Polymerase Chain Reaction Test Research Articles

Genotype profile of HPV in ASC-H cytology and histologic follow-up-prevalence, distribution, and risk: A retrospective study of 1414 cases.

A cytologic diagnosis of atypical squamous cells, cannot exclude high-grade squamous lesion (ASC-H) poses a disproportionately high risk of cervical cancer development. The objective of this study was to analyze type-specific risks by mapping human papillomavirus (HPV) genotypes in ASC-H cytology. In total, 1,048,581 Papanicolaou tests that had ASC-H cytology were retrieved. Concurrent HPV genotyping using proprietary multiplex real-time (MRT) and polymerase chain reaction (PCR) HPV tests and histologic follow-up findings were analyzed. Among 1678 patients who had ASC-H findings (0.16%), 1414 (84.3%) underwent concurrent HPV genotyping (MRT, 857; HPV PCR test, 557). The overall high-risk HPV (hrHPV)-positive rate was 84.4%. Of the 857 MRT cases, 63.9% were infected with a single hrHPV, and 24.4% had multiple genotypes. The most prevalent HPV types were HPV16/52/58/33/31. Lesions that were identified as cervical intraepithelial neoplasia 2 or worse (CIN2+) were detected in 498 of 906 cases (55.0%), including 81 cervical carcinomas (8.9%). The risk of CIN2+ for the composite group of HPV16/52/58/33/31-positive cases was 62.7%, representing 90.7% (264 of 291) of total CIN2+ lesions in ASC-H/hrHPV-positive cases by MRT. CIN2+ lesions were detected in 108 of 142 (76.1%) HPV16-positive and/or HPV18-positive women by the PCR the HPV test. Among 128 hrHPV-negative ASC-H cases by both methods, CIN2+ lesions were identified in 21 of 128 (16.4%), including five cervical carcinomas (3.9%). The sensitivity, specificity, positive predictive value, and negative predictive value for patients in the composite group with HPV16/52/58/33/31 were 88.0%, 40.8%, 62.7%, and 75.0%, respectively. Papanicolaou tests classified as ASC-H are associated with a high CIN2+ rate and warrant colposcopy, regardless of HPV status. The extent to which the risk-stratification provided by comprehensive HPV genotyping can inform the management of ASC-H cytology remains to be explored.

Comparison of perinatal and neonatal outcomes of symptomatic pregnancy infected with SARS-CoV-2.

In this study, maternal and neonatal outcomes of pregnant women with positive severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) RNA tests were evaluated according to their symptomatic status. The clinical progression of SARS-CoV-2-positive pregnant women and the effect of coronavirus disease-2019 (COVID-19) on newborns was investigated. This retrospective cohort study was conducted at a tertiary pandemic hospital specializing in caring for pregnant women infected with SARS-CoV-2. We included patients with a positive SARS-CoV-2 polymerase chain reaction test at delivery, subdividing them into symptomatic and asymptomatic groups. Two hundred and forty-nine patients were included in the study. The mean age of the pregnant women in the symptomatic group was higher than those in the asymptomatic group (p=0.001). The iatrogenic preterm birth rates in the symptomatic and asymptomatic groups were 43.37% and 8.43%, respectively (p<0.001). Cesarean section rate was higher in symptomatic group (p=0.01). Maternal death was significantly higher in symptomatic pregnant women (p<0.001). The neonatal intensive care unit admission rate was higher in symptomatic pregnant women (p<0.001). The maternal and fetal outcomes for mothers with symptomatic infections tend to be worse, highlighting the importance of careful management, good follow-up and the advisability of closer monitoring.

Las Bolitas Syndrome in Penaeus vannamei Hatcheries in Latin America.

