Polymerase Chain Reaction Positive Cases Research Articles

Association of Epstein-Barr virus (EBV) with nasopharyngeal carcinoma: Experience from a North Indian tertiary care hospital

IntroductionNasopharyngeal carcinoma (NPC), arising from nasopharyngeal epithelium is caused by Epstein-Barr virus (EBV). It is common in South China, South East Asia and North East India. The aim and objectives of this study were to determine the prevalence of EBV in formalin-fixed paraffin-embedded (FFPE) tissue sections of clinically suspected NPC patients, correlate the results of polymerase chain reaction (PCR) with histopathology findings, and to determine the utility of tissue EBV DNA as a diagnostic bio-marker. Materials and methods31 FFPE tissue samples were collected from clinically suspected NPC patients from April 2018–December 2019. Histopathological diagnosis was done by examination of Hematoxylin and Eosin stained slides. Presence of EBV was detected by EBNA-1 PCR. IHC was performed using EBV Latent Membrane Protein 1. ResultsOf the 31 clinically suspected NPC cases, 15 (48.4 %) were histopathological confirmed NPC. Of these15, 13 (86.6 %) were non-keratinising undifferentiated NPC, and one each were keratinising NPC and non-keratinising differentiated NPC respectively.EBV EBNA1 PCR was positive in 35.5 % (11/31) of clinically suspected NPC cases. Of the 11 PCR positive cases, 9 (81.8 %) were histopathological confirmed NPC.Of the 31 clinically suspected NPC cases, IHC was indicated in 23 biopsies. Of which, 12 (52.2 %) were positive for LMP1 in the abnormal cells. Of the 12 IHC positive samples, 10 were NPC cases. ConclusionEBV DNA as an indicator towards NPC among clinically suspected cases had a sensitivity of 60 % and specificity of 87.5 %. In this study, addition of EBV DNA detection by PCR from FFPE tissue sections could confirm EBV association in 20 % of cases where it was not detected by EBV LMP1 IHC, thus helped in increasing the detection of EBV positivity in NPC cases. Early diagnosis of NPC will improve the cure rate and hence reduce the morbidity and mortality rates.

Evaluation of Viral Subgenomic RNAs and Antigen Presence in SARS-CoV-2 PCR Positive Cases

Polymerase chain reaction (PCR) and antigen test (AgT) are frequently used in the diagnosis of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Routine PCR tests that detect the virus genome cannot determine whether the virus is infectious or not. However, detection of subgenomic RNA (sgRNA) produced during the replication period may indicate active viral infection. Active virus detection can offer various health and economic benefits from isolation time to treatment. Antigen tests are also considered as indicators of infectiousness since they can detect viruses above a certain load amount. The aim of this study was to use two different subgenomic RNAs and antigen test instead of genomic RNA to examine the relationship with each other and the clinic in terms of infectiousness. Evaluating the antigen test together with subgenomic RNA as an indicator of infectiousness may show the importance of this test. SARS-CoV-2 PCR positive 109 naso/oropharyngeal swab samples stored at -80 °C were included in the study. In order to confirm the PCR positivity of these samples, E gene PCR was performed and AgT, and E and N sgRNA quantitative real-time reverse transcription-PCR (RT-qPCR) detection was performed. Of the 109 SARSCoV-2 PCR positive samples, 83 (76.14%) had antigen test positivity, 88 (80.73%) had E gene sgRNA, 96 (88.07%) had N gene sgRNA and 97 (89%) had at least one sgRNA positivity.The antigen test was found positive in 77.3% of the samples in which at least one sgRNA was detected and in 66.7% of the negative samples and this difference was not statistically significant (p= 0.475). The difference between E sgRNA and AgT positivity was significant (p= 0.023). N sgRNA was positive in 98.9% of E sgRNA positive samples and 42.9% of the negative samples and this difference was statistically significant (p= 0.0001). The AgT positivity rate was found to be 98.15% (53/54) for cycle threshold (Ct) value ≤ 25, 57.14% (12/21) for Ct 25-30, and 52.94% (18/34) for Ct ≥ 30. The difference in antigen test positivity between E gRNA Ct value ≤ 25 and > 25, ≤ 29 and > 29, < 30 and ≥ 30 was statistically significant (p= 0.0001). Antigen test positivity appears to be associated with viral load and infectivity, as expected. In our study, it has been shown that sgRNAs and AgT which are indicators of infectiousness can be detected at least 10 days after the symptom period. Using these two tests together could detect infective individuals with higher accuracy and shorten the duration of hospital stay and isolation.

