scholarly journals Investigation of Viral Load Cycle Threshold Values in Patients with SARS-CoV-2 Associated Pneumonia with Real-Time PCR Method

2021 ◽  
Vol 15 (10) ◽  
pp. 1408-1414
Author(s):  
Ayfer Bakir ◽  
Tugrul Hosbul ◽  
Ferhat Cuce ◽  
Cumhur Artuk ◽  
Gurhan Taskin ◽  
...  
Keyword(s):  
Viral Load ◽  
Respiratory Tract ◽  
Load Cycle ◽  
Cross Sectional Study ◽  
Chest Ct ◽  
Upper Respiratory Tract ◽  
Cross Sectional ◽  
Cycle Threshold ◽  
Viral Loads ◽  
Ct Value

Introduction: In this study, we aimed investigate the relationship of SARS-CoV-2 viral load cycle threshold (Ct) values with pneumonia. Methodology: A total of 158 patients in whom SARS-CoV-2 was confirmed in upper respiratory tract (URT) samples with molecular method and who had computed tomography (CT) of the chest, between April 2020 and June 2020 were included in this retrospective cross-sectional study. Results: Mean age of 158 PCR positive patients was 45.22 ± 17.89 and 60.8% of them were male. Pneumonia was detected in 40.5% of the patients on their chest CT. A weak but significant correlation was found between SARS-CoV-2 Ct value detected with PCR in analysis of oropharyngeal/ nasopharyngeal (OP/NP) samples and chest CT score (Pearson’s r: 0.197, p = 0.01). No correlation was found between the first detected viral load Ct value and age, gender and mortality. There was no significant correlation between chest CT score and mortality. While the areas remaining under ROC curve for Ct value in analysis of OP/NP samples in prediction of chest CT score ≥ 1, ≥ 5 and ≥ 10 were 0.564, 0.640 and 0.703 respectively. Conclusions: We found that the amount of SARS-CoV-2 viral load (inverse relationship with Ct) detected in OP/NP samples of patients with COVID-19 pneumonia did not reflect the increasing severity of pulmonary lesions on chest CT. Although primary target of SARS-CoV-2 is all epithelial cells of the respiratory tract we believe studies comparing viral loads in lower respiratory tract samples are needed to determine the severity of pulmonary disease.

scholarly journals Viral load in upper respiratory tract of COVID-19 patients detected by digital PCR

2020 ◽  
Author(s):  
Jiankang Zhao ◽  
Haibo Li ◽  
Hui Li ◽  
Qiaoling Wu ◽  
Ke Wu ◽  
...  
Keyword(s):  
Viral Load ◽  
Respiratory Tract ◽  
Digital Pcr ◽  
Upper Respiratory Tract ◽  
Rt Pcr ◽  
Lung Lesions ◽  
Viral Loads ◽  
Ct Value ◽  
Upper Respiratory ◽  
Close Contacts

Abstract Background: Upper respiratory tract specimens are widely applicable for the diagnosis of COVID-19. To date, no study has analyzed the actual viral loads in upper respiratory tract and its relationship with the severity of lung lesions, Ct value of RT-PCR and transmission capacity in COVID-19 patients.Methods: We retrospectively enrolled nine COVID-19 patients. Clinical data and close contacts of these patients were investigated. Respiratory samples were tested for SARS-CoV-2 with both normal RT-PCR and droplet digital PCR.Results: All the COVID-19 patients complicated with pneumonia. Viral loads in nasopharyngeal swabs were accurately quantified, and they had no direct correspondence with the severity of lung lesions. The Cycle Threshold (Ct) value of RT-PCR was approximately consistent with the absolute quantification of digital PCR. The spearman correlation coefficient between them was -0.952 with P value < 0.001. Close contacts of patients with very low viral load or no detected virus were not infected.Conclusions: Viral loads in nasopharyngeal swabs, could not predict the severity of lung lesions revealed by CT in COVID-19 patients. The infectious capacity of patients with low or absent viral load in upper respiratory tract was relatively weak, and wearing mask might be helpful for lower its spread.

