Comparison of participant-collected nasal and staff-collected oropharyngeal specimens for human ribonuclease P detection with RT-PCR during a community-based study

Abstract Background Ageing affects immunity, potentially altering fever response to infection. We assess effects of biological variables on basal temperature, and during COVID-19 infection, proposing an updated temperature threshold for older adults ≥65 years. Methods Participants were from four cohorts: 1089 unaffected adult TwinsUK volunteers; 520 adults with emergency admission to a London hospital with RT-PCR confirmed SARS-CoV-2 infection; 757 adults with emergency admission to a Birmingham hospital with RT-PCR confirmed SARS-CoV-2 infection and 3972 adult community-based COVID Symptom Study participants self-reporting a positive RT-PCR test. Heritability was assessed using saturated and univariate ACE models; mixed-effect and multivariable linear regression examined associations between temperature, age, sex and BMI; multivariable logistic regression examined associations between fever (≥37.8°C) and age; receiver operating characteristic (ROC) analysis was used to identify temperature threshold for adults ≥ 65 years. Results Among unaffected volunteers, lower BMI (p=0.001), and increasing age (p<0.001) associated with lower basal temperature. Basal temperature showed a heritability of 47% 95% Confidence Interval 18-57%). In COVID-19+ participants, increasing age was associated with lower temperatures in Birmingham and community-based cohorts (p<0.001). For each additional year of age, participants were 1% less likely to demonstrate a fever ≥37.8°C (OR 0.99; p<0.001). Combining healthy and COVID-19+ participants, a temperature of 37.4°C in adults ≥65 years had similar sensitivity and specificity to 37.8°C in adults <65 years for discriminating infection. Conclusions Ageing affects temperature in health and acute infection, with significant heritability, indicating genetic factors contribute to temperature regulation. Our observations suggest a lower threshold (37.4°C/97.3°F) for identifying fever in older adults ≥65 years.

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Assessing the burden of Covid-19 in the slums of Bangalore city: Results of Rapid Community Survey

Indian Journal of Community Health ◽

10.47203/ijch.2021.v33i03.012 ◽

2021 ◽

Vol 33 (3) ◽

pp. 475-479

Author(s):

Ranganath Thimnahalli Sobagaiah ◽

Ramesh Nugehally Raju Masthi ◽

Lalitha Krishnappa ◽

Ambika Rangaiah ◽

Girish Nagaraja Rao ◽

...

Keyword(s):

Inner Core ◽

Venous Blood ◽

Sampling Technique ◽

Community Survey ◽

Age Group ◽

Rt Pcr ◽

Community Based ◽

Cross Sectional ◽

Bangalore City ◽

Cluster Random Sampling

Background: Karnataka, more so Bangalore, reported an increase in number of COVID-19 cases in early April 2021. Objective: To assess the burden of COVID-19 in the slums of Bengaluru city. Materials and Methods: A cross-sectional multi centre community-based study was done in the 2nd and 3rd week of April 2021 in 24 different slums in Bangalore city. WHO cluster random sampling technique was followed. Swabs for RTPCR test and 4 ml of venous blood was collected from 728 subjects more than 18 years of age. Results: A total of 51 (7%) subjects were positive for COVID-19 through RT-PCR. Majority 33 (56.9%) were in the age group of 18-44 years. 148 (20.3%) subjects were sero-positive on blood examination and 18-44 years was the (59.4%) preponderant age group. Overall seropositivity was 20.3% (95%CI; 17.4-23.2) and RT-PCR positivity is 7% (95%CI; 5.2-8.8%) among the subjects surveyed. In the inner core area of Bangalore, seropositivity was 24.2% (95%CI; 21.0 – 27.3) and RT-PCR positivity was 8% (95%CI; 6.1-9.9). Two doses of COVID-19 vaccine were taken only by 1.55% subjects during the study period. Conclusion: The study showed that one in 5 subjects were sero-positive to SARS-CoV-2 and one in 15 individuals had active COVID-19 infection.

