Polymerase Chain Reaction Test Results Research Articles

Hidden enemy of pulmonary arteries: COVID-19

It has been reported that COVID-19 may cause severe endothelial damage. Pulmonary Artery Stiffness (PAS) is a strong predictor of right ventricular function. PAS can reveal important information about the endothelial functions of the pulmonary bed. In this study, we aimed to elucidate the possible effect of COVID-19 on PAS. The study was performed by measuring PAS values with transthoracic echocardiography in 130 patients, 60 of whom had COVID-19 and 70 were controls. COVID-19 patients with positive polymerase chain reaction (PCR) test results were included in the study 3-6 months after their positivity. When the Maximal frequency shift (MFS) (Hz) results were examined, no significant difference was observed between the patient and control groups (2764±279.24 and 2664.8±673.91 p=0.340, respectively). There was a significant difference between the patient and control groups in favor of the patient group in pulmonary acceleration time (PAT) (msec) results (93.18±14.99 and 126.1±17.58, respectively, p<0.001). There was a significant difference between the patient and control groups in favor of the patient group in PAS (Hz/msec) results (30.28±5.07 and 21.57±7.04, respectively, p<0.001). It is possible that COVID-19 may have adverse effects on the pulmonary artery wall and bed. As a result of endothelial damage due to COVID-19, an increase in PAS values can be observed.

Predicting COVID-19 Mortality and Identifying Clinical Symptom Patterns in Hospitalized Patients: A Machine-learning Study

Background and Purpose: Identifying effective symptoms, demographic information, and underlying diseases to predict COVID-19 mortality is essential. We aimed to study the effective clinical and symptomatic characteristics of COVID-19 mortality in hospitalized patients with positive polymerase chain reaction (PCR) test results. Materials and Methods: For this study, we prospectively collected complete data on 26867 hospitalized individuals who tested PCR positive for COVID-19 from February 20, 2020, to September 12, 2021, in the Khorasan Razavi Province, Iran. We analyzed the data using artificial neural networks (ANN) and logistic regression (LR) models. Results: The accuracy of the ANN model was higher than the LR (90.27% versus 90.15%). The ten most important predictors that contributed to the prediction of death were decreasing consciousness level, cough, PO2 level, age, chronic kidney disease, fever, headache, smoking status, chronic blood diseases, and diarrhea using the ANN model. Conclusion: In conclusion, individuals suffering from chronic diseases such as cancer, kidney and blood diseases, as well as immunodeficiency are at a higher risk of mortality. This important finding can help decision-makers and medical professionals in their efforts to consider these conditions and provide effective preventative measures to reduce the risk of death.

Clinical and Molecular Detections of Lumpy Skin Disease: Possibilities of Co-infection with Foot-and-Mouth Disease

Lumpy skin disease (LSD) and foot and mouth disease (FMD) are notable viral diseases of cattle. This report aimed to highlight the possibilities of an uncommon case of LSD and FMD co-infection. The report also presents the clinical and molecular detection of LSD virus in six crossbred calves and LSD and FMD virus co-infection in a heifer at small-scale dairy farms located in northern Ethiopia. Nasal swabs and tissue samples were collected following aseptic techniques from the six calves suspected of having LSD and a tissue sample from one heifer suspected of having LSD-FMD co-infection and submitted to the laboratory for cell culture and real-time polymerase chain reaction (PCR) tests. Different-sized, firm, painful skin nodules with necrotic centers were seen on different parts of the calves’ body. Swelling of the prescapular and prefemoral lymph nodes, conjunctivitis, and corneal cloudiness were also observed. Uniquely, one heifer was seen with erosive lesions in the oral cavity and tongue, salivation, lameness, and skin nodules. Intracytoplasmic inclusion bodies, a distinctive feature of LSD virus, and the formation of syncytia, a characteristic of FMD virus, were observed in the cell lines. The heifer was diagnosed with a rare co-infection of LSDV and FMDV based on clinical signs, cell culture, and real-time PCR test results. The other six calves were diagnosed with the LSD virus. Treatment with broad-spectrum antibiotics, local wound cleansing, and anti-inflammatory drugs was initiated. Unfortunately, the heifer with LSD-FMD co-infection died while under treatment, and just three calves with LSD were recovered. It can be concluded that vaccination of animals against both diseases and promotion of bio-security protocols in farms is more helpful than treatment, and early case reporting is also warranted to avoid losses related to the diseases.

