scholarly journals Investigation about the Occurrence of Transmission Cycles of Arbovirus in the Tropical Forest, Amazon Region

Viruses ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 774 ◽  
Author(s):  
Pedro A. Araújo ◽  
Maria O. Freitas ◽  
Jannifer Oliveira Chiang ◽  
Franko Arruda Silva ◽  
Liliane Leal Chagas ◽  
...  
Keyword(s):  
Viral Genome ◽  
Cell Monolayer ◽  
Virus Genome ◽  
Field Trips ◽  
National Forest ◽  
Human Populations ◽  
Newborn Mouse ◽  
Viral Isolation ◽  
Transmission Cycles ◽  
Potential Area

Because of its ecological characteristics, the Caxiuanã National Forest (FLONA) is a potential area of arbovirus circulation. The present study aimed to investigate the occurrence of arbovirus transmission cycles at FLONA de Caxiuanã. Five field trips were performed to capture mosquitoes and sylvatic vertebrates. For these vertebrates, we attempted viral isolation by cell monolayer inoculation from blood, and hemagglutination inhibition and further seroneutralization assays from sera. For mosquitoes, we performed tests of viral genome detection. A total of 338 vertebrates were captured, and the greatest representative was birds (251/74.26%). A total of 16,725 mosquitoes were captured, distributed among 56 species. There were no viruses isolated by newborn mouse inoculation. Among birds, antibodies against Ilheus virus were the most prevalent. Catu virus, Caraparu virus, and Mucambo virus were the most prevalent among mammals and reptiles. Fragments of Mucambo virus, Ilheus virus, Bussuquara virus, and Rocio virus genome were detected in a pool of mosquito samples. These results of the study suggest the occurrence of arbovirus transmission cycles in the FLONA of Caxiuanã. The proximity of human populations with elements, involved in transmission cycles, makes surveillance necessary in this population to avoid dispersion of arboviruses to naïve locations.

First Detection of Tobacco Mosaic Virus in Tobacco Fields in Northern Lebanon

2020 ◽  
Vol 20 ◽  
Author(s):  
Rami Obeid ◽  
Elias Wehbe ◽  
Mohamad Rima ◽  
Mohammad Kabara ◽  
Romeo Al Bersaoui ◽  
...  
Keyword(s):  
Tobacco Mosaic Virus ◽  
Mosaic Virus ◽  
Viral Genome ◽  
Virus Genome ◽  
Enzyme Linked Immunosorbent Assay ◽  
Virus Family ◽  
Crop Fields ◽  
Wide Range ◽  
Almost All ◽  
Das Elisa

Background: Tobacco mosaic virus (TMV) is the most known virus in the plant mosaic virus family and is able to infect a wide range of crops, in particularly tobacco, causing a production loss. Objectives: Herein, and for the first time in Lebanon, we investigated the presence of TMV infection in crops by analyzing 88 samples of tobacco, tomato, cucumber and pepper collected from different regions in North Lebanon. Methods: Double-antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA), revealed a potential TMV infection of four tobacco samples out of 88 crops samples collected. However, no tomato, cucumber and pepper samples were infected. The TMV+ tobacco samples were then extensively analyzed by RT-PCR to detect viral RNA using different primers covering all the viral genome. Results and Discussion: PCR results confirmed those of DAS-ELISA showing TMV infection of four tobacco samples collected from three crop fields of North Lebanon. In only one of four TMV+ samples, we were able to amplify almost all the regions of viral genome, suggesting possible mutations in the virus genome or an infection with a new, not yet identified, TMV strain. Conclusion: Our study is the first in Lebanon revealing TMV infection in crop fields, and highlighting the danger that may affect the future of agriculture.

scholarly journals The evolutionary dynamics of Oropouche Virus (OROV) in South America

2019 ◽  
Author(s):  
Bernardo Gutierrez ◽  
Emma Wise ◽  
Steven Pullan ◽  
Christopher Logue ◽  
Thomas A. Bowden ◽  
...  
Keyword(s):  
Viral Genome ◽  
Amazon Basin ◽  
Evolutionary Dynamics ◽  
Surface Proteins ◽  
Human Populations ◽  
Evolutionary Processes ◽  
Viral Pathogens ◽  
Viral Genomes ◽  
Glycosylation Sites ◽  
Variable Evolutionary Rates

