SARS-COV-2 Infection in Children and Young People in Bulgaria - A Prospective, Single-Center, Cohort Study

Compared to other respiratory viruses, the proportion of hospitalizations due to SARS-CoV-2 among children is relatively low. While severe illness is not common among children and young individuals, a particular type of severe condition called multisystem inflammatory syndrome in children (MIS-C) has been reported. The aim of this prospective cohort study, which followed a group of individuals under the age of 19, was to examine the characteristics of patients who had contracted SARS-CoV-2, including their coexisting medical conditions, clinical symptoms, laboratory findings, and outcomes. The study also aimed to investigate the features of children who met the WHO case definition of MIS-C, as well as those who required intensive care. A total of 270 patients were included between March 2020 and December 2021. The eligible criteria were individuals between 0-18 with a confirmed SARS-CoV-2 infection at the Infectious Disease Hospital "Prof. Ivan Kirov"in Sofia, Bulgaria. Nearly 76% of the patients were <= 12 years old. In our study, at least one comorbidity was reported in 28.1% of the cases, with obesity being the most common one (8.9%). Less than 5% of children were transferred to an intensive care unit. We observed a statistically significant difference in the age groups, with children between 5 and 12 years old having a higher likelihood of requiring intensive care compared to other age groups. The median values of PaO2 and SatO2 were higher among patients admitted to the standard ward, while the values of granulocytes and C-reactive protein were higher among those transferred to the intensive care unit. Additionally, we identified 26 children who met the WHO case definition for MIS-C. Our study data supports the evidence of milder COVID-19 in children and young individuals as compared to adults. Older age groups were associated with higher incidence of both MIS-C and ICU admissions.Copyright © 2023 P. Velikov et al., published by Sciendo.

Validating saliva as a biological sample for cost-effective, rapid and routine screening for SARS-CoV-2

Purpose: Compared to nasopharyngeal/oropharyngeal swabs (N/OPS-VTM), non-invasive saliva samples have enormous potential for scalability and routine population screening of SARS-CoV-2. In this study, we investigate the efficacy of saliva samples relative to N/OPS-VTM for use as a direct source for RT-PCR based SARS-CoV-2 detection. Method(s): We collected paired nasopharyngeal/oropharyngeal swabs and saliva samples from suspected positive SARS-CoV-2 patients and tested using RT-PCR. We used generalized linear models to investigate factors that explain result agreement. Further, we used simulations to evaluate the effectiveness of saliva-based screening in restricting the spread of infection in a large campus such as an educational institution. Result(s): We observed a 75.4% agreement between saliva and N/OPS-VTM, that increased drastically to 83% in samples stored for less than three days. Such samples processed within two days of collection showed 74.5% test sensitivity. Our simulations suggest that a test with 75% sensitivity, but high daily capacity can be very effective in limiting the size of infection clusters in a workspace. Guided by these results, we successfully implemented a saliva-based screening in the Bangalore Life Sciences Cluster (BLiSC) campus. Conclusion(s): These results suggest that saliva may be a viable alternate source for SARS-CoV-2 surveillance if samples are processed immediately. Although saliva shows slightly lower sensitivity levels when compared to N/OPS-VTM, saliva collection is logistically advantageous. We strongly recommend the implementation of saliva-based screening strategies for large workplaces and in schools, as well as for population-level screening and routine surveillance as we learn to live with the SARS-CoV-2 virus.Copyright © 2023 Indian Association of Medical Microbiologists

[Rapid detection and genotyping of SARS-CoV-2 Omicron BA.4/5 variants using a RT-PCR and CRISPR-Cas12a-based assay].

