Viral Agents Research Articles

Clinical cases of toxic hepatitis: aspects of differential diagnosis with viral hepatitis

In modern conditions of environmental problems, practicing doctors increasingly have to provide assistance to patients with hepatitis, the cause of which is not only known viral agents, but also chemical poisons. General information about toxic, primarily drug‑induced, and viral hepatitis is given. The main hepatotoxic drugs are listed. Their classification, mechanism of action, clinical symptoms, biochemical and morphological changes in various toxic liver lesions are highlighted. Information on drugs with high hepatic extraction, for which there is a high risk of overdose, is highlighted. For patients from risk groups, it is advisable to at least halve the dose of such drugs in accordance with the decrease in hepatic blood flow. Drugs with low hepatic extraction have a minimal risk of overdose, although metabolic insufficiency with long‑term administration of such drugs may cause their accumulation. Finally, drugs that are excreted by the kidneys are practically devoid of the risk of hepatotoxicity. Other professional and household toxic substances that have a direct hepatotoxic effect are discussed (carbon tetrachloride, dichlorodiphenyltrichloromethylmethane, yellow phosphorus, amanito‑ and phallotoxins of the pale toadstool, various pesticides, etc.).
 Clinical cases of own clinical observations of various toxic hepatitises are included. The general characteristics of viral hepatitis are given, primarily with an emphasis on their differential diagnosis with hepatotoxic lesions. The main signs of viral and toxic hepatitis are grouped in the table. For a successful differential diagnosis of toxic and viral hepatitis, it is necessary to apply a modern complex of anamnestic, clinical, biochemical, virological, instrumental and morphological examination methods as fully as possible.

Occupational Health Hazards Among Veterinarians in Saudi Arabia.

Introduction Veterinarians and other professionals who interact with animals on a daily basis encounter an elevated risk of exposure to both known and as-yet-undiscovered microbial agents. Additionally, they are also exposed to physical, chemical, and environmental hazards. Enhancing occupational health and safety in this context carries significant global significance. Methods This study aimed to comprehensively identify and outline the various biological, physical, chemical, and environmental health threats that were encountered by veterinarians in Saudi Arabia. To achieve this, wedesigned a self-completed questionnaire for 529 participants. The survey encompassed potential occupational hazards such as microbial diseases, injuries resulting from animal bites and scratches, allergies, and environmental risks like sunstroke and dust storms. Results Among the 529 participating veterinarians, 45.9% (243 individuals) reported instances of zoonotic diseases within the past five years. Notably, potential viral agents included Middle East respiratory syndrome coronavirus, avian influenza, and foot-and-mouth disease virus. Bacterial diseases were also frequently documented, with brucellosis (18.7%) and salmonellosis (7.9%) being notable pathogens. Protozoal infections were led by Leishmaniosis, constituting the most commonly detected protozoa (29 /529, 5.5%). Interestingly, 345 (65.2%) of the individuals reported that they have experienced animal bites and scratches. Needle stick injuries were also a common occupational hazard, with an incidence rate of 19.1%. Additionally, chemical exposure was prevalent, particularly to disinfectants (57.5%) and veterinary drugs (23.4%). The study participants also reported their exposure to various environmental hazards, including sunstroke, dust, sandstorms, and heavy rains. Conclusion The findings of this study draw attention to a concerning trend among veterinarians in Saudi Arabia. Their personal health and safety appear to receive inadequate attention, potentially heightening the risk of occupationally related health hazards. These outcomes highlight the need for a reevaluation of safety protocols and infection control practices within the veterinary profession. The implications of this study can potentially inform the development of policies and initiatives aimed at mitigating occupationally related health hazards among veterinarians in Saudi Arabia.

Benchmarking of virome metagenomic analysis approaches using a large, 60+ members, viral synthetic community.

We report here efforts to benchmark performance of two widespread approaches for virome analysis, which target either virion-associated nucleic acids (VANA) or highly purified double-stranded RNAs (dsRNAs). This was achieved using synthetic communities of varying complexity levels, up to a highly complex community of 72 viral agents (115 viral molecules) comprising isolates from 21 families and 61 genera of plant viruses. The results obtained confirm that the dsRNA-based approach provides a more complete representation of the RNA virome, in particular, for high complexity ones. However, for viromes of low to medium complexity, VANA appears a reasonable alternative and would be the preferred choice if analysis of DNA viruses is of importance. Several parameters impacting performance were identified as well as a direct relationship between the completeness of virome description and sample sequencing depth. The strategy, results, and tools used here should prove useful in a range of virome analysis efforts.

