Polymerase Chain Reaction Test Results Research Articles

Investigating Transmission Patterns and Genome Sequencing of SARS-CoV-2 in University College Dublin

Abstract Background This study describes the investigation and management of multiple outbreaks of SARS-Cov2 during the second and third wave of the pandemic at University College Dublin, Ireland from September 2020 to September 2021. Methods Relevant data were gathered as part of the public health outbreak investigations led by the UCD Internal Covid Control Team (ICCT) in collaboration with the public health teams of the Health Service Executive (HSE). Results are presented for PCR (polymerase chain reaction) confirmed cases and their close contacts, reported to the UCD ICCT between September 2020 to September 2021. Results There were 214 cases notified to ICCT. Among these, 153 cases were in residence on-campus cases. 73 epidemiologically linked clusters identified, where the number of cases linked with each cluster varied between 1 to 27. Additional cases during this period had no obvious epidemiological link to the identified clusters. Of 902 close contacts with PCR test results, 31.5% (n = 284) tested positive. 77% (n = 219) self-reported with mild to moderately symptoms while 23% (n = 65) self-reported as asymptomatic. Retrospective Whole Genome Sequence (WGS) analysis was undertaken after the outbreaks had subsided. The test positive cases were grouped into 6 clusters, and it was shown that many of the apparent sporadic cases were included in these clusters. Conclusions The proportion of close contacts testing positive varied significantly throughout the pandemic, with testing policy and type of exposure having the greatest impact. Whole genome sequencing can give a better understanding of webs of transmission to complement epidemiological investigations. It is now possible to undertake sequencing in real time where it can make a contribution to outbreak control and resolution. Public Health professionals should become familiar with WGS and bioinformatics as useful tools in their armory for the control of all communicable diseases not only SARS-CoV-2. Key messages • Combined epidemiological investigations and Whole Genome Sequencing (WGS) provide crucial insights into campus COVID-19 outbreaks, guiding effective control measures. • WGS integration enhances understanding of transmission patterns, identifies clusters, and equips public health professionals with data-driven approaches for outbreak management beyond SARS-CoV-2.

Detection of Brucella militensis in the Serum of Patients Suspected of Brucellosis by the Omp31 Gene Amplification, Compared to the Serological Diagnostic Tests

Background and Objectives: Brucellosis is one of the most common infectious diseases with a global spread. It has a high prevalence in Iran. This study aims to diagnose brucellosis caused by Brucella melitensis in the serum of patients by the amplification of omp31 gene, compared to the serological tests. Methods: Blood samples were collected from 200 people suspected of brucellosis. The samples were evaluated by serological tests including Rose Bengal test, Wright test, Coombs-Wright test, gel agglutination test, and 2-mercaptoethanol (2ME) test. DNA extraction was done by the phenol/chloroform extraction method. Molecular detection with polymerase chain reaction (PCR) method was done using the specific primers of the Omp31 gene. Data were analyzed in SPSS software, version 23 using the analysis of variance. Results: Of 200 patients, 122 were female and 78 were male with a mean age of 45.17±17.43 years. The results of PCR test for the omp31 gene were positive in 14.5% of cases, which was consistent with the results of serological tests (13.8%). The sensitivity of Wright, Coombs-Wright, 2ME, and gel agglutination tests, compared to PCR, was 89.7, 75.9, 55.2 and 55.2%, respectively. Most of the affected people were housekeepers (41.5%) and urban residents (75.5%). Muscle pain (68%) and leg pain (62.3%) were the most common symptoms. Consumption of non-pasteurized dairy products was the highest risk factor (17%). Conclusion: The diagnosis of brucellosis by the omp31 gene amplification has higher sensitivity and accuracy compared to the serological tests. Considering the importance of rapid and timely diagnosis of brucellosis to control its clinical complications, the molecular diagnosis method is recommended as a diagnostic method.

