scholarly journals SARS-CoV-2 RNA and antibody dynamics in a Dutch household study with dense sampling frame

2021 ◽  
Author(s):  
Wanda G.H. Han ◽  
Arno Swart ◽  
Axel Bonacic Marinovic ◽  
Dirk Eggink ◽  
Johan Reimerink ◽  
...  
Keyword(s):  
Symptom Onset ◽  
Symptom Severity ◽  
Oral Fluid ◽  
Probability Of Detection ◽  
Serological Response ◽  
Sample Type ◽  
Sampling Frame ◽  
Rt Pcr ◽  
Specific Antibodies ◽  
Viral Loads

AbstractThis study investigated the dynamics of SARS-CoV-2 infection and diagnostics in household members of different ages and with different symptom severity after SARS-CoV-2 exposure during the early phase of the pandemic. Households with a SARS-CoV-2 confirmed positive case and at least one child in the Netherlands were followed for 6 weeks. Naso (NP)- and oropharyngeal (OP) swabs, oral fluid and feces specimens were analyzed for SARS-CoV-2 RNA and serum for SARS-CoV-2-specific antibodies. The dynamics of the presence of viral RNA and the serological response was modeled to determine the sampling time-frame and sample type with the highest sensitivity to confirm or reject a SARS-CoV-2 diagnosis. Transmission of SARS-CoV-2 between adults and children within a household was correlated with symptom severity of index cases. In children higher viral loads compared to adults were detected at symptom onset. Early in infection, higher viral loads were detected in NP and OP specimens, while RNA in especially feces were longer detectable. SARS-CoV-2-specific antibodies have a 90% probability of detection from 7 days (total Ig) and 18 days (IgG) since symptom onset. In conclusion this study has shown that on average, children carry higher loads of virus as compared to adults early after infection. For highest probability of detection in SARS-CoV-2 diagnostics early in infection, RT-PCR on NP and OP specimens are more sensitive than on oral fluid and feces. For SARS-CoV-2 diagnostics late after infection, RT-PCR on feces specimens and serology are more valuable.

scholarly journals SARS-CoV-2 RNA detected in blood products from patients with COVID-19 is not associated with infectious virus

2020 ◽  
Vol 5 ◽  
pp. 181
Author(s):  
Monique I. Andersson ◽  
Carolina V. Arancibia-Carcamo ◽  
Kathryn Auckland ◽  
J. Kenneth Baillie ◽  
Eleanor Barnes ◽  
...  
Keyword(s):  
Symptom Onset ◽  
Severe Disease ◽  
Acute Infection ◽  
Laboratory Diagnosis ◽  
Blood Products ◽  
Rt Pcr ◽  
Serum Samples ◽  
Blood Samples ◽  
Viral Loads ◽  
Clinical Cohort

Background: Laboratory diagnosis of SARS-CoV-2 infection (the cause of COVID-19) uses PCR to detect viral RNA (vRNA) in respiratory samples. SARS-CoV-2 RNA has also been detected in other sample types, but there is limited understanding of the clinical or laboratory significance of its detection in blood. Methods: We undertook a systematic literature review to assimilate the evidence for the frequency of vRNA in blood, and to identify associated clinical characteristics. We performed RT-PCR in serum samples from a UK clinical cohort of acute and convalescent COVID-19 cases (n=212), together with convalescent plasma samples collected by NHS Blood and Transplant (NHSBT) (n=462 additional samples). To determine whether PCR-positive blood samples could pose an infection risk, we attempted virus isolation from a subset of RNA-positive samples. Results: We identified 28 relevant studies, reporting SARS-CoV-2 RNA in 0-76% of blood samples; pooled estimate 10% (95%CI 5-18%). Among serum samples from our clinical cohort, 27/212 (12.7%) had SARS-CoV-2 RNA detected by RT-PCR. RNA detection occurred in samples up to day 20 post symptom onset, and was associated with more severe disease (multivariable odds ratio 7.5). Across all samples collected ≥28 days post symptom onset, 0/494 (0%, 95%CI 0-0.7%) had vRNA detected. Among our PCR-positive samples, cycle threshold (ct) values were high (range 33.5-44.8), suggesting low vRNA copy numbers. PCR-positive sera inoculated into cell culture did not produce any cytopathic effect or yield an increase in detectable SARS-CoV-2 RNA. There was a relationship between RT-PCR negativity and the presence of total SARS-CoV-2 antibody (p=0.02). Conclusions: vRNA was detectable at low viral loads in a minority of serum samples collected in acute infection, but was not associated with infectious SARS-CoV-2 (within the limitations of the assays used). This work helps to inform biosafety precautions for handling blood products from patients with current or previous COVID-19.

