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Topic Review
List of Virus Species
Excluded are other ranks of virus, viroids and prions. Also excluded are more recently discovered viruses such as Bourbon Virus, common names and obsolete names for viruses.
  • 1.3K
  • 31 Oct 2022
Topic Review
Efavirenz
Efavirenz (Sustiva®) is a first-generation non-nucleoside reverse transcriptase inhibitor (NNRTI) used to treat human immunodeficiency virus (HIV) type 1 infection or to prevent the spread of HIV. In 1998, the FDA authorized efavirenz for the treatment of HIV-1 infection. Patients formerly required three 200 mg efavirenz capsules daily, which was rapidly updated to a 600 mg tablet that only required one tablet per day.
  • 1.3K
  • 11 Jan 2023
Topic Review
Loop Mediated Isothermal Amplification
The recent progress of molecular diagnostics has allowed the generation of different sophisticated tools, like loop-mediated isothermal amplification (LAMP). This technique has become a well-established in different fields, including medicine, agriculture, and food industry, due to its high specificity, analytical sensitivity, technical simplicity, short analysis time, and low cost. LAMP involves isothermal amplification of target DNA and is highly accordant with point-of-care analysis. It has great potential to improve plant protection diagnostics, especially for in field analyses, detection of plant quarantine pathogens or virus pathogens in early infection stages. In this review, the authors provide detailed overview of the LAMP, describing in particular evolution of the technique, design and main features of the primer set, different visualization methods of LAMP results, its evolution and use in different fields, reporting in detail LAMP application in plant virology, and the main advantages of this technique.
  • 1.3K
  • 28 Oct 2020
Topic Review
RT-LAMP CRISPR-Cas12/13-Based SARS-CoV-2 Detection Methods
LAMP is highly specific and produces a large yield of amplicon in a short period of time, with reagents that are less expensive and more readily available. In addition, the CRISPR technology is a highly specific approach for detecting nucleic acids rapidly and accurately. Therefore, this review focuses on the CRISPR-based detection of SARS-CoV-2 RNA using Cas12 and Cas13 nucleases integrated with reverse-transcription LAMP (RT-LAMP).
  • 1.3K
  • 22 Sep 2021
Topic Review
COVID-19 Pandemic Prediction
Several epidemiological models are being used around the world to project the number of infected individuals and the mortality rates of the COVID-19 outbreak. Advancing accurate prediction models is of utmost importance to take proper actions. Due to the lack of essential data and uncertainty, the epidemiological models have been challenged regarding the delivery of higher accuracy for long-term prediction. As an alternative to the susceptible-infected-resistant (SIR)-based models, this study proposes a hybrid machine learning approach to predict the COVID-19, and we exemplify its potential using data from Hungary. The hybrid machine learning methods of adaptive network-based fuzzy inference system (ANFIS) and multi-layered perceptron-imperialist competitive algorithm (MLP-ICA) are proposed to predict time series of infected individuals and mortality rate. The models predict that by late May, the outbreak and the total morality will drop substantially. The validation is performed for 9 days with promising results, which confirms the model accuracy. It is expected that the model maintains its accuracy as long as no significant interruption occurs. This paper provides an initial benchmarking to demonstrate the potential of machine learning for future research.
  • 1.3K
  • 02 Feb 2021
Biography
Thomas Henry Flewett
Thomas Henry Flewett, MD, FRCPath, FRCP (29 June 1922 – 12 December 2006) was a founder member (and subsequently Fellow) of the Royal College of Pathologists and was elected (by distinction) a Fellow of the Royal College of Physicians of London in 1978. He was chairman of the World Health Organisation (WHO) Steering Committee on Viral Diarrhoeal Diseases, 1990–3, and a member until 1996. His
  • 1.2K
  • 02 Dec 2022
Topic Review
Virus Host Interaction and Uncoating
Influenza is a zoonotic respiratory disease of major public health interest due to its pandemic potential, and a threat to animals and the human population. The influenza A virus genome consists of eight single-stranded RNA segments sequestered within a protein capsid and a lipid bilayer envelope. During host cell entry, cellular cues contribute to viral conformational changes that promote critical events such as fusion with late endosomes, capsid uncoating and viral genome release into the cytosol. 
