Ethical issues in the use of leftover samples and associated personal data obtained from diagnostic laboratories.

Diagnostic laboratories are an integral part of the research ecosystem in biomedical sciences. Among other roles, laboratories are a source of clinically-characterized samples for research or diagnostic validation studies. Particularly during the COVID-19 pandemic, this process was entered by laboratories with different experience in the ethical management of human samples. The objective of this document is to present the current ethical framework regarding the use of leftover samples in clinical laboratories. Leftover samples are defined as the residue of a sample that has been obtained and used for clinical purposes, and would otherwise be discarded. Secondary use of samples typically demands institutional ethical oversight and informed consent by the participants, although the latter requirement could be exempted when the harm risks are sufficiently small. However, ongoing discussions have proposed that minimal risk is an insufficient argument to allow the use of samples without consent. In this article, we discuss both positions, to finally suggest that laboratories anticipating the secondary use of samples should consider the adoption of broad informed consent, or even the implementation of organized biobanking, in order to achieve higher standards of ethical compliance which would enhance their capacity to fulfill their role in the production of knowledge.

Misdiagnosis of Clostridioides difficile Infections by Standard-of-Care Specimen Collection and Testing among Hospitalized Adults, Louisville, Kentucky, USA, 2019-20201.

Although Clostridioides difficile infection (CDI) incidence is high in the United States, standard-of-care (SOC) stool collection and testing practices might result in incidence overestimation or underestimation. We conducted diarrhea surveillance among inpatients >50 years of age in Louisville, Kentucky, USA, during October 14, 2019-October 13, 2020; concurrent SOC stool collection and CDI testing occurred independently. A study CDI case was nucleic acid amplification test‒/cytotoxicity neutralization assay‒positive or nucleic acid amplification test‒positive stool in a patient with pseudomembranous colitis. Study incidence was adjusted for hospitalization share and specimen collection rate and, in a sensitivity analysis, for diarrhea cases without study testing. SOC hospitalized CDI incidence was 121/100,000 population/year; study incidence was 154/100,000 population/year and, in sensitivity analysis, 202/100,000 population/year. Of 75 SOC CDI cases, 12 (16.0%) were not study diagnosed; of 109 study CDI cases, 44 (40.4%) were not SOC diagnosed. CDI incidence estimates based on SOC CDI testing are probably underestimated.

A Cost, Time, and Demographic Analysis of Participant Recruitment and Urine Sample Collection Through Social Media Optimization.

INTRODUCTION: Clinical research can be expensive and time consuming due to high associated costs and/or duration of the study. We hypothesized that urine sample collection using online recruitment and engagement of research participants via social medial has the potential to reach a large population in a small timeframe, at a reasonable cost. METHODS: We performed a retrospective cost analysis of a cohort study comparing cost per sample and time per sample for both online and clinically recruited participants for urine sample collection. During this time, cost data were collected based on study associated costs from invoices and budget spreadsheets. The data were subsequently analyzed using descriptive statistics. RESULTS: Each sample collection kit contained 3 urine cups, 1 for the disease sample and 2 for control samples. Out of the 3,576 (1,192 disease + 2,384 control) total sample cups mailed, 1,254 (695 control) samples were returned. Comparatively, the 2 clinical sites collected 305 samples. Although the initial startup cost of online recruitment was higher, cost per sample for online recruited was found to be $81.45 compared to $398.14 for clinic sample. CONCLUSIONS: We conducted a nationwide, contactless, urine sample collection through online recruitment in the midst of the COVID-19 pandemic. Results were compared with the samples collected in the clinical setting. Online recruitment can be utilized to collect urine samples rapidly, efficiently, and at a cost per sample that was 20% of an in-person clinic, and without risk of COVID-19 exposure.

Off-line or on-line? – near-рeer assisted anatomy education in the time of Covid-19 рandemic – a single center randomized controlled study