Optimization of deoxyribonucleic acid extraction and polymerase chain reaction methods for gene detection of Toxoplasma gondii in goat milk

Abstract. Fatmawati M, Suwanti LT, Mufasirin, Subekti DT, Ekawasti F, Lastuti NDR, Lamid M, Suprihati E, Effendi MH, Al-Arif A. 2023. Optimization of deoxyribonucleic acid extraction and polymerase chain reaction methods for gene detection of Toxoplasma gondii in goat milk. Biodiversitas 24: 5905-5911. Dairy goats (Capra aegagrus hircus) are intermediate hosts that transmit Toxoplasma gondii to humans through goat milk consumption. T. gondii can invade mammary glands and secrete into milk. The method of detecting gene of the T. gondii in milk is through a Polymerase Chain Reaction (PCR) test based on specific genes. The objective of this study was to compare the efficacy methods of the T. gondii molecular assay from the extraction, master mix for PCR assay, and primer that is possible to amplify the gene of T. gondii in goat milk for PCR assay. The research method for purification used flotation using concentrated sugar. This research compared the extraction kit from Kit Extraction 1 (K1), Kit Extraction 2 (K2), and Kit Extraction 3 (K3) with the extraction method listed in the brochure. Meanwhile, for the PCR assay, three types of master mix were used, including Master Mix 1 (M1), Master Mix 2 (M2), and Master Mix 3 (M3). The specific genes used included primers B1, ROP, GRA 1, GRA 7, BAG 1, and P30. Tris borate EDTA (TBE) or Phosphate Buffer Saline Solution (PBS) as buffer milk samples gave the same PCR test results. The results show that the principle of a flotation method test using PBS can be used to prepare the milk sample. The research showed that extraction kit 1 (K1) and extraction kit 2 (K2) gave positive results for the positive control. However, in terms of price, K2 is cheaper than K1. So, to optimize DNA extraction, K2 can be used. The master mix that can be used for PCR testing of milk samples is M1 because M1 gives positive results for positive controls and negative results for negative controls. Primers for optimal results used GRA 7 and B1 with denaturation temperature of 94°C, annealing at 56°C, and an extension of 73°C 33. This research concluded that the type of DNA extraction kit affects the PCR test results for detecting T. gondii in goat milk. It is necessary to optimize the type of master mix to be used in PCR testing and primers capable of amplifying the T. gondii gene.

The association of positive sepsis PCRs tests with patient mortality, length of stay, and antibiotic management in a medical intensive care unit

Background: Polymerase chain reaction (PCR) testing amplifies a specific DNA segment through heat cycling to identify pathogens for the diagnosis of infection. This testing allows for rapid detection of pathogens, before conventional blood culture results become available. The high mortality associated with severe sepsis and septic shock stresses the importance of early diagnosis and initiation of early antibiotic therapy. This study analyzed the association of the sepsis PCR results and antibiotic management, length of stay, and mortality outcomes in a medical intensive care unit (MICU).
 Methods: This study is a retrospective, cross-sectional study on patients diagnosed with severe sepsis and septic shock based on ICD-10 codes, aged 18 years and older, admitted to the MICU at University Medical Center, Lubbock, Texas, between December 2016 to December 2020.
 Results: Clinical information from 268 patients with the diagnosis of sepsis or septic shock was collected and analyzed. The mean age was 60.9 ± 15.6 years with a predominance of men (144, 53.7%) and Caucasian race (193,73.4%). A total of 101 patients (37.6%) had positive PCR results; overall, PCR test results had a diagnostic sensitivity of 91.2 %. The concordance between positive blood culture and positive PCR was 93.3 % (p <.0001). There was a significant correlation between PCR positivity and increased serum lactate levels (p=0.03), changes in antibiotics (P<0.00010), and increased mortality rate (p=0.04). There was no significant correlation between PCR positivity and length of stay (p=0.84).
 Conclusion: In this study, PCR testing was an accurate tool for early identification of bacterial pathogens. A positive PCR was associated with higher serum lactate levels, higher mortality rates, and an increased frequency of antibiotic changes but was not associated with shorter ICU length of stay.
 Key words: Sepsis, septic shock, PCR testing, outcomes

Using Active Surveillance to Identify Monoclonal Antibody Candidates Among COVID-19-Positive Veterans in the Atlanta VA Health Care System.