Washout-Resistant, pH-Responsive Anti-TMV Nanoimmune Inducer Based on Cellulose Nanocrystals.

The application of antiplant virus agents on leaf surfaces faces challenges due to their vulnerability to wear, instability, and limited duration, which in turn jeopardizes plant health and yield. In recent years, high-aspect-ratio nanomaterials have gained prominence as powerful carriers for disease treatment, thanks to their exceptional penetrability and precise drug delivery capabilities. Here, we synthesized a pH-responsive nanoimmune inducer (CNC-AMO) with strong leaf adhesion through a Schiff base reaction, achieved by grafting amino-oligosaccharides (AMOs) on the surface of aldehyde-based CNC (CNC-CHO). Fourier transform infrared spectrometry, zeta potential, X-ray photoelectron spectroscopy, X-ray diffraction, transmission electron microscopy, atomic force microscopy, scanning electron microscopy, thermogravimetric analysis, and elemental analysis were used to characterize the CNC-AMO. The CNC-AMO displayed the capability for pH-responsive AMO release, showcasing its potential for targeted and controlled delivery. When applied to plants, the CNC-AMO exhibited impressive anti-TMV efficacy during a weeklong observation period. Meanwhile, the CNC-AMO exhibited remarkable adhesion and scouring resistance on the surfaces of the plant leaves. We strongly believe that the synergy of environmentally friendly synthetic materials, efficient plant virus control, and streamlined scalability positions CNC-AMOs as a promising pesticide for plant virus therapy.

Seasonal Trends and Interactions of Viral Pathogens in Children Presenting with Acute Respiratory Tract Infections in the Advancing Periods of SARS-CoV-2 Pandemic

Although various bacteria and viruses have been identified in the etiology of acute respiratory tract infections (ARI), 90% of acute ARIs that develop in children are of viral origin. The aim of this study was to investigate the seasonal trends and interactions between infectious agents and to determine the risk factors associated with ARI in children aged 1-15 years admitted to the Pediatric Emergency Department of Manisa Celal Bayar University Hospital in the advancing periods of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic. To determine the bacterial and viral agents, samples were taken from 314 patients attending to the hospital with symptoms suggestive for ARI, between 06/01/2021 and 05/31/2022. Viral and bacterial agents were identified by multiplex polymerase chain reaction (PCR) and automated identification system, respectively. Demographic data of the participants and possible risk factors for ARI were recorded in the questionnaires. In the study, viral agents were detected in 77.3% of the children, and the most common infectious agent was rhinovirus/enterovirus (RV/EV) (36.3%), followed by influenza viruses (11.2%), and SARS-CoV-2 (10.5%). While RV/EV positivity was found to be higher in children with moderate and below average (p< 0.001) hand hygiene, influenza positivity was found higher in those attending school/preschool institution (p< 0.001) and whose mothers working full-time (p< 0.001). Respiratory syncytial virus positivity was associated with maternal smoking (p= 0.013) and home overcrowding (p= 0.014). Bacterial colonization was detected in 33 (11.6%) of 284 children whose swabs were taken for both bacterial and viral agents and the most frequently detected agents were Staphylococcus aureus (60.6%) and Pseudomonas aeruginosa (15.2%). Having siblings (p= 0.008) and maternal smoking (p= 0.012) were found to be associated with the detection of bacterial agents. In this study, in the advanced period of the pandemic, the most detected agents and seasonal characteristics were found to be similar to the pre-pandemic period. It is thought that knowing the regional etiology and risk factors will contribute to taking the necessary local control and protective measures.

