scholarly journals Implications in the quantitation of SARS-CoV2 copies in concurrent nasopharyngeal swabs, whole mouth fluid and respiratory droplets

Author(s):  
Priya Kannian ◽  
Bagavad Gita Jayaraman ◽  
Swarna Alamelu ◽  
Chandra Lavanya ◽  
Nagalingeswaran Kumarasamy ◽  
...  

AbstractImportanceThe nasopharyngeal swab (NPS) is considered the ideal diagnostic specimen for Covid-19, while WMF is recently promoted due to collection simplicity and importance in disease transmission. There is limited knowledge on the relative viral load in these samples – NPS, whole mouth fluid (WMF) and respiratory droplets (RD; another important source in transmission), on how the loads vary with disease severity and on how much virus is shed.ObjectiveTo quantify and compare SARS-CoV2 copies in the NPS, WMF and RD samples, and correlate with disease severity.DesignCross sectional study.SettingTertiary care multi-speciality hospital with limited resources in a low-to-middle income country.ParticipantsEighty suspected COVID-19 patients were recruited from the COVID-19 out-patient clinic and hospital isolation wards.InterventionConcurrent NPS, WMF and RD samples were collected from all the recruited patients and tested for SARS-CoV2 copies by quantitative reverse transcriptase-polymerase chain reaction (RT-PCR).Main outcomes and measuresThe main outcome was COVID-19 measured by SARS-CoV2 quantitative RT-PCR in NPS samples. COVID-19 disease severity was determined according to NIH criteria. Virus shedding was defined as the presence of SARS-CoV2 copies in the WMF and RD samples.ResultsSARS-CoV2 was detected in 55/80 (69%) of the NPS samples. Of these 55, WMF and RD samples were positive in 44 (80%) and 17 (31%), respectively. The concordance of WMF with NPS was 84% (p=0.02). SARS-CoV2 copy numbers were comparable in the NPS (median: 8.74×10^5) and WMF (median: 3.07×10^4), but lower in RD samples (median: 3.60×10^2). Patients with mild disease had higher copies in the NPS (median: 3.46×10^6), while patients with severe disease had higher copies in the WMF (median: 1.34×10^6) and RD samples (median: 4.29×10^4). The 25-75% interquartile range of NPS SARS-CoV2 copies was significantly higher in the WMF (p=0.0001) and RD (p=0.01) positive patients.Conclusion and relevanceSARS-CoV2 copies are highest in NPS samples. WMF is a reliable surrogate sample for diagnosis. High copy numbers in the NPS imply initial virological phase and higher risk of virus shedding via WMF and RD.Key pointsQuestionHow the numbers of SARS-CoV2 copies in nasopharyngeal swab (NPS) samples might reflectvirus shedding from the whole upper aerodigestive tract and indicatedisease severity?FindingsIn this cross-sectional study involving 80 suspected COVID-19 patients, the data indicate higher SARS-CoV2 copies in NPS samples of patients with mild disease,and in the whole mouth fluid (WMF) and respiratory droplet (RD) samples of patients with severe disease. Patients with higher SARS-CoV2 copies in the NPS shed the virus in the WMF and RD samples at statistically higher levels.MeaningHigh SARS-CoV2 copies in NPS samples imply initial virological phase withhigh levels of shedding through both WMF and RD.

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Umar Saeed ◽  
Sara Rizwan Uppal ◽  
Zahra Zahid Piracha ◽  
Azhar Rasheed ◽  
Zubair Aftab ◽  
...  

AbstractRapid diagnosis of SARS-CoV-2 during pandemic enables timely treatment and prevention of COVID-19. Evaluating the accuracy and reliability of rapid diagnostic testing kits is crucial for surveillance and diagnosis of SARS-CoV-2 infections in general population, injection drug users, multi-transfused populations, healthcare workers, prisoners, barbers and other high risk populations. The aim of this study was to evaluate performance and effectiveness of nasopharyngeal swab (NSP) and saliva based rapid antigen detection testing kits in comparison with USFDA approved triple target gold standard real-time polymerase chain reaction. A cross-sectional study was conducted on 33,000 COVID-19 suspected patients. From RT-PCR positive patients, nasopharyngeal swab (NSP) and saliva samples were obtained for evaluation of rapid COVID-19 testing kits (RDT). 100/33,000 (0.3%) of specimens were RT-PCR positive for SARS-CoV-2. Among RT-PCR positive, 62% were males, 34% were females, and 4% were children. The NSP-RDT (Lepu Medical China) analysis revealed 53% reactivity among males, 58% reactivity among females, and 25% reactivity among children. However saliva based RDT (Lepu Medical China) analysis showed 21% reactivity among males and 23% among females, and no reactivity in children. False negative results were significantly more pronounced in saliva based RDT as compared to NSP-RDT. The sensitivity of these NSP-RDT and saliva based RDT were 52% and 21% respectively. The RDTs evaluated in this study showed limited sensitivities in comparison to gold standard RT-PCR, indicating that there is a dire need in Pakistan for development of suitable testing to improve accurate COVID-19 diagnosis in line with national demands.


