Advances in Virology最新文献

Enterovirus can cause central nervous system (CNS) infections ranging from meningitis to severe encephalitis. The aims of our study were to describe and develop the current epidemiological, biological, and clinical aspects of these infections as well as to enrich Moroccan data. This is a retrospective study conducted from January 2021 to March 2023, which included all patients admitted to the hospitals of Ibn Sina University Hospital Center in Rabat (Morocco) with clinical suspicion of CNS infection and positive cerebrospinal fluid (CSF) for enterovirus detected by BioFire® FilmArray® panel meningitis/encephalitis. 1479 CSF were analyzed by multiplex PCR. Enterovirus was detected in 19 patients (1.28%) with a median age of 5 years, predominantly affecting male patients (73.7%) and children (94.7%), especially those aged 2 years and older (68.4%). Fever was the most common symptom (77.8%), followed by headache (66.7%). The seasonal peak of enterovirus detection was also observed. For most patients, the CSF was predominantly lymphocytic (88.2%) with normal glycorrhachia (84.2%) and proteinorachia (73.7%). A notable proportion (10.5%) had a normal CSF cytology. Hyperproteinorachia was found in 26.3% of cases and hypoglycorrhachia in 5.3%. Blood analysis revealed a normal WBC count in 55.6% of cases, hyperleukocytosis in 33.3%, and leukopenia in 11.1%. CRP was elevated in 72.2% of cases. CNS enterovirus infections were particularly present among the pediatric population in this study. The lack of specificity in clinical and biological manifestations may sometimes suggest bacterial etiology. The widespread use of multiplex PCR can therefore provide a reliable and rapid method of detection and diagnosis.

Background: Human rhinovirus (HRV), traditionally recognized as the primary etiological agent of the common cold, has become the second most important viral agent in bronchopulmonary conditions, such as pneumonia and asthma exacerbations. During the COVID-19 pandemic, several viruses exhibited changes in their epidemiological behavior. This study aims to evaluate the clinical and epidemiological characteristics of children with HRV pneumonia before and during the pandemic in Mexico. Methods: A comparative ambispective longitudinal epidemiological study of two cohorts (prepandemic and pandemic periods) was carried out. Two databases were compared: one from 2010 to 2013 and the other from 2021 to 2023. Children under 5 years of age diagnosed with HRV pneumonia were included. Student's t-test, χ ² tests, and logistic regression were used to assess risk factors associated with severe pneumonia. Incidence density was calculated as HRV cases per 10 new cases of pneumonia per month for each year. Results: During the pandemic, the age of presentation shifted from 5 months to 16 months. There was a higher incidence of HRV pneumonia in children during the pandemic, particularly in the second half of 2021, with a peak in July and August. In addition, there was an increase in severity (53% vs. 63%, p=0.006) and coinfections (51.3% vs. 76% p < 0.001). A higher prevalence of all risk factors was observed in the second cohort. Conclusions: During the pandemic, a shift toward older age, a higher percentage of coinfections, and increased severity associated to HRV pneumonia were observed. These findings highlight the need for the development and implementation of targeted prevention and treatment measures for HRV.

In Africa, measles epidemics are frequently reported, despite numerous preventive measures, such as vaccination, which targets children under 5 years of age. Unfortunately, the Republic of the Congo is not an exception to this major health concern. Indeed, many cases are reported annually. Here, we provide an overview of the epidemiological characteristics of laboratory-confirmed measles cases from January 2019 to October 2022 as well as the risk factors associated with the occurrence of measles outbreak. Samples from suspected measles cases were collected across the country and sent to the National Laboratory of Public Health for confirmation. Specific IgM was tested using the enzyme-linked immunosorbent assay (ELISA). Data were analyzed using descriptive and analytic statistics (p < 0.05 was statistically significant). A total of 1330 samples were collected and analyzed. Over those 4 years, 537 samples were confirmed to be positive (40.3%) but with important disparities between years. A relatively low frequency of cases was reported in 2020. Overall, a progressive and significant evolution of positive cases was observed between 2019 and 2022, increasing from 16.8% in 2019 to 65.9% in 2022 (p < 0.0001). We report a low vaccination rate among children (44.8%) and a significantly high positivity rate in this group (46.6%) (p < 0.0008). No difference was reported according to the completeness of the vaccination scheme (p=0.094). Females were slightly more exposed to this infection than males (p=0.04; adjusted odds ratio [aOR]: 1.25 [1.01-1.6]), with an increased risk of exposure in rural areas (p=0.0001; aOR: 0.41 [0.32-0.53]). The department of Pointe-Noire had the highest positivity rate, while three other departments were considered high-risk areas: Likouala (p = 0.0001; aOR: 3.18 [1.80-5.61]), Pool (p=0.0001; aOR: 2.90 [1.70-4.95]), and Brazzaville (p=0.0005; aOR: 0.52 [0.36-0.75]). This study calls for strengthening the epidemiological surveillance system and vaccination strategy in the country. It remains important to research factors that induce a high positive rate among vaccinated children by biological verification of the immunization.