Nucleocapsid single point-mutation associated with drop-out on RT-PCR assay for SARS-CoV-2 detection

BackgroundSince its beginning, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been a challenge for clinical and molecular diagnostics, because it has been caused by a novel viral agent. Whole-genome sequencing assisted in the characterization and classification of SARS-CoV-2, and it is an essential tool to genomic surveillance aiming to identify potentials hot spots that could impact on vaccine immune response and on virus diagnosis. We describe two cases of failure at the N2 target of the RT-PCR test Xpert® Xpress SARS-CoV-2.MethodsTotal nucleic acid from the Nasopharyngeal (NP) and oropharyngeal (OP) swab samples and cell supernatant isolates were obtained. RNA samples were submitted to random amplification. Raw sequencing data were subjected to sequence quality controls, removal of human contaminants by aligning against the HG19 reference genome, taxonomic identification of other pathogens and genome recovery through assembly and manual curation. RT-PCR test Xpert® Xpress SARS-CoV-2 was used for molecular diagnosis of SARS-CoV-2 infection, samples were tested in duplicates.ResultsWe identified 27 samples positive for SARS-CoV-2 with a nucleocapsid (N) gene drop out on Cepheid Xpert® Xpress SARS-CoV-2 assay. Sequencing of 2 of 27 samples revealed a single common mutation in the N gene C29197T, potentially involved in the failed detection of N target.ConclusionsThis study highlights the importance of genomic data to update molecular tests and vaccines.

Border disease virus and chlamydophila abortus co-infection in aborted sheep foetuses

Abortion in sheep and goats is one of the most important reproductive problems that affect small ruminants breeding. Non-infectious factors and infectious agents such as bacterial, viral, mycotic and parasitic infectious agents can cause abortion in sheep and goats. A high rate of abortion (43.75%) was observed in two sheep flocks in Niğde Province in Turkey during the lambing season in 2016. To determine the reason of abortion, aborted sheep foetuses (n = 3) and EDTA whole blood samples (n = 3) from mother of the foetuses were collected from two sheep flocks. Aborted foetuses and buffy coat cells of the EDTA whole blood samples were used for total nucleic acid extraction. Extracted nucleic acids were analysed for akabane virus (AKAV), bluetongue virus (BTV), peste des petits ruminants virus (PPRV), pestiviruses, Schmallenberg virus (SBV), Brucella spp., Chlamydophila abortus (C. abortus), Coxiella burnetii and Listeria monocytogenes. Border disease virus (BDV) RNA and C. abortus DNA were detected in three aborted sheep foetuses whereas other investigated infectious agents were not detected. Additionally, EDTA whole blood samples from mother of the foetuses were also found BDV positive. To the best of my knowledge, this is the first report on BDV and C. abortus co-infection in aborted sheep foetuses.

Fluctuation of the prevalence of beak and feather disease virus in captive psittacines in Iran.

Beak and feather disease virus (BFDV) is one of the most life-threatening viral agents infecting parrot species. In this study, we investigated fluctuation in the prevalence of beak and feather disease virus (BFDV) in captive psittacines in Iran. Two series of feather samples from different psittacine species, received between July 2019 and July 2021 (n = 1009) and between July 2021 and July 2022 (n = 2020), were examined for the presence of BFDV using the PCR method, and the host species distribution and temporal prevalence of BFDV within populations were calculated. The results showed a total viral prevalence of 26.86% and 26.88% within sample series 1 and 2, respectively. By examining both sample series, the prevalence of BFDV was found to be thehighest (P < 0.05) in Nymphicus hollandicus and thelowest (P < 0.05) in Psittacus erithacus, Myiopsitta monachus, Pyrrhura molinae, and Aratinga solstitialis. The viral prevalence was significantly higher (P < 0.05)within the series 1than theseries 2 samples only in Nymphicus hollandicus. Within series 2, the viral prevalence was significant (P < 0.05) in samples from Nymphicus hollandicus collected in March. This study indicates significant prevalence of BFDV in captive Nymphicus hollandicus populations and suggests that the fluctuation in the prevalence of BFDV could be due to the combined influence of host-species and temporal factors.

New-onset heart failure in infants: when the aetiological diagnosis becomes a challenge.

