COVID-19 RT-PCR Research Articles

Clinical Characteristics of COVID-19 in Neonates and Infants Younger Than 3 Months

Background: COVID-19 is a respiratory infection that was generated in 2019 as a pandemic affecting children and adults. Objectives: To better understand COVID-19 in young children, we evaluated the epidemiological, clinical, and outcomes of SARS-CoV-2 infection in neonates and 1-3 months old infants and compared the difference between the two groups. Methods: This retrospective analysis included children admitted to Bouali and Imam Khomeini tertiary hospitals in Sari, between March 2019 and March 2022 with a COVID-19 diagnosis. Demographic data such as age, sex, comorbidity, clinical characteristics and symptoms, medications and laboratory test results were extracted from the patients' medical records. Statistical analysis was performed using SPSS software, version 22.0, and p-values less than 0.05 were considered statistically significant. Results: This study evaluated 152 children including 34(22.4%) neonates and 118(77.6%) infants with a median age of 49.5 [33-66] days. The frequencies of mild, moderate, and severe/MIS-C cases were 96(63.2%), 29(19.1%), and 27(17.8%), respectively (p=0.879). Overall, 90(59.2%) patients were boys and 62(40.8%) were girls (p=0.695). COVID-19 RT-PCR test was positive in 65(42.8%) children (p= 0.022) and 3(2%) children expired. Fever was the most common symptom (75%), followed by cough (56.6%), poor feeding (46.1%), dyspnea (32.9%), and lethargy (32.2%). 29(19.1%) patients required ICU admission and 6(3.9%) patients underwent mechanical ventilation (p=0.463 and p=0.126, respectively). The median duration of hospital stay was 5 days [IQR= 4-7 days]. The median duration of antibiotic therapy did not differ among the groups (p= 0.786). Sepsis workup was performed in 82.9% of patients, and none had a positive CSF culture.

Olfactory Dysfunction, Dysgeusia, and Clinical Outcomes in COVID-19 Patients: An Observational Study in a Tertiary COVID Referral Center in the Philippines

Objective: To describe the prevalence, onset, associated symptoms, and clinical characteristics of COVID-19 in-patients with olfactory and gustatory dysfunction at the Philippine General Hospital from March 2021 to January 2022 and determine the number of patients with olfactory dysfunction/dysgeusia who recovered or expired. Methods: Design: Prospective Cohort StudySetting: COVID-19 Referral Hospital (Tertiary National University Hospital)Participants: COVID-19 RT-PCR positive in-patients, ages 19 and older Results: A total of 207 patients were included. Sixty-four (64) patients reported olfactory dysfunction and 79 reported dysgeusia. Olfactory and gustatory dysfunction were observed early in the course of infection, before day 6 of illness. The average length of hospital stay was 20.36 days; those with olfactory dysfunction stayed for 17.53 days, dysgeusia for 19.92 days, and 21.09 days for those who noted neither. For those subsequently intubated, 0 had olfactory dysfunction, three reported dysgeusia, three had both and six had neither. Thirteen (13) patients in the study expired. Among them, none reported olfactory dysfunction and two had dysgeusia. Conclusions: Our results corroborate existing literature that olfactory and gustatory dysfunction as key indicators of COVID-19 with 42.5% of participants reporting these symptoms early, often before day 6 of illness. Ninety-two percent (92%) of those affected recovered and had shorter hospital stays, emphasizing the importance of recognizing these dysfunctions for improved disease detection and outcomes.

A case of Iatrogenic Pseudo Aneurysm of Femoral Artery

A 55-year-old woman was admitted hospital in-patient unit withfever and breathlessness for 5 days. Pertinent medical history included chronic kidney disease (CKD), poorly controlled Diabetes with retinopathy, Hypertension and Bronchial asthma. After admission patient was found to be severely anaemic and her stool was black and tarry. Blood transfusion was required for correction of anaemia. Endoscopy of upper GIT was planned after stabilization. RT PCR for COVID-19 was positive. After couple of days she became desaturated in spite of high level of oxygen delivery and was shifted to ICU. Bangladesh Crit Care J September 2024; 12 (2): 179-180

Correlation of COVID-19 vaccination and RT-PCR ct value among cases in Addis Ababa, Ethiopia: implication for future preparedness

