Viruses

32 pages, 3621 KB

Open AccessReview

Advances in Molecular Techniques for Detecting Sweet Potato (Ipomoea batatas (L.) Lam) Viruses: A Comprehensive Review

by Muhammad Abul Kalam Azad, Nanziba Ibnat, Saleh Shafique Chowdhury, Saaimatul Huq and Shahidul Islam

Viruses 2026, 18(8), 908; https://doi.org/10.3390/v18080908 - 18 Aug 2026

Abstract

Sweet potato (Ipomoea batatas (L.) Lam) is an important global food crop, but its production is threatened by numerous viral pathogens. More than 30 RNA and DNA viruses have been reported worldwide, making rapid and accurate detection essential for disease management, epidemiological [...] Read more.

Sweet potato (Ipomoea batatas (L.) Lam) is an important global food crop, but its production is threatened by numerous viral pathogens. More than 30 RNA and DNA viruses have been reported worldwide, making rapid and accurate detection essential for disease management, epidemiological surveillance, germplasm exchange, and resistance breeding. Although previous reviews have addressed sweet potato viruses and individual diagnostic methods, a comprehensive synthesis of emerging molecular technologies remains limited. This review addresses that gap by critically integrating recent advances from PCR-based and isothermal assays to high-throughput sequencing, CRISPR-based diagnostics, biosensors, nanotechnology, and artificial intelligence-driven detection platforms. Conventional approaches, including symptom observation, biological indexing, electron microscopy, and ELISA, have contributed to early virus identification but often lack the sensitivity, specificity, and speed needed for modern diagnostics. Molecular and isothermal techniques have substantially improved detection accuracy and enabled rapid identification and field-deployable diagnostics of diverse and mixed infections, while sequencing, CRISPR, biosensors, and AI-based platforms offer greater capacity for detecting novel and emerging viruses. This review discusses the comparative evaluation of molecular technologies for sweet potato virus detection in terms of diagnostic performance, cost-effectiveness, speed, and suitability for both laboratory and field applications, while highlighting future priorities for next-generation virus diagnostics. Integrating portable and high-throughput diagnostic platforms will strengthen virus surveillance, support virus-free planting material production, and promote sustainable sweet potato production worldwide. Full article

(This article belongs to the Section Viruses of Plants, Fungi and Protozoa)

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30 pages, 3276 KB

Open AccessReview

Bacteriophages as Phagobiotics: Scientific Rationale and Translational Boundaries for Gut Microbiome Modulation

by Fedor Zurabov

Viruses 2026, 18(8), 907; https://doi.org/10.3390/v18080907 - 18 Aug 2026

Abstract

Most translational work on bacteriophages has focused on antibacterial therapy or food biocontrol. A third use case is scientifically plausible but remains insufficiently defined: the intentional use of characterized phages to modulate gut microbial communities without infection-treatment claims. In this review, the term [...] Read more.

Most translational work on bacteriophages has focused on antibacterial therapy or food biocontrol. A third use case is scientifically plausible but remains insufficiently defined: the intentional use of characterized phages to modulate gut microbial communities without infection-treatment claims. In this review, the term “phagobiotics” is used for defined, purified and process-controlled bacteriophages or phage cocktails intended for selective gut microbiota modulation. The concept is evaluated across natural human phage exposure, the gut phageome, mechanisms of phage-mediated community modulation, human intervention studies, preclinical models, manufacturing quality and regulatory boundaries. Current evidence supports biological plausibility and indicates that oral phage exposure can be well tolerated and, in some contexts, can selectively affect target bacterial groups without broad microbiota disruption. Generalized clinical efficacy and broad microbiome-support claims, however, remain insufficiently established. Microbiological-modulation claims require target-linked evidence, whereas claims to treat, prevent or cure disease or replace antibiotics fall outside the proposed non-therapeutic category. A proportionate framework is proposed in which natural exposure and food-use precedents inform, but do not determine, the safety rationale; product-specific controls focus on identity, purity, production-host control, manufacturing consistency, stability, genomic characterization and claim-linked evidence. Regulatory classification remains case-specific and depends on intended use, product format, target population and claims. Full article

(This article belongs to the Special Issue Bacteriophages as Precision Tools for Microbiome Modulation)

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Graphical abstract

26 pages, 4110 KB

Open AccessArticle

Distinct Activation of Defense-Related Gene Networks in Rosetted Versus Symptomless Shoots in Rose Rosette Virus-Infected Roses

by Shakil Hosain, Venura Herath, Reghan Mutethia, Michael V. Kolomiets, Kevin Ong, Oscar Riera-Lizarazu and Jeanmarie Verchot

Viruses 2026, 18(8), 906; https://doi.org/10.3390/v18080906 - 18 Aug 2026

Abstract

Rose rosette virus (RRV) causes witches’ broom disease in roses. This study examined whether differences in disease in these spatially distinct domains are associated with local changes in defense-related hormones and transcriptional reprogramming. The levels of defense-related phytohormones salicylic acid (SA), jasmonic acid [...] Read more.

