Nasopharyngeal Specimens Research Articles

Clinical Performance of the Reverse Transcription-Loop-Mediated Isothermal Amplification Assay for the Diagnosis of COVID-19 in a Thai Community Hospital at the Thailand-Myanmar Border.

Coronavirus disease 2019 (COVID-19) continues to be a global health threat and is a public health issue in Thailand and other countries. The extensive cross-border between Thailand and Myanmar is considered to be at a potentially high risk for COVID-19 distribution in this region. In this instance, simple and cost-effective tests for rapid and early detection of COVID-19 would be useful for effective patient management and control of the disease. This study was conducted at Mae Sot Hospital on the border of Thailand-Myanmar to evaluate the diagnostic performance of a simple colorimetric reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay developed recently for the rapid detection of SARS-CoV-2. Nasopharyngeal specimens were routinely collected and processed through automated nucleic acid extraction followed by real-time reverse transcription-polymerase chain reaction (rRT-PCR) using the Molaccu® COVID-19 Detection Kit. The RT-LAMP assay was further performed on remnant RNA samples, and the visual results were compared to those of rRT-PCR as a reference. Of the 727 samples tested, the RT-LAMP assay could detect 322 out of 374 samples positive for SARS-CoV-2 by rRT-PCR with 100% (n = 353/353) negative agreement. The comparative analysis demonstrated the overall accuracy, sensitivity, specificity, positive predictive value, and negative predictive valueof the RT-LAMP at 92.85% (n = 675/727, 95% CI: 90.73-94.61), 86.10% (n = 322/374, 95% CI: 82.17-89.44), 100% (n = 353/353, 95% CI: 98.96-100), 100% (n = 322/322, 95% CI: 98.86-100), and 87.16% (n = 353/405, 95% CI: 84.06-89.73), respectively. This RT-LAMP assay showed good diagnostic performance in the hospital setting. It can increase laboratory capacity for rapid SARS-CoV-2 testing and has the potential for use as an alternative or a backup assay at the point of need, especially where alternatives are unavailable for any reason, such as a decline in COVID-19 cases.

COVID-19 in Patients with Different Hematological Malignancies: Treatment Strategy and Outcome: An Iraqi Experience

Background: Patients with hematological malignancies may have higher rates of morbidity and mortality due to SARS-COVID-19 than those in the general population. Objectives: To evaluate the outcome of SARS-COVID-19 in patients with different hematological malignancies undergoing active or modified therapy. Settings: This was a retrospective cohort, multicenter study conducted on 167 patients diagnosed with SARS-COVID-19. The selected patients had been diagnosed with different hematological malignancies and had received treatment (chemotherapy or immunosuppressive). The study was carried out in different centers across Iraq between 1 December 2020 and 1 December 2021. Patients and Methods: This study was conducted in seven hematology centers across Iraq with 167 patients; of these, this study showed that 88 (52.7%) were males and 79 (47.3%) were females (mean age 51.9 ± 18.3 years). All patients had had a COVID-19 infection confirmed through RNA-specific fragments by real-time reverse transcriptase polymerase chain reaction (RT-PCR) of the nasopharyngeal swab specimens, and by computed tomography (CT) of the chest. Demographic data were obtained from patient files, which included the type of hematological malignancy, treatment (chemotherapy, immunotherapy, supportive), severity of COVID-19, modification of treatment and disease outcome for patients, whether alive or not. Patients identified as having benign or non-hematological malignancies were excluded. Results: The treatment protocol was modified in 124 patients (74.3%), while 43 patients (25.7%) continued on the same protocol. Regarding treatment outcomes, 77.2% of patients were alive at the end of the study and 22.8% had died. The survival of COVID-19 patients did not change significantly when the treatment protocol was modified compared to those who continued on treatment as per protocol. The death rate was significantly higher among patients with severe disease compared to those with mild and moderate disease (61.4% v. 0% and 5.0%, respectively) (p<0.001). Conclusions: The management of patients with hematological malignancies during the COVID-19 pandemic may be challenging, with higher mortality in patients with concurrent hematological malignancies and COVID-19. The survival of COVID-19 patients did not change significantly when treatment was modified. Age groups, sex, type of hematological malignancy, and disease status did not affect the survival of these patients. The death rate was significantly higher among patients with hematological malignancies and severe COVID-19 compared with mild or moderate disease.

Prevalence of Co-Infections and Pathogens in Hospitalized Children with Acute Respiratory Infections: A Comparative Analysis Between SARS-CoV-2 and Non-SARS-CoV-2 Cases.

