scholarly journals Evaluation of the E gene RT-PCR Ct Values in Clinical Samples from Symptomatic and Asymptomatic COVID-19 Patients

2021 ◽  
Author(s):  
Neetu John ◽  
Rani Soni ◽  
Dev Jyoti Majumdar
Keyword(s):  
Clinical Samples ◽  
Public Health Issue ◽  
Value Analysis ◽  
The Public ◽  
E Gene ◽  
Qrt Pcr ◽  
Ct Value ◽  
Asymptomatic Patients ◽  
Significant Difference ◽  
Pcr Targeting

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread globally and is a major public health issue. Procedures that have been established to decrease the spread of the virus depend on the careful and precise detection of infected individuals using quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR). There have been many ambiguous concerns among the public regarding the severity of infection and its connection with the Cycle threshold (Ct) value and there was forceful need to inform the values to the public especially those with symptoms. The main objective of this study was to determine the association between the E (Envelop) gene Ct values of the symptomatic and asymptomatic COVID 19 patients. The study was conducted at the Virus Research and Diagnostic Laboratory (VRDL), Jagdalpur, Chhattisgarh. Between March 2020 and June 2020, samples were collected from the Bastar region as per the Indian Council of Medical Research (ICMR) guidelines. A total of 29228 clinical samples were tested by qRT-PCR targeting the E and RdRp (RNA-dependant RNA polymerase) genes as well as the ORF (open reading frame) gene that encode polyproteins of SARS-CoV-2. Of the 29228 samples tested, 75 were tested positive and 29153 were tested negative. In addition, the Ct values varied between the symptomatic and asymptomatic patients. It was observed that, the Ct values ranged from 15 to 32 in the asymptomatic patients and between 13 to 34 in the symptomatic patients. E gene Ct value analysis showed no significant difference between the asymptomatic and symptomatic COVID-19 patients. Thus, we observed that there was no association between the Ct values of symptomatic and asymptomatic patients of COVID-19.

scholarly journals Correlation between Cycle Threshold (Ct) Value and IL-6 and D-Dimer in Chip-based RT-PCR Positive COVID-19 Cases: Study from a Stand-alone Laboratory

2021 ◽  
pp. 1-9
Author(s):  
Chhavi Gandhi ◽  
H. N. Ravikumar ◽  
Vani Ravikumar ◽  
C. Vani
Keyword(s):  
Interleukin 6 ◽  
Clinical Sample ◽  
Threshold Value ◽  
Clinical Samples ◽  
Rt Pcr ◽  
Cycle Threshold ◽  
Ct Value ◽  
Asymptomatic Patients ◽  
Significant Difference ◽  
D Dimer

Background: Novel Coronavirus (SARS-COV-2) is a leading cause of morbidity and mortality since the beginning of 2020 leading to range of symptoms from mild flu to respiratory distress, which is called COVID-19. RTPCR being the main diagnostic test can confirm the presence of the virus in the clinical samples, while various studies have defined Interleukin-6 and D-dimer as potent biomarker for severity. In this study, we have attempted to correlate the severity of COVID-19 with the presence of IL-6 and D-dimer and the Cycle threshold (Ct vlue) as determined by chip based RTPCR. Aim: The study aims to correlate the Cycle threshold value obtained after chip-based RT-PCR with markers such as IL-6 and D-Dimers.                                                      Methodology: It is a retrospective, observational study done in 799 subjects  in a span of three months (August 2020 to October 2020) at R V Metropolis Diagnostic and Healthcare Pvt Ltd. All symptomatic patients who tested positive in the Laboratory for COVID-19 by chip-based RT-PCR were included. Chip based RTPCR or Truenat test was performed on Nasopharyngeal swabs of the suspected subjects. Interleukin-6 was determined by Electrochemiluminiscence assay while D-dimer was done on the principle of Chemiluminiscence. Statistical Analysis Used: SPSS 12.0 version. Results: Total number of subjects enrolled were 799, with mean age of the subjects being 46.80± 17.55 years. In the study, males were found to be affected by COVID-19 more than females with ratio of male to female being 1.65:1. 498 (62.3%) of males presented with COVID-19 while it was observed in 301 (37.6%) females. Out of 799 subjects, 289 (36.2%) were symptomatic and out of 289 subjects, 140 (17.5% of total subjects) required hospitalisation. Cycle threshold values of both screening as well as confirmatory genes were determined separately in the cases of symptomatic and asymptomatic cases and there was no significant difference between the Ct values in cases of symptomatic and asymptomatic patients. Symptomatic patients were subcategorised under hospitalised and non-hospitalised and Again, no significant difference was seen between the two subset of patients in terms of Ct-value and, indirectly, the viral load of their clinical sample. The results convey that IL-6 and D-Dimer was significantly high (p=0.001 and <0.001 respectively) in case of symptomatic patients.D-Dimer was significantly high (p= <0.001) in the patients who needed hospitalisation. IL-6 was significantly raised as well (p=0.02). Screening and confirmatory gene were found to have no significant relationship with IL-6 and D-Dimer, neither any correlation was observed with them. Conclusion: Biomarkers such as Interleukin-6 and D-dimer can very well help in determining the severity and need for hospitalisation in a COVID-19 affected patient, but they have been found to have no relationship with cycle threshold value of RTPCR in our study.