The COVID-19 pandemic significantly changed the way anatomy classes were carried out, depriving students of practical learning using real anatomical specimens. Once COVID restrictions were lifted and students returned to a normal class setting a randomized study was carried out to elevate effectiveness of practical anatomy didactics. The aim of this study was to evaluate the impact of an anatomy workshop based on demonstrating anatomical structures delivered in a face-to-face format, and to compare it with a standard course based on online learning. The randomization involved 350 students from whom 80 participants were drawn to form both a study and control group. The study consisted of three parts: exam 1, workshop, exam 2. The study group participated in all parts of the project, while the control group participated only in the exam. The workshop was held by near peer teachers (NPT). Statistical analysis showed that participation in the workshop had an effect on the passing score of exam 2 (p=0.039). It was also shown that the difference in scores was significantly higher (p=0.049) in the study group compared to the control group. The study proved that the workshops which were based on demonstrating anatomical structures by NPT significantly affected the scores obtained by trainees. In conclusion, the project confirmed the importance of student interaction with anatomical specimens and that online teaching is not a substitute for teaching in a dissecting room. Additionally, this study confirmed the high usefulness of NPT as a support for the didactic process conducted by experts. Copyright: © 2022 Jurand Domański, Marta Wanat, Jacek Ciach, Angelika Osuch, Bożena Kurc-Darak, Sławomir Woźniak, Zygmunt Domagała.

Saliva as a Viable and Simple Alternative to Nasopharyngeal and Oropharyngeal Swabs for COVID-19 Real-Time Reverse Transcriptase Polymerase Chain Reaction

Introduction: Attributable to the difficulties in specimen collection, discomfort and symptoms caused on by Nasopharyngeal (NPS) and Oropharyngeal Swab (OPS) collection, and significant risk to Healthcare Workers (HCW), evaluation of an alternative specimen for the diagnosis of Coronavirus Disease 2019 (COVID-19) is required. Saliva specimen could be an alternative specimen with many advantages over NPS and OPS, however little is known about how well it performs this purpose. Aim(s): The present study was conducted to assess the efficacy of saliva as a viable and simple alternative specimen to NPS and OPS for COVID-19 Real-Time reverse transcriptase Polymerase Chain Reaction (rRT-PCR). Material(s) and Method(s): The present cross-sectional study was conducted in the Department of Microbiology, SGT Medical College Hospital and Research Institute, Haryana, India, from July 2020 to December 2020. A total of 60 symptomatic and 20 asymptomatic COVID-19 patients were recruited for the study and specimen viz., saliva, NPS and OPS were collected at four different sampling points i.e., on day 1, 5, 7 and 14 after confirmation of COVID-19 rRT-PCR test positivity. Data obtained from the study was analysed and expressed as median, frequency, interquartile range and Chi-square test was done for comparison of categorical variables. Result(s): Majority of the patients in symptomatic hospitalised COVID-19 patients were males (n=49, 81.7%) and remaining were females (n=11, 18.3%) and in asymptomatic group 8 (40%) were males and 12 (60%) were females. Saliva was the most sensitive specimen (74.2%), followed by NPS, Naso Oropharyngeal Swab (NOPS) with 70.8% each and OPS (65.8%) for detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in symptomatic patients at four different sampling points. Comparable findings were also observed in specimens obtained from asymptomatic individuals as well. In addition, the viral load was also highest in saliva sample, as measured by Cycle Threshold (CT)-value. Across all specimen types, high viral load (lower CT-values) was observed during the early period of infection. Majority of the study participants reported discomfort during NPS and OPS collection (90% and 85%, respectively), lacrimation, sneezing and gag reflex being the most commonly reported induced symptoms. Conclusion(s): In the present study, saliva could be a viable and alternate specimen for COVID-19 diagnosis due to its ease in sample collection, specimen stability and reduced risk of transmission of infection due to droplets.Copyright © 2023 Journal of Clinical and Diagnostic Research. All rights reserved.

The Effect of SIRT1 activation on Cyclooxygenase enzyme activity in COVID-19 patients

For the third year COVID-19 pandemic is still a global health challenge, despite the availability of vaccines and protection methods, treatment protocols still being updated continuously to observe the optimum management for patients. Cyclooxegynase (COX) enzymes are involved in inflammation and thrombosis related to COVID-19. COX-Thromboxane2 pathway is one of the important pathways that results in thrombus formation. In this study the COX activity level changes were measured by ELISA technique in COVID-19 plasma samples that treated with SIRT1 activators resveratrol and linear BAS SIRT1 aptamer, a significant lowering in COX activity was observed with promising potential atrithrombotic action in COVID-19 to be further investigated in future.

