Advances in Virology最新文献

Introduction: The spike (S) gene of SARS-CoV-2 is pivotal to the processes of cell entry, immune evasion, and the adaptation of the host.

Aim: This study aimed to comprehensively characterize the SARS-CoV-2 spike gene variants circulating in Iraq and assess the functional consequences of their mutations on ACE2 receptor affinity, RBD-mediated immune escape, and viral transmissibility. It represents the first integrative genomic and functional profiling of Iraqi SARS-CoV-2 spike variants, providing novel regional insights into viral adaptation and evolution.

Methods: Whole-genome sequencing was performed on Iraqi SARS-CoV-2 isolates, followed by mutation profiling, phylogenetic classification, and comparison with global datasets. Key spike mutations-N501Y, P681R, D614G, and E484K-were analyzed to assess their structural and functional implications.

Results: Iraqi isolates clustered mainly within the Delta (21J) and 20A lineages. The mutations N501Y (91.7%), P681R (75%), and D614G (100%) were prevalent, enhancing viral binding and transmission, while E484K was absent, suggesting limited immune escape compared to Omicron-like variants.

Conclusion: The absence of E484K and the predominance of transmission-enhancing mutations indicate that Iraqi SARS-CoV-2 isolates favor adaptation through increased ACE2 affinity rather than extensive immune evasion. These findings underscore the importance of regional genomic surveillance to inform vaccination strategies and public health responses.

[This retracts the article DOI: 10.1155/2015/675921.].

Common bean (Phaseolus vulgaris L) is Kenya's second most important agricultural product after maize, serving as a vital source of protein for many rural families in Western Kenya. However, viral diseases caused by RNA and DNA viruses greatly impair bean productivity, often leading to yield losses of up to 100%, thus contributing to food insecurity. Global research has isolated 168 viruses of plants that have detrimental effects on common beans; however, no extensive profiling of these viruses has been done in Western Kenya. The scope of this study was to delineate the whole virome that infects common beans through a comprehensive disease diagnostic survey. Sixty-one diseased samples were collected, and nucleic acids were extracted using standard extraction protocols (DNA &RNA Qiagen) and sequenced on the Illumina platform. Metagenomic analysis revealed several DNA-based viruses, such as Badnavirus spp, Caulimovirus maculatractylodei, Pandanus badnavirus, Okra enation leaf curl virus, and Paper mulberry vein-banding virus, while metatranscriptomic analysis uncovered viruses like Tomato leaf curl Cameroon alphasatellite, Physalis Rugose Mosaic Virus, Citrus endogenous paretrovirus, Natevirus nate, and Bracoviriform facetosae. To the best of our knowledge, this study provides a comprehensive inventory of viral entities associated with common beans not documented in Africa. This information is essential for defining plant defense mechanisms, guiding crop protection strategies, lowering agriculture-related risks, strengthening resistance, and advancing resilience.

Human immunodeficiency virus-1 (HIV-1) is among the most genetically diverse pathogens due to expeditious molecular evolution. The rapid change in HIV genomes intricates HIV transmission and progression and attributes HIV resistance to antiretroviral therapy (ART). In East Africa, as in other parts of the globe, HIV-1 occurs in various subtypes, circulating recombinant form (CRF) and unique recombinant forms, with subtype A1 being the most predominant. Surveillance of HIV-1 molecular diversity and drug resistance mutations (DRMs) is a linchpin for monitoring viral evolution and treatment efficiency. However, consolidated reports on the same are limited, and therefore, the pursuit of meta-analysis was sought to analyze genetic diversity and drug resistance patterns of HIV-1 pol gene and their geographical distributions in four East African countries (Kenya, Uganda, Tanzania, and Ethiopia). We retrieved 7614 HIV-1 pol gene sequences, deposited between 2015 and 2025 from the Los Alamos HIV databases. The predominant HIV-1 subtypes were A1 (40.2%), C (21.5%), and D (17.7%), with geographical variability. A notable frequency of inter-subtype recombinant was observed with recombinants A1D (9.5%) and A1C (2.94%) being prevalent. Few CRFs (> 0.1%) were identified. DRM were present in 42.8% of the sequences, with the majority associated with NNRTIs (36.5%) and NRTIs (25.5%). The most frequently associated mutations were K103N and M184V. Although resistance to INSTI (3.7%) remained minimal, its presence warrants continued monitoring. A significant association between HIV-1 subtypes and DRM prevalence was observed (χ ² = 102.43, p < 0.0001), with subtypes showing varied resistance burdens. These findings underscore the variability in HIV-1 genetic diversity across studied East African countries, highlighting the need for region-specific interventions, to optimize HIV-1 control in this region.

