Nasopharyngeal Swab Specimens Research Articles

Impact of admission viral load on respiratory outcomes in hospitalized SARS-CoV-2 infected patients with cancer and without cancer: A 2-, 4- and 6-months follow-up prospective study

BackgroundThis prospective follow-up study aimed to determine the temporal changes in respiratory outcomes over 6 months period in patients with and without cancer hospitalized for severe COVID-19 and to determine the associated risk factors based on admission viral load. MethodsAll adult patients hospitalized with a confirmed diagnosis of severe SARS-CoV-2 infection were investigated using rRT-PCR on nasopharyngeal swab specimens. Patients were divided into three arbitrary groups according to their cycle threshold (CT) values obtained at admission as high (CT<25.0), medium (CT between 25.0 and 30.0), and low (CT>30.0) viral load. Patients had pulmonary function tests, chest high-resolution computed tomography (HRCT), and a 6-minute walking time distance measured at each follow-up visit. ResultsThis follow-up study had a total of 112 participants, of which 75 were cancer-free and 37 had active cancer. Overall, 29.5% had a low viral load, compared to 48.2% who had a high viral load, and 22.3% had a medium viral load. For patients who did not have cancer, the mean age was 57.3 (SD 15.4) and for those who had cancer, it was 62.3 (SD 18.4). Most patients had overall better temporal changes in pulmonary function and tolerance, as well as exercise capacity, even though severe and chronic respiratory abnormalities persisted in a fraction of the patients. In patients without cancer who had a high viral load, we have seen a substantial reduction in diffusion capacity of the lungs for carbon monoxide (DLCO) predicted value with a median of 65 (IQR 63–70) while in patients with cancer, it was 60 (IQR 56–67) at 2 months. At 4 and 6 months, the predicted DLCO values for patients without cancer were 65 (IQR 61–70), whereas the predicted DLCO values for patients with active cancer were 62 (IQR 60–67) and 67 (59−73). Importantly, radiological abnormalities persisted in 22 (29%) non-cancer patients and 16 (43%) cancer patients. Multivariate regression analysis showed an increased odds ratio of impaired HRCT associated with a high viral load of 3.04 (95% CI:1.68–6.14; p < 0.001) for patients without cancer and 5.07 (95% CI: 4.04–10.8; p < 0.0001) for patients with cancer. The CT pneumonia score at hospitalization was 2.25 (95% CI:1.76–3.08; p = 0.041) and 2.85 (95% CI:1.89–5.14; p = 0.031) for non-cancer and cancer patients respectively. ConclusionsThe evidence of persistent pulmonary abnormalities and radiographic changes was found in both patient groups who had high viral load at hospital admission and suggesting that SARS-CoV-2 viral load might serve as a useful indicator to predict the development of respiratory complications in patients with COVID-19.

Higher SARS-CoV-2 detection of oropharyngeal compared with nasopharyngeal or saliva specimen for molecular testing: a multicentre randomised comparative accuracy study

BackgroundTesting is critical for detecting SARS-CoV-2 infection, but the best sampling method remains unclear.ObjectivesTo determine whether nasopharyngeal swab (NPS), oropharyngeal swab (OPS) or saliva specimen collection has the highest detection...

Genes Involved in miRNA Biogenesis Are Not Downregulated in SARS-CoV-2 Infection.

miRNAs, small non-coding RNAs that regulate gene expression, are involved in various pathological processes, including viral infections. Virus infections may interfere with the miRNA pathway through the inhibition of genes involved in miRNA biogenesis. A reduction in the number and the levels of miRNAs expressed in nasopharyngeal swabs of patients with severe COVID-19 was lately observed by us, pointing towards the potential of miRNAs as possible diagnostic or prognostic biomarkers for predicting outcomes among patients with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. The objective of the present study was to investigate whether SARS-CoV-2 infection influences the expression levels of messenger RNAs (mRNAs) of key genes involved in miRNA biogenesis. mRNA levels of AGO2, DICER1, DGCR8, DROSHA, and Exportin-5 (XPO5) were measured by quantitative reverse-transcription polymerase chain reaction (RT-qPCR) in nasopharyngeal swab specimens from patients with COVID-19 and controls, as well as in cells infected with SARS-CoV-2 in vitro. Our data showed that the mRNA expression levels of AGO2, DICER1, DGCR8, DROSHA, and XPO5 were not significantly different in patients with severe COVID-19 when compared to patients with non-severe COVID-19 and controls. Similarly, the mRNA expression of these genes was not affected by SARS-CoV-2 infection in NHBE and Calu-3 cells. However, in Vero E6 cells, AGO2, DICER1, DGCR8, and XPO5 mRNA levels were slightly upregulated 24 h after infection with SARS-CoV-2. In conclusion, we did not find evidence for downregulation of mRNA levels of miRNA biogenesis genes during SARS-CoV-2 infection, neither ex vivo nor in vitro.