Children's scabies survey indicates high prevalence and misdiagnosis in Auckland educational institutions.

Here, we present results of a survey of scabies prevalence in childcare centres and primary schools in Auckland. Children whose parents agreed to take part in participating centres in the Auckland region were examined for scabies by general practitioners and given questionnaires of relevant symptoms. Diagnoses of clinical or suspected scabies were made according to the International Alliance for the Control of Scabies (IACS) criteria. The survey was a stratified random sample of schools and early childcare centres. A quantitative polymerase chain reaction (PCR) test was also used to complement the IACS criteria. A total of 181 children were examined, with 145 children with history information, 16 of whom (11.0%) met the criteria for 'clinical' or 'suspected' scabies. Weighted analysis, accounting for the survey design, indicated that the prevalence of scabies in early childcare centres was 13.2% (95% CI: 4.3 to 22.1), with no school-aged children fulfilling these criteria. A higher proportion had clinical signs of scabies with 23 (12.7%) having typical scabies lesions and a further 43 (23.8%) had atypical lesions. A total of 64 PCR tests were taken and 15 (23%) were positive. None of these cases were receiving treatment for scabies. Five were undergoing topical skin treatment: three with topical steroid and two with calamine lotion. The prevalence of children with scabies is high in early childcare centres in Auckland. Misdiagnosis is suggested by several PCR positive cases being treated by topical agents used to treat other skin conditions.

Incidence of herpes simplex virus type 2 positivity among women living with human immunodeficiency virus in South Africa.

For women living with HIV (WLHIV), co-infection with herpes simplex virus type 2 (HSV-2) causes severe genital ulcers and presents additional challenges for their HIV care. To inform preventive strategies, we aimed to determine the incidence and risk factors of HSV-2 positivity in a prospective cohort of South African women. The CAPRISA 002 study enrolled women at acute HIV infection between 2004 and 2020. HSV-2 testing was conducted by multiplex polymerase chain reaction (PCR) assay on collected vaginal swabs up to twice annually during follow-up. We calculated incidence as the number of new cases per 100 person-years (PYs) and used Cox-proportional-hazard regression to identify factors associated with time-to-HSV-2 PCR positivity. At enrolment, the median age of 171 women was 24years, interquartile range (IQR 21-28), and the estimated median days since HIV infection was 42 (IQR 22-65). Of participants tested at enrolment, HSV-2 antibody prevalence was 81.4% (105/129), and 10.6% (12/113) were positive by PCR. Among 147 women with a prior negative HSV-2 PCR diagnosis, we observed 47 new HSV-2 PCR positive cases over 424.4 PYs of follow-up, yielding an incidence rate of 11.1 cases per-100-PYs. HSV-2 PCR positivity incidence was higher among younger women (<25years: adjusted Hazard Ratio [aHR] = 5.91, 95%CI 3.02-11.6), those with bacterial vaginosis (BV) (Nugent score 7-10: aHR = 2.17, 95%CI 1.15-4.10) and lower CD4 counts (<500cells/μl: aHR = 2.04, 95%CI 1.08-3.87). After acute HIV infection in women, the incidence of HSV-2 PCR positivity was associated with younger age, BV diagnosis and lower CD4 count.