2020 ◽  
Vol 26 (Supplement_1) ◽  
pp. S11-S12
Author(s):  
Cole Johnson ◽  
Edward Barnes ◽  
Xian Zhang ◽  
Millie Long

Abstract Background and Aims There are currently several recruitment challenges in randomized controlled trials (RCT) for inflammatory bowel disease (IBD) which prolong the drug approval process and affect the generalizability of study results. The purpose of this study is to characterize individuals who participate in IBD RCTs and identify factors which could influence future recruitment strategies. Methods We performed a cross-sectional study within the IBD Partners cohort comparing patients with current or prior participation in an interventional randomized controlled trial (RCT) of a medical therapy for IBD to those without any RCT participation. Bivariate statistics were used to compare RCT participation by IBD subtype and by other demographic and disease characteristics, and predictive modeling was used to identify factors predictive of RCT participation. We calculated the percent of the cohort that participated an in RCT during each calendar year from 2011–2018 and Clinicaltrials.gov was accessed to determine the number of active RCTs for IBD therapies per year during that same period. Results A total of 14,747 patients with IBD were included in the analysis and 1,116 (7.6%) reported RCT participation at any time. Demographic factors predictive of RCT participation (Table 1) included following at an academic institution (OR=1.8; 95%CI: 1.51–2.04) and age 36–75 (OR=1.6; 95%CI: 1.43–1.87). Patients with Crohn’s disease (CD) were more likely to participate than those with ulcerative colitis (UC) (OR=1.5; 95%CI: 1.35–1.77). Patients with more severe disease were more likely to participate, including those with prior IBD-related hospitalization (OR=2.6; 95%CI: 2.19–2.99), IBD-related surgery (OR=2.5; 95%CI: 2.24–2.87), biologic exposure (OR=3.2; 95%CI: 2.76–3.65), and “Poor” or worse quality of life (OR=1.7; 95%CI: 1.45–1.93). Steroid-free remission was associated with lower likelihood of RCT participation (OR=0.6; 95%CI: 0.53–0.70). While the number of active RCTs for IBD more than doubled between 2011 and 2018, RCT participation rates during that same time period decreased from 1.1% to 0.7% of the cohort (Figure 1). Conclusions RCT participation rates declined within this cohort between 2011–2018. Groups underrepresented in RCTs for IBD included younger patients, patients followed in community settings, and patients with more mild disease. The non-RCT group had mean sCDAI and SCCAI scores that did not meet remission thresholds, demonstrating populations in need of alternate therapies for whom clinical trials could be an option. Given anti-TNF exposure rates in this national cohort, studies should focus on anti-TNF failure populations. Investigators should make every effort to offer RCTs to all patients and network with community providers to increase awareness of RCTs.


Author(s):  
Umar Saeed ◽  
Sara Rizwan Uppal ◽  
Zahra Zahid Piracha ◽  
Aftab Ahmad Khan ◽  
Azhar Rasheed ◽  
...  