Sensitivity of nasopharyngeal swab and saliva specimens in the detection of SARS-CoV-2 virus among boarding school girls

With the reopening of schools, the detection of coronavirus disease 2019 (COVID-19) in children is very important in order to prevent outbreaks in schools and to reduce the risk of more severe post-COVID-19 complications. Various specimens can be used to detect the SARS-CoV-2 virus, and saliva has been considered as an alternative specimen in adults. However, data in children are lacking, especially among the female population. This study compared the efficacy of saliva specimens with nasopharyngeal swab specimens for the detection of severe acute respiratory syndrome coronavirus-2 using reverse transcriptase polymerase chain reaction. This study evaluated the diagnostic performance of saliva among boarding school girls at three time points: diagnosis, and days 7 and 14 since first confirmation using a nasopharyngeal swab specimen. Eighty-four paired samples from 36 individuals were compared. Nasopharyngeal samplings were carried out by trained health officers, while saliva samplings were performed independently by children. The overall percentage agreement (OPA) between saliva and nasopharyngeal swabs was 50.2%. The OPA was 52.8% at diagnosis, and this increased slightly to 54.2% at day 7, and subsequently decreased to 45.8% at day 14. Saliva specimens had sensitivity of 44.6%, specificity of 80.0%, positive predictive value of 94.2% and negative predictive value of 16.3% compared with nasopharyngeal swab specimens for the diagnosis of COVID-19. The use of saliva as an alternative specimen for the diagnosis of COVID-19 in children should be considered carefully. Thorough sampling instructions should be given in order to minimize bias in the findings.

Use of saliva as an alternative diagnostic method for diagnosis of COVID-19

Mass population testing has been recommended to contain the spread of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. However, the use of nasopharyngeal swab specimens has caused many logistic challenges. This study investigated the sensitivity and specificity of saliva as a non-invasively-obtained specimen for molecular detection of SARS-CoV-2 RNA. In total, 153 patients with confirmed coronavirus disease 2019 (COVID-19) who had been admitted to the regional referral hospital or who self-isolated at home were included in this study. Nasopharyngeal swab specimens and saliva samples were collected on the same day, and were tested for SARS-CoV-2 infection using reverse transcriptase polymerase chain reaction. The sensitivity and specificity of saliva samples were 81.5% and 76.4%, respectively, in cases that had been confirmed as COVID-19 using nasopharyngeal swab samples. Positive predictive values and negative predictive values were 92.3% and 54.1%, respectively. The highest detection rates were found among samples collected 4-7 days since symptom onset. Saliva samples showed comparable performance to nasopharyngeal swab specimens for the diagnosis of COVID-19 in adults. The performance of saliva as a diagnostic specimen for COVID-19 testing is particularly significant during the first week of symptoms.

Investigation of Blood Plasma Viral Nucleocapsid Antigen as a Marker of Active Severe Acute Respiratory Syndrome Coronavirus 2 Omicron Variant Infection.