1457. Epidemiology of Human Herpesvirus-6 Meningoencephalitis in Los Angeles County, 2016-2020

Abstract Background Human herpesvirus 6 (HHV-6) is ubiquitous and a known central nervous system (CNS) pathogen. However, HHV-6 in cerebrospinal fluid (CSF) without clinical findings of meningoencephalitis (ME) may not represent true infection, but rather, asymptomatic viral reactivation, chromosomal integration, or latent activation. With the introduction in 2015 of a rapid polymerase chain reaction (PCR) multiplex panel that simultaneously tests for 14 CNS pathogens, reports of HHV-6 PCR positive ME have increased. We sought to understand the epidemiology of HHV-6 ME by evaluating reported cases in Los Angeles County (LAC) between 2016-2020. Methods ME is a reportable condition in LAC. We reviewed clinical, laboratory, and radiologic data for all HHV-6 PCR positive cases reported in LAC between 2016-2020. We developed case classification categories, “unlikely,” “possible,” and “likely”, based on symptoms, CSF profile, and alternative diagnoses (see Table 1). Results A total of 67 HHV-6 ME cases were reported (see Table 2). Reports increased over time, with one in 2016, 12 in 2017, 17 in 2018, 20 in 2019, and 17 in 2020. Median age was 9 months (range 0d-78y), and 47 (70%) were &amp;lt; three years old. Forty-four (66%) were male. Six (9%) were immunocompromised, including one hematopoietic stem cell transplant recipient. Nineteen (28%) had abnormal CSF, and eight (12%) received therapy for HHV-6. Five cases (7%) were classified as “likely” HHV-6 ME, 12 (18%) “possible,” and 50 (75%) “unlikely”. The “likely” cases ranged in age from 7 months to 12 years old, and none were immunocompromised. One received antiviral therapy and was discharged to a rehabilitation facility, the other four were discharged home with full recovery. Conclusion The significance of HHV-6 in CSF remains challenging to determine both clinically and epidemiologically. In the setting of increased testing, increasing detection of HHV-6 in CSF may not reflect increasing rates of HHV-6 ME. The majority of reported HHV-6 ME cases were “unlikely” based on our classification. Classifying cases with alternative diagnoses as ‘unlikely” may miss cases with multiple true infections, particularly in the immunocompromised. It is important to consider clinical presentation, CSF profile and other diagnoses to understand the true burden of HHV-6 ME. Disclosures All Authors: No reported disclosures.

The relationship between new PCR positive cases and going out in public during the COVID-19 epidemic in Japan.

The suppression of the first wave of COVID-19 in Japan is assumedly attributed to people's increased risk perception after acquiring information from the government and media reports. In this study, going out in public amidst the spread of COVID-19 infections was investigated by examining new polymerase chain reaction (PCR) positive cases of COVID-19 and its relationship to four indicators of people going out in public (the people flow, the index of web searches for going outside, the number of times people browse restaurants, and the number of hotel guests, from the Regional Economic and Social Analysis System (V-RESAS). Two waves of COVID-19 infections were examined using cross-correlation analysis. In the first wave, all four indicators of going out changed to be opposite the change in new PCR positive cases, showing a lag period of -1 to +6 weeks. In the second wave, the same relationship was only observed for the index of web searches for going outside, and two indicators showed the positive lag period of +6 to +12 weeks after the change in new PCR positive cases. Moreover, each indicator in the second wave changed differently compared to the first wave. The complexity of people's behaviors around going out increased in the second wave, when policies and campaigns were implemented and people's attitudes were thought to have changed. In conclusion, the results suggest that policies may have influenced people's mobility, rather than the number of new PCR positive cases.

SARS-CoV-2 infection in pregnant women assisted in a high-risk maternity hospital in Brazil: Clinical aspects and obstetric outcomes

BackgroundThe spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, the possible development of serious illness, and the possibility of severe obstetric outcomes highlight the importance of addressing SARS-CoV-2 infection in obstetric management.Methods and findingsA cross-sectional study of pregnant women assisted in a high-risk maternity hospital in Brazil in 2020. All patients admitted for delivery or miscarriage care were tested for SARS-CoV-2 using polymerase chain reaction (PCR) and for immunoglobulin (I)gM, and/or IgG by immunochromatography. Clinical aspects and obstetric outcomes were analyzed. A total of 265 pregnant women were included in the study. There were 38 (14.4%) PCR positive cases during pregnancy, 12 (31.6%) on admission screening, and 71(27.2%) patients were IgM- and/or IgG-positive. Among the participants, 86 (32.4%) had at least one positive test during pregnancy. SARS-CoV-2 positive patients had greater contact with known positive patients (p = 0.005). The most frequently reported symptoms were runny nose, cough, loss of smell and taste, headache, and fever. There was also a 35% rate of asymptomatic infections and a 4.6% rate of severe or critical infections. Patients exposed or infected with SARS-CoV-2 had a higher incidence of preterm delivery, cesarean section, need for resuscitation in the delivery room, Apgar score <7 at 5 min, admission to the neonatal intensive care unit, and jaundice. Newborns with at least one positive test had a significantly greater need for phototherapy after delivery (p = 0.05). The results showed a high rate of positive tests among newborns (37.5%), which seems to be compatible with both neonatal and perinatal infection.ConclusionsIt is important to further investigate SARS-CoV-2 infection during pregnancy, including the clinical course and the possibility of adverse outcomes with impact on maternal and fetal health, regardless of the development of symptoms.

Delayed Influenza Treatment in Children With False-Negative Rapid Antigen Test: A Retrospective Single-Center Study in Korea 2016-2019.