Objectives. We aimed to compare the prevalence of co-infections, pathogens, and factors associated with SARS-CoV-2 acute respiratory infection (ARI) and non-SARS-CoV-2 ARI, among hospitalized children. Methods. We conducted an observational cross-sectional study of hospitalized children <15 years with ARI, and lasting respiratory symptoms <14 days, using polymerase chain reaction on nasopharyngeal specimens. Results. Of the 184 children with ARI analyzed, 122 were infected with SARS-CoV-2 and 62 were not. SARS-CoV-2 ARI had a significantly lower rate of co-infection than non-SARS-CoV-2 ARI (2.5% vs14.5%, P = .003). SARS-CoV-2 ARI children were significantly associated with a less empirical antibiotics (aOR = 0.09, CI = 0.03-0.21; P = .000), more pneumonia (aOR = 5.15, CI = 1.77-14.95; P = .003), and more abnormal chest X-ray (aOR = 2.81, CI = 1.38-5.71; P = .004). Conclusions. Although SARS-CoV-2 ARI in hospitalized children was associated with pneumonia and abnormal chest x-rays, empirical antibiotics may not be necessary for treating mild to moderate cases.

Evaluation of Two Commercial Kits for Qualitative Detection of SARS-CoV-2 Antigens in Nasopharyngeal Specimens.

Two rapid antigen tests (RATs) for COVID-19 targeting the nucleocapsid protein of SARS-CoV-2 were compared with real-time RT-PCR as the reference method. Ninety-six nasopharyngeal swab samples, comprising 56 positive and 40 negative samples confirmed through rRT-PCR were collected and retested to determine the reliability of the two nasopharyngeal RATs. The overall sensitivity and specificity of both RATs were 64.3% (95% confidence interval 50.4 - 76.6%) and 100% (95% confidence interval 91.2 - 100%), respectively. Cohen's kappa coefficient of agreement of both RATs to rRT-PCR was 0.600 (95% confidence interval 0.457 - 0.743) (p < 0.001), showing almost perfect agreement when the Ct values were less than 25 in rRT-PCR. A significant difference in Ct values between true positives and false negatives was observed (Mann-Whitney-Wilcoxon test; p < 0.001). Compared to rRT-PCR, RATs have fewer false negatives. In suspected COVID-19 cases, negative RAT results should be retested using either RAT or rRT-PCR.

Rate and Risk Factors of Reinfection, Recurrence, and Hospital Readmission Among SARS-Cov-2 Hospitalized Patients; a National Cohort Study.

Reinfection and hospital readmission due to COVID-19 were significant and costly during the pandemic. This study aimed to assess the rate and risk factors of SARS-Cov-2 reinfection, recurrence, and hospital readmission, by analyzing the national data registry in Iran. This study was a retrospective cohort conducted from March 2020 to May 2021. A census method was used to consider all of the possible information in the national Medical Care Monitoring Center (MCMC) database obtained from the Ministry of Health and Medical Education; the data included information from all confirmed COVID-19 patients who were hospitalized and diagnosed using at least one positive Polymerase Chain Reaction (PCR) test by nasopharyngeal swab specimens. Univariate and multivariable Cox regression analyses were performed to assess the factors related to each studied outcome. After analyzing data from 1,445,441 patients who had been hospitalized due to COVID-19 in Iran, the rates of overall reinfection, reinfection occurring at least 90 days after the initial infection, recurrence, and hospital readmission among hospitalized patients were 67.79, 26.8, 41.61, and 30.53 per 1000 person-years, respectively. Among all cases of hospitalized reinfection (48292 cases), 38.61% occurred more than 90 days from the initial SARS-Cov-2 infection. Getting infected with COVID-19 in the fifth wave of the disease compared to getting infected in the first wave (P<0.001), having cancer (P<0.001), chronic kidney disease (P<0.001), and age over 80 years (P<0.001) were respectively the most important risk factors for overall reinfection. In contrast, age 19-44 years (P<0.001), intubation (P<0.001), fever (P<0.001), and cough (P<0.001) in the initial admission were the most important protective factors of overall reinfection, respectively. Reinfection and recurrence of COVID-19 after recovery and the rate of hospital readmission after discharge were remarkable. Advanced or young age, as well as having underlying conditions like cancer and chronic kidney disease, increase the risk of infection and readmission.