Increasing the Level of Neopterin in patients infected with SARS-CoV-2 Indicates Fatal Mortality

Background: The severity of Coronavirus Disease-2019 (COVID-19) cases is associated with hyperinflammation. Patients with critical and severe COVID-19 have been observed to have high amounts of circulating cytokines. Neopterin, a crucial cytokine in the antiviral immune response that is released by macrophages upon stimulation with interferon-gamma, can be utilized to forecast the severity of illness in COVID-19 patients. Methods: The study included 185 patients with COVID-19. The patients with COVID-19 were divided into three groups according to disease severity as critical disease (n=51), severe disease (n=81), and moderate disease (n=53). All basic demographic and clinical data of the patients were recorded and blood samples were collected. Results: Neopterin levels were significantly higher in critical COVID-19 patients compared with severe and moderate COVID-19 patients (p < 0.0001). Further, neopterin showed significantly higher levels in the age group >50 years of patients with COVID-19 than in the age group <50 years. Neopterin levels were correlated with WBCs, Platelet, CRP, D-Dimer, Ferritin, Fibrinogen, IL-6, and Procalcitonin levels positively (ρ= 0.569, 0.474, 0.338, 0.696, 0.605, 0.77, 0.727, and 0.585;p < 0.01 respectively), and correlated with BMI, SpO2, and lymphocyte negatively (ρ= - 0.165;p < 0.05, p= - 0.754, - 0. 548;p < 0.01 respectively). A cutoff value of 23.62 nmol/L for neopterin predicted COVID-19 with a sensitivity of 95.7% and a specificity of 95.5% (AUC: 0.986;p < 0.0001). Conclusion: Neopterin may be a useful prognostic biomarker for assessing the severity of COVID-19.

Pre-analytical considerations in the development of a prototype SARS-CoV-2 antigen ARCHITECT automated immunoassay.

OBJECTIVES: To evaluate pre-analytical challenges related to high-volume central laboratory SARS-CoV-2 antigen testing with a prototype qualitative SARS-CoV-2 antigen immunoassay run on the automated Abbott ARCHITECT instrument. METHODS: Contrived positive and negative specimens and de-identified nasal and nasopharyngeal specimens in transport media were used to evaluate specimen and reagent on-board stability, assay analytical performance and interference, and clinical performance. RESULTS: TCID50/mL values were similar for specimens in various transport media. Inactivated positive clinical specimens and viral lysate (USA-WA1/2020) were positive on the prototype immunoassay. Within-laboratory imprecision was ≤0.10 SD (<1.00 S/C) with a ≤10% CV (≥1.00 S/C). Assay reagents were stable on board the instrument for 14 days. No high-dose hook effect was observed with a SARS-CoV-2 stock of Ct 13.0 (RLU>1.0 × 106). No interference was observed from mucin, whole blood, 12 drugs, and more than 20 cross-reactants. While specimen stability was limited at room temperature for specimens with or without viral inactivation, a single freeze/thaw cycle or long-term storage (>30 days) at -20 °C did not adversely impact specimen stability or assay performance. Specificity of the prototype SARS-CoV-2 antigen immunoassay was ≥98.5% and sensitivity was ≥89.5% across two ARCHITECT instruments. Assay sensitivity was inversely correlated with Ct and was similar to that reported for the Roche Elecsys® SARS-CoV-2 Ag immunoassay. CONCLUSIONS: The prototype SARS-CoV-2 antigen ARCHITECT immunoassay is sensitive and specific for detection of SARS-CoV-2 in nasal and nasopharyngeal specimens. Endogenous proteases in mucus may degrade the target antigen, which limits specimen storage and transport times and complicates assay workflow.

Patient and Healthcare Professional Insights of Home- and Remote-Based Clinical Assessment: A Qualitative Study from Spain and Brazil to Determine Implications for Clinical Trials and Current Practice.

INTRODUCTION: The SARS-CoV-2 virus pandemic has accelerated the growing trend towards using home- and remote-based medical testing (H/RMT). The aim of this study was to gather insights and explore the opinions of patients and healthcare professionals (HCPs) in Spain and Brazil regarding H/RMT and the impact of decentralised clinical trials. METHODS: This qualitative study consisted of in-depth open question interviews of HCPs and patients/caregivers followed by a workshop that aimed to determine the advantages and barriers to H/RMT in general, and in the context of clinical trials. RESULTS: There were 47 participants in the interviews (37 patients, 2 caregivers, 8 HCPs) and 32 in the validation workshops (13 patients, 7 caregivers, 12 HCPs). The main advantages for the use of H/RMT in current practice were the comfort and convenience, the ability to improve the relationship between HCPs and patients and personalise patient care, and the increased patient awareness towards their disease. Barriers to H/RMT included accessibility, digitalisation, and the training requirements for both HCPs and patients. Furthermore, according to the Brazilian participants, there is a general distrust in the logistical management of H/RMT. Patients indicated that the convenience of H/RMT did not influence their decision to participate in a clinical trial, with the main reason for participating in a clinical trial being to improve health; however, H/RMT in clinical research does aid adherence to the long-term follow-up associated with trials and provides access to patients living far from the clinical sites. CONCLUSION: Insights from patients and HCPs suggest that the advantages of H/RMT may outweigh the barriers, and that social, cultural and geographical factors and the HCP-patient relationship are critical aspects to be considered. Moreover, the convenience of H/RMT does not appear to be a driver for participating in a clinical trial but can facilitate patient diversity and study adherence.