AbstractThe Amazon basin is host to numerous arthropod-borne viral pathogens that cause febrile disease in humans. Among these,Oropouche orthobunyavirus(OROV) is a relatively understudied member of the Peribunyavirales that causes periodic outbreaks in human populations in Brazil and other South American countries. Although several studies have described the genetic diversity of the virus, the evolutionary processes that shape the viral genome remain poorly understood. Here we present a comprehensive study of the genomic dynamics of OROV that encompasses phylogenetic analysis, evolutionary rate estimates, inference of natural selective pressures, recombination and reassortment, and structural analysis of OROV variants. Our study includes all available published sequences, as well as a set of new OROV genomes sequences obtained from patients in Ecuador, representing the first set of viral genomes from this country. Our results show that differing evolutionary processes on the three segments that encompass the viral genome lead to variable evolutionary rates and TMRCAs that could be explained by cryptic reassortment. We also present the discovery of previously unobserved putative N-linked glycosylation sites, and codons which evolve under positive selection on the viral surface proteins, and discuss the potential role of these features in the evolution of the virus through a combined phylogenetic and structural approach.

scholarly journals Involvement of Creatine Kinase B in Hepatitis C Virus Genome Replication through Interaction with the Viral NS4A Protein

2009 ◽  
Vol 83 (10) ◽  
pp. 5137-5147 ◽  
Author(s):  
Hiromichi Hara ◽  
Hideki Aizaki ◽  
Mami Matsuda ◽  
Fumiko Shinkai-Ouchi ◽  
Yasushi Inoue ◽  
...  
Keyword(s):  
Creatine Kinase ◽  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Viral Genome ◽  
Proteome Analysis ◽  
Virus Genome ◽  
Genome Replication ◽  
Creatine Kinase B ◽  
Efficient Replication

ABSTRACT Persistent infection with hepatitis C virus (HCV) is a major cause of chronic liver diseases. The aim of this study was to identify host cell factor(s) participating in the HCV replication complex (RC) and to clarify the regulatory mechanisms of viral genome replication dependent on the host-derived factor(s) identified. By comparative proteome analysis of RC-rich membrane fractions and subsequent gene silencing mediated by RNA interference, we identified several candidates for RC components involved in HCV replication. We found that one of these candidates, creatine kinase B (CKB), a key ATP-generating enzyme that regulates ATP in subcellular compartments of nonmuscle cells, is important for efficient replication of the HCV genome and propagation of infectious virus. CKB interacts with HCV NS4A protein and forms a complex with NS3-4A, which possesses multiple enzyme activities. CKB upregulates both NS3-4A-mediated unwinding of RNA and DNA in vitro and replicase activity in permeabilized HCV replicating cells. Our results support a model in which recruitment of CKB to the HCV RC compartment, which has high and fluctuating energy demands, through its interaction with NS4A is important for efficient replication of the viral genome. The CKB-NS4A association is a potential target for the development of a new type of antiviral therapeutic strategy.

scholarly journals Dengue Virus Genome Uncoating Requires Ubiquitination

mBio ◽  
2016 ◽  
Vol 7 (3) ◽  
Author(s):  
Laura A. Byk ◽  
Néstor G. Iglesias ◽  
Federico A. De Maio ◽  
Leopoldo G. Gebhard ◽  
Mario Rossi ◽  
...  
Keyword(s):  
Dengue Virus ◽  
Capsid Protein ◽  
Viral Genome ◽  
Dengue Infection ◽  
Ubiquitin Proteasome System ◽  
Virus Genome ◽  
Proteasome Activity ◽  
Viral Translation ◽  
Ubiquitin Proteasome ◽  
Molecular Aspects

ABSTRACTThe process of genome release or uncoating after viral entry is one of the least-studied steps in the flavivirus life cycle. Flaviviruses are mainly arthropod-borne viruses, including emerging and reemerging pathogens such as dengue, Zika, and West Nile viruses. Currently, dengue virus is one of the most significant human viral pathogens transmitted by mosquitoes and is responsible for about 390 million infections every year around the world. Here, we examined for the first time molecular aspects of dengue virus genome uncoating. We followed the fate of the capsid protein and RNA genome early during infection and found that capsid is degraded after viral internalization by the host ubiquitin-proteasome system. However, proteasome activity and capsid degradation were not necessary to free the genome for initial viral translation. Unexpectedly, genome uncoating was blocked by inhibiting ubiquitination. Using different assays to bypass entry and evaluate the first rounds of viral translation, a narrow window of time during infection that requires ubiquitination but not proteasome activity was identified. In this regard, ubiquitin E1-activating enzyme inhibition was sufficient to stabilize the incoming viral genome in the cytoplasm of infected cells, causing its retention in either endosomes or nucleocapsids. Our data support a model in which dengue virus genome uncoating requires a nondegradative ubiquitination step, providing new insights into this crucial but understudied viral process.IMPORTANCEDengue is the most significant arthropod-borne viral infection in humans. Although the number of cases increases every year, there are no approved therapeutics available for the treatment of dengue infection, and many basic aspects of the viral biology remain elusive. After entry, the viral membrane must fuse with the endosomal membrane to deliver the viral genome into the cytoplasm for translation and replication. A great deal of information has been obtained in the last decade regarding molecular aspects of the fusion step, but little is known about the events that follow this process, which leads to viral RNA release from the nucleocapsid. Here, we investigated the fate of nucleocapsid components (capsid protein and viral genome) during the infection process and found that capsid is degraded by the ubiquitin-proteasome system. However, in contrast to that observed for other RNA and DNA viruses, dengue virus capsid degradation was not responsible for genome uncoating. Interestingly, we found that dengue virus genome release requires a nondegradative ubiquitination step. These results provide the first insights into dengue virus uncoating and present new opportunities for antiviral intervention.