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Different diagnostic methods for detection of influenza epidemics

Epidemiology and Infection ◽

10.1017/s0950268899003751 ◽

2000 ◽

Vol 124 (3) ◽

pp. 515-522 ◽

Cited By ~ 12

Author(s):

H. REBELO-de-ANDRADE ◽

M. C. ZAMBON

Keyword(s):

Virus Isolation ◽

Diagnostic Techniques ◽

Influenza Viruses ◽

Diagnostic Methods ◽

Specific Method ◽

Surveillance Systems ◽

Rt Pcr ◽

Community Based ◽

Surveillance Network ◽

Influenza Activity

Linking continuous community-based morbidity recording of influenza-like illness (ILI) with virological sampling has consistently proved its value as one of the earliest indicators of circulating influenza activity. The clinical morbidity recording in the Portuguese national surveillance network, during a 7-year period, and the contribution of different diagnostic techniques, including virus isolation, multiplex RT–PCR, immunocapture enzyme linked immunoassay (EIA) and complement fixation tests (CFTs) for the detection of influenza in such a community-based setting is described and evaluated in this study. There was good correlation between the increase of morbidity, total samples taken and the detection of influenza virus by all the methods although this was less evident for virus isolation and EIA than for RT–PCR or serology. From a total of 1685 throat swabs collected from cases of ILI, 43·6% were RT–PCR positive, 17·5% were positive by capture EIA and in 5% virus isolates were made. The detection of influenza by RT–PCR occurred earlier than by any other method and showed the best correlation with epidemic patterns of morbidity registration. We conclude that in surveillance systems where virus culture is sub-optimal, RT–PCR provides a rapid, sensitive, specific method for detecting influenza viruses from community-based sampling.

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A primary care approach to the COVID-19 pandemic: clinical features and natural history of 2,073 suspected cases in the Corona São Caetano programme, São Paulo, Brazil

10.1101/2020.06.23.20138081 ◽

2020 ◽

Cited By ~ 5

Author(s):

Fabio E Leal ◽

Maria C Mendes-Correa ◽

Lewis F Buss ◽

Silvia F Costa ◽

Joao CS Bizario ◽

...

Keyword(s):

Primary Care ◽

Natural History ◽

Clinical Features ◽

Older Patients ◽

Population Based ◽

Rt Pcr ◽

Community Based ◽

Care Approach ◽

History Of ◽

At Home

ABSTRACTBackgroundDespite most cases not requiring hospital care, there are limited community-based clinical data on COVID-19.Methods and findingsThe Corona São Caetano program is a primary care initiative offering COVID-19 care to all residents of São Caetano do Sul, Brazil. After triage of potentially severe cases, consecutive patients presenting between 13th April and 13th May 2020 were tested at home with SARS-CoV-2 reverse transcriptase (RT) PCR; positive patients were followed up for 14 days. RT-PCR-negative patients were offered SARS-CoV-2 serology. We describe the clinical features, virology and natural history of this prospective population-based cohort. Of 2,073 suspected COVID-19 cases, 1,583 (76·4%) were tested by RT-PCR, of whom 444 (28·0%, 95%CI: 25·9% - 30·3%) were positive; 604/1,136 (53%) RT-PCR-negative patients underwent serology, of whom 52 (8·6%) tested SARS-CoV-2 seropositive. The most common symptoms of COVID-19 were cough, fatigue, myalgia and headache; whereas self-reported fever, anosmia, and ageusia were most associated with a positive COVID-19 diagnosis. RT-PCR cycle thresholds were lower in men, older patients, those with fever and arthralgia, and around symptom onset. The rates of hospitalization and death among 444 RT-PCR-positive cases were 6·7% and 0·7%, respectively, with older age and obesity more frequent in the hospitalized group.ConclusionsCOVID-19 presents similarly to other mild respiratory disease in primary care. Some symptoms assist the differential diagnosis. Most patients can be managed at home.

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Salivary detection of COVID-19. Clinical performance of oral sponge sampling for SARS-CoV-2 testing

10.1101/2021.02.17.21251556 ◽

2021 ◽

Author(s):

Charles Hugo Marquette ◽

Jacques Boutros ◽

Jonathan Benzaquen ◽

Marius Ilié ◽

Mickelina Labaky ◽

...