Acceptability of serosurveys in southern Zambia: data collector and caregiver perspectives.

Background: Factors associated with whether individuals choose to participate in serosurveys are not well understood. Understanding perceptions from multiple perspectives, including the perspectives of both data collectors and participants, through a holistic model such as the socio-ecological model contextualizes individual, interpersonal, and structural level influences on survey research participation. We used a multiple methods approach to characterize reasons for serosurvey participation in communities in Southern Province, Zambia where a serosurvey was conducted in 2016. Methods: The first phase conducted focus group discussions and in-depth interviews with 24 data collectors who participated in a measles-rubella serosurvey in 2016. The second phase surveyed 34 caregivers at health facilities to identify barriers and facilitators to serosurvey participation. Emergent themes were then classified into a socio-ecological model using individual, interpersonal, and structural level constructs. Results: Common themes emerged from data collectors as well as caregivers surveyed. At the individual level, providing incentives was a facilitator, and some religious beliefs were described as a barrier to serosurvey participation. At the interpersonal level, family dynamics and community peer influences could help or hinder serosurvey participation. Community health workers were consistently named as facilitators of participation. At the structural level, concerns about specimen collection, who was selected for serosurveys, and not receiving test results arose as potential barriers. The most frequently reported facilitator was provision of information about the purpose of the serosurvey (85% of respondents). The most frequently reported barrier was lack of clarity regarding use of their blood specimen (53% of respondents). For specimen collection type, caregivers consistently preferred finger prick blood collection over both venous blood draw and oral swabs. Conclusion: Serosurvey participation was deemed acceptable to most study participants. The socio-ecological model revealed barriers and facilitators for participation to guide strategies to improve participation which can be applied to ongoing serosurveys for SARS-CoV-2. Serosurveys should continue to develop engagement plans to provide information about blood collection ahead of the serosurvey and communicate the objectives of such studies through trusted sources such as community health workers and traditional leaders.

A large series of molecular and serological specimens to evaluate mother-to-child SARS-CoV-2 transmission: a prospective study from the Italian Obstetric Surveillance System.

OBJECTIVES: To assay the presence of the SARS-CoV-2 genome in vaginal, rectal, and placental swabs among pregnant women and in newborn nasopharyngeal swabs and to investigate the immunological response and maternal antibody transfer through the umbilical cord blood and milk of unvaccinated mothers. METHODS: Vaginal, rectal, and placental specimens, maternal and neonatal serum, and milk were collected from a wide cohort of pregnant Italian women with confirmed SARS-CoV-2 infection admitted to the hospital between February 25, 2020 and June 30, 2021. Samples were tested in selected reference laboratories according to a shared interlaboratory protocol. RESULTS: Among 1086 enrolled women, the SARS-CoV-2 positive rate detected in all specimens ranged from 0.7% to 8.4%. Respectively, 45.2% of maternal sera collected during pregnancy and 39.7% of those collected at birth tested positive for immunoglobulin G, whereas 50.5% tested positive among neonates. Nasopharyngeal swabs were positive in 0.8% of the newborns, and immunoglobulin G was detected in 3.0% of the milk samples. The highest immunological response was recorded within 30 days during pregnancy and within 60 days of birth and in the neonatal population. CONCLUSION: Vertical transmission should be considered a rare event; although, a good maternal immunological response and antibodies transfer throughout the umbilical cord blood was detected.