Rose rosette virus (RRV) causes witches’ broom disease in roses. This study examined whether differences in disease in these spatially distinct domains are associated with local changes in defense-related hormones and transcriptional reprogramming. The levels of defense-related phytohormones salicylic acid (SA), jasmonic acid (JA), 9-lipoxygenase (9-LOX), 13-lipoxygenase (13-LOX), and derived oxylipins were different in these distinct tissues. We curated differentially expressed genes involved in the biosynthesis, storage, and signaling of SA, JA, and oxylipins to reveal how specific defense pathways correlate with these distinct disease states. Gene ontology (GO) analysis and the Disease Resistance Analysis and Gene Orthology 3 (DRAGO3) pipeline revealed stress-associated genes and classical resistance (R) gene families that were differently expressed in these distinct tissue domains. Promoter analysis of defense-associated transcription factors and histone modifiers revealed hormone responsive elements, suggesting complex hormone crosstalk is involved in defense-related gene expression. We confirmed by RT-qPCR, a notable subset of defense genes in the chromosome 5 hotspot, specifically in the linkage group 5 (LG5) quantitative trait loci, linked to reduced RRV susceptibility, was altered in both field-infected and greenhouse-inoculated plants. The association of high versus low disease states with distinct defense hormone signatures and gene expression patterns suggests that local immune states, rather than whole-plant defenses, determine whether a cane becomes rosetted or remains asymptomatic. Full article

(This article belongs to the Special Issue Common Pathogenic Mechanisms of Plant Viruses)

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16 pages, 1256 KB

Open AccessArticle

Virological Failure and Mortality Among People Living with HIV Transitioned to Second- or Third-Line Antiretroviral Therapy in Rwanda: A Competing-Risks Survival Analysis of National Case-Based Surveillance Data, 2019–2025

by Gallican N. Rwibasira, Jean Claude Kwizera, Tafadzwa Dzinamarira, Steven Karera, Gatete Gaetan, Albert Tuyishime, Eric Remera, Daniel Henry Paris and Tracy R. Glass

Viruses 2026, 18(8), 905; https://doi.org/10.3390/v18080905 - 17 Aug 2026

Abstract

Background: Despite Rwanda’s achievement of the UNAIDS 95–95–95 targets, national evidence on virological failure (VF) and mortality after transition to second- or third-line antiretroviral therapy (ART) remains limited. We estimated the incidence of these outcomes and examined associated factors among people living with [...] Read more.

Background: Despite Rwanda’s achievement of the UNAIDS 95–95–95 targets, national evidence on virological failure (VF) and mortality after transition to second- or third-line antiretroviral therapy (ART) remains limited. We estimated the incidence of these outcomes and examined associated factors among people living with HIV (PLWH) transitioned to second- or third-line ART in Rwanda between 2019 and 2025. Methods: We conducted a retrospective cohort study using Rwanda’s national HIV case-based surveillance (CBS) system. PLWH aged ≥15 years who transitioned to second- or third-line ART between 1 January 2019 and 31 December 2025 were followed from transition until the first recorded outcome, last clinical contact, or administrative censoring. The primary operational VF endpoint was the first viral load >1000 copies/mL recorded ≥180 days after transition; a prespecified sensitivity analysis required two consecutive measurements >1000 copies/mL. We used Kaplan–Meier estimation and facility-clustered Cox regression for the composite outcome of VF or death, and Aalen–Johansen cumulative incidence functions and Fine–Gray regression for VF with death treated as a competing event. Results: Among 778 PLWH followed for 3564 person-years (median follow-up, 60.0 months), 81 (10.4%) met the primary operational VF endpoint, and 13 (1.7%) had death recorded as the first event. The composite incidence rate was 2.64 per 100 person-years (95% CI 2.10–3.17). In adjusted Cox regression, a PI-based regimen (adjusted hazard ratio [aHR] 2.14, 95% CI 1.37–3.36), WHO stage III (aHR 1.92, 95% CI 1.10–3.34), and WHO stage IV (aHR 3.59, 95% CI 1.61–8.02) were associated with the composite outcome. In Fine–Gray analysis, a PI-based regimen (subdistribution hazard ratio [sHR] 3.37, 95% CI 1.96–5.78) and WHO stage IV (sHR 4.44, 95% CI 1.91–10.4) were associated with VF. Conclusions: PI-based regimen use and advanced WHO clinical stage were associated with poorer outcomes after ART line transition. These findings support intensified viral load monitoring, adherence and resistance assessment, and individualized regimen review for patients receiving PI-based therapy, together with systematic implementation of the WHO advanced HIV disease package for patients with stage III or IV disease. Full article

(This article belongs to the Special Issue HIV Infection, Latency, Pathogenesis and Associated Comorbidities, Including Cancer and Inflammation in the Context of Drugs of Abuse and ART)

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16 pages, 959 KB

Open AccessArticle

Deep Sequencing of Hepatitis B Virus Reveals Clinically Relevant Low-Frequency Variants Among People Living with HIV in Botswana

by Tsholofelo Sethibe, Wonderful Tatenda Choga, Florence G. Gaongalelwe, Bonolo B. Phinius, Gorata G. A. Mpebe, Kabo Baruti, Chanana Dorcus Tsayang, Goabaone Mbae, Basetsana Katlo S. Phakedi, Patience Motshosi, Linda Mpofu-Dobo, Mosimanegape Jongman, Sikhulile Moyo, Motswedi Anderson and Simani Gaseitsiwe

Viruses 2026, 18(8), 904; https://doi.org/10.3390/v18080904 - 17 Aug 2026

Abstract

(1) Background: The Hepatitis B virus (HBV) is characterized by extensive genetic diversity, including low-frequency variants that contribute to disease progression. We aimed to characterize low-frequency variants and evaluate their potential clinical impact. (2) Methods: We utilized 104 HBV near-full-length sequences generated using [...] Read more.