Strategies for optimizing identification and outreach to potential candidates for monoclonal antibody (Mab) therapy for COVID-19 are not clear. Using a centralized, active surveillance system, the Atlanta Veterans Affairs Health Care System (AVAHCS) infectious disease (ID) team identified candidates for Mab infusion and provided treatment. As part of a quality improvement project from December 28, 2020, to August 31, 2021, a clinical team consisting of ID pharmacists and physicians reviewed each outpatient with a positive COVID-19 polymerase chain reaction test daily at the AVAHCS. The clinical team used Emergency Use Authorization (EUA) criteria to determine eligibility. Eligible patients were contacted on the same day of review via telephone to confirm eligibility and obtain verbal consent. Telehealth follow-up occurred on day 1 and day 7 postinfusion to assess for adverse events. In total, 2028 patients with COVID-19 were identified; 289 patients (14%) were eligible, and 132 (46%) received Mab therapy. Similar to AVAHCS demographics, a majority of those who received Mab therapy were non-Hispanic Black patients (65%). The most common comorbidities were hypertension (59%) and diabetes (37%). The median time from symptom onset to positive COVID-19 polymerase chain reaction (PCR) test result was 6 days (range, 0-9), and the median time from positive COVID-19 PCR test result to Mab infusion was 2 days (range, 0-8). Twelve patients (9%) required hospitalization for worsening COVID-19 symptoms postinfusion. No deaths occurred. Combining laboratory surveillance and active screening led to high uptake of Mab therapy and minimized delay from symptom onset to Mab infusion, thereby optimizing outpatient treatment of COVID-19. This approach also successfully screened and treated Black patients in the AVAHCS population.

The Efficacy and Safety of Adding Chlorpromazine to Atazanavir/Ritonavir Regimen in the Treatment of Moderate COVID-19 Patients, a Randomized Double-blind Clinical Trial

Background: According to COVID-19 mutation and no defined treatment, it is necessary to find effective treatment. Chlorpromazine, a phenothiazine antipsychotic drug, has been shown in animal studies to have antiviral effects by inhibiting clathrin-mediated endocytosis. The aim of this study was to evaluate the effectiveness of adding chlorpromazine to the atazanavir/ritonavir regimen in the treatment of moderate COVID-19 patients. Methods: In this randomized double-blind clinical trial, sixty hospitalized patients with moderate COVID-19 confirmed by CT findings or polymerase chain reaction (PCR) were enrolled. All patients received atazanavir/ritonavir 300mg/100mg once daily. In two parallel groups, chlorpromazine 25 mg three times a day or a placebo was administered for up to 14 days. Complete blood count with differential, C-reactive protein (CRP), liver enzymes, and erythrocyte sedimentation rate was measured on days 1, 3, 5, 7, and 10. The primary outcome was the improvement of oxygen saturation and the secondary outcome was the duration of hospitalization and conversion of PCR test results. Results: Oxygen saturation during the hospitalization was not different among the two groups. The mean duration of hospitalization in the chlorpromazine group was 7.4±2.7 days and in the placebo was 8.2±3 days (P=0.2). Compared to baseline, both groups showed an increase in white blood cell count (P=0.04) and polymorphonuclear cells (P=0.04) but lymphocyte count decreased. At the end of the study, the PCR test was negative in 100% of patients in the chlorpromazine group and 95% of patients in the placebo group. Conclusion: In adult hospitalized patients with moderate symptomatic COVID-19, adding chlorpromazine to the atazanavir/ritonavir regimen did not improve outcomes.

Musculoskeletal system symptoms in patients with COVID-19 and the impact of these symptoms on quality of life.

Coronavirus disease 2019 (COVID-19) is a respiratory disease caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and also affects the musculoskeletal system. This study was conducted to investigate the musculoskeletal symptoms, type of pain and effect on quality of life in patients presenting with pain after COVID-19. This prospective, descriptive study included 97 patients aged 18 years or older who were diagnosed with COVID-19 based on a positive polymerase chain reaction test result, with or without musculoskeletal pain prior to COVID-19 infection. Patients who applied to the post-COVID-19 outpatient clinic with the complaint of pain at least 1 month and maximum 1 year after the diagnosis of COVID-19 were included. Patients' demographic characteristics and musculoskeletal examination findings were evaluated. The patients were examined, and the questionnaire forms were completed. The pain was assessed using the visual analog scale (VAS), the Douleur-Neuropathique-4 (DN-4) questionnaire, while the quality of life was assessed using the Short Form-36 (SF-36) survey. Patients were divided into groups in terms of gender, age, body mass index. Shapiro-Wilk's test, the independent samples t-test and the Mann-Whitney U test were used for statistical analyses. The mean age of the patients was 46.5 ± 13.5 years, 30 of them were male. Pain increased in patients with pre-COVID-19 arthralgia and myalgia (p< 0.001). Post-COVID-19 VAS was significantly higher than pre-COVID-19 VAS (7 ± 1.2 vs. 3.2 ± 1.9, p< 0.05). Pre-COVID-19 patients with myalgia had significantly worse SF-36 physical function, social function, pain, general health perception (p< 0.05). The mean scores of females in the SF-36 physical function, pain were significantly worse than males (p< 0.05). According to DN-4, 41 (42.3%) patients had neuropathic pain. There was moderate negative correlation between VAS, DN-4 and SF-36 (p< 0.05). Arthralgia, myalgia, and neuropathic pain, all of which negatively affect the quality of life, are often observed in the patients infected with COVID-19.