OBJECTIVE: To establish a rapid detection and genotyping method for SARS-CoV-2 Omicron BA.4/5 variants using CRISPPR-Cas12a gene editing technology. METHODS: We combined reverse transcription-polymerase chain reaction (RT-PCR) and CRISPR gene editing technology and designed a specific CRISPPR RNA (crRNA) with suboptimal protospacer adjacent motifs (PAM) for rapid detection and genotyping of SARS- CoV-2 Omicron BA.4/5 variants. The performance of this RT- PCR/ CRISPPR-Cas12a assay was evaluated using 43 clinical samples of patients infected by wild-type SARS-CoV-2 and the Alpha, Beta, Delta, Omicron BA. 1 and BA. 4/5 variants and 20 SARS- CoV- 2-negative clinical samples infected with 11 respiratory pathogens. With Sanger sequencing method as the gold standard, the specificity, sensitivity, concordance (Kappa) and area under the ROC curve (AUC) of RT-PCR/CRISPPR-Cas12a assay were calculated. RESULTS: This assay was capable of rapid and specific detection of SARS- CoV-2 Omicron BA.4/5 variant within 30 min with the lowest detection limit of 10 copies/µL, and no cross-reaction was observed in SARS-CoV-2-negative clinical samples infected with 11 common respiratory pathogens. The two Omicron BA.4/5 specific crRNAs (crRNA-1 and crRNA-2) allowed the assay to accurately distinguish Omicron BA.4/5 from BA.1 sublineage and other major SARS-CoV-2 variants of concern. For detection of SARS-CoV-2 Omicron BA.4/5 variants, the sensitivity of the established assay using crRNA-1 and crRNA-2 was 97.83% and 100% with specificity of 100% and AUC of 0.998 and 1.000, respectively, and their concordance rate with Sanger sequencing method was 92.83% and 96.41%, respectively. CONCLUSION: By combining RT-PCR and CRISPPR-Cas12a gene editing technology, we successfully developed a new method for rapid detection and identification of SARS-CoV-2 Omicron BA.4/5 variants with a high sensitivity, specificity and reproducibility, which allows rapid detection and genotyping of SARS- CoV-2 variants and monitoring of the emerging variants and their dissemination.

Circulation of SARS-CoV-2 Among Asylum Seekers: A Real-Life Experience to Address Health Equity in Piacenza, Italy

Aim of the Study: We aimed to evaluate the virus spreading among a migrant population previously excluded by community surveillance programs. Method(s): We conducted a retrospective study, collecting data about people without SARS-CoV-2-related symptoms who attended the outpatient clinic for undocumented migrants from November 1, 2020, to April 30, 2021. Patients who performed a nasopharyngeal swab and serologic test to evaluate the presence of antibody anti-SARS-CoV-2 were enrolled. Result(s): Overall, 240 people were included in our study. Of them, 15 (6.3%) were female, with a median age of 27.0 years (interquartile range [IQR], 24.3-32.1 years). Thirty-seven patients (15.4%) tested positive for SARS-CoV-2 at the nasopharyngeal swab during the study period. Of these, 16 had positive or low positive results for immunoglobulin G (IgG) and 3 tested positive for both IgG and IgM. Besides, 22 participants (9.2%) resulted positive to serological testing, but negative to polymerase chain reaction testing. The median age of SARS-CoV-2 positive patients (n = 59) was significantly higher than negative (29.6 [IQR, 25.0-35.0] vs 26.8 [IQR, 24.2-31.5], P = 0.022). Among positive patients, the most frequent nationality was Bangladeshi, with 24 people (40.7%, P < 0.001). The highest percentage of positive was found among the same nationality (51.1% of Bangladeshi tested positive). Conclusion(s): Our data underline the significantly higher prevalence of SARS-CoV-2 infection in the undocumented migrant population in respect of the general population of Piacenza province in the same period (15.4% vs 5.9%, P < 0.001). The extension of surveillance programs to the whole population, thus including undocumented people, is crucial to curb the spreading of the virus.Copyright © 2022 Wolters Kluwer Health, Inc. All rights reserved.

A one-enzyme rt-qpcr assay for sars-cov-2, and procedures for reagent production

Given the scale of the ongoing COVID-19 pandemic, the need for reliable, scalable testing, and the likelihood of reagent shortages, especially in resource-poor settings, we have developed an RTqPCR assay that relies on an alternative to conventional viral reverse transcriptases, a thermostable reverse transcriptase/DNA polymerase (RTX) (Ellefson et al., 2016). Here we show that RTX performs comparably to the other assays sanctioned by the CDC and validated in kit format. We demonstrate two modes of RTX use - (i) dye-based RT-qPCR assays that require only RTX polymerase, and (ii) TaqMan RT-qPCR assays that use a combination of RTX and Taq DNA polymerases (as the RTX exonuclease does not degrade a TaqMan probe). We also provide straightforward recipes for the purification of this alternative reagent RTX. We anticipate that in low resource or point-of-need settings researchers could obtain the available constructs and begin to develop their own assays, within whatever regulatory framework exists for them.Copyright © 2021 Bio-protocol LLC. All Rights Reserved.

