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Viral population genetics

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https://read.qxmd.com/read/30901142/a-wild-circ-ulation-high-presence-of-porcine-circovirus-3-in-different-mammalian-wild-hosts-and-ticks
#1
Giovanni Franzo, Laura Grassi, Claudia Maria Tucciarone, Michele Drigo, Marco Martini, Daniela Pasotto, Alessandra Mondin, Maria Luisa Menandro
Porcine circovirus 3 (PCV-3) has emerged as a potential threat for swine industry, being consistently reported in presence of several clinical signs all around the world. Recently, its presence in wild boar has been demonstrated at high prevalence. This evidence is surprising since the lower density of wild populations might not be expected to sustain such efficient viral transmission. Porcine circoviruses were proven to exhibit a certain plasticity in the host tropism and were detected in unrelated species, like mice, dogs and ruminants...
March 22, 2019: Transboundary and Emerging Diseases
https://read.qxmd.com/read/30899574/diagnostic-tests-for-crimean-congo-haemorrhagic-fever-a-widespread-tickborne-disease
#2
Laura T Mazzola, Cassandra Kelly-Cirino
Crimean-Congo haemorrhagic fever (CCHF) is a widespread tickborne disease that circulates in wild and domestic animal hosts, and causes severe and often fatal haemorrhagic fever in infected humans. Due to the lack of treatment options or vaccines, and a high fatality rate, CCHF virus (CCHFV) is considered a high-priority pathogen according to the WHO R&D Blueprint. Several commercial reverse transcriptase PCR (RT-PCR) and serological diagnostic assays for CCHFV are already available, including febrile agent panels to distinguish CCHFV from other viral haemorrhagic fever agents; however, the majority of international laboratories use inhouse assays...
2019: BMJ Global Health
https://read.qxmd.com/read/30894851/inflation-vs-exhaustion-of-antiviral-cd8-t-cell-populations-in-persistent-infections-two-sides-of-the-same-coin
#3
Emanuele Marchi, Lian Ni Lee, Paul Klenerman
Persistent virus infection can drive CD8+ T-cell responses which are markedly divergent in terms of frequency, phenotype, function, and distribution. On the one hand viruses such as Lymphocytic Choriomeningitis Virus (LCMV) Clone 13 can drive T-cell "exhaustion", associated with upregulation of checkpoint molecules, loss of effector functions, and diminished control of viral replication. On the other, low-level persistence of viruses such as Cytomegalovirus and Adenoviral vaccines can drive memory "inflation," associated with sustained populations of CD8+ T-cells over time, with maintained effector functions and a distinct phenotype...
2019: Frontiers in Immunology
https://read.qxmd.com/read/30876864/an-accurate-approximation-for-the-expected-site-frequency-spectrum-in-a-galton-watson-process-under-an-infinite-sites-mutation-model
#4
John L Spouge
If viruses or other pathogens infect a single host, the outcome of infection often hinges on the fate of the initial invaders. The initial basic reproduction number R0 , the expected number of cells infected by a single infected cell, helps determine whether the initial viruses can establish a successful beachhead. To determine R0 , the Kingman coalescent or continuous-time birth-and-death process can be used to infer the rate of exponential growth in an historical population. Given M sequences sampled in the present, the two models can make the inference from the site frequency spectrum (SFS), the count of mutations that appear in exactly k sequences (k=1,2,…,M)...
March 12, 2019: Theoretical Population Biology
https://read.qxmd.com/read/30875126/concise-review-targeting-cancer-stem-cells-and-their-supporting-niche-using-oncolytic-viruses
#5
Mathieu J F Crupi, John C Bell, Ragunath Singaravelu
Cancer stem cells (CSCs) have the capacity to self-renew and differentiate to give rise to heterogenous cancer cell lineages in solid tumors. These CSC populations are associated with metastasis, tumor relapse and resistance to conventional anti-cancer therapies. Here, we focus on the use of oncolytic viruses (OVs) to target CSCs as well as the OV-driven interferon production in the tumor microenvironment (TME) that can repress CSC properties. We explore the ability of OVs to deliver combinations of immune-modulating therapeutic transgenes, such as immune checkpoint inhibitor antibodies...