scholarly journals Sociodemographic Factors, Cycle Threshold Values, and Clinical Outcomes of COVID-19

2021 ◽  
Vol 1 (S1) ◽  
pp. s18-s19
Author(s):  
Frida Rivera ◽  
Cameron Gmehlin ◽  
Liliana Pezzin ◽  
Ann B. Nattinger ◽  
Ryan Hanson ◽  
...  
Keyword(s):  
Viral Load ◽  
Clinical Outcomes ◽  
Quantitative Polymerase Chain Reaction ◽  
Sociodemographic Factors ◽  
Load Cycle ◽  
Cross Sectional Study ◽  
Area Deprivation ◽  
Sectional Study ◽  
Cross Sectional ◽  
Cycle Threshold

Background: The gold standard for diagnosis of COVID-19 has been SARS-CoV-2 detection by reverse-transcriptase-quantitative polymerase chain reaction (RT-qPCR), which provides a semiquantitative indicator of viral load (cycle threshold, Ct). Our research group previously described how African American race and poverty were associated with an increased likelihood of hospitalization due to COVID-19. We sought to characterize the relationship between Ct values and clinical outcomes while controlling for sociodemographic factors. Methods: We conducted a cross-sectional study of SARS-CoV-2–positive patients admitted to Froedtert Health between March 16 and June 1, 2020. Ct values were obtained by direct interrogation of either cobas SARS-CoV-2 or Cepheid Xpert Xpress platforms. Patient demographics, comorbidities, symptoms at admission, health insurance, and hospital course were collected using electronic medical records. A proxy for socioeconomic disadvantage, area-deprivation index (ADI), was assigned using ZIP codes. Multivariate models were performed to assess associations between Ct values and clinical outcomes while controlling for ADI, race, and type of insurance. Results: Overall, 302 patients were included. The mean age was 60.89 years (SD, 18.2); 161 (53%) were men, 177 (58%) were African Americans; and 156 (51%) had Medicaid or were uninsured. Of the 302 inpatients, 158 (52%) required admission to the ICU, 199 (65.9%) were discharged to home, 49 (16.2%) were discharged to a nursing home, and 54 (17.9%) died. Lower Ct values (higher viral load) were associated with Medicaid or lack of insurance (coefficient, −2.88, 95% confidence interval [CI], −4.96 to −0.79, P = .007) and age >60 years old (coefficient, −2.98, 95% CI −4.87 to −1.08, P = .002). Contrary to what was expected, higher CT values (lower viral load) were associated with higher ADI scores (coefficient, 2.62, 95% CI, 0.52–4.85; P = .017). However, when patients were stratified into low, medium, and high ADI, those with Medicaid or no insurance had the lowest mean Ct values (23.3, 25.9, and 27.6, respectively) compared to Medicare or other insurance (Figure 1). Body mass index (odds ratio [OR], 1.04; 95% CI, 1.02–1.07; P = .001) and male sex (OR, 2.15; 95% CI, 1.28–3.60; P = .004) were independently associated with ICU admission. Every increase of a CT point (OR, 0.90; 95% CI, 0.85–0.95; p <0.001) and age >60 years old (OR 2.62, 95% CI; 1.14-6.04; p=0.023) was associated with death. Conclusions: In this cross-sectional study of adults tested for COVID-19 in a large midwestern academic health system, lower Ct values were independently associated with poverty and age >60 years old.Funding: NoDisclosures: None

scholarly journals 425. The Utility of Paired Upper and Lower COVID-19 Sampling in Patients with Artificial Airways

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S279-S279
Author(s):  
Eimear Kitt ◽  
Julia S Sammons ◽  
Kathleen Chiotos ◽  
Susan E Coffin ◽  
Susan E Coffin ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Lower Respiratory Tract ◽  
Diagnostic Testing ◽  
Cross Sectional Study ◽  
Upper Respiratory Tract ◽  
Cross Sectional ◽  
Mechanically Ventilated ◽  
Paired Samples ◽  
Control And Prevention ◽  
Polymerase Chain