In September 2023, several hatcheries in Latin America experienced significant mortality rates, up to 90%, in zoea stage 2 of Penaeus vannamei. Observations of fresh mounts revealed structures resembling lipid droplets, similar to those seen in a condition known as "las bolitas syndrome". Routine histopathological examinations identified detached cells and tissues in the digestive tracts of affected zoea, contrasting with the typical algal cell contents seen in healthy zoea. Polymerase chain reaction (PCR) testing for over 20 known shrimp pathogens indicated minimal differences between diseased and healthy batches. Both groups tested negative for acute hepatopancreatic necrosis disease (AHPND) but positive for Vibrio species and Rickettsia-like bacteria in the diseased samples. Histological analyses of the affected zoea revealed characteristic tissue degeneration in the hepatopancreas, forming spheres that eventually migrated into the upper gut, midgut, and midgut caeca, a pathology identified as bolitas syndrome (BS). Microbiological assessments revealed Vibrio species at concentrations of 106 CFU zoea/g in affected zoea, approximately two orders of magnitude higher than in healthy zoea. Bacterial isolation from both healthy and BS-affected zoea on thiosulphate-citrate-bile salts-sucrose (TCBS) agar and CHROMagar™ (Paris, France), followed by identification using API 20E, identified six strains of Vibrio alginolyticus. Despite similarities to "las bolitas syndrome" in fresh mounts, distinct histopathological differences were noted, particularly the presence of sloughed cells in the intestines and variations in hepatopancreatic lobes. This study highlights the critical need for further research to fully understand the etiology and pathology of bolitas syndrome in zoea stage 2 of P. vannamei to develop effective mitigation strategies for hatchery operations.

The impact of comorbidity status in COVID-19 vaccines effectiveness before and after SARS-CoV-2 omicron variant in northeastern Mexico: a retrospective multi-hospital study.

The end of the coronavirus disease 2019 (COVID-19) pandemic has been declared by the World Health Organization on May 5, 2023. Several vaccines were developed, and new data is being published about their effectiveness. However, the clinical trials for the vaccines were performed before the Omicron variant appeared and there are population groups where vaccine effectiveness still needs to be tested. The overarching goal of the present study was to analyze the effects of COVID-19 vaccination before and after the Omicron variant in patients considering comorbidities in a population from Nuevo Leon, Mexico. Epidemiological COVID-19 data from the Mexican Social Security Institute were collected from 67 hospitals located in northeastern Mexico, from July 2020 to May 2023, and a total of 669,393 cases were compiled, 255,819 reported a SARS-CoV-2 positive reverse transcription quantitative polymerase chain reaction (RT-qPCR) test or a positive COVID-19 antigen rapid test. Before Omicron (BO, 2020-2021), after 14 days of two doses of COVID-19 vaccine, BNT162b2 and ChAdOx1 vaccines were effective against infection in non-comorbid and all comorbid subgroups, whereas after Omicron (AO, 2022- 2023) there was no significant effectiveness against infection with none of the vaccines. Regarding hospitalization BO, BNT162b2, ChAdOx1, CoronaVac and mRNA-1273 significantly protected non-comorbid patients whereas BNT162b2, ChAdOx1, and mRNA-1273, protected all comorbid subgroups against hospitalization. AO, BNT162b2, ChAdOx1, CoronaVac and mRNA-1273 were effective against hospitalization in non-comorbid patients whereas for most comorbid subgroups BNT162b2, ChAdOx1 and CoronaVac were effective against hospitalization. Non-comorbid patients were protected against death as an outcome of COVID-19 during the BO period with most vaccines whereas a reduction in effectiveness was observed AO with mRNA-1273 vaccines in patients with hypertension, and diabetes mellitus. BO, COVID-19 vaccines were effective against infection, hospitalization, and death whereas AO, COVID-19 vaccines failed to protect the population from COVID-19 infection. A varying effectiveness against hospitalization and death is observed AO.

Prevalence and predictors of antibiotic prescription among patients hospitalized with viral lower respiratory tract infections in Southern Province, Sri Lanka.

Antimicrobial overprescription is common for lower respiratory tract infections (LRTI), as viral and bacterial infections generally present with similar clinical features. Overprescription is associated with downstream antimicrobial resistance. This study aims to identify the prevalence and predictors of antibiotic prescription among patients hospitalized with viral LRTI. A prospective cohort study was conducted among patients aged ≥1 year hospitalized with viral LRTI in a tertiary care hospital in Southern Province, Sri Lanka from 2018-2021. Demographic, clinical, and laboratory data were recorded. Nasopharyngeal and blood samples were collected for multiplex polymerase chain reaction testing for 21 respiratory pathogens and procalcitonin (PCT) detection, respectively. Demographic and clinical features associated with antibiotic prescription were identified using Chi Square and t-tests; significant variables (p<0.05) were further included in multivariable logistic regression models. The potential impact of biomarker testing on antibiotic prescription was simulated using standard c-reactive protein (CRP) and PCT cut-offs. Of 1217 patients enrolled, 438 (36.0%) had ≥1 respiratory virus detected, with 48.4% of these patients being male and 30.8% children. Influenza A (39.3%) and human rhinovirus/ enterovirus (28.3%) were most commonly detected. A total of 114 (84.4%) children and 266 (87.8%) adults with respiratory viruses were treated with antibiotics. Among children, neutrophil percentage (median 63.6% vs 47.6%, p = 0.04) was positively associated with antibiotic prescription. Among adults, headache (60.6% vs 35.1%, p = 0.003), crepitations/crackles (55.3% vs 21.6%, p<0.001), rhonchi/wheezing (42.9% vs 18.9%, p = 0.005), and chest x-ray opacities (27.4% vs 8.1%, p = 0.01) were associated with antibiotic prescription. Access to CRP and procalcitonin test results could have potentially decreased inappropriate antibiotic prescription in this study by 89.5% and 83.3%, respectively. High proportions of viral detection and antibiotic prescription were observed among a large inpatient cohort with LRTI. Increased access to point-of-care biomarker testing may improve antimicrobial prescription.

