Viral Infection Process Research Articles

The association of increased incidence of congenital heart disease in newborns with maternal COVID-19 infection during pregnancy

This paper aims to examine the potential link between maternal COVID-19 infection during pregnancy and the increased risk of congenital heart disease (CHD) in newborns. A comparative analysis was conducted involving two groups: mothers infected with COVID-19 during pregnancy and a control group. Data on maternal characteristics, pregnancy-related complications, and newborn outcomes were collected and analyzed. Additionally, the annual incidence rates of CHD from 2020 to 2023 were evaluated to assess trends over time. No significant differences were found between the COVID-19 cases and the control group in terms of maternal age, BMI, gravidity, parity, use of assisted reproductive technology, adverse obstetric history, or complications during pregnancy, including diabetes mellitus, preeclampsia, and thyroid abnormalities. For newborn outcomes, there were no significant differences in sex distribution, rate of cesarean delivery, Apgar scores, or birth weight. However, a significantly higher prevalence of cardiac ultrasound abnormalities was observed in the COVID-19 group (10.08%) compared to the control group (4.13%, p = 0.012). Further analysis revealed that the majority of cardiac abnormalities in the COVID-19 group occurred in mothers infected before 8 weeks of pregnancy. The annual incidence rates of CHD showed a significant increase during the COVID-19 pandemic, with the highest rate in 2023 (5.46%) compared to previous years. Maternal COVID-19 infection during pregnancy may adversely affect the development of the newborn’s heart. This could be due to the inflammatory response caused by the viral infection or other pathological processes. The findings underscore the importance of vigilant prenatal care and early detection of cardiac abnormalities during the pandemic and suggest the need for further research to explore potential mechanisms and intervention strategies.

Study of non-silent and deletion mutations of SARS-CoV-2 in relation to viral behavior in the infectious process

SARS-CoV-2 is a 30,000-nucleotide single-stranded RNA virus encoding structural, non-structural and accessory proteins. Its origin is uncertain, with hypotheses suggesting evolution from bats or pangolins. Genetic recombination events between strains may have resulted in the emergence of SARS-CoV-2, making it capable of infecting humans and increasing its transmissibility. Its mutability rate is similar to that of other coronaviruses, however, due to the occurrence of the pandemic and the propagation clusters, there was an intensification in the number of mutations generated, which evolutionarily gave rise to lineages, sublineages, variants and strains, consecutively. Such mutations, especially non-synonymous ones, phenotypically reflect a variation in virulence, associated with factors of transmissibility, pathogenicity, multiplication, immunological evasion that differ from their ancestors, which are accumulating and becoming fixed in the lineages of this sarbecovirus. In this way, this study aims to understand such non-silent mutations by correlating changes to the viral infectious process.

Unveiling the Dynamic Mechanism of SARS-CoV-2 Entry Host Cells at the Single-Particle Level.

Understanding the dynamic features of severe acute respiratory coronavirus 2 (SARS-CoV-2) binding to the cell membrane and entry cells is crucial for comprehending viral pathogenesis and transmission and facilitating the development of effective drugs against COVID-19. Herein, we employed atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) to study the binding dynamics between the virus and cell membrane. Our findings revealed that the Omicron variant of SARS-CoV-2 virus-like particles (VLPs) exhibited a slightly stronger affinity for the angiotensin-converting enzyme-2 (ACE2) receptor compared with the Delta variant and was significantly higher than the wild-type (WT). Using a real-time force-tracing technique, we quantified the dynamic parameters for a single SARS-CoV-2 VLP entry into cells, showing that approximately 200 ms and 60 pN are required. The parameters aligned with the analysis obtained from coarse-grained molecular dynamics (CGMD) simulations. Additionally, the Omicron variant invades cells at a higher entry cell speed, smaller force, and higher probability. Furthermore, single-particle fluorescence tracking visually demonstrated clathrin-dependent endocytosis for SARS-CoV-2 entry into A549 cells. The dynamic features of endocytosis provide valuable insights into the SARS-CoV-2 entry mechanism and possible intervention strategies targeting the viral infection process.

