Viral Culture Research Articles

Rocky Mountain Spotted Fever Encephalitis and "Starry Sky" Pattern on MRI: A Case Report.

Rocky Mountain Spotted Fever (RMSF) is a tick-borne disease caused by Rickettsia rickettsii (R. rickettsii). RMSF presents after a tick bite with fever, rash, and headache but can also cause more serious neurological manifestations. We report a case of RMSF encephalitis presenting with altered sensorium and rapid progression to coma, fever, and petechial rash, and an magnetic resonance imaging (MRI) brain notable for a "starry sky" pattern. A 61-year-old woman presented with confusion and fever and was diagnosed with a urinary tract infection. Two days later, she became comatose. MRI brain revealed lacunar infarcts in the right centrum semiovale and splenium of the corpus callosum. Lumbar puncture was notable for neutrophilic pleocytosis and elevated protein with negative bacterial and viral cultures. Empiric meningitis therapy was initiated, and she was transferred to our institution. On transfer, she was febrile, comatose, and had a diffuse petechial rash. Repeat MRI brain demonstrated diffuse, innumerable punctate foci of diffusion restriction with susceptibility-weighted signal attenuation throughout cerebral hemispheres in a "starry sky" pattern. Skin biopsy revealed perivascular lymphocytic infiltrates. Serologic RSMF antibody titers were obtained, and doxycycline was initiated for presumed RMSF encephalitis. The family opted to pursue palliative measures, given no clinical improvement. RSMF titers and postmortem PCR from brain tissue were positive for R. rickettsii. This case report highlights the clinical presentation of RMSF encephalitis. RMSF encephalitis should be suspected in a patient presenting with encephalopathy, fever, petechial rash, and MRI brain findings of diffuse punctate foci of diffusion restriction and susceptibility-weighted signal attenuation in a "starry-sky" pattern.

7504 A Case of Methicillin Sensitive Staphylococcus Aureus Thyroiditis

Abstract Disclosure: K. Patel: None. P. Kachhadia: None. S. Khan: None. F. Akanbi: None. A. Abu Limon: None. S.A. Aldasouqi: None. Introduction: Acute suppurative thyroiditis refers to bacterial infection of the thyroid gland. It is rare as the thyroid gland is typically protected from infection due to isolation of the gland from neighboring structures as well as its rich blood supply and adequate lymphatic drainage. It shares characteristics with subacute and autoimmune thyroiditis which make for difficult diagnosis. Here we present a case of acute suppurative thyroiditis in the setting of methicillin sensitive staphylococcus aureus (MSSA) bacteremia. Case Presentation: We have a 45 year old gentleman with a history of polysubstance abuse who was admitted after a drug overdose. He was being treated for rhabdomyolysis and approximately ten days after admission he became febrile with Tmax 103.3 Farenheit with a sore throat and dysphagia. Workup showed leukocytosis, ESR 86 mm/h [0-15], CRP 45.5 mg/dL [0-1], blood cultures with MSSA, negative viral upper respiratory panel, throat culture, Syphilis and HIV testing. He had a positive Hepatitis C antibody without a detectable viral load. Echocardiogram ruled out vegetations. He was treated with cefazolin. CT neck was obtained and showed thyroid enlargement. Subsequent ultrasound showed heterogeneous echotexture and increased color flow and a left inferior pole nodule 2.3 x 2.1 x 2.0 cm. Thyroid labs showed TSH 0.16 [0.35 - 4.01 u[IU]/mL,] Free T4 3.91 ng/dL [0.61 - 1.37], TPO <0.3. The nodule was biopsied and endocrinology was consulted. On exam thyroid was nontender. He was started on beta blockers and thyroid labs were monitored. TSI and TRAB were negative. TSH, Free T4 and Free T3 improved to normal range. Nodule biopsy results showed benign follicular cells with abundant acute inflammation suggestive of an abscess. Metronidazole was added after biopsy results. Post antibiotic therapy, CRP improved to 1.7 mg/dL. Discussion/Conclusion: Incidence of acute suppurative thyroiditis has been published as occurring <1% of all thyroid diseases. One systematic review found 200 cases reported from January 2000 to January 2020. Prior case reports have described acute suppurative thyroiditis in adult patients with prior thyroid gland pathology or an immunocompromised state and some demonstrated a correlation with intravenous drug users. The most common culprits include Staphylococcus spp, Streptococcus spp, Salmonella spp, Escherichia spp. Management includes antimicrobial therapy and/or needle aspiration. Non-responders can undergo incision and drainage of abscess or thyroidectomy. Mortality was reported in about 8% of the reported 200 cases. In our patient, his history of drug use and Hepatitis C likely made him prone to infection. Although there was no description of pus during biopsy, pathology suggested acute inflammation. This along with elevated inflammatory markers led to the diagnosis. This case highlights an uncommon but potential cause of thyroiditis. Presentation: 6/3/2024

