RT-PCR Test Research Articles

Assessment of porcine reproductive and respiratory syndrome virus (PRRSV) farm surface contamination through environmental sampling

BackgroundDuring the fall of 2020, the porcine reproductive and respiratory syndrome virus (PRRSV) L1C.5 variant emerged and rapidly spread throughout southern Minnesota generating questions regarding possible transmission routes. This study aimed to investigate whether PRRSV could be detected on surfaces inside and outside pig barns housing L1C.5 variant PRRSV-positive pigs to illustrate the potential for indirect transmission of PRRSV. Seven Midwestern U.S. PPRS-positive breeding or growing pig farms and one PRRS-negative farm were conveniently selected. Internal and external barn surfaces were wiped using a PBS moistened cloth and the resulting liquid was submitted to the University of Minnesota Veterinary Diagnostic Laboratory for PRRSV RT-PCR testing and virus isolation.ResultsAll (n = 26) samples from PRRSV-negative farm tested negative. Nineteen (13%) out of 143 samples from positive farms yielded positive RT-PCR results. Positive samples originated primarily from exhaust fan cones and doorknobs, followed by anteroom floor and mortality carts/sleds. Virus isolation attempted on two samples did not yield positive results.ConclusionsPRRSV contamination can occur on surfaces inside and outside pig barns that are in frequent contact with farm personnel. Although virus isolation attempts were negative, our results illustrate the potential for PRRSV to be transmitted indirectly through contaminated materials or farm personnel. The study supports the implementation of biosecurity practices by farm personnel to prevent the introduction of PRRSV into farms and the prevention of PRRSV transmission between farms.

Comparison of Abbot ID Now Method with Eurobioplex RT-PCR SARS-Cov-2 Multiplex Method for Detection of SARS-Cov-2 from Nasopharyngeal and Oropharyngeal Samples

Background: COVID 19 created an urgent demand for rapid diagnosis to encircle this pandemic and improve patient management. In this context, we evaluated the concordance of the ID NOW test compared to the Eurobioplex RT-PCR test in the rapid diagnosis of SARS-CoV-2. Methods: To evaluate the concordance of the assay at different viral loads, 154 positive samples were selected to represent the full range of Ct values observed on the Eurobioplex RT-PCR assay, ranging from 14 to 38 cycles. Positive concordance for the ID Now assay was calculating dusing Eurobioplex RT-PCR as the reference test. An additional 70 negative samples were selected to assess negative concordance. Results: Compared to Eurobioplex RT-PCR, the overall positive agreement was 79% with ID Now. Negative agreement was 100% for ID Now. ID Now showed 100% positive agreement for medium and high viral concentrations (Ct value <30). However, for Ct values >30, the positive agreement was 33.3% for ID Now. Conclusions: This study shows a major limitation of ID Now for specimens collected in universal transport media with lower viral concentrations. Further studies are necessary to evaluate the performance of ID Now for dry nasopharyngeal swabs (manufacturer's recommended method).

COVID-19 breakthrough infections in vaccinated individuals at BPKIHS, Nepal

BackgroundAlthough there have been reports of COVID-19 breakthrough infections in vaccinated individuals, the vaccines have demonstrated a high efficacy in preventing severe illness and death. Nepal has reported fewer studies of COVID-19 breakthrough infections. Hence, this study has objective to assess the prevalence, and to describe clinical characteristics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) breakthrough infection.MethodsThis descriptive study was conducted from January to December 2022. The study enrolled 200 individuals who had received the recommended doses of the COVID-19 vaccine and they were RT-PCR positive diagnosed with vaccine breakthrough infections after 14 days of completing the vaccination course. The patient’s demographic and clinical profiles, as well as their outcomes in terms of severity, length of hospital stay, and mortality were recorded.ResultsThe prevalence of SARS-CoV2 infection was 6.3% (547/8682). Among fully vaccinated personnel, the prevalence of breakthrough infections was 6.2% (200/3175). This study found the Omicron variants in respondents. The mean age of the patients was 38.28 years, and 41.5% (83/200) of the breakthrough cases were healthcare workers. The mean time gap between the second dose of vaccination and a positive RT-PCR test was 354.68 days. Of the 200 breakthrough cases, 89% (178) had mild symptoms, 9% (17) had moderate symptoms requiring hospitalization, and 2% (4) were severe cases that required intensive care facility. Among the severe cases, 3 out 4 were above 60 years old. Furthermore, the patients greater than 60 years had longer hospital stays (p < 0.0001) however no deaths were recorded.ConclusionFully vaccinated individuals can experience COVID-19 breakthrough infections and the majority of cases present with mild symptoms. Elderly patients have a higher likelihood of severe disease and longer hospital stay compared to younger patients. The results of this study emphasize the importance of vaccination in mitigating the severity of the disease.