The role of the neutrophil/lymphocyte ratio as a biomarker predicting the severity of COVID-19 infection

At the end of 2019, several cases of pneumonia provoked by an unknown causative agent were identified in China. In March 2020, the World Health Organization announced a pandemic of a new strain of Coronavirus - SARS-CoV-2. The neutrophil/lymphocyte ratio (NLR) is a biomarker that has recently become an important diagnostic and prognostic indicator in many diseases. The study&amp;lsquo;s objective was to look for a relationship between NLR and the outcome of Covid-19 infection. Retrospectively, we studied 288 patients (mean age 69.1 &amp;plusmn; 12.5) treated in an intensive pulmonology unit over ten months since 01.08.2021. All patients had severe pneumonia caused by SARS-CoV-2 infection, proven by a polymerase chain reaction (PCR) test. Leukocytes, lymphocytes, neutrophils, and NLR were traced. Hundred and seventy-four (60.4%) of the patients died, and the rest were discharged with improvement. Concerning NLR, we found values of 9.52 in the group of the deceased and 7.87 in those discharged, respectively, at the beginning. In the end, this indicator increased in the group of deceased to 15.04, while we found a drop to 7.3 in those discharged. A statistically significant difference was found regarding the outcome of the disease and the change in the NLR values in dynamics (p = 0.005). NLR is a cheap and reliable biomarker that can predict the outcome of Covid-19 infection.

Self-swabbing versus assisted swabbing for viral detection by qRT-PCR: the experience from SARS-CoV-2 based on a meta-analysis of six prospectively designed evaluations conducted in a UK setting

PurposeIn April 2020, the UK Government implemented NHS Test and Trace to provide SARS-CoV-2 quantitative reverse transcription polymerase chain reaction (qRT-PCR) testing for the public, with nose-and-throat swabbing for samples performed by trained staff. Self-swabbing (SS) would allow rapid scale-up of testing capacity and access. Six studies were undertaken to determine whether SS was as effective for detecting SARS-CoV-2 as swabbing performed by trained staff.MethodsSix prospective studies were conducted between April–October 2020, using six swab/media combinations. Differences between assisted swabbing (AS) and SS were evaluated for concordance, positivity, sensitivity, cycle threshold (Ct) values and void rates. Statistical analysis was performed using 95% confidence intervals (CIs), paired t-tests and model-based methods.ResultsOverall, 3,253 individuals were recruited (median age 37 years, 49% female), with 2,933 having valid paired qRT-PCR results. Pooled concordance rate was 98% (95% CI: 96%, 99%). Positivity rate differences for SS (8.1%) and AS (8.4%) and differences in pooled sensitivities between SS (86%; 95% CI: 78%, 92%) and AS (91%; 95% CI: 78%, 96%) were nonsignificant. Both types of swabbing led to pooled void rates below 2% and strongly correlated Ct values. Age, sex and previous swabbing experience did not have a significant impact on concordance or sensitivity.ConclusionThe UK adopted a policy to promote self-testing for SARS-CoV-2 based on data demonstrating equivalence of SS versus AS. Positive outcomes with SS are likely generalisable to testing for other respiratory pathogens, and we consider self-sampling and self-testing essential for future pandemic preparedness.

Use of a diagnostic Puumala virus real-time RT-PCR in an orthohantavirus endemic region in the Netherlands.