Clinical characters of COVID-19 patient in a Saudi intensive care unit: A single-center experience

Objectives Address and assess the clinical characteristics and outcomes of COVID-19 patients admitted to the intensive care unit (ICU) of King Saud Hospital Unaizah/Qassim, Saudi Arabia. Material and Methods A single-center observational retrospective study in King Saud Hospital, including 82 critically ill COVID-19 patients admitted to the ICU, confirmed by positive polymerase chain reaction testing of nasopharyngeal specimens. Results The study was conducted on 82 COVID-19 patients from April to October 2020. The mean patient age was 58.48 years. Males were more affected by the virus, accounting for 74% of admissions. Hypertension was our patients’ most common chronic disease (45%). Most (82.9%) of the patients presented with a cough. Leukocytosis, high ferritin, lactate dehydrogenase (LDH), and D-Dimer were associated with an increased risk for mortality. Tocilizumab was associated with good outcomes among our patients. Conclusion In this retrospective study, hypertension and being male are more common factors for disease severity. Patients improved with early intervention with tocilizumab and antibiotics, and in most cases, non-invasive ventilation was associated with good outcomes.

Correlation of lymphocyte subsets and inflammatory biomarkers with disease severity in COVID-19 patients.

To determine the correlation of lymphocyte subsets and soluble serum inflammatory biomarkers with disease severity in coronavirus disease-2019 infection. The retrospective study was conducted at the Department of Immunology, Sindh Institute of Urology and Transplantation (SIUI), Karachi, Pakistan from September 1 to November 30, 2021, and comprised data of patients admitted from June to July 2021 who tested positive for coronavirus disease-2019 on the basis of reverse transcription-polymerase chain reaction of nasopharyngeal swab specimens. The patients were categorised into severe group A and non-severe group B. Initial investigations included complete blood count, neutrophil-to-lymphocytes ratio, C-reactive protein, D-Dimers and serum ferritin levels. Lymphocyte subsets included cluster of differentiation-3+, cluster of differentiation-4+/ cluster of differentiation-3+, cluster of differentiation-8+ T lymphocytes, cluster of differentiation-19+B lymphocytes, cluster of differentiation-16+ cluster of differentiation-56+ Natural Killer cells and serum cytokine levels of interleukin-2, interleukin- 4, interleukin-6, interleukin-10, tumour necrosis factor-alpha and interferon gamma. They were correlated with disease severity. Data was analysed using SPSS 20. Of the 54 patients, 33(61.1%) were males and 21(38.9%) were females. There were 29(53.70%) patients in group A with median age 52 years (interquartile range: 43.5-65 years), and 25(46.29%) in group B with median age 50 years (interquartile range: 36.5-59 years) (p=0.241). Disease was significantly more severe in male patients compared to female (p=0.002). In group A, cluster of differentiation-3+ T cells were reduced in 21(72.4%) patients, cluster of differentiation-8+ T cells in 16(55.2%), cluster of differentiation-4+ T cells in 23(79.3%) and cluster of differentiation-19+ B cells in 8(27.6%). In group B, cluster of differentiation-3+ T cells were reduced in 10(40%) subjects, cluster of differentiation-8+ T cells in 7(28%), cluster of differentiation-4+ T cells in 12(48%) and cluster of differentiation-19+ B cells in 4(16%) patients. Serum cytokine levels were not significantly different between the groups (p>0.05). In group A, 7(24.13%) patients died, and in such cases, the neutrophil-to-lymphocytes ratio was significantly higher (p=0.037). Pro-inflammatory markers and cytokine levels increased, while lymphocyte subsets decreased with increasing severity of the disease.

Perception of Fomite Route of Transmission, Usage of Masks and Role of Saliva in coronavirus Disease-19 Infections: A Cross-sectional Survey among Dental Health Care Professionals in Saudi Arabia

Background: Coronavirus Disease-19 has been spreading globally with the rise of many variants after being declared as a pandemic on 11th March 2020. There is a lack of scientific literature focused on fomite transmission of COVID-19, especially the potential of saliva as a contributing factor in the spread and diagnosis of COVID-19 in dental healthcare practice. Hence, the aim was to comprehend the level of awareness of dental health care professionals/practitioners (DHCPs) about the role of fomite route of transmission and the role of saliva in Coronavirus Disease-19 (COVID-19) infections. Methods: An electronic questionnaire using Google Forms was circulated online after ethical approval and validation to dental health practitioners in Saudi Arabia, via emails and social media platforms. Results: Three hundred and eighty-nine responses were recorded. The female DHCPs had statistically significant awareness of the fomite route of transmission among various dental health professionals (p=0.04) and dental students, and dental interns had the maximum awareness (p&lt;0.05). The DHCPS preferred to learn and collect nasopharyngeal specimens by themselves for COVID-19 testing. Doctoral DHCPs had maximum awareness about WHO guidelines for social distancing, while dental nurses were more informed about infection control methods against COVID-19. Conclusion: DHCPs have adequate information about the fomite route of transmission and the role of saliva in COVID-19. Saliva specimen collection is specifically preferred for COVID-19 testing by dental assistants and hygienists for testing in the dental health center/clinic/university. The DHCPs and dental hygienists were less aware of the fomite route of transmission through asymptomatic COVID-19 infected patients.