Autoimmune Sequelae After Delta or Omicron Variant SARS-CoV-2 Infection in a Highly Vaccinated Cohort

Studies have reported increased risk of autoimmune sequelae after SARS-CoV-2 infection. However, risk may potentially be attenuated by milder Omicron (B.1.1.529) variant infection and availability of booster vaccination. To estimate the 300-day risk of new-incident autoimmune sequelae after SARS-CoV-2 Delta or Omicron BA.1 or BA.2 variant infection in adults who received COVID-19 vaccines and boosters, compared with a contemporary control group without infection. This cohort study in Singapore enrolled adults from September 1, 2021, to March 7, 2022, and followed up for 300 days. Participants were adults aged 18 years or older with SARS-CoV-2 infection during the predominance of the Delta and Omicron BA.1 or BA.2 variants and were still alive at 30 days after COVID-19 diagnosis. The national SARS-CoV-2 testing registry was used to construct cohorts of adults with SARS-CoV-2 Delta or Omicron BA.1 or BA.2 variant infection (hereafter, cases) and a contemporaneous group with negative polymerase chain reaction or rapid antigen test results (hereafter, controls). New-incident autoimmune diagnoses after SARS-CoV-2 infection. This information was recorded in the MediClaims national health care claims database and identified 31 to 300 days after index date of infection. Risks and excess burdens were estimated using Cox proportional hazards regression model with overlap weights applied. In total, 1 766 036 adults (915 096 females [51.9%]; mean [SD] age, 49 [18] years) were included in the study population, with 480 082 (27.2%) categorized as cases and 1 285 954 (72.8%) as controls. Of these adults, 73.1% had Chinese, 13.7% Malay, and 9.9% Indian ethnicity. There were 104 179 cases and 666 575 controls included during the Delta variant-predominance transmission, while 375 903 cases and 619 379 controls were included during the Omicron variant-predominance transmission. During the Delta variant period, 81.1% of cases had completed primary vaccination; during the Omicron variant period, 74.6% of cases received boosters. No significantly elevated risk of 12 prespecified autoimmune sequelae was recorded across the Omicron and Delta variant cohorts. Elevated risks of inflammatory bowel disease (adjusted hazard ratio [AHR], 2.23; 95% CI, 1.45-3.46; P < .001) and bullous skin disorders (AHR, 4.88; 95% CI, 2.47-9.66; P < .001) were observed only in the subset of COVID-19 cases requiring hospitalization during the predominance of the Omicron variant. While elevated risk of vasculitis (AHR, 5.74; 95% CI, 1.48-22.23; P = .01) was observed in vaccine-breakthrough Omicron variant infections, no increased risk of vasculitis was observed in the corresponding subgroup who received boosters. This cohort study observed no significantly elevated long-term risk of autoimmune sequelae after SARS-CoV-2 Delta and Omicron BA.1 or BA.2 variant infection, except for a modestly increased risk of inflammatory bowel disease and bullous skin disorders in the hospitalized subgroup during the predominance of the Omicron variant. Booster vaccination appeared to mitigate the risk of long-term autoimmune sequelae.

Evaluation of general characteristics of patients diagnosed with COVID-19 who were admitted to the ward and intensive care unit from the emergency department: a retrospective clinical study

Aims: COVID-19 has caused many negative biological and psychological effects all over the world for a long time. Our aim is to present the general characteristics of patients who were diagnosed with COVID-19 by applying to the emergency department and who were admitted to the intensive care unit or service. Methods: 1210 patients who were hospitalized in the emergency department, treated between 1 June 2020 and 1 January 2021, who had a positive COVID-19 Polymerase Chain Reaction test result and were examined retrospectively, were included in the study. p

Risk of intensive care unit admission and mortality in patients hospitalized due to influenza A or B and SARS‑CoV‑2 variants Omicron or Delta

AbstractBackgroundRespiratory viral infections have significant global health impacts. We compared 30‐day intensive care unit (ICU) admission and all‐cause mortality risks in patients with severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) Delta and Omicron variants versus influenza A and B (A/B).MethodsData from two retrospective inpatient cohorts in Capital Region of Denmark were analyzed. Cohorts included hospitalized influenza A/B patients (2017–2018) and SARS‐CoV‐2 Delta/Omicron patients (2021–2022), aged ≥18 years, admitted within 14 days of a positive real‐time polymerase chain reaction test result. Cumulative ICU admission and mortality rates were estimated using the Aalen–Johansen estimator. Cox regression models calculated hazard ratios (HRs) for ICU admission and mortality.ResultsThe study encompassed 1459 inpatients (Delta: 49%; Omicron: 26%; influenza A: 6.4%; and influenza B: 18%). Cumulative incidence of ICU admission was 11%, 4.0%, 7.5%, and 4.1%, for Delta, Omicron, influenza A, and B, respectively. For ICU admission, adjusted HRs (aHRs) were 3.1 (p &lt; .001) and 1.5 (p = .34) for Delta and Omicron versus influenza B, and 1.5 (p = .36) and 0.71 (p = .48) versus influenza A. For mortality, aHRs were 3.8 (p &lt; .001) and 3.4 (p &lt; .001) for Delta and Omicron versus influenza B, and 2.1 (p = .04) and 1.9 (p = .11) versus influenza A.ConclusionDelta but not Omicron inpatients had an increased risk for ICU admission compared to influenza B; however, both variants were associated with higher risks of mortality than influenza B. Only Delta inpatients had a higher risk of mortality than influenza A inpatients.