Is Autophagy a Friend or Foe in SARS-CoV-2 Infection?

As obligate parasites, viruses need to hijack resources from infected cells to complete their lifecycle. The interaction between the virus and host determines the viral infection process, including viral propagation and the disease's outcome. Understanding the interaction between the virus and host factors is a basis for unraveling the intricate biological processes in the infected cells and thereby developing more efficient and targeted antivirals. Among the various fundamental virus-host interactions, autophagy plays vital and also complicated roles by directly engaging in the viral lifecycle and functioning as an anti- and/or pro-viral factor. Autophagy thus becomes a promising target against virus infection. Since the COVID-19 pandemic, there has been an accumulation of studies aiming to investigate the roles of autophagy in SARS-CoV-2 infection by using different models and from distinct angles, providing valuable information for systematically and comprehensively dissecting the interplay between autophagy and SARS-CoV-2. In this review, we summarize the advancements in the studies of the interaction between SARS-CoV-2 and autophagy, as well as detailed molecular mechanisms. We also update the current knowledge on the pharmacological strategies used to suppress SARS-CoV-2 replication through remodeling autophagy. These extensive studies on SARS-CoV-2 and autophagy can advance our understanding of virus-autophagy interaction and provide insights into developing efficient antiviral therapeutics by regulating autophagy.

Dynamics of Acute Infection with Mammarenavirus Wenzhouense in Rattus norvegicus.

While Mammarenavirus Wenzhouense (WENV) is broadly distributed across Asia, the dynamics of WENV infection remain unclear. In this study, a field-derived strain of WENV was used to inoculate Sprague Dawley (SD) rats by intramuscular injection, and the process of viral infection was observed over the course of 28 d. Viral RNA became detectable in the blood at 3 dpi and remained detectable for about 12 d. In most organ tissues, viral RNA peaked at 7 dpi, and then began to decline by 14 d, but remained detectable in intestine and brain tissues at 21 and 28 dpi. Viral shedding was detected from fecal samples for 5 d, from 6 to 11 dpi using qRT-PCR, and was recovered from feces collected at 8 dpi. Horizontal contact infection occurred among cage-mates at 14 and 21 dpi. Antibodies against the nucleocapsid were detected at 5 dpi, and then increased and persisted until the end of the experiment. These results enabled us to determine the kinetics of viremic response, viral shedding in feces, and horizontal transmission dynamics, as well as the potential sites for WENV replication and viral maintenance in nature.

The dynamics of the cytokine profile of the lungs and liver of BALB/C male mice infected with the H1N1 subtype avian influenza virus

The increasing number of reported cases of direct transmission of avian influenza viral strains to humans is obviously associated with the threat of a new pandemic and the need for a more detailed study of the pathogenesis of the viral infectious process. The aim of the research was to study the pathogenesis of influenza infection and in particular to establish the role of proinflammatory cytokines in the pathogenesis of the inectious process caused by influenza virus subtype A/WSN/1/33(H1N1). The experiment involved 21 male BALB/c mice aged 4-6 weeks weighing 16-18 g, which16were infected intranasally with influenza A/WSN/1/33(H1N1) virus under ether anesthesia by inoculation of 50 µl of allantoic fluid containing 10 LD50 of the virus. Histological studies were performed on samples of lung and liver tissues. It was evidenced that infection caused by the highly pathogenic for mice influenza virus A/WSN/1/33(H1N1) initiates the spreading of dystrophic and necrotic processes mainly in the lungs and liver. This can occur due the increase of proinflammatory cytokines leading to the violation of the circulatory system triggered by the active reproduction of the virus and toxic manifestations on behalf of cellular immunity. Structural changes in the lung and liver tissues of mice experimentally infected with the influenza A/WSN/1/33(H1N1) virus indicated the presence of a large amount of the virus at all stages of the experiment that requires further research.

Epidemiological Study in Antiviral Innate Immunity.