455. Changing epidemiology of SARS-CoV-2 testing, positivity rates, and variant distribution in children and adults over multiple pandemic waves in New York City

Abstract Background Children and adults have had different experiences during the COVID-19 pandemic, especially in the context of new SARS-CoV-2 variants and changing vaccine eligibility. We aimed to compare the changing epidemiology of SARS-CoV-2 testing, positivity, and variants in adults versus children over multiple pandemic waves in a multi-hospital health system in New York City. Methods We analyzed SARS-CoV-2 RT-PCR testing data from 10/1/20 to 9/11/22 from children (0-21 years) and adults ( &amp;gt; 21 years) and compared positivity rates during 5 pandemic waves in New York City: Wave 2 (10/1/20-6/30/21), Wave 3 (7/1/21-12/1/21), Wave 4 (12/2/21-3/5/22), Wave 5 (3/6/22-6/12/22), and Wave 6 (6/13/22-9/11/22). The first test per patient per wave was included. If a patient had a positive test, the first positive test was included. Whole genome sequencing was performed on a subset of nasopharyngeal specimens with Ct values &amp;lt; 33 from 12/1/20 to 5/22/22. Results From 10/1/20 to 9/11/2022, 243,457 adults and 33,298 children were tested for SARS-CoV-2 with 15095 (6.2%) adults and 1961 (5.9%) children testing positive. Distribution of cases, positivity rates, and vaccine coverage over time are presented in Figure 1. Positivity rate was higher in adults compared to children in Wave 2 (adults 6.1%, children 4.5%, p&amp;lt; 0.001), similar in Wave 3 (adults 2.4%, children 2.2%, p = 0.2), higher in children in Wave 4 (adults 12%, children 16%, p&amp;lt; 0.001) and similar in Wave 5 (3.5%, 3.8%, p = 0.6) and Wave 6 (6.8%, 7.2%, p = 0.7). In Wave 4, the high positivity rate in children was driven by younger age groups, outpatient testing, and unvaccinated children (Figures 2-4). WGS of 1996 adult and 381 pediatric SARS-CoV-2 isolates demonstrated a mix of Alpha (13%), Iota (22%), and B lineages (61%) in Wave 2, predominance of Delta (87.4%) in Wave 3, predominance of Omicron (BA.1) (81%) in Wave 4, and predominance of BA.2 (84%) in Wave 5, with no difference in distribution between adults and pediatrics over time (Figure 5).Figure 1.Distribution of SARS-CoV-2 PCR testing, positive tests, positivity rate, and vaccination rate in children and adults. Number of tested and positive cases presented as daily case counts. Positivity rates presented as 14-day rolling averages. Due to low testing numbers, rolling average of pediatric positivity rate was excluded in Waves 5 and 6. Vaccination rates indicate daily proportion of patients with 2 or more vaccines doses.Figure 2.SARS-CoV-2 positivity rates in adults and children by pandemic wave and vaccine status.Positivity rates between fully vaccinated adults and children, and not fully vaccinated adults and children compared within each wave using Pearson’s Chi-squared test. Total number tested and positive for SARS-CoV-2 indicated in table. **p&amp;lt;0.01, ***p&amp;lt;0.001.Figure 3.SARS-CoV-2 positivity rates by age group and pandemic wave.Total number tested and positive for SARS-CoV-2 indicated in table. Conclusion Despite multiple wave-specific differences, SARS-CoV-2 variant distribution did not differ between adults and children over time. Additional work is indicated to understand if the difference in positivity rates is related to differences in immune response or exposure patterns between children and adults.Figure 4.SARS-CoV-2 positivity rates in adults and children by testing site.Total number tested and positive for SARS-CoV-2 indicated in table. ED, emergency department.Figure 5.Monthly distribution of SARS-CoV-2 variants in adults and children during Waves 2, 3, 4, and 5.Proportion of each SARS-CoV-2 variant in adults (red line) and children (blue line) over time. Variants indicated by WHO classification and include following Pango lineages: Delta (B.1.617.2, AY), Omicron (BA.1, BA.2), Alpha (B.1.1.7), Iota (B.1.526), B lineages (B.1/B1.1 lineages). The distribution of each variant was compared between adults and children over time using the Kolmogorov-Smirnov test. Disclosures Melissa Cushing, MD, Cerus Corporation: Advisor/Consultant|Haemonetics: Advisor/Consultant|Octapharma: Advisor/Consultant