scholarly journals Assessment of Successful qRT-PCR of SARS-CoV-2 Assay in Pool Screening Using Isopropyl Alcohol Purification Step in RNA Extraction

2021 ◽  
Vol 2021 ◽  
pp. 1-6
Author(s):  
Mayank Gangwar ◽  
Alka Shukla ◽  
Virendra Kumar Patel ◽  
Pradyot Prakash ◽  
Gopal Nath
Keyword(s):  
Isopropyl Alcohol ◽  
Rna Extraction ◽  
Group Testing ◽  
Research Work ◽  
Rt Pcr ◽  
Purification Step ◽  
E Gene ◽  
Qrt Pcr ◽  
Pcr Targeting ◽  
Pooled Samples

The study is aimed at establishing the optimal parameters for RNA purification of pooled specimens, in SARS-CoV-2 assay. This research work evaluates the difference of extracted RNA purity of pooled samples with and without treatment with isopropyl alcohol and its effect on real-time RT-PCR. As per the protocol of the Indian Council of Medical Research (ICMR), 5 sample pools were analysed using qRT-PCR. A total of 100 pooled samples were selected for the study by mixing 50 μL of one COVID-19 positive nasopharyngeal/oropharyngeal (NP/OP) specimen and 50 μL each of 4 known negative specimens. Pool RNA was extracted using the column-based method, and 1 set of pooled extracted RNA was tested as such, while RNA of the second set was treated additionally with chilled isopropyl alcohol (modified protocol). Further, the purity of extracted RNA in both the groups was checked using Microvolume Spectrophotometers (Nanodrop) followed by RT-PCR targeting E-gene and RNaseP target. The results showed that the purity index of extracted RNA of untreated pooled specimens was inferior to isopropyl alcohol-treated templates, which was observed to be 85% sensitivity and 100% specificity. The average Cq (E gene) in the unpurified and purified pool RNA group was 34.66 and 31.48, respectively. The nanodrop data suggested that purified RNA concentration was significantly increased with an average value of 24.73 ± 1.49   ng / uL , which might be the reason for high sensitivity and specificity. Thus, this group testing of SARS-CoV-2 cases using pools of 5 individual samples would be the best alternative for saving molecular reagents, personnel time, and can increase the overall testing capacity. However, purity of RNA is one of the important determinants to procure unfailing results, thus, this additional purification step must be included in the protocol after RNA has been extracted using commercially available kit before performing qRT-PCR.