Automated sample-to-answer system for rapid and accurate diagnosis of emerging infectious diseases

Automated sample-to-answer systems that promptly diagnose emerging infectious diseases, such as zoonotic diseases, are crucial to preventing the spread of infectious diseases and future global pandemics. However, automated, rapid, and sensitive diagnostic testing without professionals and sample capacity and type limitations remains unmet needs. Here, we developed an automated sample-to-answer diagnostic system for rapid and accurate detection of emerging infectious diseases from clinical specimens. This integrated system consists of a microfluidic platform for sample preparation and a bio-optical sensor for nucleic acid (NA) amplification/detection. The microfluidic platform concentrates pathogens and NAs in a large sample volume using adipic acid dihydrazide and a low-cost disposable chip. The bio-optical sensor allows label-free, isothermal one-step NA amplification/detection using a ball-lensed optical fiber-based silicon micro-ring resonator sensor. The system is integrated with software to automate testing and perform analysis rapidly and simply;it can distinguish infection status within 80 min. The detection limit of the system (0.96 × 101 PFU) is 10 times more sensitive than conventional methods (0.96 × 102 PFU). Furthermore, we validated the clinical utility of this automated system in various clinical specimens from emerging infectious diseases, including 20 plasma samples for Q fever and 13 (11 nasopharyngeal swabs and 2 saliva) samples for COVID-19. The system showed 100% sensitivity and specificity for detecting 33 samples of emerging infectious diseases, such as Q fever, other febrile diseases, COVID-19, human coronavirus OC43, influenza A, and respiratory syncytial virus A. Therefore, we envision that this automated sample-to-answer diagnostic system will show high potential for diagnosing emerging infectious diseases in various clinical applications. © 2023 Elsevier B.V.

Concordance in COVID-19 serology, bone mineralization, and inflammatory analytes between venous and self-collected capillary blood samples exposed to various pre-analytical conditions.

BACKGROUND: The COVID-19 has led to a significant increase in demand for remote blood sampling in clinical trials. This study aims to ascertain the concordance between venous versus capillary samples, processed immediately or exposed to various pre-analytical conditions. METHODS: Participants (≥12 years old) provided a venous blood sample (processed immediately) and capillary samples allocated to one of the following conditions: processed immediately or exposed to 12-, 24-, or 36-h delays at room temperature or 36-h delays with a freeze-thaw cycle. The analytes of interest included SARS-CoV-2 IgG, 25-hydroxy vitamin D (25(OH)D), alkaline phosphate (ALP), calcium (Ca), phosphate (Ph), and c-reactive protein (CRP). Paired samples were considered interchangeable if they met three criteria: minimal within-subject mean difference, 95% of values within desirable total errors, and inter-class correlation (ICC) > 0.90. RESULTS: 90 participants (44.1% male) were enrolled. When comparing rapidly processed venous with capillary samples, 25(OH)D, ALP, and CRP met all three criteria; SARS-CoV-2 IgG met two criteria (mean difference and ICC); and Ca and Ph met one criterion (mean difference). When considering all three criteria, concentrations of 25(OH)D, CRP, and ALP remained unchanged after delays of up to 36 h; SARS-CoV-2 IgG met two criteria (mean difference and ICC); Ca and Ph met one criterion (mean difference). CONCLUSION: These findings suggest that remote blood collection devices can be used to measure anti-SARS-CoV-2 IgG, 25(OH)D, CRP, and ALP. Further analysis is required to evaluate the interchangeability between venous and capillary testing in Ca and Ph levels, which are more sensitive to pre-analytical conditions.

Correlations of Myeloperoxidase (MPO), Adenosine deaminase (ADA), C-C motif chemokine 22 (CCL22), Tumour necrosis factor alpha (TNFα) and Interleukin-6 (IL-6) mRNA expression in the nasopharyngeal specimens with the diagnosis and severity of SARS-CoV-2 infections.

Cytokine dynamics in patients with coronavirus disease 2019 (COVID-19) have been studied in blood but seldomly in respiratory specimens. We studied different cell markers and cytokines in fresh nasopharyngeal swab specimens for the diagnosis and for stratifying the severity of COVID-19. This was a retrospective case-control study comparing Myeloperoxidase (MPO), Adenosine deaminase (ADA), C-C motif chemokine ligand 22 (CCL22), Tumour necrosis factor alpha (TNFα) and Interleukin-6 (IL-6) mRNA expression in 490 (327 patients and 163 control) nasopharyngeal specimens from 317 (154 COVID-19 and 163 control) hospitalized patients. Of the 154 COVID-19 cases, 46 died. Both total and normalized MPO, ADA, CCL22, TNFα, and IL-6 mRNA expression levels were significantly higher in the nasopharyngeal specimens of infected patients when compared with controls, with ADA showing better performance (OR 5.703, 95% CI 3.424-9.500, p < 0.001). Receiver operating characteristics (ROC) curve showed that the cut-off value of normalized ADA mRNA level at 2.37 × 10-3 had a sensitivity of 81.8% and specificity of 83.4%. While patients with severe COVID-19 had more respiratory symptoms, and elevated lactate dehydrogenase, multivariate analysis showed that severe COVID-19 patients had lower CCL22 mRNA (OR 0.211, 95% CI 0.060-0.746, p = 0.016) in nasopharyngeal specimens, while lymphocyte count, C-reactive protein, and viral load in nasopharyngeal specimens did not correlate with disease severity. In summary, ADA appears to be a better biomarker to differentiate between infected and uninfected patients, while CCL22 has the potential in stratifying the severity of COVID-19.