Abstract Background The Centers for Disease Control and Prevention (CDC) recommends upper respiratory tract (URT) polymerase chain reaction (PCR) testing as the initial diagnostic test for Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Lower respiratory tract (LRT) testing for patients requiring mechanical ventilation is also recommended. The goal of this study was to evaluate concordance between paired URT and LRT specimens in children undergoing pre-admission/procedure screening or diagnostic testing. We hypothesized that &lt; 10% of paired tests would have discordant results. Methods Single center cross-sectional study including children with artificial airways who had paired URT and LRT SARS-CoV-2 PCR testing between 4/1/2020 and 6/8/2020. URT specimens included nasopharyngeal (NP) swabs and aspirates. LRT specimens included tracheal aspirates and bronchoalveolar lavages. URT and LRT specimens were classified as paired if the two specimens were collected within 24 hours. Artificial airways included tracheostomies and endotracheal tubes. Tests were classified as diagnostic versus screening based on the indication selected in the order. Results 102 paired specimens were obtained during the study period. Fifty-nine were performed for screening and 43 were performed for diagnosis of suspected SARS-CoV-2. Overall, 94 specimens (92%) were concordant, including 89 negative from both sources and 5 positive from both sources. Eight specimens (8%) were discordant, all of which were positive from the URT and negative from the LRT (Figure 1). Among patients undergoing screening, 3 of 4 positive tests were discordant and among symptomatic patients, 5 of 9 positive tests were discordant. There were no instances of a positive LRT specimen with a negative URT specimen. Figure 1. Performance of upper and lower respiratory tract SARS-CoV-2 PCR testing in children with artificial airways Conclusion Overall, most paired samples from the URT and LRT yielded concordant results with no pairs positive from the LRT and negative from the URT. These data support the CDC recommendation that URT specimens are the preferred initial SARS-CoV-2 test, while LRT specimens should be collected only from mechanically ventilated with suspected SARS-CoV-2. Disclosures All Authors: No reported disclosures

scholarly journals A cross sectional study on prescription pattern of drugs in upper respiratory tract infections in a tertiary care hospital

2020 ◽  
Vol 9 (2) ◽  
pp. 271
Author(s):  
Divya Bade ◽  
Shivashankaramurthy K. G. ◽  
Kiran L. J. ◽  
Raghuprasada M. S. ◽  
Harishkumar V. S. ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Respiratory Tract Infections ◽  
Cross Sectional Study ◽  
Prescribing Patterns ◽  
Essential Medicines ◽  
Upper Respiratory Tract Infections ◽  
Upper Respiratory Tract ◽  
Cross Sectional ◽  
Upper Respiratory ◽  
Tract Infections

Background: Upper respiratory tract infections are one of the leading causes of hospital visits worldwide. Judicious use of antibiotics is challenging for upper respiratory tract infections (URTIs) in developing countries like India. This leads to inappropriate use of antibiotics causing many dreaded conditions like antibacterial resistance among other things. Hence rational use of drugs, mainly antibacterial, is a priority to reduce the burden of treatment failure. The objective of this study is to study the prescribing patterns and rationality of drugs prescribed in the management of URTIs.Methods: This was a cross-sectional study. Data was collected from records of 300 outpatients clinically diagnosed as URTIs from SSIMS and RC Hospital, Davangere between January 2015 and June 2016. The prescribing patterns, approval status and listing of drugs in World Health Organization (WHO) essential medicines list/ National List of Essential Medicines (NLEM) were analysed. The data was presented as percentages, mean and standard deviations.Results: A total of 300 cases were studied. Among these, acute pharyngitis (29%) and acute sinusitis (26%) are the most common infections. Of the 300 cases studied, 283 (94.3%) were prescribed antimicrobials. Of the total 740 medications prescribed, 393 (53.1%) were fixed-dose combinations (FDCs). A total of 724 medications (97.8%) were approved by Drugs Controller General of India and 248 (33.5%) by Food and Drug Administration. Only 5.8% of the prescribed drugs have been listed in WHO’s and NLEM. The most common class of antibacterials prescribed was Beta-lactams.Conclusions: Oral formulations were preferred over parenteral formulations and FDCs were preferred over single drug formulations. Beta-lactams comprised the major class of antibacterial prescribed.