scholarly journals Large Evolutionary Rate Heterogeneity among and within HIV-1 Subtypes and CRFs

Viruses ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 1689
Author(s):  
Arshan Nasir ◽  
Mira Dimitrijevic ◽  
Ethan Romero-Severson ◽  
Thomas Leitner
Keyword(s):  
Evolutionary Rate ◽  
Virus Genome ◽  
Rate Variation ◽  
Human Populations ◽  
Host Immune System ◽  
Virus Spread ◽  
Rate Heterogeneity ◽  
Hiv 1 ◽  
Subtype 3 ◽  
Diverse Virus

HIV-1 is a fast-evolving, genetically diverse virus presently classified into several groups and subtypes. The virus evolves rapidly because of an error-prone polymerase, high rates of recombination, and selection in response to the host immune system and clinical management of the infection. The rate of evolution is also influenced by the rate of virus spread in a population and nature of the outbreak, among other factors. HIV-1 evolution is thus driven by a range of complex genetic, social, and epidemiological factors that complicates disease management and prevention. Here, we quantify the evolutionary (substitution) rate heterogeneity among major HIV-1 subtypes and recombinants by analyzing the largest collection of HIV-1 genetic data spanning the widest possible geographical (100 countries) and temporal (1981–2019) spread. We show that HIV-1 substitution rates vary substantially, sometimes by several folds, both across the virus genome and between major subtypes and recombinants, but also within a subtype. Across subtypes, rates ranged 3.5-fold from 1.34 × 10−3 to 4.72 × 10−3 in env and 2.3-fold from 0.95 × 10−3 to 2.18 × 10−3 substitutions site−1 year−1 in pol. Within the subtype, 3-fold rate variation was observed in env in different human populations. It is possible that HIV-1 lineages in different parts of the world are operating under different selection pressures leading to substantial rate heterogeneity within and between subtypes. We further highlight how such rate heterogeneity can complicate HIV-1 phylodynamic studies, specifically, inferences on epidemiological linkage of transmission clusters based on genetic distance or phylogenetic data, and can mislead estimates about the timing of HIV-1 lineages.

scholarly journals Evolutionary origins of epidemic potential among human RNA viruses

2019 ◽  
Author(s):  
Lu Lu ◽  
Liam Brierley ◽  
Gail Robertson ◽  
Feifei Zhang ◽  
Samantha Lycett ◽  
...  
Keyword(s):  
Rna Viruses ◽  
Rna Virus ◽  
Virus Genome ◽  
Human Populations ◽  
Infective Virus ◽  
Genome Sequences ◽  
Evolutionary Origins ◽  
Virus Diversity ◽  
Human Viruses ◽  
Do So

AbstractTo have epidemic potential, a pathogen must be able to spread in human populations, but of human-infective RNA viruses only a minority can do so. We investigated the evolution of human transmissibility through parallel analyses of 1755 virus genome sequences from 39 RNA virus genera. We identified 57 lineages containing human-transmissible species and estimated that at least 74% of these lineages have evolved directly from non-human viruses in other mammals or birds, a public health threat recently designated “Disease X”. Human-transmissible viruses rarely evolve from virus lineages that can infect but not transmit between humans. This result cautions against focussing surveillance and mitigation efforts narrowly on currently known human-infective virus lineages and supports calls for a better understanding of RNA virus diversity in non-human hosts.

scholarly journals Evaluation of lockdown effect on SARS-CoV-2 dynamics through viral genome quantification in waste water, Greater Paris, France, 5 March to 23 April 2020