Discovery of novel and known viruses associated with toxigenic and non-toxigenic bloom forming diatoms from the Northern Adriatic Sea

Algal blooms impact trophic interactions, community structure and element fluxes. Despite playing an important role in the demise of phytoplankton blooms, only few viruses infecting diatoms have been cultured. Pseudo-nitzschia is a widespread diatom genus that commonly blooms in coastal waters and contains toxin-producing species. This study describes the characterization of a novel virus infecting the toxigenic species Pseudo-nitzschia galaxiae isolated from the northern Adriatic Sea. The ssRNA virus PnGalRNAV has 29.5 nm ± 1.2 nm icosahedral virions and a genome size of 8.8 kb. It belongs to the picorna-like Marnaviridae family and shows high specificity for P. galaxiae infecting two genetically and morphologically distinct strains. We found two genetically distinct types of this virus and screening of the global virome database revealed matching sequences from the Mediterranean region and China, suggesting its global distribution. Another virus of similar shape and size infecting Pseudo-nitzschia calliantha was found, but its genome could not be determined. In addition, we have obtained and characterized a new virus that infects Chaetoceros tenuissimus. The replicase protein of this virus is very similar to the previously described ChTenDNAV type-II virus, but it has a unique genome and infection pattern. Our study is an important contribution to the collective diatom virus culture collection and will allow further investigation into how these viruses control diatom bloom termination, carbon export and toxin release in the case of Pseudo-nitzschia.

(Re-)Emergence of Oropouche Virus (OROV) Infections: Systematic Review and Meta-Analysis of Observational Studies.

Oropouche Virus (OROV; genus of Orthobunyavirus) is the causal agent of Oropouche Fever (OF). Due to the lack of specific signs and symptoms and the limited availability of diagnostic tests, the actual epidemiology of OROV infections and OF has been extensively disputed. In this systematic review with meta-analysis, a literature search was carried out in PubMed, Scopus, EMBASE, and MedRxiv in order to retrieve relevant articles on the documented occurrence of OROV infections. Pooled detection rates were then calculated for anti-OROV antibodies and virus detection (i.e., viral RNA detected by viral cultures and/or real-time polymerase chain reaction [RT-qPCR]). Where available, detection rates for other arboviruses (i.e., Dengue [DENV], Chikungunya [CHKV], and Zika Virus [ZIKV]) were calculated and compared to those for OROV. A total of 47 studies from South America and the Caribbean were retrieved. In individuals affected by febrile illness during OROV outbreaks, a documented prevalence of 0.45% (95% confidence interval [95%CI] 0.16 to 1.12) for virus isolation, 12.21% (95%CI 4.96 to 27.09) for seroprevalence (including both IgM and IgG class antibodies), and 12.45% (95%CI 3.28 to 37.39) for the detection of OROV-targeting IgM class antibodies were eventually documented. In the general population, seroprevalence was estimated to be 24.45% (95%CI 7.83 to 55.21) for IgG class antibodies. The OROV detection rate from the cerebrospinal fluids of suspected cases of viral encephalitis was estimated to be 2.40% (95%CI 1.17 to 5.03). The occurrence of OROV infections was consistently lower than that of DENV, CHKV, and ZIKV during outbreaks (Risk Ratio [RR] 24.82, 95%CI 21.12 to 29.16; RR 2.207, 95%CI 1.427 to 3.412; and RR 7.900, 95%CI 5.386 to 11.578, respectively) and in the general population (RR 23.614, 95%CI 20.584 to 27.129; RR 3.103, 95%CI 2.056 to 4.685; and RR 49.500, 95%CI 12.256 to 199.921, respectively). In conclusion, our study stresses the possibly high underestimation of OROV prevalence in the general population of South America, the potential global threat represented by this arbovirus infection, and the potential preventive role of a comprehensive "One Health approach".