Genotyping of Corona virus infections in Baghdad city

Background: The discovery of genotypes linked to geographic and temporal infectious clusters suggests that genotyping analysis can be used to track and monitor the transmission of corona virus. Objective: To explore the clinical value of causative agent for corona virus infection (CoVI) by using different genes (SARS-HCoV2 ORFlab JINZA1 and JINZA2 gene and HCoV NL63, HCoV OC43 and HCoV 229E in the diagnosis of causative agent for corona virus disease and severity of infection to know speed transmission this pandemic and control of disease. Patients and methods: Different types from human samples included nasal swabs, throat swabs and blood samples(plasma) from patients with CoVI and pneumonia. To diagnosis SARS-HCoV2 ORFlab JINZA1 and JINZA2 gene, and HCoV NL63 gene, HCoV OC43 gene and HCoV 229E gene. The positive ratio of SARS-HCoV2 ORFlab gene in the diagnosis of COVID-19 pneumonia confirmed by conventional PCR then gene sequencing by sanger method by using PCR product were sent for Sanger sequencing using ABI3730XL, automated DNA sequences, by Macrogen Corporation Korea. The results were received by email then analyzed using geneious software. Results: Assay for CoV the results shown P = 0.001 Highly sign. (P<0.01) within NL63 gene from nasal and throat swab positive n = 2 (10.53%) while negative n =17 (89.47 %) and P = 0.00 Highly sign. (P<0.01) within CT for NL63 gene positive n = 2 (4 %) while negative n = 48 (96 %). In addition to CoV result by PCR were P = 0.033 Sign. (P<0.05), positive n =17 (34%) and negative n =33 (66 %) from total n =50, and P = 0.019 Sign. (P<0.05) within SARSHCOV2 ORFlab gene from nasal swab by PCR positive n =4(21.05%), negative n = 15(78.95%) from total n =19 and P = 0.648 Non sign. (P>0.05) 229E gene from nasal and throat swab positive n =11(57.9%), negative n =8 (42.1%) from total n=19 (100%). While undetectable from OC43HCOV gene by real time PCR and by conventional PCR that indicated all results were negative for blood samples and from nasal and throat swab: Conclusion: Genotyping very important to know type of gene caused corona virus infection by using PCR real time PCR and conventional PCR indicated the study on the present other types of corona virus were HCOV 229E and NL63 HCOV and PCR product confirmed by Sanger sequencing using ABI3730XL, automated DNA sequences, the results concluded discovery two new isolates called SARSHCOV2ORF1ab JINZA1 gene and SARSHCOV2ORF1ab JINZA2 gene in Baghdad/Iraq patients and submitted in National Center for Biotechnology Information. SARSHCOV2ORF1ab JINZA1 OK486620 gene and JINZA2 OK586822 gene. The names of both genes according to name of PhD student Jnan Jafar Baksh, Supervisal Prof. Dr. Nazar Shiyaa Mohammed and Assist prof. Dr. Ahmed Saadi Hassan. BLAST results indicated because transmission by travel between Iraq and USA. Both of two patient's loss of their life due to severity of infection for JINZA1 and JINZA2 and were critical class for this pandemic.Recommendation: 1) Chosen specific primers for specific gene to avoid coinfection with other viruses and using confirmed tests include real time PCR or conventional PCR and gene sequencing for genotyping for corona virus to know speed viral transmission and control of disease: 2) Nasal swab and throat swab for detection from corona virus mostly greatest than blood samples because viral load higher and development molecular techniques and instruments for detection from virus when very low viral load.

