Comparison of T-cell immune responses to SARS-CoV-2 spike (S) and nucleocapsid (N) protein using an in-house flow-cytometric assay in laboratory employees with and without previously confirmed COVID-19 in South Africa: nationwide cross-sectional study.

AIMS: To compare specific T-cell responses between laboratory employees in South Africa with and without previously diagnosed SARS-CoV-2 infection. METHODS: Employees at a private pathology laboratory in South Africa were invited to participate in a nationwide cross-sectional study. T-cell proliferation to SARS-CoV-2 nucleocapsid (N)-proteins and spike (S)-proteins was measured by flow cytometry and compared between participants. RESULTS: Based on classification according to SARS-CoV-2 reverse transcription (RT)-PCR results, a total of 81% (42/52) of positive participants demonstrated T-cell proliferation to SARS-CoV-2 N-proteins or S-proteins (95% CI 67.5% to 90.4%), while 62% (68/110) of negative participants also had detectable T-cell responses to SARS-CoV-2 proteins (95% CI 52.1% to 70.9%). When classified according to SARS-CoV-2 serology results, 92.6% (50/54) of positive participants demonstrated T-cell proliferation to SARS-CoV-2 proteins (95% CI 82.1 to 97,9 %), while 56% (60/108) of negative participants demonstrated T-cell proliferation (95% CI 45.7% to 65.1%). The magnitude of the T-cell responses as determined by a stimulation index, was significantly higher in the group previously infected by SARS-CoV-2 than in the negative group. A statistically significant difference in T-cell proliferation was noted between high risk and low risk groups for exposure to SARS-CoV-2 within the negative group, but no significant difference in magnitude of the response. CONCLUSIONS: A significant proportion of South African laboratory employees who were not previously diagnosed with COVID-19 demonstrated T-cell reactivity to SARS-CoV-2 N-proteins and S-proteins. The pre-existing T-cell proliferation responses may be attributable to cross-reactive immune responses to other human coronaviruses, or possibly asymptomatic infection.

Consensus of the Liaison-Psychiatry Committee of the Colombian Psychiatric Association on the Diagnosis and Treatment of Delirium in the Context of the COVID-19 Pandemic. / Consenso del Comité de Psiquiatría de Enlace de la Asociación Colombiana de Psiquiatría sobre el diagnóstico y tratamiento del delirium en el contexto de la pandemia por COVID-19.

The pandemic caused by the new coronavirus named SARS-CoV-2 poses unprecedented challenges in the health care. Among them is the increase in cases of delirium. The severe SARS-CoV-2 disease, COVID-19, has common vulnerabilities with delirium and produces alterations in organs such as the lungs or the brain, among others, which have the potential to trigger the mental disorder. In fact, delirium may be the first manifestation of the infection, before fever, general malaise, cough or respiratory disturbances. It is widely supported that delirium increases the morbidity and mortality in those who suffer from it during hospitalization, so it should be actively sought to carry out the relevant interventions. In the absence of evidence on the approach to delirium in the context of COVID-19, this consensus was developed on three fundamental aspects: diagnosis, non-pharmacological treatment and pharmacological treatment, in patients admitted to the general hospital. The document contains recommendations on the systematic use of diagnostic tools, when to hospitalize the patient with delirium, the application of non-pharmacological actions within the restrictions imposed by COVID-19, and the use of antipsychotics, taking into account the most relevant side effects and pharmacological interactions.

Impact of COVID-19 pandemic on HbA1c management and results in pediatric and adult outpatients with diabetes.