Bridging basic science and applied diagnostics: Comprehensive viral diagnostics enabled by graphene-based electronic biosensor technology advancements

This study presents a graphene field-effect transistor (gFET) biosensor with dual detection capabilities for SARS-CoV-2: one RNA detection assay to confirm viral positivity and the other for nucleocapsid (N-)protein detection as a proxy for infectiousness of the patient. This technology can be rapidly adapted to emerging infectious diseases, making an essential tool to contain future pandemics. To detect viral RNA, the highly conserved E-gene of the virus was targeted, allowing for the determination of SARS-CoV-2 presence or absence using nasopharyngeal swab samples. For N-protein detection, specific antibodies were used. Tested on 213 clinical nasopharyngeal samples, the gFET biosensor showed good correlation with RT-PCR cycle threshold values, proving its high sensitivity in detecting SARS-CoV-2 RNA. Specificity was confirmed using 21 pre-pandemic samples positive for other respiratory viruses. The gFET biosensor had a limit of detection (LOD) for N-protein of 0.9 pM, establishing a foundation for the development of a sensitive tool for monitoring active viral infection. Results of gFET based N-protein detection corresponded to the results of virus culture in all 16 available clinical samples and thus it also proved its capability to serve as a proxy for infectivity. Overall, these findings support the potential of the gFET biosensor as a point-of-care device for rapid diagnosis of SARS-CoV-2 infection and indirect assessment of infectiousness in patients, providing additional information for clinical and public health decision-making.

Real-world performance of a single-use, analyser-free, molecular point-of-care test for COVID-19 used in the emergency department: Results of a prospective trial (ED-POC)

A novel single-use, analyser-free, molecular point-of-care test for SARS-CoV-2 (Veros COVID-19 test, Sherlock Biosciences) could reduce time to results and improve patient care and flow in the emergency department (ED), but its performance in this setting is unknown. Adults aged ≥18 years presenting to Southampton General Hospital (UK) with suspected COVID-19 were tested with the Veros COVID-19 test in addition to standard of care near-patient PCR. Measures of diagnostic accuracy were calculated for the Veros COVID-19 test stratified by Ct value. Discrepant results underwent viral culture. Between Jan 16 and May 2, 2023, 400 patients were enrolled with a median (IQR) age of 60 (34-77) and 141 (35·3%) were SARS-CoV-2 positive by PCR. The Veros test gave valid results on the first test in 384 (96·0%), and sensitivity and specificity were 127/141 (90·1%, 95%CI 83·9-94·5) and 258/259 (99·6%, 95%CI 97·9-100) overall. For those with high or moderate viral load (Ct ≤30), sensitivity was 125/129 (96·9%, 95%CI 92·3-99·2). One (7·1%) of 14 PCR positive/Veros test negative samples was culture positive. Median (IQR) time from sample collection to result was 19 (18-20) mins with the Veros test versus 73 (59-92) mins with PCR (p<0·0001). The Veros COVID-19 test generated results in near real-time, around 1h sooner than rapid, near-patient, analyser-based PCR, and accuracy was excellent for samples with moderate and high viral loads. The Veros test represents a step-change in molecular diagnostics for infection and could significantly reduce time to results and improve patient management in EDs and other settings.

New methods to detect bacterial or viral infections in patients with chronic obstructive pulmonary disease.