Background: Since 2023, Cameroon has recorded numerous cases of seasonal influenza caused by the A/H3N2 subtype, which is the strain most commonly encountered worldwide in 2024. Methods: To describe the evolutionary dynamics of influenza A/H3N2 viruses, whole genome sequencing was performed using the Oxford Nanopore Technologies sequencing platform and the SQK-LSK109, EXP-NBD196 reagent kit (Oxford Nanopore Technologies, catalog no. SQK-LSK109). Subsequently, mutational analysis was performed on the 8 genes of the H3N2 influenza strains isolated between 2023 and 2024 in Cameroon by aligning our protein sequences with the reference sequences recommended by the WHO in the northern hemisphere during the 2023-2024 influenza season using MEGA 11 software. The trimeric and tetrameric structures of the HA, NA, and M proteins were downloaded from the protein website https://www.rcsb.org/ and imported into the PyMOL Version 2.6.1 software for visualization and annotation of the observed amino acid substitutions. Results: All Cameroonian A(H3N2) strains from 2023 to 2024 belonged to clade 3c.2a. The mutations I208F, K156I, E66K, N112S, G69N, V239I, K292E, Q189R, G241D, A202D, T3A, S70R, N161S, N138D, N394S, and N120D were detected in most HA1 gene samples (Supporting Table S1). Among these mutations, the important A202D and N161S mutations in HA1 in 2023 and 2024 led to the virulence of the virus and consequently resulted in the rapid evolution of the A/H3N2 virus and the generation of the new clades 3C.2a1b.2a.2a.3 and 3c.2a1b.2a.2a.3a.1, respectively. Similarly, amino acid substitutions at sites I469T, I65V, and H275Y in the NA protein were observed compared to the 2024 vaccine strain A/Darwin/6/2021. We noted the presence of the H275Y substitution in 30% of Cameroonian strains associated with major resistance to neuraminidase inhibitors, particularly oseltamivir. In general, the number of amino acid mutations observed between circulating strains and the vaccine strain for the following year was higher, indicating that circulating strains would evolve away from vaccine strains for the year 2023-2024. Conclusions: These results highlight the evolutionary nature of the human influenza virus.

[This corrects the article DOI: 10.1155/av/7990876.].

Background and Aims: Herpes simplex virus Type 1 (HSV-1) causes a wide spectrum of diseases in humans, including skin and mucosal ulcers, encephalitis, and keratitis. Acyclovir is regarded as the gold standard for treating infections with this virus. However, there are certain drawbacks to using this drug, such as its ineffectiveness against treatment-resistant virus strains. Therefore, the development of novel and effective drugs to combat this virus is urgently needed. The present work aims to explore the efficacy of magnesium oxide nanoparticles (MgONPs) against HSV-1 in vitro as a potential novel antiviral agent. Methods: MgONPs were characterized by X-ray diffraction, energy-dispersive X-ray spectroscopy, field-emission scanning electron microscope, ultraviolet-visible spectrophotometry, Fourier-transform infrared spectroscopy, dynamic light scattering, and zeta potential. To assess the cytotoxic effects of MgONPs on Vero cells, the neutral red uptake assay was used. The effects of MgONPs at nontoxic concentrations on HSV-1 were then examined using a quantitative real-time PCR assay. Results: No toxic effect was observed in all used concentrations of MgONPs (up to a concentration of 1000 μg/mL). Three-hour incubation of HSV-1 with MgONPs at concentrations of 900 and 1000 μg/mL resulted in a remarkable decrease in viral load with an inhibition rate of 93.6% and 96.8%, respectively. The results from the posttreatment assay also showed that MgONPs at concentrations of 300 and 1000 μg/mL led to a significant decrease in viral load with an inhibition rate of 99.5% and 99.7%, respectively. Conclusion: MgONPs can exert their inhibitory effects on HSV-1 in a dose-dependent manner, both directly and through interfering with the replication cycle of the virus.