Comparative Analysis of the Mitochondrial Genome of Eggplant (Solanum melongena L.) to Identify Cytoplasmic Male Sterility Candidate Genes.

Cytoplasmic male sterility (CMS) is important for commercial hybrid seed production. However, it is still not used in eggplant (Solanum melongena L.), and corresponding regulatory genes and mechanisms of action have not been reported. We report CMS line 327A, which was derived from the hybridization between cultivated and wild eggplants. By looking at different stages of anther development under a microscope, we saw that the 327A anther's tapetum layer vacuolized during meiosis, which caused abortion. To investigate the 327A CMS regulatory genes, the mitochondrial genomes of 327A and its maintainer line 327B were assembled de novo. It was found that 15 unique ORFs (Open Reading Frame) were identified in 327A. RT-PCR and RT-QPCAR tests confirmed that orf312a and orf172a, 327A-specific ORFs with a transmembrane domain, were strongly expressed in sterile anthers of 327A. In addition, orf312a has a chimeric structure with the ribosomal protein subunit rpl16. Therefore, orf312a and orf172a can be considered strong candidate genes for CMS. Concurrently, we analyzed the characteristics of CMS to develop a functional molecular marker, CMS312, targeting a future theoretical basis for eggplant CMS three-line molecular breeding.

SARS-COV-2 breakthrough infection and its covariates among healthcare providers of a hospital in Bangladesh during the omicron wave

IntroductionBreakthrough infection by SARS-COV-2 virus among vaccinated individuals has been reported from all over the world and it has created a substantial challenge in designing strategies to live with the virus in the post-pandemic era. Factors affecting the extent and nature of breakthrough infection are still not fully understood and those are known to vary depending on host and agent factors. Health Care Workers (HCWs), especially in hospital settings, are front-liners in combating the epidemic and, consequently, they are more vulnerable to breakthrough infection by SARS-COV-2. Like most of the countries of the world, Bangladesh went through several waves of COVID-19 and the last (3rd wave) was the widespread Omicron wave during the winter of 2022. HCWs in Bangladesh have been disproportionately affected by the virus. Under this context, the aim of the present study was to explore breakthrough infection (BTI) and its host-related covariates among HCWs of a COVID-dedicated city-based hospital during the Omicron wave in Bangladesh. Materials and methodsAn observational cross-sectional study was conducted on 267 HCWs of the Narayanganj Tertiary (300-bed) hospital during February–March 2022 which coincided with the terminal part of the 3rd wave. Data were collected by trained Field Assistants using Interviewer-administered Data Collection Forms with Questionnaires as instruments. Previous COVID-19 status (any time after the onset of the pandemic and within last 3 months) was explored by the history of specific symptoms as well as by the confirmatory rtPCR test reports from DGHS approved laboratories Anti-nucleocapsid antibody (Anti-N-Ab) in venous blood samples, assayed by a chemiluminescent ELISA technique, was used as a seroprevalence-based marker of breakthrough infection during the preceding few months. Data were analyzed by bivariate as well as multivariate statistics using the IBM-SPSS software. ResultsThe median age (range) of the HCWs was 38 (21–65) years; Body Mass Index (BMI, kg/m2) 25 (15–49); and Waist-Hip Ratio (WHR) was 0.92 (0.46–1.21). The male subjects had significantly higher median age (p = 0.01) and higher WHR (p = 0.001) as compared to the female subjects. As per the BMI category, subjects with overweight and obesity constituted 83.3 % of the male subjects as compared to 61.6 % of the female subjects (p = 0.001). The time lapse between receiving of 3rd dose and blood sampling was significantly higher among females compared to males (median days 60 vs 49, p < 0.02) indicating earlier vaccination with 1st booster dose among females. A proportion of 51.85 % male and 49.68 % female subjects showed Anti-N-Ab positivity; there was no significant difference between the gender groups. Also, there was no significant difference among male and female subjects regarding the Ab levels. On Spearman correlation analysis, a tendency of association of WHR with Ab level was observed among the male subjects; however, the association did not show statistical significance (p = 0.09). On binary logistic regression Ab positivity was found to be independently associated with WHR (p = 0.03), and prior SARS-COV-2 infection within the last 3 months (p = 0.02) among males. When all the subjects were considered together, COVID symptom positivity during the last 3 months (p = 0.067) and receiving the 1st booster dose (p = 0.07) showed a tendency of association with Ab positivity. On multiple regression analysis, Ab levels showed a negative association with WHR (p = 0.035) among males. ConclusionsMore than 50 % of the vaccinated hospital-based HCWs in Bangladesh suffered from BTI during the winter of 2022 when the Omicron wave (the 3rd wave) of COVID-19 was at its peak. The data also indicate that overweight and obesity are major host-related risk factors underlying BTI. Inadequate coverage by a booster dose seems to be another determinant of BTI and the level of immune response in this population.