BackgroundThe COVID-19 disease requires accurate diagnosis to effectively manage infection rates and disease progression. The study aims to assess the relationship between vaccination status and RT-PCR cycle threshold (Ct) values by comparing clinical, RDT and RT-PCR results.MethodsA total of 453 suspected COVID-19 cases were included in this study. Nasopharyngeal swabs were collected for both RDT and RT-PCR testing, with RDTs conducted on-site and RT-PCR at the Ethiopian Public Health Institute (EPHI) genomics laboratory. Detailed clinical, RDT, and RT-PCR results were analyzed. Data analysis included descriptive statistics, cross-tabulation, and Chi-Square tests to investigate the connections between diagnostic outcomes and vaccination status, with a focusing on Ct values.ResultsRDT results showed 34.0% negative and 65.8% positive, while RT-PCR results indicated 35.8% negative and 64.2% positive cases. The discrepancies between RDT and RT-PCR results emphasize the importance of thorough testing. No significant association was found between vaccination status and viral load, as indicated by Ct values. Among RT-PCR positive cases, 49.8% had been vaccinated, suggesting challenges in interpreting results among vaccinated individuals. Further analysis revealed that vaccination (first or second dose) had minimal impact on Ct values, indicating limited influence of vaccination status on viral load dynamics in infected individuals.ConclusionsThe study highlights the significant differences between RDT and RT-PCR outcomes, underscoring the need for a comprehensive testing approach. Additionally, the findings suggest that vaccination status does not significantly impact RT-PCR Ct values, complicating the interpretation of diagnostic results in vaccinated individuals, especially in breakthrough infections and potential false positives.

Epidemiological overlaps in COVID-19 and malaria within healthcare and community settings of Southern Ghana.

COVID-19 disruptions including lockdowns and prioritization of COVID-19 control programs in Africa in 2020-2022 contributed to reductions in malaria control activities including malaria diagnosis, treatment and resistance monitoring. This study investigated the malaria burden and distribution on the background of active transmission of SARS-CoV-2 in Southern Ghana; utilizing community health education and medical screening (CHEMS) approach to determine epidemiological overlaps in COVID-19 and malaria. Between October-December 2022, prospective cross-sectional surveys, with CHEMS were conducted in Greater Accra and Central regions, where 994 participants enrolled either at a hospital or community setting provided demographic and clinical data including history of clinical malaria infection and antimalarial treatment in the past 2 weeks. Of this study population, 953 provided nasal/throat swabs for COVID-19 RT-PCR testing, with a subset of 136 participants also providing finger-prick blood for malaria RDT testing. The study population comprised of 73.6% adults, with 54.6% COVID-19 vaccination rate. Overall, 18.1% of participants had a history of clinical malaria, which was associated (adjusted odds ratio > 1.50, p-value ≤0.022) with COVID-19 symptoms and positivity, study area and hospital setting, suggestive of overlaps in the epidemiological risk for malaria. On a background of widespread SARS-CoV-2 infections (12-37%), malaria parasitaemia was detected in 6%, with 2% being co-infections with SARS-CoV-2. Among the malaria positives, 9.5% had a history of antimalarial treatment, which suggested that their infections were recrudescent parasitaemia. The epidemiological and clinical overlap between malaria and COVID-19 within the hospital and community settings underscores the need for accurate case diagnosis to inform effective clinical treatments. Innovative surveillance programs, with community engagement are needed to maximize control interventions including treatment of asymptomatic malaria infections.

Prediction of Mortality Using the Sequential Organ Failure Assessment Score in Critically Ill COVID-19 Patients.

To determine the accuracy and reliability of the sequential organ failure assessment (SOFA) score in predicting the risk of mortality in ICU-admitted COVID-19 patients. Cross-sectional study. Place and Duration of the Study: COVID Intensive Care Unit (ICU), The Aga Khan University Hospital, Karachi,from January to June 2022. A total of 62 patients with a positive RT-PCR for COVID-19, admitted into the intensive care unit (ICU), were included in this descriptive cross-sectional study. Written informed consent was obtained after explaining the risks and benefits of the study to the patients / next of kin. SOFA score at the time of admission and 48 hours after admission was calculated. The outcome variable, i.e., mortality, was assessed in association with the SOFA score. Results: The study had a predominantly male population of 54.8% (n = 34). The SOFA score >7 at admission and 48 hours after admission was observed in 46.8% (n = 29) patients. Among 62 COVID-19 patients, the majority were found to have a severe nature of the disease, i.e., 69.4% (n = 43), followed by moderate / mild cases 30.6% (n = 19). Depending on the requirement of the patient, 74.2% (n = 46) were invasively ventilated while 77.4% (n = 48) were on non-invasive ventilation. Overall the mortality rate of the present study was 43.5% (n = 27). The scores both at the time of admission and 48 hours after admission for the survivors had a significant difference (p = 0.001) with the non-survivors. The SOFA score on admission and 48 hours after had a significant positive association with the severity of COVID-19 infection and its risk of mortality. COVID-19, Mortality prediction, SOFA score.