(1) Background: The Hepatitis B virus (HBV) is characterized by extensive genetic diversity, including low-frequency variants that contribute to disease progression. We aimed to characterize low-frequency variants and evaluate their potential clinical impact. (2) Methods: We utilized 104 HBV near-full-length sequences generated using next-generation sequencing (NGS) from people living with HIV (PLHIV). We used an in-house bioinformatics suite (HBVgenomeR v5.9.7) to filter for low-frequency variants (5–50%), which were compared to escape and drug resistance mutations (DRMs) and hepatocellular carcinoma (HCC)-associated mutations reported at the consensus level. Unclassified variants were characterized by HBV open reading frames (ORFs) to determine mutation frequency per genomic region. (3) Results: A total of six escape mutations were detected in 8/104 (7.7%) sequences, with _surfaceN131T being the most prevalent (5/8). We also observed six DRMs in 30/104 (28.8%), with _rtV173L being the most prevalent (21/30). Truncation mutations were also observed with _rtA181T/_sW172* and _rtM204I/_sW196L being the most prevalent. A total of 8/104 (7.7%) sequences had four variants associated with HCC. The _xP46S was the highest observed HCC-associated mutation at 5/8. We report 1152 unique uncharacterized variants across all ORFs, and these were found in 94/104 (90.4%) sequences. The RNaseH domain had the highest burden (330/1152, 28.6%). (4) Conclusions: Deep sequencing results identified clinically significant mutations, including those below the 20% detection limit of traditional sequencing, that would go unreported. This highlights the possible underreporting of mutational burden in people living with HBV/HIV, indicating the importance of deep sequencing to aid in HBV/HIV understanding and management. Full article

(This article belongs to the Section Human Virology and Viral Diseases)

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15 pages, 924 KB

Open AccessArticle

Seroepidemiology of Enterovirus D68 in Xiamen Children: A Cross-Sectional Study in 2022

by Liting Wang, Qiguo Zhu, Yi Lu, Yuanyuan Wu, Zhifeng Ke, Qingbing Zheng, Longfa Xu, Tong Cheng, Rui Zhu and Jun Shen

Viruses 2026, 18(8), 903; https://doi.org/10.3390/v18080903 - 17 Aug 2026

Abstract

Enterovirus D68 (EV-D68) is a re-emerging pathogen associated with severe acute flaccid myelitis (AFM) and pneumonia, predominantly in children but also capable of causing severe disease in immunocompromised adults. Seroprevalence data are essential for understanding population immunity, age-specific susceptibility, and viral transmission dynamics; [...] Read more.

Enterovirus D68 (EV-D68) is a re-emerging pathogen associated with severe acute flaccid myelitis (AFM) and pneumonia, predominantly in children but also capable of causing severe disease in immunocompromised adults. Seroprevalence data are essential for understanding population immunity, age-specific susceptibility, and viral transmission dynamics; yet, such data for the period after the COVID-19 pandemic are scarce. We conducted a cross-sectional serological survey to characterize the neutralizing antibody profile of EV-D68 among children in Xiamen, China, in 2022. A total of 453 children aged 0–16 years (217 with acute respiratory tract infection [ARTI] and 236 without) were enrolled. Neutralizing antibody (NtAb) titers against the EV-D68 STL strain were measured using a microneutralization assay, seropositivity was defined as a titer ≥1:16. Multivariable regression and analysis of covariance were used to adjust for age and sex. Overall seroprevalence was 96.0% (435/453), exceeding 90.0% in every age subgroup (0–1 y: 100%; 1–3 y: 97.6%; 3–5 y: 92.6%; ≥5 y: 96.2%). The geometric mean titer (GMT) was 76.78 (95% CI: 68.32–85.24). After adjustment, ARTI status was not significantly associated with seropositivity (adjusted OR = 1.42, 95% CI: 0.46–4.41, p = 0.542). In an exploratory comparison, children with ARTI showed nominally higher antibody titers than those without (Mann–Whitney U test, p = 0.003), although the absence of EV-D68-specific PCR testing precludes etiologic attribution of respiratory symptoms to EV-D68 infection. Infants < 1 year showed the highest GMT (86.31), while children aged 1–3 years had the lowest GMT (63.52) and the largest low-titer fraction, indicating a susceptibility gap. Our study revealed EV-D68 circulated endemically in this pediatric population, establishing a high population immune baseline (>90.0%) with distinct age-dependent patterns. These findings provide key reference data for ongoing serosurveillance, outbreak risk assessment, and the evaluation of future vaccines or immunoprophylactic strategies should they become available. Full article

(This article belongs to the Special Issue Enteric Viruses in Environment and Humans: Identification, Surveillance and Control)

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14 pages, 2509 KB

Open AccessArticle

Possible Volumetric Changes in the Hippocampus and Olfactory Bulbs After COVID-19: A Stereological MRI Study

by Gamze Altun, Aynur Atilla, Kerim Aslan, Kıymet Kübra Tüfekci, Barış Genç, Arife Ahsen Kaplan, Özgür Kemal, Murat Terzi, Hüseyin Akan and Süleyman Kaplan

Viruses 2026, 18(8), 902; https://doi.org/10.3390/v18080902 - 16 Aug 2026

Abstract

COVID-19 affects the olfactory system and the hippocampus, leading to severe olfactory and cognitive impairments. This study aimed to quantify volumetric changes in the olfactory bulbs and hippocampus in patients with COVID-19, and to investigate these differences in relation to loss of smell [...] Read more.