Nasopharyngeal qualitative reverse-transcription polymerase chain reaction (RT-PCR) is the gold standard for diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, but it is not practical or sufficient in every clinical scenario due to its inability to distinguish active from resolved infection. Alternative or adjunct testing may be needed to guide isolation precautions and treatment in patients admitted to the hospital. We performed a single-center, retrospective analysis of residual clinical specimens and medical record data to examine blood plasma nucleocapsid antigen as a candidate biomarker of active SARS-CoV-2. Adult patients admitted to the hospital or presenting to the emergency department with SARS-CoV-2 ribonucleic acid (RNA) detected by RT-PCR from a nasopharyngeal swab specimen were included. Both nasopharyngeal swab and a paired whole blood sample were required to be available for analysis. Fifty-four patients were included. Eight patients had positive nasopharyngeal swab virus cultures, 7 of whom (87.5%) had concurrent antigenemia. Nineteen (79.2%) of 24 patients with detectable subgenomic RNA and 20 (80.0%) of 25 patients with N2 RT-PCR cycle threshold ≤ 33 had antigenemia. Most individuals with active SARS-CoV-2 infection are likely to have concurrent antigenemia, but there may be some individuals with active infection in whom antigenemia is not detectable. The potential for high sensitivity and convenience of a blood test prompts interest in further investigation as a screening tool to reduce reliance on nasopharyngeal swab sampling and as an adjunct diagnostic test to aid in clinical decision making during the period after acute coronavirus disease 2019.

Dry loop-mediated isothermal amplification assay for detection of SARS-CoV-2 from clinical specimens.

To establish a point-of-care test for coronavirus disease 2019 (COVID-19), we developed a dry loop-mediated isothermal amplification (LAMP) method to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA. We carried out reverse transcription (RT)-LAMP using the Loopamp SARS-CoV-2 Detection kit (Eiken Chemical, Tokyo, Japan). The entire mixture, except for the primers, is dried and immobilized inside the tube lid. To determine the specificity of the kit, 22 viruses associated with respiratory infections, including SARS-CoV-2, were tested. The sensitivity of this assay, determined by either a real-time turbidity assay or colorimetric change of the reaction mixture, as evaluated by the naked eye or under illumination with ultraviolet light, was 10 copies/reaction. No LAMP product was detected in reactions performed with RNA from any pathogens other than SARS-CoV-2. After completing an initial validation analysis, we analyzed 24 nasopharyngeal swab specimens collected from patients suspected to have COVID-19. Of the 24 samples, 19 (79.2%) were determined by real-time RT-PCR analysis as being positive for SARS-CoV-2 RNA. Using the Loopamp SARS-CoV-2 Detection kit, we detected SARS-CoV-2 RNA in 15 (62.5%) of the 24 samples. Thus, the sensitivity, specificity, positive predictive value, and negative predictive values of the Loopamp 2019-CoV-2 detection reagent kit were 78.9%, 100%, 100%, and 55.6%, respectively. The dry LAMP method for detecting SARS-CoV-2 RNA is fast and easy to use, and its reagents can be stored at 4°C, solving the cold chain problem; thus, it represents a promising tool for COVID-19 diagnosis in developing countries.

Diagnostic Performance and Tolerability of Saliva and Nasopharyngeal Swab Specimens in the Detection of SARS-CoV-2 by RT-PCR.

Saliva is a promising alternative for a nasopharyngeal swab (NPS) in specimen collection to detect SARS-CoV-2. We compared the diagnostic performance and tolerability of saliva collection versus NPS in a clinical setting. Paired NPS and saliva specimens were collected sequentially from participants (n = 250) at the Turku University Hospital drive-in coronavirus testing station in the spring of 2022, with Omicron BA.2 as the dominant SARS-CoV-2 variant. Discomfort and preference for the sampling method were assessed. The specimens were analyzed for SARS-CoV-2 using real-time multiplex reverse transcriptase PCR (RT-PCR) with a laboratory-developed test (LDT) and two commercial kits (PerkinElmer SARS-CoV-2 and PerkinElmer SARS-CoV-2 Plus) for several target genes. Among the 250 participants, 246 had respiratory symptoms. With LDT, SARS-CoV-2 was detected in 135 and 134 participants from NPS and saliva, respectively. Of the 250 specimens, 11 gave a discordant outcome, resulting in excellent agreement between the specimen types (Cohen's kappa coefficient of 0.911; P = 0.763). The cycle threshold (CT) values of LDT and commercial kit target genes were significantly lower from NPS than from saliva. A total of 172 (69%) participants assessed saliva sampling as more tolerable than NPS (P < 0.0001). Our findings present saliva as an applicable alternative for SARS-CoV-2 diagnostics. However, the lower CT values obtained from NPS indicate that NPS may be a slightly more sensitive specimen type. Participants preferred saliva sampling, although delivering an adequate volume of saliva was challenging for some participants. IMPORTANCE The extensive testing of SARS-CoV-2 is vital in controlling the spread of COVID-19. The reference standard for specimen collection is a nasopharyngeal swab (NPS). However, the discomfort of NPS sampling, the risk of nosocomial infections, and global material shortages have accelerated the development of alternative testing methods. Our study demonstrates that patients tolerate saliva sampling better than NPS. Of importance, although the RT-PCR qualitative test results seem to correspond between NPS and saliva, we show significantly lower CT values for NPS, compared to saliva, thus contradicting the suggested superiority of the saliva specimen over NPS in the detection of the Omicron variants of SARS-CoV-2. Future research is still required to enable individual planning for specimen collection and to determine the effects of different SARS-CoV-2 variants on the sensitivity of the saliva matrix.