Evaluation of a commercial Real Time PCR for clinical samples without RNA extraction for detection of SARS-CoV-2

RT-PCR is the gold standard for diagnosis of COVID-19. All RT-PCR kits are based on RNA extraction from the clinical sample. There was a sudden increase in demand of these kits, both RNA extraction and COVID-19 RT-PCR kits during the pandemic. This sudden spurt in global demand created a situation of shortage of consumables, especially the RNA extraction kits. Hence, this study was carried out to evaluate and compare COVID-19 RT-PCR without RNA extraction step using buffer R3. Sensitivity, specificity and accuracy of RT-PCR kit without RNA extraction were 89.16 %, 100% and 89.6% respectively. This approach saved more than 50 % time compared to the RT-PCR kit with RNA extraction approach allowing enhanced daily sample processing capability. RT-PCR kit without RNA extraction help in managing a greater number of samples, reduces cost and turnaround time.

Comprehensive Study of the IBMP ELISA IgA/IgM/IgG COVID-19 Kit for SARS-CoV-2 Antibody Detection.

COVID-19 laboratory diagnosis primarily relies on molecular tests, highly sensitive during early infection stages with high viral loads. As the disease progresses, sensitivity decreases, requiring antibody detection. Since the beginning of the pandemic, serological tests have been developed and made available in Brazil, but their diagnostic performance varies. This study evaluated the IBMP ELISA IgA/IgM/IgG COVID-19 kit performance in detecting SARS-CoV-2 antibodies. A total of 90 samples, including 64 from COVID-19 patients and 26 pre-pandemic donors, were assessed based on time post symptom onset (0-7, 8-14, and 15-21 days). The kit showed 61% sensitivity, 100% specificity, and 72% accuracy overall. Sensitivity varied with time, being 25%, 57%, and 96% for 0-7, 8-14, and 15-21 days, respectively. Similar variations were noted in other commercial tests. The Gold ELISA COVID-19 (IgG/IgM) had sensitivities of 31%, 71%, and 100%, while the Anti-SARS-CoV-2 NCP ELISA (IgG) and Anti-SARS-CoV-2 NCP ELISA (IgM) showed varying sensitivities. The IBMP ELISA kit displayed high diagnostic capability, especially as the disease progressed, complementing COVID-19 diagnosis. Reproducibility assessment revealed minimal systematic and analytical errors. In conclusion, the IBMP ELISA IgA/IgM/IgG COVID-19 kit is a robust tool for detecting anti-SARS-CoV-2 antibodies, increasing in efficacy over the disease course, and minimizing false negatives in RT-PCR COVID-19 diagnosis.

Metabolic Syndrome as A Prognostic Factor for Outcome of Severe SARS-COV-2 Cases

Abstract Background SARS-COV-2 (Coronavirus Disease-2019), a disease caused by the coronavirus. SARS-CoV-2 (Sever Acute Respiratory Syndrome-Coronavirus-2) has emerged as a rapidly spreading communicable disease affecting more than 100 countries across the globe at present. Aim of the Work To illuminate to what extent metabolic syndrome can be used as a prognostic factor for outcomes of patients infected with SARS-COV-2. Primary outcome measure is ICU stay and outcome. Secondary outcome measures are Patients requiring MV and mortality. Patients and Methods This was a retrospective study in order to illuminate to what extent metabolic syndrome can be used as a prognostic factor for outcomes of patients infected with SARS-COV-2, with Primary outcome measure which was ICU stay and outcome, and Secondary outcome measures were Patients requiring MV and mortality. Ninety patients admitted to ICU for Pneumonic COVID-19 with a confirmed positive RT-PCR for COVID-19 and chest computed tomography was divided into two groups in Ain-shams University hospitals. Results Components of metabolic syndrome such as hypertension, type 2 diabetes mellitus (T2DM), and obesity are highly prevalent and significantly increase the risk of hospitalization and mortality in SARS-COV-2 patients. Conclusion MetS is a better prognostic indicator for severe disease outcomes in patients with COVID-19 than its individual components. Patients with MetS had a significantly higher need for ICU admission irrespective of their age, sex, or race. The need for mechanical ventilation was also higher across all patients with MetS. The association of MetS with higher mortality was significant for females, patients younger than 65 years of age.