HEMATOLOGICAL CHANGES ASSOCIATED WITH COVID-19 INFECTION IN ADEN/ YEMEN

Chronic Hematological alterations in COVID-19 patients range from mild to severe, with common changes including lymphopenia, neutrophilia, and thrombocytopenia. The gold standard for diagnosis is the polymerase chain reaction (PCR) test, which is highly specific and sensitive for detecting SARS-CoV-2 genetic material. The study was a single isolation center retrospective analysis of 200 patients with COVID-19 confirmed cases. The hematological indicators were taken after sample blood collected from the staff of Central Public Health Laboratory to determine the changes, and compared between different grades of severity and prognosis with the hematological indicators. The data was analyzed using Statistical Package for the Social Sciences (SPSS) version 22.0. simple frequencies and percentage were used, while chi-square test used to determine the association between variables. Males consisted 73.5% in this study, while 63% of participants suffered from moderate severity. Related to the hematological changes; and comparisons made according to real-time PCR test results revealed that the Lymphocytopenia and leukocytosis presented among 47.5% and 46.5% respectively with significance association with illness severity and outcome of patients with p-value&lt; 0.05. hematological changes in COVID-19 patients are a common and significant aspect of the disease. Lymphopenia, neutrophilia, thrombocytopenia, and increased levels of inflammatory markers are frequently observed. These hematological abnormalities are associated with disease severity, poor clinical outcomes. Blood parameters aid in COVID-19 diagnosis and prognosis, with abnormal hematological parameters providing early evidence. However, interpretation should consider limitations, sample size, and potential biases. Further research needed.

Influenza Infection and Acute Myocardial Infarction

BackgroundAcute respiratory infections can trigger acute myocardial infarction. We aimed to quantify the association between laboratory-confirmed influenza infection and acute myocardial infarction, particularly in patients with and without known coronary artery disease.MethodsThis observational, registry-based, self-controlled case series study evaluated the association between laboratory-confirmed influenza infection and occurrence of acute myocardial infarction. Laboratory records on respiratory virus polymerase chain reaction (PCR) testing from 16 laboratories across the Netherlands were linked to national mortality, hospitalization, medication, and administrative registries. Influenza infection was defined as a positive PCR test result. Acute myocardial infarction was defined as a registered diagnostic code for either acute myocardial infarction hospitalization or death. Using a self-controlled case series method, we then compared the incidence of acute myocardial infarction during the risk period (days 1 to 7 after influenza infection) versus the control period (1 year before and 51 weeks after the risk period).ResultsBetween 2008 and 2019, we identified 158,777 PCR tests for influenza in the study population; 26,221 were positive for influenza, constituting 23,405 unique influenza illness episodes. A total of 406 episodes were identified with acute myocardial infarction occurring within 1 year before and 1 year after confirmed influenza infection and were included in analysis. Twenty-five cases of acute myocardial infarction occurred during the risk period versus 394 during the control period. The adjusted relative incidence of acute myocardial infarction during the risk period compared with the control period was 6.16 (95% confidence interval [CI], 4.11 to 9.24). The relative incidence of acute myocardial infarction in individuals without prior hospitalization for coronary artery disease was 16.60 (95% CI, 10.45 to 26.37) compared with 1.43 (95% CI, 0.53 to 3.84) for those with prior admission for coronary artery disease.ConclusionsInfluenza infection was associated with an increased risk of acute myocardial infarction, especially in individuals without a prior hospitalization for coronary artery disease. (Funded by the Dutch Research Council [NWO].)

Dysnatremia as a Mortality Marker in Intensive Care Patients with SARS-CoV-2 Infection: A Retrospective Study.