Evaluation of the AdvanSure One-Stop COVID-19 Plus Kit for SARS-CoV-2 Detection Using a Streamlined RNA Extraction Method.

Real-time reverse transcription (rRT)-PCR, which is the reference standard for the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, generally involves a time-consuming and costly RNA extraction step prior to amplification. We evaluated the performance of the AdvanSure One-Stop COVID-19 Plus Kit (LG Chem, Seoul, Korea), a novel rRT-PCR assay that can detect SARS-CoV-2 within 90 minutes using a streamlined RNA extraction method. In total, 509 nasopharyngeal swab (NPS) specimens (SARS-CoV-2 positive: N=205; SARS-CoV-2 negative: N=304) previously tested using the PowerChek SARS-CoV-2 Real-time PCR Kit (Kogene Biotech, Seoul, Korea) were tested using the AdvanSure assay. The limit of detection (LOD) of the AdvanSure assay was determined using serially diluted inactivated SARS-CoV-2. The positive and negative percent agreements between the AdvanSure and PowerChek assays were 99.5% (204/205) and 99.3% (302/304), respectively. The LODs of the AdvanSure assay for SARS-CoV-2 nucleocapsid and spike/RNA-dependent RNA polymerase genes were 672 and 846 copies/mL, respectively. The results show that the performance of the AdvanSure assay is comparable to that of the PowerChek assay used for routine SARS-CoV-2 testing, suggesting that the AdvanSure assay is a useful diagnostic tool for rapid and accurate detection of SARS-CoV-2 infection.

Evaluation of saliva and nasopharyngeal swab sampling for genomic detection of SARS-CoV-2 in children accessing a pediatric emergency department during the second pandemic wave.

SARS-CoV-2 infection is mainly detected by multiplex real-time RT-PCR from upper respiratory specimens, which is considered the gold-standard technique for SARS-CoV-2 infection diagnosis. A nasopharyngeal (NP) swab represents the clinical sample of choice, but NP swabbing can be uncomfortable to the patients, especially for pediatric-age participants, requires trained healthcare personnel, and may generate an aerosol, increasing the intrinsic exposure risk of healthcare workers. The objective of this study was to compare paired NP and saliva samples (SS) collected from pediatric patients to evaluate whether the saliva collection procedure may be considered a valuable alternative to the classical NP swab (NPS) sampling in children. In this study, we describe a SARS-CoV-2 multiplex real-time RT-PCR protocol for SS, comparing the results with the paired NPS specimens from 256 pediatric patients (mean age 4.24 ± 4.40 years) admitted to the hospital emergency room of Azienda Ospedaliera Universitaria Integrata (AOUI), Verona, and randomly enrolled between September 2020 and December 2020. The saliva sampling demonstrated consistent results when compared to NPS use. The SARS-CoV-2 genome was detected in 16 out of 256 (6.25%) NP samples, among which 13 (5.07%) were positive even when paired SS were analyzed. Moreover, SARS-CoV-2-negative NPS and SS were consistent, and the overall concordances between NPS and SS were detected in 253 out of 256 samples (98.83%). Our results suggest that saliva samples may be considered a valuable alternative to NPS for SARS-CoV-2 direct diagnosis with multiplex real-time RT-PCR in pediatric patients.