Abstract COVID-19 pandemic has urged the need of rapid detection of SARS-CoV-2 in limited time frame. To cope with current, COVID-19 expanding scenario, accurate diagnosis of SARS-CoV-2 should be ensured by both national and international health organizations. Sporadic marketing of SARS-CoV-2 rapid detection kits raises questions regarding quality control and assurance. To aim of this study was to examine the effectiveness of SARS-CoV-2 nasopharyngeal swab based rapid detection kits, in comparison to gold standard USFDA approved triple target real-time polymerase chain reaction. A cross-sectional study of 1500 suspected COVID-19 patients was conducted. 100 RT-PCR confirmed patients nasopharyngeal swabs were evaluated for RDT. The COVID-19/SARS-CoV-2 NSP based RDT analysis showed 78% reactivity. Among RT-PCR confirmed negative subjects, 49.3% showed false positivity. The positive predictive analysis revealed 67.82% values, while the negative predictive vales of were 64.40%. The NSP RDTs showed limited sensitivities and specificities compared to gold standard RT-PCR. Accurate surveillance of COVID-19 is dependent upon authentic and validated SARS-CoV-2 detection nation-wide, which needs to be monitored by higher authorities. This study is critical for designing adequate measures by several COVID-19 strategic organizations to prevent future viral epidemics.


2020 ◽  
Vol 66 (9) ◽  
pp. 1258-1263
Author(s):  
Hamad Dheir ◽  
Savas Sipahi ◽  
Selcuk Yaylaci ◽  
Ahmed Cihad Genc ◽  
Fevziye Turkoglu Genc ◽  
...  

SUMMARY INTRODUCTION: This study aims to determine the incidence of de novo nephritic syndrome (NS) in COVID-19 patients and identify its associated factors. METHODS: All ward patients with COVID-19 pneumonia were investigated. After determining the inclusion and exclusion criteria, the study population was identified. The urine dipstick test and urine protein creatinine ratio (UPCR) measurements were performed. Patients with de novo NS findings, nasopharyngeal swab, and urine RT-PCR tests were performed simultaneously RESULTS: This descriptive cross-sectional study was conducted with 21 patients with COVID-19. The mean age of the patients was 42.2±8.8 years, and 71.4% of them were male. The mean duration of follow-up was 28.4±9.3 days. The urine RT-PCR test was positive in one patient (4.8%). Improvements were observed in hematuria by 71.4%, and proteinuria by 85.7% at the end of the follow-up. A significant decrease in the measured UPCR was found in comparison to the baseline(P=0.000). Also, improvements were recorded in the complete blood counts, inflammatory parameters, ferritin, and coagulation tests, compared to the baseline. There was a positive correlation between baseline UPCR and ferritin, and a negative correlation between baseline UPCR and sodium values CONCLUSION: COVID-19-induced de novo nephritic syndrome may occur mainly due to tubulointerstitial involvement and often results in spontaneous remission. However, why these findings were not present in all patients who had no comorbidities is not clear.


2021 ◽  
Author(s):  
Hani A. Naseef ◽  
Ula Mohammad ◽  
Nimeh Al-Shami ◽  
Yousef Sahoury ◽  
Abdallah D. Abukhalil ◽  
...  

AbstractDiagnosis of co-infections with multiple pathogens among hospitalized COVID-19 patients can be jointly challenging and very essential for appropriate treatment, shortening hospital stay and preventing antimicrobial resistance. This study proposes to investigate the burden of bacterial and fungal co-infections outcomes on COVID-19 patients. It is a single centre cross-sectional study of hospitalized COVID-19 patients at Beit-Jala hospital in Palestine. The study included 321 hospitalized patients admitted to the ICU between June 2020 and March 2021 aged ≥ 20 years, with a confirmed diagnosis of COVID-19 via RT-PCR conducted on a nasopharyngeal swab. The patient’s information was gathered using graded data forms from electronic medical reports. The diagnosis of bacterial and fungal infection was proved through the patient’s clinical presentation and positive blood or sputum culture results. All cases had received empirical antimicrobial therapy before the ICU admission, and different regimens during the ICU stay. The rate of bacterial co-infection was 51.1%, mainly from gram-negative isolates (Enterobacter species and K.pneumoniae). The rate of fungal co-infection caused by A.fumigatus was 48.9%, and the mortality rate was 8.1%. However, it is unclear if it had been attributed to SARS-CoV-2 or coincidental.


2020 ◽  
Author(s):  
Shima Nabavi ◽  
Zahra Javidarabshahi ◽  
Abolghasem Allahyari ◽  
Mohammad Ramezani ◽  
Mohsen Seddigh-Shamsi ◽  
...  