Patients with chronic obstructive pulmonary disease (COPD) are frequently colonized and infected by respiratory pathogens. Identifying these infectious etiologies is critical for understanding the microbial dynamics of COPD and for the appropriate use of antimicrobials during exacerbations. Traditional methods, such as bacterial and viral cultures, have been standard in diagnosing respiratory infections. However, these methods have significant limitations, including lack of sensitivity and prolonged turnaround time. Modern molecular approaches offer rapid, sensitive, and specific detection, though they also come with their own challenges. This review explores and evaluates the clinical utility of the latest advancements in detecting bacterial and viral respiratory infections in COPD, encompassing molecular techniques, biomarkers, and emerging technologies. In the evolving landscape of COPD management, integrating molecular diagnostics and emerging technologies holds great promise. The enhanced sensitivity of molecular techniques has significantly advanced our understanding of the role of microbes in COPD. However, many of these technologies have primarily been developed for pneumonia diagnosis or research applications, and their clinical utility in managing COPD requires further evaluation.

Febrile young infants and the association with enterovirus infection

BackgroundEnterovirus is a common pediatric infectious disease, but the epidemiological data in young infants were lacking. This study aims to evaluate the role of enterovirus in febrile young infants and identify risk factors for severe infections. MethodsWe enrolled febrile infants younger than 90 days admitted to National Taiwan University Hospital from January 2010 to June 2021. Enterovirus infection was confirmed via viral isolation or pan-enterovirus PCR. Central nervous system involvement was defined by positive culture or PCR in cerebrospinal fluid. Severe complications included sepsis, hepatic failure, myocarditis, shock, encephalitis, acute kidney injury, respiratory failure, and multiorgan failure. ResultsOut of 840 febrile infants, 17.4% (n = 146) had enterovirus infection. Among these, 46% (n = 67) presented with meningitis and/or encephalitis. Early-onset enterovirus infection within the first two weeks of life was significantly linked to increased risks of anemia (hemoglobin <9 g/dL), ICU admission, central nervous system involvement, shock, hepatic failure, and mortality. Multivariable logistic regression identified high-risk serotypes (aOR 17.4, [95% CI 1.58, 191.5], p = 0.019) and hemoglobin <9 g/dL (aOR 44.9, [95% CI 5.6, 357.6], p < 0.001) as significant risk factors for severe complications. ConclusionsEnterovirus accounted for 17.4% of the etiology in febrile young infants and the case-fatality rate was 2%. Febrile young infants who had risk factors of enterovirus infection should consider viral culture or PCR examination for confirmation.

Clinical symptoms and faecal shedding of SARS-CoV-2 RNA among hospitalized COVID-19 patients: Implication for transmission.

SARS-CoV-2 shedding in human stool has been suggested as a probable route for faeco-oral transmission of the virus due to the availing evidence on the infectivity and pathogenicity of similar highly infectious respiratory viruses. Determining association of SARS-CoV-2 shedding in stools and presenting clinical status might be useful for prediction of the viral transmission spectrum and disease outcome. This study involved a descriptive cross-sectional survey of 91 consenting hospitalized, confirmed COVID-19 patients in Infectious Disease Isolation Centre, Oyo State, Nigeria. Socio-demographic characteristics and other ancillary data were collected from patient's hospital records with the aid of a structured investigator administered questionnaire. The laboratory detection of SARS-CoV-2 RNA in the stool of patients was performed using RT-PCR method. 27 (29.7%) of the 91 COVID-19 patients shed SARS-CoV-2 in their stools. The frequency of male (38.3%) patients shedding the virus in stools was higher than female (12.9%) patients (P = 0.012). Higher proportion of patients who had symptoms (41.2%) at admission shed the virus in their stool (P <0.007); particularly, fever (0.001), fatigue (0.003), headache (0.003), catarrh (0.001), and loss of smell (0.009). The frequency of viral shedding in stool was higher among patients with loss of taste (p = 0.028). Viral shedding in stool was significantly associated with low CT values (47.2%) and moderate CT value (21.4%) (P<0.05). Multivariate analysis showed that patients with moderate CT-value (OR = 0.28, 95% CI: 0.08-0.94, P = 0.039) and high CT-value (OR = 0.08, 95% CI: 0.01-0.80, P = 0.033) were less likely to shed the virus in stool. The gastrointestinal tract could be a route of SARS-CoV-2 transmission irrespective of the patients' clinical status. The low and moderate CT values of the nasopharyngeal swab is associated with shedding of the virus in patients' stools, although infectivity will depend on viral activity obtainable from further laboratory test analyses, such as viral culture.