Development of a clinical prediction score for Ebola virus disease screening at triage centers in the Democratic Republic of the Congo.

The 2018-2020 Ebola virus disease (EVD) outbreak in the Democratic Republic of the Congo (DRC) was the largest since the disease's discovery in 1976. Rapid identification and isolation of EVD patients are crucial during triage. This study aimed to develop a clinical prediction score for EVD using clinical and epidemiological predictors. We conducted a retrospective cross-sectional study using surveillance data from EVD outbreak, collected during routine clinical care at the Ebola Transit Center (ETC) in Beni, DRC, from 2018 to 2020. The Spiegelhalter and Knill-Jones method was used for score development, including potential predictors with an adjusted likelihood ratio above 2 or below 0.50. Validation was performed using a dataset previously published in PLOSOne by Tshomba et al. Among 3725 patients screened, 3698 fulfilled the inclusion criteria, with 571 (15.4%) testing positive for EVD via RT-PCR Test. Seven predictive factors were identified: asthenia, sore throat, conjunctivitis, bleeding gums, hematemesis, contact with a sick person, and contact with a traditional healer. The prediction score achieved an Area under the receiver operating characteristic (AUROC) of 0.764, with 81.4% sensitivity and 53.6% specificity at a -1 cutoff. External validation demonstrated an AUROC of 0.766, with 80.8% sensitivity and 41.4% specificity at the -1 cutoff. Our study developed a screening tool to assess the risk of suspected patients developing EVD and being admitted to ETUs for RT-PCR testing and treatment. External validation results affirmed the model's reliability and generalizability in similar settings, suggesting its potential integration into clinical practice. Given the severity and urgency of EVD as well as the risk nosocomial EVD transmission, it is essential to continuously update these models with real-time data on symptoms, disease progression, patient outcomes and validated RDT during EVD outbreaks. This approach will enhance model accuracy, enabling more precise risk assessments and more effective outbreak management.

Surveillance of SARS-CoV-2 prevalence from repeated pooled testing: application to Swiss routine data.

Surveillance of SARS-CoV-2 through reported positive RT-PCR tests is biased due to non-random testing. Prevalence estimation in population-based samples corrects for this bias. Within this context, the pooled testing design offers many advantages, but several challenges remain with regards to the analysis of such data. We developed a Bayesian model aimed at estimating the prevalence of infection from repeated pooled testing data while (i) correcting for test sensitivity; (ii) propagating the uncertainty in test sensitivity; and (iii) including correlation over time and space. We validated the model in simulated scenarios, showing that the model is reliable when the sample size is at least 500, the pool size below 20, and the true prevalence below 5%. We applied the model to 1.49 million pooled tests collected in Switzerland in 2021-2022 in schools, care centres, and workplaces. We identified similar dynamics in all three settings, with prevalence peaking at 4-5% during winter 2022. We also identified differences across regions. Prevalence estimates in schools were correlated with reported cases, hospitalizations, and deaths (coefficient 0.84 to 0.90). We conclude that in many practical situations, the pooled test design is a reliable and affordable alternative for the surveillance of SARS-CoV-2 and other viruses.

Evaluation of the COVID-19 vaccine effectiveness on the outcomes of COVID 19 disease in Iran: a test-negative case-control study.

This study measures the COVID-19 vaccine effectiveness (CVE) against hospital admission and severe COVID-19. This study is a test-negative case-control design using data from eight provinces in April, 2021 until March, 2022. The individuals were classified as cases and controls based on the results of the RT-PCR test for SARS-CoV-2 and matched based on the timing of the test being conducted as well as the timing of hospital admission. The measure of association was an odds ratio (OR) by univariate and multiple logistic regression. The multiple logistic regression has been carried out to take confounding factors and potential effect modifiers into account. The CVE was computed as CVE = (1 - OR)*100 with 95% confidence interval. Among 19314 admitted patients, of whom 13216 (68.4%) were cases and 6098 (31.6%) were controls, 1313 (6.8%) died. From total, 5959 (30.8%) patients had received the vaccine in which one, two, and booster doses were 2443 (12.6%), 2796 (14.5٪), and 720 (3.7٪), respectively. The estimated adjusted effectiveness of only one dose, two doses and booter vaccination were 22% (95% CI: 14%-29%), 35% (95% CI: 29%-41%) and 33% (95% CI: 16%-47%), respectively. In addition, the adjusted vaccine effectiveness against severe outcome was 33% (95% CI: 19%- 44%), 34% (95% CI: 20%- 45%) and 20% (95% CI: -29%- 50%) for those who received one, two and booster vaccinations, respectively. Our study concluded that full vaccination, though less effective compared to similar studies elsewhere, decreased hospital admissions and deaths from COVID-19 in Iran, particularly during the Delta variant period, with an observed decline during the Omicron variant dominance.