scholarly journals Delayed rise of oral fluid antibodies, elevated BMI, and absence of early fever correlate with longer time to SARS-CoV-2 RNA clearance in a longitudinally sampled cohort of COVID-19 outpatients

2021 ◽  
Author(s):  
Annukka A R Antar ◽  
Tong Yu ◽  
Nora Pisanic ◽  
Razvan Azamfirei ◽  
Jeffrey A Tornheim ◽  
...  
Keyword(s):  
Symptom Onset ◽  
Oral Fluid ◽  
Gingival Crevicular Fluid ◽  
Rna Virus ◽  
Cox Proportional Hazards ◽  
Viral Rna ◽  
Antibody Detection ◽  
Upper Respiratory Tract ◽  
Rt Pcr ◽  
Virus Culture

Abstract Background Sustained molecular detection of SARS-CoV-2 RNA in the upper respiratory tract (URT) in mild to moderate COVID-19 is common. We sought to identify host and immune determinants of prolonged SARS-CoV-2 RNA detection. Methods Ninety-five symptomatic outpatients self-collected mid-turbinate nasal, oropharyngeal (OP), and gingival crevicular fluid (oral fluid) samples at home and in a research clinic a median of 6 times over 1-3 months. Samples were tested for viral RNA, virus culture, and SARS-CoV-2 and other human coronavirus antibodies, and associations were estimated using Cox proportional hazards models. Results Viral RNA clearance, as measured by SARS-CoV-2 RT-PCR, in 507 URT samples occurred a median (IQR) 33.5 (17-63.5) days post-symptom onset. Sixteen nasal-OP samples collected 2-11 days post-symptom onset were virus culture positive out of 183 RT-PCR positive samples tested. All participants but one with positive virus culture were negative for concomitant oral fluid anti-SARS-CoV-2 antibodies. The mean time to first antibody detection in oral fluid was 8-13 days post-symptom onset. A longer time to first detection of oral fluid anti-SARS-CoV-2 S antibodies (aHR 0.96, 95% CI 0.92-0.99, p=0.020) and BMI ≥ 25kg/m2 (aHR 0.37, 95% CI 0.18-0.78, p=0.009) were independently associated with a longer time to SARS-CoV-2 viral RNA clearance. Fever as one of first three COVID-19 symptoms correlated with shorter time to viral RNA clearance (aHR 2.06, 95% CI 1.02-4.18, p=0.044). Conclusions We demonstrate that delayed rise of oral fluid SARS-CoV-2-specific antibodies, elevated BMI, and absence of early fever are independently associated with delayed URT viral RNA clearance.

scholarly journals A novel RT-LAMP workflow for rapid salivary diagnostics of COVID-19 and effects of age, gender and time from symptom onset

2021 ◽  
Author(s):  
Gerson Shigeru Kobayashi ◽  
Luciano Abreu Brito ◽  
Danielle De Paula Moreira ◽  
Angela May Suzuki ◽  
Gabriella Shih Ping Hsia ◽  
...  
Keyword(s):  
Viral Load ◽  
Symptom Onset ◽  
Clinical Performance ◽  
Point Of Care ◽  
Rapid Diagnostics ◽  
Rt Pcr ◽  
Point Of Care Testing ◽  
Viral Loads ◽  
Peak Viral Load ◽  
Salivary Diagnostics