Objectives: Diabetes mellitus intensify the risks and complications related to COVID-19 infection. A major effect of the pandemic has been a drastic reduction of in-person visits. The aim of this study was to evaluate the impact of the COVID-19 pandemic on HbA1c management and results among pediatric and adult outpatients with diabetes, considering the laboratory and point-of-care testing (POCT) HbA1c measurements. Methods: Observational retrospective study including patients from pediatric and adult diabetes units was conducted. HbA1c results obtained in the laboratory and POCT over 3 years (2019-2021) were collected from the laboratory information system. Results: After the lockdown, the number of HbA1c plummeted. Children returned soon to routine clinical practice. The number of HbA1c increased gradually in adults, especially in POCT. Globally, HbA1c results were lower in children compared with adults (p<0.001). HbA1c values in children (p<0.001) and adults (p=0.002) decreased between pre-pandemic and post-pandemic periods, though lower than the HbA1c reference change value. The percentage of HbA1c results above 8% remained stable during the study period. Conclusions: Continuous glucose monitoring and a telemedicine have been crucial, even allowing for improvements in HbA1c results. During the lockdown, patients with better metabolic control were managed in the laboratory whereas patients with poorer control or a severe clinical situation were attended in diabetes units by POCT. Adults returned to pre-pandemic management slowly because they were more susceptible to morbidity and mortality due to COVID-19. Coordination among all health professionals has been essential to offering the best management, especially in difficult scenarios such as the COVID-19 pandemic.

Efficacy of Nucleic Acid Extraction by Manual versus Automated Magnetic Bead-based Method to Detect SARS-CoV-2

Introduction: In December 2019, a rapid spread of highly infectious, Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), was reported in Wuhan, China. The gold standard for diagnosis of SARS-CoV-2 infection is nucleic acid amplification technology by detecting its viral Ribonucleic Acid (RNA) from respiratory swabs (oropharyngeal and nasopharyngeal) by Reverse Transcription-Polymerase Chain Reaction (RT-PCR) whose specificity is approximately 95%. Magnetic bead RNA extraction was benchmarked against the commercial QIAcube extraction platform. Aim(s): To compare the efficacy of nucleic acid extraction by manual method and automated magnetic bead-based method to detect SARS-CoV-2. Material(s) and Method(s): The present observational comparative study was conducted in the Department of Microbiology, Autonomous State Medical College, Firozabad, Uttar Pradesh, India. Duration of the study was from February to March 2022. A total of 470 oropharyngeal and nasopharyngeal samples were included in this study to observe the efficacy of nucleic acid extraction by manual extraction and automated extraction for SARS-CoV-2. Data were entered in Microsoft Excel software and analysed using Statistical Package for the Social Sciences (SPSS) version 26.0. Result(s): During this study period, a total of 470 individual samples were tested in 94 pools. Out of these 470 individuals, 331 were males (70.5%) and 139 were females (29.5%). All 94 pools were found negative by both automatic and manual extraction methods. Envelope (E) gene was found in one pool (1.06%) by the manual RNA extraction method. E gene was absent in 93 pools (98.94%) by manual method. Internal control was found highest in 88 pools (93.62%) by the automated extraction method. Conclusion(s): Automated workflows avoid human error from the sample processing pipeline and also ensure as well as enhance the meaningful output, diagnostic precision, and testing capacity. Automated instruments are in wide usage because of their capability of processing thousands of samples per day with the support of minimal staff. Copyright © 2022 Journal of Clinical and Diagnostic Research. All rights reserved.

Consensus of the Liaison-Psychiatry Committee of the Colombian Psychiatric Association on the diagnosis and treatment of delirium in the context of the COVID-19 pandemic.

The pandemic caused by the new coronavirus named SARS-CoV-2 poses unprecedented challenges in the health care. Among them is the increase in cases of delirium. The severe SARS-CoV-2 disease, COVID-19, has common vulnerabilities with delirium and produces alterations in organs such as the lungs or the brain, among others, which have the potential to trigger the mental disorder. In fact, delirium may be the first manifestation of the infection, before fever, general malaise, cough or respiratory disturbances. It is widely supported that delirium increases the morbidity and mortality in those who suffer from it during hospitalization, so it should be actively sought to carry out the relevant interventions. In the absence of evidence on the approach to delirium in the context of COVID-19, this consensus was developed on three fundamental aspects: diagnosis, non-pharmacological treatment and pharmacological treatment, in patients admitted to the general hospital. The document contains recommendations on the systematic use of diagnostic tools, when to hospitalize the patient with delirium, the application of non-pharmacological actions within the restrictions imposed by COVID-19, and the use of antipsychotics, taking into account the most relevant side effects and pharmacological interactions.