A Laboratory Validation of Self-Collected Nasal Swab and Rhinoswab for the Detection of Sars-Cov-2

Intro: In Australia, the main methods to diagnose COVID-19 are through rapid antigen tests (RATs) and through nucleic acid amplification testing (NAAT, including polymerase chain reaction) on healthcare worker (HCW)-collected combined nose/throat swabs. With self-collection widely used by the public for RATs, the aim of this study was to evaluate the performance of self-collected samples using commercial NAAT for SARS-CoV-2. Method(s): Consenting participants aged 14 years and older were provided with a self-collection pack containing instructions and either a FLOQSwab (Copan) or a Rhinoswab (Rhinomed). Participants collected their own nasal sample unsupervised prior to having a HCW-collected combined nose and throat swab taken for standard of care NAAT. Paired self-collected and HCW samples were tested on the cobas SARS-CoV-2 assay (Roche) and the Aptima SARS-CoV-2 assay (Hologic). Finding(s): We demonstrated comparable sensitivity, specificity, and agreement between self-collected nasal and Rhinoswab samples, compared to HCW- collected samples tested using the cobas SARS-CoV-2 and Aptima SARS-CoV-2 assays. In our study the clinical performance of self-collected specimens was comparable to HCW-collected samples, with both self-collect nasal and Rhinoswab samples resulting in 90-95% sensitivity, and in most cases >95% specificity. Discussion(s): Without the availability of samples for NAAT the ability to perform genomic testing is limited, reducing surveillance and public health investigations. We showed that genomic sequencing from self-collected samples can correctly identify the virus lineage and that the main determination of successful genomic testing is a high viral load rather than collection method. Conclusion(s): These data support self-collection as an accessible method for community testing for COVID-19 and introduces a novel collection device, the Rhinoswab as an alternative to the standard nasal swab. The testing method of self-collection can be expanded from the widely used RATs to NAAT and genomic testing which may inform the management and public health response to the COVID-19 pandemic.Copyright © 2023

Expert consensus on laboratory testing for sars-COV-2.

With the global outbreak of the coronavirus disease 2019, the laboratory testing for the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) has become the key to the epidemic prevention and control. Based on the questions, issues from the clinical practice and the latest research, the Sub-committee of Clinical Microbiology Laboratory, Chinese Hospital Association proposed "Expert Consensus on Laboratory Testing for SARS-CoV-2". The consensus panel is composed by experts in clinical microbiology, molecular biology and immunology laboratory medicine. The consensus describes the technological characteristics, precautions of clinical application, and biosafety requirements. It also includes the coping strategies for the most frequent problems and the challenges in testing and results explanation of commonly used clinical methods including nucleic acid, antibody and antigen tests, and combined testing of nucleic acid and antibody. We expect this consensus could provide guidances and reference opinions on how to conduct the precise laboratory testing for SARS-CoV-2 on the epidemic prevention and control.Copyright © 2021, Peking Union Medical College Hospital. All rights reserved.

Nucleic Acid Point-of-Care Testing to Improve Diagnostic Preparedness.

Testing programs for severe acute respiratory syndrome coronavirus 2 have relied on high-throughput polymerase chain reaction laboratory tests and rapid antigen assays to meet diagnostic needs. Both technologies are essential; however, issues of cost, accessibility, manufacturing delays, and performance have limited their use in low-resource settings and contributed to the global inequity in coronavirus disease 2019 testing. Emerging low-cost, multidisease point-of-care nucleic acid tests may address these limitations and strengthen pandemic preparedness, especially within primary healthcare where most cases of disease first present. Widespread deployment of these novel technologies will also help close long-standing test access gaps for other diseases, including tuberculosis, human immunodeficiency virus, cervical cancer, viral hepatitis, and sexually transmitted infections. We propose a more optimized testing framework based on greater use of point-of-care nucleic acid tests together with rapid immunologic assays and high-throughput laboratory molecular tests to improve the diagnosis of priority endemic and epidemic diseases, as well as strengthen the overall delivery of primary healthcare services.