Prevalence, Risk Factors, Prognosis, and Management of Pericardial Effusion in COVID-19.

Background: There is limited data in the literature about the clinical importance and prognosis of pericardial effusion (PE) in patients discharged after recovering from COVID-19, but large-scale studies have yet to be available. This study investigated the prevalence, risk factors, prognosis, late clinical outcomes, and management of PE in COVID-19. Materials and Methods: Between August 2020 and March 2021, 15,689 patients were followed up in our pandemic hospital due to COVID-19. Patients with positive polymerase chain reaction (PCR) test results and PE associated with COVID-19 in computed tomography (CT) were included in the study. The patients were divided into three groups according to PE size (mild, moderate, and large). Transthoracic echocardiography (TTE) records, laboratory data, clinical outcomes, and medical treatments of patients discharged from the hospital were retrospectively reviewed. Results: According to the PE size (mild, moderate, large) of 256 patients with PE at admission or discharge, the mean age was 62.17 ± 16.34, 69.12 ± 12.52, and 72.44 ± 15.26, respectively. The mean follow-up period of the patients was 25.2 ± 5.12 months. Of the patients in the study population, 53.5% were in the mild group, 30.4% in the moderate group, and 16.1% in the large group. PE became chronic in a total of 178 (69.6%) patients at the end of the mean three months, and chronicity increased as PE size increased. Despite the different anti-inflammatory treatments for PE in the acute phase, similar chronicity was observed. In addition, as the PE size increased, the patients' frequency of hospitalization, complications, and mortality rates showed statistical significance between the groups. Conclusions: The clinical prognosis of patients presenting with PE was quite poor; as PE in size increased, cardiac and noncardiac events and mortality rates were significantly higher. Patients with large PE associated with COVID-19 at discharge should be monitored at close intervals due to the chronicity of PE and the increased risk of tamponade.

Evaluating the effectiveness of first-Line anti-tuberculosis in Al Dhafra Hospitals

Background: Tuberculosis (TB) continues to be a significant public health issue despite extensive efforts to control it. The standard treatment for TB involves the use of first-line anti-TB drugs administered at a standard dose. However, the effectiveness of this treatment can vary between individual patients, resulting in differing cure rates.&#x0D; Methodology: The objective of this retrospective study was to assess the effectiveness and safety of first-line generic anti-TB medications administered at Liwa Hospital in the Al Dhafra Region. Data was collected from the electronic medical records of 140 TB patients admitted to Liwa Hospital from January to December 2022. The study included patients with positive acid-fast bacillus (AFB) or polymerase chain reaction (PCR) test results, indicating active TB infection. Patients resistant to first-line anti-TB medications or with lung cancer were excluded. Data collected included demographic information, length of stay conversion time, hospital admission, prescribed medications, treatment duration, and treatment outcomes.&#x0D; Results: This study observed an average length of stay of 21 days for patients treated with first-line generic anti-TB medications at Liwa Hospital. Over 80% of the patients were discharged within 30 days of admission, indicating a positive response to the medications. Approximately 13% of the patients required a longer duration of treatment and were discharged between 30 and 60 days after admission. Only 5% of the patients had a prolonged stay of over 60 days, most of whom had co-morbidities or rifampicin resistance, but achieved AFB conversion within three months. The average conversion time for patients was 25 days, with over 92% achieving conversion within two months.&#x0D; Conclusion: This study demonstrated the efficacy and safety of first-line generic anti-TB medications in treating TB patients at Liwa Hospital. The majority of patients responded well to the medications, leading to discharge within 30 days.&#x0D; Keywords: Tuberculosis, Ethambutol, Pyrazinamide, Rifampicin, Isoniazid, First line drugs, Anti TB drugs