BackgroundWe aimed to examine the delay in antiviral initiation in rapid antigen test (RAT) false-negative children with influenza virus infection and to explore the clinical outcomes. We additionally conducted a medical cost-benefit analysis.MethodsThis single-center, retrospective study included children (aged < 10 years) with influenza-like illness (ILI), hospitalized after presenting to the emergency department during three influenza seasons (2016–2019). RAT-false-negativity was defined as RAT-negative and polymerase chain reaction-positive cases. The turnaround time to antiviral treatment (TAT) was from the time when RAT was prescribed to the time when the antiviral was administered. The medical cost analysis by scenarios was also performed.ResultsA total of 1,430 patients were included, 7.5% were RAT-positive (n = 107) and 2.4% were RAT-false-negative (n = 20). The median TAT of RAT-false-negative patients was 52.8 hours, significantly longer than that of 4 hours in RAT-positive patients (19.2–100.1, P < 0.001). In the multivariable analysis, TAT of ≥ 24 hours was associated with a risk of severe influenza infection and the need for mechanical ventilation (odds ratio [OR], 6.8, P = 0.009 and OR, 16.2, P = 0.033, respectively). The medical cost varied from $11.7–187.3/ILI patient.ConclusionAntiviral initiation was delayed in RAT-false-negative patients. Our findings support the guideline that children with influenza, suspected of having severe or progressive infection, should be treated immediately.

Usefulness of Nested PCR Assay for the Molecular Diagnosis of Human Rickettsial Infection: A Study in Bangladesh

Background: Rickettsial infections are re-emerging arthropods born worldwide zoonotic disease caused by Rickettsia, which is responsible for spotted fever and typhus fever. The diagnosis of a rickettsial illness is important for appropriate antibiotic treatment.&#x0D; Aims: The study aimed to determine the diagnostic accuracy and clinical usefulness of using nested polymerase chain reaction (PCR) by comparing nested PCR, ELISA, and Weil-Felix (WF) tests. &#x0D; Methodology: This was a prospective type of cross-sectional study. A total of 135 clinically suspected rickettsial infection cases were enrolled. Peripheral blood was taken to detect gltA, 17 kDa lipoprotein antigen gene (17 kDa), ompA, and ompB gene of Rickettsia by nested PCR. ELISA and Weil-Felix tests were done to compare with nested PCR.&#x0D; Results: Out of 135 cases, we detected Rickettsia in 70(51.85%) cases by nested PCR assay (p&lt;0.01), 33((24.4%) by Weil- Felix test, 34 (25.18%) by ELISA. Only 26.66% of cases were PCR positive, which were negative by both ELISA and Weil-Felix test. Fifteen (11.11%) cases were positive by all three tests. Among 70 PCR positive rickettsia cases most frequently detected gene was ompB 42(60%), followed by 17kDa 34(48.58%); gltA 21(30%), and ompA 3(4.28%). Multiple gene combinations (ompB, 17kDa and gltA) detected in 98.57 % cases.&#x0D; Conclusion: Nested PCR assays showed the highest rate of detection of rickettsia cases than ELISA and Weil-Felix test. Multiple gene combinations (ompB, 17kDa, and gltA) showed the highest positivity. Therefore, diagnosis of rickettsial infection can be confirmed by PCR assay, and clinicians can plan appropriate treatment for these patients.

Relation of Gut Lactobacillus Acidophilus and Atherosclerosis in type 2 diabetic patients with and without atherosclerosis