SARS-CoV-2 Delta and Omicron Variants Surge in Curitiba, Southern Brazil, and Its Impact on Overall COVID-19 Lethality.

Screening efforts and genomic surveillance are essential tools to evaluate the course of the COVID-19 pandemic and assist the public healthcare system in dealing with an increasing number of infections. For the analysis of COVID-19 cases scenarios in Curitiba, Paraná, Brazil, we performed a diagnosis of positive cases, coupled with genotyping, for symptomatic and asymptomatic members of the Federal University of Paraná. We achieved over 1000 samples using RT-qPCR for diagnosis. The posterior genotyping allowed us to observe differences in the spread of strains in Curitiba, Brazil. The Delta variant was not associated with an infection wave, whereas the rapid Omicron variant spread became dominant in less than one month. We also evaluated the general vaccination coverage in the state, observing a striking reduction in lethality correlated to the vaccinated fraction of the population; although lower lethality rates were not much affected by the Omicron variant wave, the same effect was not translated in the number of infections. In summary, our results provide a general overview of the pandemic's course in Paraná State and how there was reduction in lethality after a combination of multiple infection waves and a large-scale vaccination program.

Syphilis self-testing to expand test uptake among men who have sex with men: a theoretically informed mixed methods study in Zimbabwe.

OBJECTIVES: Self-testing for STIs such as HIV and syphilis may empower sexual minorities and expand uptake of STI testing. While much is known about HIV self-testing (HIVST), less is known about syphilis self-testing, particularly in low-income settings. The objective of this study is to determine context-specific facilitators and barriers for self-testing and to assess the usability of syphilis self-testing in Zimbabwe among men who have sex with men (MSM). METHODS: This mixed methods study was conducted in Harare as part of a larger syphilis self-testing trial. The study included in-depth interviews (phase I) followed by usability testing and a second interview (phase II). In-depth interviews were conducted with MSM and key informants prior to syphilis self-testing. The same MSM then used the syphilis self-test, quantitatively assessed its usability and participated in a second in-depth interview. Phase I data were analysed using a thematic approach, guided by an adapted social ecological model conceptual framework. Phase II interviews were analysed using rapid assessment procedure methodology, and usability was assessed using a pre-established index, adapted from existing HIVST scales. RESULTS: Twenty MSM and 10 key informants were recruited for phase I in-depth interviews, and 16 of these MSM participated in phase II by completing a syphilis self-test kit. Facilitating factors for self-testing included the potential for increased privacy, convenience, autonomy, and avoidance of social and healthcare provider stigma. Barriers included the fear to test and uncertainty about linkage to care and treatment. Data from the Usability Index suggested high usability (89.6% on a 0-100 scale) among the men who received the self-test. CONCLUSIONS: MSM in Zimbabwe were willing to use syphilis self-test kits and many of the barriers and facilitators were similar to those observed for HIVST. Syphilis self-testing may increase syphilis test uptake among sexual minorities in Zimbabwe and other low-income and middle-income countries.

Fast, simple and cheap: method modified from conventional cultivation for tuberculosis diagnosis allows seeding on Löwenstein-Jensen of any swab-embedded pulmonary samples decontaminated with sodium hydroxide.

BACKGROUND: Few tuberculosis (TB) control programmes in low-income countries have access to culture facilities in their primary care diagnostic centres and this scenario may have worsened with the coronavirus disease 2019 pandemic. Thus the aim was to develop and evaluate a simpler TB test that allows seeding on Löwenstein-Jensen (LJ) medium of several swab-embedded samples decontaminated with sodium hydroxide (NaOH). METHODS: A cotton swab containing each sample was decontaminated in NaOH before being dipped into a slightly acidic solution to neutralize the pH in order to allow the culture to develop on LJ medium. Samples (n=543) from suspected or confirmed pulmonary TB were analysed in two phases: standardization (n=167) and evaluation of the study method (n=376). RESULTS: The study method showed sensitivity >95% and specificity >93% using Ogawa-Kudoh (OK) and modified Petroff (MP) as standards and was comparable to MP-LJ (p>0.05) and slightly superior to OK (p=0.03) for sputum culture and more comprehensive than the latter for other pulmonary specimens. CONCLUSIONS: This article reports a more comprehensive, simpler and less costly method for diagnosing TB in the laboratory with fewer economic resources and biosafety equipment. Thus a patent application was filed (BR1020190103841).