The addition of a real-time reverse transcription polymerase chain reaction test to routine orthohantavirus diagnostics may better aid clinical decision making than the use of standard serology tests alone. Awareness by clinicians and clinical microbiologists of this advantage may ultimately lead to a reduction in over-hospitalization and unnecessary invasive diagnostic procedures.

Screening blood donors for malaria, can we increase the number of eligible donors? An observational retrospective study

BackgroundIn non-endemic countries, malaria can be transmitted through blood donations from imported cases. To ensure standards of quality and safety of human blood, the European Union and Spanish national law, requires a deferral period, or a screening by immunological or genomic test among those donors with potential risk of malaria. Scientific societies, European Committee on Blood Transfusion, and Spanish Society of Haematology and Haemotherapy, refer only to the result of the immunological test.MethodsAn observational retrospective study was performed in potential donors with a positive immunological test for malaria done in the Regional Transfusion Center in Madrid and referred to the National Reference Unit for Tropical Diseases in Madrid between 2015–2020. At consultation a Polymerase Chain Reaction (PCR) for malaria was performed.ResultsDuring the study period, 121 possible donors attended for consultation at NRU-Trop. Median age: 38.5 (IQR:33–48); median time to consultation was 32 months (IQR:12.5–110). Eighty-two (67.8%) donors were migrants and thirty-nine were travellers (32.2%). ELISA values were available for 109 subjects (90.1%), 56 individual left malaria endemic area > 3 years before. All donors tested negative for Plasmodium spp PCR test (n = 121, 100%).ConclusionsNone of the subjects with a positive immunologic test deferred as blood donors had a positive genomic test. The presence of Plasmodium spp in collected blood was not detected by molecular techniques. To avoid the loss of potential blood donors, especially those with low incidence red blood cell antigens, as more precise microbiology techniques become available, updating the existing legislation becomes necessary to increase the availability of donated blood.

Prevalence, under-reporting, and epidemiological surveillance of COVID-19 in the Araguaína City of Brazil.

Asymptomatic and underreported individuals remain a source of coronafig disease 2019 (COVID-19) transmission to others. Data on the prevalence and epidemiological factors influencing transmission are fundamental for establishing control measures, especially in vulnerable regions such as the Amazon. This study aimed to determine the point prevalence and active infection of COVID-19 among the population in Araguaína, a Brazilian city located in the Amazon region, analyzed the socioeconomic and behavioral variables of a statistically representative sample of this population using an epidemiological survey, and identify the viral genomic diversity in the region. During the sixth epidemiological week of 2021 (February 8 to 12), samples of 497 inhabitants of the municipality asymptomatic for respiratory syndromes underwent reverse transcription-quantitative polymerase chain reaction and serological tests (immunoglobulin M and immunoglobulin G). A questionnaire collated data on socioeconomic factors, prevention measures, and health status history. The active infection rate was 6.2%, and the prevalence was 13.5% of the study population. Active infection cases were under-reported; each reported positive case represented 14-28 under-reported cases. Lineages P.2, P.1, and B.1.1 were detected. Working from home was a protective factor against the infection, and clinical signs of fever, dry cough, and loss of taste or smell were associated with testing positive (p <0.05). A descriptive analysis of the indicators revealed that the entire population was susceptible to the disease. Intensified vaccination strategies are required regardless of socioeconomic factors, health conditions, and preventive measures. Implementation of objective, comprehensive, and efficient management tools to minimize the spread of COVID-19 in this municipality can serve as a model for other regions of Brazil.

The impact of mild and moderate COVID-19 infection on the progression of kidney dysfunction in patients with IgA nephropathy.