The hidden dangers of SARS-CoV-2 testing

A foreign body can be intentionally or accidentally ingested. Timing of endoscopy relies on foreign body shape and size, location in gastrointestinal tract, patient's clinical conditions, occurrence of symptoms or onset of complications. In this short case, we present a middle age woman, who accidentally swallowed a portion of a nasopharyngeal swab half-broken during a diagnostic test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Upper gastrointestinal endoscopy was promptly performed to prevent the swab from crossing the pylorus leading to serious complications and, therefore, risk of surgical intervention. The broken nasopharyngeal swab was detected in the gastric body, and immediately removed with a foreign body forceps. Our hospital performs many nasopharyngeal swabs and to our knowledge, this is only the second reported swab ingestion during SARS-CoV-2 test.Copyright © 2021 The Gastroenterological Society of Taiwan, The Digestive Endoscopy Society of Taiwan and Taiwan Association for the Study of the Liver.

Rapid Detection of Sars Cov-2 Infection in Comparision with Rt-Pcr in Tertiary Care Hospital

Objectives: The goal of the present study was to assess the SARS-CoV-2 antigen detection test's performance features and compare them to the real-time reverse transcription polymerase chain reaction (RT-PCR) test, the gold standard test for the diagnosis of COVID-19 cases. Method(s): From October 2020 to May 2021, patients attending the OPD, including those undergoing surgery, at a Tertiary Care Teaching Hospital in Telangana provided 1000 respiratory samples, primarily nasopharyngeal swabs. A skilled technician had collected two nasopharyngeal swabs from each person in a COVID sample collection room while wearing personal protective equipment and following strict infection control procedures. One swab was used for the rapid antigen test given by the standard Q COVID-19 Ag test kit and placed into the extraction buffer tube. Second swab was kept in the viral transport medium and used for AllplexTM 2019-nCoV Assay (Seegene, Korea), which targets envelope gene (E), and RNA dependent RNA polymerase (RdRp) and nucleocapsid (N) genes of SARS CoV-2, was used for SARS-CoV-2 RNA detection according to the manufacturer's instructions. Result(s): Out of 1000 samples tested for COVID-19, 623 (63.7%) were males and 377 (36.3%) were females. Out of 1000 samples, 347 samples were RT-PCR positive and 653 were RT-PCR negative. Out of 347 RT-PCR samples positive, 341 were Rapid antigen test positive samples and six were negative. Overall sensitivity and specificity are 98.27% and 99.85%, respectively. Conclusion(s): The real-time RT-PCR assay's sensitivity and specificity were comparable to those of the rapid assay for SARS-CoV-2 antigen detection. It can be utilized for contact tracing measures to control the COVID-19 pandemic in places such as border crossings, airports, interregional bus and train stations, and mass testing campaigns needing quick findings. This is especially true in areas with a high prevalence of the disease.Copyright © 2023 The Authors. Published by Innovare Academic Sciences Pvt Ltd.

What contributes to the re-positive nucleic acid test results for the omicron variant of SARS-CoV-2 in the shelter cabin hospital in Shanghai, China?