Evaluation of the effect of COVID-19 infection in pregnancy and puerperium in a suburban medical college in West Bengal, India

ABSTRACT Background: The pandemic of SARS-CoV-2 was a novel situation, there was no conclusive knowledge, particularly concerning its effect on pregnant women and infants. Eminent obstetric organizations have introduced an array of guidelines to assist clinicians in countering this prior unknown outbreak. The primary objective of this study was to summarize the clinical characteristics, complications, and maternal and neonatal outcomes of COVID-19 during pregnancy and puerperium. Methods: This was a cross-sectional observational study conducted in the Outpatient/Emergency/Inpatient or COVID ward in the Department of Obstetrics and Gynaecology, of a tertiary hospital in Nadia district, West Bengal, India, from 1.7.2020 to 30.6.2021 including 104 pregnant or puerperal mothers with laboratory-confirmed, i.e., RT-PCR or Rapid Antigen Test positive reports after informed consent. The obstetric outcome, modes of delivery, and neonatal status including any complications or SNCU admission within six weeks postpartum were recorded. Results: The majority were in the ≥ 20–24 years age group, primigravida, residents of Nadia with no significant travel or contact history. 73.08% were affected in the third trimester and the comorbidities detected were chiefly anemia (15.38%), hypertensive or chronic liver diseases, and hypothyroidism. 45.19% of the mothers were asymptomatic while the other complaints were fever (18.27%), cough (11.55%), anosmia and/or ageusia (10.58%), sore throat (9.61%), respiratory distress, loose stools, and chest pain. The medical complications were predominantly low SpO2, convulsions, pneumonitis, and two maternal deaths. The obstetric complications were preterm birth (26.9%), pre-eclampsia/eclampsia (17.3%), antepartum (3.9%) and postpartum hemorrhage (4.4%), and sepsis (5.8%). Fourteen mothers had first-trimester termination, 63 had vaginal deliveries, and the rest had cesarean section. Out of 90 neonates, most were in the range of ≥ 2–2.5 kg birth weight and normal 1-min APGAR score. None tested positive for COVID-19 RTPCR and no detectable congenital anomaly or neonatal death was recorded.

The Enhancement of COVID-19 Severity on Coagulation Markers: a Cross-sectional Study in West Sumatra, Indonesia

Objective: This study aimed to determine the description of the coagulation marker and how it implicates COVID-19 patients based on clinical outcomes in the form of enhancement severity and death. Method: The subjects were collected from patients with positive COVID-19 RT-PCR with medical records including demographic data, and laboratory results such as hemoglobin, hematocrit, leukocytes, platelets, coagulation markers (D-dimer, PT, and APTT), and patients outcomes post-treatment. Statistical analysis is performed by using chi-square and Mann-Whitney tests were considered statistically difference level of significant between variables. Result: The COVID-19 patients is classified into mild group with 27 subjects (44.2%) and moderate-severe group 34 subjects (55.8%). Leukocytes, D-dimer, and PT levels significantly differed between mild and moderate-severe groups. All coagulation markers had a symptomatic effect on Covid-19 patients, increased D-dimer and prolonged prothrombin time in adult COVID-19 patients tend to be followed by the enhancement of severe symptoms and death

Outcome of RT-PCR in the Diagnosis of Patients with COVID-19 Symptoms: A Study in a COVID-19 Referral Hospital