Inactivation Validation of Ebola, Marburg, and Lassa Viruses in AVL and Ethanol-Treated Viral Cultures.

High-consequence pathogens such as the Ebola, Marburg, and Lassa viruses are handled in maximum-containment biosafety level 4 (BSL-4) laboratories. Genetic material is often isolated from such viruses and subsequently removed from BSL-4 laboratories for a multitude of downstream analyses using readily accessible technologies and equipment available at lower-biosafety level laboratories. However, it is essential to ensure that these materials are free of viable viruses before removal from BSL-4 laboratories to guarantee sample safety. This study details the in-house procedure used for validating the inactivation of Ebola, Marburg, and Lassa virus cultures after incubation with AVL lysis buffer (Qiagen) and ethanol. This study's findings show that no viable virus was detectable when high-titer cultures of Ebola, Marburg, and Lassa viruses were incubated with AVL lysis buffer for 10 min, followed by an equal volume of 95% ethanol for 3 min, using a method with a sensitivity of ≤0.8 log10 TCID50 as the limit of detection.

QuickFit: A High-Throughput RT-qPCR-Based Assay to Quantify Viral Growth and Fitness In Vitro.

Quantifying viral growth rates is key to understanding evolutionary dynamics and the potential for mutants to escape antiviral drugs. Defining evolutionary escape paths and their impact on viral fitness allows for the development of drugs that are resistant to escape. In the case of HIV, combination antiretroviral therapy can successfully prevent or treat infection, but it relies on strict adherence to prevent escape. Here, we present a method termed QuickFit that enables the quantification of viral fitness by employing large numbers of parallel viral cultures to measure growth rates accurately. QuickFit consistently recapitulated HIV growth measurements obtained by traditional approaches, but with significantly higher throughput and lower rates of error. This method represents a promising tool for rapid and consistent evaluation of viral fitness.

Development of highly adaptable RT-PCR methods for identifying Delta and BA.1 variants in inactivated COVID-19 vaccines.

Background The emergence and rapid spread of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), poses a significant threat to human health and public safety. While next-generation sequencing (NGS) is capable of detecting and tracking new COVID-19 variants for disease diagnosis and prevention, its high cost and time-consuming nature limit its widespread use. In this study, our aim was to develop a highly adaptable and accurate RT-PCR method for identifying the Delta or BA.1 variants in inactivated COVID-19 vaccine. We devised three two-plex RT-PCR methods targeting specific mutation sites: S: Δ156-157, S: N211-, L212I, and S: Δ142-144, Y145D. The RT-PCR method targeting the S: Δ156-157 mutation site was able to distinguish the Delta variant from other COVID-19 virus strains, while the RT-PCR methods targeting the S: N211-, L212I or S: Δ142-144, Y145D mutation sites were able to distinguish the BA.1 variant from other COVID-19 virus strains. We separately validated these three two-plex RT-PCR methods, and the results demonstrated good linearity, repeatability, reproducibility, and specificity for each method. Moreover, all three methods can be applied in the production of SARS-CoV-2 variant inactivated vaccines, enabling the identification of Delta or BA.1 variants in virus cultures as well as in inactivated vaccine stocks. This study presents a systematic approach to identify COVID-19 variants using multiple RT-PCR methods. We successfully developed three two-plex RT-PCR methods that can identify Delta and BA.1 variants based on specific mutation sites, and we completed the validation of these three methods.

Enteroviral meningitis in children: Clinical and laboratory features with and without pleocytosis.

