV-2 in saliva based on reverse transcription loop-mediated isothermal amplification. The test has two steps: (1) heat saliva with a stabilization solution and (2) detect virus by incubating with a primer/enzyme mix. After incubation, saliva samples containing the SARS-CoV-2 genome turn bright yellow. Because this test is pH dependent, it can react falsely to some naturally acidic saliva samples. We report unique saliva stabilization protocols that rendered 295 healthy saliva samples compatible with the test, producing zero false positives. We also evaluated the test on 278 saliva samples from individuals who were infected with SARS-CoV-2 but had no symptoms at the time of saliva collection, and from 54 matched pairs of saliva and anterior nasal samples from infected individuals. The Saliva TwoStep test described herein identified infections with 94% sensitivity and >99% specificity in individuals with sub-clinical (asymptomatic or pre-symptomatic) infections.


Subject(s)
COVID-19/diagnosis , COVID-19/virology , Carrier State/diagnosis , Carrier State/virology , SARS-CoV-2/isolation & purification , Saliva/virology , COVID-19/metabolism , COVID-19 Testing , Humans , Molecular Diagnostic Techniques/methods , Nucleic Acid Amplification Techniques/methods , RNA, Viral/genetics , SARS-CoV-2/genetics , Sensitivity and Specificity , Specimen Handling/methods
19.
Lancet Infect Dis ; 21(7): 929-938, 2021 07.
Article in English | MEDLINE | ID: covidwho-1145005

ABSTRACT

BACKGROUND: Routine viral testing strategies for SARS-CoV-2 infection might facilitate safe airline travel during the COVID-19 pandemic and mitigate global spread of the virus. However, the effectiveness of these test-and-travel strategies to reduce passenger risk of SARS-CoV-2 infection and population-level transmission remains unknown. METHODS: In this simulation study, we developed a microsimulation of SARS-CoV-2 transmission in a cohort of 100 000 US domestic airline travellers using publicly available data on COVID-19 clinical cases and published natural history parameters to assign individuals one of five health states of susceptible to infection, latent period, early infection, late infection, or recovered. We estimated a per-day risk of infection with SARS-CoV-2 corresponding to a daily incidence of 150 infections per 100 000 people. We assessed five testing strategies: (1) anterior nasal PCR test within 3 days of departure, (2) PCR within 3 days of departure and 5 days after arrival, (3) rapid antigen test on the day of travel (assuming 90% of the sensitivity of PCR during active infection), (4) rapid antigen test on the day of travel and PCR test 5 days after arrival, and (5) PCR test 5 days after arrival. Strategies 2 and 4 included a 5-day quarantine after arrival. The travel period was defined as 3 days before travel to 2 weeks after travel. Under each scenario, individuals who tested positive before travel were not permitted to travel. The primary study outcome was cumulative number of infectious days in the cohort over the travel period without isolation or quarantine (population-level transmission risk), and the key secondary outcome was the number of infectious people detected on the day of travel (passenger risk of infection). FINDINGS: We estimated that in a cohort of 100 000 airline travellers, in a scenario with no testing or screening, there would be 8357 (95% uncertainty interval 6144-12831) infectious days with 649 (505-950) actively infectious passengers on the day of travel. The pre-travel PCR test reduced the number of infectious days from 8357 to 5401 (3917-8677), a reduction of 36% (29-41) compared with the base case, and identified 569 (88% [76-92]) of 649 actively infectious travellers on the day of flight; the addition of post-travel quarantine and PCR reduced the number of infectious days to 2520 days (1849-4158), a reduction of 70% (64-75) compared with the base case. The rapid antigen test on the day of travel reduced the number of infectious days to 5674 (4126-9081), a reduction of 32% (26-38) compared with the base case, and identified 560 (86% [83-89]) actively infectious travellers; the addition of post-travel quarantine and PCR reduced the number of infectious days to 3124 (2356-495), a reduction of 63% (58-66) compared with the base case. The post-travel PCR alone reduced the number of infectious days to 4851 (3714-7679), a reduction of 42% (35-49) compared with the base case. INTERPRETATION: Routine asymptomatic testing for SARS-CoV-2 before travel can be an effective strategy to reduce passenger risk of infection during travel, although abbreviated quarantine with post-travel testing is probably needed to reduce population-level transmission due to importation of infection when travelling from a high to low incidence setting. FUNDING: University of California, San Francisco.


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , Carrier State/diagnosis , Pandemics/prevention & control , Aircraft/statistics & numerical data , Asymptomatic Infections , COVID-19/transmission , COVID-19/virology , Carrier State/virology , Computer Simulation , Diagnostic Tests, Routine/statistics & numerical data , Humans , SARS-CoV-2/pathogenicity , Travel/statistics & numerical data
20.
Emerg Infect Dis ; 27(4): 1249-1251, 2021 04.
Article in English | MEDLINE | ID: covidwho-1145546
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