Abstract 252: Resuscitation in Prehospital Stage: Effectiveness and Influencing Factors

Circulation ◽  
2020 ◽  
Vol 142 (Suppl_4) ◽  
Author(s):  
Anita Abula ◽  
Aija Maca ◽  
Oskars Kalejs
Keyword(s):  
Cardiac Arrest ◽  
Influencing Factors ◽  
Sudden Cardiac Arrest ◽  
Heart Rhythm ◽  
Public Health Issue ◽  
Public Places ◽  
Successful Resuscitation ◽  
The Public ◽  
Significant Difference ◽  
Hospital Cardiac Arrest

Background: Sudden cardiac arrest or sudden cardiac death is one of the leading causes of death all over the world. Of particular importance is out-of-hospital cardiac arrest (OHCA) - an important overworld public health issue. In order to help these people and improve their chances of survival, it is necessary to provide assistance as soon as possible. Bystanders are usually non-medical persons why it is more complicated to implement. The objectives of the study were to research effectiveness and influencing factors of resuscitation in prehospital stage and create suggestions and methodical recommendations as possible. Materials and Methods: A retrospective study was developed, which summarizes and analyzes the electronic call cards (IEK) of the Emergency Medical service of Latvia (EMS) for 2018 and 2019. IEK were selected that identified “successful resuscitation” and “unsuccessful resuscitation” as a complication of diagnosis (classification developed and validated by EMS of Latvia). Results: Overall 2538 resuscitations were performed, of which 27,6% were successful resuscitation. About a quarter (24,2%) of all resuscitations happened in a public place. The increase in the number of successful resuscitations is observed for resuscitation events that happened in public places. In most of cardiac arrest cases, bystanders did not perform CPR (60,3%). Arrival time of EMS in 2018 was 7,52 - 8,44 minutes and in 2019 was 7,75 - 8,23 minutes. The research shows that approximately 23% of cases the first monitored rhythm by EMS were VF/pVT. There is a significant difference in the increase in successful resuscitations if EMS performed defibrillation during the call. Conclusions: The most important influencing factors in the outcome of resuscitation are the patient’s age, the location, the first aid provided by bystanders, the time until the arrival of EMS and the first observed heart rhythm in a patient with cardiac arrest. It is necessary to create a register of AED (automated external defibrillator) devices in Latvia and their locations, to ensure the availability of data to the EMS service and the public.

scholarly journals Microbial Contamination of Handmade Sauce Used by Street Food Vendors in Jashore, Bangladesh

2019 ◽  
Author(s):  
M. Hossain ◽  
B.K. Dey
Keyword(s):  
Microbial Contamination ◽  
Public Health Issue ◽  
Microbial Count ◽  
Bacterial Cells ◽  
Salmonella Spp ◽  
Street Food ◽  
The Public ◽  
E Coli ◽  
Food Borne ◽  
Significant Difference

Background: Contaminated handmade street foods are often claimed to occur food-borne diseases, especially in developing countries. Therefore, considering the public health issue, this study was conducted to assess the microbial contamination of handmade sauce used by street food vendors in Jashore, Bangladesh. Methods: A total of 30 samples of Plum Sauce (PS) and Tomato Sauce (TS) were collected from Jashore district, Bangladesh. The quantitative microbial tests were done by dilution plate technique. Identification of particular bacterial group or species was performed using selective media. All the data related to microbial count were subjected to ANOVA test using SPSS version 21.0. Results: All the sauce samples contained viable Enterobacteriaceae cells; whereas 80% and 83.33% of the total samples were found to be contaminated with Salmonella spp. and Escherichia coli, respectively. Total viable bacterial cells found in the samples ranged from 1.2×103 to 4.2×109 Colony Forming Unit (CFU)/g. In addition, total Enterobacteriaceae and E. coli counts ranged from 30 to 2.0×107 and from 0 to 7.0×105 CFU/g, respectively. Although PS samples contained a higher amount of Enterobacteriaceae and E. coli compared to TS, no significant difference (p>0.05) was found. Conclusion: The consumption of street foods is of great concern in Bangladesh. Making the vendors aware of sanitary practices is too crucial that could be achieved through training of the vendors at the root level of the country. Furthermore, it is necessary to monitor the street foods frequently by the national authorities.