Objectives: Rapid diagnostics is pivotal to curb SARS-CoV-2 transmission, and saliva has emerged as a practical alternative to naso/oropharyngeal (NOP) specimens. We aimed to develop a direct RT-LAMP workflow for viral detection in saliva, and to provide more information regarding its potential in COVID-19 diagnostics. Methods: Clinical and contrived specimens were used to screen/optimize formulations and sample processing protocols. Salivary viral load was determined in symptomatic patients to evaluate clinical performance (n = 90) and to characterize saliva based on age, gender and time from onset of symptoms (n = 49). Results: The devised workflow achieved 93.2% sensitivity, 97% specificity, and 0.895 Kappa for salivas containing >102 copies/μL. Further analyses in saliva showed peak viral load in the first days of symptoms and lower viral loads in females, particularly among young individuals (<38 years). NOP RT-PCR data did not yield relevant associations. Conclusions: This novel saliva RT-LAMP workflow can be applied to point-of-care testing. This work reinforces that saliva better correlates with transmission dynamics than NOP specimens, and reveals gender differences that may reflect higher transmission by males. To maximize detection, testing should be done immediately after symptom onset, especially in females.

scholarly journals Clinical Course of SARS-CoV-2 Infection in Adults with ESKD Receiving Outpatient Hemodialysis

Kidney360 ◽  
2021 ◽  
Vol 2 (12) ◽  
pp. 1917-1927
Author(s):  
Ana Cecilia Bardossy ◽  
Lauren Korhonen ◽  
Sabrina Schatzman ◽  
Paige Gable ◽  
Carolyn Herzig ◽  
...  
Keyword(s):  
Symptom Onset ◽  
Neutralizing Antibodies ◽  
Clinical Course ◽  
Rt Pcr ◽  
Convenience Sample ◽  
Content Type ◽  
Specific Antibodies ◽  
Viral Culture ◽  
Maintenance Dialysis ◽  
Dialysis Facilities

BackgroundPatients with ESKD on maintenance dialysis receive dialysis in common spaces with other patients and have a higher risk of severe SARS-CoV-2 infections. They may have persistently or intermittently positive SARS-CoV-2 RT-PCR tests after infection. We describe the clinical course of SARS-CoV-2 infection and the serologic response in a convenience sample of patients with ESKD to understand the duration of infectivity.MethodsFrom August to November 2020, we enrolled patients on maintenance dialysis with SARS-CoV-2 infections from outpatient dialysis facilities in Atlanta, Georgia. We followed participants for approximately 42 days. We assessed COVID-19 symptoms and collected specimens. Oropharyngeal (OP), anterior nasal (AN), and saliva (SA) specimens were tested for the presence of SARS-CoV-2 RNA, using RT-PCR, and sent for viral culture. Serology, including neutralizing antibodies, was measured in blood specimens.ResultsFifteen participants, with a median age of 58 (range, 37‒77) years, were enrolled. Median duration of RT-PCR positivity from diagnosis was 18 days (interquartile range [IQR], 8‒24 days). Ten participants had at least one, for a total of 41, positive RT-PCR specimens ≥10 days after symptoms onset. Of these 41 specimens, 21 underwent viral culture; one (5%) was positive 14 days after symptom onset. Thirteen participants developed SARS-CoV-2–specific antibodies, 11 of which included neutralizing antibodies. RT-PCRs remained positive after seroconversion in eight participants and after detection of neutralizing antibodies in four participants; however, all of these samples were culture negative.ConclusionsPatients with ESKD on maintenance dialysis remained persistently and intermittently SARS-CoV-2–RT-PCR positive. However, of the 15 participants, only one had infectious virus, on day 14 after symptom onset. Most participants mounted an antibody response, including neutralizing antibodies. Participants continued having RT-PCR–positive results in the presence of SARS-CoV-2–specific antibodies, but without replication-competent virus detected.

scholarly journals SARS-CoV-2 RNA detected in blood samples from patients with COVID-19 is not associated with infectious virus

2020 ◽  
Author(s):  
Monique I Andersson ◽  
Carolina V Arancibia-Cárcamo ◽  
Kathryn Auckland ◽  
J Kenneth Baillie ◽  
Eleanor Barnes ◽  
...  
Keyword(s):  
Symptom Onset ◽  
Severe Disease ◽  
Acute Infection ◽  
Laboratory Diagnosis ◽  
Rt Pcr ◽  
Serum Samples ◽  
Blood Samples ◽  
Viral Loads ◽  
Clinical Cohort ◽  
Copy Numbers