Background and Objectives: The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection may cause acute respiratory failure, but also remains responsible for many other pathologies, including electrolyte disorders. SARS-CoV-2 infection causes disorders in many systems and can disrupt water homeostasis with thirst and appetite abnormalities. Dysnatremia affects prognosis, and may be associated with mortality in patients admitted to an intensive care unit (ICU) diagnosed with SARS-CoV-2. Materials and Methods: The study included 209 patients admitted to the ICU between 12 April 2021 and 1 March 2022 who were over 18 years old and diagnosed with SARS-CoV-2 infection by clinical and thoracic tomography findings or with a positive reverse transcription polymerase chain reaction (RT-PCR) test result. The laboratory markers, treatment modalities, nutritional, and respiratory support also for outcome evaluation, length of stay in the ICU, total hospitalization duration, and mortality in the ICU were recorded. The laboratory marker comparison was made using admission with the final assessment performed before the time of mortality in the ICU or after discharge. Results: Inotropic requirements among patients were high, which reflected mortality in the ICU. Hypernatremia presence was associated with an increase in enteral support, the inotropic support requirement, and mortality. Hypernatremia was correlated with diabetes mellitus, chronic renal failure, and a longer duration under mechanical ventilation. Conclusions: Hypernatremia was an important risk factor in ICU patients hospitalized for SARS-CoV-2 infection, which was also affected by the treatment regimens given themselves. This complex relationship underlies the importance of proper electrolyte management, especially in patients who were under severe stress and organ failure.

The Impact of Polymerase Chain Reaction Urine Testing on Clinical Decision-Making in the Management of Complex Urinary Tract Infections.

While urinary polymerase chain reaction (PCR) testing is effective in organism identification in patients with complex urinary tract infections (cUTI), limited data exists on the clinical usefulness of this test. We serially surveyed physicians treating symptomatic patients with cUTI both at presentation and after PCR, and urine culture (UC) results were available to ascertain how the test results modified the therapy. A total of 96 unique surveys completed by 21 providers were included in the data analysis. The mean age for female and male patients was 69.4 ± 15.5 and 71.6 ± 12.7 years, respectively. The test positivity and line-item concordance for UC and PCR were consistent with prior reports. The PCR results modified or confirmed treatment in 59/96 (61.5%) and 25/96 (26.0%) of the cases, respectively, with 12/29 (41.4%) and 47/67 (70.1%) having negative and positive PCR results, respectively, resulting in treatment change (difference 28.7%, p < 0.01). Of these, 55/59 (57.3%) were alterations in the antibiotic regimen. PCR use to modify treatment was similar across providers and not statistically different when stratified by patient age, gender, or prior empiric therapy. In 31/59 (52.5%) of the cases, the PCR results modified the treatment where UC would not; conversely, UC would have modified the treatment in 3/37 (8.1%) of the cases where PCR did not (difference 44.4%, p < 0.01). We find that PCR test results are used by clinicians in managing cUTI, and use of this test provides an opportunity to improve antibiotic stewardship in this difficult-to-treat subset of patients.

The Emergence of Linezolid-Resistant Staphylococcus Epidermidis in the COVID-19 Hospitalized Intubated Patients in North Khorasan, Iran.

The present study aimed to investigate secondary bacterial infections among patients infected with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Coagulase-negative Staphylococci can infect immunocompromised patients. Linezolid resistance among Staphylococcus epidermidis is one of the most critical issues. In 2019, 185 SARS-CoV-2-positive patients who were admitted to North Khorasan Province Hospital (Bojnurd, Iran), were investigated. Patients having positive SARS-CoV-2 reverse transcriptase real-time polymerase chain reaction (RT-PCR) test results, who had a history of intubation, mechanical ventilation, and were hospitalized for more than 48 hours were included. After microbiological evaluation of pulmonary samples, taken from intubated patients with clinical manifestation of pneumonia, co-infections were found in 11/185 patients (5.94%) with S. epidermidis, Staphylococcus aureus, and Acinetobacter baumani, respectively. Remarkably, seven out of nine S. epidermidis isolates were linezolid resistant. Selected isolates were characterized using antimicrobial resistance patterns and molecular methods, such as Staphylococcal cassette chromosome mec (SCCmec) typing, and gene detection for ica, methicillin resistance (mecA), vancomycin resistance (vanA), and chloramphenicol-florfenicol resistance (cfr) genes. All of the isolates were resistant to methicillin, and seven isolates were resistant to linezolid. Nine out of 11 isolated belonged to the SCCmec I, while two belonged to the SCCmec IV. It should be noted that all patients had the underlying disease, and six patients had already passed away. The increasing linezolid resistance in bacterial strains becomes a real threat to patients, and monitoring such infections, in conjunction with surveillance and infection prevention programs, is very critical for reducing the number of linezolid-resistant Staphylococcal strains. A preprint of this study was published at https://europepmc.org/article/ppr/ppr417742.