Keyword(s):

Mass Screening ◽

Clinical Performance ◽

Close Contact ◽

Low Cost ◽

Sampling Technique ◽

Contact Tracing ◽

Rt Pcr ◽

Community Based ◽

Attending Physician ◽

Close Contacts

ABSTRACTBackgroundThe current diagnostic standard for coronavirus 2019 disease (COVID-19) is reverse transcriptase-polymerase chain reaction (RT-PCR) testing with naso-pharyngeal (NP) swabs. The invasiveness and need for trained personnel make the NP technique unsuited for repeated community-based mass screening. We developed a technique to collect saliva in a simple and easy way with the sponges that are usually used for tamponade of epistaxis. This study was carried out to validate the clinical performance of oral sponge (OS) sampling for SARS-CoV-2 testing.MethodsOver a period of 22 weeks, we collected prospectively 409 paired NP and OS samples from consecutive subjects presenting to a public community-based free screening center. Subjects were referred by their attending physician because of recent COVID-19 symptoms (n=147) or by the contact tracing staff of the French public health insurance since they were considered as close contacts of a laboratory-confirmed COVID-19 case (n=262).ResultsIn symptomatic subjects, RT-PCR SARS-CoV-2 testing with OS showed a 96.5% (95%CI: 89.6-94.8) concordance with NP testing, and, a 93.3% [95%CI: 89.1-97.3] sensitivity. In close contacts the NP-OS concordance (93.8% [95%CI: 90.9-96.7]) and OS sensitivity (71.9% [95%CI: 66.5-77.3]) were slightly lower.ConclusionThese results strongly suggest that OS testing is a straightforward, low-cost and high-throughput sampling method that can be used for frequent RT-PCR testing of COVID-19 patients and mass screening of populations.Summary of the “take home” messageOS sampling for SARS-CoV2 RT-PCR is an easy to perform, straightforward self-administered sampling technique, which has a sensitivity of up to 93.3% in symptomatic patients and 71% in close contact subjects.

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Diagnostic accuracy of two commercial SARS-CoV-2 Antigen-detecting rapid tests at the point of care in community-based testing centers

10.1101/2020.11.20.20235341 ◽

2020 ◽

Cited By ~ 4

Author(s):

Alice Berger ◽

Marie Therese Ngo Nsoga ◽

Francisco Javier Perez-Rodriguez ◽

Yasmine Abi Aad ◽

Pascale Sattonnet-Roche ◽

...

Keyword(s):

Diagnostic Tests ◽

Point Of Care ◽

Rapid Test ◽

Diagnostic Value ◽

Rapid Diagnostic Tests ◽

Ease Of Use ◽

Rt Pcr ◽

Test Device ◽

Community Based ◽

Rapid Tests

AbstractBackgroundAntigen-detecting rapid diagnostic tests for SARS-CoV-2 offer new opportunities for the quick and laboratory-independent identification of infected individuals for control of the SARS-CoV-2 pandemic.MethodsWe performed a prospective, single-center, point of care validation of two antigen-detecting rapid diagnostic tests (Ag-RDT) in comparison to RT-PCR on nasopharyngeal swabs.FindingsBetween October 9th and 23rd, 2020, 1064 participants were enrolled. The Panbio™Covid-19 Ag Rapid Test device (Abbott) was validated in 535 participants, with 106 positive Ag-RDT results out of 124 positive RT-PCR individuals, yielding a sensitivity of 85.5% (95% CI: 78.0–91.2). Specificity was 100.0% (95% CI: 99.1–100) in 411 RT-PCR negative individuals. The Standard Q Ag-RDT (SD Biosensor, Roche) was validated in 529 participants, with 170 positive Ag-RDT results out of 191 positive RT-PCR individuals, yielding a sensitivity of 89.0% (95%CI: 83.7–93.1). One false positive result was obtained in 338 RT-PCR negative individuals, yielding a specificity of 99.7% (95%CI: 98.4–100). For individuals presenting with fever 1-5 days post symptom onset, combined Ag-RDT sensitivity was above 95%.InterpretationWe provide an independent validation of two widely available commercial Ag-RDTs, both meeting WHO criteria of ≥80% sensitivity and ≥97% specificity. Although less sensitive than RT-PCR, these assays could be beneficial due to their rapid results, ease of use, and independence from existing laboratory structures. Testing criteria focusing on patients with typical symptoms in their early symptomatic period onset could further increase diagnostic value.FundingFoundation of Innovative Diagnostics (FIND), Fondation privée des HUG, Pictet Charitable Foundation.