Abstract: Background Recent researches show that alteration of GUT bacterial population is found to be an important factor for development of atherosclerosis either directly or indirectly through augmenting other known risk factors for atherosclerosis like; diabetes and dyslipidemia. On the other hand, many members of the gut microbiota are probiotics; Bifidobacterium and Lactobacillus are two well-known probiotics, many studies show their athero-protective role and their protective effect against insulin resistance and metabolic syndrome. Aim of the work To study the role of gut Lactobacillus Acidophilus in the development of atherosclerosis in type 2 diabetic patients (T2DM). Patients and methods The study was conducted on 64 type 2 diabetic patients, with their age ranging between 25 and 60 years old. They will be divided into two groups; Group 1: 32 Type 2 diabetic patients with atherosclerosis. Group 2: 32 Type 2 diabetic patients without atherosclerosis. All subjects in this study were subjected to Full medical history taking. Thorough clinical examination (including weight, height, BMI, blood pressure). The following laboratory investigations were done: Fasting blood glucose, two-hour post prandial, HbA1c, Fasting insulin (for HOMA IR), Lipid profile (Total cholesterol-LDL-HDL-Triglycerides), and Liver and kidney function test. Identification of stool Lactobacillus Acidophilus by Polymerase chain reaction (PCR) semi- quantitative technique. Carotid ultrasonography for estimation of intimamedia thickness (IMT). Results As regards PCR for Lactobacillus Acidophilus 68.8% of group one patients were positive for PCR for Lactobacillus Acidophilus, compared to 75.0% of group two, but there was no statistical difference among the two groups (P value = 0.578).As regards PCR cut-off time in PCR positive cases, there was a statistically significant difference among the two groups (P value= 0.016). Applying Receiver operating characteristic curve (ROC), it showed that PCR cut-off time more than 26.82 can be used as a predictor for atherosclerosis in type two diabetic patients (T2DM) with sensitivity of 72.73%, specificity of 70.83% and area under curve (AUC) of 0.723. In group one, there was a statistically significant positive correlation between PCR cut off time and the two hours post prandial blood sugar (P value= 0.005), the glycated hemoglobin (HBa1c) (P value= 0.049) and intimal media thickness (IMT) (P-value= 0.045). Conclusion Lactobacillus Acidophilus concentration is higher in type 2 diabetes patients without atherosclerosis than in atherosclerotic patients and detection of their level in stool using PCR can be used as a predictor for atherosclerosis in type two diabetes patients.

Evaluation of implantation markers and immune cell infiltration in endometrial biopsy of female genital tuberculosis

BackgroundFemale genital tuberculosis (FGTB) causes infertility in a significant number of females. The immunological impact of tuberculosis on endometrium in infertile females has not been studied before. The present study was designed to evaluate markers related to infiltrating immune cells and implantation in endometrial aspiration from infertile females and correlate with conventional tests and polymerase chain reaction (PCR) for tuberculosis (TB). MethodsIt was a prospective cohort study with 385 patients out of which IHC was done in 306 over a period of 3 years from 2013 to 2016 in a tertiary care hospital. Women with infertility, 20–35 years of age, without history of pulmonary TB or intake of antitubercular therapy were included. Endometrial samples were subjected to PCR for TB along with microbiological and histological examination for TB. Immunohistochemistry for CD45, CD3, CD20, CD4, CD8, CD68, CD138, Interferon gamma, Interleukin 10 (IL-10) and implantation markers MUC1 and Notch 1 were done on the endometrial samples along with 25 control subjects. ResultsConventional tests for tuberculosis like staining for acid fast bacilli (AFB), granuloma on histology or culture positivity were seen in 2.61% (6/306; 1.96% had granulomas, 1/306; 0.32% was AFB positive, 2/306; 0.6% were liquid culture positive). PCR was positive in 190/306 (62.09%). CD3, CD20, CD45, CD68, CD4, CD8 and CD 138 expressing infiltrating cells were not significantly related to PCR positive cases. Interferon gamma expressing lymphocytes were significantly higher (38.94%) in PCR positive endometria compared to 26.72% in the PCR negative (p = 0.04). Notch −1 expression correlated significantly with the occurrence of pregnancy. A trend towards high intensity expression of Notch1 was seen in PCR negative cases. MUC-1 expression did not correlate with pregnancy although interferon gamma expression was significantly related to low intensity MUC1 expression. ConclusionsImmunohistochemical markers are not reliable tests in diagnosis of FGTB. Notch 1 expression though showing correlation with pregnancy has to be further evaluated with a panel of other implantation markers. Study fundingIndian Council of Medical Research, New Delhi, India.

Association of Serum Hyaluronic Acid and Laminin with Polymerase Chain Reaction Findings in Hepatitis C Patients.

To find the association of serum hyaluronic acid and laminin levels with polymerase chain reaction (PCR) results in hepatitis C sero-positive patients; and the correlation among viral load, serum hyaluronic acid, and serum laminin levels. Cross-sectional descriptive study. Department of Chemical Pathology and Endocrinology, Armed Forces Institute of Pathology (AFIP), Rawalpindi, Pakistan from December 2019 to July 2020. One hundred and eighty diagnosed cases of hepatitis C patients were included in this study. To find association, cross tabulation was done after dividing into two groups according to their median by applying Chi-square test. Correlation of viral load, duration of disease, serum hyaluronic acid and laminin levels were calculated using Spearman's correlation. There were 124 (68.9%) males and 56 (31.1%) females. Median (IQR) age was 36 (32.3 - 45.0) years; while median duration of disease was 12 (8 - 18) months. There was a strong association between PCR positive cases with hyaluronic acid (p <0.001) and serum laminin levels (p <0.001). A strong relationship was found between viral load and serum hyaluronic acid (r =0.889, p <0.001), as well as with serum laminin (r =0.889, p <0.001). Current study established a strong significant association between PCR results and disease duration with levels of serum laminin and hyaluronic acid. The levels of serum laminin and serum hyaluronic acid also correlate well with viral load and duration of disease. Key Words: Hepatitis C, Hepatic fibrosis, Hyaluronic acid, Laminin.