Previous research indicates that coronavirus disease 2019 (COVID-19) infection may have a role in triggering immunoglobulin A (IgA) nephropathy. However, limited research has explored the clinical implications of COVID-19 infection in individuals already diagnosed with IgA nephropathy. This study aimed to determine whether COVID-19 infection independently affects the subsequent trajectory of kidney function in IgA nephropathy patients. This was a single-center cohort study. The study included 199 patients diagnosed with IgA nephropathy. The COVID-19 infection status was determined using a combined method: a questionnaire and the Health Code application, both administered at the end of 2022 in northern China. Kidney function trajectory was assessed by the estimated glomerular filtration rate (eGFR), calculated based on serum creatinine levels measured during follow-up outpatient visits. The primary endpoint of interest was the eGFR trajectory. Out of the 199 participants, 75% (n=181) reported a confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, determined through antigen or polymerase chain reaction tests, accounting for 79% (n=143) of the infected patients. A significant majority (98%) experienced mild to moderate symptoms. Over a median follow-up period of 10.7months post-COVID-19 infection, notable clinical events included gross hematuria in 30 patients (16.6%), which normalized within an average of 3days. Additionally, a 2-fold increase in proteinuria or progression to the nephrotic range was observed in 10 individuals (5.5%). No cases of acute kidney injury were noted. COVID-19 exposure was associated with an absolute change in eGFR of 2.98mL/min/1.73m2 per month (95% confidence interval 0.46 to 5.50). However, in a fully adjusted model, the estimated changes in eGFR slope post-COVID-19 were -0.39mL/min/1.73m2 per month (95% confidence interval -0.83 to 0.06, P=.088) which included the possibility of no significant effect. Notably, a higher rate of kidney function decline was primarily observed in patients with a baseline eGFR <45mL/min/1.73m2 [-0.56mL/min/1.73m2 (-1.11 to -0.01), P=.048]. In the cohort, there were few instances of severe COVID-19 cases. The absence of long-term follow-up outcomes was observed. Overall, mild to moderate COVID-19 infection does not appear to significantly exacerbate the subsequent decline in kidney function among IgA nephropathy patients, particularly in those with preserved baseline kidney function.

Prospective follow-up of overactive bladder symptoms in patients with prior SARS-CoV-2 infection.

SARS-CoV-2 infection can result in genitourinary symptoms, such as frequency, urgency, nocturia, and pain/pressure. In this study, we followed the progression of overactive bladder (OAB) symptoms in patients that reported new or worsening OAB symptoms after coronavirus disease-19 (COVID-19) diagnosis. Individuals from a COVID-19 serology study were invited to participate in a follow-up study. Respondents were divided into three groups based on prior COVID-19 testing. Patients scored symptoms retrospectively before the pandemic, at study onset, and prospectively during 12-month follow-up. Genitourinary symptoms were assessed using international consultation on incontinence questionaire for OAB (ICIQ-OAB). Change in ICIQ-OAB scores from baseline were calculated. The minimal important difference of one on ICIQ-OAB is considered a significant change. 26.0% of participants previously had positive COVID polymerase chain reaction (PCR) test (PCR+), 5.6% a positive serology test only (Ser+), and 65.5% were COVID naïve (COVID-). 23.8% of participants reported a significant increase in ICIQ-OAB score at study onset compared to prepandemic. ICIQ-OAB scores were similar at prepandemic but significantly higher at study start (p < 0.001) in PCR+ group. During follow-up, change in ICIQ-OAB scores from baseline remained unchanged for COVID- group, but gradually reduced for PCR+, reaching similar levels as COVID- group by 12 months. By 12 months, 71.4% of PCR+, 42.9% of Ser+, and 68.8% of COVID- participants still reported significant increase in ICIQ-OAB scores. Most COVID-19 patients experienced return of symptoms to baseline, indicative of the potential resolution of COVID-associated cystitis. A subset of cases did not, raising questions about the underlying factors contributing to this outcome. Additional research is needed to assess long COVID on urological health.

A case of a cerebellar form of progressive multifocal leukoencephalopathy in a patient undergoing peritoneal dialysis.

Progressive multifocal leukoencephalopathy (PML), a severe demyelinating disease of the central nervous system, is caused by the reactivation of the polyomavirus JC virus (JCV). It favors the cerebrum and typically occurs in patients with immunodeficiencies, with a progressive course and fatal outcome in the majority of cases. However, the cerebellar form of PML, characterized by isolated posterior fossa lesions, such as those in the cerebellum or brainstem at disease onset, is rare, and reports of its occurrence in peritoneal dialysis (PD) patients are lacking. In this paper, we describe a rare case of a cerebellar form of PML in a PD patient. A 64-year-old man undergoing PD was referred to our hospital for anorexia, nausea, and vomiting in the past month. He had finger-to-nose test abnormalities, gaze-directed nystagmus, and scanning speech. He was diagnosed with the cerebellar form of PML based on his progressive cerebellar symptoms, the typical magnetic resonance imaging findings, and the presence of JCV-DNA in the cerebrospinal fluid polymerase chain reaction test. He developed nocturnal delirium, aggravated disquiet, and died of pneumonia on the 69th day. Clinicians should consider the cerebellar form of PML as a differential diagnosis if PD patients develop progressive cerebellar symptoms.