2020 ◽  
Vol 25 (50) ◽  
Author(s):  
S Wurtzer ◽  
V Marechal ◽  
JM Mouchel ◽  
Y Maday ◽  
R Teyssou ◽  
...  
Keyword(s):  
Waste Water ◽  
Viral Genome ◽  
Time Course ◽  
Human Populations ◽  
Additional Information ◽  
Quantitative Monitoring ◽  
Stool Samples ◽  
Important Additional Information ◽  
Specific Symptoms

Introduction Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent of coronavirus disease (COVID-19). People infected with SARS-CoV-2 may exhibit no or mild non-specific symptoms; thus, they may contribute to silent circulation of the virus among humans. Since SARS-CoV-2 RNA can be detected in stool samples, monitoring SARS-CoV-2 RNA in waste water (WW) has been proposed as a complementary tool to investigate virus circulation in human populations. Aim To test if the quantification of SARS-CoV-2 genomes in WW correlates with the number of symptomatic or non-symptomatic carriers. Method We performed a time-course quantitative analysis of SARS-CoV-2 by RT-qPCR in raw WW samples collected from several major WW treatment plants in Greater Paris. The study period was 5 March to 23 April 2020, including the lockdown period in France (from 17 March). Results We showed that the increase of genome units in raw WW accurately followed the increase of human COVID-19 cases observed at the regional level. Of note, the viral genome could be detected before the epidemic grew massively (around 8 March). Equally importantly, a marked decrease in the quantities of genome units was observed concomitantly with the reduction in the number of new COVID-19 cases, 29 days following the lockdown. Conclusion This work suggests that a quantitative monitoring of SARS-CoV-2 genomes in WW could generate important additional information for improved monitoring of SARS-CoV-2 circulation at local or regional levels and emphasises the role of WW-based epidemiology.

Abstract 1: Molecular Basis of Hypertriglyceridemia Associated with the APOA5 c553.G>T SNP

2013 ◽  
Vol 33 (suppl_1) ◽  
Author(s):  
Vineeta Sharma ◽  
Trudy M Forte ◽  
Robert O Ryan
Keyword(s):  
Gene Transfer ◽  
Free Fraction ◽  
Immunoblot Analysis ◽  
Virus Genome ◽  
Human Populations ◽  
Loss Of Function ◽  
Wild Type ◽  
V Protein ◽  
Asian Populations ◽  
Free Region

Objectives Apolipoprotein (apo) A-V is a low abundance protein with profound effects on plasma triglyceride (TG) levels. Several APOA5 SNPs correlate with hypertriglyceridemia (HTG). The c.553 G>T SNP, substituting a Cys for Gly at position 162 of mature apoA-V, is prevalent in Asian populations and correlates with HTG. To investigate the mechanism underlying this association, gene transfer studies were performed in apoa5-/- mice. Methods Adeno-associated virus (AAV2/8) harboring the coding sequence for wild type apoA-V (AAV2/8-apoA-V), G162C apoA-V (AAV2/8-G162C) and LacZ (AAV2/8-LacZ) were injected (1x10e12 virus genome) into the tail vein of 8 apoa5-/- mice per group. Blood samples were collected weekly for 4 weeks and TG and apoA-V levels measured. FPLC was performed on plasma obtained from AAV2/8-apoA-V and AAV2/8-G162C mice. VLDL, LDL, HDL and the lipoprotein-free region were characterized. Results Compared to AAV2/8-LacZ mice, AAV2/8-apoA-V mice had significantly lower plasma TG levels (50% ±5). Unlike AAV2/8-apoA-V, mice injected with AAV2/8-G162C displayed little or no reduction in TG despite similar amounts of plasma apoA-V protein. Immunoblot analysis of FPLC fractionated plasma revealed that, whereas wild-type apoA-V was lipoprotein associated (VLDL and HDL), G162C apoA-V was largely recovered in the lipoprotein-free fraction. Immunoblot analysis following SDS-PAGE under non-reducing conditions revealed that lipoprotein-associated wild type apoA-V and G162C apoA-V are monomeric; by contrast, the electrophoretic mobility of G162C apoA-V recovered in the lipoprotein-free fraction was retarded. Conclusions Gene transfer of wild type apoA-V induces a significant reduction in plasma TG levels of apoa5-/- mice. By contrast, G162C apoA-V failed to induce a corresponding decrease in plasma TG, recapitulating effects observed in human populations harboring this SNP. The propensity of G162C apoA-V to form a disulfide bond with one or more plasma proteins interferes with its lipoprotein binding ability, resulting in loss of function. The results provide a molecular explanation for HTG associated with a common APOA5 SNP. The gene transfer strategy employed provides a platform for studies of other common apoA-V SNPs.