Transmission of SARS-CoV-2 in Different Districts of a County in Istanbul, March to September 2020.

Epidemics caused by airborne viruses in cities with large populations create a big problem as in the current COVID-19 pandemic. Cramped lifestyle, busy workplaces, crowded public transportation, and higher household member counts are responsible for the transmission of the disease. In Turkey, Istanbul has taken the lead in the number of cases since the beginning of the epidemic. The excess population density is the major cause for disease transmission. It is essential to monitor the contaminated regions with geographical information systems on city maps. Outbreak maps visualize and help analyze the patterns of transmission and serve as a communication and education tool. A dynamic heat map video of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) polymerase chain reaction positive cases in a county of Istanbul was generated. The heat map visualizes how the epidemic spread to all the districts and the cumulative cases increased in one county of Istanbul with real attack rates.

SARS-CoV-2 Prevalence in Saliva and Gastric and Intestinal Fluid in Patients Undergoing Gastrointestinal Endoscopy in COVID-19 Endemic Areas: Prospective Cross-Sectional Study in Japan

Background: Gastrointestinal endoscopy (GIE) is useful for the early detection and treatment of many diseases; however, GIE is considered a high-risk procedure in the coronavirus disease 2019 (COVID-19) pandemic era. This study aimed to explore the rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positivity in saliva and gastric and intestinal fluids to which endoscopy medical staff are exposed.Methods: The study was a single-center cross-sectional study. From June 1 to July 31, 2020, all patients who underwent GIE at Yokohama City University Hospital endoscopy center were registered. All patients provided 3 ml of saliva. For upper GIE, 10 ml of gastric fluid was collected through the endoscope. For lower GIE, 10 ml of intestinal fluid was collected through the endoscope. The primary outcome was the positive rate of SARS-CoV-2 in saliva and gastric and intestinal fluids. We also analyzed serum-specific antibodies for SARS-CoV-2 and patients’ background information.Findings: A total of 783 samples (560 upper GIE and 223 lower GIE samples) were analyzed. Polymerase chain reaction (PCR) on saliva samples did not show any positive results in either upper or lower GIE samples. However, 2.0% (16/783) of gastrointestinal fluid samples tested positive for SARS-CoV-2. No significant differences in age, sex, purpose of endoscopy, medication, or rate of antibody test positivity were found between PCR positive and PCR negative cases.Interpretation: Asymptomatic patients, even those with no detectable virus in their saliva, had SARS-CoV-2 in their gastrointestinal tract. Endoscopy medical staff should be aware of infection when performing procedures.Trial Registration: The study was registered in the University Hospital Medical Information Network Clinical Trials Registry as UMIN000040587. Funding: This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.Declaration of Interests: The authors declare that they have no conflicts of interests.Ethics Approval Statement: The institutional review board at YCU Hospital approved this prospective study on May 17, 2020 (approval number: B200500054). Written consent for participation in the study was obtained from all patients.

Evaluation of SARS-CoV-2 PCR Positive Cases in the Pediatric Emergency Department