  • 1.2K
  • 03 Sep 2021
Topic Review
T-Cell Receptor Signalosome
Human immunodeficiency virus type-1 (HIV-1) can undergo either a lytic pathway to cause productive systemic infection or enter a latent state in which the integrated provirus remains transcriptionally silent for decades. The ability to latently infected T-cells enables HIV-1 to establish persistent infections in resting memory CD4+ T-lymphocytes which become reactivated following disruption or cessation of intensive drug therapy. Maintenance of viral latency occurs through epigenetic and non-epigenetic mechanisms. Epigenetic mechanisms of HIV latency regulation involve deacetylation and methylation of histone proteins within Nucleosome 1 (nuc -1) at the viral long terminal repeats (LTR) such that inhibition of histone deacetyltransferase and histone lysine methyltransferase activities, respectively, reactivates HIV from latency. Non-epigenetic mechanisms involve nuclear restriction of critical cellular transcription factors such as Nuclear factor-kappa Beta (NF-kB) or Nuclear factor of activated T-cells (NFAT) which activate transcription from the viral LTR, limiting nuclear levels of viral transcription transactivator protein Tat and its cellular co-factor; positive transcription elongation factor b (P-TEFb) which together regulate HIV transcriptional elongation. The T-cell receptor (TCR) activation efficiently induces NF-kB, NFAT, and activator protein 1 (AP-1) transcription factors through multiple signal pathways and how these factors efficiently regulate HIV LTR transcription through the non-epigenetic mechanism. Elongation factor P-TEFb induced through an extracellular signal-regulated kinase (ERK) dependent mechanism regulates HIV transcriptional elongation before Tat is synthesized and the role of AP-1 in the modulation of HIV transcriptional elongation through functional synergy with NF-kB. The TCR signaling induces critical posttranslational modifications of the Cyclin-dependent kinase 9 (CDK9) subunit of P-TEFb which enhances interactions between P-TEFb and viral Tat protein and the resultant enhancement of HIV transcriptional elongation.
  • 1.2K
  • 13 Aug 2020
Topic Review
Newcastle Disease Viruses
Newcastle disease viruses (NDVs), also known as avian paramyxoviruses type 1, are members of the genus Orthoavulavirus, species Avian orthoavulavirus 1 in the family Paramyxoviridae. They are negative-sense, single-stranded, non-fragmented RNA viruses, distributed worldwide, and they are able to infect wild, peridomestic and domestic avian species.
  • 1.2K
  • 27 Jan 2021
Topic Review
Human Cytomegalovirus (HCMV)
Human cytomegalovirus (HCMV) is a β-herpesvirus, also known as human herpes virus 5. Compared with other human herpesviruses, the prevalence of HCMV is high, and more than 90% of the general population is an HCMV carrier. HCMV infection can disrupt homeostasis by affecting the host cell autophagy, apoptosis, proliferation, invasion, angiogenesis, and immune response [5]. Increasing evidence indicates that HCMV causes the occurrence and progression of inflammation [6], atherosclerosis, Crohn’s disease, and various cancers. More seriously, HCMV can trigger life-threatening diseases in immunosuppressed individuals. Thus, it is necessary to elucidate the pathogenic mechanism of HCMV and discover novel targets and strategies for anti-HCMV treatment. Apoptosis is a form of programmed cell death, which is essential for maintaining normal physiology and tissue function by cleaning up cells that are damaged, dysfunctional, or no longer necessary. The survival and accumulation of damaged or unnecessary cells contribute to numerous diseases, such as cancers, in addition to immunological, neurodegenerative, cardiovascular, and infectious diseases. Apoptosis generally occurs through two distinct pathways: intrinsic and extrinsic. Interestingly, both extrinsic and intrinsic apoptotic pathways can be activated by pathogenic infection.
  • 1.2K
  • 13 Jul 2021
Topic Review
Novel Respirovirus in Alpine Chamois
The Alpine chamois is a free-living wild ruminant distributed across the mountainous areas of France, Italy, Switzerland, Liechtenstein, Germany, Austria, Slovenia and Croatia. This wide distribution favours interactions with other wild ruminants and livestock, implying the risk of cross-transmission of pathogens. Due to the impact of lung diseases on chamois populations, the investigation of respiratory pathogens is important for wildlife conservation and for the understanding of infection transmission at the livestock–wildlife interface. A novel respirovirus was isolated from a chamois with lung lesions in Italian Alps. The genome characterization of this novel virus revealed similarities to domestic ruminant respiroviruses, mainly of caprine and ovine origin. Overall, phylogenetic analyses indicated that the chamois virus is distinct from already defined species and suggested that it is a putative novel member of the genus Respirovirus. The present investigation contributes to the knowledge of respiratory infections in wild ruminants and raises questions on the epidemiological link between chamois and other animal species.