Background: Despite the increasing reports of re-positive SARS-CoV-2 cases after recovery and discharge from hospitals, our knowledge remains very limited regarding the contributing factors of re-positivity and its roles in the transmission and epidemiology of the Omicron variant. Methods: In this retrospective study, re-positivity is defined as the positive nucleic acid result (Ct < 35) following two consecutive negative results during hospitalization. A total of 751 patients from Shanghai Shelter Cabin Hospital were enrolled and divided with a ratio of about 1:2 into the re-positivity group and the non-re-positivity group. Patients required three consecutive negative results daily as the de-isolation criterion. The follow-up time of discharged patients lasted five weeks. Univariate regression analysis was used to compare variables between the re-positivity and non-re-positivity groups, and the single re-positivity and multiple re-positivity groups, with P < 0.05 defined as the statistical significance of differences. Subsequently, variables with P < 0.2 were subjected to multivariate logistic regression analysis to investigate the odds ratio (OR) of re-positivity and the influencing factors of re-positivity of the Omicron variant. Results: The re-positivity group had a higher proportion of males (68.1% vs 58.1%, p = 0.000), a higher education level (31.9% vs 12.7%, p = 0.007), a longer hospitalization duration (13 days vs 8 days, p = 0.000), and a higher Convidecia vaccination rate (6.0% vs 2.4%, p = 0.011). Further multivariable analysis showed male (OR = 2.168, p = 0.000), Convidecia vaccination (OR = 2.634, p = 0.014), hospitalization duration (OR = 2.146, p = 0.000) and education level (OR = 1.595, p = 0.007) were associated with re-positivity. The average rate of re-positivity was 25% during hospitalization and decreased to 0.4% among discharged patients. Re-positivity was more common in the period with a larger number of hospitalized patients and in larger wards with a larger number of patients. Conclusion: A large number of hospitalized patients, large-sized wards, and gender are significant contributing factors to re-positivity. Division of the shelter cabin hospital into small independent wards and requirement of three consecutive results daily as the de-isolation criterion might be more beneficial to the control and prevention of the spread of the Omicron variant.

Evaluation of the ePlex Respiratory pathogen panel 2 to detect viral and bacterial pathogens, including SARS-CoV-2 Omicron in nasopharyngeal swabs

The simultaneous detection and specific identification of multiple pathogens from patients exhibiting respiratory symptoms is important for directing pathogen-specific treatments. The ePlex Respiratory Pathogen Panel 2 (ePlex RP2 panel) is a multiplex molecular test for the qualitative detection of many viral and bacterial pathogens including SARS-CoV-2 in respiratory tract infections. The ePlex RP2 panel received FDA emergency use authorization for nasopharyngeal swab specimens collected in viral transport media. In the evaluation using the ePlex RP2, a total of 67 nasopharyngeal swab specimens were compared to the ePlex RP panel and the CDC 2019-nCoV Real-Time RT-PCR assay as the reference methods. The overall agreement of the ePlex RP2 panel was 100%. The ePlex RP2 panel could detect Omicron BA1 and BA2. The ePlex RP2 panel is a rapid, sensitive and specific "specimen-to-answer" platform to detect simultaneously multiple viruses and bacteria in the upper respiratory tract.Copyright © 2022 The Authors

Comparison of a point-of-care and a standard RT-PCR assay for COVID-19 detection in the emergency department

Introduction: With the rapid spreading of the coronavirus (COVID-19) pandemic and the limited capacities of realtime reverse transcriptase-PCR (RT-PCR) at the laboratory level, there is an emerging need for rapid, point-of-care (POC), molecular testing in the Emergency Department (ED). Aims and objectives: To compare the diagnostic performance of ID NOW COVID-19 assay (Abbott, Chicago, Il, USA) performed by ED doctors with a gold standard reference RT-PCR test (GeneXpert assay developed by Cepheid). Method(s): Paired nasopharyngeal swabs were collected from consecutive adult patients suspected of having COVID-19 in the ED of a tertiary hospital in Athens (Greece);the first swab was directly used for the ID NOW COVID-19 assay in POC by an emergency physician and the second was analyzed with reference RT-PCR by a central laboratory technician. Cohen's kappa was run to determine if there was sufficient agreement between the two diagnostic methods. Result(s): Seventy one consecutive patients (36 female, mean age 64.6) were enrolled in the present study from 15th January to 21th February, 2022. The two tests agreed on 20 positive and 50 negative results. On the contrary, ID NOW COVID-19 assay was found positive in one patient with a negative reference RT-PCR test. There was very good agreement between the two diagnostic methods [kappa = 0.966 (95% CI, 0.900 to 1.032), p < 0.0001]. Conclusion(s): Comparison of a POC and a standard laboratory RT-PCR test in an ED patient population yielded high positive (95%) and negative percent agreement (100%). ID NOW COVID-19 assay seems to be a highly reliable POC test for early screening and triage of suspected COVID-19 patients.