This chapter summarizes the epidemiological study design of natural immune epidemiology studies based on recent COVID-19-related research. The epidemiological studies on antiviral innate immunity have mainly included randomized controlled trials (RCTs) and observational studies. Importantly, this chapter will discuss how to use these methodologies to answer an epidemiological question of natural immunity in the viral infection process based on previous studies. An observational case- or cohort-based study of antiviral innate immunity may support this theoretical hypothesis but is not appropriate for clinical practice or treatment. RCTs are the gold standard for epidemiological studies and occupy a greater role in the hierarchy of evidence.

HnRNPs in antiviral innate immunity.

During virus infection, many host proteins are redirected from their normal cellular roles to restrict and terminate infection. Heterogeneous nuclear ribonucleoproteins (hnRNPs) are cellular RNA-binding proteins critical to host nucleic acid homeostasis, but can also be involved in the viral infection process, affecting virus replication, assembly and propagation. It has become evident that hnRNPs play important roles in modulation of host innate immunity, which provides critical initial protection against infection. These novel findings can potentially lead to the leveraging of hnRNPs in antiviral therapies. We review hnRNP involvement in antiviral innate immunity, in humans, mice and other animals, and discuss hnRNP targeting as a potential novel antiviral therapeutic.

A C-Degron Structure-Based Approach for the Development of Ligands Targeting the E3 Ligase TRIM7.

TRIM7 is a ubiquitin E3 ligase with key regulatory functions, mediating viral infection, tumor biology, innate immunity, and cellular processes, such as autophagy and ferroptosis. It contains a PRYSPRY domain that specifically recognizes degron sequences containing C-terminal glutamine. Ligands that bind to the TRIM7 PRYSPRY domain may have applications in the treatment of viral infections, as modulators of inflammation, and in the design of a new class of PROTACs (PROteolysis TArgeting Chimeras) that mediate the selective degradation of therapeutically relevant proteins (POIs). Here, we developed an assay toolbox for the comprehensive evaluation of TRIM7 ligands. Using TRIM7 degron sequences together with a structure-based design, we developed the first series of peptidomimetic ligands with low micromolar affinity. The terminal carboxylate moiety was required for ligand activity but prevented cell penetration. A prodrug strategy using an ethyl ester resulted in enhanced permeability, which was evaluated using confocal imaging.

Genome-wide identification of ATG genes and their expression profiles under biotic and abiotic stresses in Fenneropenaeus chinensis

BackgroundAutophagy is a conserved catabolic process in eukaryotes that contributes to cell survival in response to multiple stresses and is important for organism fitness. Extensive research has shown that autophagy plays a pivotal role in both viral infection and replication processes. Despite the increasing research dedicated to autophagy, investigations into shrimp autophagy are relatively scarce.ResultsBased on three different methods, a total of 20 members of the ATGs were identified from F. chinensis, all of which contained an autophagy domain. These genes were divided into 18 subfamilies based on their different C-terminal domains, and were found to be located on 16 chromosomes. Quantitative real-time PCR (qRT-PCR) results showed that ATG genes were extensively distributed in all the tested tissues, with the highest expression levels were detected in muscle and eyestalk. To clarify the comprehensive roles of ATG genes upon biotic and abiotic stresses, we examined their expression patterns. The expression levels of multiple ATGs showed an initial increase followed by a decrease, with the highest expression levels observed at 6 h and/or 24 h after WSSV injection. The expression levels of three genes (ATG1, ATG3, and ATG4B) gradually increased until 60 h after injection. Under low-salt conditions, 12 ATG genes were significantly induced, and their transcription abundance peaked at 96 h after treatment.ConclusionsThese results suggested that ATG genes may have significant roles in responding to various environmental stressors. Overall, this study provides a thorough characterization and expression analysis of ATG genes in F. chinensis, laying a strong foundation for further functional studies and promising potential in innate immunity.

Hour-Long, Kilohertz Sampling Rate Three-Dimensional Single-Virus Tracking in Live Cells Enabled by StayGold Fluorescent Protein Fusions.