In December 2019, a previously unknown type of coronavirus was detected in China and named as "severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)". The World Health Organization has named the SARS-CoV-2 related as coronavirus disease-2019 (COVID-19) and declared it as a pandemic. There is a limited data about the COVID-19 disease for the pediatric patients. In this study, it was aimed to evaluate the epidemiological, clinical, laboratory and radiologic findings, treatment and clinical outcomes of patients admitted to the pediatric emergency department with the suspicion of COVID-19. Between March 11 and June 16, 2020, patients aged between 1 month-18 years admitted to the pediatric emergency department and who have an indication for sampling for the polymerase chain reaction (PCR) method with the suspicion of COVID-19 according to the current guidelines published by the Ministry of Health were included in the study. The demographic characteristics, symptoms, durations and the history of contact with the suspected/definite COVID-19 cases were questioned in the patients with positive results. Physical examination, laboratory and imaging data of the patients were recorded. According to clinical severity, patients were divided into five groups. Treatment methods, ward/intensive care unit admission, length of stay at hospital, and prognosis were recorded. Of the 237 patients included in the study, 45 (18.9%) of the samples were positive and 192 (81.1%) were negative. There was a history of contact with COVID-19 positive case in 38 (85.6%) of COVID-19 PCR positive patients. The mean time for onset of symptoms after contact was 3.5 ± 1.7 days. Twenty-one of the patients (46.6%) were asymptomatic and the most common symptom was fever (34.1%) and cough (27.3%). Of the patients whose laboratory tests were requested, lymphopenia wasdetected in 50% and 52.3% of procalcitonin, 23.5% of C-reactive protein and 64.7% of D-dimer values were found to be high. Chest radiography was obtained from 45.4% of the patients; 90.0% were evaluated as normal, bronchovascular change, pleural effusion and consolidation were detected in one of each (5.0%) patient. Thorax computed tomography (CT) was obtained from 4 (9.0%) patients. One patient had normal CT findings, two patients had consolidation, one patient had peripheral ground-glass appearance and one patient had pleural effusion. Antibiotics were started in 38.6% of the patients and the most commonly used antibiotic was azithromycin (34.1%). Oseltamivir was started in one (2.3%) patient, and 10 (24.7%) patients were treated with hydroxychloroquine. There were no serious and critical cases according to the clinical severity. Pediatric patients constitute a small part of COVID-19 individuals in the community, and a significant part of them are asymptomatic, and patients who are symptomatic present with a mild clinic. In our study, most of the patients had a history of contact with COVID-19 positive cases, therefore, it should be questioned when evaluating a pediatric patient. There were no specific findings for COVID-19 positive patients in terms of laboratory and radiology.

A High Malaria Prevalence Identified by PCR among Patients with Acute Undifferentiated Fever in India.

BackgroundApproximately one million malaria cases were reported in India in 2015, based on microscopy. This study aims to assess the malaria prevalence among hospitalised fever patients in India identified by PCR, and to evaluate the performance of routine diagnostic methods.MethodsDuring June 2011-December 2012, patients admitted with acute undifferentiated fever to seven secondary level community hospitals in Assam (Tezpur), Bihar (Raxaul), Chhattisgarh (Mungeli), Maharashtra (Ratnagiri), Andhra Pradesh (Anantapur) and Tamil Nadu (Oddanchatram and Ambur) were included. The malaria prevalence was assessed by polymerase chain reaction (PCR), routine microscopy, and a rapid diagnostic test (RDT) with PCR as a reference method.ResultsThe malaria prevalence by PCR was 19% (268/1412) ranging from 6% (Oddanchatram, South India) to 35% (Ratnagiri, West India). Among malaria positive patients P. falciparum single infection was detected in 46%, while 38% had P. vivax, 11% mixed infections with P. falciparum and P. vivax, and 5% P. malariae. Compared to PCR, microscopy had sensitivity of 29% and specificity of 98%, while the RDT had sensitivity of 24% and specificity of 99%.ConclusionsHigh malaria prevalence was identified by PCR in this cohort. Routine diagnostic methods had low sensitivity compared to PCR. The results suggest that malaria is underdiagnosed in rural India. However, low parasitaemia controlled by immunity may constitute a proportion of PCR positive cases, which calls for awareness of the fact that other pathogens could be responsible for the febrile disease in submicroscopic malaria.

Plasma Epstein Barr virus (EBV) DNA as a biomarker for EBV associated Hodgkin lymphoma.

To assess plasma Epstein-Barr virus (EBV) DNA as a biomarker of tumour burden at diagnosis and during therapy in children with Hodgkin lymphoma. Case-control study, with prospective follow-up of the Hodgkin lymphoma cohort (2007-2012). Pediatric Hematology Oncology unit of a tertiary care hospital in Delhi. Thirty children with Hodgkin lymphoma and 70 sex and age-matched controls (benign lymphadenopathy 19, non-lym-phoid malignancy 29, Burkitt lymphoma 5, healthy children 17). Positive EBV-staining on immunohistochemistry was defined as EBV-associated Hodgkin lymphoma. Plasma EBV real-time quantitative polymerase chain reaction (PCR) was tested at presentation, after first and last chemotherapy cycles, and on follow-up. Plasma EBV quantitative PCR was compared between cases and controls. Its kinetics was assessed during and after chemotherapy. EBV quantitative PCR was positive in 19 (63%) Hodgkin lymphoma cases (range 500 to 430,000 copies/mL), with 87.5% accuracy (kappa=0.69) as compared with EBV immunohistochemistry. Sensitivity and specificity of the quantitative PCR were 87.5% and 81.8%, respectively. Only boys showed positive EBV immunohistochemistry and,or quantitative PCR positivity. All controls were quantitative PCR negative. All quantitative PCR positive cases with follow up blood sample showed EBV clearance after the first cycle. A quantitative PCR negative case in long-term remission became positive at relapse. EBV status did not influence survival. Plasma EBV-DNA, detectable in EBV-associated Hodgkin lymphoma, becomes undetectable early after initiating therapy. It can be used as a biomarker of treatment response in EBV-associated Hodgkin lymphoma.