Evaluation of Viral Respiratory Pathogens Among Patients Initially Tested Negative for SARS-CoV-2

Background: A number of ribonucleic acid (RNA) and deoxyribonucleic acid (DNA) viruses commonly circulating among vertebrates, such as influenza H1N1, respiratory syncytial virus (RSV), adenoviruses, and human coronavirus (HCoV)-229E, cause symptoms similar to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). These viruses are important causes of cold, pneumonia, and shortness of breath in humans, which have been overlooked during the coronavirus disease 2019 (COVID-19) pandemic. Furthermore, the diagnosis of infection with these viruses mostly relies on physical examination and clinical history, despite the fact that accurate molecular diagnosis is available. Objectives: This study aimed to evaluate the presence of respiratory viruses in patients who were suspected to be infected with COVID-19 yet initially tested negative for SARS-CoV-2, as it could be beneficial in developing effective control measures and more reliable testing and surveillance of such viruses. Methods: In this study, laboratory samples of 123 patients referred to Ghaem Hospital of Mashhad, Iran, were evaluated that tested negative for SARS-CoV-2 in the initial assessment while showing the clinical symptoms of COVID-19. Initial testing for SARS-CoV-2 was carried out by the TaqMan real-time polymerase chain reaction (PCR) method using a kit approved by the Ministry of Health (Pishtaz Teb, Iran). Further analysis for the presence of 17 respiratory viruses was carried out using Genova kits based on the virus genome conserved sequences of influenza H1N1, influenza B, influenza A, SARS-CoV-2, HCoV-HKU1, HCoV-OC43, HCoV-NL63, HCoV-229E, metapneumovirus, RSV, human bocavirus 1, 2, 3, parainfluenza 1, 2, 3, and adenovirus. Results: According to the results of the present evaluations, out of 123 samples that were acquired using nasal and throat swabs and that initially tested negative for SARS-CoV-2, 8 cases of influenza A (47.1%), 1 case of parainfluenza (5.9%), 1 case of HKU1/OC-43 (5.9%), 4 cases of RSV (23.5%), 1 case of HCoV-NL63/HCoV-229-E (5.9%), and 2 cases of SARS-CoV-2 (11.8%) were detected. Conclusions: Based on the results of real-time PCR tests obtained from patients who had clinical symptoms of SARS-CoV-2 infections, it can be mentioned that due to the similar symptoms of patients with respiratory viral infections, individuals with respiratory symptoms could be examined for other viral infections in addition to SARS-CoV-2 infection, and a suitable basis for their prevalence in the community could be provided.

Hematological and Extra-Hematological Manifestations of Parvovirus B19 Disease

Abstract Objective Parvovirus B19 (PVB19) is a virus that can present with many hematological and extra-hematological findings. Its prognosis is relatively good in immunocompetent patients, but severe disease may develop in immunocompromised patients. We retrospectively reviewed a series of children who presented with PVB19 during a 6-year period at our institution. Methods Nine children with positive polymerase chain reaction and serological test results for PVB19 were studied. Their demographic data, atypical clinical and laboratory findings, treatment regiments, clinical course, and prognosis were noted. Results The hematological abnormalities associated with PVB19 were anemia, neutropenia, and thrombocytopenia, and the extra-hematological abnormalities were systemic lupus erythematosus-like syndrome, hemophagocytic lymphohistiocytosis, and acute kidney injury. All patients had good outcomes with no significant sequelae. Conclusion This case review suggests that clinicians should not consider PVB19 only as a cause of hematological events; they should also be alert to the possibility that it may cause extra-hematological diseases.

Lipoprotein(a): A New Intensive Care Unit Admission Predictor in Coronavirus Disease 2019 Patients.