Enteroviruses (EV) are most common causes of the etiologically known aseptic meningitis in children. EV can be detected with polymerase chain reaction (PCR) in cerebrospinal fluid (CSF) samples. We aimed to evaluate the clinical and laboratory characteristics of children diagnosed with PCR-confirmed EV meningitis in CSF samples. Patients aged 1 month to 17 years who underwent lumbar puncture (LP) with suspected meningitis and had CSF viral PCR and culture results between September 2012 and January 2021 at a tertiary care hospital in Turkey were included. Patients with no virus detected in CSF samples by PCR was comprised PCR-negative group. The EV PCR-positive patients were divided into two groups based on CSF pleocytosis as enteroviral meningitis (EVM) with CSF pleocytosis and EVM without CSF pleocytosis, and compared in terms of clinical and laboratory features. 78 (38.2%) were EV PCR-positive, and 126 (61.8%) were PCR-negative. Pleocytosis was detected in 55 (70.5%) EV PCR-positive patients and 94 (74.6%) of PCR-negative patients. Convulsion was significantly frequent (p=0.017) in EV PCR-positive patients with no pleocytosis. Protein and lactate concentrations in CSF were significantly higher in EV PCR-positive patients with pleocytosis (p=0.048, p=0.001, respectively). Median hospital stay was significantly longer in PCR-negative group (p<0.001). Diagnosing EVM with PCR prevents long-term hospitalization, unnecessary antibiotic use and healthcare-related complications.

Diagnostic Strategies in the Era of Monkeypox Resurgence: A Comprehensive Analysis.

The resurgence of monkeypox (Mpox), an orthopoxvirus infection closely related to smallpox, presents a significant global health challenge. This study presents a comprehensive overview of Mpox, focusing on its clinical manifestations, diagnostic strategies, and testing methodologies. A thorough review of the literature and available data on Mpox, emphasizing diagnostic assays, clinical indicators, and laboratory testing, constitutes the core of this analysis. The study involves insights from Mpox patients and healthcare professionals engaged in its diagnosis and management. Contextualizing the research within the global spread of Mpox addresses the complexities associated with the diagnosis of the disease. The findings illuminate diverse Mpox diagnostic techniques, encompassing viral culture, immunological methods, serology,quantitative polymerase chain reaction (qPCR), electron microscopy, and advanced technologies such as artificial intelligence (AI) and the GeneXpert system. qPCR is highlighted as the benchmark for MPXV detection and quantification. These diagnostic advancements have significantly enhanced the precision and efficiency of Mpox diagnosis, facilitating prompt identification and treatment of infected individuals. The study underscores the critical importance of accurate and timely diagnosis, proper handling and transportation of clinical specimens, and the imperative for point-of-care (POC) testing to control the global spread of Mpox.

Clinical Evaluation of the Accuracy of the Panbio™ COVID-19/Flu A&B Rapid Panel: A Combination Antigen Rapid Diagnostic Test for the Omicron Variant and Influenza A Virus.

It is difficult to differentiate between coronavirus disease 2019 (COVID-19) and influenza based on the symptoms. In the present study, a newly developed antigen rapid diagnostic test (Ag-RDT) called Panbio™ COVID-19/Flu A&B that can simultaneously detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A/B virus was evaluated. Its accuracy was evaluated using 235 pairs of nasopharyngeal samples collected from patients with respiratory symptoms and fever (>37.5°C). Reverse transcription polymerase chain reaction was used as a reference method to evaluate the accuracy of the SARS-CoV-2 detection. We confirmed the accuracy of the developed Ag-RDT against the Omicron variant where the sensitivity and specificity were 94.8% and 100%, respectively. In addition, to identify the influenza A virus, a noninferiority test was conducted using a commercial Ag-RDT, which has a sensitivity and specificity in comparison with viral culture of 94.8% and 98.4%, respectively. The positive and negative predictive values for influenza A virus were 98.5% and 98.1%, respectively, for the Panbio COVID-19/Flu A&B test. The evaluation of this newly developed Ag-RDT using clinical samples suggests that it has a high efficacy in clinical settings.

Profiling of viral load, antibody and inflammatory response of people with monkeypox during hospitalization: a prospective longitudinal cohort study in China