Comparison of Real-time RT-PCR cycle threshold (Ct) values with clinical features and severity of COVID-19 disease among hospitalized patients in the first and second waves of COVID-19 pandemic in Chennai, India

IntroductionReal-time reverse transcriptase-polymerase chain reaction (rRT-PCR) of nasopharyngeal/ oropharyngeal swab has been the gold standard test for detection of SARS-CoV-2 infection The relationship between cycle threshold (Ct) values of rRT-PCR and severity of disease remain disputable and not clearly defined in COVID-19. MethodologyThis is a single-centered retrospective observational study conducted at Government Corona Hospital (GCH), Guindy, Chennai. In the present study, we compared the Ct value of rRT-PCR from nasopharyngeal swab specimens with a diverse range of symptoms and disease severity among 240 individuals who were hospitalized with COVID-19, viz., mild cases (MC; n = 160), moderately severe cases (MSC; n = 46) and severe cases (SC; n = 34) in the first and second waves of COVID-19 pandemic. ResultsThe study included 240 hospitalized COVID-19 patients with a median age of 52 years (range 21 to 90 years). MC, MSC, and SC all had median Ct values of 25.0 (interquartile range – IQR 20.0 to 30.5), 29.5 (IQR 23.0 to 34.0), and 29.0 (IQR 24 to 37.5) for the ORF1ab gene. The Ct value differed significantly between mild vs moderate, and mild vs severe cases. The Ct value of SC group with co-morbidity of type 2 diabetes have a significant difference compared to non-diabetes group (p value <0.05). There was a significant difference in the median Ct value of ORF1ab gene among the MSC group and MC but not in the SC group in the first and second waves of the pandemic (p<0.05). ConclusionWe conclude that SARS-CoV-2 Ct values of rRT-PCR alone does not have a role in aiding severity stratification among patients with COVID-19 since the viral dynamics and Ct value may vary due to the emerging variants that occur in different waves of the pandemic.

Evaluate the Sars- Cov-2 diagnostic value of quantitative antigen test

One of the most successful strategies to halt the spread of the COVID-19 pandemic is to quickly screen by testing to identify infected individuals, leading to effectively isolating patients. However, in order to ensure the test's value, the diagnostic value must be thoroughly analyzed before using it. In this research, we used a cross-sectional descriptive study to evaluate the diagnostic efficacy of the Lumipulse G SARS-COV-2 Ag test on salivary and nasopharyngeal swab specimens. The results showed that at the manufacturer's recommended cut-off of 0.67 pg/mL, the sensitivity and specificity were 70.00% and 68.87% on saliva samples, respectively. The test's sensitivity and specificity for nasopharyngeal swab samples were 100% and 95.9%, respectively, at the 1.34 pg/mL cut-off, and it could achieve high sensitivity of 99.4% and specificity of 99.3% at the cut-off value of 17.66 pg/mL. With nasopharyngeal swab samples, we found that the Lumipulse G SARS-COV-2 Ag test achieved the WHO testing standards for the diagnosis and screening of COVID-19. The sensitive diagnostic of this test in nasopharyngeal swab samples is high even the viral load is low and higher than in saliva swab samples.

Population-level median cycle threshold (Ct) values for asymptomatic COVID-19 cases can predict the trajectory of future cases.