<i>Introduction: </i>Corona virus (SARS-CoV-2) (COVID-19) outbreak was first reported in China rapidly spread around the world within short period causing global public health emergency. COVID 19 is a highly infectious disease caused by severe acute respiratory syndrome corona virus 2 (SARS-CoV-2). The initial symptoms were fever, cough, dyspnea, myalgia or fatigue, headache, hemoptysis, diarrhea and acute respiratory distress syndrome (ARDS). Hence in diagnosis of COVID-19 RT-PCR of viral nucleic acid is regarded as the reference standard to detect the COVID-19 positive cases. <i>Objective: </i>The aim of this study was to determine the outcome of RT-PCR of the patients with COVID-19 symptoms. <i>Methodology: </i>This was a cross-sectional prospective study carried out in the department of Radiology and imaging in collaboration with the department of Virology and COVID unit in IbnSina Hospital, Dhaka, Bangladesh during January, 2022 to June, 2022. A total of 239 OPD patients with COVID-19 symptoms aged above 18 years were enrolled in this study. The collected data were cleaned, edited and entered into computer for analysis. The data were analyzed using Statistical Package for Social Sciences (SPSS) software, version 23.0. The ethical clearance of this study was obtained from the Ethics Committee of School of Public Health & Life Science, University of South Asia, and Dhaka, Bangladesh. <i>Results: </i>In this study a total of (n=239) patients with COVID-19 symptoms were enrolled. According to age distribution, the majority., 142 (59.42%) patients belonged to the age group >52 years, which was the highest and followed by 44 (18.42%) age group (43-52) years, 36 (15.06%) (33-42) years, 14 (5.85%) (22-32) years and 3 (1.25%) <22 years. According to sex distribution, the majority, 167 (69.85%) were male and 72 (30.12%) were female. Distribution by symptoms, all the patients239 (100%) had general weakness and followed by sneezing 221 (92.46%), fever 236 (98.74%), headache 228 (95.39%), cough 232 (97.07%), respiratory distress, 225 (94.14%), cough and SOB, 237 (99.16%), loss of smell, 212 (88.74%), lac of apatite, 224 (73.72%), asthma 218 (91.21%) and pneumonia, 118 (49.37%). In RT_PCR lab test results, the majority 195 (81.58%) were observed COVID-19 Negative (-) and 44 (18.41%) were observed COVID-19 Positive (+). Among the positive cases, the majority 26 (60%) were male and 18 (40%) were female. <i>Conclusion: </i>This study prevailed around 20 % of the patients with COVID-19 symptoms got COVID-19 Positive in RT-PCR lab test results. Therefore, the patients with COVID-19 symptoms must conduct RT-PCR lab test for their being sure of their COVID-19 affection. At the same time, the male are more vulnerable to COVID-19 than their counter part female.

Final assessment of the COVID-19 pandemic impact between the different social and economic strata population of the city of Buenos Aires

BackgroundDuring the pandemic, epidemiological communications reported an estimation of excess deaths. However, the final calculation requires a detailed analysis. The study aim was to ascertain the number and distribution of COVID-19 fatalities among various socio-economic strata in a large, moderate to low-income city. Study designObservational time series analysis in a large city, treated as a natural experiment. MethodsAnalysis of death certificates, demographic data, and health system records of positive RT-PCR COVID-19 tests from 2015 to 2021, categorizing by age, sex, and place of residence. The study measured the pandemic's impact on mortality, including COVID and non-COVID deaths, using corrected Poisson regression models for different demographics and assessing socio-economic status impact via ecological community-level analysis. ResultsCompared to the pre-pandemic period (2015–2019, IRR = 1.00), the sex- and age-adjusted rate of all-cause death increased significantly during the pandemic (2020–2021) IRR = 1.109 [1.054–1.167], p < 0.0001. This was observed in both males (IRR = 1.158 [1.1–1.219], p < 0.0001) and females (IRR = 1.068 [1.016–1.124], p = 0.01). There was no observed effect of the pandemic on the historical trend in the progressive reduction of mortality in people under 35 years of age. The increase in deaths was at the expense of COVID (+11,175 deaths) and cardiovascular causes (IRR = 1.114 [1.020–1.217] p = 0.017). During the pandemic, there was a significant increase in deaths at home (IRR = 1.219 [1197–1.242], p < 0.0001), especially in people dying of cardiovascular causes (IRR = 1.391 [1.360–1.422], p < 0.0001). The increase in the adjusted mortality rate during the pandemic was socially conditioned. ConclusionsThe pandemic not only led to increased COVID-19 mortality but also heightened fatalities from non-COVID causes, reflecting a potential bias in healthcare resource allocation towards SARS-CoV-2 at the expense of chronic pathologies care.