Predictive value of methicillin-resistant staphylococcus aureus nasal swab in patients with COVID-19 pneumonia and secondary bacterial pneumonia

ObjectiveTo determine the performance measures of admission methicillin-resistant Staphylococcus aureus (MRSA) nasal swabs for MRSA bacterial pneumonia in patients co-infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). MethodsThe study included patients admitted with SARS-CoV-2-positive nasopharyngeal specimens, MRSA nasal screens, and bacterial cultures to assess secondary MRSA pneumonia. Results293 patients and 662 microbiological cultures evaluated. Overall, the specificity (91.8% [95% CI 88.6% to 95%]) and negative predictive value (NPV 97.4% [95% CI 95.4% – 99.3%]) of MRSA nasal swabs was high. However, the sensitivity (46.2%; 95% CI 19.1% to 73.3%) and positive predictive value (PPV 20.7%; 95% CI 59.5 – 35.4%) were low. Those patients in the MRSA nasal swab negative group had a shorter median duration of linezolid therapy. ConclusionsSARS-CoV-2 infection doesn't reduce the specificity or negative predictive value of MRSA nasal swabs for secondary MRSA pneumonia.

Clinical and Laboratory Diagnosis of Exanthems Among Japanese Children Younger Than 6 Years Old in the Post-Measles-Rubella Vaccine Era.

Exanthems are a common reason for visits to the pediatric emergency department. However, epidemiological data in the post-measles-rubella vaccine era is limited. We sought to determine the recent causes of exanthems in children younger than 6 years old in the pediatric emergency department. A prospective single-center study was conducted in Japan from August 2019 to March 2020. Children younger than 6 years old with exanthems were enrolled. Exanthems were classified into 7 morphological patterns. Varicella, herpes zoster, impetigo, urticaria and Kawasaki disease were diagnosed clinically. Nasopharyngeal swab specimens were collected from patients with nonspecific exanthems and evaluated by polymerase chain reaction (PCR) assays capable of detecting 24 pathogens. The final diagnosis was made by discussion of 3 physicians based on clinical course and microbiology. There were 9705 pediatric visits, of which 296 (3%) had exanthems and were younger than 6 years old. Clinical diagnosis was possible for 160 (54%), including urticaria in 110 (37%), Kawasaki disease in 29 (10%), impetigo in 10 (3%), varicella or herpes zoster in 7 (2%) and group A Streptococcus in 4 (1%). Among the remaining 136 (46%) children, 75 (25%) underwent testing by PCR. One or more pathogens were detected in 49 (65%), specifically enterovirus in 14 (19%), cytomegalovirus in 13 (17%), human herpesvirus type-6 in 12 (16%), adenovirus in 11 (15%) and human herpesvirus type-7 in 8 (11%). Final infectious disease diagnoses were roseola infantum in 11 (15%), enterovirus in 9 (12%), adenovirus in 6 (8%), mixed virus infection in 5 (7%), group A Streptococcus in 3 (4%), parechovirus-A in 3 (4%) and influenza in 3 (4%). The most common causes of pediatric exanthems were noninfectious diseases and viral exanthema. PCR assay was instrumental for etiological diagnosis of nonspecific exanthems.

Clinical and molecular characteristics of the 2022 Enterovirus-D68 outbreak among hospitalized children, Ohio, USA

BackgroundEnterovirus-D68 (EV-D68) has appeared biennially in the United States following the 2014 outbreak. It has gained epidemiologic and clinical relevance and was identified as an important pathogen associated with severe respiratory and central nervous system diseases. We aim to describe the clinical and molecular characteristics of the post-pandemic 2022 Enterovirus-D68 outbreak in children evaluated in a tertiary pediatric hospital in Columbus, Ohio. MethodsEV-D68 RT-PCR was performed on nasopharyngeal specimens collected during Jun—Nov 2022 from children (<18 years), identified by 1) physician-order or 2) random selection of 10–15 specimens weekly that were Rhinovirus/Enterovirus-positive by physician-ordered respiratory virus panel. Patients who tested positive for EV-D68 were identified and clinical data and outcomes were analyzed. Partial viral VP1 region was sequenced and characterized. ResultsForty-four children positive for EV-D68 were identified, among which 88.6 % of patients presented with respiratory symptoms and 61.4 % required PICU admission. Two patients presented with AFM that was attributed to EV-D68. EV-D68 sequences from 2022 clustered within the B3 subclade. ConclusionsA significant proportion of children identified with EV-D68 during the 2022 outbreak had respiratory compromise requiring PICU admission. As the virus continues evolving, it is important to monitor the activity of EV-D68, characterizing these strains clinically and genetically, which will help to understand the viral pathogenicity and virulence.