Assessment of COVID-19 Related Misinformation among the Community in Basrah, Iraq

2020 ◽  
Vol 2 (CSI) ◽  
pp. 12-18
Author(s):  
Ali Al-Rubaye ◽  
Dhurgham Abdulwahid ◽  
Aymen Albadran ◽  
Abbas Ejbary ◽  
Laith Alrubaiy
Keyword(s):  
Cross Sectional Study ◽  
Bachelor's Degree ◽  
Public Knowledge ◽  
Age Group ◽  
Cross Sectional ◽  
Educational Levels ◽  
The Public ◽  
First Case ◽  
Significant Difference ◽  
Central District

Background: There has been a rapid rise in cases of COVID-19 infection and its mortality rate since the first case reported in February 2020. This led to the rampant dissemination of misinformation and rumors about the disease among the public. Objectives: To investigate the scale of public misinformation about COVID-19 in Basrah, Iraq. Methods: A cross-sectional study based on a 22-item questionnaire to assess public knowledge and understanding of information related to the COVID-19 infection. Results: A total of 483 individuals completed the questionnaire. The most frequent age group was 26–35 years (28.2%); there were 280 (58%) males and 203 (42%) females. Of the participants, 282 (58.4%) were with an education level below the Bachelor’s degree, 342 (70.8%) were married, and 311 (64%) were living in districts in Basra other than the central district. Overall, 50.8% (11.8/ 22 * 100%) of individuals had the correct information regarding COVID-19. There was a significant association between the level of COVID-19 related misinformation and participants’ educational levels and occupation (p <0.05). However, there was no significant difference found across sex, age group, marital state, and area of residence. Conclusions: Misinformation related to COVID-19 is widely spread and has to be addressed in order to control the pandemic. Keywords: COVID-19, misinformation, knowledge, Iraq

scholarly journals Molecular detection of cattle Sarcocystis spp. in North-West Italy highlights their association with bovine eosinophilic myositis

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Selene Rubiola ◽  
Tiziana Civera ◽  
Felice Panebianco ◽  
Davide Vercellino ◽  
Francesco Chiesa
Keyword(s):  
18S Rdna ◽  
Inflammatory Myopathy ◽  
Molecular Techniques ◽  
Diaphragm Muscle ◽  
Economic Losses ◽  
Intermediate Hosts ◽  
Slaughter Cattle ◽  
Significant Difference ◽  
Pcr Targeting

Abstract Background Cattle are intermediate hosts of six Sarcocystis species, among which Sarcocystis hominis and Sarcocystis heydorni can infect humans through the consumption of raw or undercooked meat. In addition to the zoonotic potential, there is increasing interest in these protozoa because of the evidence supporting the role of Sarcocystis spp. in the occurrence of bovine eosinophilic myositis (BEM), a specific inflammatory myopathy which leads to carcass condemnation and considerable economic losses. Actually, all the prevalence studies carried out on cattle in Italy have been based on either morphological or 18S rDNA-based molecular techniques, most likely leading to misidentification of closely related species. Therefore, there is a strong need for new data on the prevalence of the different Sarcocystis spp. in cattle in Italy and their association with bovine eosinophilic myositis. Methods To reach our aim, individual striated muscle samples from BEM condemned carcasses (N = 54) and diaphragm muscle samples from randomly sampled carcasses (N = 59) were obtained from Northwest Italy slaughterhouses. Genomic DNA was extracted and analyzed by multiplex-PCR targeting 18S rDNA and cox1 genes. PCR products amplified using the genus-specific primer set in absence of the specific fragment for S. hirsuta, S. cruzi, S. hominis or S. bovifelis were sequenced to achieve species identification. Results Sarcocystis DNA was detected in 67.8% of the samples from slaughter cattle and in 90.7% of the samples from BEM condemned carcasses. S. cruzi was identified as the most prevalent species in slaughter cattle (61%), followed by S. bovifelis (10.2%), S. hominis (8.5%) and S. hirsuta (1.7%). Notably, among the different Sarcocystis spp. detected, the presence of S. bovifelis and S. hominis was significantly higher in samples isolated from BEM condemned carcasses (46.3% and 40.7% respectively), while there was no statistically significant difference between the presence of S. cruzi or S. hirsuta in BEM condemned carcasses (42.6% and 1.8%, respectively) and randomly sampled carcasses. Furthermore, DNA sequence analysis revealed the presence of a putative new species in two carcasses. Conclusions Our study contributes to updating the data on the prevalence of the different Sarcocystis spp. in cattle in Italy, highlighting the presence of three Sarcocystis spp., S. cruzi, S. hominis and S. bovifelis, in BEM lesions and allowing us to speculate on the possible role of S. hominis and S. bovifelis as the major sarcosporidian species involved in bovine eosinophilic myositis. Graphic Abstract