Endothelium-related events in patients with coronavirus disease 2019 are linked to a poor prognosis. Lipoprotein(a) plays a role in vascular endothelial cell dysfunction. This research aims to investigate whether baseline serum lipoprotein(a) levels could be a predictor for intensive care unit admission and related clinical parameters in coronavirus disease 2019 patients. The research covers 126 patients who were hospitalized in intensive care unit or the non-intensive care unit in our hospital. This prospective cohort study was conducted from January 2021 to June 2021. The patients who were positive for severe acute respiratory syndrome coronavirus 2 according to real-time polymerase chain reaction test results were included in the study. Two groups were created according to the status of intensive care unit admission. Lipoprotein(a) was studied from blood samples taken at the time of hospital admission. According to the results of the first clinical evaluation, 46 patients were admitted to the intensive care unit and 80 patients were admitted to non-intensive care unit in the hospital. Patients with intensive care unit admission had significantly higher serum lipoprotein(a) levels than patients without intensive care unit admission (40.9 ng/mL and 17.4 ng/mL, P < .001, respectively). The regres- sion analysis revealed that serum lipoprotein(a) levels were independently related to intensive care unit admission (odds ratio 1.242, 95% CI 1.109-1.391, P < .001). In receiver operating characteristic curve analysis, lipoprotein(a) level ≥31.42 ng/mL had 82.6% sensitivity and 72.5% specificity in predicting intensive care unit admission. The risk of intensive care unit admission was seen to be 12.522-fold higher in cases with lipoprotein(a) level ≥31.42. Lipoprotein(a) could be used as a useful biomarker for the triage of coronavirus disease 2019 patients. Baseline serum lipoprotein(a) levels may serve as a useful prognostic biomarker in patients hospitalized for coronavirus disease 2019.

Investigating the prevalence of and predictive and risk factors for pulmonary embolism in patients with COVID-19 in Nemazee Teaching Hospital.

Pulmonary thromboembolism (PTE) is a significant contributing factor to vascular diseases. This study aimed to determine the prevalence of pulmonary thromboembolism and its predisposing factors in patients with COVID-19. This cross-sectional study included 284 patients with COVID-19 who were admitted to Nemazee Teaching Hospital (Shiraz, Iran) between June and August 2021. All patients were diagnosed with COVID-19 by a physician based on clinical symptoms or positive polymerase chain reaction (PCR) test results. The collected data included demographic data and laboratory findings. Data were analyzed using the SPSS software. P≤0.05 was considered statistically significant. There was a significant difference in the mean age between the PTE group and non-PTE group (P=0.037). Moreover, the PTE group had a significantly higher prevalence of hypertension (36.7% vs. 21.8%, P=0.019), myocardial infarction (4.5% vs. 0%, P=0.006), and stroke (23.9% vs. 4.9%, P=0.0001). Direct bilirubin (P=0.03) and albumin (P=0.04) levels significantly differed between the PTE and non-PTE groups. Notably, there was a significant difference in the partial thromboplastin time (P=0.04) between the PTE and non-PTE groups. A regression analysis indicated that age (OR, 1.02; 95% CI, 1.00‒1.004; P=0.005), blood pressure (OR, 2.07; 95% CI, 1.12‒3.85; P=0.02), heart attack (OR, 1.02; 95% CI, 1.28‒6.06; P=0.009), and albumin level (OR, 0.39; 95% CI, 0.16‒0.97; P=0.04) were all independent predictors of PTE development. Regression analysis revealed that age, blood pressure, heart attack, and albumin levels were independent predictors of PTE.

Public knowledge of SARS-CoV-2 serological and viral lineage laboratory testing and result interpretation: A GENCOV study cross-sectional survey

ObjectivesConcepts related to SARS-CoV-2 laboratory testing and result interpretation can be challenging to understand. A cross-sectional survey of COVID-19 positive adults residing in Ontario, Canada was conducted to explore how well people understand SARS-CoV-2 laboratory tests and their associated results. Design and methodsParticipants were recruited through fliers or by prospective recruitment of outpatients and hospitalized inpatients with COVID-19. Enrolled participants included consenting adults with a positive SARS-CoV-2 polymerase chain reaction test result. An 11-item questionnaire was developed by researchers, nurses, and physicians in the study team and was administered online between April 2021 to May 2022 upon enrolment into the study. ResultsResponses were obtained from 940 of 1106 eligible participants (85% participation rate). Most respondents understood 1) that antibody results should not influence adherence to social distancing measures (n = 602/888, 68%), 2) asymptomatic SARS-CoV-2 infection following test positivity (n = 698/888, 79%), 3) serological test sensitivity in relation to post-infection timeline (n = 540/891, 61%), and 4) limitations of experts’ knowledge related to SARS-CoV-2 serology (n = 693/887, 78%). Conversely, respondents demonstrated challenges understanding 1) conflicting molecular and serological test results and their relationship with immune protection (n = 162/893, 18%) and 2) the impact of SARS-CoV-2 variants on vaccine effectiveness (n = 235/891, 26%). Analysis of responses stratified by sociodemographic variables identified that respondents who were either: 1) female, 2) more educated, 3) aged 18–44, 4) from a high-income household, or 5) healthcare workers responded expectedly more often. ConclusionsWe have highlighted concepts related to SARS-CoV-2 laboratory tests and associated results which may be challenging to understand. The findings of this study enable us to identify 1) misconceptions related to various SARS-CoV-2 test results, 2) groups of individuals at risk, and 3) strategies to improve people’s understanding of their test results.