Recent studies indicate that the population-level SARS-CoV-2 cycle threshold (Ct) values can inform the trajectory of the pandemic. The presented study investigates the potential of Ct values in predicting the future of COVID-19 cases. We also determined whether the presence of symptoms could change the correlation between Ct values and future cases. We examined the individuals (n = 8660) that consulted different sample collection points of a private diagnostic center in Pakistan for COVID-19 testing between June 2020 and December 2021. The medical assistant collected clinical and demographic information. The nasopharyngeal swab specimens were taken from the study participants and real-time reverse transcriptase polymerase chain reaction (RT-PCR) was used to detect SARS-CoV-2 in these samples. We observed that median Ct values display significant temporal variations, which show an inverse relationship with future cases. The monthly overall median Ct values negatively correlated with the number of cases occurring one month after specimen collection (r = -0.588, p <0.05). When separately analyzed, Ct values for symptomatic cases displayed a weak negative correlation (r = -0.167, p<0.05), while Ct values from asymptomatic cases displayed a stronger negative correlation (r = -0.598, p<0.05) with the number of cases in the subsequent months. Predictive modeling using these Ct values closely forecasted the increase or decrease in the number of cases of the subsequent month. Decreasing population-level median Ct values for asymptomatic COVID-19 cases appear to be a leading indicator for predicting future COVID-19 cases.

Maternal and neonatal outcomes in pregnant women with COVID-19 in a tertiary care hospital

Background: The first case of the new Corona virus was identified in Wuhan, China in December 2019 and since then it spread around the world to other countries. The World health Organisation declared that the CoV-19 pandemic as a public health emergency of international concern (PHEIC) on 30 Jan 2020. In our hospital we managed Covid-19 positive patients as per guidelines. Here we are presenting the data of management and clinical outcomes of COVID-19 positive pregnant patients in our institution.Materials & Methodology: In this study we retrospectively reviewed the medical records of all COVID-19 positive pregnant women who were admitted to PESIMSR from January 2021 to August 2021, after obtaining permission from the institute. The infection status was determined via real-time polymerase chain reaction (RT-PCR) of nasopharyngeal swab specimen. In a pre-constructed data form the details regarding obstetric data, clinical status, symptoms, maternal and fetal outcomes were noted. Patients treated in an outpatient setting were not included.Results: 125 COVID-19 positive pregnant women were admitted in our hospital during study period. Mean maternal age was 23.9+_4.2 years. The mean gestational age calculated was 37.5±1.5 weeks. Cesare an section was performed in 33.6% of cases and 65.6% cases delivered vaginally. Most of the cases were asymptomatic. Patients with mild disease, without acute respiratory distress syndrome (ARDS), responded well to the supportive treatment. 10 babies required the admission in the new born intensive care unit and were discharged. All neonates tested negative for COVID-19, which showed no evidence of vertical transmission of COVID-19 in study group. Neither maternal nor neonatal deaths occurred.Conclusion: Our data showed that the course of Corona virus disease, COVID -19 in pregnancy is mild in the majority of cases and neonatal outcomes also appeared favourable.

The Outcome of COVID-19 Infection in Patients With Gastrointestinal Diseases: An Experience at a Tertiary Center.

Observing the impact of the coronavirus disease 2019 (COVID-19) pandemic on digestive diseases in hospitalized patients at the Department of Gastroenterology-Hepatology in "Mother Teresa" University Hospital Center (UHC),Tirana. This retrospective study was carried out from June 2020 to December 2021 involving 41 cases of patients >18 years who were positive for COVID-19 infection detected by RT-PCR (Reverse Transcription-Polymerase Chain Reaction) assays of nasopharyngeal swab specimens. The severity of COVID-19 infection was evaluated by hematological/biochemical parameters, blood oxygenation/need for oxygen, radiological data on pulmonary CT imaging. Out of 2527 hospitalized cases, 1.6% (41) were positive for the infection. The average age was 60.05 +/- 15.008 years. The group of age with more patients (48.8%) was 41-60 years. Infected males were higher than females (p<0.001). Out of the total, 21% were vaccinated at the diagnosis. Most patients came from urban areas, more than a half from the capital. Frequency of the digestive diseases was: cirrhosis 31.7%, pancreatitis 21.9%, alcoholic liver disease 21.9%, gastrointestinal hemorrhage 19.5%, digestive cancer 14.6%, biliary diseases 7.3%, inflammatory bowel disease (IBD) 2.4%, other digestive diseases 4.8%. Fever (90%) and fatigue (78.04%) were the dominant clinical signs. Biochemical and hematological parameters showed elevation of average value of aspartate amino transferase (AST), alanine transaminase (ALT) (AST>ALT, p<0.001), and bilirubin in all the patients. Higher levels of creatinine andsignificantly predictive value of systemic inflammation indices NLR (neutrophil to lymphocyte ratio) and MLR (monocyte to lymphocyte ratio) were found in the fatality cases. Patients with cirrhosis had more severe form of COVID-19, lower blood oxygenationand needed treatment by O2-therapy (p<0.046). Death rate was 12%. A strong correlation was found between the need for O2-therapy and deaths (p<0.001) and between characteristic findings for COVID-19 in pulmonary CT imaging and low blood oxygenation (p<0.003). Comorbiditywith chronic diseases, such as liver cirrhosis, has an important impact on the severity and mortality of the patients with COVID-19 infection. Inflammatory indices, such as NLR (neutrophil to lymphocyte ratio) and MLR (monocyte to lymphocyte ratio), are useful tools in predicting the evolution toward severe forms of the disease.