The onset of heart dysfunction in infants can result from either inherited factors or viral infections, both of which may involve inflammation. However, the precise role of EMB and CMR in determining the etiology of such cases remains poorlydefined. While CMR demonstrates high sensitivity in detecting inflammation, our experience suggests that it may not effectively differentiate between these two groups. A comprehensive diagnostic approach is essential when addressing this challenge, which includes considering EMB (with attention to the number of T-lymphocytes and the presence of oedema), specific CMR criteria, notably LGE and tissue mappings, as well as the identification of viral agents in cardiac tissue andtroponin levels. Additionally, genetic tests should be conducted when evaluating these patients. • EMB is the gold standard diagnostic test for myocarditis but it is notuniversally accepted. • The diagnostic value of the 2018-LLC in pediatric patients is still undefined. • Both EMB and CMR may show inflammation in infants with new-onset heart failure of any aetiology. • A global approach should be used when facing this diagnostic challenge, including the EMB (number of T-lymphocytes and oedema), some CMR criteria, specially LGE and mappings, the detection of viral agents in cardiac tissue and troponins. Genetic tests should also be performed when studying these patients.

Aptamer-based electrochemical biosensor with S protein binding affinity for COVID-19 detection: Integrating computational design with experimental validation of S protein binding affinity

Aptamer-based biosensors capable of rapid one-step detection of viruses provide new capabilities for large-scale detection of COVID-19. Here we report a combined aptamer-based electrochemical and computational approach to characterize the interaction between a 60 base single stranded (ss)DNA aptamer and the viral S protein using molecular docking and bioinformatics tools. To construct the biosensor, the DNA aptamer was immobilized to the surface of a gold nanoparticles (AuNPs) modified electrode and methylene blue (MB) was used as redox indicator. Based on thermodynamic calculations for the aptamer sequence as well as several runs in APBS (Adaptive Poisson-Boltzmann Equation), we found that S protein GLN104-ASP115 pocket is the candidate for DNA 30–39(GGGAGTGGTT) sequence interaction. In the presence of S-protein, the target induced conformational changes in the aptamer’s structure, generating an increase in the MB redox signal, with a linear range between 10 pM to 6 nM and a limit of detection of 91.1 pM using differential pulse voltammetry (DPV). The aptasensor was investigated in spiked human saliva and serum samples, demonstrating performance in both media. This study demonstrates the potential of the MB-labeled electrochemical aptasensor for direct one-step detection of viral proteins, COVID-19 and potentially other viral agents.

Inhibition of herpes simplex virus by wedelolactone via targeting viral envelope and cellular TBK1/IRF3 and SOCS1/STAT3 pathways

Development of novel antiherpes simplex virus (HSV) agents with active mechanisms different from nucleoside analogues is of high importance. Herein, we investigated the anti-HSV activities and mechanisms of wedelolactone (WDL) both in vitro and in vivo. Cytopathic effect (CPE) inhibition assay, plaque assay, and western blot assay were used to evaluate the anti-HSV effects of WDL in vitro. The immunofluorescence assay, RT-PCR assay, plaque reduction assay, sandwich ELISA assay, syncytium formation assay, tanscriptome analysis and western blot assay were used to explore the anti-HSV mechanisms of WDL. The murine encephalitis and vaginal models of HSV infection were performed to evaluate the anti-HSV effects of WDL in vivo. WDL possessed inhibitory effects against both HSV-1 and HSV-2 in different cells with low toxicity, superior to the effects of acyclovir. WDL can directly inactivate the HSV particle via destruction of viral envelope and block HSV replication process after virus adsorption, different from the mechanisms of acyclovir. WDL may influence the host genes and signaling pathways related to HSV infection and immune responses. WDL can mainly interfere with the TBK1/IRF3 and SOCS1/STAT3 pathways to reduce HSV infection and inflammatory responses. Importantly, WDL treatment markedly improved mice survival, attenuated inflammatory symptoms, and reduced the virus titres in both HSV-1 and HSV-2 infected mice. Thus, the natural compound WDL has the potential to be developed into a novel anti-HSV agent targeting both viral envelope and cellular TBK1/IRF3 and SOCS1/STAT3 pathways.