A viral infection process covers a large range of spatiotemporal scales. Tracking the viral infection process with fluorescent labels over long durations while maintaining a fast sampling rate requires bright and highly photostable labels. StayGold is a recently identified green fluorescent protein that has a greater photostability and higher signal intensity under identical illumination conditions compared to existing fluorescence protein variants. Here, StayGold protein fusions were used to generate virus-like particles (StayGold-VLPs) to achieve hour-long 3D single-virus tracking (SVT) with 1000 localizations per second (kHz sampling rate) in live cells. The expanded photon budget from StayGold protein fusions prolonged the tracking duration, facilitating a comprehensive study of viral trafficking dynamics with high temporal resolution over long time scales. The development of StayGold-VLPs presents a simple and general VLP labeling strategy for better performance in SVT, enabling exponentially more information to be collected from single trajectories and allowing for the future possibility of observing the entire life cycle of a single virus.

Molecular characterization of SARS-CoV-2 nucleocapsid protein

Corona Virus Disease 2019 (COVID-19) is a highly prevalent and potent infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Until now, the world is still endeavoring to develop new ways to diagnose and treat COVID-19. At present, the clinical prevention and treatment of COVID-19 mainly targets the spike protein on the surface of SRAS-CoV-2. However, with the continuous emergence of SARS-CoV-2 Variants of concern (VOC), targeting the spike protein therapy shows a high degree of limitation. The Nucleocapsid Protein (N protein) of SARS-CoV-2 is highly conserved in virus evolution and is involved in the key process of viral infection and assembly. It is the most expressed viral structural protein after SARS-CoV-2 infection in humans and has high immunogenicity. Therefore, N protein as the key factor of virus infection and replication in basic research and clinical application has great potential research value. This article reviews the research progress on the structure and biological function of SARS-CoV-2 N protein, the diagnosis and drug research of targeting N protein, in order to promote researchers’ further understanding of SARS-CoV-2 N protein, and lay a theoretical foundation for the possible outbreak of new and sudden coronavirus infectious diseases in the future.

Homeostasis imbalance process ontology: a study on COVID-19 infectious processes.

One significant challenge in addressing the coronavirus disease 2019 (COVID-19) pandemic is to grasp a comprehensive picture of its infectious mechanisms. We urgently need a consistent framework to capture the intricacies of its complicated viral infectious processes and diverse symptoms. We systematized COVID-19 infectious processes through an ontological approach and provided a unified description framework of causal relationships from the early infectious stage to severe clinical manifestations based on the homeostasis imbalance process ontology (HoIP). HoIP covers a broad range of processes in the body, ranging from normal to abnormal. Moreover, our imbalance model enabled us to distinguish viral functional demands from immune defense processes, thereby supporting the development of new drugs, and our research demonstrates how ontological reasoning contributes to the identification of patients at severe risk. The HoIP organises knowledge of COVID-19 infectious processes and related entities, such as molecules, drugs, and symptoms, with a consistent descriptive framework. HoIP is expected to harmonise the description of various heterogeneous processes and improve the interoperability of COVID-19 knowledge through the COVID-19 ontology harmonisation working group.

Identification of the Hub Genes Involved in Chikungunya Viral Infection.

Background Chikungunya virus (CHIKV) infection poses a significant global health threat, necessitating a deeper understanding of its molecular mechanisms for effective management and treatment. This study aimed to understand the molecular and geneticmechanisms of CHIKV infection by analyzing microarray expression data. Methodology National Center for Biotechnology Information (NCBI) GEO2R with an adjusted p-value cut-off of <0.05 and |log2FC ≥ 1.5| was used to identify the differentially expressed genes involved in CHIKV infection using microarray data from the Gene Expression Omnibus (GEO) database, followed by enrichment analysis, protein-protein interaction (PPI) network construction, and, finally, hub gene identification. Results Analysis of the microarray dataset revealed 25 highly significant differentially expressed genes (DEGs), including 21 upregulated and four downregulated genes. PPI network analysis elucidated interactions among these DEGs, with hub genes such as ACTB and CTNNB1 exhibiting central roles. Enrichment analysis identified crucial pathways, including leukocyte transendothelial migration, regulation of actin cytoskeleton, and thyroid hormone signaling, implicating their involvement in CHIKV infection. Furthermore, the study highlights potential therapeutic targets such as ACTB and CTNNB1, which showed significant upregulation in infected cells. Conclusions These findings underscore the complex interplay between viral infection and host cellular processes, shedding light on novel avenues for diagnostic marker discovery and advancing antiviral strategies. In this study, we shed light on the molecular and genetic mechanisms of CHIKV infection and the potential role of ACTB and CTNNB1 genes.