Evaluation of an immunochromatography-based rapid antigen test, Inspecter Kowa® SARS-CoV-2, using saliva specimens for the detection of SARS-CoV-2

BackgroundIn the context of the coronavirus disease 2019 (COVID-19) pandemic, a rapid and reliable point-of-care test is an essential tool for controlling the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In particular, an immunochromatography test (ICT) that uses saliva specimens for rapid antigen detection not only reduces the risk of secondary infections but also reduces the burden on medical personnel. MethodsThe newly developed salivary antigen test kit “Inspecter Kowa® SARS-CoV-2” is an ICT to which saliva specimens can be directly applied. We evaluated its usefulness in comparison with reverse transcription quantitative PCR (RT-qPCR) and the Espline® SARS-CoV-2 Kit for the detection of SARS-CoV-2 using nasopharyngeal swab specimens. In this study, 140 patients with suspected symptomatic COVID-19 who visited our hospital were enrolled, and nasopharyngeal swab and saliva specimens were collected after they consented to participate in the study. ResultsInspector Kowa SARS-CoV-2 was positive in 45 of 61 (73.8%) saliva that were positive by RT-qPCR and the Espline® SARS-CoV-2 Kit was also positive in 56 of 60 (93.3%) Np swabs that were positive by RT-qPCR. Good antigen detection was achieved by ICT with saliva and nasopharyngeal swab specimens when viral load was ≥105 copies/mL, whereas detection sensitivity was low when viral load was <105 copies/mL, especially in saliva specimens. ConclusionThis ICT for the detection of SARS-CoV-2 salivary antigen is an attractive tool that does not require specialized equipment and allows patients to perform the entire process from sample collection to self-diagnose and to reduce the burden on medical care during a pandemic.

Impact of G29179T mutation on two commercial PCR assays for SARS-CoV-2 detection

Nucleic acid amplification test (NAAT) is the gold standard for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection. However, genetic mutations in the virus can affect the result. Cycle threshold (Ct) values of N genes and their association with mutations using SARS-CoV-2 positive specimens diagnosed by the Xpert Xpress SARS-CoV-2 were examined in this study. In total, 196 nasopharyngeal swab specimens were tested for SARS-CoV-2 infection using the Xpert Xpress SARS-CoV-2, and 34 were positive. WGS was performed for four outlier samples with increased ΔCt identified by Scatterplot analysis as well as seven control samples without increased ΔCt in the Xpert Xpress SARS-CoV-2. The presence of the G29179T mutation was identified as a cause of increased ΔCt. PCR using the Allplex™ SARS-CoV-2 Assay did not show a similar increase in ΔCt. Previous reports focusing on N-gene mutations and their effects on SARS-CoV-2 testing including the Xpert Xpress SARS-CoV-2 were also summarized. While a single mutation that impacts one target of a multiplex NAAT is not a true detection failure, mutation compromising NAAT target region can cause confusion of the results and render the assay susceptible to diagnostic failure.