Geometry optimization, impact of solvation on the spectral (FT-IR, UV, NMR) analysis, Quantum chemical parameters, and the bioactivity of feruloyltyramine as a potential anti-Lassa virus agent via molecular docking

The unrelenting menace of the Lassa virus, characterized by its high mortality rate and the potential for global dissemination, underscores an urgent call for its comprehensive eradication to safeguard global public health. In light of this, this research embarked on an extensive investigation of trans-N-feruloyltyramine (FLTM), a compound derived from Cissampelos pareira. This study encompassed a thorough examination of its structural characteristics, utilizing spectroscopic analyses including FT-IR, UV, and NMR, with the aim of elucidating its electronic, structural, and biological properties. Seamlessly integrating experimental and theoretical approaches at the DFT/B3LYP/def2SVP level of theory in FLTM_dmso, FLTM_gas, FLTM_H2O, and FLTM_MeOH solvation. Moreover, solvation dynamic simulation highlighted FLTM's heightened total energy and enhanced solubility across dimethyl sulfoxide (DMSO), water (H2O), and methanol (MeOH) phases, signifying efficient distribution to target sites and emphasizing its potential as a drug candidate. Conversely, FLTM_gas exhibited lower total energy. Electronic properties further elucidated FLTM's reactivity and kinetic stability, with FLTM_DMSO displaying the lowest energy gap among solvents and corresponding values of 1.4168, 4.2159, 4.2175, and 4.2749 eV. These findings mirrored the compound's higher reactivity and lower kinetic stability compared to FLTM_H2O, FLTM_gas, and FLTM_MeOH, aligning with principles of chemical hardness and softness. Results of the molecular docking introduced FLTM as a potential Lassa fever treatment candidate, surpassing Ribavirin in binding affinities with Lassa virus target receptors. FLTM exhibited binding energies of -6.5 kcal/mol, -7.2 kcal/mol, and -8.2 kcal/mol in 7UOT, 3MX5, and 3MX2, respectively, establishing interactions with crucial amino acid residues. These findings strongly advocate for FLTM's efficacy, meriting further in vitro and in vivo investigations for clinical validation.

Long-term quantitative hepatitis B surface antigen (HBsAg) trajectories in persons with and without HBsAg loss on tenofovir-containing antiretroviral therapy.

Improving the understanding of the patterns of quantitative hepatitis B surface antigen (qHBsAg) trajectories associated with HBsAg loss is important in light of novel anti-hepatitis B virus agents being developed. We evaluated long-term qHBsAg trajectories in persons with HIV and HBV during tenofovir-containing antiretroviral therapy in the Swiss HIV Cohort Study. We included 29 participants with and 29 without HBsAg loss, defined as qHBsAg <0.05 IU/mL. We assessed qHBsAg decline during therapy in both groups and used agglomerative hierarchical clustering to identify different qHBsAg trajectory profiles in persons with HBsAg loss. The median follow-up time was 11.9 years (IQR 8.4-14.1), and the median time to HBsAg loss was 48 months (IQR 12-96). Among participants with HBsAg loss, 79% had a qHBsAg decline ≥1 log10 IU/mL 2 years after starting tenofovir. The trajectories in qHBsAg levels during tenofovir therapy were heterogeneous, characterized by five distinct profiles. Among participants without HBsAg loss, only 7% had a qHBsAg decline ≥1 log10 IU/ml after 2 years. Most persons with HIV who experienced HBsAg loss had an early decline in qHBsAg levels, with diverse trajectories during long-term tenofovir therapy. In persons without HBsAg loss, qHBsAg levels remained remarkably stable over time.

Effectiveness of monochloramine for inactivation of coronavirus in reclaimed water