SARS-CoV-2 immunoassays in a predominantly vaccinated population: Performances and qualitative agreements obtained with two analytical approaches and four immunoassays.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) serosurveys are typically analysed by applying a fixed threshold for seropositivity ('conventional approach'). However, this approach underestimates the seroprevalence of anti-nucleocapsid (N) in vaccinated individuals-who often exhibit a difficult-to-detect anti-N response. This limitation is compounded by delays between the onset of infection and sample collection. To address this issue, we compared the performance of four immunoassays using a new analytical approach ('ratio-based approach'), which determines seropositivity based on an increase in anti-N levels. Two groups of plasma donors and four immunoassays (Elecsys total anti-N, VITROS total anti-N, Architect anti-N Immunoglobulin G (IgG) and in-house total anti-N) were evaluated. First-group donors (N = 145) had one positive SARS-CoV-2 polymerase chain reaction (PCR) test result and had made two plasma donations, including one before and one after the PCR test (median = 27 days post-PCR). Second-group donors (N = 100) had made two plasma donations early in the Omicron wave. Among first-group donors (97.9% vaccinated), sensitivity estimates ranged from 60.0% to 89.0% with the conventional approach, compared with 94.5% to 98.6% with the ratio-based approach. Among second-group donors, Fleiss's κ ranged from 0.56 to 0.83 with the conventional approach, compared with 0.90 to 1.00 with the ratio-based approach. With the conventional approach, the sensitivity of four immunoassays-measured in a predominantly vaccinated population based on samples collected ~1 month after a positive test result-fell below regulatory agencies requirement of ≥95%. The ratio-based approach significantly improved the sensitivities and qualitative agreement among immunoassays, to the point where all would meet this requirement.

The significance of monitoring respiratory sample cultures and polymerase chain reaction tests for detecting bacterial pathogens in severely and critically ill patients with COVID-19

Background. Bacterial superinfection is one of the most common and potentially lethal complications in severely and critically ill patients with COVID-19. Objectives. To determine the colonisation time frame and the spectrum of potential bacterial pathogens in respiratory samples from patients with severe and critical COVID-19, using routine culture and polymerase chain reaction (PCR) tests. Methods. A prospective observational study was conducted on patients aged ≥18 years with confirmed severe and critical COVID-19 who were admitted to or transferred to the intensive care unit (ICU). Respiratory samples were collected for microbial culture and PCR testing within the first 2 days after ICU admission/transfer, between days 3 and 6, and after 7 days of ICU stay. Results. A total of 82 patients, with a median (interquartile range) age of 74.5 (67.3 - 81.0) years and a median Charlson comorbidity index of 4 (3 - 5), were enrolled in the study. Colonisation with any pathogen was observed in 67% of patients, after a median of 4 (2 - 6) days in the ICU. On days 0 - 2 of the ICU stay, micro-organisms were detected in 18% of patients, with Klebsiella pneumoniae (without acquired antibiotic resistance) and methicillin-susceptible Staphylococcus aureus being most frequently identified. Later, Acinetobacter baumannii and carbapenem-resistant K. pneumoniae became the predominant micro-organisms, identified in nearly half of the patients. In 74% of the samples, the results of microbial culture and PCR tests were identical. In 17%, PCR revealed bacterial pathogens not identified by culture. Conclusion. Our study confirms that colonisation of the respiratory tract occurs early in the course of ICU stay. Superinfections are predominantly caused by multidrug-resistant Gram-negative bacteria.

Wastewater Surveillance of US Coast Guard Installations and Seagoing Military Vessels to Mitigate the Risk of COVID-19 Outbreaks, March 2021-August 2022.

