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.

Borderline SARS-CoV-2 patients: the trace behind.

BACKGROUND: Effective and precise SARS-CoV-2 detection assays are crucial for maintaining regular hospital routines and identifying infected hospital employees and infected patients before hospital admission. Inconclusive PCR test results of potentially infectious borderline SARS-CoV-2 patients can confuse clinicians and delay appropriate infection control. OBJECTIVES AND STUDY DESIGN: In this retrospective study, we followed up borderline SARS-CoV-2 patients who were tested (from the second sample with the same method) at the Clinical Department of Clinical Microbiology. We aimed to determine the positivity conversion ratio within 7 days after inconclusive PCR test results. RESULTS: Out of 247 borderline patients, who were resampled and retested in the same laboratory, 60 patients (29.4%) showed conversion of the borderline viral load (inconclusive RT-PCR test) to a positive RT-PCR test result. CONCLUSIONS: Our results highlight the need for retesting of borderline patients with inconclusive SARS-CoV-2 results. Follow-up testing of inconclusive PCR results within 7 days can identify additional positive results and reduce the potential risk of intrahospital transmission.

Diagnostic Efficacy of RealStar SARS-CoV-2 Reverse Transcription-Polymerase Chain Reaction (RT-PCR) in Comparison to GeneXpert System for the Detection of COVID-19.

Background and objective The coronavirus disease 2019 (COVID-19) pandemic has become a major health concern due to the rapid transmission of the virus that causes it: severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To address the growing demand on healthcare systems to control this pandemic, more effective diagnostic methods need to be applied. In this study, we aimed to compare the efficacy of RealStar® SARS-CoV-2 reverse transcription-polymerase chain reaction (RT-PCR) versus the GeneXpert® system. Methods A retrospective cross-sectional study was conducted in the central lab of King Abdulaziz Medical City (KAMC) in Riyadh, Saudi Arabia. Data from all nasopharyngeal swabs (NPS) (150,000) submitted for SARS-CoV-2 analysis from July 2020 to July 2021 were reviewed retrospectively. Furthermore, all NPS (n=384) that were analyzed on both the RealStar® SARS-CoV-2 RT-PCR and GeneXpert® systems for confirmatory purposes were included in the study. Acute respiratory illness (ARI) screening forms of the selected samples were reviewed from the electronic database (BestCare system), and they were analyzed and compared at one point in time; therefore, a cross-sectional study was found to be the best suitable study design. Using the statistical analysis software, the receiver operating characteristic (ROC) curve was obtained to compare the sensitivity (Sn), specificity (Sp), positive predictive value (PPV), and negative predictive value (NPV). The test was considered significant if the area under the curve (AUC) value was >0.5. Results The diagnostic performance of the RealStar® and GeneXpert® assays in detecting SARS-CoV-2 was evaluated using ROC curve analysis, which showed AUCs of 0.597 and 0.637, respectively. In addition, 35% of the total results fell into a substantial agreement of 0.76 (95% CI: 0.6626-0.8732). The majority of the NPS were reported negative by both RealStar® (246, 80.66%) and GeneXpert® (226, 74.10%). Most samples (210, 68.85%) were obtained from asymptomatic patients, scoring less than 4 (ARI <4) based on the ARI screening form. Conclusion Based on the AUC of ROC, there is no significant difference in the performance characteristics between the RealStar® RT-PCR and GeneXpert® in detecting COVID-19.

SARS-CoV-2 detection by RT-qPCR using saliva in outpatients tested for COVID-19

Background: The COVID-19 pandemic has affected millions of people around the world. Part of control strategies is testing a large proportion of the population to identify and isolate the infected sub-jects. Aim(s): To evaluate the SARS-CoV-2 detection by the performance of a reverse transcription and quantitative polymerase chain reaction (RT-qPCR) against SARS-CoV-2, using saliva as a matrix compared to a nasopharyngeal swab (NPS) to simplify obtaining a diagnostic sample. Method(s): Adults in outpatient care were recruited, 95% of them symptomatic. We studied 530 paired saliva and NPS samples by SARS-CoV-2 RT-qPCR. Result(s): Fifty-nine individuals tested positive in NPS and 54 in saliva samples. Sensitivity for saliva sample was 91%, specificity 100%, positive predictive value (PPV) 100%, negative predictive value (NPV) 98%. The Kappa index was 0.95 and LR-0.08. On average, the cycle threshold (CT) of saliva was 3.99 points higher than those of NPS (p < 0.0001) showing that viral load (VL) is lower in saliva than in NPS. Viral load in both decreased over the time after onset of symptoms. Saliva sampling was preferred by subjects instead of NPS. Conclusion(s): This study demonstrates that SARS-CoV-2 RT-qPCR using saliva, even with lower VL, is suitable for the diagnosis of COVID-19 in outpatient adults, especially at early stage of symptoms. Copyright © 2022, Sociedad Chilena de Infectologia. All rights reserved.