Attitudes about COVID-19 Testing among Black Adults in the United States.

Purpose: Black Americans are disproportionately affected by coronavirus disease 2019 (COVID-19) hospitalizations and deaths. Decreasing health disparities requires widespread uptake of COVID-19 testing, but attitudes about COVID-19 testing among Black Americans have not been studied. We aimed to characterize knowledge, attitudes, and beliefs about COVID-19 testing among Black parents. Methods: Semi-structured interviews were conducted and analyzed using a phenomenology approach with 26 self-identified Black parents after telemedicine visits with a children's health center. Interviews were recorded and transcribed; 65% were double coded with a resultant free-marginal interrater kappa score of 86.8%. Results: Most participants were women, spent time inside the homes of friends or family members, and almost half knew someone diagnosed with COVID-19. Three central themes emerged regarding COVID-19 testing decision making, including: 1) perceived COVID-19 disease susceptibility; 2) barriers to testing, with subthemes including trust in test accuracy and safety, perceived stigma of a positive test result, and impact of racism on self-efficacy; and 3) cues to action. Conclusions: When considering these themes as constructs of the Health Belief Model, we are better able to understand Black Americans' views of COVID-19 testing and motivations for accessing testing. Culturally responsive educational campaigns delivered by trusted community members should aim to improve understanding about disease transmission and types of tests available. Importantly, framing testing as a means to ensure safety may improve self-efficacy to obtain testing. Lastly, the health community should learn from these conversations with Black Americans so that disease prevention and mitigation strategies prioritize health equity.

Large-Scale Screening of Asymptomatic Persons for SARS-CoV-2 Variants of Concern and Gamma Takeover, Brazil.

We performed a large-scale severe acute respiratory syndrome coronavirus 2 screening campaign using 2 PCR-based approaches, coupled with variant genotyping, aiming to provide a safer environment for employees of Federal University in Curitiba, Brazil. We observed the rapid spread of the Gamma variant of concern, which replaced other variants in <3 months.

Probable Pain on the Pain Assessment in Impaired Cognition (PAIC15) Instrument: Assessing Sensitivity and Specificity of Cut-Offs against Three Standards.

Observational pain scales can help to identify pain in persons with dementia who may have difficulty expressing pain verbally. The Pain Assessment in Impaired Cognition-15 (PAIC15) covers 15 items that indicate pain, but it is unclear how probable pain is, for each summed score (range 0-45). We aimed to determine sensitivity and specificity of cut-offs for probable pain on the PAIC15 against three standards: (1) self-report when able, (2) the established Pain Assessment in Advanced Dementia (PAINAD) cut-off of 2, and (3) observer's overall estimate based on a series of systematic observations. We used data of 238 nursing home residents with dementia who were observed by their physician in training or nursing staff in the context of an evidence-based medicine (EBM) training study, with re-assessment after 2 months in 137 residents. The area under the ROC curve was excellent against the PAINAD cut-off (≥0.8) but acceptable or less than acceptable for the other two standards. Across standards and criteria for optimal sensitivity and specificity, PAIC15 scores of 3 and higher represent possible pain for screening in practice, with sensitivity and specificity against self-report in the 0.5 to 0.7 range. While sensitivity for screening in practice may be too low, a cut-off of 4 is reasonable to indicate probable pain in research.

Performance of a SARS-CoV-2 antigen rapid immunoassay in patients admitted to the emergency department.