Military training centers and seagoing vessels are often environments at high risk for the spread of COVID-19 and other contagious diseases, because military trainees and personnel arrive after traveling from many parts of the country and live in congregate settings. We examined whether levels of SARS-CoV-2 genetic material in wastewater correlated with SARS-CoV-2 infections among military personnel living in communal barracks and vessels at US Coast Guard training centers in the United States. The Coast Guard developed and established 3 laboratories with wastewater testing capability at Coast Guard training centers from March 2021 through August 2022. We analyzed wastewater from barracks housing trainees and from 4 Coast Guard vessels for the presence of SARS-CoV-2 genes N and E and quantified the results relative to levels of a fecal indicator virus, pepper mild mottle virus. We compared quantified data with the timing of medically diagnosed COVID-19 infection among (1) military personnel who had presented with symptoms or had been discovered through contact tracing and had medical tests and (2) military personnel who had been discovered through routine surveillance by positive SARS-CoV-2 antigen or polymerase chain reaction test results. Levels of viral genes in wastewater at Coast Guard locations were best correlated with diagnosed COVID-19 cases when wastewater testing was performed twice weekly with passive samplers deployed for the entire week; such testing detected ≥1 COVID-19 case 69.8% of the time and ≥3 cases 88.3% of the time. Wastewater assessment in vessels did not continue because of logistical constraints. Wastewater testing is an effective tool for measuring the presence and patterns of SARS-CoV-2 infections among military populations. Success with wastewater testing for SARS-CoV-2 infections suggests that other diseases may be assessed with similar approaches.

Analysis of Plasmid-Mediated Quinolone Resistance (PMQR) Genes Among Escherichia coli Strains Isolated from Patients with Urinary Tract Infection in Eastern Turkey

Aim: Urinary tract infections are a common occurrence worldwide, with females being more susceptible than males. Infections can manifest as asymptomatic bacteriuria or more severe forms such as sepsis. This study aims to analyse the plasmid-mediated quinolone resistance genes of Escherichia coli (E. coli) responsible for causing urinary tract infections.&#x0D; Material and Method: Microbiological evaluation was conducted using conventional culture method, API 20E (API-bioMérieux, France), antibiotic susceptibility tests, and polymerase chain reaction (PCR).&#x0D; Results: During the study period, 145 E. coli strains were collected from 96 (66.2%) outpatients and 49 (33.8%) hospitalised patients with urinary tract infections (UTI). The resistance rates of E. coli strains to quinolone antibiotics were as follows: nalidixic acid in 102 strains (70.3%), ciprofloxacin in 96 strains (66.2%), ofloxacin in 73 strains (50.3%), gatifloxacin in 47 strains (32.4%), levofloxacin in 41 strains (28.3%) and moxifloxacin in 32 (22%) strains. Based on the PCR test results, it was found that 80% (116) of the isolates carried at least one PMQR gene. Furthermore, 31.9% (37/116) of the isolates were found to carry two or three PMQR markers simultaneously.&#x0D; Discussion and Conclusion: The objective of this study was to establish the prevalence of quinolone resistance among E. coli strains isolated from patients with UTI. To control the high rate of spread of antibiotic-resistant microorganisms, it is crucial for all healthcare facilities to implement more careful management of antibiotic use and adhere to procedures set by infection control programmes.

Role of exosomes in false-positive COVID-19 PCR tests: Non-specificity of SARS-CoV-2-RNA in vivo detection explains artificial post-pandemic peaks

Background: The COVID-19 pandemic priorities have focused on prevention by detection and response. National governments’ prevention response decisions are based upon detection statistics from PCR (polymerase chain reaction) tests that are used to define numbers of (i) COVID-19 infected persons, (ii) COVID-19 hospitalisations, and (iii) COVID-19 deaths. These statistics assume a priori that PCR tests are nigh 100% true detectors of COVID-19 infections. Here we will provide an alternative interpretation, along with the compelling evidence, that false positives have distorted to some degree the statistics of the primary outbreaks, and account for almost the whole of the 2nd and subsequent apparent COVID-19 outbreak peaks in various countries. Methods: We extract from the published literature on PCR-test outcomes graphical data that reveals the evidence for a very large percentage of false positive results. We review the role of exosomes in the immune response to all respiratory viral infections and its effect on PCR tests. We hypothesise that exosomes, triggered by all viral respiratory infections, are largely responsible for positive outcomes from PCR tests for COVID-19. We test our alternative interpretation for consistency with the empirical epidemiological trends as published by the World Health Organization (WHO). The Scientific Method is used to direct our research efforts. Findings: We find that PCR testing data for the second and following waves of the COVID-19 pandemic indicate that these waves are mainly artefacts of false-positive results. We find that this interpretation provides a more consistent explanation of the known epidemiology of COVID-19 than the hitherto consensus notion of extremely contagious and rapidly mutating viruses. Interpretation: The RNA (ribonucleic acid) code detected in PCR tests, previously attributed to SARS-CoV-2, belongs instead to a respiratory-virus-induced immune system response by human cells that liberate exosomes, and that vitiate PCR test results. PCR tests have zero specificity in vivo due to the exosome RNA. PCR tests exhibit excellent specificity in vitro on pure samples of other respiratory viruses. The low success rate of vaccines in preventing COVID-19 is explained by the inexact identification of the SARS-CoV-2 RNA.