A comparative study of SAR-CoV-2 detection using RT-PCR based testing from a nasopharyngeal swab versus indwelling tracheostomy in patients with a tracheostomy

Background Nasopharyngeal swab RT-PCR is the standard procedure for COVID-19 testing. In patients with tracheostomy with an altered airway that bypasses the nasopharynx, the yield of samples from different sites is unknown. This information will be essential for formulating a sample collection method for COVID-19 RT-PCR testing in patients undergoing tracheostomy. Methods This was a cross-sectional study. Nasopharyngeal swabs and tracheal secretion (via closed-circuit secretion suction) samples were collected from 100 patients with a non-plugging tracheostomy tube at Thammasat University Hospital, Pathum Thani, Thailand. The participants were aged between 1-96 years old for screening purposes during the pandemic. The detection results and cycle threshold (Ct) values from each site were analyzed using McNemar’s test with a 95% confidence interval. Results Four participants had positive results. One patient tested positive only for the nasopharyngeal swab, whereas the other tested positive only for the tracheal secretion sample. No statistically significant difference was found between the discordant and concordant groups (P = 1). Conclusions We found two discordant results among the four positive cases in the 100 patients. One patient tested positive only from the nasopharyngeal swab, whereas the other tested positive only from the tracheal sample. The percentage of agreement was 98, and the kappa coefficient value was 65.64% (p &lt;0.001). According to these results, one sample from the nasopharynx or tracheal tube should be sufficient to determine the infection status of low-risk patients. For highly suspicious cases, multisite sampling should be performed. This study showed discordance in COVID-19 RT-PCR screening results using samples from nasopharyngeal swabs and tracheal secretions in tracheotomized patients. A multiple-site sample is suggested for highly suspicious patients with tracheostomy.

Incidence of perioperative complications in COVID-19 survivors: Prospective observational clinical trial.

As long as the COVID-19 pandemic continued, the continuation of elective surgery had been unavoidable. There is still no consensus on the timing of elective surgery in patients who have recovered from COVID-19. The primary aim of this study was to determine the effect of time after COVID-19 infection on perioperative complications. This prospective observational single center included adult patients who had recovered from COVID-19 and underwent surgery between February and July 2021. Data were prospectively collected from the patient and hospital database, the preoperative evaluation form and the perioperative anesthesia forms. A total of 167 patients were included in our study. Preoperative COVID-19 RT-PCR test results were negative in all patients. The mean time of positive COVID-19 diagnosis was 151.0 ± 74.0 days before the day of surgery. Intraoperative general and airway complications occurred in 33 (19.8%) and 17 (10.2%) patients, respectively. Although the time from COVID-19 positivity to surgery was shorter in patients with intraoperative general and airway complications, the difference between the groups did not reach statistical significance (P = .241 and P = .133, respectively). The median time from COVID-19 positivity to surgery in patients with and without postoperative complications was 156.0 (min: 27.0-max: 305.0) and 148.5 (min: 14.0-max: 164.0) days, respectively (P = .757). In patients with and without oxygen support in the postoperative period, the median time from COVID-19 positivity to surgery was 98.0 (min: 27.0-max: 305.0) and 154.0 (min: 14.0-max: 364.0) days, respectively. In patients who received oxygen support in the postoperative period, the time from COVID-19 positivity to surgery was shorter and the difference between the groups was statistically significant (P = .014). The incidence of perioperative complications decreased with increasing time after a positive SARS-CoV-2 infection, but there was no difference in perioperative complications between the groups. As the time between COVID-19 positivity and surgery increased, the need for oxygen support in the postoperative period decreased. It is not possible to share clear data on the timing of operation after SARS-CoV-2 infection.

Association of chest computed tomography severity score at ICU admission and respiratory outcomes in critically ill COVID-19 patients.