Automated sample-to-answer system for rapid and accurate diagnosis of emerging infectious diseases

Automated sample-to-answer systems that promptly diagnose emerging infectious diseases, such as zoonotic diseases, are crucial to preventing the spread of infectious diseases and future global pandemics. However, automated, rapid, and sensitive diagnostic testing without professionals and sample capacity and type limitations remains unmet needs. Here, we developed an automated sample-to-answer diagnostic system for rapid and accurate detection of emerging infectious diseases from clinical specimens. This integrated system consists of a microfluidic platform for sample preparation and a bio-optical sensor for nucleic acid (NA) amplification/detection. The microfluidic platform concentrates pathogens and NAs in a large sample volume using adipic acid dihydrazide and a low-cost disposable chip. The bio-optical sensor allows label-free, isothermal one-step NA amplification/detection using a ball-lensed optical fiber-based silicon micro-ring resonator sensor. The system is integrated with software to automate testing and perform analysis rapidly and simply;it can distinguish infection status within 80min. The detection limit of the system (0.96 × 101 PFU) is 10 times more sensitive than conventional methods (0.96 × 102 PFU). Furthermore, we validated the clinical utility of this automated system in various clinical specimens from emerging infectious diseases, including 20 plasma samples for Q fever and 13 (11 nasopharyngeal swabs and 2 saliva) samples for COVID-19. The system showed 100% sensitivity and specificity for detecting 33 samples of emerging infectious diseases, such as Q fever, other febrile diseases, COVID-19, human coronavirus OC43, influenza A, and respiratory syncytial virus A. Therefore, we envision that this automated sample-to-answer diagnostic system will show high potential for diagnosing emerging infectious diseases in various clinical applications.

Development of a non-contact mobile screening center for infectious diseases: Effects of ventilation improvement on aerosol transmission prevention.

Under the global landscape of the prolonged COVID-19 pandemic, the number of individuals who need to be tested for COVID-19 through screening centers is increasing. However, the risk of viral infection during the screening process remains significant. To limit cross-infection in screening centers, a non-contact mobile screening center (NCMSC) that uses negative pressure booths to improve ventilation and enable safe, fast, and convenient COVID-19 testing is developed. This study investigates aerosol transmission and ventilation control for eliminating cross-infection and for rapid virus removal from the indoor space using numerical analysis and experimental measurements. Computational fluid dynamics (CFD) simulations were used to evaluate the ventilation rate, pressure differential between spaces, and virus particle removal efficiency in NCMSC. We also characterized the airflow dynamics of NCMSC that is currently being piloted using particle image velocimetry (PIV). Moreover, design optimization was performed based on the air change rates and the ratio of supply air (SA) to exhaust air (EA). Three ventilation strategies for preventing viral transmission were tested. Based on the results of this study, standards for the installation and operation of a screening center for infectious diseases are proposed.

The US Department of Veterans Affairs Science and Health Initiative to Combat Infectious and Emerging Life-Threatening Diseases (VA SHIELD): A Biorepository Addressing National Health Threats.

Background: The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has demonstrated the need to share data and biospecimens broadly to optimize clinical outcomes for US military Veterans. Methods: In response, the Veterans Health Administration established VA SHIELD (Science and Health Initiative to Combat Infectious and Emerging Life-threatening Diseases), a comprehensive biorepository of specimens and clinical data from affected Veterans to advance research and public health surveillance and to improve diagnostic and therapeutic capabilities. Results: VA SHIELD now comprises 12 sites collecting de-identified biospecimens from US Veterans affected by SARS-CoV-2. In addition, 2 biorepository sites, a data processing center, and a coordinating center have been established under the direction of the Veterans Affairs Office of Research and Development. Phase 1 of VA SHIELD comprises 34 157 samples. Of these, 83.8% had positive tests for SARS-CoV-2, with the remainder serving as contemporaneous controls. The samples include nasopharyngeal swabs (57.9%), plasma (27.9%), and sera (12.5%). The associated clinical and demographic information available permits the evaluation of biological data in the context of patient demographics, clinical experience and management, vaccinations, and comorbidities. Conclusions: VA SHIELD is representative of US national diversity with a significant potential to impact national healthcare. VA SHIELD will support future projects designed to better understand SARS-CoV-2 and other emergent healthcare crises. To the extent possible, VA SHIELD will facilitate the discovery of diagnostics and therapeutics intended to diminish COVID-19 morbidity and mortality and to reduce the impact of new emerging threats to the health of US Veterans and populations worldwide.

Primary healthcare providers challenged during the COVID-19 pandemic: a qualitative study.