Virus detection light diffraction fingerprints for biological applications.

The transmission of viral diseases is highly unstable and highly contagious. As the carrier of virus transmission, cell is an important factor to explore the mechanism of virus transmission and disease. However, there is still a lack of effective means to continuously monitor the process of viral infection in cells, and there is no rapid, high-throughput method to assess the status of viral infection. On the basis of the virus light diffraction fingerprint of cells, we applied the gray co-occurrence matrix, set the two parameters effectively to distinguish the virus status and infection time of cells, and visualized the virus infection process of cells in high throughput. We provide an efficient and nondestructive testing method for the selection of excellent livestock and poultry breeds at the cellular level. Meanwhile, our work provides detection methods for the recessive transmission of human-to-human, animal-to-animal, and zoonotic diseases and to inhibit and block their further development.

Study of Oxadiazole derivatives as precursor for multi-functional inhibitor to SARS-CoV-2: A detailed virtual screening analysis

SARS-CoV-2, the virus responsible for the COVID-19 pandemic, is highly contagious and has caused widespread loss of life. In the quest to find effective antiviral agents, attention has turned to oxadiazole derivatives, which are known for their potential antiviral properties in such as CoViTris2020, ChloViD2020, etc. To evaluate their effectiveness, molecular docking and molecular dynamics simulations are conducted for various oxadiazole derivative in interactions with critical proteins involved in the viral infection process. These proteins encompass transmembrane-serine-2 (TMPRSS2), 3-chymotrypsin-like-protease (3CLpro), angiotensin-converting-enzyme-2 (ACE2), and papain-like-protease (PLpro). The study shows that the oxadiazole derivatives exhibited their most stable complexes when interacting with TMPRSS2 in comparison to 3CLpro, ACE2, and PLpro. In particular, Oxa8 displayed a binding energy of -6.52 kcal/mol with TMPRSS2. In contrast, the binding energies with ACE2, 3CLpro, and PLpro were -5.74, -4.56, and -5.56 kcal/mol, respectively. RMSD analysis during MD simulations demonstrated that the complex structure remained consistently stable. During the initial 2 ns, the RMSD value for the ligand concerning its interaction with the protein backbone hovered around 2 Å, indicating a sustained level of structural stability. In conclusion, this study suggests that oxadiazole derivative Oxa8 holds promise as a potential inhibitor of SARS-CoV-2, particularly due to its strong binding affinity with TMPRSS2 and its enduring structural stability observed in molecular dynamics simulations.

Uncovering the Multifaceted Roles of DDX21: Bridging Biological Insights and Medical Applications

DDX21 belongs to the DEAD-box (DDX) family of helicases but deviates from the characteristic sequence Asp–Glu–Ala–Asp (DEAD) to Asp–Glu–Val–Asp. In addition to the typical helicase activity associated with the DEAD-box family, DDX21 also possesses foldase and adenosine triphosphatase activities. It plays crucial roles in various molecular processes, including the regulation of transcription, ribosomal RNA processing, modification, and unwinding of RNA spatial structures. DDX21 is subject to intricate regulation by multiple upstream factors, including expression control and posttranslational modification. In numerous cancer types, abnormal expression of DDX21 has been observed to influence cancer cell behaviors, such as the cell cycle, proliferation, invasion, migration, and apoptosis. In addition, DDX21 modulates innate immunity following viral infection and plays a dual role in the viral infection process. This review comprehensively explores the protein structure, molecular regulatory mechanisms, and pathophysiological functions of DDX21. Consequently, this study not only offers potential avenues for future research but also sparks novel ideas for targeted treatments for both cancer and viral infections.