To evaluate the association of a validated chest computed tomography (Chest-CT) severity score in COVID-19 patients with their respiratory outcome in the Intensive Care Unit. A single-center, prospective study evaluated patients with positive RT-PCR for COVID-19, who underwent Chest-CT and had a final COVID-19 clinical diagnosis needing invasive mechanical ventilation in the ICU. The admission chest-CT was evaluated according to a validated Chest-CT Severity Score in COVID-19 (Chest-CTSS) divided into low ≤50% (<14 points) and >50% high (≥14 points) lung parenchyma involvement. The association between the initial score and their pulmonary clinical outcomes was evaluated. 121 patients were clustered into the > 50% lung involvement group and 105 patients into the ≤ 50% lung involvement group. Patients ≤ 50% lung involvement (<14 points) group presented lower PEEP levels and FiO2 values, respectively GEE P = 0.09 and P = 0.04. The adjusted COX model found higher hazard to stay longer on invasive mechanical ventilation HR: 1.69, 95% CI, 1.02-2.80, P = 0.042 and the adjusted logistic regression model showed increased risk ventilator-associated pneumonia OR = 1.85 95% CI 1.01-3.39 for COVID-19 patients with > 50% lung involvement (≥14 points) on Chest-CT at ICU admission. COVID-19 patients with >50% lung involvement on Chest-CT admission presented higher chances to stay longer on invasive mechanical ventilation and more chances to developed ventilator-associated pneumonia.

Non-Invasive Specimen Collection in COVID-19 RT-PCR Testing: An Observational Study at an Indonesian Tertiary Hospital

Background: COVID-19 is a disease of SARS-CoV2 beta coronavirus infection. One way to control the progression of COVID-19 symptoms is a rapid and accurate diagnosis. The current gold standard of COVID-19 diagnostic method uses RT-PCR from nasopharyngeal (NP) swabs and sputum specimens. Objective: To assess the efficacy of saliva and rectal swabs as non-invasive alternatives to the conventional nasopharyngeal swab for RTPCR testing in COVID-19 diagnosis, with a focus on the potential benefits for healthcare providers and patient comfort. Methods: This observational study was conducted with 80 confirmed cases at a tertiary hospital in Indonesia, the study compared RTPCR positivity rates among different collection methods. Results: A high positivity rate of 92% for nasopharyngeal swabs, with saliva and rectal swabs yielding 36% and 34%, respectively. Notably, the positivity rates for saliva and rectal samples increased to 60% and 50% when testing occurred between five to seven days post-symptom onset. Crucially, in older patients, both saliva and rectal swabs demonstrated higher positivity rates than in younger patients within the initial four days of symptom onset, with rates of 43% and 17%, respectively. Furthermore, a significant correlation was found between rectal swab positivity on day one and mortality in the older cohort, where lower Ct values on day seven were significantly associated with the deceased group. Conclusion: These findings support the potential of saliva and rectal swabs in predicting disease severity and patient outcomes, suggesting a safer and more convenient testing strategy for COVID- 19.

IJCM_296A: Assessment of burden of Long Covid, and it's determinants among patients with Long Covid in the rural community in Bengaluru Rural District – A community based cross sectional study.

Background: Longer-term consequences after SARS-CoV-2 infection are becoming an important burden to societies and healthcare systems. Long COVID-19 and post COVID-19 conditions are terms used clinically to describe ongoing or new symptoms that occur beyond 12 weeks of recovery from an acute infection, that cannot be explained by an alternative medical diagnosis. It is now understood that COVID-19 can impact on multiple organ systems, which can lead to a diverse range of persistent symptoms including fatigue, breathlessness, cough, loss of taste and/or smell, myalgia, memory issues and gastrointestinal problems. Very few studies have been conducted globally to assess the burden of Long Covid which are in hospital setting and none published in Karnataka state. This community based cross sectional study intends to bridge the gap in existing evidence pool and to influence evidence-based policy decisions at local administrative level. Objectives: To assess the prevalence of Long covid among people infected with COVID-19 in rural community Bengaluru rural district. Methodology: Community based cross sectional study was conducted between October 2023 to November 2023 in Orohalli &amp; Jadigenahalli Panchayaths of Hoskote Taluk. After obtaining written and informed consent from the participants, all adults &gt; 18years of age residing in identified villages, with COVID-19 RTPCR positive status, tested at least 12 weeks/ 3 months prior to the date of interviewed using a prevalidated questionare and Fatigue Assessment Scale. Data is analysed using SPSS trial version 21. Results: 420 participants were interviewed in 17 villages. Mean period between date of COVID positivity to date of interview was 490 days. 27 (6.4%) participants reported residual symptoms from COVID 19 infection suggestive of Long Covid. Majority of them complained of fatigue. Out 25 respondents with fatigue, 18 people had a score &gt; 22 on FAS, indicative of clinical fatigue. Older age &gt;60years, female gender, and ICU admission during infection, were associated with higher prevalence of long covid and are statistically significant (p value&lt; 0.05) Conclusion: It is essential to determine the burden of longer-term consequences of SARS-CoV-2 infection and the needs of affected individuals, to successfully plan healthcare services and efficiently allocate public health resources.