The dynamics of viral shedding and the specific humoral response against monkeypox virus (MPXV) have not been well characterized in patients across their disease course during hospitalisation. The aim of this study was to determine the viral load and the levels of antibodies against MPXV using longitudinal paired-collected samples from hospitalized patients. Patients who were hospitalised with mpox were recruited at Beijing Ditan Hospital Capital Medical University in China between June 2 and September 23, 2023. Paired samples, including samples from skin lesions, the oropharynx, saliva, faeces, urine, plasma, and serum, were serially collected at days 1, 3, 7, and 14 after admission until discharge. Not all of the patients had samples obtained at all of the timepoints. All the samples were analysed via quantitative PCR. Virus isolation was performed by using clinical samples and Vero cells. The presence of IgM, IgA, IgG, and neutralising antibodies (NAbs) against MPXV was evaluated. The first collected plasma sample was taken when the patient was hospitalised, and the levels of cytokines and chemokines were measured in the sample. The demographic data, smallpox vaccination status, history of known exposure to MPVX, HIV status and other clinical data were collected using a standard case report form. A total of 510 specimens were serially collected from 39 recruited people with mpox. Among all the samples, the skin lesions had the highest viral DNA detection rates and viral loads, and the saliva samples had the second highest rates and viral loads. One day before discharge, 85% of the dry scrabs (median Ct 28.2, range 19.0-38.3) and 70% of the saliva samples (median Ct 32.4, range 24.5-38.1) were positive for viral DNA, Of which, 23.1% of dry scrabs were positive in viral culture. The rate of viral DNA detection in the oropharyngeal, saliva, and faecal samples decreased with time, while the rates in the plasma, serum, and urine samples increased quickly before 10 days post symptom onset (PSO). The median days of appearance of MPXV-IgM, MPXV-IgA, MPXV-IgG, and NAb were at 8(interquartile range [IQR] 7-9), 9 (7-10), 12 (9-15), and 12 (9-15) PSO, respectively. The IgM, IgA, IgG, and NAb titres increased with time. Between days 11 and 21 PSO, the NAb titres were lower in people living with HIV (PWH) than in people living without HIV (PWOH). Increased NAb titres were associated with decreased viral loads in the saliva (r=0.28, p=0.025), faeces (r=0.35, p=0.021), plasma (r=0.30, p=0.0044), and serum samples (r=0.37, p=0.001). Compared with PWOH, PWH had higher plasma levels of MIP-1α, MIP-1β, G-CSF, IL-4, and FGF-basic. The high positive viral culture rate of clinical samples of patients when they are discharged from the hospital indicates that effective public health management strategies are needed for people with mpox. The low NAb titres and high levels of cytokines in PWH shows that earlier treatment is needed to control inflammation in high-risk populations. National Natural Science Foundation of China, Chinese Academy of Medical Sciences, Fundamental Research Funds for the Central Universities for Peking Union Medical College, National Key R&D Program of China.

Emerging Methods in the Identification of Bacterial Respiratory Tract Pathogens.

Here, we will review different bacterial causes of respiratory tract infections and discuss the available diagnostic methods. Moreover, we will provide some recently published patents and newer techniques, such as respiratory panels and omics approaches, and express the challenges in this path. Respiratory tract infections (RTIs) include those infections that can lead to the involvement of different respiratory parts, including the sinuses, throat, airways, and lungs. Acute respiratory tract infection is the leading cause of death from infectious illnesses worldwide. According to the World Health Organization, 1.6 to 2.2 million deaths have occurred due to acute respiratory infections in children under five years of age. About 4 million people die annually from respiratory infections, 98% of which are caused by lower respiratory infections. Depending on the type of pathogen, the severity of the infection can vary from mild to severe and even cause death. The most important pathogens involved in respiratory tract infections include Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis. The symptoms are often similar, but the treatment can vary greatly. Therefore, correct diagnosis is so important. There are several methods for diagnosing respiratory infections. Traditional tests include the culture of respiratory samples, considered the primary tool for diagnosing respiratory infections in laboratories, and less common standard tests include rapid and antigenic tests. It is essential to think that the culture method is reliable. In the original method of diagnosing respiratory infections, some bacteria were challenging to grow successfully, and many clinical laboratories needed to be equipped for viral cultures. Another issue is the time to get the results, which may take up to 7 days. Rapid and antigenic tests are faster but need to be more accurate. The clinical laboratories are trying to be equipped with molecular methods for detecting respiratory pathogens and identifying the genetic material of the infectious agent in these new methods as the primary method in their agenda.

Inefficient tissue immune response against MPXV in an immunocompromised mpox patient.