Human-virus protein-protein interactions maps assist in revealing the pathogenesis of viral infection.

Many significant viral infections have been recorded in human history, which have caused enormous negative impacts worldwide. Human-virus protein-protein interactions (PPIs) mediate viral infection and immune processes in the host. The identification, quantification, localization, and construction of human-virus PPIs maps are critical prerequisites for understanding the biophysical basis of the viral invasion process and characterising the framework for all protein functions. With the technological revolution and the introduction of artificial intelligence, the human-virus PPIs maps have been expanded rapidly in the past decade and shed light on solving complicated biomedical problems. However, there is still a lack of prospective insight into the field. In this work, we comprehensively review and compare the effectiveness, potential, and limitations of diverse approaches for constructing large-scale PPIs maps in human-virus, including experimental methods based on biophysics and biochemistry, databases of human-virus PPIs, computational methods based on artificial intelligence, and tools for visualising PPIs maps. The work aims to provide a toolbox for researchers, hoping to better assist in deciphering the relationship between humans and viruses.

Occult hepatic B viral infection in children: important public health issues

Introduction. Occult hepatitis B virus infection (OBI) is of important clinical significance and represents a specific phase of the viral infectious process in which HBsAg-negative individuals have reduced viral DNA replication, detectable or undetectable in serum but present in the liver. Materials and methods. A review of the Pub Med database on occult HBV infection from January 2013 to April 2023 was performed, selecting publications pertaining to children. Results. Of the 914 identified articles, 111 publications met the selection criteria of “occult HBV infection in children”. In this phase, covalently closed circular DNA (cccADN) is in a low replication state. Mechanisms of suppression of HBV replication activity have been shown to be related to host immune control and epigenetic factors. The prevalence of occult HBV infection in adults varies widely in different geographic regions and depends on risk factors for parenteral infections and the sensitivity of tests used to detect HBsAg and HBV DNA. Occult HBV infection in children is a poorly understood problem, with a prevalence of 20-54%. HBV can be transmitted parenterally, by blood transfusion, habitual transmission, or liver transplantation, causing acute hepatitis, reactivating with immunosuppression, accelerating the progression of chronic hepatitis to cirrhosis, and contributing to malignancy. Conclusions. Occult HBV infection in children is one of the clinical forms of chronic HBV infection with varying overall prevalence. Anti-HBcor is an important diagnostic marker, and their testing for hepatitis of unknown etiology in children will detect chronic HBV infection.

Rescue of a Cilevirus from infectious cDNA clones

Reverse genetics systems represent an important tool for studying the molecular and functional processes of viral infection. Citrus leprosis virus C (CiLV-C) (genus Cilevirus, family Kitaviridae) is the main pathogen responsible for the citrus leprosis (CL) disease in Latin America, one of the most economically important diseases of the citrus industry. Molecular studies of this pathosystem are limited due to the lack of infectious clones. Here, we report the construction and validation of a CiLV-C infectious cDNA clone based on an agroinfection system. The two viral RNA segments (RNA1 and RNA2) were assembled into two binary vectors (pJL89 and pLXAS). Agroinfiltrated Nicotiana benthamiana plants showed a response similar to that observed in the natural infection process with the formation of localized lesions restricted to the inoculated leaves. The virus recovered from the plant tissue infected with the infectious clones can be mechanically transmitted between N. benthamiana plants. Detection of CiLV-C subgenomic RNAs (sgRNAs) from agroinfiltrated and mechanically inoculated leaves further confirmed the infectivity of the clones. Finally, partial particle-purification preparations or sections of CiLV-C-infected tissue followed by transmission electron microscopy (TEM) analysis showed the formation of CiLV-C virions rescued by the infectious clone. The CiLV-C reverse genetic system now provides a powerful molecular tool to unravel the peculiarities of the CL pathosystem.