scholarly journals Differences in Viral Disinfection Mechanisms as Revealed by Quantitative Transfection of Echovirus 11 Genomes

2019 ◽  
Vol 85 (14) ◽  
Author(s):  
Jason Torrey ◽  
Urs von Gunten ◽  
Tamar Kohn
Keyword(s):  
Viral Genome ◽  
Uv Light ◽  
Virus Genome ◽  
Host Cells ◽  
Protein Damage ◽  
Heat Inactivation ◽  
Genome Replication ◽  
Virus Inactivation ◽  
Genome Damage ◽  
A Genome

ABSTRACTVirus inactivation mechanisms can be elucidated by methods that measure the loss of specific virus functionality (e.g., host attachment, genome internalization, and genome replication). Genome functionality is frequently assessed by PCR-based methods, which are indirect and potentially inaccurate; genome damage that affects detection by high-fidelity PCR enzymes may not adversely affect the ability of actual cellular enzymes to produce functional virus. Therefore, we developed here a transfection-based assay to quantitatively determine viral genome functionality by inserting viral RNA into host cells directly to measure their ability to produce new functional viruses from damaged viral genomes. Echovirus 11 was treated with ozone, free chlorine (FC), UV light at 254 nm (UV254), or heat, and then the reductions in genome functionality and infectivity were compared. Ozone reduced genome functionality proportionally to infectivity, indicating that genome damage is the main mechanism of virus inactivation. In contrast, FC caused little or no loss of genome functionality compared to infectivity, indicating a larger role for protein damage. For UV254, genome functionality loss accounted for approximately 60% of virus inactivation, with the remainder presumably due to protein damage. Heat treatment resulted in no reduction in genome functionality, in agreement with the understanding that heat inactivation results from capsid damage. Our results indicate that there is a fundamental difference between genome integrity reductions measured by PCR enzymes in previous studies and actual genome functionality (whether the genome can produce virus) after disinfection. Compared to PCR, quantitative transfection assays provide a more realistic picture of actual viral genome functionality and overall inactivation mechanisms during disinfection.IMPORTANCEThis study provides a new tool for assessing virus inactivation mechanisms by directly measuring a viral genome’s ability to produce new viruses after disinfection. In addition, we identify a potential pitfall of PCR for determining virus genome damage, which does not reflect whether a genome is truly functional. The results presented here using quantitative transfection corroborate previously suggested virus inactivation mechanisms for some virus inactivation methods (heat) while bringing additional insights for others (ozone, FC, and UV254). The developed transfection method provides a more mechanistic approach for the assessment of actual virus inactivation by common water disinfectants.

scholarly journals Fluorescent Tagged Vaccinia Virus Genome Allows Rapid and Efficient Measurement of Oncolytic Potential and Discovery of Oncolytic Modulators

Biomedicines ◽  
2020 ◽  
Vol 8 (12) ◽  
pp. 543
Author(s):  
Franck Gallardo ◽  
Doris Schmitt ◽  
Renée Brandely ◽  
Catherine Brua ◽  
Nathalie Silvestre ◽  
...  
Keyword(s):  
Vaccinia Virus ◽  
Viral Genome ◽  
Human Tumor ◽  
Virus Genome ◽  
Living Cells ◽  
Biologic Agent ◽  
Target Sequence ◽  
Human Tumor Cells ◽  
Efficient Measurement ◽  
Oncolytic Activity

As a live biologic agent, oncolytic vaccinia virus has the ability to target and selectively amplify at tumor sites. We have previously reported that deletion of thymidine kinase and ribonucleotide reductase genes in vaccinia virus can increase the safety and efficacy of the virus. Here, to allow direct visualization of the viral genome in living cells, we incorporated the ANCH target sequence and the OR3-Santaka gene in the double-deleted vaccinia virus. Infection of human tumor cells with ANCHOR3-tagged vaccinia virus enables visualization and quantification of viral genome dynamics in living cells. The results show that the ANCHOR technology permits the measurement of the oncolytic potential of the double deleted vaccinia virus. Quantitative analysis of infection kinetics and of viral DNA replication allow rapid and efficient identification of inhibitors and activators of oncolytic activity. Our results highlight the potential application of the ANCHOR technology to track vaccinia virus and virtually any kind of poxvirus in living cells.

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