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Diagnostic accuracy of two commercial SARS-CoV-2 antigen-detecting rapid tests at the point of care in community-based testing centers

PLoS ONE ◽

10.1371/journal.pone.0248921 ◽

2021 ◽

Vol 16 (3) ◽

pp. e0248921

Author(s):

Alice Berger ◽

Marie Therese Ngo Nsoga ◽

Francisco Javier Perez-Rodriguez ◽

Yasmine Abi Aad ◽

Pascale Sattonnet-Roche ◽

...

Keyword(s):

Diagnostic Accuracy ◽

Point Of Care ◽

Rapid Test ◽

Diagnostic Value ◽

Ease Of Use ◽

Lower Sensitivity ◽

Rt Pcr ◽

Test Device ◽

Community Based ◽

Rapid Tests

Objectives Determine the diagnostic accuracy of two antigen-detecting rapid diagnostic tests (Ag-RDT) for SARS-CoV-2 at the point of care and define individuals’ characteristics providing best performance. Methods We performed a prospective, single-center, point of care validation of two Ag-RDT in comparison to RT-PCR on nasopharyngeal swabs. Results Between October 9th and 23rd, 2020, 1064 participants were enrolled. The PanbioTM Covid-19 Ag Rapid Test device (Abbott) was validated in 535 participants, with 106 positive Ag-RDT results out of 124 positive RT-PCR individuals, yielding a sensitivity of 85.5% (95% CI: 78.0–91.2). Specificity was 100.0% (95% CI: 99.1–100) in 411 RT-PCR negative individuals. The Standard Q Ag-RDT (SD Biosensor, Roche) was validated in 529 participants, with 170 positive Ag-RDT results out of 191 positive RT-PCR individuals, yielding a sensitivity of 89.0% (95%CI: 83.7–93.1). One false positive result was obtained in 338 RT-PCR negative individuals, yielding a specificity of 99.7% (95%CI: 98.4–100). For individuals presenting with fever 1–5 days post symptom onset, combined Ag-RDT sensitivity was above 95%. Lower sensitivity of 88.2% was seen on the same day of symptom development (day 0). Conclusions We provide an independent validation of two widely available commercial Ag-RDTs, both meeting WHO criteria of ≥80% sensitivity and ≥97% specificity. Although less sensitive than RT-PCR, these assays could be beneficial due to their rapid results, ease of use, and independence from existing laboratory structures. Testing criteria focusing on patients with typical symptoms in their early symptomatic period onset could further increase diagnostic value.

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Autism and COVID-19: A Case Series in a Neurodevelopmental Unit

Journal of Clinical Medicine ◽

10.3390/jcm9092937 ◽

2020 ◽

Vol 9 (9) ◽

pp. 2937

Author(s):

Leslie Nollace ◽

Cora Cravero ◽

Alice Abbou ◽

Brice Mazda-Walter ◽

Alexandre Bleibtreu ◽

...

Keyword(s):