Comparative analysis of a hup B gene based diagnostic PCR with other conventional techniques for pediatric tuberculous meningitis

Tuberculous meningitis, an extrapulmonary manifestation of tuberculosis, is associated with poor prognosis and high mortality in the pediatric age group with delayed treatment. The main causative agent in humans is Mycobacterium tuberculosis but other members of the M. tuberculosis complex especially Mycobacterium bovis, have also been implicated as potential human pathogens. Our study utilizes the hup B gene (Rv2986c in M. tuberculosis and Mb3010c in M. bovis) as a target for a two-step 'in house' nested polymerase chain reaction (PCR) in cerebrospinal fluid samples and can differentiate between M. tuberculosis and M. bovis. The products obtained for M. tuberculosis and M. bovis are 116 and 89 base pair respectively due to a 27 base pair deletion at the C-terminal of hup B gene of M. bovis. Fifty cases, suggestive of tuberculous meningitis, and fifty controls (admitted for other causes) were chosen as per Modified Ahuja's criteria and correlated with response to therapy. They were regrouped retrospectively as definitive tuberculous meningitis [25] and non-tuberculous meningitis [75]. Of the non-tuberculous meningitis category, 45 patients were diagnosed as pyogenic meningitis while the rest were diagnosed as febrile seizures [16], hypocalcemic seizures [11] and enteric encephalopathy [3]. Mycobacterial DNA extracted from cerebrospinal fluid samples were subjected to a two-step nested PCR. A sensitivity of 92% and specificity of 98.7% was obtained. M. tuberculosis and M. bovis infection was seen in 56% and 35% of the PCR positive cases respectively while 9% showed co-infection with both species. Thus this novel gene target shows promising potential as a rapid molecular diagnostic aid in pediatric tuberculous meningitis where rapid institution of antituberculosis therapy is essential.

Prevalence of canid herpesvirus-1 infection in stillborn and dead neonatal puppies in Denmark.

BackgroundCanid herpesvirus-1 (CaHV-1) infection in puppies less than three weeks of age is often reported to be associated with a lethal generalized necrotizing inflammation and since the discovery of the virus in 1965 several reports of neonatal infections have been published. However, the significance of CaHV-1 for peri- and neonatal mortality in puppies remains unclear. Therefore, we examined stillborn and dead neonatal puppies in Denmark to determine the prevalence of infection and further to correlate infection levels with necropsy findings to assess the possible significance of the infection.ResultsFrom a cross-sectional study of 57 dead puppies, 22.8% (n = 13) were confirmed positive for CaHV-1 by real-time polymerase chain reaction (PCR) of tissue pools of lung/liver and/or spleen/kidney. Specimens from PCR positive cases were further investigated by histology and in situ hybridization (ISH). High levels of CaHV-1 DNA were present in only one case in which lesions and ISH staining consistent with CaHV-1 infection were found as well. CaHV-1 concentrations in the other cases were low and a range of lesions not consistent with CaHV-1 were found. Similar, ISH staining was mostly negative in these except for one case with a few positive cells.ConclusionCaHV-1 infection in stillborn and dead neonatal puppies in Denmark seems to be common, but the direct significance for puppy mortality remains unclear as only one of 13 PCR positive puppies (7.7%) had pathognomonic lesions.Electronic supplementary materialThe online version of this article (doi:10.1186/s13028-014-0092-9) contains supplementary material, which is available to authorized users.

Effectiveness of pertussis vaccines for adolescents and adults: case-control study

Objective To assess the effectiveness of reduced acellular pertussis (Tdap) vaccines in adolescents and adults.Setting Kaiser Permanente Northern California.Design Case-control study.Participants All polymerase chain reaction (PCR) confirmed cases of pertussis...