Sociodemographic and clinical characteristics of SARS-CoV-2 infected population during the second and third epidemiological waves in Sri Lanka

Objective: To analyze data on socio-demographic and clinical characteristics of SARS-CoV-2 infected population whose samples were received from Medical Research Institute, Sri Lanka. Method(s): Laboratory based retrospective study was done on patient samples which were tested positive for SARS-CoV-2 by National Reference Virology Laboratory at the Medical Research Institute, Sri Lanka, from November, 2020 to November, 2021. Data on socio-demographic characteristics and clinical presentation of 13 126 patients were examined. Result(s): The mean age of the study population was (36.0+/-7.2) years and the majority were men (64.0%). The highest number of positive cases were found in the 21-30 years-of-age group. Two distinct peaks were noted in the incidence of SARS-CoV-2 positive individuals. In addition, 42.5% of the positive samples tested positive (42.5%) were from Medical Officer of Health collection centres. Furthermore, 60.6% (7 951) of the infected subjects were asymptomatic whereas the remaining were symptomatic. The highest percentage of symptomatic patients were observed in the 91-100 years-of-age group while the highest asymptomatic subjects were found in the 31-40 years-of-age group. The percentage of asymptomatic children (65.3%) was significantly (P<0.05) higher than that of adults (43.4%). Conclusion(s): The findings of this study aid decision makers to focus on the vulnerable groups, and geographic and temporal distribution of patients in the public health strategies that aim at preventing the spread of the disease and reducinig its mortalities.Copyright © 2023 Wolters Kluwer Medknow Publications. All rights reserved.

The Circulation of Common Respiratory Viruses and Their Co-infection with Severe Acute Respiratory Syndrome Coronavirus 2 Before and After Coronavirus Disease of 2019 Vaccination

Background: Respiratory viruses play important roles in respiratory tract infections;they are the major cause of diseases such as the common cold, bronchiolitis, pneumonia, etc., in humans that circulate more often in the cold seasons. During the COVID-19 pandemic, many strict public health measures, such as hand hygiene, the use of face masks, social distancing, and quarantines, were implemented worldwide to control the pandemic. Besides controlling the COVID-19 pandemic, these introduced measures might change the spread of other common respiratory viruses. Moreover, with COVID-19 vaccination and reducing public health protocols, the circulation of other respiratory viruses probably increases in the community. Objective(s): This study aims to explore changes in the circulation pattern of common respiratory viruses during the COVID-19 pan-demic. Method(s): In the present study, we evaluated the circulation of seven common respiratory viruses (influenza viruses A and B, rhi-novirus, and seasonal human Coronaviruses (229E, NL63, OC43, and HKU1) and their co-infection with SARS-CoV-2 in suspected cases of COVID-19 in two time periods before and after COVID-19 vaccination. Clinical nasopharyngeal swabs of 400 suspected cases of COVID-19 were tested for SARS-CoV-2 and seven common respiratory viruses by reverse transcription real-time polymerase chain reaction. Result(s): Our results showed common respiratory viruses were detected only in 10% and 8% of SARS-CoV-2-positive samples before and after vaccination, respectively, in which there were not any significant differences between them (P-value = 0.14). Moreover, common viral respiratory infections were found only in 12% and 32% of SARS-CoV-2-negative specimens before and after vaccination, respectively, in which there was a significant difference between them (P-value = 0.041). Conclusion(s): Our data showed a low rate of co-infection of other respiratory viruses with SARS-CoV-2 at both durations, before and after COVID-19 vaccination. Moreover, the circulation of common respiratory viruses before the COVID-19 vaccination was lower, probably due to non-pharmaceutical interventions (NPI), while virus activity (especially influenza virus A) was significantly in-creased after COVID-19 vaccination with reducing strict public health measures.Copyright © 2023, Author(s).