Cell and cytokine analyses from bronchoalveolar lavage in non-critical COVID-19 pneumonia.

Cell and cytokine analyses from bronchoalveolar lavage (BAL) in non-critically ill patients with COVID-19 pneumonia are poorly described. This study focused on patients hospitalized in the non-intensive care unit for either suspected COVID-19 pneumonia or persistent respiratory symptoms following proven COVID-19 pneumonia. Overall, 54 patients who underwent BAL between April 2020 and February 2021 for suspected or follow-up of proven COVID-19 pneumonia were included. Based on SARS-CoV-2 polymerase chain reaction test results and clinical follow-up, three pulmonary disease groups were defined: non-COVID-19 (n = 20), acute COVID-19 (n = 13), and post-COVID-19 (n = 24) pneumonia patients. Cytological and cytokine analyses were performed on BAL fluid (IL-1β, IL-6, IL-8, IL-10, TNF-α, IFN-γ, HGF, and TGF-β), with investigators blinded to the patient groups. Lymphocytic alveolitis with plasmocytes was observed in acute COVID-19 pneumonia, returning to normal post-COVID-19. The highest cytokine levels were observed in COVID-19 patients, with significantly increased IFN-γ, IL-10, and HGF levels compared to non-COVID-19 patients, while significantly decreased IL-6, IL-8, IL-10, IFN-γ, TNF-α, and HGF levels were noted in post-COVID-19 patients. In COVID-19 patients, correlations between IL-10, TNF-α and IFN-γ concentrations were found. Lymphocytic alveolitis with plasmacytosis was found in non-critical COVID-19 pneumonia This alveolitis is associated with the presence of IL-6, IL-8, IL-10, TNF-α, IFN-γ and HGF. Alveolitis and cytokines levels decreased in post-COVID-19 pneumonia.

Determining the Prevalence of Avian Chlamydiosis in Wild Amazona Species From Brazil Using Molecular Testing and Clinical Signs.

Avian chlamydiosis is a disease that occurs in birds, especially parrots, and is caused by the Gram-negative bacterium Chlamydia psittaci. Wild Animal Screening Centers in Brazil receive, maintain, treat, and place (preferably to nature) wild animals recovered from illegal trafficking. We performed molecular testing for avian chlamydiosis in parrots from the genus Amazona that were presented to these centers. Cloacal swab samples were collected from 59 parrots (Amazona species) and transported in aqueous or culture medium. The samples were subsequently submitted for DNA extraction by the boiling method, polymerase chain reaction (PCR) amplification using CPF/CPR primers, and agarose gel electrophoresis. Conjunctivitis, nasal discharge, and poor body condition were the clinical signs associated with a differential disease diagnosis of avian chlamydiosis. Transport medium did not have an effect on the test results. The prevalence of C psittaci in the samples was 37% (22/59, 95% confidence interval: 25-49). There was a significant (P = 0.009) association between the PCR test results and clinical signs. Follow-up testing was conducted on a subgroup of 14 individuals that initially tested negative on PCR; 50% (7/14) of these birds were found to be positive within 24 days of the first test. The results of this study confirm the feasibility of using the CPF/CFP primer-based PCR to detect C psittaci in Amazona species, describe a less costly method of transporting biological material for DNA extraction, and evaluate the temporal aspect for obtaining positive results through molecular testing for C psittaci in Amazona species.

A retrospective review of COVID-19 testing and mitigation strategies at a psychiatric hospital and subsequent COVID-19 acquisition

Behavioral health settings present increased challenges in preventing the transmission of infectious agents. Characterizing the relative effectiveness of various strategies, including testing for asymptomatic carriage of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, will inform transmission reduction efforts in behavioral health settings. Asingle-center retrospective study was conducted in an inpatient behavioral health hospital by reviewing COVID-19 mitigation and testing strategies with information collected from discharges between July 1, 2020and February 28, 2021. During the study period, there were 3,694 total discharges and 3,229 unique admitted patients, including 86 (2.7%) patients who had positive SARS-CoV-2 polymerase chain reactiontest results. Preadmission testing from noncongregate care settings (38, 44.1%), and testing after an in-hospital exposure (27, 31.4%) were the most common indications for testing among patients with a positive test. Up to 29 (33.7%) potentially acquired the infection during their hospitalization. Asymptomatic screening tests identified approximately two-thirds (55, 64.0%) of potentially contagious patients. Asymptomatic screening testing on admission and after exposure and universal masking were strong interventions to prevent SARS-CoV-2 transmission in this investigation Future studies of SARS-CoV-2 and other pathogens in behavioral health settings should endeavor to characterize the effectiveness of infection prevention interventions.