Challenging Behaviors ◽

Case Series ◽

Rt Pcr ◽

Community Based ◽

Respiratory Dysfunction ◽

Upper Respiratory Infection ◽

Staff Members ◽

Viral Spread ◽

Close Cooperation

Background: COVID-19 has become pandemic and can impact individuals with autism as well. Here, we report a case series admitted to a neurobehavioral unit dedicated to challenging behaviors in patients with autism. Methods: We describe 16 patients (mean age 20.8 years; range 12–43 years; 76% male) with autism hospitalized between March 2020 and mid-April 2020 for challenging behaviors, for which COVID-19 disease has been suspected and who needed both psychiatric and medical care. A close cooperation with the Infectious and Tropical Diseases Department was organized to limit viral spread and training sessions (e.g., hygiene, clinical COVID-19 monitoring, virus testing) were given to staff members. Results: Most patients had severe autism and severe/moderate intellectual disability. Eleven patients were already in the unit when it was hit by the pandemic, and five were admitted from the community. Based on a virus search via reverse transcriptase polymerase chain reaction (RT-PCR) or serology at the 2-month follow-up, we had 11 confirmed COVID-19 cases. The main COVID-19 symptoms included benign upper respiratory infection signs (N = 9, 81.8%), diarrhea (N = 7, 63.6%), fatigue (N = 7, 63.6%), and respiratory signs (N = 5, 45.5%), including one patient who needed oxygen therapy. Three patients remained asymptomatic and COVID-19-free (including two under immunosuppressive treatments). Among the symptomatic patients, five showed atypical behaviors that we understood as idiosyncratic manifestations (e.g., irrepressible licking behavior). On day 14, only one patient with respiratory dysfunction still had a positive RT-PCR SARS-CoV-2 test. Conclusions: Organizing a COVID+ unit for patients with autism is realistic and requires close collaboration with infectologists. We believe that this initiative should be promoted to limit both the spread of the virus and the ostracism of patients with autism and challenging behaviors.

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Salivary detection of COVID-19. Clinical performance of oral sponge sampling for SARS-CoV-2 testing

ERJ Open Research ◽

10.1183/23120541.00396-2021 ◽

2021 ◽

pp. 00396-2021

Author(s):

Jacques Boutros ◽

Jonathan Benzaquen ◽

Charles Hugo Marquette ◽

Marius Ilié ◽

Mickelina Labaky ◽

...

Keyword(s):

Mass Screening ◽

Sampling Method ◽

Clinical Performance ◽

Low Cost ◽

Contact Tracing ◽

Rt Pcr ◽

Community Based ◽

Polymerase Chain ◽

Attending Physician ◽

Close Contacts

BackgroundThe current diagnostic standard for coronavirus 2019 disease (COVID-19) is reverse transcriptase-polymerase chain reaction (RT-PCR) testing with naso-pharyngeal (NP) swabs. The invasiveness and need for trained personnel make the NP technique unsuited for repeated community-based mass screening. We developed a technique to collect saliva in a simple and easy way with the sponges that are usually used for tamponade of epistaxis. This study was carried out to validate the clinical performance of oral sponge (OS) sampling for SARS-CoV-2 testing.MethodsOver a period of 22 weeks, we collected prospectively 409 paired NP and OS samples from consecutive subjects presenting to a public community-based free screening center. Subjects were referred by their attending physician because of recent COVID-19 symptoms (n=147) or by the contact tracing staff of the French public health insurance since they were considered as close contacts of a laboratory-confirmed COVID-19 case (n=262).ResultsIn symptomatic subjects, RT-PCR SARS-CoV-2 testing with OS showed a 96.5% (95%CI: 89.6–94.8) concordance with NP testing, and, a 93.2% (95%CI: 89.1–97.3)] sensitivity when using the IdyllaTM platform and a sensitivity of 76.3% [69.4–83.2] on the Synlab Barla laboratory platform. In close contacts the NP-OS concordance (93.8% [95%CI: 90.9–96.7]) and OS sensitivity (71.9% [95%CI: 66.5–77.3]) were slightly lower.ConclusionThese results strongly suggest that OS testing is a straightforward, low-cost and high-throughput sampling method that can be used for frequent RT-PCR testing of COVID-19 patients and mass screening of populations.

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Symptoms and symptom clusters associated with SARS-CoV-2 infection in community-based populations: Results from a statewide epidemiological study

10.1101/2020.10.11.20210922 ◽

2020 ◽

Cited By ~ 1

Author(s):

Brian E. Dixon ◽

Kara Wools-Kaloustian ◽

William F. Fadel ◽

Thomas J. Duszynski ◽

Constantin Yiannoutsos ◽

...