Bacterial sepsis causes more dramatic pathogenetic changes in the Th1 pathway than does viral (COVID-19) sepsis: a prospective observational study of whole blood transcriptomes

ObjectivesThis study aimed to comprehensively compare host responses of patients with bacterial sepsis and those with viral (COVID-19) sepsis by analyzing messenger RNA (mRNA) and microRNA (miRNA) profiles to shed light on their distinct pathophysiological mechanisms.DesignProspective observational study.SettingWhole blood RNA sequencing was used to analyze mRNA and miRNA profiles of patients diagnosed as having bacterial sepsis or viral (COVID-19) sepsis at the Department of Trauma and Emergency Medicine, Osaka University Graduate School of Medicine.PatientsTwenty-two bacterial sepsis patients, 35 viral (COVID-19) sepsis patients, and 15 healthy subjects admitted to the department were included. We diagnosed bacterial sepsis patients according to the sepsis-3 criterion that the Sequential Organ Failure Assessment score must increase to 2 points or more among patients with suspected infections. Viral (COVID-19) sepsis patients were diagnosed using SARS-CoV-2 RT-PCR testing, and presence of pneumonia was assessed through chest computed tomography scans.InterventionsNone.Measurements and main resultsFor RNA sequencing, 14,500 mRNAs, 1121 miRNAs, and 2556 miRNA-targeted mRNAs were available for analysis in the bacterial sepsis patients. Numbers of genes showing upregulated: downregulated gene expression (false discovery rate < 0.05, |log2 fold change| > 1.5) were 256:2887 for mRNA, 53:5 for miRNA, and 49:2507 for miRNA-targeted mRNA. Similarly, in viral (COVID-19) sepsis patients, 14,500 mRNAs, 1121 miRNAs, and 327 miRNA-targeted mRNAs were analyzed, with numbers of genes exhibiting upregulated: downregulated gene expression of 672:1147 for mRNA, 3:4 for miRNA, and 165:162 for miRNA-targeted mRNA. This analysis revealed significant differences in the numbers of upregulated and downregulated genes expressed and pathways between the bacterial sepsis and viral (COVID-19) sepsis patients. Bacterial sepsis patients showed activation of the PD-1 and PD-L1 cancer immunotherapy signaling pathway and concurrent suppression of Th1 signaling.ConclusionOur study illuminated distinct molecular variances between bacterial sepsis and viral (COVID-19) sepsis. Bacterial sepsis patients had a greater number of upregulated and downregulated genes and pathways compared to viral (COVID-19) sepsis patients. Especially, bacterial sepsis caused more dramatic pathogenetic changes in the Th1 pathway than did viral (COVID-19) sepsis.

Comparison of Clinical, Laboratory, and Radiological Symptoms of Patients Hospitalized in the COVID-19 Wards of Imam Reza Hospital in Mashhad During the First, Second, and Third Peaks of COVID-19

Background: Considering that few studies have investigated the differences in clinical, laboratory, and imaging symptoms of patients with coronavirus disease 2019 (COVID-19) during different peaks of the disease in Iran, the present study compares the patients who were admitted to the COVID-19 departments of Imam Reza Hospital during the first, second, and third peaks of the disease. Methods: In this cross-sectional study, data were collected by reviewing the files of patients with a definite diagnosis of COVID-19 based on the RT-PCR test in Imam Reza Hospital in Mashhad. The patients were divided into three groups based on the time of admission: The first peak from March 2020 to June 2020, the second peak from July to September 2020, and the third peak from October to December 2020. The variables evaluated in this study included demographic information, clinical signs and symptoms, and laboratory and radiological findings. Descriptive qualitative data were reported using frequency tables, while quantitative descriptive data were reported using measures of central tendency and dispersion. A comparison of qualitative data among the three peaks was conducted using the chi-square test, while for quantitative data, the ANOVA test was used followed by appropriate post-hoc tests. Results: A total of 561 patients with an average age of 58.90 ± 16.80 years were included in the study, of which 336 (59.9%) were male. Regarding underlying diseases, significant differences were found in age (P &lt; 0.001), smoking (P &lt; 0.001), diabetes (P = 0.003), high blood pressure (P &lt; 0.001), asthma (P = 0.025), and ischemic heart disease (P &lt; 0.001). For vital signs, significant differences were observed in heart rate (P &lt; 0.001), respiration rate (P &lt; 0.001), diastolic blood pressure (P = 0.010), and SPO2 (P &lt; 0.001). In clinical characteristics, significant differences were found in fever (P &lt; 0.001), nausea (P = 0.011), vomiting (P = 0.031), headache (P &lt; 0.001), weakness (P &lt; 0.001), and sore throat (P &lt; 0.001). In laboratory characteristics, significant differences were observed in white blood cell (WBC) count (P = 0.024), neutrophil percentage (P &lt; 0.001), lymphocyte percentage (P &lt; 0.001), and C-reactive protein (CRP) (P = 0.001). The CT score values of the patients were significantly different between the three peaks. Patient mortality was significantly different across the three peaks. Less than 15% of hospitalized patients died in the first peak, while over 24% died in the second peak and nearly 40% of inpatients died in the third peak. In our study, the first and third surges and the second and third surges had different mortalities. Conclusions: The third and first peaks had the highest and lowest mortality rates, respectively. Underlying diseases and unstable vital signs were more common in the second and third peaks. Patients in the second peak had significantly higher CT scores compared to the other peaks.