Background: There is a dire need for the establishment of active dengue surveillance to continuously detect cases, circulating serotypes, and determine the disease burden of dengue fever (DF) in the country and region. Predicting dengue PCR results using machine learning (ML) models represents a significant advancement in pre-emptive healthcare measures. This study outlines the comprehensive process of data preprocessing, model selection, and the underlying mechanisms of each algorithm employed to accurately predict dengue PCR outcomes. Methods: We analyzed data from 300 suspected dengue patients in Islamabad and Rawalpindi, Pakistan, from August to October 2023. NS1 antigen ELISA, IgM and IgG antibody tests, and serotype-specific real-time polymerase chain reaction (RT-PCR) were used to detect the dengue virus (DENV). Representative PCR-positive samples were sequenced by Sanger sequencing to confirm the circulation of various dengue serotypes. Demographic information, serological test results, and hematological parameters were used as inputs to the ML models, with the dengue PCR result serving as the output to be predicted. The models used were logistic regression, XGBoost, LightGBM, random forest, support vector machine (SVM), and CatBoost. Results: Of the 300 patients, 184 (61.33%) were PCR positive. Among the total positive cases detected by PCR, 9 (4.89%), 171 (92.93%), and 4 (2.17%) were infected with serotypes 1, 2, and 3, respectively. A total of 147 (79.89%) males and 37 (20.11%) females were infected, with a mean age of 33 ± 16 years. In addition, the mean platelet and leukocyte counts and the hematocrit percentages were 75,447%, 4189.02%, and 46.05%, respectively. The SVM was the best-performing ML model for predicting RT-PCR results, with 71.4% accuracy, 97.4% recall, and 71.6% precision. Hyperparameter tuning improved the recall to 100%. Conclusion: Our study documents three circulating serotypes in the capital territory of Pakistan and highlights that the SVM outperformed other models, potentially serving as a valuable tool in clinical settings to aid in the rapid diagnosis of DF.

Nucleic acid-based vaccines allow scalable, rapid, and cell-free vaccine production in response to an emerging disease such as the current COVID-19 pandemic. Here, we objected to the design of a multiepitope mRNA vaccine against the structural proteins of SARS-CoV-2. Through an immunoinformatic approach, promising epitopes were predicted for the spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins. Fragments rich in overlapping epitopes were selected based on binding affinities with HLA classes I and II for the specific presentation to B and T lymphocytes. Two constructs were designed by fusing the fragments in different arrangements via GG linkers. Construct 1 showed better structural properties and interactions with toll-like receptor 2 (TLR-2), TLR-3, and TLR-4 during molecular docking and dynamic simulation. A 50S ribosomal L7/L12 adjuvant was added to its N-terminus to improve stability and immunogenicity. The final RNA sequence was used to design a trans-amplifying RNA (taRNA) vaccine in a split-vector system. It consists of two molecules: a nonreplicating RNA encoding a trans-acting replicase to amplify the second one, a trans-replicon (TR) RNA encoding the vaccine protein. Overall, the immune response simulation detected that activated B and T lymphocytes and increased memory cell formation. Macrophages and dendritic cells proliferated continuously, and IFN-γ and cytokines like IL-2 were released highly.

Chronic hepatitis B virus (HBV) infection affects 257-291 million people worldwide. The World Health Organization reported 890,000 HBV-related deaths in 2019, higher than reported previously. There are 10 HBV genotypes (A-J) subdivided into several subgenotypes that differ considerably by geography. Various virologic factors, including genotype and subgenotype, impact the odds of acquiring a chronic HBV infection, the type of treatment prescribed, and the risk of developing hepatocarcinoma. Information on the HBV genotypes and subgenotypes that circulate in Ecuador remains low. To address this gap, the current study took a preliminary look at HBV-infected human samples from this region to identify the most common genotypes and subgenotypes. Samples from 44 patients in the Andean, Coastal, and Amazon regions of Ecuador were amplified and two major genotypes were identified, genotype F (42/44; 95.5%) and genotype E (2 patients; 4.5%). The genotype F subgenotypes were F3 (35/42; 83.33%), F4 (6/42; 14.28%), and F1b (1/42, 2.39%). This is the first epidemiological study to assess the distribution of HBV genotypes in Ecuador. The findings can inform antiviral drug effectivity studies specific to HBV genotypes prevalent in South America.