Keyword(s):

Public Health ◽

Chest Pain ◽

Hospitalized Patients ◽

Symptom Clusters ◽

Urgent Care ◽

Shortness Of Breath ◽

Robust Methods ◽

Rt Pcr ◽

Community Based ◽

Clinical Screening

AbstractBackgroundPrior studies examining symptoms of COVID-19 are primarily descriptive and measured among hospitalized individuals. Understanding symptoms of SARS-CoV-2 infection in pre-clinical, community-based populations may improve clinical screening, particularly during flu season. We sought to identify key symptoms and symptom combinations in a community-based population using robust methods.MethodsWe pooled community-based cohorts of individuals aged 12 and older screened for SARS-CoV-2 infection in April and June 2020 for a statewide seroprevalence study. Main outcome was SARS-CoV-2 positivity. We calculated sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) for individual symptoms as well as symptom combinations. We further employed multivariable logistic regression and exploratory factor analysis (EFA) to examine symptoms and combinations associated with SARS-CoV-2 infection.ResultsAmong 8214 individuals screened, 368 individuals (4.5%) were RT-PCR positive for SARS-CoV-2. Although two-thirds of symptoms were highly specific (>90.0%), most symptoms individually possessed a PPV <50.0%. The individual symptoms most greatly associated with SARS-CoV-2 positivity were fever (OR=5.34, p<0.001), anosmia (OR=4.08, p<0.001), ageusia (OR=2.38, p=0.006), and cough (OR=2.86, p<0.001). Results from EFA identified two primary symptom clusters most associated with SARS-CoV-2 infection: (1) ageusia, anosmia, and fever; and (2) shortness of breath, cough, and chest pain. Moreover, being non-white (13.6% vs. 2.3%, p<0.001), Hispanic (27.9% vs. 2.5%, p<0.001), or living in an Urban area (5.4% vs. 3.8%, p<0.001) was associated with infection.ConclusionsSymptoms can help distinguish SARS-CoV-2 infection from other respiratory viruses, especially in community or urgent care settings where rapid testing may be limited. Symptoms should further be structured in clinical documentation to support identification of new cases and mitigation of disease spread by public health. These symptoms, derived from asymptomatic as well as mildly infected individuals, can also inform vaccine and therapeutic clinical trials.Research in ContextEvidence before this studyUsing multiple journal articles queried from MEDLINE as well as a Cochrane systematic review, we examined all studies that described symptoms known to be associated with COVID-19. We further examined the guidelines from WHO and CDC on the symptoms those public health authorities consider to be associated with COVID-19. Most of the evidence comes from China, Italy, and the United States. Collectively prior research and guidance suggests there are a dozen symptoms reported by individuals who tested positive for COVID-19 in multiple countries. Symptoms include fever, cough, fatigue, anosmia, ageusia, shortness of breath, chills, myalgias, headache, sore throat, chest pain, and gastrointestinal issues. The evidence is generally of low quality as it is descriptive in nature, and it is biased towards hospitalized patients. Most studies report the proportion of patients hospitalized or testing positive for infection who report one or more symptoms within 3-14 days prior to hospitalization or infection. There has been little validation of symptoms among hospitalized or non-hospitalized patients. Furthermore, according to a Cochrane review, no studies to date assess combinations of different signs and symptoms.Added value of this studyThis study employs multiple, rigorous methods to examine the ability of specific symptoms as well as symptom combinations/groups to predict laboratory-confirmed (RT-PCR) infection of SARS-CoV-2. Furthermore, the study is unique in its large sample drawn exclusively from community-based populations rather than hospitalized patients.Implication of all the available evidenceCombining the evidence from this study with prior research suggests that anosmia and ageusia are key symptoms that differentiate COVID-19 from influenza-like symptoms. Clinical screening protocols for COVID-19 should look for these symptoms, which are not commonly asked of patients who present to urgent care or hospital with flu-like symptoms.Key pointsImportant symptoms specific to COVID-19 are fever, anosmia, ageusia, and cough. Two-thirds of symptoms were highly specific (>90.0%), yet most symptoms individually possessed a PPV <50.0%. This study confirms using robust methods the key symptoms associated with COVID-19 infection, and it also identifies combinations of symptoms strongly associated with positive infection

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