OBJECTIVES: Given the ongoing pandemic emergency, there is a need to identify SARS CoV-2 infection in various community settings. Rapid antigen testing is spreading worldwide, but diagnostic accuracy is extremely variable. Our study compared a microfluidic rapid antigen test with a reference molecular assay in patients admitted to the emergency department (ED) of a general hospital from October 2020 to January 2021. METHODS: Nasopharyngeal swabs collected in patients with suspected COVID-19 and in patients with no symptoms suggesting COVID-19, but requiring hospitalization, were obtained. RESULTS: 792 patients of median age 71 years were included. With a prevalence of 21%, the results showed: 68.7% (95% confidence interval [CI]: 60.9-75.5) sensitivity; 95.2% (95% CI: 93.1-96.7) specificity; 79.2% (95% CI: 71.4-85.3) positive predictive value (PPV); 91.9% (95% CI: 89.5-93.9) negative predictive value; 3.8 (95% CI: 2.7-5.3) positive likelihood ratio (LR+); and 0.09 (95% CI: 0.07-0.1) negative likelihood ratio (LR-). In the symptomatic subgroup, sensitivity increased to 81% (95% CI: 70.3-88.6) and PPV to 96.9% (95% CI: 88.5-99.5), along with an LR+ of 32 (95% CI: 8.2-125.4). CONCLUSIONS: The new rapid antigen test showed an overall excellent diagnostic performance in a challenging situation, such as that of an ED during the COVID-19 emergency.

Development of a qualitative real-time RT-PCR assay for the detection of SARS-CoV-2: a guide and case study in setting up an emergency-use, laboratory-developed molecular microbiological assay.

Developing and deploying new diagnostic tests are difficult, but the need to do so in response to a rapidly emerging pandemic such as COVID-19 is crucially important. During a pandemic, laboratories play a key role in helping healthcare providers and public health authorities detect active infection, a task most commonly achieved using nucleic acid-based assays. While the landscape of diagnostics is rapidly evolving, PCR remains the gold-standard of nucleic acid-based diagnostic assays, in part due to its reliability, flexibility and wide deployment. To address a critical local shortage of testing capacity persisting during the COVID-19 outbreak, our hospital set up a molecular-based laboratory developed test (LDT) to accurately and safely diagnose SARS-CoV-2. We describe here the process of developing an emergency-use LDT, in the hope that our experience will be useful to other laboratories in future outbreaks and will help to lower barriers to establishing fast and accurate diagnostic testing in crisis conditions.

Interventional procedure plans generated by telemedicine visits in spine patients are rarely changed after in-person evaluation.

BACKGROUND AND OBJECTIVES: The role of telemedicine in the evaluation and treatment of patients with spinal disorders is rapidly expanding, brought on largely by the COVID-19 pandemic. Within this context, the ability of pain specialists to accurately diagnose and plan appropriate interventional spine procedures based entirely on telemedicine visits, without an in-person evaluation, remains to be established. In this study, our primary objective was to assess the relevance of telemedicine to interventional spine procedure planning by determining whether procedure plans established solely from virtual visits changed following in-person evaluation. METHODS: We reviewed virtual and in-person clinical encounters from our academic health system's 10 interventional spine specialists. We included patients who were seen exclusively via telemedicine encounters and indicated for an interventional procedure with documented procedural plans. Virtual plans were then compared with the actual procedures performed following in-person evaluation. Demographic data as well as the type and extent of physical examination performed by the interventional spine specialist were also recorded. RESULTS: Of the 87 new patients included, the mean age was 60 years (SE 1.4 years) and the preprocedural plan established by telemedicine, primarily videoconferencing, did not change for 76 individuals (87%; 95% CI 0.79 to 0.94) following in-person evaluation. Based on the size of our sample, interventional procedures indicated solely during telemedicine encounters may be accurate in 79%-94% of cases in the broader population. CONCLUSIONS: Our findings suggest that telemedicine evaluations are a generally accurate means of preprocedural assessment and development of interventional spine procedure plans. These findings clearly demonstrate the capabilities of telemedicine for evaluating spine patients and planning interventional spine procedures.

Correlation between lung ultrasound and chest CT patterns with estimation of pulmonary burden in COVID-19 patients.