Potato virus Y (PVY) is a highly diverse and genetically variable virus with various strains. Differential evolutionary routes have been reported in the genus Potyvirus, caused by natural selection pressure, mutation, and recombination, with their virulence being dependent on different environmental conditions. Despite its significance and economic impact on Solanaceous species, the understanding of PVY's phylogeography in Kenya remains limited and inadequately documented. The study centers on the molecular characterization of a Kenyan PVY isolate, GenBank accession number PP069009. In-depth phylogenetic analysis unveiled a strong evolutionary association between the Kenyan isolate and isolate [JQ924287] from the United States of America, supported by a robust 92% probability. Recombinant analyses exposed a mosaic-like genetic architecture within the Kenyan isolate, indicating multiple gene recombination events. Selection pressure scrutiny identified specific sites under selective pressure, with evidence of positive/diversifying and negative/purifying selection. Population genetics analysis revealed a calculated nucleotide diversity (π) of 0.00354881, while analysis of molecular variance (AMOVA) unveiled a structured genetic landscape with an øST value of 0.45224. The extensive haplotype network depicted the possibility of diverse PVY strains occurring across continents. This analysis provides valuable insights into the genetic diversity and distribution of PVY globally, highlighting the importance of understanding evolutionary dynamics for effective management and control strategies of PVY on a global scale.

The omicron variant and its sublineages are highly contagious, and they still constitute a global source of concern despite vaccinations. Hospitalizations and mortality rates resulting from infections by these variants of concern are still common. The existing therapeutic alternatives have presented various setbacks such as low potency, poor pharmacokinetic profiles, and drug resistance. The need for alternative therapeutic options cannot be overemphasized. Plants and their phytochemicals present interesting characteristics that make them suitable candidates for the development of antiviral therapeutic agents. This study aimed to investigate the antiviral potential of Imperata cylindrica (I. cylindrica). Specifically, the objective of this study was to identify I. cylindrica phytochemicals that display inhibitory effects against SARS-CoV-2 main protease (M^pro), a highly conserved protein among coronaviruses. Molecular docking and in silico pharmacokinetic assays were used to assess 72 phytocompounds that are found in I. cylindrica as ligands and M^pro (6LU7) as the target. Only eight phytochemicals (bifendate, cylindrene, tabanone, siderin, 5-hydroxy-2-[2-(2-hydroxyphenyl)ethyl]-4H-1-benzopyran-4-one, maritimin, 5-methoxyflavone, and flavone) displayed high binding affinities with M^pro with docking scores ranging from -5.6 kcal/mol to -9.1 kcal/mol. The in silico pharmacokinetic and toxicological assays revealed that tabanone was the best and safest phytochemical for the development of an inhibitory agent against coronavirus main protease. Thus, the study served as a baseline for further in vitro and in vivo assessment of this phytochemical against M^pro of SARS-CoV-2 variants of concern to validate these in silico findings.

[This corrects the article DOI: 10.1155/2014/859090.].

Group A rotavirus (RVA), which causes acute gastroenteritis (AGE) in children worldwide, is categorized mainly based on VP7 (genotype G) and VP4 (genotype P) genes. Genotypes that circulate at <1% are considered unusual. Important genes also include VP6 (genotype I) and NSP4 (genotype E). VP6 establishes the group and affects immunogenicity, while NSP4, as an enterotoxin, is responsible for the clinical symptoms. The aim of this study was to genotype the VP6 and NSP4 genes and molecularly characterize the NSP4 and VP6 genes of unusual RVA. Unusual RVA strains extracted from fecal samples of children ≤16 years with AGE were genotyped in VP6 and NSP4 genes with Sanger sequencing. In a 15-year period (2007-2021), 54.8% (34/62) of unusual RVA were successfully I and E genotyped. Three different I and E genotypes were identified; I2 (73.5%, 25/34) and E2 (35.3%, 12/34) were the most common. E3 genotype was detected from 2017 onwards. The uncommon combination of I2-E3 was found in 26.5% (9/34) of the strains and G3-P[9]-I2-E3 remained the most frequent G-P-I-E combination (20.6%, 7/34). Children infected with RVA E2 strains had a statistically higher frequency of dehydration (50%) than those infected with RVA E3 strains (p = 0.019). Multiple substitutions were detected in NSP4, but their functional effect remains unknown. The result indicates the genetic diversity of RVA strains. Continuous surveillance of the RVA based on the whole genome will provide better knowledge of its evolution.