The recent outbreak of monkeypox virus (MPXV) was unprecedented in its size and distribution. Those living with uncontrolled HIV and low CD4 T cell counts might develop a fulminant clinical mpox course with increased mortality, secondary infections, and necrotizing lesions. Fatal cases display a high and widespread MPXV tissue burden. The underlying pathomechanisms are not fully understood. We report here the pathological findings of an MPXV-driven abscess in gastrocnemius muscle requiring surgery in an immunocompromised patient with severe mpox. Presence of virus particles and infectivity were confirmed by electron microscopy, expansion microscopy, and virus culture, respectively. MPXV tissue distribution by immunohistochemistry (IHC) showed a necrotic core with infection of different cell types. In contrast, at the lesion rim fibroblasts were mainly infected. Immune cells were almost absent in the necrotic core, but were abundant at the infection rim and predominantly macrophages. Further, we detected high amounts of alternatively activated GPNMB+-macrophages at the lesion border. Of note, macrophages only rarely colocalized with virus-infected cells. Insufficient clearance of infected cells and infection of lesion-associated fibroblasts sustained by the abundance of profibrotic macrophages might lead to the coalescing of lesions and the severe and persistent clinical mpox course observed in immunocompromised patients.

Establishment of a multisite umbrella cohort study protocol to describe the epidemiology and aetiologies of acute undifferentiated febrile illness in Latin America

IntroductionAcute undifferentiated febrile illnesses (AUFIs) impose a large burden in the tropics. Understanding of AUFI’s epidemiology is limited. Insufficient diagnostic capacity hinders the detection of outbreaks. The lack of interconnection...

Viral Kinetics of SARS-CoV-2 in Nursing Home Residents and Staff

Background: Nursing home (NH) residents are at high risk of COVID-19 from exposure to infected staff and other residents. Understanding SARS-CoV-2 viral RNA kinetics in residents and staff can guide testing, isolation, and return to work recommendations. We sought to determine the duration of antigen test and polymerase chain reaction (PCR) positivity in a cohort of NH residents and staff. Methods: We prospectively collected data on SARS-CoV-2 viral kinetics from April 2023 through November 2023. Staff and residents could enroll prospectively or upon a positive test (identified through routine clinical testing, screening, or outbreak response testing). Participating facilities performed routine clinical testing; asymptomatic testing of contacts was performed within 48 hours if an outbreak or known exposure occurred and upon (re-) admission. Enrolled participants who tested positive for SARS-CoV-2 were re-tested daily for 14 days with both nasal antigen and nasal PCR tests. All PCR tests were run by a central lab with the same assay. We conducted a Kaplan-Meier survival analysis on time to first negative test restricted to participants who initially tested positive (day zero) and had at least one test ≥10 days after initially testing positive with the same test type; a participant could contribute to both antigen and PCR survival curves. We compared survival curves for staff and residents using the log-rank test. Results: Twenty-four nursing homes in eight states participated; 587 participants (275 residents, 312 staff) enrolled in the evaluation, participants were only tested through routine clinical or outbreak response testing. Seventy-two participants tested positive for antigen; of these, 63 tested PCR-positive. Residents were antigen- and PCR-positive longer than staff (Figure 1), but this finding is only statistically significant (p=0.006) for duration of PCR positivity. Five days after the first positive test, 56% of 50 residents and 59% of 22 staff remained antigen-positive; 91% of 44 residents and 79% of 19 staff were PCR-positive. Ten days after the first positive test, 22% of 50 residents and 5% of 22 staff remained antigen-positive; 61% of 44 residents and 21% of 19 staff remained PCR-positive. Conclusions: Most NH residents and staff with SARS-CoV-2 remained antigen- or PCR-positive 5 days after the initial positive test; however, differences between staff and resident test positivity were noted at 10 days. These data can inform recommendations for testing, duration of NH resident isolation, and return to work guidance for staff. Additional viral culture data may strengthen these conclusions.Disclosure: Stefan Gravenstein: Received consulting and speaker fees from most vaccine manufacturers (Sanofi, Seqirus, Moderna, Merck, Janssen, Pfizer, Novavax, GSK, and have or expect to receive grant funding from several (Sanofi, Seqirus, Moderna, Pfizer, GSK). Lona Mody: NIH, VA, CDC, Kahn Foundation; Honoraria: UpToDate; Contracted Research: Nano-Vibronix