COVID-19 affects the olfactory system and the hippocampus, leading to severe olfactory and cognitive impairments. This study aimed to quantify volumetric changes in the olfactory bulbs and hippocampus in patients with COVID-19, and to investigate these differences in relation to loss of smell and taste. This stereological MRI study included 60 COVID-19 (+) participants and 54 non-COVID-19 participants. Using OsiriX software, the volumes of the olfactory bulb and hippocampus were manually measured from 3T MRI images. Compared with controls, participants with loss of smell and taste had smaller olfactory bulb volumes. This decrease was especially noticeable in the left olfactory bulb of female patients. Furthermore, the right hippocampal volume in male patients with loss of smell and taste was significantly decreased. These findings suggest that atrophy of the olfactory bulb and hippocampus may be specific to certain regions and sexes following SARS-CoV-2 infection. Stereological MRI assessments can effectively identify these changes. Prospective longitudinal studies are needed to determine the clinical significance of these changes and their impact on patient management. Full article

(This article belongs to the Section Coronaviruses)

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15 pages, 5164 KB

Open AccessArticle

Whole-Genome Sequencing of RSV and Phylogeographic Assessment of Viral Importations into Russia

by German V. Roev, Ekaterina V. Pimkina, Dmitry V. Svetlichnyy, Arina V. Peresadina, Maksim I. Nadtoka, Kamil F. Khafizov and Vasiliy G. Akimkin

Viruses 2026, 18(8), 901; https://doi.org/10.3390/v18080901 - 15 Aug 2026

Abstract

Lower respiratory tract infections caused by the respiratory syncytial virus (RSV) pose a major global public health challenge. The use of next-generation sequencing technologies enables detailed monitoring of viral genetic variability, which is crucial for evaluating the efficacy of immunoprophylactic measures. In this [...] Read more.

Lower respiratory tract infections caused by the respiratory syncytial virus (RSV) pose a major global public health challenge. The use of next-generation sequencing technologies enables detailed monitoring of viral genetic variability, which is crucial for evaluating the efficacy of immunoprophylactic measures. In this study, whole-genome sequencing of RSV was performed on 106 samples collected in the Russian Federation between September 2021 and April 2025. Three NGS platforms were employed: Illumina MiSeq, Oxford Nanopore Technologies MinION, and Qitan Tech QNome-3841. Using discrete phylogeographic methods, we estimated a minimum of 45 introduction events into Russia for RSV-A and 39 for RSV-B among the genomes included in the analysis. Most events were represented by a single Russian genome. These results indicate recurrent introductions of RSV into Russia from abroad. Given the limited genomic sampling available, most of these introductions were not associated with detectable transmission within the country. Full article

(This article belongs to the Special Issue RSV Epidemiological Surveillance: 3rd Edition)

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14 pages, 15849 KB

Open AccessArticle

Innate Immune Responses Induced by H9N2 Influenza A Virus and Klebsiella pneumoniae Co-Infection

by Yong-Jie Zhu, Rui-Rui Du, Feng Xiao, Ling-Yi Shao, Jia-Xin Sun, Yu-Jun Zhou, Yu-Xin Shi, Ya-Wen Jin and Zhi-Jing Xie

Viruses 2026, 18(8), 900; https://doi.org/10.3390/v18080900 - 14 Aug 2026

Abstract

Klebsiella pneumoniae infection following H9N2 Influenza A virus (IAV) infection causes severe pneumonia. But the underlying pathogenic mechanisms of H9N2 IAV and K. pneumoniae co-infection are complex and need to be further explored. In this study, the lung transcriptomes of mice with H9N2 [...] Read more.

Klebsiella pneumoniae infection following H9N2 Influenza A virus (IAV) infection causes severe pneumonia. But the underlying pathogenic mechanisms of H9N2 IAV and K. pneumoniae co-infection are complex and need to be further explored. In this study, the lung transcriptomes of mice with H9N2 IAV and K. pneumoniae co-infection were characterized by transcriptomic profiling. As a result, GO enrichment analysis revealed that the differential genes were primarily involved in the activation of immune responses, cellular components of membranes and extracellular spaces, and defense responses against pathogen infections. According to KEGG enrichment, the differentially expressed genes (DEGs) were concentrated in TLR signaling pathways, RLR signaling pathways, TNF signaling pathways and NLRP3 signaling pathways. Furthermore, in vitro cell models were established to investigate the innate immune responses induced by H9N2 IAV and K. pneumoniae CPS co-stimulation. K. pneumoniae CPS stimulation influenced the cytokine profiles of mink lung epithelial cells infected with H9N2 IAV, worsened cell viability, and aggravated apoptosis, indirectly inhibiting H9N2 IAV replication. The findings demonstrated that K. pneumoniae superinfection modulated the innate immune responses induced by H9N2 IAV infection, contributing to its pathogenesis. Full article

(This article belongs to the Section Viral Immunology, Vaccines, and Antivirals)

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16 pages, 554 KB

Open AccessArticle

Hepatitis B in Isolated Anti-HBc Carriers: Predictors of Detectable HBV DNA and Implications for Risk-Stratified Screening

by Hasan Zeybek

Viruses 2026, 18(8), 899; https://doi.org/10.3390/v18080899 - 14 Aug 2026

Abstract

Background/Objectives: Isolated anti-HBc (IAHBc)—anti-HBc reactivity without HBsAg or anti-HBs—may indicate occult HBV infection (OBI) and confers reactivation risk under immunosuppression, yet most evidence derives from single specialties. We assessed the frequency, predictors, and diagnostic yield of detectable HBV DNA across multiple clinical specialties [...] Read more.