Symptoms Predicting SARS-CoV-2 Test Results in Resident Physicians and Fellows in New York City

Accurate prediction of SARS-CoV-2 infection based on symptoms can be a cost-efficient tool for remote screening in healthcare settings with limited SARS-CoV-2 testing capacity. We used a machine learning approach to determine self-reported symptoms that best predict a positive SARS-CoV-2 test result in physician trainees from a large healthcare system in New York. We used survey data on symptoms history and SARS-CoV-2 testing results collected retrospectively from 328 physician trainees in the Mount Sinai Health System, over the period 1 February 2020 to 31 July 2020. Prospective data on symptoms reported prior to SARS-CoV-2 test results were available from the employee health service COVID-19 registry for 186 trainees and analyzed to confirm absence of recall bias. We estimated the associations between symptoms and IgG antibody and/or reverse transcriptase polymerase chain reaction test results using Bayesian generalized linear mixed effect regression models adjusted for confounders. We identified symptoms predicting a positive SARS-CoV-2 test result using extreme gradient boosting (XGBoost). Cough, chills, fever, fatigue, myalgia, headache, shortness of breath, diarrhea, nausea/vomiting, loss of smell, loss of taste, malaise and runny nose were associated with a positive SARS-CoV-2 test result. Loss of taste, myalgia, loss of smell, cough and fever were identified as key predictors for a positive SARS-CoV-2 test result in the XGBoost model. Inclusion of sociodemographic and occupational risk factors in the model improved prediction only slightly (from AUC = 0.822 to AUC = 0.838). Loss of taste, myalgia, loss of smell, cough and fever are key predictors for symptom-based screening of SARS-CoV-2 infection in healthcare settings with remote screening and/or limited testing capacity.

Viral Respiratory Tract Infection Agents Detected Between Years 2019-2021, COVID-19, and Co-Infections

Respiratory tract infections are a major cause of morbidity and mortality at all ages and are seen as a very important public health problem all over the world. In this study, we aimed to evaluate the effect of the pandemic on the epidemiological and seasonal characteristics of the agents by analyzing the respiratory viral infection agents, viral co-infections and associations with Coronavirus diseases-2019 (COVID-19) studied by multiplex polymerase chain reaction (PCR) test in the molecular microbiology laboratory in a three-year period, including the one-year period before the pandemic. Between March 2019 and December 2021, 8825 respiratory tract specimens accepted to the molecular microbiology laboratory with respiratory tract multiplex PCR test requests were included in the study. In addition, severe acute respiratory syndrome (SARS-CoV-2) PCR test results of the patients with positive results with respiratory tract multiplex PCR test, which were studied within ± 3 days, were evaluated retrospectively. Respiratory viral pathogens were detected using FTD Respiratory Pathogens 21 kit (Fast Tract Diagnostics, Siemens Healthineers Company). Two different kits based on real-time reverse transcription PCR were used for SARS-CoV-2 RNA detection in different periods. According to our results, at least one viral agent was detected in 2156 (24.4%) of a total of 8825 samples and a single agent was detected in 1843 (85.5%) of these. The distribution of viruses in the samples with a single agent was determined as RV, RSV A/B, HCoVs, AdV, flu A virus, MPV A/B, PIV 1-4, flu B virus, EV, BoV and PeV, in order of frequency. Multiple agents were found in 313 (14.5%) of these 2156 samples. They were found to be two agents in 291 samples, three in 21 samples and four in one sample. When the SARS-CoV-2 PCR test results of the patients who had positive results with respiratory tract multiplex PCR and who were studied within ± 3 days were evaluated retrospectively, SARS-CoV-2 RNA was detected in 45 (3.5%) of 1277 samples in which at least one agent was detected. In four of these patients, SARS-CoV-2 was found together with multiple agents. Consequently, there was a sharp decrease in the prevalence of all viral agents during the pandemic period. It was evaluated that besides the COVID-19 infection, the restrictions applied during the pandemic period were also effective in this situation.