Clinical epidemiology, determinants, and outcomes of viral encephalitis in Ghana; a cross-sectional study.

Viral encephalitis is a rare, yet severe neurological disorder. It poses a significant public health threat due to its high morbidity and mortality. Despite the disproportionate burden of the disease in impoverished African countries, the true extent of the problem remains elusive due to the scarcity of accurate diagnostic methods. The absence of timely and effective diagnostic tools, particularly Real-time Polymerase Chain Reaction, has led to misguided treatment, and an underestimation of the disease burden in Ghana. We conducted a prospective cross-sectional study to determine the viral aetiologies of encephalitis among patients presenting to a major referral hospital in Ghana from May 2019 and August 2022. The study aimed at providing a comprehensive information on the clinical epidemiology, and outcomes of viral encephalitis in Ghana. Clinical samples were collected from patients presenting with signs and symptoms of encephalitis and tested for viral agents using real-time polymerase chain reaction. We assessed the clinical epidemiology, risk factors and outcome of individuals using descriptive and logistic regression analysis. Seventy-seven (77) patients were enrolled unto the study. The participants frequently presented with fever (85.7%), seizures (80.5%), lethargy (64.9%) and headache (50.6%). Viruses were detected in 40.3% of the study participants in either cerebrospinal fluid, rectal or oral swab samples. The most frequently detected viruses were cytomegalovirus (48.4%), enteroviruses (38.7%) and HSV (29.0%). Twenty-one (27.3%) of the patients died while on hospital admission. Gender (OR = 5.70 (1.536-1.172), p = 0.01), and negative polymerase chain reaction test results were identified as significant factors associated with death. Antiviral treatment increased the chance of survival of viral encephalitis patients by 21.8%. Our results validate the crucial role of molecular tools as essential for the rapid diagnosis of viral encephalitis, enabling effective treatment and improved patient outcomes. This study contributes valuable epidemiological and clinical insight into viral encephalitis in Ghana.

Clinical Diagnosis Is Highly Predictive of Laboratory-Confirmed Mpox in a Sexual Health Clinic.

Promptly recognizing mpox can facilitate earlier diagnosis and appropriate treatment. How accurately clinicians can diagnose mpox based on clinical data and before receiving molecular test results is not known. Leveraging public health and clinical data collected in Seattle-King County's Sexual Health Clinic (SHC) from July 29, 2022, to September 30, 2022, we analyzed the proportion of patients who received presumptive versus results-based tecovirimat when clinicians had a high, intermediate, or low suspicion for mpox after clinical evaluation. We calculated the sensitivity, specificity, and positive (PPV) and negative predictive value (NPV) of this approach against criterion standard mpox polymerase chain reaction (PCR) results. Of 321 patients evaluated for mpox in the SHC, median age was 34.5 years and 88% were cisgender men. Overall, 121 of 319 (38%) tested positive by mpox PCR. Clinicians had high suspicion for mpox in 122 patients and offered empiric tecovirimat to 92 (88%), of whom 85 (92%) tested PCR positive. Of 13 intermediate suspicion patients offered presumptive therapy, all accepted but none tested positive by PCR. The sensitivity, specificity, PPV, and NPV of high/intermediate clinical suspicion for mpox were 99%, 90%, 86%, and 99%, respectively. A higher proportion of people with HIV were diagnosed with mpox (57% vs. 36%, P = 0.01, χ2 test), and sensitivity and PPV of high/intermediate clinical suspicion in this subgroup were 100% and 86%, respectively. Clinical providers working in a high-volume, public SHC were able to both accurately identify and rule out mpox based on clinical examination before receiving PCR test results.

Oral Mucosal Manifestations Associated with PCR Positivity in Patients with COVID-19.