ABSTRACTBackgroundLaboratory diagnosis of SARS-CoV-2 infection (the cause of COVID-19) uses PCR to detect viral RNA (vRNA) in respiratory samples. SARS-CoV-2 RNA has also been detected in other sample types, but there is limited understanding of the clinical or laboratory significance of its detection in blood.MethodsWe undertook a systematic literature review to assimilate the evidence for the frequency of vRNA in blood, and to identify associated clinical characteristics. We performed RT-PCR in serum samples from a UK clinical cohort of acute and convalescent COVID-19 cases (n=212), together with convalescent plasma samples collected by NHS Blood and Transplant (NHSBT) (n=111 additional samples). To determine whether PCR-positive blood samples could pose an infection risk, we attempted virus isolation from a subset of RNA-positive samples.ResultsWe identified 28 relevant studies, reporting SARS-CoV-2 RNA in 0-76% of blood samples; pooled estimate 10% (95%CI 5-18%). Among serum samples from our clinical cohort, 27/212 (12.7%) had SARS-CoV-2 RNA detected by RT-PCR. RNA detection occurred in samples up to day 20 post symptom onset, and was associated with more severe disease (multivariable odds ratio 7.5). Across all samples collected ≥28 days post symptom onset, 0/143 (0%, 95%CI 0.0-2.5%) had vRNA detected. Among our PCR-positive samples, cycle threshold (ct) values were high (range 33.5-44.8), suggesting low vRNA copy numbers. PCR-positive sera inoculated into cell culture did not produce any cytopathic effect or yield an increase in detectable SARS-CoV-2 RNA.ConclusionsvRNA was detectable at low viral loads in a minority of serum samples collected in acute infection, but was not associated with infectious SARS-CoV-2 (within the limitations of the assays used). This work helps to inform biosafety precautions for handling blood products from patients with current or previous COVID-19.

scholarly journals 513. Viral kinetics of SARS-CoV-2 in patients with COVID-19

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S322-S323
Author(s):  
Da Young Kim ◽  
Ju-Hyung Lee ◽  
Hyeon Jeong Oh ◽  
Jun-won Seo ◽  
Na Ra Yun ◽  
...  
Keyword(s):  
Chest Radiograph ◽  
Symptom Onset ◽  
Supplemental Oxygen ◽  
University Hospital ◽  
Upper Respiratory Tract ◽  
Rt Pcr ◽  
Viral Kinetics ◽  
Viral Loads ◽  
Severe Group ◽  
Kinetics Of

Abstract Background As only few studies have analyzed viral kinetics between the incubation and symptomatic periods of COVID-19 patients, we investigated the viral kinetics and compared viral loads between patients with mild and severe COVID-19. Methods We determined the viral kinetics of 10 patients diagnosed with COVID-19 at Chosun University Hospital. Six patients were classified into the “mild” group and 4 into the “severe” group according to supplemental oxygen use during admission. Samples were collected via nasopharyngeal swabs and sputum specimens. SARS-CoV-2 was detected using real-time reverse transcription-polymerase chain reaction (RT-PCR). Chest radiograph scores during hospitalization were obtained Results Ct values of the upper respiratory tract specimens were low during the early stages after symptom onset but gradually increased over time in both groups. The severe group had lower Ct values than the mild group. The Ct values of the RdRP and E genes on day 6 after symptom onset were significantly lower in the severe group than in the mild group (p &lt; 0.05). Three of 6 patients had positive results on RT-PCR even before symptom onset; 2 of them had the lowest Ct values. The chest radiograph scores were higher in the severe group than in the mild group, and the score in the severe group was the highest at approximately 3 weeks after symptom onset. Ct values when the RdRP gene and E gene were targeted to detect SARS-CoV-2 on the basis of the days after symptom onset in all the patients Conclusion Viral load and chest radiograph scores were significantly different between the severe and mild groups of COVID-19 patients. Disclosures All Authors: No reported disclosures

scholarly journals Mycoplasma hyopneumoniae Surveillance in Pig Populations: Establishing Sampling Guidelines for Detection in Growing Pigs