scholarly journals Retinal microvascular signs in COVID-19

2021 ◽  
pp. bjophthalmol-2020-318236
Author(s):  
Ralene Sim ◽  
Gemmy Cheung ◽  
Daniel Ting ◽  
Edmund Wong ◽  
Tien Yin Wong ◽  
...  
Keyword(s):  
Medical History ◽  
Vital Signs ◽  
Plexiform Layer ◽  
Nasopharyngeal Swab ◽  
Inner Plexiform Layer ◽  
Cross Sectional ◽  
Imaging Device ◽  
Asymptomatic Patients ◽  
Significant Difference ◽  
Retinal Microvascular Signs

Background/aimsTo explore if retinal findings are associated with COVID-19 infection.MethodsIn this prospective cross-sectional study, we recruited participants positive for COVID-19 by nasopharyngeal swab, with no medical history. Subjects underwent retinal imaging with an automated imaging device (3D OCT-1 Maestro, Topcon, Tokyo, Japan) to obtain colour fundus photographs (CFP) and optical coherence tomographic (OCT) scans of the macula. Data on personal biodata, medical history and vital signs were collected from electronic medical records.Results108 patients were recruited. Mean age was 36.0±5.4 years. 41 (38.0%) had symptoms of acute respiratory infection (ARI) at presentation. Of 216 eyes, 25 (11.6%) had retinal signs—eight (3.7%) with microhaemorrhages, six (2.8%) with retinal vascular tortuosity and two (0.93%) with cotton wool spots (CWS). 11 eyes (5.1%) had hyper-reflective plaques in the ganglion cell-inner plexiform layer layer on OCT, of which two also had retinal signs visible on CFP (CWS and microhaemorrhage, respectively). There was no significant difference in the prevalence of retinal signs in symptomatic versus asymptomatic patients (12 (15.0%) vs 13 (9.6%), p=0.227). Patients with retinal signs were significantly more likely to have transiently elevated blood pressure than those without (p=0.03).ConclusionOne in nine had retinal microvascular signs on ocular imaging. These signs were observed even in asymptomatic patients with normal vital signs. These retinal microvascular signs may be related to underlying cardiovascular and thrombotic alternations associated with COVID-19 infection.

scholarly journals Comparison of saliva with healthcare workers- and patient-collected swabs in the diagnosis of COVID-19 in a large cohort

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Mitnala Sasikala ◽  
Yelamanchili Sadhana ◽  
Ketavarapu Vijayasarathy ◽  
Anand Gupta ◽  
Sarala Kumari Daram ◽  
...  
Keyword(s):  
Healthcare Workers ◽  
Early Stage ◽  
Cost Effective ◽  
Hospitalized Patients ◽  
Detection Sensitivity ◽  
Nasopharyngeal Swab ◽  
Predictive Values ◽  
Qrt Pcr ◽  
Asymptomatic Patients ◽  
Sensitivity Specificity