Abstract Objectives: Coronavirus disease 2019 (COVID-19) can present with a variety of symptoms. Severity of the disease may be associated with several factors. Here, we review clinical features of COVID-19 patients with different severities.Methods: This cross-sectional study was performed in Imam Reza hospital, Mashhad, Iran, during February-April 2020. COVID-19 patients with typical computed tomography (CT) patterns and/or positive reverse-transcriptase polymerase chain reaction (RT-PCR) were included. The patients were classified into three groups of moderate, severe, and critical based on disease severity. Demographic, clinical, laboratory, and radiologic findings were collected and compared. P<0.05 was considered statistically significant.Results: Overall, 200 patients with mean age of 69.75±6.39 years, of whom 82 (41%) were female were studied. Disease was severe/critical in the majority of patients (167, 83.5%). Disease severity was significantly associated with age, malignant comorbidities, dyspnea, nausea/vomiting, confusion, respiratory rate, pulse rate, O2 saturation, extent of CT involvement, serum C-reactive protein (CRP), pH, pO2, and aspartate transaminase (P<0.05). Moreover, complications including shock, coagulopathy, acidosis, sepsis, acute respiratory distress syndrome (ARDS), intensive care unit (ICU) admission, and intubation were significantly higher in patients with higher severities. O2 saturation, nausea/vomiting, and extent of lung CT involvement were independent predictors of severe/critical COVID-19 (OR=0.342, 45.93, and 25.48, respectively; P<0.05).Conclusions: Our results indicate O2 saturation, nausea/vomiting, and extent of lung CT involvement as independent predictors of severe COVID-19 conditions. Serum CRP levels and pO2 were also considerably higher patients with higher severity and can be used along with other factors as possible predictors of severe disease in COVID-19 patients.


2021 ◽  
pp. 101053952110177
Author(s):  
Eslam Moradi-Asl ◽  
Davoud Adham ◽  
Hassan Ghobadi ◽  
Abbas Abbasi-Ghahramanloo

This study aimed to identify subgroups of coronavirus disease 2019 (COVID-19) symptoms and assess the role that preexisting comorbidity on membership of specific subgroup. This cross-sectional study took place in Ardabil, northwest of Iran. All patients (16 183) who were admitted to the hospitals of Ardabil province were recruited. Six indicator variables were selected to identify latent subgroups of patients using the result of polymerase chain reaction (PCR) test as a grouping variable. Data analysis was performed using χ2, independent t test, and latent class analysis. This study found that among PCR-positive patients, there were 3 latent classes: (1) mild disease (16.1%), (2) semi-severe disease (62.5%), and (3) severe disease (21.3%). This study showed that having preexisting comorbidity increase the odds of membership in semi-severe disease (odds ratio = 2.30) and severe disease (odds ratio = 1.60) classes compared with mild disease class. Focusing on patients who experience co-occurrence of more symptoms may be helpful in control of COVID-19.


Author(s):  
Fausto Salaffi ◽  
Marco Di Carlo ◽  
Laura Bazzichi ◽  
Fabiola Atzeni ◽  
Marcello Govoni ◽  
...  

Abstract Objective To establish optimal cut-off values for the scores of the revised Fibromyalgia Impact Questionnaire (FIQR), the modified Fibromialgia Assessment Scale (FAS 2019mod), and the Polysymptomatic Distress Scale (PDS) in order to distinguish five levels of FM disease severity. Methods Consecutive FM patients were evaluated with the three clinimetric indices, and each patient was required to answer the anchor question: ‘In general, would you say your health is 1 = very good, 2 = good, 3 = fair, 4 = poor, or 5 = very poor?’—which represented the external criterion. Cut-off points were established through the interquartile reconciliation approach. Results The study sample consisted of 2181 women (93.2%) and 158 men (6.8%), with a mean age of 51.9 (11.5) years, and mean disease duration was 7.3 (6.9) years. The overall median FIQR, FAS 2019 mod and PDS scores (25th–75th percentiles) were respectively 61.16 (41.16–77.00), 27.00 (19.00–32.00) and 19.0 (13.00–24.00). Reconciliation of the mean 75th and 25th percentiles of adjacent categories defined the severity states for FIQR: 0–23 for remission, 24–40 for mild disease, 41–63 for moderate disease, 64–82 for severe disease and &gt;83 for very severe disease; FAS 2019 mod: 0–12 for remission, 13–20 for mild disease, 21–28 for moderate disease, 29–33 for severe disease and &gt;33 for very severe disease; PDS: 0–5 for remission, 6–15 for mild disease, 16–20 for moderate disease, 21–25 for severe disease and &gt;25 for very severe disease. Conclusions Disease severity cut-offs can represent an important improvement in interpreting FM.