HIV is a major cause of tuberculosis. The objective of current study was to isolate clinical determinants associated with viral load count among adult TB/HIV co-infected patients. This study was done at the University of Gondar Comprehensive Specialized Hospital from March 2017 to March 2022. In this study, linear mixed-effects models were used for repeated measure viral load count. Results from the analysis show that baseline viral load count (β = 465.1,  p value = 0.0026), hemoglobin levels (β = -493.5,  p value = 0.0107), CD4 cell count (β = -38.2,  p value = 0.0027), CPT (β = -326.8,  p value = 0.0363), functional status (β = 416.0,  p value = 0.0059), OCC (β = 123.0,  p value = 0.0028), tuberculosis type (β = 430.3,  p value = 0.0336), platelet cell count (β = -2.5,  p - value = 0.0005), lymphocyte count (β = -7.9,  p value = 0.0219), and visit time (β = -2.2,  p value = 0.001) were clinical determinants that affected repeated measure viral load count at a 5% level of significance. The study examined clinical determinants of repeated measure viral load count among TB/HIV co-infected patients. The clinical determinants like hemoglobin levels ≥ 11 g/dL, CD4 cell count ≥ 200 cell/mm³, CPT drug users, and platelet cell count, lymphocyte count, and visit time were decreased viral load count. Inversely, baseline viral load count (≥ 10,000 copies/mL), bedridden patients, patients with OCC, and those with extrapulmonary tuberculosis had a higher viral load count. Extensive monitoring and counseling can be beneficial for patients with hemoglobin, CD4 cell count, CPT, platelet cell count, lymphocyte count, visit time, baseline viral load count, and functional status, OCC, and TB type. Finally, further studies should be done in order to address major clinical determinants and enhance continuous follow-ups, monitor TB/HIV progression, and improve the life expectancy of patients living with TB/HIV.

Yunnan Province is an area in China with a major prevalence of biting arthropods (including mosquitos, ticks, and Culicoides) and arboviruses including dengue virus (DENV), bluetongue virus (BTV), and epizootic hemorrhagic disease virus (EHDV). Therefore, attempts to isolate and detect arboviruses are frequently conducted in Yunnan during the past decades. In this study, a total of three viral strains/isolates (LF6-4, LF3-1, and LF6C2) previously isolated from cattle, goat, and Culicoides in Lufeng County, Yunnan Province, between 2022 and 2023 were used for whole-genome sequencing, phylogenetic analysis, and electron microscopic analysis. As a result, these viruses were completely sequenced. Strain LF6-4 isolated from cattle was identified as a putative Serotype 1 Yunnan orbivirus (YUOV). Strain LF3-1 isolated from goats was identified as Guangxi orbivirus (GXOV), and it is the first GXOV strain isolated from this animal. Isolate LF6C2 represented the first totivirus strain isolated from Culicoides. The viral particles of all three isolates collected from the infected C6/36 cells were all icosahedral particles with a diameter of approximately 45 nm. However, MDBK cells yielded YUOV and GXOV particles with diameters of approximately 75 nm. This difference may be caused by different viral proliferation/package modes in the different types of host cells.

This research concentrated on the molecular diagnosis of Molluscum contagiosum (MC) in clinically suspected individuals from Diyala Province, Iraq, through the identification of the MC021L gene in skin tissue samples between October 2020 and April 2021. A total of 101 skin lesion samples were collected from patients suspected of MC infection, ranging in age from 5 months to 60 years and including both males and females. Samples were gathered from Baquba Teaching Hospital, the dermatology clinic, and multiple basic healthcare centers, where a tailored questionnaire was developed to capture sociodemographic and clinical details. All samples were analyzed using conventional PCR to detect the MC021L gene with specific primers, followed by gene sequencing and phylogenetic analysis. Data were analyzed using SPSS Version 27, with statistical significance set at p < 0.05. PCR results showed that 19 samples (18.8%) tested positive, with distinct bands at 979 bp. Sequencing of the MC021L locus uncovered 52 nucleic acid variations that are present in almost all samples (including missense mutations in the MC021L-encoded glycoprotein). These variations were uniformly distributed across the MC021L gene in the viral samples. Phylogenetic analysis revealed that all viral strains belonged to a putative new clade that was located between Subtypes-I and -II. Four isolates were submitted to the NCBI database and assigned the accession numbers LC629162, LC629163, LC629164, and LC629165. The unique genetic sequences of these isolates of the MC021L gene confirmed that they do not match any previously identified subtypes, paving the way for further scientific exploration.