Evaluation of diagnostic performance of SARS-CoV-2 detection kits: a comparative study

BackgroundCoronavirus Disease 2019 (COVID-19) pandemic has hit many countries worldwide. Rapid and accurate diagnosis is crucial to reduce disease burden. Many commercial kits have become available, but their performance needs to be assessed. This study aimed at evaluation of the diagnostic performance of real-time polymerase chain reaction (RT-PCR) and Rapid Antigen detection (RAD) kits for detecting Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Five hundred sixty-four Nasopharyngeal swab specimens sent to Molecular Laboratory at Ain Shams University Specialized Hospital for SARS-CoV-2 PCR testing collected from 564 subjects who attended the outpatient clinic for sample collection were randomly selected. All samples were tested for SARS-CoV-2 PCR using Viasure. Each time a recent kit was introduced, 94 samples, previously tested using Viasure, were used to determine the performance characteristics of the recent kit in comparison with Viasure, including Fast Track Diagnostics (FTD), DNA Technology, QiaPrep, Xpress SARS-CoV-2, ID NOW COVID-19 assay and Artron COVID-19 Antigen test kit.ResultsUpon comparison, FTD, DNA Technology, QiaPrep, Xpress SARS-CoV-2 and ID Now showed positive percent agreement, 100%, 100%, 97.7%, 100%, 100% negative percent agreement, 86%, 100%, 98.8%, 90%, 100%, respectively. The RAD kit results, when compared with RT-PCR, showed high sensitivity at cycle threshold (Ct) < 30, low sensitivity at Ct ≥ 30, while specificity was 100%.ConclusionFast track, DNA Technology, QiaPrep, Xpress SARS-CoV-2 and ID Now showed good diagnostic performance. Positive RAD rule in SARS-CoV-2 infection, however negative results should be correlated with clinical condition and molecular testing.

Incidence and Transmission Dynamics of Bordetella pertussis Infection in Rural and Urban Communities, South Africa, 2016‒2018.

We conducted 3 prospective cohort studies (2016-2018), enrolling persons from 2 communities in South Africa. Nasopharyngeal swab specimens were collected twice a week from participants. Factors associated with Bordetella pertussis incidence, episode duration, and household transmission were determined by using Poisson regression, Weibull accelerated time-failure, and logistic regression hierarchical models, respectively. Among 1,684 participants, 118 episodes of infection were detected in 107 participants (incidence 0.21, 95% CI 0.17-0.25 infections/100 person-weeks). Children <5 years of age who had incomplete vaccination were more likely to have pertussis infection. Episode duration was longer for participants who had higher bacterial loads. Transmission was more likely to occur from male index case-patients and persons who had >7 days infection duration. In both communities, there was high incidence of B. pertussis infection and most cases were colonized.

Verification of the Performance of the Panbio COVID-19 Ag Rapid Test Device for Implementation in the Clinical Laboratory

Objectives: The Panbio COVID-19 Ag Rapid Test Device (Panbio COVID-19 Ag, Abbott Rapid Diagnostics) is a lateral flow immunochromatographic assay targeting the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleoprotein in nasopharyngeal specimens for the diagnosis of coronavirus disease 2019 (COVID-19). This study aimed to verify the performance of the Panbio COVID-19 Ag for implementation in clinical laboratories. Methods: Sixty nasopharyngeal swab specimens (30 positive and 30 negative) dipped in transport medium, and COVID-19 was confirmed using real-time RT-PCR using Allplex SARS-CoV-2 assay (Seegene), were tested using the Panbio COVID-19 Ag. Reproducibility was evaluated using positive and negative control materials. Sensitivity and specificity were calculated based on the results of real-time RT-PCR as the standard test method. Results: Reproducibility was confirmed by the consistent results of repeated tests of the quality control materials. The overall sensitivity and specificity of Panbio COVID-19 Ag were 50.0% and 100.0%, respectively. Panbio COVID-19 Ag demonstrated high sensitivity (88.2%) in analyzing the detection limit cycle threshold (Ct) value of 26.67 provided by the manufacturer as a positive criterion, and the sensitivity was 100.0% for the positive criterion of Ct values &lt;25, although it was less sensitive for Ct ≥25. Conclusion: Considering the high sensitivity for positive samples with Ct values &lt;25 and the rapid turnaround of results, Panbio COVID-19 Ag can be used in clinical laboratories to diagnose COVID-19 in limited settings.