scholarly journals Induction of interferon response by high viral loads at early stage infection may protect against severe outcomes in COVID-19 patients

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Eric C. Rouchka ◽  
Julia H. Chariker ◽  
Brian Alejandro ◽  
Robert S. Adcock ◽  
Richa Singhal ◽  
...  
Keyword(s):  
Gene Expression ◽  
Viral Load ◽  
Respiratory Tract ◽  
Disease Severity ◽  
Critical Factor ◽  
Interferon Response ◽  
Upper Respiratory Tract ◽  
Viral Loads ◽  
Antiviral Responses ◽  
Upper Respiratory

AbstractKey elements for viral pathogenesis include viral strains, viral load, co-infection, and host responses. Several studies analyzing these factors in the function of disease severity of have been published; however, no studies have shown how all of these factors interplay within a defined cohort. To address this important question, we sought to understand how these four key components interplay in a cohort of COVID-19 patients. We determined the viral loads and gene expression using high throughput sequencing and various virological methods. We found that viral loads in the upper respiratory tract in COVID-19 patients at an early phase of infection vary widely. While the majority of nasopharyngeal (NP) samples have a viral load lower than the limit of detection of infectious viruses, there are samples with an extraordinary amount of SARS-CoV-2 RNA and a high viral titer. No specific viral factors were identified that are associated with high viral loads. Host gene expression analysis showed that viral loads were strongly correlated with cellular antiviral responses. Interestingly, however, COVID-19 patients who experience mild symptoms have a higher viral load than those with severe complications, indicating that naso-pharyngeal viral load may not be a key factor of the clinical outcomes of COVID-19. The metagenomics analysis revealed that the microflora in the upper respiratory tract of COVID-19 patients with high viral loads were dominated by SARS-CoV-2, with a high degree of dysbiosis. Finally, we found a strong inverse correlation between upregulation of interferon responses and disease severity. Overall our study suggests that a high viral load in the upper respiratory tract may not be a critical factor for severe symptoms; rather, dampened antiviral responses may be a critical factor for a severe outcome from the infection.

scholarly journals Evaluation of swabbing methods for estimating the prevalence of bacterial carriage in the upper respiratory tract: a cross sectional study

BMJ Open ◽  
2014 ◽  
Vol 4 (10) ◽  
pp. e005341 ◽  
Author(s):  
A L Coughtrie ◽  
R N Whittaker ◽  
N Begum ◽  
R Anderson ◽  
A Tuck ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Large Population ◽  
Population Based ◽  
Cross Sectional Study ◽  
Research Network ◽  
Upper Respiratory Tract ◽  
Sectional Study ◽  
Baseline Measure ◽  
Cross Sectional ◽  
Upper Respiratory