Performance of STANDARD™ M10 SARS-CoV-2 Assay for the Diagnosis of COVID-19 from a Nasopharyngeal Swab.

The STANDARD™ M10 severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) assay (M10 assay) (SD Biosensor Inc., Suwon, Korea) is a rapid, fully-automated, cartridge-type molecular diagnostic assay that detects SARS-CoV-2 RNA using primers and probes for each target gene (ORF1ab gene, E gene). This study evaluated its performance by assessing its concordance with the approved SARS-CoV-2 real-time PCR assay. Tests were performed on 80 nasopharyngeal samples. The sensitivity and specificity of the M10 assay were 100%. The M10 assay effectively diagnosed SARS-CoV-2 infection, and it was comparable to the approved SARS-CoV-2 real-time PCR assay. It is a viable point-of-care test due to its short turnaround time.

The Ocular Surface

This is a study of patients who were diagnosed with COVID-19 between December 30 and February 7, 2020 with a clinical diagnosis of COVID-19, a total of 102 patients (48 males and 47 percent and 54 are female 53 percent) were diagnosed with clinical symptoms, Respiratory therapy and chest computer Tomography (CT) abnormalities. Patient's gestational age is 57.63 [14.90] year on average [SD].A total of 102 patients were recognize, with 72 of them being men (50%) and women (50%) respectively. Only two patients (2.78 percent) were found to have conjunctivitis out of 62 patients with laboratory confirmed COVID-19. SARS-COV2 RT-PCR detected ocular discharges in only one of two patients, SARS-COV-2 fragments. Covid-19 infected about 80,000 people in just three months, according to estimates with the help of 300 medical personal. It attacks the respiratory tract first and foremost, although it also affects extra-pulmonary locations, the gastrointestinal tract, as well as other organs. Fever, tiredness, and cough are the early symptoms of SARS-COV-2 infection,. Which rapidly develops into pneumonia. A large number of patients experience symptoms such as headaches, diarrhea, nausea, and vomiting at the start of their disease, and some patients also experience nausea and vomiting some patients occur with asymptomatic infection. Despite the fact that SARS-COV2 infection via the ocular surface is rare was shown to be astonishingly low in this investigation SARS-COV2 infection transmitted through the eyes as a nosocomial illness following occupation exposure is a viable route. the reduced positive rate of SARS-COV-2 conjunctival swab samples could be due to an ineffective diagnosis technique and a sampling time lag. © The Electrochemical Society

Comparison of Initial CT Findings and CO-RADS Stage in COVID-19 Patients with PCR, Inflammation and Coagulation Parameters in Diagnostic and Prognostic Perspectives.

Objectives: This study aims to determine whether COVID-19 patients with different initial reverse transcriptase-polymerase chain reaction (RT-PCR), computed tomography (CT) and laboratory findings have different clinical outcomes. Materials and Methods: In this multi-center retrospective cohort study, 895 hospitalized patients with the diagnosis of COVID-19 were included. According to the RT-PCR positivity and presence of CT findings, the patients were divided into four groups. These groups were compared in terms of mortality and need for intensive care unit (ICU). According to the COVID-19 Reporting and Data System (CO-RADS), all patients' CT images were staged. Multivariate binary logistic regression analysis was used to examine the relationship between CO-RADS and predictive inflammation and coagulation parameters. Results: RT-PCR test positivity was 51.5%, the CT finding was 70.7%, and 49.7% of the patients were in the CO-RADS 5 stage. The need for ICU and mortality rates was higher in the group with only CT findings compared to the group with only RT-PCR positivity, (14.9% vs. 4.0%, p < 0.001; 9.3% vs. 3.3%, p > 0.05; respectively). Mortality was 3.27 times higher in patients with CO-RADS 4 compared to those with CO-RADS 1-2. Being in the CO-RADS 4 stage and LDH were discovered to be the most efficient parameters in determining mortality risk. Conclusion: Performing only the RT-PCR test in the initial evaluation of patients in SARS-CoV-2 infection may lead to overlooking groups that are more at risk for severe disease. The use of a chest CT to perform CO-RADS staging would be beneficial in terms of providing both diagnostic and prognostic information.