March 15, 2019: Stem Cells
https://read.qxmd.com/read/30863382/human-immunodeficiency-virus-1-diversity-in-the-moscow-region-russia-phylodynamics-of-the-most-common-subtypes
#6
Aleksey Lebedev, Natalya Lebedeva, Fedor Moskaleychik, Alexander Pronin, Elena Kazennova, Marina Bobkova
This study analyzes the HIV-1 subtype diversity and its phylodynamics in Moscow region, which is the most densely populated area of Russia characterized by high rates of internal and external migration. The demographic and viral data from 896 HIV-infected individuals collected during 2011-2016 were analyzed. The study revealed broad diversity in the HIV-1 subtypes found in Moscow, which included A6 (85.1%), B (7.6%), CRF02_AG (1.2%) and URF_A6/B recombinants (4.2%). Other HIV-1 subtypes were detected as single cases...
2019: Frontiers in Microbiology
https://read.qxmd.com/read/30859951/22-using-light-to-unveil-depression-the-role-of-optogenetics
#7
Aurelio Lourenco Diniz, Freddy Escobar-Montealegre, Marcela Pellegrini Peçanha
IntroductionMajor depressive disorder (MDD) is a highly prevalent and often debilitating condition with a vast impact on modern societies worldwide. Although it interferes significantly with functioning, MDD is frequently unresponsive to conventional treatment approaches and pharmacotherapy failure has been reported in approximately one third of patients. Current knowledge of the exact underlying disease mechanisms is insufficient, and may thus largely contribute to such therapeutic limitations. Optogenetics, a novel study field employing the expression of genetically-encodable light-sensitive proteins in specific cell types, circumvents the limitations of other forms of neuromodulation and enables temporally precise, bidirectional control of cellular activity in well-defined neuronal populations...
February 2019: CNS Spectrums
https://read.qxmd.com/read/30849988/molecular-detection-and-phylogenetic-analysis-of-peste-des-petits-ruminants-virus-circulating-in-small-ruminants-in-eastern-amhara-region-ethiopia
#8
Biruk Alemu, Getachew Gari, Geneviève Libeau, Olivier Kwiatek, Menbere Kidane, Rediet Belayneh, Bewuket Siraw, Barbara Wieland, Wondwoson Asfaw, Reta D Abdi
BACKGROUND: Peste des Petits Ruminants (PPR) is a severe, highly infectious and fatal viral disease of small ruminants. Four lineages of PPR virus have been identified globally based on sequence analysis of the nucleoprotein (N) and fusion (F) gene. The aim of this study was to isolate and genetically characterize recently circulating PPR virus in small ruminants in the eastern Amhara region in Ethiopia. A total of 28 anti-mortem samples (gum debris, nasal and ocular swab) were collected from clinically suspicious animals and examined for the presence of PPRV by a one-step RT-PCR assay...
March 8, 2019: BMC Veterinary Research
https://read.qxmd.com/read/30845200/tracking-dengue-virus-type-1-genetic-diversity-during-lineage-replacement-in-an-hyperendemic-area-in-colombia
#9
Mauricio A Salvo, Matthew T Aliota, Louise H Moncla, Ivan D Velez, Andrea I Trujillo, Thomas C Friedrich, Jorge E Osorio
Dengue virus (DENV) is a flavivirus responsible for the most common and burdensome arthropod-borne viral disease of humans[1]. DENV evolution has been extensively studied on broad geographic and time scales, using sequences from a single gene[2,3]. It is believed that DENV evolution in humans is dominated primarily by purifying selection due to the constraint of maintaining fitness in both humans and mosquitoes[4,5]. Few studies have explored DENV evolutionary dynamics using whole genome sequences, nor have they explored changes in viral diversity that occur during intra-epidemic periods...
2019: PloS One
https://read.qxmd.com/read/30842944/genetically-engineered-crops-importance-of-diversified-integrated-pest-management-for-agricultural-sustainability
#10
REVIEW
Jennifer A Anderson, Peter C Ellsworth, Josias C Faria, Graham P Head, Micheal D K Owen, Clinton D Pilcher, Anthony M Shelton, Michael Meissle
As the global population continues to expand, utilizing an integrated approach to pest management will be critically important for food security, agricultural sustainability, and environmental protection. Genetically engineered (GE) crops that provide protection against insects and diseases, or tolerance to herbicides are important tools that complement a diversified integrated pest management (IPM) plan. However, despite the advantages that GE crops may bring for simplifying the approach and improving efficiency of pest and weed control, there are also challenges for successful implementation and sustainable use...