Comparison of seven commercial RT-PCR kits with the NIV kit for the diagnosis of Covid-19

Objectives Coronavirus disease 2019 (COVID-19) caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) spread across the globe in an unprecedented manner and was declared a pandemic on March 11, 2020 by the World Health Organization (WHO). This study was carried out with the aim to compare the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and agreement of the eight different RT-PCR kits for the diagnosis of COVID-19. Material and Methods This observational cross-sectional study was carried out in the Department of Microbiology of a tertiary care hospital in Central Delhi from July to October 2021. A total of 45 nasopharyngeal and/or oropharyngeal swabs in Viral Transport Medium (VTM) from suspected COVID-19 patients were received in the laboratory for RT-PCR. These samples were tested by eight different Indian Council of Medical Research (ICMR)-approved RT-PCR kits with different gene targets. The comparison was made with the National Institute of Virology (NIV), the Pune COVID-19 RT-PCR kit. Statistical analysis: sensitivity, specificity, PPV, and NPV were calculated for each kit and compared using the McNemar test. Agreement of different kits was evaluated using Kappa analysis. Results The results of the 45 samples of suspected COVID-19 cases were recorded as per the cycle threshold (Ct) provided in the kit insert. Of these, 15 samples detected both E and RdRp genes and 30 were negative for both the genes of SARS CoV-2 by NIV, the Pune COVID-19 RT-PCR kit. All kits showed 100% sensitivity and had 100% NPV when compared with the NIV kit. However, specificity, PPV, and agreement were variable as compared to the NIV kit. Conclusion The reporting should be carried out as per the manufacturer’s instructions. However, positive results with Ct values ≥ 36 showed variable results with different RT PCR kits and hence should be interpreted with caution.

Novel COVID-19 biomarkers identified through multi-omics data analysis: N-acetyl-4-O-acetylneuraminic acid, N-acetyl-L-alanine, N-acetyltriptophan, palmitoylcarnitine, and glycerol 1-myristate.

This study aims to apply machine learning models to identify new biomarkers associated with the early diagnosis and prognosis of SARS-CoV-2 infection.Plasma and serum samples from COVID-19 patients (mild, moderate, and severe), patients with other pneumonia (but with negative COVID-19 RT-PCR), and healthy volunteers (control) from hospitals in four different countries (China, Spain, France, and Italy) were analyzed by GC-MS, LC-MS, and NMR. Machine learning models (PCA and PLS-DA) were developed to predict the diagnosis and prognosis of COVID-19 and identify biomarkers associated with these outcomes.A total of 1410 patient samples were analyzed. The PLS-DA model presented a diagnostic and prognostic accuracy of around 95% of all analyzed data. A total of 23 biomarkers (e.g., spermidine, taurine, L-aspartic, L-glutamic, L-phenylalanine and xanthine, ornithine, and ribothimidine) have been identified as being associated with the diagnosis and prognosis of COVID-19. Additionally, we also identified for the first time five new biomarkers (N-Acetyl-4-O-acetylneuraminic acid, N-Acetyl-L-Alanine, N-Acetyltriptophan, palmitoylcarnitine, and glycerol 1-myristate) that are also associated with the severity and diagnosis of COVID-19. These five new biomarkers were elevated in severe COVID-19 patients compared to patients with mild disease or healthy volunteers.The PLS-DA model was able to predict the diagnosis and prognosis of COVID-19 around 95%. Additionally, our investigation pinpointed five novel potential biomarkers linked to the diagnosis and prognosis of COVID-19: N-Acetyl-4-O-acetylneuraminic acid, N-Acetyl-L-Alanine, N-Acetyltriptophan, palmitoylcarnitine, and glycerol 1-myristate. These biomarkers exhibited heightened levels in severe COVID-19 patients compared to those with mild COVID-19 or healthy volunteers.