Understanding the dissemination of viruses and viroids identified through virome analysis of major grapevine rootstocks and RPA-based detection of prevalent grapevine virus B

Grapevine stocks are generally vegetatively propagated for the commercial cultivation. The propagation is predominantly done on rootstocks with >90 % of plant stocks propagated on Dogridge rootstock alone in India. Three additional rootstocks i.e. Paulsen, SO4 and Ramsey are also used for grapevine propagation on a limited scale. However, no information is available on the health status of these rootstocks being used by nurserymen and growers. Therefore, these rootstocks were collected from nurseries of five different locations and subjected to high-throughput sequencing (HTS) to determine the spectrum of viruses and viroids. The de novo assembly of unaligned reads revealed the presence of genome sequences of nine viruses viz. grapevine rupestris stem pitting-associated virus (GRSPaV), grapevine leafroll-associated virus 3 (GLRaV-3), grapevine leafroll-associated virus 4 (GLRaV-4), grapevine virus A (GVA), grapevine virus B (GVB), grapevine virus D (GVD), grapevine virus F (GVF), grapevine virus L (GVL), grapevine fleck virus (GFkV) and five viroids viz. hopstunt viroid (HSVd), grapevine yellow speckle viroid 1 and 2 (GYSVd-1 and GYSVd-2), Australian grapevine viroid (AGVd) and grapevine latent viroid (GLVd). The identified viruses and viroids were further confirmed through RT-PCR and Sanger sequencing. Indexing for the presence of these graft-transmissible pathogens in 43 rootstocks and 23 scion samples collected through field surveys indicated that infected rootstocks are the probable source for dissemination of these viruses and viroids in grapevine scions. As GVB was the most prevalent virus in all the rootstocks and scions as observed in RT-PCR testing, a simplified crude sap-based recombinase polymerase amplification (RPA) assay was optimized for its rapid detection. The present study highlights that grapevine rootstocks are reservoir of viruses and viroids and source for their dissemination in grapevine vineyards. Findings of the study including the optimized simplified cost-effective isothermal nucleic acid-based detection technique for GVB will be highly useful for production of certified clean rootstocks of grapevine in India.

Detection and typing of influenza viruses in vaccinated and non- vaccinated children in central Greece during 2018-2019

During the 2018-2019 influenza season in central Greece, 388 respiratory samples were collected from children presented with influenza symptoms and tested for the detection of influenza viruses. Real-time RT-PCR testing of the samples revealed the presence of influenza A (H1N1) (pdm09), influenza A (H3N2), seasonal influenza A (H1N1), and influenza B viruses. All samples tested were found negative for influenza A(H5) HA gene sequence. The majority of influenza viruses detected were type A (90%), of which the majority, (61%), were influenza A (H1N1) (pdm09) viruses, indicating that these viruses were the dominant influenza subtype circulating in central Greece during the winter and early spring of the aforementioned season.

Clinical and Genomic Perspective of SARS CoV-2 Infection in Liver Disease Patients: A Single-Centre Retrospective Study.