PURPOSE: The capability of lung ultrasound (LUS) to distinguish the different pulmonary patterns of COVID-19 and quantify the disease burden compared to chest CT is still unclear. METHODS: PCR-confirmed COVID-19 patients who underwent both LUS and chest CT at the Emergency Department were retrospectively analysed. In both modalities, twelve peripheral lung zones were identified and given a Severity Score basing on main lesion pattern. On CT scans the well-aerated lung volume (%WALV) was visually estimated. Per-patient and per-zone assessments of LUS classification performance taking CT findings as reference were performed, further revisioning the images in case of discordant results. Correlations between number of disease-positive lung zones, Severity Score and %WALV on both LUS and CT were assessed. The area under receiver operating characteristic curve (AUC) was calculated to determine LUS performance in detecting %WALV ≤ 70 %. RESULTS: The study included 219 COVID-19 patients with abnormal chest CT. LUS correctly identified as positive 217 (99 %) patients, but per-zone analysis showed sensitivity = 75 % and specificity = 66 %. The revision of the 121 (55 %) cases with positive LUS and negative CT revealed COVID-compatible lesions in 42 (38 %) CT scans. Number of disease-positive zones, Severity Score and %WALV between LUS and CT showed moderate correlations. The AUCs for LUS Severity Score and number of LUS-positive zones did not differ in detecting %WALV ≤ 70 %. CONCLUSION: LUS in COVID-19 is valuable for case identification but shows only moderate correlation with CT findings as for lesion patterns and severity quantification. The number of disease-positive lung zones in LUS alone was sufficient to discriminate relevant disease burden.

Laboratory diagnosis of COVID-19.

OBJECTIVES: This was a non-systematic review of the literature on the laboratory diagnosis of COVID-19. DATA SOURCES: Searches in PubMed and Google Scholar for articles made available in 2020, using the terms "diagnosis" OR "diagnostic" OR "diagnostic tests" OR "tests" AND "COVID-19" OR "SARS-CoV-2" in the title. SUMMARY OF FINDINGS: Tests for the etiological agent identify genetic material of SARS-CoV-2 or humoral responses to it. The gold standard for diagnosis is the identification of viral genome targets by real-time polymerase chain reaction (RT-PCR) in respiratory tract materials during the first week of symptoms. Serological tests should be indicated from the second week of symptoms onwards. A wide range of different tests is available, with variable sensitivity and specificity, most of which require validation. Laboratory tests such as complete blood count, C-reactive protein (CRP), D-dimer, clotting tests, lactic dehydrogenase (LDH), ferritin, and procalcitonin identify risk of disease with greater severity, thromboembolic complications, myocardial damage, and/or worse prognosis. Imaging tests may be useful for diagnosis, especially when there is a compatible clinical picture, and other tests presented negative results or were unavailable. CONCLUSIONS: The identification of genetic material of the virus by RT-PCR is the gold standard test, but its sensitivity is not satisfactory. The diagnosis of COVID-19 should be based on clinical data, epidemiological history, tests for etiological diagnosis, and tests to support the diagnosis of the disease and/or its complications. New diagnostic methods with higher sensitivity and specificity, as well as faster results, are necessary.

Adjusting RT-qPCR conditions to avoid unspecific amplification in SARS-CoV-2 diagnosis.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in December 2019 and quickly spread around the world, forcing global health authorities to develop protocols for its diagnosis. Here we report dimer formation in the N2 primers-probe set (CDC 2019-nCoV Real-Time RT-PCR) used in the diagnostic routine, and propose alternatives to reduce dimerization events. Late unspecific amplifications were visualized in 56.4% of negative samples and 57.1% of no-template control, but not in positive samples or positive control. In silico analysis and gel electrophoresis confirmed the dimer formation. The RT-qPCR parameters were optimized and the late unspecific amplifications decreased to 11.5% in negative samples and no-template control. The adjustment of PCR parameters was essential to reduce the risk of false-positives results and to avoid inclusive results requiring repeat testing, which increases the costs and generates delays in results or even unnecessary requests for new samples.