  • 1.2K
  • 29 Oct 2020
Topic Review
ZIKA Virus and Male Infertility
Zika virus (ZIKV) has been reported by several groups as an important virus causing pathological damage in the male reproductive tract. ZIKV can infect and persist in testicular somatic and germ cells, as well as spermatozoa, leading to cell death and testicular atrophy. ZIKV has also been detected in semen samples from ZIKV-infected patients. This has huge implications for human reproduction. Global scientific efforts are being applied to understand the mechanisms related to arboviruses persistency, pathogenesis, and host cellular response to suggest a potential target to develop robust antiviral therapeutics and vaccines. Here, we discuss the cellular modulation of the immunologic and physiologic properties of the male reproductive tract environment caused by arboviruses infection, focusing on ZIKV. We also present an overview of the current vaccine effects and therapeutic targets against ZIKV infection that may impact the testis and male fertility.
  • 1.2K
  • 01 Nov 2020
Topic Review
Nuclear Egress of HSV-1
Herpes simplex virus 1 (HSV-1) replicates its genome and packages it into capsids within the nucleus. HSV-1 has evolved a complex mechanism of nuclear egress whereby nascent capsids bud on the inner nuclear membrane to form perinuclear virions that subsequently fuse with the outer nuclear membrane, releasing capsids into the cytosol. The viral-encoded nuclear egress complex (NEC) plays a crucial role in this vesicle-mediated nucleocytoplasmic transport. Nevertheless, similar system mediates the movement of other cellular macromolecular complexes in normal cells. Therefore, HSV-1 may utilize viral proteins to hijack the cellular machinery in order to facilitate capsid transport. 
  • 1.2K
  • 22 Sep 2021
Topic Review
Tanzania Peste des Petits Ruminants
Peste des petits ruminants (PPR) is an important transboundary animal disease of domestic small ruminants, camels, and wild artiodactyls. The disease has significant socio-economic impact on communities that depend on livestock for their livelihood and is a threat to endangered susceptible wild species. 
  • 1.2K
  • 22 Jun 2021
Topic Review
Viral Vector-Based Gene Therapy
Gene therapy is a technique involving the modification of an individual’s genes for treating a particular disease. The key to effective gene therapy is an efficient carrier delivery system. Viral vectors that have been artificially modified to lose their pathogenicity are used widely as a delivery system, with the key advantages of their natural high transduction efficiency and stable expression. With decades of development, viral vector-based gene therapies have achieved promising clinical outcomes. Long-term gene therapy involves the administration of a specific genetic material (i.e., DNA or RNA) via a carrier, referred to as a “delivery vector,” which facilitates the entry of the foreign genetic material into target cells. The delivery vectors are of two types: viral vectors and non-viral vectors. The commonly used viral vectors are adeno-associated viruses (AAVs), adenoviruses (Ads), or lentiviruses (LVs).
  • 1.2K
  • 09 May 2023
Topic Review
Latent Infection by Tobamoviruses
Tobamoviruses are among the most well-studied plant viruses and yet there is still a lot to uncover about them. On one side of the spectrum, there are damage-causing members of this genus: such as the tobacco mosaic virus (TMV), tomato brown rugose fruit virus (ToBRFV) and cucumber green mottle mosaic virus (CGMMV), on the other side, there are members which cause latent infection in host plants. New technologies, such as high-throughput sequencing (HTS), have enabled people to discover viruses from asymptomatic plants, viruses in mixed infections where the disease etiology cannot be attributed to a single entity and more and more researchers a looking at non-crop plants to identify alternative virus reservoirs, leading to new virus discoveries. However, the diversity of these interactions in the virosphere and the involvement of multiple viruses in a single host is still relatively unclear. For such host–virus interactions in wild plants, symptoms are not always linked with the virus titer.