Background/Objectives: Isolated anti-HBc (IAHBc)—anti-HBc reactivity without HBsAg or anti-HBs—may indicate occult HBV infection (OBI) and confers reactivation risk under immunosuppression, yet most evidence derives from single specialties. We assessed the frequency, predictors, and diagnostic yield of detectable HBV DNA across multiple clinical specialties in a large real-world cohort to inform risk-based testing. Methods: In this 8-year, single-center retrospective study from an intermediate-endemic setting, 36,506 patients were screened for HBsAg, anti-HBs, and anti-HBc IgG. Patients with the IAHBc pattern who underwent HBV DNA testing formed the analytic cohort. Predictors of HBV DNA positivity were identified by multivariable logistic regression, and the number needed to screen (NNS) was calculated per specialty. Results: IAHBc prevalence was 4.16% (1517/36,506); 1412 patients comprised the analytic cohort (median age 60 years; 55.2% male). HBV DNA was detectable in 117 patients (8.3% of the cohort; 0.32% of all screened). Positivity varied more than fifteen-fold across specialties, with NNS ranging from 4.3 in gastroenterology to 66 in other clinics. High-intensity immunosuppression was the strongest independent predictor (adjusted OR 14.5), alongside younger age and gastroenterology or infectious diseases referral; the model showed good discrimination (AUC 0.810), while male sex was not an independent predictor. Among positive patients, 47% had HBV DNA below 200 IU/mL, consistent with low-level occult infection. Conclusions: These findings support guideline-recommended HBV DNA testing in all anti-HBc-positive patients before immunosuppression and, where universal testing is not feasible, provide local denominators for prioritizing it as an exercise in diagnostic stewardship. The proposed algorithm is institution-level rather than generalizable. Full article

(This article belongs to the Special Issue Hepatitis Viruses: Detection, Diagnosis and Treatment)

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27 pages, 4266 KB

Open AccessReview

Unraveling HBV Life Cycle by Fluorescent Microscopy Imaging

by Vanessa Sarabia Vega, Virgile Rat, Florian Seigneuret, Sébastien Eymieux, Philippe Chouteau and Hugues de Rocquigny

Viruses 2026, 18(8), 898; https://doi.org/10.3390/v18080898 - 14 Aug 2026

Abstract

The hepatitis B virus (HBV) is a worldwide hepatotropic virus despite the availability of a highly effective vaccine. Currently, the most efficacious treatment against HBV infection is the use of interferon and nucleos(t)ide analogs, which effectively suppress viral replication but do not eradicate [...] Read more.

The hepatitis B virus (HBV) is a worldwide hepatotropic virus despite the availability of a highly effective vaccine. Currently, the most efficacious treatment against HBV infection is the use of interferon and nucleos(t)ide analogs, which effectively suppress viral replication but do not eradicate infection. Consequently, studies are still ongoing to identify novel molecules with antiviral properties. Interfering with HBV trafficking in infected cells is an approach that would greatly benefit from the diverse techniques of microscopy. However, several challenges arise in employing such techniques for HBV, given the unique characteristics of this virus. Notably, HBV predominantly produces non-infectious subviral particles in addition to infectious virions. Moreover, both virions and SVPs are small objects, measuring only 20 to 40 nm, which challenges their observation using conventional optical microscopy. Additional obstacles include the small size of the HBV genome and its high compaction, which restrict reverse genetics and the introduction of DNA sequences coding for fluorescent polypeptides. In this review, we will provide an overview of ongoing research efforts aimed at visualizing the different stages of the HBV life cycle within infected cells. Furthermore, we will explore solutions successfully applied to the visualization of other viruses that could potentially be adapted to HBV. Full article

(This article belongs to the Special Issue Microscopy Methods for Virus Research, 2nd Edition)

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42 pages, 15278 KB

Open AccessArticle

Phylogenetic Evidence of Local HIV-1 Transmission and Antiretroviral Drug Resistance in the Middle East and North Africa

by Esraa Al-Fraihat, Amal Irshaid, Mohammed Sallam, Johan Snygg, Rasha Awawdeh, Hasanain Al-Shakerchi, Sama Al-Baidhani and Malik Sallam

Viruses 2026, 18(8), 897; https://doi.org/10.3390/v18080897 - 14 Aug 2026

Abstract

The molecular epidemiology and antiretroviral (ARV) drug resistance of human immunodeficiency virus type 1 (HIV-1) remain incompletely outlined in the Middle East and North Africa (MENA). The aim of this retrospective molecular epidemiology study was to analyze MENA HIV-1 sequences for phylogenetic clustering [...] Read more.

The molecular epidemiology and antiretroviral (ARV) drug resistance of human immunodeficiency virus type 1 (HIV-1) remain incompletely outlined in the Middle East and North Africa (MENA). The aim of this retrospective molecular epidemiology study was to analyze MENA HIV-1 sequences for phylogenetic clustering and to delineate surveillance drug-resistance mutations (SDRMs) for nucleoside reverse-transcriptase inhibitors (NRTIs), non-nucleoside reverse-transcriptase inhibitors (NNRTIs), and protease inhibitors (PIs) across various periods, locations, and subtypes/circulating recombinant forms (CRFs). Viral sequences were retrieved from the Los Alamos HIV Sequence Database as of 15 April 2026. Analyses were done using multiple sub-gene regions (two env regions (n = 224 and n = 60) and PR (n = 2413) and RT (n = 2103) of the pol gene). Phylogeny construction was conducted using maximum-likelihood estimation, while ARV drug resistance analysis was conducted using the Stanford HIVdb algorithm. The HIV-1 MENA sequences showed a remarkable genetic diversity, with co-circulation of multiple subtypes/CRFs, including subtype B in the Maghreb, Levant, and Egypt sub-regions, subtypes A1, G, CRF01_AE, and CRF02_AG in the Gulf Cooperation Council (GCC) and Yemen sub-region, and subtypes C and D in the Horn of Africa and Sudan sub-region. The percentage of MENA HIV-1 sequences in clusters was 10.3% for env1, 8.3% for env2, 22.0% for PR and 37.2% for RT. Phylogenetic reconstruction hinted at a structured epidemic dominated by small transmission units, with most clusters comprising dyads (n = 260) or networks (n = 142) and a limited number of large clusters (n = 8) that were largely confined within national boundaries, with only occasional cross-border linkages (n = 8). Overall SDRM prevalence was 3.2% in the PR region and 14.9% in the RT region, with a higher percentage of NNRTI-associated mutations (10.0%) than NRTI-associated mutations (9.1%) and dual-class resistance observed in 4.1% of sequences. Phylogenetic clustering was not associated with the probability of harboring SDRMs; however, negative binomial models showed that non-clustered sequences had a greater burden of NRTI-associated mutations, whereas no such association was observed for NNRTI- or PI-associated mutations. The findings showed predominantly localized and fragmented MENA HIV-1 transmission dynamics. Heterogeneous ARV drug resistance dynamics indicated that resistance emergence might be shaped by broader epidemiologic and treatment-related factors rather than ongoing clustered transmission. There is a need for coordinated molecular surveillance and optimized ART strategies across the MENA countries. Full article