Fecal shedding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by infected persons into wastewater was documented early during the COVID-19 pandemic, thereby stimulating inquiries into the effectiveness of municipal wastewater treatment processes for the reduction of infectious viruses. In wastewater treatment plants, free chlorine has traditionally been the disinfectant utilized due to its low cost and high efficacy. However, regulations limiting disinfection by-products have prompted a shift to chloramination in many areas of the United States. While studies regarding the effectiveness of free chlorine against many viral agents are abundant, the efficacy of monochloramine (NH2Cl) has been less well researched. This study aimed to determine the effectiveness of pre-formed monochloramine for disinfection of human coronavirus 229E (HCoV-229E) in both phosphate-buffered saline (PBS) and reclaimed water from a water reclamation plant in Tucson, Arizona. Reclaimed water was sampled over the course of six months (August 2020 to November 2020), and dosed with monochloramine at 3 mg/L. An additional 1 mg/L free ammonia was added to simulate the operational conditions of the treatment plant. Viability was determined using MRC-5 host cell monolayers, using the TCID50 assay method. An average Ct99.9 (concentration of disinfectant multiplied by the contact time to achieve a 99.9 % reduction of the target organism) of 176 mg*min/L monochloramine was determined. No significant difference in inactivation rate was observed between the dosed reclaimed water and phosphate buffered saline (PBS). These data indicate that monochloramine is an effective disinfectant for coronaviruses. They also indicate that the water matrix type did not significantly impact the disinfection efficacy of monochloramine against HCoV-229E in reclaimed wastewater compared to PBS.

Detection of the Genetic Material of the Viruses Tacheng uukuvirus and Sara tick phlebovirus in Taiga Ticks Collected in the Sverdlovsk, Tomsk Regions and Primorsky Territory of Russia and Their Phylogeny

Extensive spread of tick-borne diseases poses a significant problem for public health and the health of the population living in endemic areas.The aim of the study was to search, analyze genetic material and identify new viral agents of the Phenuiviridae family in taiga ticks collected in Asian regions of Russia using the method of high throughput sequencing.Materials and methods. The study involved 1460 taiga ticks collected in suburban areas of the Tomsk, Yekaterinburg and Primorsky Territory. The genetic material isolated from ticks was sequenced using Illumina technology followed by phylogenetic analysis.Results and discussion. Analysis of the sequencing results made it possible to detect extended nucleotide sequences of the L-gene fragment characteristic of the Phenuiviridae family viruses. We were able to identify 20 nucleotide sequences the length of 250 bp on average in homogenates of Ixodes persulcatus ticks. Eighteen isolates have been identified as members of the genus Uukuvirus and two isolates have been assigned to the genus Phlebovirus, Phenuiviridae family. Phylogenetic analysis has shown that all isolates of the genus Uukuvirus fall under the cluster of Tacheng tick virus 2 belonging to the species Tacheng uukuvirus. They form a separate phylogenetic group which is closely related to two Romanian variants of 2019. Tacheng tick virus 2 was detected in all three surveyed regions of the Asian part of Russia. Two Tomsk isolates of phlebovirus were classified as Sara tick phlebovirus and they clustered with two isolates of phleboviruses from Karelia. Thus, the genetic material of Tacheng tick virus 2 and Sara tick phlebovirus belonging to two genera of the family Phenuiviridae was found in I. persulcatus ticks collected in three geographically different regions of the Asian part of Russia.

Prevalence of Rotavirus, Adenovirus, and Hepatitis A Virus in a Tertiary Care Hospital in Somalia

Rotavirus, one of the viral infectious agents that is transmitted mainly through the fecal-oral route and spreads easily in regions with poor sanitation conditions, is the most common causative agent of acute gastroenteritis in children under five years of age worldwide, and enteric adenoviruses are other frequently encountered causative agents of gastroenteritis in childhood. Hepatitis A virus (HAV) is also transmitted in similar routes and is endemic in regions with poor sanitation conditions and limited access to clean water and is usually acquired in early childhood in these regions. In this study conducted in Mogadishu Somalia, rotavirus and adenovirus antigen test (immunochromatographic rapid test) results in patients admitted to a tertiary hospital in the 9-month period between February 2019 and October 2019 and ELISA based HAV antibody test results studied in 2018-2019 were retrospectively examined and it was aimed to determine the distribution of positivity rates of these viruses by age, gender, and year. During the study period, 1136 patients (mean age 6.33±12.36) were tested for rotavirus and adenovirus antigens, and 362 patients (mean age 21.26±18.45) were tested for anti-HAV IgM/IgG antibodies. The positivity rates of rotavirus and adenovirus were found as 17.8% and 5.1%, respectively. The positivity rates of anti-HAV IgM and IgG antibodies were 26.5% and 85.4%. The age group with the highest rotavirus test positivity was babies under one year old (27.3%), positivity rate was also high in children aged 1-2 years old (20.9%), and this distribution was similar for adenovirus. Although a small number of patients were tested in under five years of age, anti-HAV IgG seropositivity was 60% and above in all age groups. The highest anti-HAV IgM positivity rates were observed in children 2-&lt;5 and 5-15 years of age, 52.9% and 44% respectively. Rotavirus antigen positivity was found at high levels in the three-month period covering June, July, and August 2019. In July (2019), it was observed that the number of rotavirus and adenovirus antigen test requests were increased, and also, at the same time the highest positivity rates for both viruses were observed; 31.2% and 9.5% for rotavirus and adenovirus. Rotavirus and enteric adenovirus co-infection was detected in 2.4% (27/1136) of the patients, and 23 (85.2%) of these were under five years of age children. Our study results show that children under the age of two are especially affected by rotavirus and adenovirus infections in Somalia and indicate that HAV infections are acquired at an early childhood. We can say that it may be useful to review vaccination programs as an important public health measure to reduce the burden of mortality and morbidity associated with HAV and rotavirus, which have a high prevalence and also have protective vaccines.