2019: Frontiers in Bioengineering and Biotechnology
https://read.qxmd.com/read/30842757/natural-hosts-and-genetic-diversity-of-the-emerging-tomato-leaf-curl-new-delhi-virus-in-spain
#11
Miguel Juárez, María Pilar Rabadán, Luis Díaz Martínez, Monia Tayahi, Ana Grande-Pérez, Pedro Gómez
Knowledge about the host range and genetic structure of emerging plant viruses provides insights into fundamental ecological and evolutionary processes, and from an applied perspective, facilitates the design and implementation of sustainable disease control measures. Tomato leaf curl New Delhi virus (ToLCNDV) is an emerging whitefly transmitted begomovirus that is rapidly spreading and inciting economically important diseases in cucurbit crops of the Mediterranean basin. Genetic characterization of the ToLCNDV Mediterranean populations has shown that they are monophyletic in cucurbit plants...
2019: Frontiers in Microbiology
https://read.qxmd.com/read/30842323/evidence-for-both-intermittent-and-persistent-compartmentalization-of-hiv-1-in-the-female-genital-tract
#12
Batsirai M Mabvakure, Bronwen E Lambson, Kavisha Ramdayal, Lindi Masson, Dale Kitchin, Mushal Allam, Salim Abdool Karim, Carolyn Williamson, Jo-Ann Passmore, Darren P Martin, Cathrine Scheepers, Penny L Moore, Gordon W Harkins, Lynn Morris
HIV-1 has been shown to evolve independently in different anatomical compartments but studies in the female genital tract have been inconclusive. Here we examined evidence of compartmentalization using HIV-1 subtype C envelope (Env) glycoprotein genes (gp160) obtained from matched cervico-vaginal lavage (CVL) and plasma samples over 2-3 years of infection. HIV-1 gp160 amplification from CVL was achieved for only four of 18 acutely infected women and this was associated with the presence of pro-inflammatory cytokines and/or measurable viremia in the CVL...
March 6, 2019: Journal of Virology
https://read.qxmd.com/read/30837341/crispr-spacers-indicate-preferential-matching-of-specific-virioplankton-genes
#13
Daniel J Nasko, Barbra D Ferrell, Ryan M Moore, Jaysheel D Bhavsar, Shawn W Polson, K Eric Wommack
Viral infection exerts selection pressure on marine microbes, as virus-induced cell lysis causes 20 to 50% of cell mortality, resulting in fluxes of biomass into oceanic dissolved organic matter. Archaeal and bacterial populations can defend against viral infection using the clustered regularly interspaced short palindromic repeat (CRISPR)-associated (Cas) system, which relies on specific matching between a spacer sequence and a viral gene. If a CRISPR spacer match to any gene within a viral genome is equally effective in preventing lysis, no viral genes should be preferentially matched by CRISPR spacers...
March 5, 2019: MBio
https://read.qxmd.com/read/30826932/unique-genetic-features-of-canine-adenovirus-type-1-cadv-1-infecting-red-foxes-vulpes-vulpes-in-northern-norway-and-arctic-foxes-vulpes-lagopus-in-svalbard
#14
Andrea Balboni, Morten Tryland, Torill Mørk, Siw T Killengreen, Eva Fuglei, Mara Battilani
Canine adenovirus type 1 (CAdV-1) is the aetiological agent of infectious canine hepatitis (ICH) in domestic dogs (Canis familiaris). In spite of the widespread use of vaccination, CAdV-1 continues to circulate in the dog population. Although a high number of serological screenings have indicated that CAdV-1 is widespread in fox species, little is known about the potential role of foxes as reservoirs of CAdV-1. Furthermore, very little data exist on the molecular features of this virus in foxes. To add to existing knowledge on CAdV-1 circulating in wild carnivores, tissue samples from CAdV-seropositive red foxes (Vulpes vulpes, n = 10) from the northern mainland of Norway and arctic foxes (Vulpes lagopus, n = 10) from the Svalbard archipelago, Norway, were investigated using a molecular approach to detect CAdV-1 DNA and important structural and non-structural genes of the detected viruses were sequenced and analysed...
March 2, 2019: Veterinary Research Communications
https://read.qxmd.com/read/30819129/molecular-pathogenesis-of-cholangiocarcinoma
#15
REVIEW
Peter L Labib, George Goodchild, Stephen P Pereira
BACKGROUND: Cholangiocarcinomas are a heterogeneous group of malignancies arising from a number of cells of origin along the biliary tree. Although most cases in Western countries are sporadic, large population-based studies have identified a number of risk factors. This review summarises the evidence behind reported risk factors and current understanding of the molecular pathogenesis of cholangiocarcinoma, with a focus on inflammation and cholestasis as the driving forces in cholangiocarcinoma development...