(This article belongs to the Section Human Virology and Viral Diseases)

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12 pages, 1086 KB

Open AccessArticle

Weight Gain Is Associated with Short-Term FIB-4 Increase and Concurrent Metabolic Change in People with HIV and Metabolic Dysfunction-Associated Steatotic Liver Disease

by Wei Xu, Li Liu, Meiyan Sun, Renfang Zhang, Jun Chen and Yinzhong Shen

Viruses 2026, 18(8), 896; https://doi.org/10.3390/v18080896 - 14 Aug 2026

Abstract

Background: Short-term variation in the Fibrosis-4 index (FIB-4) may identify people who warrant further liver assessment. We evaluated longitudinal FIB-4 changes and associated metabolic factors in people with HIV (PWH) and metabolic dysfunction-associated steatotic liver disease (MASLD). Methods: This retrospective cohort included 683 [...] Read more.

Background: Short-term variation in the Fibrosis-4 index (FIB-4) may identify people who warrant further liver assessment. We evaluated longitudinal FIB-4 changes and associated metabolic factors in people with HIV (PWH) and metabolic dysfunction-associated steatotic liver disease (MASLD). Methods: This retrospective cohort included 683 PWH with ultrasound-defined MASLD who underwent routine clinical and laboratory assessments approximately every three months. A prespecified FIB-4 increase required both a ≥20% rise and crossing to ≥1.3 among participants with baseline FIB-4 < 1.3, or a ≥20% rise among those with baseline FIB-4 ≥ 1.3. Results: Of 683 enrolled participants, 655 were analyzed longitudinally. Over a median follow-up of 12.0 months, 59 (9.0%) met the FIB-4 increase definition, corresponding to 8.8 events per 100 person-years. Weight gain was associated with this outcome (adjusted hazard ratio 1.19 per 1% increase, 95% CI 1.14–1.24), whereas HIV- and antiretroviral therapy-related variables were not. Transition from non-obesity to obesity was associated with the outcome (odds ratio 8.45, 95% CI 3.57–20.02). Weight change also correlated with concurrent changes in total cholesterol, triglycerides, fasting glucose, and liver enzymes (all p < 0.01). Conclusions: Weight gain was associated with short-term FIB-4 increase and with concurrent metabolic change in PWH with MASLD. Full article

(This article belongs to the Special Issue HIV in the Context of Chronic Disorders and Aging)

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20 pages, 2608 KB

Open AccessReview

LINE-1 Epigenetic Repression and Regulation of Immunity

by Holly Jefferson and Helen M. Rowe

Viruses 2026, 18(8), 895; https://doi.org/10.3390/v18080895 - 14 Aug 2026

Abstract

The long interspersed element-1 (LINE-1) family is the sole remaining transposable element family that is capable of autonomous retrotransposition in humans. LINE-1 expression, tightly controlled through epigenetic mechanisms, has complex effects on gene regulation. Due to their similarity to retroviruses, once activated, LINE-1s [...] Read more.

The long interspersed element-1 (LINE-1) family is the sole remaining transposable element family that is capable of autonomous retrotransposition in humans. LINE-1 expression, tightly controlled through epigenetic mechanisms, has complex effects on gene regulation. Due to their similarity to retroviruses, once activated, LINE-1s have the ability to trigger pathways involved in innate and adaptive immunity with both beneficial and detrimental effects. This review will explore the mechanisms and importance of LINE-1 epigenetic repression and the potential outcomes of LINE-1 expression, with a focus on their immunogenic roles in innate and adaptive immunity. Full article

(This article belongs to the Special Issue Control and Contributions of Transposable Elements: Implications for Development and Disease)

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3 pages, 140 KB

Open AccessEditorial

Closing Remarks for the Special Issue on Coronaviruses and Influenza Viruses: Evolution, Cross-Species Transmission, and Recombination

by Maged Gomaa Hemida

Viruses 2026, 18(8), 894; https://doi.org/10.3390/v18080894 - 13 Aug 2026

Abstract

The completion of this Special Issue, “Coronaviruses and Influenza Viruses: Evolution, Cross-Species Transmission, and Recombination”, offers a valuable opportunity to reflect on the remarkable scientific progress in understanding two of the most critical groups of emerging and re-emerging viral pathogens that affect both [...] Read more.