Asymptomatic Children as a Missing Link in Preventing COVID-19 Transmission.

Investigating the prevalence of the coronavirus disease 2019 (COVID-19) infection in asymptomatic children who have been in close contact with symptomatic individuals is instrumental for refining public health approaches, protecting vulnerable populations, and mitigating the broader impact of the pandemic. Accordingly, this study aimed to evaluate the incidence of COVID-19 infection in asymptomatic children who had been in close contact with parents exhibiting COVID-19 symptoms. Study Design: A cross-sectional study. The present cross-sectional study was conducted on 175 asymptomatic children who had been in close contact with COVID-19 confirmed cases in Hamadan County from March 2021 to August 2021. Reverse transcription polymerase chain reaction (RT-PCR) testing was performed on all asymptomatic children who had been in close contact with an individual with COVID-19. Furthermore, multiple logistic regressions were conducted to determine the predictors of COVID-19 transmission from family members to children. Out of the 175 children in close contact with index cases, 53 (30.29%) tested positive for COVID-19 through PCR. Regarding factors related to the index case, male cases (Adjusted odds ratio [AOR]=2.29; 95% confidence interval [CI]: 1.03-5.09, P=0.041), rural dwellers (AOR=3.22; 95% CI: 1.02-10.16, P=0.046), illiterate cases (AOR=8.45; 95% CI: 1.76-40.65, P=0.008), and cases presenting with nasal congestion symptoms (AOR=9.12; 95% CI: 2.22-37.40, P=0.002) were more prone to transmitting the virus to children who had close contact with them. The findings of the present study suggested that asymptomatic COVID-19 infection in household contacts is significant in children who were in close contact with a COVID-19-positive patient. Therefore, it is crucial to continue to monitor this group closely.

Epidemiology of measles in southern Iran: trends, challenges, and vaccination insights

Background: Measles, a highly contagious and vaccine-preventable disease, continues to present global public health challenges. This retrospective study focused on measles outbreaks in Hormozgan province, southern Iran, spanning from 2014 to 2019. Methods: Between 2014 and 2019, patients suspected of having measles, as reported by medical centers in Hormozgan, were subject to a comprehensive evaluation. The diagnosis of measles was conclusively established through the use of real-time polymerase chain reaction (RT-PCR) testing. A detailed collection of pertinent data was undertaken. SPSS software, version 21, was employed for statistical analysis. Results: In the current study, out of 1291 clinically suspected measles cases, 151 were PCR-confirmed, with an average age of 16.77 years (±10.46), comprising 50.9% males and 49.1% females. The annual distribution showed varied incidence: 8.4% in 2014, peaking at 18.8% in 2015, then fluctuating to 11.4% in 2016, 0.8% in 2017, and 17.9% in 2018, with no cases in 2019. Among confirmed cases, 16.5% were vaccinated, while 68.2% were not, and 15.23% had unknown vaccination status. Conclusion: This retrospective study highlights the ongoing challenge of measles in Hormozgan province, Iran, from 2014 to 2019. Despite measles being preventable by vaccination, a significant number of cases were confirmed among both vaccinated and unvaccinated individuals, indicating gaps in immunization coverage and effectiveness. The fluctuating annual incidence, with a peak in 2015 and no cases in 2019, suggests variable success in disease control efforts. This underscores the need for enhanced surveillance, improved vaccination strategies, and public health interventions to effectively combat measles outbreaks in this region.

Herpes simplex (HSV-1) encephalitis in an infant: a case report study

Introduction and importance: The herpes simplex virus (HSV) is the most common cause of acute sporadic encephalitis, a severe and often fatal disease in humans. It is associated with high mortality and morbidity rates in untreated patients. Case presentation: An 11-month-old child was admitted to the hospital presenting with acute fever and seizures characterized by staring episodes and spastic movements affecting the left side of the body. Diagnostic workup revealed abnormal T2 flair hyperintense foci in bi-temporoparietal lobes and right thalamus, and bilateral otomastoiditis were detected. A positive result for HSV-1 was obtained through HSV type 1/2 polymerase chain reaction (PCR) testing, leading to a diagnosis of herpes encephalitis. Clinical discussion: While acyclovir has proven to be an effective therapeutic option, mortality and neurological sequelae continue to be reported in a notable fraction of patients. HSV encephalitis is mainly caused by two strains of the herpes simplex virus: HSV-1, more frequently observed in children and adults, and HSV-2, commonly seen in neonates and those with compromised immune systems. MRI scans often reveal that the brain lesions are localized to certain areas, although temporal involvement may not always be evident. The symptoms of herpetic encephalitis can greatly vary, making early diagnosis and treatment vital for improving patient outcomes. Conclusion: This case report highlights the clinical presentation, diagnostic challenges, and treatment strategies for HSV-1 encephalitis and underscores the importance of early recognition and prompt initiation of antiviral therapy in suspected cases of HSV-1 encephalitis.