2021 ◽  
Vol 59 (5) ◽  
Author(s):  
Maria Jose Clavijo ◽  
Dapeng Hu ◽  
Seth Krantz ◽  
Jean Paul Cano ◽  
Thairê Pereira Maróstica ◽  
...  
Keyword(s):  
Oral Fluid ◽  
Mycoplasma Hyopneumoniae ◽  
Growing Pigs ◽  
Probability Of Detection ◽  
Sample Type ◽  
Sample Sizes ◽  
Serum Samples ◽  
Content Type ◽  
Large Sample ◽  
Oral Fluids

ABSTRACT Antemortem detection of Mycoplasma hyopneumoniae infection in swine production systems has relied on antibody testing, but the availability of tests based on DNA detection and novel diagnostic specimens, e.g., tracheal swabs and oral fluids, has the potential to improve M. hyopneumoniae surveillance. A field study was performed over a 14-week period during which 10 pigs in one pen at the center of a room with 1,250 6-week-old pigs housed in 46 pens were intratracheally inoculated with M. hyopneumoniae. Thereafter, one tracheal sample, four serum samples, and one oral fluid sample were collected from every pen at 2-week intervals. Tracheal and oral fluid samples were tested for M. hyopneumoniae DNA and serum samples for M. hyopneumoniae antibody. Test results were modeled using a hierarchical Bayesian model, based on a latent spatial piecewise exponential survival model, to estimate the probability of detection by within-pen prevalence, number of positive pens in the barn, sample allocation, sample size, and sample type over time. Analysis showed that tracheal samples provided the earliest detection, especially at large sample sizes. While serum samples are more commonly collected and are less expensive to test, high probability of detection estimates were only obtained 30 days postexposure at large sample sizes. In all scenarios, probability of detection estimates for oral fluids within 30 days were significantly lower than those for tracheal and serum samples. Ultimately, the choice of specimen type, sample number, and assay will depend on testing objectives and economics, but the estimates provided here will assist in the design of M. hyopneumoniae surveillance and monitoring programs for different situations.

scholarly journals Evaluation and modelling of the performance of an automated SARS-CoV-2 antigen assay according to sample type, target population and epidemic trends

2022 ◽  
Author(s):  
Nicolas Yin ◽  
Cyril Debuysschere ◽  
Valery Daubie ◽  
Marc Hildebrand ◽  
Charlotte Martin ◽  
...  
Keyword(s):  
Viral Load ◽  
Target Population ◽  
Daily Routine ◽  
Sample Type ◽  
Rt Pcr ◽  
Viral Loads ◽  
Detection Assay ◽  
Assay Performance ◽  
Antigen Assay ◽  
Risk Patients

The Lumipulse® G SARS-CoV-2 Ag assay performance was evaluated on prospectively collected saliva and nasopharyngeal swabs (NPS) of recently ill in- and outpatients and according to the estimated viral load. Performances were calculated using RT-PCR positive NPS from patients with symptoms ≤ 7 days and RT-PCR negative NPS as gold standard. In addition, non-selected positive NPS were analyzed to assess the performances on various viral loads. This assay yielded a sensitivity of 93.1% on NPS and 71.4% on saliva for recently ill patients. For NPS with a viral load > 103 RNA copies/mL, sensitivity was 96.4%. A model established on our daily routine showed fluctuations of the performances depending on the epidemic trends but an overall good negative predictive value. Lumipulse® G SARS-CoV-2 assay yielded good performance for an automated antigen detection assay on NPS. Using it for the detection of recently ill patient or to screen high-risk patients could be an interesting alternative to the more expensive RT-PCR.

scholarly journals Serological Response to SARS-CoV-2 in Health Care Workers Employed in a Large Tertiary Hospital in Lombardy, Northern Italy

2021 ◽  
Vol 9 (3) ◽  
pp. 488
Author(s):  
Agnese Comelli ◽  
Emanuele Focà ◽  
Emanuele Sansone ◽  
Cesare Tomasi ◽  
Elisa Albini ◽  
...  
Keyword(s):  
Health Care ◽  
Health Care Workers ◽  
Online Survey ◽  
Northern Italy ◽  
Spike Protein ◽  
Serological Response ◽  
Rt Pcr ◽  
Specific Antibodies ◽  
First Semester ◽  
Care Workers