  • 1.2K
  • 07 Sep 2022
Topic Review
Septins in Infections
Human septins comprise a family of 13 genes that encode conserved GTP-binding proteins. They form nonpolar complexes, which assemble into higher-order structures, such as bundles, scaffolding structures, or rings. Septins are counted among the cytoskeletal elements. They interact with the actin and microtubule networks and can bind to membranes. Many cellular functions with septin participation have been described in the literature, including cytokinesis, motility, forming of scaffolding platforms or lateral diffusion barriers, vesicle transport, exocytosis, and recognition of micron-scale curvature. Septin dysfunction has been implicated in diverse human pathologies, including neurodegeneration and tumorigenesis. Moreover, septins are thought to affect the outcome of host–microbe interactions. Implication of septins has been demonstrated in fungal, bacterial, and viral infections. Knowledge on the precise function of a particular septin in the different steps of the virus infection and replication cycle is still limited. Published data for vaccinia virus (VACV), hepatitis C virus (HCV), influenza A virus (H1N1 and H5N1), human herpesvirus 8 (HHV-8), and Zika virus (ZIKV), all of major concern for public health, will be discussed here.
  • 1.2K
  • 26 Mar 2021
Topic Review
Neutrophils during Arboviral Infections
Arboviruses are known to cause large-scale epidemics in many parts of the world. These arthropod-borne viruses are a large group consisting of viruses from a wide range of families. The ability of their vector to enhance viral pathogenesis and transmission makes the development of treatments against these viruses challenging. Neutrophils are generally the first leukocytes to be recruited to a site of infection, playing a major role in regulating inflammation and, as a result, viral replication and dissemination. However, the underlying mechanisms through which neutrophils control the progression of inflammation and disease remain to be fully understood. In this review, we highlight the major findings from recent years regarding the role of neutrophils during arboviral infections. We discuss the complex nature of neutrophils in mediating not only protection, but also augmenting disease pathology. Better understanding of neutrophil pathways involved in effective protection against arboviral infections can help identify potential targets for therapeutics. 
  • 1.2K
  • 05 Jul 2021
Topic Review
Raptors in WNV Epidemiology
West Nile virus exists in a natural cycle between mosquitoes and wild birds, with humans and horses acting as dead-end hosts. Avian species are key in WNV transmission cycle and, therefore, have been the focus of surveillance across many countries. Raptors appear particularly susceptible to WNV infection, resulting in higher prevalence, resulting in clinical disease and death. Birds of prey are known to play an important role as WNV reservoir and potentially act as amplifying hosts of infection. Importantly, raptor higher susceptibility/prevalence may indicate infection through predation of infected prey. Consequently, becoming and important target species when designing cost-effective surveillance for monitoring both seasonal WNV circulation in endemic countries and its emergence into new areas, even outside the mosquito season. 
  • 1.2K
  • 27 Oct 2020
Topic Review
Gene annotation for 'Flaviviridae' genomes
Responding to the ongoing and severe public health threat of viruses of the family Flaviviridae, including dengue, hepatitis C, West Nile, yellow fever, and Zika, demands a greater understanding of how these viruses emerge and spread. Updated phylogenies are central to this understanding. Most cladograms of Flaviviridae focus on specific lineages and ignore outgroups, thus hampering the efficacy of the analysis to test ingroup monophyly and relationships. This is due to the lack of annotated Flaviviridae genomes, which has gene content variation among genera. This variation makes analysis without partitioning difficult. Therefore, we developed an annotation pipeline for the genera of Flaviviridae (Flavirirus, Hepacivirus, Pegivirus, and Pestivirus), named “Fast Loci Annotation of Viruses” (FLAVi: flavi-web.com), that combines ab initio and homology-based strategies. FLAVi recovered 100% of the genes in Flavivirus and Hepacivirus genomes. In Pegivirus and Pestivirus, annotation efficiency was 100% except for one partition each. There were no false positives. The combined phylogenetic analysis of multiple genes made possible by annotation has clear impacts over the tree topology compared to phylogenies that we inferred without outgroups or data partitioning. The final tree is largely congruent with previous hypotheses and adds evidence supporting the close phylogenetic relationship between dengue and Zika.
  • 1.2K
  • 27 Oct 2020
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