February 28, 2019: BMC Cancer
https://read.qxmd.com/read/30814317/genotypic-and-phenotypic-diversity-of-herpes-simplex-virus-2-within-the-infected-neonatal-population
#16
Lisa N Akhtar, Christopher D Bowen, Daniel W Renner, Utsav Pandey, Ashley N Della Fera, David W Kimberlin, Mark N Prichard, Richard J Whitley, Matthew D Weitzman, Moriah L Szpara
More than 14,000 neonates are infected with herpes simplex virus (HSV) annually. Approximately half display manifestations limited to the skin, eyes, or mouth (SEM disease). The rest develop invasive infections that spread to the central nervous system (CNS disease or encephalitis) or throughout the infected neonate (disseminated disease). Invasive HSV disease is associated with significant morbidity and mortality, but the viral and host factors that predispose neonates to these forms are unknown. To define viral diversity within the infected neonatal population, we evaluated 10 HSV-2 isolates from newborns with a range of clinical presentations...
February 27, 2019: MSphere
https://read.qxmd.com/read/30808620/no-cost-of-complexity-in-bacteriophages-adapting-to-a-complex-environment
#17
Andrew M Sackman, Darin R Rokyta
A longstanding prediction in evolutionary biology is that organisms experience a so-called "cost of complexity" manifested as a decreasing rate of adaptation in populations as organisms or selective environments become increasingly complex. This theory assumes the ubiquity of antagonistic pleiotropy, or tradeoffs in fitness, for mutations affecting multiple traits or phenotypes. A particular manifestation of antagonism thought to be at play in adaptive dynamics involves the relationship between viral growth rate and capsid stability, an interaction that may impede the adaptation of viral pathogens to novel hosts and environments...
February 26, 2019: Genetics
https://read.qxmd.com/read/30790699/phenotyping-of-lewis-and-secretor-hbga-from-saliva-and-detection-of-new-fut2-gene-snps-from-young-children-from-the-amazon-presenting-acute-gastroenteritis-and-respiratory-infection
#18
Marcia Terezinha Baroni de Moraes, Alberto Ignácio Olivares Olivares, Alexandre Madi Fialho, Fábio Correia Malta, Sergio da Silva E Mouta Junior, Romanul de Souza Bispo, Alvaro Jorge Velloso, Gabriel Azevedo Leitão, Carina Pacheco Cantelli, Johan Nordgren, Lennart Svenson, Marize Pereira Miagostovich, José Paulo Gagliardi Leite
The Histo-blood group antigens (HBGA) are host genetic factors associated with susceptibility to rotavirus (RV) and human norovirus (HuNoV), the major etiological agents of viral acute gastroenteritis (AGE) worldwide. The FUT2 gene expressing the alpha-1, 2-L- fucosyltransferase enzyme is important for gut HBGA expression, and also provides a composition of the phenotypic profile achieved through mutations occurring in populations with different evolutionary histories; as such, it can be considered a genetic population marker...
February 18, 2019: Infection, Genetics and Evolution
https://read.qxmd.com/read/30785873/secondary-contact-between-diverged-host-lineages-entails-ecological-speciation-in-a-european-hantavirus
#19
Moritz Saxenhofer, Sabrina Schmidt, Rainer G Ulrich, Gerald Heckel
The diversity of viruses probably exceeds biodiversity of eukaryotes, but little is known about the origin and emergence of novel virus species. Experimentation and disease outbreak investigations have allowed the characterization of rapid molecular virus adaptation. However, the processes leading to the establishment of functionally distinct virus taxa in nature remain obscure. Here, we demonstrate that incipient speciation in a natural host species has generated distinct ecological niches leading to adaptive isolation in an RNA virus...
February 2019: PLoS Biology
https://read.qxmd.com/read/30781655/loss-of-mybbp1a-induces-cancer-stem-cell-activity-in-renal-cancer
#20
Blanca Felipe-Abrio, Eva Maria Verdugo-Sivianes, Carmen Sáez, Amancio Carnero
Tumors are cellular ecosystems where different populations and subpopulations of cells coexist. Among these cells, cancer stem cells (CSCs) are considered to be the origin of the tumor mass, being involved in metastasis and in the resistance to conventional therapies. Furthermore, tumor cells have an enormous plasticity and a phenomenon of de-differentiation of mature tumor cells to CSCs may occur. Therefore, it is essential to identify genetic alterations that cause the de-differentiation of mature tumor cells to CSCs for the future design of therapeutic strategies...
February 18, 2019: Cancers
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