Performance of and Severe Acute Respiratory Syndrome Coronavirus 2 Diagnostics Based on Symptom Onset and Close Contact Exposure: An Analysis From the Test Us at Home Prospective Cohort Study.

Understanding changes in diagnostic performance after symptom onset and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exposure within different populations is crucial to guide the use of diagnostics for SARS-CoV-2. The Test Us at Home study was a longitudinal cohort study that enrolled individuals across the United States between October 2021 and February 2022. Participants performed paired antigen-detection rapid diagnostic tests (Ag-RDTs) and reverse-transcriptase polymerase chain reaction (RT-PCR) tests at home every 48 hours for 15 days and self-reported symptoms and known coronavirus disease 2019 exposures immediately before testing. The percent positivity for Ag-RDTs and RT-PCR tests was calculated each day after symptom onset and exposure and stratified by vaccination status, variant, age category, and sex. The highest percent positivity occurred 2 days after symptom onset (RT-PCR, 91.2%; Ag-RDT, 71.1%) and 6 days after exposure (RT-PCR, 91.8%; Ag-RDT, 86.2%). RT-PCR and Ag-RDT performance did not differ by vaccination status, variant, age category, or sex. The percent positivity for Ag-RDTs was lower among exposed, asymptomatic than among symptomatic individuals (37.5% (95% confidence interval [CI], 13.7%-69.4%) vs 90.3% (75.1%-96.7%). Cumulatively, Ag-RDTs detected 84.9% (95% CI, 78.2%-89.8%) of infections within 4 days of symptom onset. For exposed participants, Ag-RDTs detected 94.0% (95% CI, 86.7%-97.4%) of RT-PCR-confirmed infections within 6 days of exposure. The percent positivity for Ag-RDTs and RT-PCR tests was highest 2 days after symptom onset and 6 days after exposure, and performance increased with serial testing. The percent positivity of Ag-RDTs was lowest among asymptomatic individuals but did not differ by sex, variant, vaccination status, or age category.

Aetiology of pleural effusions in children living in a high TB endemic setting.

<sec id="st1"><title>BACKGROUND</title>Confirming the aetiology of pleural effusion in children may be difficult in TB-endemic settings. We investigated the role of polymerase chain reaction (PCR) and routine biochemical tests in discriminating pleural effusion caused by bacteria from other aetiologies.</sec><sec id="st2"><title>METHODS</title>This is a cross-sectional post-hoc analysis among children with pleural effusion in a tertiary hospital in South Africa, incorporating new data from PCR testing of stored pleural fluid. Aetiological classification was defined by microbiological confirmation.</sec><sec id="st3"><title>RESULTS</title>Ninety-one children were enrolled; the median age 31 months (IQR 12-102). The aetiology of pleural effusion was 40% (36/91) bacteria, 11% (10/91) TB, 3% (3/91) viruses, 11% (10/91) polymicrobial and 35% (32/91) had no pathogen identified. The most common pathogen was Staphylococcus aureus (27/91, 30%) with similar yields on culture and PCR, followed by Streptococcus pneumoniae (12/91, 13%), detected more commonly by PCR. PCR reduced the number of children with unconfirmed aetiologies from 48 to 32. Characteristics of children with no pathogen most resembled those with TB. Pleural fluid lactate dehydrogenase ≥1,716 U/L best discriminated bacterial pleural effusion from other aetiologies (sensitivity of 86%; specificity 95%).</sec><sec id="st4"><title>CONCLUSION</title>PCR improved detection of pathogens and reduced number of children with unconfirmed aetiologies in presumed exudative pleural effusion.</sec>.

Occurrence of Secondary Non-Hodgkin Lymphomas Among Our Classical Hodgkin Lymphoma Patients: A Single-Centre Experience.