Performance evaluation of the cobas SARS-CoV-2 Duo, a novel qualitative and quantitative assay, for the detection of SARS-CoV-2 RNA.

Viral load quantification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a critical measure for monitoring clinical responses of patients with COVID-19. The cobas SARS-CoV-2 Duo (Roche Molecular Systems, Inc.) uses the cobas 6800/8800 platform and is an automated real-time reverse transcription PCR (RT-PCR) assay for the qualitative detection of SARS-CoV-2 RNA (ORF1a and ORF1a/b non-structural regions) in nasal and nasopharyngeal specimens. This assay also performs quantitation of the SARS-CoV-2 RNA level in the collected specimen. The precision, accuracy, and linearity of the cobas SARS-CoV-2 Duo test were assessed and correlated with the cycle threshold (Ct) value of the cobas SARS-CoV-2 assay, and the cobas Liat SARS-CoV-2 and influenza A/B assay (Inf A/B) (cobas Liat) in 201 clinical nasopharyngeal swab specimens. The analytical measurement range of the cobas SARS-CoV-2 Duo has been verified to be 1.0E + 02 IU/mL to 1.0E + 09 IU/mL. The between- and within-run precision evaluation and the linearity results (R 2 = 0.9961) of the cobas SARS-CoV-2 Duo were acceptable based on the verification criteria. A total of 201 nasopharyngeal specimens were evaluated. The positive, negative, and total agreements between the cobas SARS-CoV-2 Duo and the cobas SARS-CoV-2 assay were 93.5% (157 of 168), 75% (33 of 44), and 92.5% (186 of 201), respectively. The qualitative results (Ct values) from the cobas SARS-CoV-2 and the cobas Liat demonstrated good agreement with the quantitative results from the cobas SARS-CoV-2 Duo assay. In conclusion, the diagnostic performance of the cobas SARS-CoV-2 Duo assay is appropriate. It is a precise, accurate, and sensitive method for the detection of SARS-CoV-2 RNA and is comparable to two qualitative assays. IMPORTANCE Quantitative SARS-CoV-2 tests for viral load are necessary to guide patient treatment, as well as to determine infection control measures and policies. Although the real-time RT-PCR assays can report the Ct value to estimate the viral load, there are several serious concerns regarding the use of Ct values. Importantly, Ct values can vary significantly among between- and within-run methods. The diagnostic performance of the cobas SARS-CoV-2 Duo is appropriate. It is a precise, accurate, and sensitive method for the detection of SARS-CoV-2 RNA and is comparable to two qualitative assays (the cobas SARS-CoV-2 and the Liat cobas SARS-CoV-2 and Inf A/B). In contrast, using the Ct value to estimate viral load is not reliable, and utilization of a quantitative detection test, such as the cobas SARS-CoV-2 Duo, to accurately measure the viral load is needed.

Tracking severe acute respiratory syndrome coronavirus 2 transmission and co-infection with other acute respiratory pathogens using a sentinel surveillance system in Rift Valley, Kenya.

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been the most significant public health challenge in over a century. SARS-CoV-2 has infected over 765 million people worldwide, resulting in over 6.9 million deaths. This study aimed to detect community transmission of SARS-CoV-2 and monitor the co-circulation of SARS-CoV-2 with other acute respiratory pathogens in Rift Valley, Kenya. We conducted a cross-sectional active sentinel surveillance for the SARS-CoV-2 virus among patients with acute respiratory infections at four sites in Rift Valley from January 2022 to December 2022. One thousand two hundred seventy-one patients aged between 3 years and 98 years presenting with influenza-like illness (ILI) were recruited into the study. Nasopharyngeal swab specimens from all study participants were screened using a reverse transcription-quantitative polymerase chain reaction (RT-qPCR) for SARS-CoV-2, influenza A, influenza B and respiratory syncytial virus (RSV). The samples that tested positive for influenza A (n = 73) and RSV (n = 12) were subtyped, while SARS-CoV-2 (n = 177) positive samples were further screened for 12 viral and seven bacterial respiratory pathogens. We had a prevalence of 13.9% for SARS-CoV-2, 5.7% for influenza A, 2% for influenza B and 1% for RSV. Influenza A-H1pdm09 and RSV B were the most dominant circulating subtypes of influenza A and RSV, respectively. The most common co-infecting pathogens were Streptococcus pneumoniae (n = 29) and Haemophilus influenzae (n = 19), accounting for 16.4% and 10.7% of all the SARS-CoV-2 positive samples. Augmenting syndromic testing in acute respiratory infections (ARIs) surveillance is crucial to inform evidence-based clinical and public health interventions.