Patient characteristics associated with conversion from negative to positive severe acute respiratory syndrome coronavirus-2 polymerase chain reaction test results: Implications for clinical false-negativity from a single-center: A case-control study.

BACKGROUND: Accurate diagnosis of coronavirus disease 2019 is essential to limiting transmission within healthcare settings. The aim of this study was to identify patient demographic and clinical characteristics that could impact the clinical sensitivity of the nasopharyngeal severe acute respiratory syndrome coronavirus-2 (SARS-CoV2) reverse transcription polymerase chain reaction (RT-PCR) test. METHODS: We conducted a retrospective, matched case-control study of patients who underwent repeated nasopharyngeal SARS-CoV2 RT-PCR testing at a tertiary care academic medical center between March 1 and July 23, 2020. The primary endpoint was conversion from negative to positive PCR status within 14 days. We conducted conditional logistic regression modeling to assess the associations between demographic and clinical features and conversion to test positivity. RESULTS: Of 51,116 patients with conclusive SARS-CoV2 nasopharyngeal RT-PCR results, 97 patients converted from negative to positive within 14 days. We matched those patients 1:2 to 194 controls by initial test date. In multivariate analysis, clinical suspicion for a respiratory infection (adjusted odds ratio [aOR] 20.9, 95% confidence interval [CI]: 3.1-141.2) and lack of pulmonary imaging (aOR 4.7, 95% CI: 1.03-21.8) were associated with conversion, while a lower burden of comorbidities trended toward an increased odds of conversion (aOR 2.2, 95% CI: 0.9-5.3). CONCLUSIONS: Symptoms consistent with a respiratory infection, especially in relatively healthy individuals, should raise concerns about a clinical false-negative result. We have identified several characteristics that should be considered when creating institutional infection prevention guidelines in the absence of more definitive data and should be included in future studies.

THE ROLE OF WORLD THE FIGHT AGAINST COVID-19

In under two decades, the world has encountered three flare-ups of fatal Coronaviruses, including the ongoing pandemic of Coronavirus Disease 2019 (COVID-19) in China. COVID-19 represented a crisis of worldwide concerns, and cases have been accounted for more than 200 nations/districts that came about in wellbeing, lives, and monetary misfortunes. China's financial development is anticipated to tumble to 5.6% this year, the International Monetary Fund (IMF) anticipated that arrangement venture and expense strategies to execute $3.3 trillion and contributes further $4.5 trillion. IMF conjectures develop from 3.7% of worldwide total national output (GDP) in 2019 to 9.9% in 2020. Gross domestic product proportion anticipated from 3.0% in 2019 to become 10.7% in 2020, the US proportion expected to increment from 5.8-15.7%. There is a desperate requirement for local and universal co-activity to stretch out hands to forestall further spreading of COVID-19. The IMF has reacted to the COVID emergency with exceptional speed and greatness of financial aid. This paper shows the response of the world against COVID-19. How the countries are helping each other to control the spread and discovering the cure of this virus. Asia has survived usefully and also defending the second wave of virus, but on the other hand, the Europe is the most infected region with the highest rate of death. Why Asia is near to win this fight with a stable economy, but the Europe is not, instead of this the economy is going to be crashed. These questions raises to the Economy, Behavior and Policies, of respective Countries.

Sudden sensorineural hearing loss in a post-COVID-19 patient.

A detailed history and diagnostic evaluation for recent or past COVID-19 infection is vital in patients presenting with Sudden Sensorineural Hearing Loss (SSNHL) since SSNHL could be a sequelae of COVID-19 and timely diagnosis and intervention could significantly improve hearing and quality of life.

Differing Sensitivity of COVID-19 PCR Tests and Consequences of the False-negative Report: A Small Observation.