ObjectivesBacterial carriage in the upper respiratory tract is usually asymptomatic but can lead to respiratory tract infection (RTI), meningitis and septicaemia. We aimed to provide a baseline measure of Streptococcus pneumoniae, Moraxella catarrhalis, Pseudomonas aeruginosa, Staphylococcus aureus, Haemophilus influenzae and Neisseria meningitidis carriage within the community. Self-swabbing and healthcare professional (HCP) swabbing were compared.DesignCross-sectional study.SettingIndividuals registered at 20 general practitioner practices within the Wessex Primary Care Research Network South West, UK.Participants10 448 individuals were invited to participate; 5394 within a self-swabbing group and 5054 within a HCP swabbing group. Self-swabbing invitees included 2405 individuals aged 0–4 years and 3349 individuals aged ≥5 years. HCP swabbing invitees included 1908 individuals aged 0–4 years and 3146 individuals aged ≥5 years.Results1574 (15.1%) individuals participated, 1260 (23.4%, 95% CI 22.3% to 24.5%) undertaking self-swabbing and 314 (6.2%, 95% CI 5.5% to 6.9%) undertaking HCP-led swabbing. Participation was lower in young children and more deprived practice locations. Swab positivity rates were 34.8% (95% CI 32.2% to 37.4%) for self-taken nose swabs (NS), 19% (95% CI 16.8% to 21.2%) for self-taken whole mouth swabs (WMS), 25.2% (95% CI 20.4% to 30%) for nasopharyngeal swabs (NPS) and 33.4% (95% CI 28.2% to 38.6%) for HCP-taken WMS. Carriage rates of S. aureus were highest in NS (21.3%). S. pneumoniae carriage was highest in NS (11%) and NPS (7.4%). M. catarrhalis carriage was highest in HCP-taken WMS (28.8%). H. influenzae and P. aeruginosa carriage were similar between swab types. N. meningitidis was not detected in any swab. Age and recent RTI affected carriage of S. pneumoniae and H. influenzae. Participant costs were lower for self-swabbing (£41.21) versus HCP swabbing (£69.66).ConclusionsHigher participation and lower costs of self-swabbing as well as sensitivity of self-swabbing favour this method for use in large population-based respiratory carriage studies.

scholarly journals Characterising HIV transmission risk among US patients with HIV in care: a cross-sectional study of sexual risk behaviour among individuals with viral load above 1500 copies/mL

2017 ◽  
Vol 94 (3) ◽  
pp. 206-211 ◽  
Author(s):  
Michael J Stirratt ◽  
Gary Marks ◽  
Christine O’Daniels ◽  
Edward R Cachay ◽  
Meg Sullivan ◽  
...  
Keyword(s):  
Viral Load ◽  
Sexual Risk ◽  
Hiv Transmission ◽  
Risk Behaviour ◽  
Cross Sectional Study ◽  
Transmission Risk ◽  
Sexual Risk Behaviour ◽  
Sexually Active ◽  
Cross Sectional ◽  
Viral Loads

ObjectivesViral load and sexual risk behaviour contribute to HIV transmission risk. High HIV viral loads present greater transmission risk than transient viral ‘blips’ above an undetectable level. This paper therefore characterises sexual risk behaviour among patients with HIV in care with viral loads>1500 copies/mL and associated demographic characteristics.MethodsThis cross-sectional study was conducted at six HIV outpatient clinics in USA. The study sample comprises 1315 patients with HIV with a recent viral load >1500 copies/mL. This study sample was drawn from a larger sample of individuals with a recent viral load >1000 copies/mL who completed a computer-assisted self-interview (CASI) regarding sexual risk practices in the last 2 months. The study sample was 32% heterosexual men, 38% men who have sex with men (MSM) and 30% women.ResultsNinety per cent of the sample had their viral load assay within 60 days of the CASI. Thirty-seven per cent reported being sexually active (vaginal or anal intercourse) in the last 2 months. Most of the sexually active participants reported always using condoms (56.9%) or limiting condomless sex to seroconcordant partners (serosorting; 29.2% overall and 42.9% among MSM). Among sexually active participants who reported condomless anal or vaginal sex with an at-risk partner (14%), most had viral loads>10 000 copies/mL (62%).ConclusionsA relatively small number of patients with HIV in care with viral loads above 1500 copies/mL reported concurrent sexual transmission risk behaviours. Most of the individuals in this small group had markedly elevated viral loads, increasing the probability of transmission. Directing interventions to patients in care with high viral loads and concurrent risk behaviour could strengthen HIV prevention and reduce HIV infections.Trial registration numberNCT02044484, completed.

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