Clinical comparison of three SARS-CoV-2 nucleic acid amplification tests for routine diagnostic testing

BackgroundCycle threshold (Ct) values from SARS-CoV-2 nucleic acid amplification tests have been used to estimate viral load for treatment decisions. Additionally, there is a need for high-throughput testing, consolidating a variety of assays on one random-access analyzer. ObjectivesIn this study, the clinical performance of the Alinity m SARS-CoV-2, RealTime SARS-CoV-2, and GeneXpert Xpress SARS-CoV-2/Flu/RSV assays was assessed. MethodsAlinity precision and detection rates were evaluated using a dilution series of the Alinity m SARS-CoV-2 positive control. In a retrospective study, 7 remnant external quality assessment (EQA) specimens and 200 remnant nasopharyngeal swab specimens (100 positive and 100 negative) were tested in the three assays. ResultsAlinity had 100 % detection rate at 50 copies/mL and high reproducibility (Ct value coefficient of variation ≤3.1 %). All three assays correctly detected positive and negative EQA samples with comparable Ct values (max difference 2.38) and high linearity. In patient samples, positive percent agreement was 95 % (95 % CI 89–98 %) and negative percent agreement was 100 % (95 % CI 96–100 %) for Alinity, compared to the other two assays. Four specimens detected on Alinity m but not RealTime or Xpert had Ct values above 40. Assay results were highly correlated (r ≥ 0.94). Ct values (after addition of 10 unread cycles to the reported Ct of RealTime) were comparable across the three assays. ConclusionsAlinity m had high precision and accuracy and Ct values comparable to those of the RealTime and Xpert assays. The assays could be used interchangeably, with no need for adjustment of patient management decisions based on Ct values from each assay.

Multi-center clinical evaluation of the Panther Fusion SARS-CoV-2/Flu A/B/RSV assay in nasopharyngeal swab specimens from symptomatic individuals.

The symptomology is overlapping for respiratory infections due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), influenza A/B viruses, and respiratory syncytial virus (RSV). Accurate detection is essential for proper medical management decisions. This study evaluated the clinical performance of the Panther Fusion SARS-CoV-2/Flu A/B/RSV assay in nasopharyngeal swab (NPS) specimens from individuals of all ages with signs and symptoms of respiratory infection consistent with COVID-19, influenza, or RSV. Retrospective known-positive and prospectively obtained residual NPS specimens were collected during two respiratory seasons in the USA. Clinical performance was established by comparing Panther Fusion SARS-CoV-2/Flu assay results to a three-molecular assay composite comparator interpretation for SARS-CoV-2 and to the FDA-cleared Panther Fusion Flu A/B/RSV assay results for all non-SARS-CoV-2 targets. A total of 1,900 prospective and 95 retrospective NPS specimens were included in the analyses. The overall prevalence in prospectively obtained specimens was 20.7% for SARS-CoV-2, 6.7% for influenza A, and 0.7% for RSV; all influenza B-positive specimens were retrospective specimens. The positive percent agreement of the Panther Fusion assay was 96.9% (378/390) for SARS-CoV-2, 98.0% (121/123) for influenza A virus, 95.2% (20/21) for influenza B virus, and 96.6% (57/59) for RSV. The negative percent agreement was ≥98.5% for all target viruses. Specimens with discordant Panther Fusion SARS/Flu/RSV assay results all had cycle threshold values of ≥32.4 (by comparator or by Panther Fusion SARS/Flu/RSV assay). Only five co-infections were detected in the study specimens. The Panther Fusion SARS-CoV-2/Flu/RSV assay provides highly sensitive and specific detection of SARS-CoV-2, influenza A virus, influenza B virus, and RSV in NPS specimens.

Microbiological characterization of Pneumocystis jirovecii pneumonia using quantitative PCR from nasopharyngeal specimens: a retrospective study in a Canadian province from 2019 to 2023.

Bronchoalveolar lavage is usually employed for molecular diagnosis of Pneumocystis jirovecii but requires a specialized procedure. By contrast, nasopharyngeal (NP) specimens are easily obtained. In this retrospective study of 35 patients with paired NP and bronchoscopy specimens, NP specimens had a 100% negative percent agreement (95% CI 80.5-100) but only 72.2% positive percent agreement (95% CI 46.5-90.3).

Elevated A-to-I RNA editing in COVID-19 infected individuals.