The limited literature on the clinical course of COVID-19 among patients with underlying liver disease (LD) is available from India. The present study aimed to evaluate the clinical and mutational profile of SARS-CoV-2 among LD cases. This was a retrospective study including admitted LD cases in whom SARS-CoV-2 RT-PCR testing was performed. Complete demographic and clinical details were retrieved from Hospital Information System. Detailed mutational analysis was performed by comparing LD COVID-19 positive study group, i.e. LD-CoV(+) with COVID-19 positive outpatients without any underlying LD as control, i.e. NLD-CoV(+). Out of 232 enrolled LD cases, 137 (59.1%) were LD-CoV(+). LD cases with existing co-morbidities were affected more (P = 0.002) and had 2.29 times (OR 2.29, CI 95%, 1.25-4.29) higher odds of succumbing to COVID-19 (P = 0.006). On multivariate regression analysis, ascites (P = 0.05), severe COVID-19 pneumonia (P = 0.046), and an increased levels of bilirubin (P = 0.005) and alkaline phosphatase (P = 0.003) were found to be associated with adverse outcome in LD-CoV(+).On mutational analysis, we found certain differences between LD- and NLD-CoV(+) infected with Delta [LD- and NLD-CoV (+ /D)] and Omicron [LD- and NLD-CoV(+/O)]. More mutations were shared between LD- and NLD-CoV(+/O) compared to LD- and NLD-CoV(+/D). There were differences in prevalence of indel mutations specific to LD-CoV ( +) for both Delta and Omicron. Moreover, we also reported an interesting genic bias between LD- and NLD-CoV( +) in harbouring deleterious/tolerated mutations. To conclude, LD cases with comorbidities were affected more and had higher odds of mortality due to COVID-19. The definite difference between LD- and NLD-CoV(+) groups with respect to frequency of harboured mutations and an inherent genic bias between them is of noteworthy importance.

Long Term Health Problems and Associated Factors among COVID-19 Recovered Patients

A cross-sectional, descriptive study was conducted among 181 individuals recovered from COVID-19 infection and had been missing infection (negative rt-PCR test) or signs-symptoms for minimum three months. The study aims determine newly developed health problems in patients, which was conducted at Post-COVID Unit of Anwer Khan Modern Medical College Hospital, Dhaka, Bangladesh, between July 2021 and June 2022. Through convenient sampling, data were collected by face-to-face interview and history of signs/ symptoms during the infection were recorded from reviewing prescription and interview as well by using a semi-structured questionnaire. The mean age of the participants was 39.56±6.92 years and male-female ratio was 1.45:1. The mean monthly family income of the participants was 36,022.09±4130.56 BDT which represents lower middle to middle class family in terms of Bangladesh context. During COVID-19 infection most of the (97%) respondents had fever, and 87%, 79% of the patients had sore throat and cough respectively as common symptoms; in addition, more than one-third (34%) had diarrhea. Several constitutional symptoms also recorded during their course of illness like headache (74%) and malaise (54%). More than one-third (34%) of the respondents required admission in hospital. During the course of infection, 41%, 26% and 31% participants were suffered from mild, moderate and severe form of COVID-19 illness. Most of the respondents developed long term health problems following COVID infection and post-viral fatigue was the most prevalent (85%) among the post COVID individuals and this long-term health problem-post viral fatigue was found to be associated with monthly income and it was statistically significant (p&lt;0.05). Others long term health problems including shortness of breath (74%), loss of memory (38%), difficulty in concentration (41%), loss of hair (30%), fast beating or pounding heart (33%) were also noticed. Insomnia (56%), persistent cough (35%), loss of taste (32%) and change of bowel habit (28%) were other health problems revealed in this study. Association between loss of memory and gender (p&lt;0.0001), diabetes mellitus and severity of COVID-19 (p&lt;0.05), sore throat, cough and severity of COVID-19 (P&lt;0.05) were also found significant. diabetes mellitus (35%), hypertension (34%) and bronchial asthma (24%) were observed to be most common comorbidities. Shortness of breath – one of the post-COVID consequence was found significantly associated with diabetes mellitus and bronchial asthma (p&lt;0.05). Our study found that persistence of various signs and symptoms from COVID-19 infection and newly yield complications in individual who recovered from COVID-19 infection are collectively comprise long term health problems of post-COVID patients. This long-term health problem of post-COVID people is a major public health concern. Fatigue, dyspnea, difficulty to concentrate, memory loss, persistent cough, fast beating or pounding heart, loss of smell, loss of taste, insomnia are the most common long term health problems in COVID-19 recovered people. Long-term follow up may be recommended to understand future consequences of COVID-19 patients and well-being for the post-COVID people. CBMJ 2024 July: vol. 13 no. 02 P: 158-168