Objective Non-Hodgkin lymphoma (NHL) arising as a secondary malignancy in patients treated for classical Hodgkin lymphoma (cHL) is an infrequent and challenging clinical scenario. NHL can be presented synchronously with cHL or may develop later, sequentially, up to years after treatment for cHL. The relationship between the two lymphomas is unclear, and there are no clear guidelines forthe management ofthese patients. We would like to find a better clinical understanding of this issueso this study investigates the occurrence and clinical characteristics of secondary NHL. Materials and methods In this retrospective cohort examination, we collected cHL cases when NHL occurred during or after the course of treating cHL. We performed the histopathologic revisions of the samples, and in every case where the quality of the sample was lower, we performed molecular examinations to find the association between cHL and NHL. We performed next-generation genome sequencing (NGS) and immunoglobulin heavy-chain variable region gene (IgHV) clonality testing. Results In a cohort of 164 cHL patients diagnosed between 2011 and 2020, six patients were identified with NHL during rebiopsy prompted by lymphoma relapse or progression. Among these, five patients were diagnosed with post-germinalcenter-originated diffuse large B-cell lymphoma (post-GC DLBCL), and one patient presented high-grade B-cell lymphoma (HG-BCL). The NHL manifestation differed in its timing: three cases emerged after successful cHL treatment, with at least 18 months of complete remission, while the other three patients faced primary refractory cHL. Notably, the primary refractory cases did not exhibit a confirmed clonal relationship between cHL and NHL, but NGS data raised the possibility of synchronous NHL in one case. In contrast, among the patients with sequentially occurring NHL, polymerase chain reaction (PCR) testing of the IgHV gene affirmed a clonal connection between cHL and secondary DLBCL in one case, while the high morphological similarity suggested a potential clonality between the two lymphomas in another case. Conclusion This study reveals that secondary NHL may manifest both synchronously and sequentially following cHL. Our results suggest that synchronous NHL has a worse prognosis compared to sequentialcaseswhen the different lymphomas are not recognized at the time of diagnosis. As our data showed, in some cases, mutations that accompany the tumor cells throughout their clonal evolution can be identified, with additional mutations later on. In the future, next-generation sequencing (NGS)-based processing of liquid biopsy samples can overcome the limitations resulting from the spatial heterogeneity of lymphoid malignancies. Over the long term, this identification could lead to early patient selection and alternative treatment strategies, ultimately leading to improved prospects for cure.

Development of custom amplicon-based test systems for detecting KRAS, NRAS, and BRAF gene mutations in colorectal cancer using next-generation sequencing (NGS).

e15061 Background: Polymerase chain reaction (PCR)-based mutation diagnostics in colorectal cancer is widely available. However, PCR has limitations in identifying rare mutations and precise mutation coordinates. Targeted sequencing, though promising, often incurs high costs and longer research durations, demanding higher DNA sample quality. Our study demonstrates the benefits of using a customized amplicon test system for diagnosing somatic mutations in tumor tissue, including detecting rare mutations not captured by PCR, requiring less input biomaterial, and similar research costs. Methods: A targeted NGS assay system was developed using region-specific primers for KRAS (exons 2, 3, and 4), NRAS (exons 2, 3, and 4), and BRAF (exon 15). Library preparation involved a three-step PCR process: Target PCR incorporating Illumina overhang adapter sequences, Index PCR introducing multiplexing indices and sequencing adapters, and PCR cleanup using magnetic beads. Sequencing utilized MiSeq v2 reagents with paired 300‐bp reads, generating high-quality, full-length reads. Validation included re-testing known samples. Tumor cell percentages in FFPE specimens were determined, and DNA was extracted using the QIAamp DNA FFPE Tissue Kit. Data analysis utilized proprietary software. Results: Out of 1234 samples, 1133 were tested, with mutations detected in 685 samples (60.45%). KRAS mutations were found in 548 (48.36%), NRAS mutations in 40 (3.5%), and BRAF mutations in 88 (7.7%) samples. Double mutations were observed in 9 samples (0.79%). Data on rare and double mutations are presented in the table. Conclusions: The developed test system accurately identifies essential mutations in colorectal cancer, including rare and potentially clinically significant variants. The required DNA amount ranged from 10 to 30 ng in 5 μl, nearly ten times less than well-known commercial PCR test systems like COBAS (Roche) and therascreen (QIAGEN). The cost of the study is comparable to PCR with a minimum study duration of 4 days. [Table: see text]