Comparison of bacterial culture with BioFire® FilmArray® multiplex PCR screening of archived cerebrospinal fluid specimens from children with suspected bacterial meningitis in Nigeria

BackgroundDiagnosis of bacterial meningitis remains a challenge in most developing countries due to low yield from bacterial culture, widespread use of non-prescription antibiotics, and weak microbiology laboratories. The objective of this study was to compare the yield from standard bacterial culture with the multiplex nested PCR platform, the BioFire® FilmArray® Meningitis/Encephalitis Panel (BioFire ME Panel), for cases with suspected acute bacterial meningitis.MethodsFollowing Gram stain and bacterial culture on cerebrospinal fluid (CSF) collected from children aged less than 5 years with a clinical suspicion of acute bacterial meningitis (ABM) as defined by the WHO guidelines, residual CSF specimens were frozen and later tested by BioFire ME Panel.ResultsA total of 400 samples were analyzed. Thirty-two [32/400 (8%)] of the specimens were culture positive, consisting of; three Salmonella spp. (2 Typhi and 1 non-typhi), three alpha hemolytic Streptococcus, one Staphylococcus aureus, six Neisseria meningitidis, seven Hemophilus influenzae, 11 Streptococcus pneumoniae and 368 were culture negative. Of the 368 culture-negative specimens, the BioFire ME Panel detected at least one bacterial pathogen in 90 (24.5%) samples, consisting of S. pneumoniae, N. meningitidis and H. influenzae, predominantly. All culture positive specimens for H. influenzae, N. meningitidis and S. pneumoniae also tested positive with the BioFire ME Panel. In addition, 12 specimens had mixed bacterial pathogens identified. For the first time in this setting, we have data on the viral agents associated with meningitis. Single viral agents were detected in 11 (2.8%) samples while co-detections with bacterial agents or other viruses occurred in 23 (5.8%) of the samples.ConclusionsThe BioFire® ME Panel was more sensitive and rapid than culture for detecting bacterial pathogens in CSF. The BioFire® ME Panel also provided for the first time, the diagnosis of viral etiologic agents that are associated with meningoencephalitis in this setting. Institution of PCR diagnostics is recommended as a routine test for suspected cases of ABM to enhance early diagnosis and optimal treatment.

Alarming signs of localized and generalized lymphadenopathy referred to two pediatric tertiary centers