To date various oral manifestations in patients with coronavirus disease 2019 (COVID-19) have been reported. In the present study, we investigated the relationship between Polymerase Chain Reaction (PCR) positivity and oral signs in patients with suspected COVID-19. A total of 383 patients who presented to the emergency department for the first time with any symptoms associated with COVID-19 were included in the study. Oral examinations were performed and the findings, PCR status, and thorax computerized tomography (CT) reports were recorded. Oral mucosa was involved in 246 (64.2%) patients. 175 (78,4%) of patients with COVID-19 confirmed the diagnosis with PCR test or CT results had oral manifestation. Dry mouth, microvesicles on the tonsils or pharynx, and petechiae in the oropharynx were significantly higher in patients with positive PCR tests (P = 0.001, P < 0.001, P < 0.001, respectively). The ratio of intact oral mucosa was statistically significantly higher in patients with negative PCR tests compared to those with positive PCR tests (P < 0.001). Microvesicles on the tonsils or pharynx were most associated with PCR positivity in patients without lung involvement (P < 0.001). Dry mouth, erythema of the tonsils and pharynx, petechiae in the oropharynx, and primary/secondary herpes infection are more related to PCR positivity in patients without lung involvement (P < 0.05). Lung involvement in patients with PCR positivity is related to only cheilitis (P = 0.034). Our study revealed that especially microvesicles, petechiae, erythema on the tonsils or pharynx, and some other oral lesions such as dry mouth, oral aphthae, and primary/secondary herpes infection are associated with PCR positivity.

Deciphering Factors Linked With Reduced Severe Acute Respiratory Syndrome Coronavirus 2 Susceptibility in the Swiss HIV Cohort Study.

Factors influencing susceptibility to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remain to be resolved. Using data from the Swiss HIV Cohort Study on 6270 people with human immunodeficiency virus (HIV) and serologic assessment for SARS-CoV-2 and circulating human coronavirus (HCoV) antibodies, we investigated the association of HIV-related and general parameters with SARS-CoV-2 infection. We analyzed SARS-CoV-2 polymerase chain reaction test results, COVID-19-related hospitalizations, and deaths reported to the Swiss HIV Cohort Study between 1 January 2020 and 31 December 2021. Antibodies to SARS-CoV-2 and HCoVs were determined in prepandemic (2019) and pandemic (2020) biobanked plasma samples and compared with findings in HIV-negative individuals. We applied logistic regression, conditional logistic regression, and bayesian multivariate regression to identify determinants of SARS-CoV-2 infection and antibody responses to SARS-CoV-2 in people with HIV. No HIV-1-related factors were associated with SARS-CoV-2 acquisition. High prepandemic HCoV antibodies were associated with a lower risk of subsequent SARS-CoV-2 infection and with higher SARS-CoV-2 antibody responses on infection. We observed a robust protective effect of smoking on SARS-CoV-2 infection risk (adjusted odds ratio, 0.46 [95% confidence interval, .38-.56]; P < .001), which occurred even in previous smokers and was highest for heavy smokers. Our findings of 2 independent protective factors, smoking and HCoV antibodies, both affecting the respiratory environment, underscore the importance of the local immune milieu in regulating susceptibility to SARS-CoV-2.

Hidden enemy of pulmonary arteries: COVID-19

It has been reported that COVID-19 may cause severe endothelial damage. Pulmonary Artery Stiffness (PAS) is a strong predictor of right ventricular function. PAS can reveal important information about the endothelial functions of the pulmonary bed. In this study, we aimed to elucidate the possible effect of COVID-19 on PAS. The study was performed by measuring PAS values with transthoracic echocardiography in 130 patients, 60 of whom had COVID-19 and 70 were controls. COVID-19 patients with positive polymerase chain reaction (PCR) test results were included in the study 3-6 months after their positivity. When the Maximal frequency shift (MFS) (Hz) results were examined, no significant difference was observed between the patient and control groups (2764±279.24 and 2664.8±673.91 p=0.340, respectively). There was a significant difference between the patient and control groups in favor of the patient group in pulmonary acceleration time (PAT) (msec) results (93.18±14.99 and 126.1±17.58, respectively, p&lt;0.001). There was a significant difference between the patient and control groups in favor of the patient group in PAS (Hz/msec) results (30.28±5.07 and 21.57±7.04, respectively, p&lt;0.001). It is possible that COVID-19 may have adverse effects on the pulmonary artery wall and bed. As a result of endothelial damage due to COVID-19, an increase in PAS values can be observed.