Background: COVID-19 pandemic is requesting unprecedented efforts by health-care workers (HCWs) in all countries, and especially in Italy during the first semester of 2020. Methods: This is a retrospective, observational study conducted at the Spedali Civili General Hospital, in Brescia, Northern Italy during the SARS CoV-2 pandemic in the first semester of 2020. Serum samples from HCWs were tested for SARS-CoV-2 spike protein-specific antibodies. An online survey was used to collect demographic, clinical, and epidemiological data. Results: Of the 1893 HCWs included, 433 (22.9%) were found seropositive for SARS-CoV-2 IgG. The cumulative prevalence of SARS-CoV-2 infection (antibodies production or past positive RT-PCR on nasal/throat swab) was 25.1% (475/1893). Fifty-six out of 433 (13%) seropositive participants declared to have been asymptomatic during the study period. The development of COVID-19 signs or symptoms is the main determinant of seropositivity (OR: 11.3, p < 0.0001) along with their duration and severity. 40/290 (14.5%) HCWs with documented positive RT-PCR during the study period did not show any detectable antibody response. IgG levels positively correlate with age, COVID-19-compatible signs and symptoms experienced and their duration. Conclusions: In this study, carried out in one of the most affected areas in Europe, we demonstrate that most HCWs with COVID-19 related symptoms develop a spike protein-specific antibodies with potential neutralizing effect.

scholarly journals Delayed rise of oral fluid antibodies, elevated BMI, and absence of early fever correlate with longer time to SARS-CoV-2 RNA clearance in an longitudinally sampled cohort of COVID-19 outpatients

2021 ◽  
Author(s):  
Annukka A. R. Antar ◽  
Tong Yu ◽  
Nora Pisanic ◽  
Razvan Azamfirei ◽  
Jeffrey A. Tornheim ◽  
...  
Keyword(s):  
Symptom Onset ◽  
Oral Fluid ◽  
Gingival Crevicular Fluid ◽  
Rna Virus ◽  
Cox Proportional Hazards ◽  
Viral Rna ◽  
Antibody Detection ◽  
Upper Respiratory Tract ◽  
Rt Pcr ◽  
Virus Culture

ABSTRACTBackgroundSustained molecular detection of SARS-CoV-2 RNA in the upper respiratory tract (URT) in mild to moderate COVID-19 is common. We sought to identify host and immune determinants of prolonged SARS-CoV-2 RNA detection.MethodsNinety-five outpatients self-collected mid-turbinate nasal, oropharyngeal (OP), and gingival crevicular fluid (oral fluid) samples at home and in a research clinic a median of 6 times over 1-3 months. Samples were tested for viral RNA, virus culture, and SARS-CoV-2 and other human coronavirus antibodies, and associations were estimated using Cox proportional hazards models.ResultsViral RNA clearance, as measured by SARS-CoV-2 RT-PCR, in 507 URT samples occurred a median (IQR) 33.5 (17-63.5) days post-symptom onset. Sixteen nasal-OP samples collected 2-11 days post-symptom onset were virus culture positive out of 183 RT-PCR positive samples tested. All participants but one with positive virus culture were negative for concomitant oral fluid anti-SARS-CoV-2 antibodies. The mean time to first antibody detection in oral fluid was 8-13 days post-symptom onset. A longer time to first detection of oral fluid anti-SARS-CoV-2 S antibodies (aHR 0.96, 95% CI 0.92-0.99, p=0.020) and BMI ≥ 25kg/m2 (aHR 0.37, 95% CI 0.18-0.78, p=0.009) were independently associated with a longer time to SARS-CoV-2 viral RNA clearance. Fever as one of first three COVID-19 symptoms correlated with shorter time to viral RNA clearance (aHR 2.06, 95% CI 1.02-4.18, p=0.044).ConclusionsWe demonstrate that delayed rise of oral fluid SARS-CoV-2-specific antibodies, elevated BMI, and absence of early fever are independently associated with delayed URT viral RNA clearance.

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