Comparison of Cepheid Xpert Xpress SARS-CoV-2 Assay with Standard RTPCR Test for Detection of COVID-19 Infection: A Retrospective Cohort Study

Introduction: Real time Reverse Transcription-Polymerase Chain Reaction (RT-PCR) test, the gold standard test for Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) detection, is a tedious process and requires proficient workforce. Accurate and fast test results may permit more efficient use of protective and isolation resources and allow rapid therapeutic interventions. Aim(s): To evaluate the analytical performance characteristics of the Cepheid Xpert Xpress SARS-CoV-2 test, a rapid, automated molecular test for SARS-CoV-2 with gold standard RT-PCR test. Material(s) and Method(s): This retrospective cohort study was conducted in Virus Research and Diagnostic Laboratory (VRDL) in Department of Microbiology at GGS Medical College, Faridkot from January 2021-June 2021. A total of 100 nasopharyngeal samples, collected from clinically suspected Coronavirus Diseae-2019 (COVID-19) cases admitted at GGSMC during 1st January-30th June 2021 were tested both by Xpert assay and RT-PCR test simultaneously, taking RT-PCR as the gold standard test. The data was analysed by MedCalc statistical software version 19.6.4., and sensitivity, specificity, predictive values, likelihood ratios and the agreement between the two tests were calculated. Result(s): The mean age of the study participants was 46 years. Of these, 55 were males and 45 were females. The overall sample sensitivity and specificity of the Xpert assay were both 100% and there was perfect agreement across specimens, if authors, set a cut-off Cycle threshold-value (Ct-value) at 40 cycles for Xpert. Of 100 samples, 32 were positive for SARS-CoV-2 by either of the tests and 68 were negative. Xpert assay could detect 100% positive cases and RT-PCR test could detect 84.37% positive cases. Out of the 32 samples which were positive by Xpert assay, 5 (15.62%) samples had a Ct-value greater than 40. Conclusion(s): The Xpert assay found to be useful as a point-of-care test in acute scenario, where rapid and authentic diagnosis is essential, but do not have expertise and infrastructure to perform RT-PCR.Copyright © 2023 Journal of Clinical and Diagnostic Research. All rights reserved.

Diagnosing COVID-19: diagnostic importance of detecting E gene of the SARS-CoV-2 genome

Aim: To evaluate the significance of E gene analysis in addition to N and RdRp genes of SARS-CoV-2, and to compare the specificity and sensitivity of targets. Material(s) and Method(s): We used two reverse transcription-PCR assays: one targeting N, E and RdRp and the other targeting N and RdRp genes and analyzed variation in threshold cycle (Ct) values. Result(s): Of the 155 samples, 70.32% tested positive: all three genes were detected in 45.87%, N and RdRp in 19.27% and only N in 34.86%. Patients negative for the E gene were tested after symptoms disappeared and Ct values were significantly higher. Conclusion(s): Samples negative for the E gene were potentially false positive and clinical conditions should be assessed while interpreting results.Copyright © 2023 Future Medicine Ltd.

SARS-CoV-2 Positive Patients and the Associated Risk Factors During the Third Wave: A Study in a Tertiary Care Hospital of Punjab

Background: SARS-CoV-2 has a high mutation rate, resulting in the emergence of multiple variants in a shorter time frame, starting with Wuhan strain during first wave, then Delta during second wave and Omicron during third wave. World faced distressing spread of novel corona virus. The reason for this study was to look at the third flood of SARS-CoV-2, clinical highlights and risk factors in northern India. Method(s): This study involved 1,43,983 individuals for testing the presence of SARS-CoV-2 infection during January 2022 by RT-PCR. The epidemiological record was collected as per the guidelines of ICMR from the patient forms. Result(s): A total of 12.24% individuals were found positive with mean age of 29+/-10 years. Large portion of positive population (63.87%) was asymptomatic. Among the positive population, higher positivity rate was observed in males (57.51%) with age band of 21-40 years (51.17%). Significant association (p value = <0.00001) was found between positivity rate with age, gender and status (symptomatic/ asymptomatic). SARS-CoV-2 was shown to be more prevalent in Patiala, (49.66%) district followed by Ludhiana (24.24%), Sangrur (10.06%), Mansa (7.06%), Shaheed Bhagat Singh Nagar (6.90%) and Malerkotla (2.08%) during second and third week of January 2022. Hypertension and bronchial asthma were the most well-known comorbidities found in the current study. Conclusion(s): In totality, current study showed positivity rate of 12.24% from large population size for SARS CoV-2 from period of 1st January 2022 to 31 January 2022. Current findings include younger age group (21-40 years), high percent of asymptomatic individuals, less disease severity and a little need of hospitalization.Copyright © 2023, Institute of Medico-legal Publication. All rights reserved.