COVID-19 Frequency in Hospitalized Psychiatric Patients: A Systematic Review

Objective The COVID-19 pandemic affected individuals in different contexts (e.g. long-term care facilities, schools, communities), including psychiatric hospitals. Thus, the objective of this systematic review, duly registered and approved on PROSPERO (CRD42023427835), is to assess the frequency of positive COVID-19 cases among patients hospitalized in psychiatric hospitals. Methods A total of 4,922 articles were identified in the database searches, and 17 studies conducted in psychiatric hospitals from different regions of the world were selected. Results The frequency of positive COVID-19 cases among patients hospitalized in psychiatric hospitals ranged from 1.8% to 98.8%. Out of a total of 19,573 patients hospitalized in psychiatric hospitals, the pooled mean frequency of positive COVID-19 cases was 11.9%. The majority of patients presented COVID-19 symptoms (e.g. cough, fever and others). The COVID-19 diagnosis was primarily conducted through RT-PCR testing in 88.9% of the studies. Conclusion In conclusion, there is discrepancy in the methodology of the studies assessing the frequency of positive COVID-19 cases in psychiatric hospitals. However, this review allowed us to understand how the COVID-19 pandemic has impacted the population hospitalized in psychiatric hospitals.

Incidence of laboratory-confirmed influenza and RSV and associated presenteeism and absenteeism among healthcare personnel, Israel, influenza seasons 2016 to 2019.

BackgroundHealthcare personnel (HCP) are at high risk for respiratory infections through occupational exposure to respiratory viruses.AimWe used data from a prospective influenza vaccine effectiveness study in HCP to quantify the incidence of acute respiratory infections (ARI) and their associated presenteeism and absenteeism.MethodsAt the start and end of each season, HCP at two Israeli hospitals provided serum to screen for antibodies to influenza virus using the haemagglutination inhibition assay. During the season, active monitoring for the development of ARI symptoms was conducted twice a week by RT-PCR testing of nasal swabs for influenza and respiratory syncytial virus (RSV). Workplace presenteeism and absenteeism were documented. We calculated incidences of influenza- and RSV-associated ARI and applied sampling weights to make estimates representative of the source population.ResultsThe median age of 2,505 participating HCP was 41 years, and 70% were female. Incidence was 9.1 per 100 person-seasons (95% CI: 5.8-14.2) for RT-PCR-confirmed influenza and 2.5 per 100 person-seasons (95% CI: 0.9-7.1) for RSV illness. Each season, 18-23% of unvaccinated and influenza-negative HCP seroconverted. The incidence of seroconversion or RT-PCR-confirmed influenza was 27.5 per 100 person-seasons (95% CI: 17.8-42.5). Work during illness occurred in 92% (95% CI: 91-93) of ARI episodes, absence from work in 38% (95% CI: 36-40).ConclusionInfluenza virus and RSV infections and associated presenteeism and absenteeism were common among HCP. Improving vaccination uptake among HCP, infection control, and encouraging sick HCP to stay home are important strategies to reduce ARI incidence and decrease the risk of in-hospital transmission.

The impact of COVID pandemic on quality of life in patients with chronic cough

Introduction. A chronic cough (CC) significantly impairs patients’ quality of life. During COVID-19 pandemic cough has been considered as a cardinal symptom of SARS-CoV-2 infection. Aim. The aim of this study was to assess the impact of COVID-19 pandemic on functioning of patients with a chronic cough. Material and methods. A survey of 13 closed questions, was conducted among 100 adults with CC who were treated in a cough clinic between November 2021 and February 2023. At the same time cough severity was measured by 100 mm Visual Analogue Scale (VAS) and cough related quality of life using Leicester Cough Questionnaire (LCQ). Results. Median VAS was 40 mm (20-64 mm) and median LCQ was 14.8 points (IQR 11.6-17.6). 68 patients with CC experienced unfavorable social reactions and 40 patients declared that they avoided going out because of cough. Wearing masks led to increase in cough severity in 53 patients. Despite limitations in regular medical visits, only 20 patients (21%) declared worse quality of medical care. When it comes to 48 patients, they had SARS-CoV-2 infection confirmed by antigen or RT-PCR test, but only in 27 of them (56%) cough became more severe during COVID-19 infection and only 15 patients (15/48, 31%) required modification of previous antitussive treatment due to COVID-19 infection. Conclusion. The comparison of patients who had SARS-CoV-2 infection with those who did not, revealed that patients with COVID-19 infection were younger, more often experienced unfavorable social reactions in public places, their cough seemed alarming to the relatives to a greater extent and wearing masks was more burdensome for them. Authors findings suggest that COVD-19 had a negative impact mainly on social and psychological aspects of life in adults with CC. Keywords: COVID-19, chronic cough, quality of life.