The completion of this Special Issue, “Coronaviruses and Influenza Viruses: Evolution, Cross-Species Transmission, and Recombination”, offers a valuable opportunity to reflect on the remarkable scientific progress in understanding two of the most critical groups of emerging and re-emerging viral pathogens that affect both human and animal health [...] Full article

(This article belongs to the Special Issue Coronaviruses and Influenza Viruses: Evolution, Cross-Species Transmission, and Recombination)

63 pages, 21877 KB

Open AccessReview

RNA Cis-Elements Involved in Animal Virus Stop Codon Readthrough: Stop Codon Context and Downstream RNA Structures

by Nobuhiko Kamoshita

Viruses 2026, 18(8), 893; https://doi.org/10.3390/v18080893 - 13 Aug 2026

Abstract

Stop codon readthrough is a noncanonical translation strategy employed by certain RNA viruses, in which a viral termination codon is either decoded by host near-cognate tRNAs or canonically recognized by the class I release factor (RF, eRF1 in eukaryotes). Ribosomal A-site competition between [...] Read more.

Stop codon readthrough is a noncanonical translation strategy employed by certain RNA viruses, in which a viral termination codon is either decoded by host near-cognate tRNAs or canonically recognized by the class I release factor (RF, eRF1 in eukaryotes). Ribosomal A-site competition between near-cognate tRNAs and eRF can shift decoding toward near-cognate tRNAs, thereby promoting non-canonical decoding events by transiently pausing termination and favoring readthrough. This review focuses on two viral cis-elements that modulate readthrough across four viral genera in which this decoding event has been experimentally validated: (i) primary sequences surrounding the stop codon (stop codon context), and (ii) downstream RNA structures. Effects of stop codon context have been observed more broadly in cellular genes, including nonsense suppression in bacteria, with mechanisms including inefficient RF association or tRNA interactions at adjacent sense codons. In eukaryotic systems, interactions with the ribosomal mRNA entry channel have been suggested. Diverse downstream structures, including gammaretroviral pseudoknots and specific structures in alpha- and coltiviruses, further stimulate readthrough in a location- and structure-sensitive manner. This effect has not been consistently observed in chikungunya and triatoviral structures, suggesting a strong dependence on local sequence and structural context. Compared with the larger number of cellular readthrough occurrences that can be detected at low efficiency by ribosome profiling, viral readthrough in mammalian systems is consistently high (>2%). Understanding the interplay between viral RNA elements and host translational machinery, including potential kinetic trapping at the termination codon, provides insights into this unusual elongation mechanism. These findings may have implications for antiviral strategies targeting these RNA elements. Full article

(This article belongs to the Special Issue Viral Strategies and Cellular Countermeasures That Regulate mRNA Access to the Translation Apparatus: 2nd Edition)

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20 pages, 1685 KB

Open AccessArticle

Identification of Partitivirus-like RdRPs in the Brevipalpus yothersi Genome Supports Viral-to-Arthropod Horizontal Gene Transfer

by Bruno Afonso Corrêa, Thaís Medinilha Pancher, Denis Calandriello Calio, Aline Daniele Tassi, Laura Rossetto Pereira, Daniel Carrillo, Ricardo Harakava, Valdenice Moreira Novelli, Elliot Watanabe Kitajima, Pedro Luis Ramos-González, Juliana Freitas-Astúa and Daniel Gonzalez-Ibeas

Viruses 2026, 18(8), 892; https://doi.org/10.3390/v18080892 - 13 Aug 2026

Abstract

RNA-dependent RNA polymerases (RdRPs) are essential enzymes involved in RNA virus replication and eukaryotic RNA silencing. They are generally absent in vertebrates but present in some invertebrate lineages, such as nematodes and certain arthropods. Brevipalpus yothersi is a phytophagous mite of agricultural relevance [...] Read more.

RNA-dependent RNA polymerases (RdRPs) are essential enzymes involved in RNA virus replication and eukaryotic RNA silencing. They are generally absent in vertebrates but present in some invertebrate lineages, such as nematodes and certain arthropods. Brevipalpus yothersi is a phytophagous mite of agricultural relevance due to its role as a vector of plant-infecting viruses. We have identified two RdRPs on the genome of this mite species that, unexpectedly, are not of eukaryotic origin. Phylogenetic reconstruction and comparisons of 3D protein structures revealed similarity with viral RdRPs of the Partitiviridae family. Both RdRPs retain conserved catalytic motifs at the protein sequence level, and expression was confirmed by RNAseq and qPCR across mite developmental stages, with a peak during the nymphal stage. K-mer profiles showed similarity with mite endogenous genes, suggesting gene amelioration after the integration, or being derived from a viral donor already adapted to the mite. Our study also identified orthologs in other Brevipalpus species, but not in other Acari relatives, supporting that the horizontal gene transfer event is circumscribed to the Brevipalpus genus. These findings highlight an intriguing case of viral gene domestication in arthropods that might influence their developmental biology and the host–virus interaction. Full article

(This article belongs to the Section Invertebrate Viruses)

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23 pages, 3316 KB

Open AccessArticle

Protective Efficacy Evaluation of Various Inactivated Vaccines Against the Newly Circulated Highly Pathogenic Avian Influenza Virus H5N1 of Clade 2.3.4.4b in Pekin Ducks

by Eman Abd El Menum Shosha, Ibrahim Eldaghayes, Ahmed Abd-Elsamie H. Ali, Waleed Senosy Ali and Eman Hafez Elhayani

Viruses 2026, 18(8), 891; https://doi.org/10.3390/v18080891 - 13 Aug 2026

Abstract

Highly pathogenic avian influenza (HPAI) virus H5N1of clade 2.3.4.4b has emerged as the predominant lineage circulating in poultry flocks worldwide, raising concerns regarding the protective efficacy of currently available commercial vaccines, particularly in domestic ducks, which play an important role in virus maintenance [...] Read more.