Given the current status of coronavirus disease 2019 (COVID-19) as a global pandemic, it is of high priority to gain a deeper understanding of the disease's development and how the virus impacts its host. Adenosine (A)-to-Inosine (I) RNA editing is a post-transcriptional modification, catalyzed by the ADAR family of enzymes, that can be considered part of the inherent cellular defense mechanism as it affects the innate immune response in a complex manner. It was previously reported that various viruses could interact with the host's ADAR enzymes, resulting in epigenetic changes both to the virus and the host. Here, we analyze RNA-seq of nasopharyngeal swab specimens as well as whole-blood samples of COVID-19 infected individuals and show a significant elevation in the global RNA editing activity in COVID-19 compared to healthy controls. We also detect specific coding sites that exhibit higher editing activity. We further show that the increment in editing activity during the disease is temporary and returns to baseline shortly after the symptomatic period. These significant epigenetic changes may contribute to the immune system response and affect adverse outcomes seen in post-viral cases.

Multicenter evaluation of the Acaruiter Respiratory Panel for diagnosis of respiratory tract infections in Chinese children.

Respiratory tract infection represents the most frequent infectious disease afflicting children worldwide. This study was to evaluate the performance of Acaruiter Respiratory Panel (fluorescent PCR) in the detection of respiratory tract infection pathogens in children. Clinical trials were conducted in three representative pediatric hospitals in Shanghai, Chengdu, and Beijing. With reference to another widely used multiplex assay and first-generation sequencing, the sensitivity, specificity, accuracy, and consistency coefficient kappa (κ) value of the assay were evaluated to verify the accuracy and effectiveness in the detection of clinical respiratory pathogens, so as to objectively evaluate the clinical performance and application value of Acaruiter Respiratory Panel (fluorescent PCR). A total of 1,540 samples were screened in this clinical trial project, of which 1,404 were valid samples. Based on the comprehensive analysis of the clinical trial data of 1,404 effective samples, the detection ability of Acaruiter Respiratory Panel (fluorescent PCR) for various pathogens compared with the results of clinical diagnosis, the positive percent agreement was 97.04%-100%, the negative percent agreement was 99.31%-100%, the total percent agreement was 99.36%-100%, and the kappa value was 0.982-1.000, which had good consistency and high accuracy.IMPORTANCECompared to multiplex PCR assays that are available in the Chinese market, the Acaruiter Respiratory Panel (fluorescent PCR) covers a wider range of pathogens including eight viruses, five bacteria, Mycoplasma pneumoniae and Chlamydia pneumoniae, and has high accuracy and effectiveness in the detection of pathogens. This is the first study to evaluate the performance of the Acaruiter Respiratory Panel. This regent may be a promising assay for comprehensive testing for respiratory pathogens from nasopharyngeal swab specimens in Chinese children.

Comparison of the safety, effectiveness, and usability of swab robot vs. manual nasopharyngeal specimen collection

BackgroundHealthcare workers face a risk of infection during aerosol-generating procedures, such as nasal swabbing. Robot-assisted nasopharyngeal sampling aims to minimize this risk and reduce stress for healthcare providers. However, its effectiveness and safety require validation. MethodsWe conducted a controlled trial with 80 subjects at two teaching hospitals and compared robot-collected vs manually-collected nasopharyngeal swabs. The primary outcomes included specimen quality and success rate of nasopharyngeal swab collection. We also recorded the pain index, duration of the collection, and psychological stress using a post-collection questionnaire. ResultsDuring the study period, from September 23 to October 27, 2020, 40 subjects were enrolled in both the robotic and manual groups. The cycle threshold (Ct) value for nasopharyngeal specimens was statistically higher in the robotic group compared to the manual group (30.9 vs 28.0, p < 0.01). Both groups had Ct values under 35, indicating good quality specimens. In the robotic group, 3 out of 40 subjects required a second attempt at specimen collection, resulting in a success rate of 92.5 %. Further, although the pain levels were lower in the robotic group, the difference was not statistically significant (2.8 vs 3.6, p = 0.07). The manual group had a shorter sampling time, which was 29 s (201 vs 29, p < 0.05). However, when factoring in the time needed to put on personal protective equipment, the average time for the manual group increased to 251 s (201 vs 251, p < 0.05). Participants' questionnaire results show comparable psychological stress in both groups. Medical staff expressed that using a robot would reduce their psychological stress. ConclusionsWe propose a safe and effective robotic technology for collecting nasopharyngeal specimens without face-to-face contact, which may reduce the stress of physicians and nurses. This technology can also be optimized for efficiency, making it useful in situations where droplet-transmitted infectious diseases are a concern.