2021 ◽  
Author(s):  
Umar Saeed ◽  
Sara Rizwan Uppal ◽  
Zahra Zahid Piracha ◽  
Azhar Rasheed ◽  
Zubair Aftab ◽  
...  

Abstract Rapid diagnosis of SARS-CoV-2 during pandemic enables timely treatment and prevention of COVID-19. Evaluating the accuracy and reliability of rapid diagnostic testing kits is crucial for surveillance and diagnosis of SARS-CoV-2 infections in general population, injection drug users, multi-transfused populations, healthcare workers, prisoners, barbers and other high risk populations. The aim of this study was to evaluate performance and effectiveness of nasopharyngeal swab (NSP) and saliva based rapid antigen detection testing kits in comparison with USFDA approved triple target gold standard real-time polymerase chain reaction. A cross-sectional study was conducted on 33,000 COVID-19 suspected patients. From RT-PCR positive patients, nasopharyngeal swab (NSP) and saliva samples were obtained for evaluation of rapid COVID-19 testing kits (RDT). 100/33000 (0.3%) of specimens were RT-PCR positive for SARS-CoV-2. Among RT-PCR positive, 62% were males, 34% were females, and 4% were children. The NSP-RDT (Lepu Medical China) analysis revealed 53% reactivity among males, 58% reactivity among females, and 25% reactivity among children. However saliva based RDT (Lepu Medical China) analysis showed 21% reactivity among males and 23% among females, and no reactivity in children. False negative results were significantly more pronounced in saliva based RDT as compared to NSP-RDT. The sensitivity of these NSP-RDT and saliva based RDT were 52% and 21% respectively. The RDTs evaluated in this study showed limited sensitivities in comparison to gold standard RT-PCR, indicating that there is a dire need in Pakistan for development of suitable testing to improve accurate COVID-19 diagnosis in line with national demands.


2020 ◽  
Vol 6 (3) ◽  
pp. 08-11
Author(s):  
Shaheen Ali Khan ◽  
Muhammad Naveed Anwar ◽  
Laraib Saeed ◽  
Wajeeha Qayyum ◽  
Zuhayr Ahmad Mufti ◽  
...  

Introduction: Research has implicated an exaggerated or self-directed immune response as a factor in determining patient outcome in COVID-19. Initial reports identify lymphopenia as having a predictive role in COVID-19 related disease severity.Objective: To document the occurrence of lymphopenia in COVID-19 patients and explore its association with demographic factors and disease course.Materials & Methods: This cross sectional, observational study was conducted at Rehman Medical Institute, Peshawar from May, 2020 to August, 2020. All patients admitted to the hospital with COVID-19 diagnosis were included. Relevant information including demographics, disease severity, laboratory findings & outcomes were noted in a predesigned Performa. The data were analyzed on SPSS 22 for descriptive and comparative statistics; p≤0.05 denoted significance.Results: A total of 216 patients were included, of whom 172 (79.6%) were males. The mean age was 54.61 ± 14.35 years. Classic lymphopenia was found in 67 (31.5%), 66 (31.0%) had borderline lymphopenia, and 80 (37.6%) had no lymphopenia. Of the classic lymphopenia group, 14 (20.9%) had mild disease, 21 (31.3%) had moderate disease, 18 (26.9%) had severe disease & 14 (20.9%) had critical disease. In patients with borderline lymphopenia 31 (47.0%) had mild disease, 17 (25.8%) moderate disease, 14 (21.2%) had severe disease and 04 (6.1%) had critical disease. In patients with no lymphopenia, 32 (40.0%) had mild, 32 (40.0%) had moderate, 14 (17.5%) had severe & 02 (2.5%) had critical disease. Mortality associated with classical lymphopenia was 37.3% (n=25) whereas 43.3% (n=29) patients recovered. Male gender, disease severity and outcome were statistically linked to lymphopenia; no statistical significance was observed with age.Conclusion: A statistically significant association of lymphopenia with severe/critical disease and adverse outcomes was noted.Keywords: Lymphopenia, COVID-19, Pandemic.


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