Highly pathogenic avian influenza (HPAI) virus H5N1of clade 2.3.4.4b has emerged as the predominant lineage circulating in poultry flocks worldwide, raising concerns regarding the protective efficacy of currently available commercial vaccines, particularly in domestic ducks, which play an important role in virus maintenance and transmission. Thus, this study evaluated the immunogenicity along with the protective efficacy of four inactivated H5 vaccines against a recently isolated local HPAI-H5N1 (Newvalley-3-H5N1-2024, clade 2.3.4.4b) strain in Pekin ducks in Egypt. A total of 150 seronegative ducks were divided into vaccinated and control groups (10 groups) and vaccinated at 10 days of age. At 31 days of age, the vaccinated and positive control groups were challenged using 10^6.5 EID₅₀/0.5 mL/duck with the local isolate (Newvalley-3-H5N1-2024) via the oculo-nasal route. The vaccine efficacy was assessed through clinical signs, survival rate, hemagglutination inhibition (HI) antibody titer, tracheal and cloacal viral shedding quantified by real-time RT-PCR, and histopathological examination of trachea, lung, pancreas, and brain tissues. Generally, all ducks vaccinated with the ValleyVac Avian Flu H5 plus and MEFLUVAC^TM H5 PLUS 8 showed a significantly higher survival rate (100%) at 10 days post-vaccination (DPV) than those in the positive control (66.7% mortality rate). In contrast, ducks exhibited mortality rates ranging from 6.7% in the SERVAC Flu H5N1 group to 13.4% in the Sinder Fluvac group. The ValleyVac Avian Flu H5 plus and MEFLUVAC™ H5 PLUS 8 vaccines induced the highest HI antibody titers at 7, 14, 21, and 28 DPV in both homologous and heterologous AIV antigens, resulting in a significant reduction in viral load among all vaccinated duck groups (p-value < 0.05) comparable to the positive control group. Conversely, the SERVAC Flu H5N1 and Sinder Fluvac vaccines provided partial protection, suboptimal immunogenicity at different time points, and elevated viral shedding. Histopathological findings in ValleyVac Avian Flu H5 plus and MEFLUVAC™ H5 PLUS 8 vaccines exhibited mild tissue alterations following AIV challenge. Marked pathological lesions were observed in the SERVAC Flu H5N1 and Sinder Fluvac vaccinated groups. Among tested vaccines, both ValleyVac Avian Flu H5 plus and MEFLUVAC^TM H5 PLUS 8 showed the highest level of protective efficacy against the circulating AIV strain compared with other commercial vaccines. This study highlights the need for continuous molecular surveillance, antigenic matching, and regular updating of vaccine seed strains to ensure efficient HPAI control in Egypt. Full article

(This article belongs to the Section Animal Viruses)

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41 pages, 11112 KB

Open AccessArticle

Trimeric Class I Viral Fusion Protein Vaccine Immunogens Using a Trimeric Autotransporter in a Killed Whole-Cell Bacteria Vaccine Platform: Applications to HIV MPER

by Juan Sebastian Quintero-Barbosa, Yufeng Song, Frances Mehl, Shubham Mathur, Lauren Livingston, Xiaoying Shen, David C. Montefiori and Steven L. Zeichner

Viruses 2026, 18(8), 890; https://doi.org/10.3390/v18080890 - 13 Aug 2026

Abstract

Background: Trimeric envelope-proximal domains in viral class I fusion proteins are conserved targets of broadly neutralizing antibodies (bNAbs), but it has proven difficult to develop vaccines against those targets. The HIV-1 gp41 membrane-proximal external region (MPER) is one such target. Induction of a [...] Read more.

Background: Trimeric envelope-proximal domains in viral class I fusion proteins are conserved targets of broadly neutralizing antibodies (bNAbs), but it has proven difficult to develop vaccines against those targets. The HIV-1 gp41 membrane-proximal external region (MPER) is one such target. Induction of a neutralizing response likely depends on the immunogen having a close-to-native structure. Methods: Native sequence MPER was displayed on genome-reduced bacteria as a coiled-coil homotrimer using a Haemophilus influenzae Hia trimeric autotransporter. Vaccine designs incorporated additional features, including trimerization domains to stabilize MPER, tandem MPER repeats to increase antigen valency, and immunomodulatory elements. Antigen exposure was assessed by flow cytometry, antibody responses were evaluated by ELISA, and functional activity was measured using HIV-1 pseudovirus neutralization assays. Results: Trimer stabilization improved MPER exposure, but immunogen visibility alone did not predict neutralization. After three immunizations, neutralizing activity was detected only in the most extensively engineered vaccine, which neutralized tier 2 virus CNE55. After five immunizations, the same vaccine also neutralized the tier 2 virus 25710-2.43. A further design modification that included an extended Hia-derived spacer increased MPER exposure and antibody binding, with neutralization detected against MN.3, X1632_S2_B10, and 25710-2.43 viruses in subsets of animals. Conclusions: As a proof-of-concept, native-sequence MPER can induce detectable, though modest and virus-dependent, HIV-1 neutralizing activity when displayed in a carefully controlled trimeric bacterial surface-display platform. The results show that MPER vaccine performance depends not only on antigen exposure, but also on multimeric organization, immunomodulatory context, and antigen-scaffold geometry. Analogous coiled-coil trimeric bacterial surface display immunogens may inform vaccine development for stem/stalk regions of other Class I fusion protein viruses. Full article

(This article belongs to the Section Viral Immunology, Vaccines, and Antivirals)

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