Evaluating diagnostic accuracy of an RT-PCR test for the detection of SARS-CoV-2 in saliva

Background and objectiveSaliva has been proposed as a potential more convenient, cost-effective, and easier sample for diagnosing SARS-CoV-2 infections, but there is limited knowledge of the impact of saliva volumes and stages of infection on its sensitivity and specificity.MethodsIn this study, we assessed the performance of SARS-CoV-2 testing in 171 saliva samples from 52 mostly mildly symptomatic patients (aged 18 to 70 years) with a positive reference standard result at screening. The samples were collected at different volumes (50, 100, 300, and 500 µl of saliva) and at different stages of the disease (at enrollment, day 7, 14, and 28 post SARS-CoV-2 diagnosis). Imperfect nasopharyngeal (NP) swab nucleic acid amplification testing was used as a reference. We used a logistic regression with generalized estimating equations to estimate sensitivity, specificity, PPV, and NPV, accounting for the correlation between repeated observations.ResultsThe sensitivity and specificity values were consistent across saliva volumes. The sensitivity of saliva samples ranged from 70.2% (95% CI, 49.3–85.0%) for 100 μl to 81.0% (95% CI, 51.9–94.4%) for 300 μl of saliva collected. The specificity values ranged between 75.8% (95% CI, 55.0–88.9%) for 50 μl and 78.8% (95% CI, 63.2–88.9%) for 100 μl saliva compared to NP swab samples. The overall percentage of positive results in NP swabs and saliva specimens remained comparable throughout the study visits. We observed no significant difference in cycle number values between saliva and NP swab specimens, irrespective of saliva volume tested.ConclusionsThe saliva collection offers a promising approach for population-based testing.

Function and Global Regulation of Type III Secretion System and Flagella in Entomopathogenic Nematode Symbiotic Bacteria.

Currently, it is widely accepted that the type III secretion system (T3SS) serves as the transport platform for bacterial virulence factors, while flagella act as propulsion motors. However, there remains a noticeable dearth of comparative studies elucidating the functional disparities between these two mechanisms. Entomopathogenic nematode symbiotic bacteria (ENS), including Xenorhabdus and Photorhabdus, are Gram-negative bacteria transported into insect hosts by Steinernema or Heterorhabdus. Flagella are conserved in ENS, but the T3SS is only encoded in Photorhabdus. There are few reports on the function of flagella and the T3SS in ENS, and it is not known what role they play in the infection of ENS. Here, we clarified the function of the T3SS and flagella in ENS infection based on flagellar inactivation in X. stockiae (flhDC deletion), T3SS inactivation in P. luminescens (sctV deletion), and the heterologous synthesis of the T3SS of P. luminescens in X. stockiae. Consistent with the previous results, the swarming movement of the ENS and the formation of biofilms are dominated by the flagella. Both the T3SS and flagella facilitate ENS invasion and colonization within host cells, with minimal impact on secondary metabolite formation and secretion. Unexpectedly, a proteomic analysis reveals a negative feedback loop between the flagella/T3SS assembly and the type VI secretion system (T6SS). RT-PCR testing demonstrates the T3SS's inhibition of flagellar assembly, while flagellin expression promotes T3SS assembly. Furthermore, T3SS expression stimulates ribosome-associated protein expression.

An all-out assault on a dominant resistance gene: Local emergence, establishment, and spread of strains of tomato spotted wilt orthotospovirus (TSWV) that overcome Sw-5b-mediated resistance in fresh market and processing tomatoes in California.

Tomato spotted wilt orthotospovirus (TSWV) causes substantial economic loss to tomato production, and the Sw-5b resistance gene is widely deployed for management. Here, we show (i) the emergence of resistance-breaking (RB) TSWV strains in processing and fresh market tomato production in California over the past ten years, and (ii) evolutionary relationships with RB strains from other areas. A specific RT-PCR test was used to show the C118Y RB strain that emerged in Fresno County in 2016 quickly became predominant in the central production area and remained so through this study. In 2021, the C118Y strain was detected in the Northern production area, and was predominant in 2022. However, in 2023, the C118Y strain was unexpectedly detected in fewer spotted wilt samples from resistant varieties. This was due to emergence of the T120N RB strain, previously known to occur in Spain. A specific RT-PCR test was developed and used to show that the T120N RB strain was predominant in Colusa and Sutter counties (detected in 75-80% of samples), and detected in ~50% of samples from Yolo County. Pathogenicity tests confirmed California isolates of the T120N strain infected Sw-5b tomato varieties and induced severe symptoms. Another RB strain, C118F, was associated with spotted wilt samples of Sw-5 varieties from fresh market tomato production in southern California. Phylogenetic analyses with complete NSm sequences revealed that the C118Y and T120N RB strains infecting resistant processing tomato in California emerged locally, whereas those from fresh market production were more closely related to isolates from Mexico. Thus, widespread deployment of this single dominant resistance gene in California has driven the local emergence of multiple RB strains in different tomato production areas and types. These results further emphasize the need for ongoing monitoring for RB strains, and identification of sources of resistance to these strains.