The world at large cannot afford to miss even a single case of COVID-19 because of its far-reaching consequences; therefore, the diagnostic development to achieve test with much higher sensitivity should be made available at a mass level as early as possible. HOW TO CITE THIS ARTICLE: Garg SK. Differing Sensitivity of COVID-19 PCR Tests and Consequences of the False-negative Report: A Small Observation. Indian J Crit Care Med 2021;25(9):1077-1078.

Effectiveness of Abbott BinaxNOW Rapid Antigen Test for Detection of SARS-CoV-2 Infections in Outbreak among Horse Racetrack Workers, California, USA.

The Abbott BinaxNOW rapid antigen test is cheaper and faster than real-time reverse transcription PCR (rRT-PCR) for detecting severe acute respiratory syndrome coronavirus 2. We compared BinaxNOW with rRT-PCR in 769 paired specimens from 342 persons during a coronavirus disease outbreak among horse racetrack workers in California, USA. We found positive percent agreement was 43.3% (95% CI 34.6%-52.4%), negative percent agreement 100% (95% CI 99.4%-100%), positive predictive value 100% (95% CI 93.5%-100%), and negative predictive value 89.9% (95% CI 87.5%-92.0%). Among 127 rRT-PCR-positive specimens, the 55 with paired BinaxNOW-positive results had a lower mean cycle threshold than the 72 with paired BinaxNOW-negative results (17.8 vs. 28.5; p<0.001). Of 100 specimens with cycle threshold <30, a total of 51 resulted in positive virus isolation; 45 (88.2%) of those were BinaxNOW-positive. Our comparison supports immediate isolation for BinaxNOW-positive persons and confirmatory testing for negative persons.

Comparison of SARS-CoV-2 N gene real-time RT-PCR targets and commercially available mastermixes.

BACKGROUND: This study aimed to evaluate the impact of four different reverse transcription quantitative PCR (RT-qPCR) master mixes on the performance of SARS-CoV-2 diagnostic PCRs using three primer/probe assays targeting the N gene (A, B and C). The dynamic range and lowest detected quantity was determined using a SARS-CoV-2 partial N gene RNA transcript dilution series (100,000-1 copy/µl) and verified using 72 nose and throat swabs, 29 of which tested positive for SARS-CoV-2 RNA. RESULTS: Assay C consistently detected the lowest quantity of partial N gene RNA transcript with all mastermixes. The Takara One Step PrimeScript™ III RT-PCR Kit mastermix enabled all primer pairs to detect the entire dynamic range evaluated, with the Qiagen Quantifast and Thermofisher TaqPath 1-Step kits also performing well. Sequences from all three primer/probe sets tested in this study (assay A, B and C) have 100 % homology to ≥97 % of the of SARS-CoV-2 sequences available up to 31st December 2020 (n = 291,483 sequences). CONCLUSIONS: This work demonstrates that specific assays (in this case assay C) can perform well in terms of dynamic range and lowest detected quantity regardless of the mastermix used. However we also show that, by choosing the most appropriate mastermix, poorer performing primer pairs are also able to detect all of the template dilutions investigated. This work increases the potential options when choosing assays for SARS-CoV-2 diagnosis and provides solutions to enable them to work with optimal analytical sensitivity.

Recent Advances in the Evaluation of Serological Assays for the Diagnosis of SARS-CoV-2 Infection and COVID-19.

Introduction: Few data on the diagnostic performance of serological tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are currently available. We evaluated sensitivity and specificity of five different widely used commercial serological assays for the detection of SARS-CoV-2-specific IgG, IgM, and IgA antibodies using reverse transcriptase-PCR assay in nasopharyngeal swab as reference standard test. Methods: A total of 337 plasma samples collected in the period April-June 2020 from SARS-CoV-2 RT-PCR positive (n = 207) and negative (n = 130) subjects were investigated by one point-of-care lateral flow immunochromatographic assay (LFIA IgG and IgM, Technogenetics) and four fully automated assays: two chemiluminescence immunoassays (CLIA-iFlash IgG and IgM, Shenzhen YHLO Biotech and CLIA-LIAISON® XL IgG, DiaSorin), one electrochemiluminescence immunoassay (ECLIA-Elecsys® total predominant IgG, Roche), and one enzyme-linked immunosorbent assay (ELISA IgA, Euroimmune). Results: The overall sensitivity of all IgG serological assays was >80% and the specificity was >97%. The sensitivity of IgG assays was lower within 2 weeks from the onset of symptoms ranging from 70.8 to 80%. The LFIA and CLIA-iFlash IgM showed an overall low sensitivity of 47.6 and 54.6%, while the specificity was 98.5 and 96.2%, respectively. The ELISA IgA yielded a sensitivity of 84.3% and specificity of 81.7%. However, the ELISA IgA result was indeterminate in 11.7% of cases. Conclusions: IgG serological assays seem to be a reliable tool for the retrospective diagnosis of SARS-CoV-2 infection. IgM assays seem to have a low sensitivity and IgA assay is limited by a substantial rate of indeterminate results.