Abstract Background Lymphadenopathy (LN) affects as many as 90% of young children. A common cause of cervical LN is viral agents. The second most common cause is bacterial infections. While cancer is the most feared cause of generalized LN [2]. Objectives To define the etiology of localized versus generalized LN in children and adolescents in two tertiary centers (Ain Shams and Sultan Qaboos University Hospitals).Define the alarming signs for possible malignancy. Methods All children 2–16 years of both sexes presented to the two centers during the period 2018–2022, we divided them into patients with single lymph node enlargement and those with multiple LNs. Also with viral infection,either EBV or cytomegalovirus (CMV), and those with oncological diagnosis such as lymphoma and leukemia. Results Six hundred twenty-four children, 62% males aged 2–16 years (median, 6.5 years) over a period of 4 years,and acute both bacterial and granulomatous-related LNs were excluded (n=236). Meanwhile, 388 were enrolled from two centers, Ain Shams Children’s hospital (90%) and Sultan Qaboos (10%). In Ain Shams, 40% were referred to the general pediatrics clinic (n=155), only 1.9% were malignant, while of those referred to the pediatric oncology clinic(n=233), 42 (mostly 18%) were malignant, either leukemia (n=21) or lymphoma (four Hodgkin and seven NHL), and 10 were IMLN. Viral infection was the commonest; two-thirds were EBV and one third were CMV infection. Affected children with leukemia or NHL were commonly younger than 5 years.Boys were affected more with either EB or CMV often (two-thirds). No difference in the frequency of high temperature and sore throat between examined children in both viruses, but stomachaches, eyelid swelling, and skin rash were more common in CMV, while the frequency of LN and hepatosplenomegaly was not different. Alarming signs for risk for leukemia were associated with fever for more than 2 weeks. Purpura, bone aches and LNs. Generalized, nonregressive, firm and nontender, and splenomegaly were more at risk for noninfectious. Delay in diagnosis was 9–56 days comparable in both localized and generalized LN(mean, 17±3.1 days). Conclusion EBV was the commonest viral cause of LN in young children. Alarming signs for more serious illness were bone aches, splenomegaly, and purpura.

Validation of a Bovine Viral Diarrhea Virus (BVDV) absolute quantification method by digital droplet PCR (ddPCR).

A increasingly common way for the diagnostics of viral agents is to carry out PCR from biological samples, which can detect their nucleic acid during the acute phase of the disease. Taking into account the need for quality control of PCR tests in laboratories accredited by ISO/IEC 17025:2017, we intend to carry out feasibility studies for the production of Reference Materials (MR) for these molecular tests, using BVDV in the matrix serum as a model. The first step for this goal was the validation of an analytical method for quantification of viral RNA to characterize the material under study. Primers and probe from a commercial qualitative assay kit designed for Real Time RT-PCR (VetMax Gold BVDV - Thermo Fisher) were used for quantification of BVDV by ddPCR. The technique was optimized and a Detection Limit of 13 copies/μL was determined, allowing a Quantification Limit of 38 copies/μL. The method showed to be linear over two orders of magnitude. The method will be used in the homogeneity study and long-term stability tests for the pilot batch of BVDV in Fetal Bovine Serum MR, a model for the production of MR intended for PCR of BVDV and other Flaviviridae.

Severe viral lower respiratory tract infections in Brazilian children: Clinical features of a national cohort

BackgroundThe accurate etiological diagnosis of lower respiratory tract infections (LRTI) is essential for their effective clinical management. The extensive use of molecular methods during the COVID-19 pandemic has enabled massive data acquisition on viral lower respiratory tract infections. The current study aims to identify clinical features associated with eight viral agents among children presenting severe LRTI. Methodsretrospective cohort study of data from the Brazilian Influenza Epidemiological Surveillance Information System. Patients under 20 years-old who had severe LRTI with etiological confirmation through RT-PCR between 2020 and 2022 were included. Binary logistic regressions were used to examine associations between pathogens and symptoms. Results60,657 cases were assessed. The main viral agents detected were Sars-CoV-2 (COV2) (41.2%), Respiratory Syncytial Virus (29.1%), Human Rhinovirus (HRV) (12.1%), and Influenza (FLU) (5.5%). A general mortality rate of 4.3% was observed. The multivariate analysis evidenced that COV2 less likely presented with cough (OR: 0.34; 95%CI: 0.32–0.36), respiratory discomfort (Adjusted Odds Ratio (aOR): 0.61; 95%Confidence Interval (CI): 0.59–0.64), and desaturation (aOR: 0.71; 95%CI: 0.69–0.75). RSV strongly associated with cough (aOR: 2.59; 95%CI: 2.45–2.75) and respiratory discomfort (aOR: 1.54; 95%CI: 1.46–1.62), whereas FLU was linked to fever (aOR: 2.27; 95%CI: 2.06–2.50) and sore throat (aOR: 1.48; 95%CI: 1.34–1.64). ConclusionsThe viral agents responsible for severe LRTI have distinct associations with clinical features in children.