BACKGROUND: Primary healthcare (PHC) providers are widely acknowledged for putting the most efficient and long-lasting efforts for addressing community health issues and promoting health equity. This study aimed to explore PHC providers' experiences with coronavirus pandemic preparedness and response in Armenia. METHODS: We applied a qualitative study design using semi-structured in-depth interviews and structured observation checklists. Study participants were recruited using theoretical and convenience sampling techniques throughout Armenia. Inductive conventional content analysis was utilized to analyze the in-depth interviews. Nineteen in-depth interviews were conducted with 21 participants. Observations took place in 35 PHC facilities. The data collected during the observations was analyzed using the "SPSS22.0.0.0" software. RESULTS: Five main themes of primary healthcare providers' experiences were drawn out based on the study findings: 1) the gap in providers' risk communication skills; 2) uneven supply distributions; 3) difficulties in specimen collection and testing processes; 4) providers challenged by home visits; 5) poor patient-provider relationships. The results revealed that primary care providers were affected by uneven supply distribution throughout the country. The lack of proper laboratory settings and issues with specimen collection were challenges shaping the providers' experiences during the pandemic. The study highlighted the health systems' unpreparedness to engage providers in home visits for COVID-19 patients. The findings suggested that it was more challenging for healthcare providers to gain the trust of their patients during the pandemic. The study results also underlined the need for trainings to help primary care providers enhance their risk communication expertise or assign other responsible bodies to carry out risk communication on PHC providers' behalf. CONCLUSION: The study discovered that PHC providers have a very important role in healthcare system's preparedness and response to handle public health emergencies such as the COVID-19 pandemic. Based on the findings the study team recommends prioritizing rural PHC development, ensuring appropriate supply distributions, developing comprehensive protocols on safe home visits and specimen collection and testing processes, and trainings PHC providers on risk communication, patient-centeredness, as well as proper use of personal protective equipment.

Direct Nasal Swab for Rapid Test and Saliva as an Alternative Biological Sample for RT-PCR in COVID-19 Diagnosis.

Accurate and early diagnoses are prerequisites for prompt treatment. For coronavirus disease 2019 (COVID-19), it is even more crucial. Currently, choice of methods include rapid diagnostic tests and reverse transcription polymerase chain reaction (RT-PCR) using samples mostly of respiratory origin and sometimes saliva. We evaluated two rapid diagnostic tests with three specimen types using viral transport medium (VTM) containing naso-oropharyngeal (NOP) swabs, direct nasal and direct nasopharyngeal (NP) samples from 428 prospective patients. We also performed RT-PCR for 428 NOP VTM and 316 saliva samples to compare results. The sensitivity of the SD Biosensor Standard Q COVID-19 antigen (Ag) test kit drastically raised from an average of 65.55% (NOP VTM) to 85.25% (direct nasal samples), while RT-PCR was the gold standard. For the CareStart kit, the sensitivity was almost similar for direct NP swabs; the average was 84.57%. The specificities were ≥95% for both SD Biosensor Standard Q and CareStart COVID-19 Ag tests in all platforms. The kits were also able to detect patients with different variants as well. Alternatively, RT-PCR results from saliva and NOP VTM samples showed high sensitivities of 96.45% and 95.48% with respect to each other as standard. The overall results demonstrated high performance of the rapid tests, indicating the suitability for regular surveillance at clinical facilities when using direct nasal or direct NP samples rather than NOP VTM. Additionally, the analysis also signifies not showed that RT-PCR of saliva can be used as an choice of method to RT-PCR of NOP VTM, providing an easier, non-invasive sample collection method. IMPORTANCE There are several methods for the diagnosis of coronavirus disease 2019 (COVID-19), and the choice of methods depends mostly on the resources and level of sensitivity required by the user and health care providers. Still, reverse transcription polymerase chain reaction (RT-PCR) has been chosen as the best method using direct naso-oropharyngeal swabs. There are also other methods of fast detection, such as rapid diagnostic tests (RDTs), which offer result within 15 to 20 min and have become quite popular for self-testing and in the clinical setting. The major drawback of the currently used RT-PCR method is compliance, as it may cause irritation, and patients often refuse to test in such a way. RDTs, although inexpensive, suffer from low sensitivity due to technical issues. In this article, we propose saliva as a noninvasive source for RT-PCR samples and evaluate various specimen types at different times after infection for the best possible output from COVID-19 rapid tests.