Abstract Background A considerable amount of evidence demonstrates the potential of saliva in the diagnosis of COVID-19. Our aim was to determine the sensitivity of saliva versus swabs collected by healthcare workers (HCWs) and patients themselves to assess whether saliva detection can be offered as a cost-effective, risk-free method of SARS-CoV-2 detection. Methods This study was conducted in a hospital involving outpatients and hospitalized patients. A total of 3018 outpatients were tested. Of these, 200 qRT-PCR-confirmed SARS-CoV-2-positive patients were recruited for further study. In addition, 101 SARS-CoV-2-positive hospitalized patients with symptoms were also enrolled in the study. From outpatients, HCWs collected nasopharyngeal swabs (NPS), saliva were obtained. From inpatients, HCWs collected swabs, patient-collected swabs, and saliva were obtained. qRT-PCR was performed to detect SARS-CoV-2 by TAQPATH assay to determine the sensitivity of saliva detection. Sensitivity, specificity and positive/negative predictive values (PPV, NPV) of detecting SARS-CoV-2 were calculated using MedCalc. Results Of 3018 outpatients (asymptomatic: 2683, symptomatic: 335) tested by qRT-PCR, 200 were positive (males: 140, females: 60; aged 37.9 ± 12.8 years; (81 asymptomatic, 119 symptomatic). Of these, saliva was positive in 128 (64%); 39 of 81 asymptomatic (47%),89 of 119 symptomatic patients (74.8%). Sensitivity of detection was 60.9% (55.4–66.3%, CI 95%), with a negative predictive value of 36%(32.9–39.2%, CI 95%).Among 101 hospitalized patients (males:65, females: 36; aged 53.48 ± 15.6 years), with HCW collected NPS as comparator, sensitivity of saliva was 56.1% (47.5–64.5, CI 95%), specificity 63.5%(50.4–75.3, CI95%) with PPV of 77.2% and NPV of 39.6% and that of self-swab was 52.3%(44–60.5%, CI95%), specificity 56.6% (42.3–70.2%, CI95%) with PPV 77.2% and NPV29.7%. Comparison of positivity with the onset of symptoms revealed highest detection in saliva on day 3 after onset of symptoms. Additionally, only saliva was positive in 13 (12.8%) hospitalized patients. Conclusion Saliva which is easier to collect than nasopharyngeal swab is a viable alternate to detect SARS-COV-2 in symptomatic patients in the early stage of onset of symptoms. Although saliva is currently not recommended for screening asymptomatic patients, optimization of collection and uniform timing of sampling might improve the sensitivity enabling its use as a screening tool at community level.

scholarly journals Phenotypic Detection of Carbapenemase Production in Carbapenem-Resistant Enterobacteriaceae by Modified Hodge Test and Modified Strip Carba NP Test

2021 ◽  
Author(s):  
Nisha Patidar ◽  
Nitya Vyas ◽  
Shanoo Sharma ◽  
Babita Sharma
Keyword(s):  
Carbapenem Resistance ◽  
Nonparametric Test ◽  
Multidrug Resistant ◽  
Clinical Samples ◽  
Chi Square ◽  
Carbapenem Resistant ◽  
The Social ◽  
Significant Difference ◽  
High Degree ◽  
Carbapenem Resistant Enterobacteriaceae

Abstract Objective Carbapenems are last resort antibiotics for multidrug-resistant Enterobacteriaceae. However, resistance to carbapenem is increasing at an alarming rate worldwide leading to major therapeutic failures and increased mortality rate. Early and effective detection of carbapenemase producing carbapenem-resistant Enterobacteriaceae (CRE) is therefore key to control dissemination of carbapenem resistance in nosocomial as well as community-acquired infection. The aim of present study was to evaluate efficacy of Modified strip Carba NP (CNP) test against Modified Hodge test (MHT) for early detection of carbapenemase producing Enterobacteriaceae (CPE). Material and Methods Enterobacteriaceae isolated from various clinical samples were screened for carbapenem resistance. A total of 107 CRE were subjected to MHT and Modified strip CNP test for the detection of CPE. Statistical Analysis It was done on Statistical Package for the Social Sciences (SPSS) software, IBM India; version V26. Nonparametric test chi-square and Z-test were used to analyze the results within a 95% level of confidence. Results Out of 107 CRE, 94 (88%) were phenotypically confirmed as carbapenemase producer by Modified strip CNP test and 46 (43%) were confirmed by Modified Hodge Test (MHT). Thirty-eight (36%) isolates showed carbapenemase production by both MHT and CNP test, 56 isolates (52%) were CNP test positive but MHT negative, eight (7%) isolates were MHT positive but CNP test negative and five (5%) isolates were both MHT and CNP test negative. There is statistically significant difference in efficiency of Modified CNP test and MHT (p < 0.05). Conclusion Modified strip CNP test is simple and inexpensive test which is easy to perform and interpret and gives rapid results in less than 5 minutes. It has high degree of sensitivity and specificity. Modified strip CNP test shows significantly higher detection capacity for carbapenemase producers as compared with MHT.

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