Eastern Cape Healthcare Workers Acquisition of SARS-CoV-2 (ECHAS): Cross-Sectional (Nested Cohort) Study Protocol.

Healthcare workers (HCWs) are at increased risk of infection by the virulent severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Though data exist on the positivity rate of the SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR) test as well as COVID-19-related deaths amongst HCWs in South Africa, the overall infection rate remains underestimated by these indicators. It is also unclear whether the humoral immune response after SARS-CoV-2 infection offers durable protection against reinfection. This study will assess the SARS-CoV-2 seroprevalence amongst HCWs in the Eastern Cape (EC) and examine the longitudinal changes (rate of decay) in the antibody levels after infection in this cohort. Using a multi-stage cluster sampling of healthcare workers in selected health facilities in the EC, a cross-sectional study of 2250 participants will be recruited. In order to assess the community infection rate, 750 antenatal women in the same settings will be recruited. Relevant demographic and clinical characteristics will be obtained by a self-administered questionnaire. A chemiluminescent microparticle immunoassay (CMIA) will be used for the qualitative detection of IgG antibodies against SARS-CoV-2 nucleocapsid protein. A nested cohort study will be conducted by performing eight-weekly antibody assays (X2) from 201 participants who tested positive for both SARS-CoV-2 RT-PCR and serology. Logistic regression models will be fitted to identify the independent risk factors for SARS-CoV-2 infection. The cumulative SARS-CoV-2 infection rate and infection fatality rate among the frontline HCWs will be estimated. In addition, the study will highlight the overall effectiveness of infection prevention and control measures (IPC) per exposure sites/wards at the selected health facilities. Findings will inform the South African Department of Health's policies on how to protect HCWs better as the country prepares for the second wave of the SARS-CoV pandemic.

Diagnostic yield of repeat testing for SARS-CoV-2: Experience from a large health system in Los Angeles.

OBJECTIVE: To determine the diagnostic yield of repeat testing for SARS-CoV-2. METHODS: A retrospective analysis was performed of all SARS-CoV-2 test results within the UCLA Health System between March 9th and April 29th, 2020. All patients with repeat test results were identified and those with discordant results were reviewed. RESULTS: Between March 9th and April 29th there were 10,165 SARS-CoV-2 test results, of which 630 (6.2%) were positive. Among the 904 patients with repeat test results, 808 (89.4%) were initially negative and 96 (10.6%) were initially positive. Among the 808 patients with an initial negative test, 15 (1.9%) subsequently tested positive. Eleven cases with an initial negative SARS-CoV-2 test and without a known prior positive SARS-CoV-2 test were reviewed; 6 were employed as healthcare workers and 10 were positive on the second test. CONCLUSIONS: We found a low diagnostic yield of repeat testing for SARS-CoV-2 in our health system. Repeat testing might prove useful in certain clinical scenarios, such as in healthcare workers, when symptoms develop after a negative test, and in hospitalized patients with a high clinical suspicion for COVID-19.

The clinical sensitivity of a single SARS-CoV-2 upper respiratory tract RT-PCR test for diagnosing COVID-19 using convalescent antibody as a comparator.

The clinical false negative rate of reverse transcriptase polymerase chain reaction (RT-PCR) testing for SARS-CoV-2 on a single upper respiratory tract sample was calculated using convalescent antibody testing as a comparator. The sensitivity in symptomatic individuals was 86.2% (25/29). Of the missed cases, one (3.5%) was detected by repeat RT-PCR, one by CT thorax and two (7.1%) by convalescent antibody. The clinical false negative rate of a single RT-PCR on an upper respiratory tract sample of 14% in symptomatic patients is reassuring when compared to early reports. This report supports a strategy of combining repeat swabbing, use of acute and convalescent antibody testing and CT thorax for COVID-19 diagnosis.