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Viral population genetics

Mohammadreza Sadeghi, Eda Altan, Xutao Deng, Christopher M Barker, Ying Fang, Lark L Coffey, Eric Delwart
Metagenomic analysis of whole mosquitoes allows the genetic characterization of all associated viruses, including arboviruses and insect-specific viruses, plus those in their diet or infecting their parasites. We describe here the virome in mosquitoes, primarily Culex pipiens complex, Cx. tarsalis and Cx. erythrothorax, collected in 2016 from 31 counties in California, USA. The nearly complete genomes of 56 viruses, including 32 novel genomes, some from potentially novel RNA and DNA viral families or genera, were assembled and phylogenetically analyzed, significantly expanding the known Culex-associated virome...
August 8, 2018: Virology
Eugène Kroon, Phuc T Pham, Sunee Sirivichayakul, Rapee Trichavaroj, Donn J Colby, Suteeraporn Pinyakorn, Nittaya Phanuphak, Eric Sanders-Buell, Frits Van Griensven, Gustavo H Kijak, Jerome H Kim, Nelson L Michael, Merlin L Robb, Jintanat Ananworanich, Mark S De Souza, Sodsai Tovanabutra
OBJECTIVE: To assess transmission characteristics in a predominantly men who have sex with men (MSM) cohort initiating anti-retroviral therapy (ART) immediately following diagnosis of acute HIV-1infection (AHI). METHODS: A longitudinal study (2009-2017) was performed in participants with AHI (n = 439) attending a single clinic in Bangkok. Plasma samples obtained prior to ART were used to obtain HIV-1 pol sequences and combined with clinical and epidemiologic data to assess transmission dynamics (cluster formation and size) using phylogenetic analysis...
August 8, 2018: AIDS
Marina Laplana, José Luis Royo, Joan Fibla
INTRODUCTION: Vitamin-D plays a role regulating the immune response against to viral infection. In this sense, vitamin-D deficiency may confer increased susceptibility to enveloped virus infection such as HIV, Hepatitis, Dengue and Respiratory Syncytial virus infection, among others. Vitamin D activity is mediated by its receptor (VDR), which acts as a transcription factor modulating the expression of genes triggering the response against viruses. To date, six major VDR polymorphisms (Cdx, A1012G, FokI, BsmI, ApaI and TaqI) have been studied in the context of viral infection susceptibility...
August 6, 2018: Gene
Juliana de Paoli, André Castagna Wortmann, Mirelli Gabardo Klein, Vagner Reinaldo Zingalli Bueno Pereira, Adriana Cirolini, Bibiane Godoy, Nelson Jurandi Rosa Fagundes, Jonas Michel Wolf, Vagner Ricardo Lunge, Daniel Simon
BACKGROUND: Hepatitis B virus (HBV) infection is a major public health problem in Brazil. HBV endemicity is usually moderate to low according to geographic regions, and high prevalence of this virus has been reported in people of some specific Brazilian counties, including those with a strong influence of Italian colonization in southern Brazil. Analysis of HBV diversity and identification of the main risk factors to HBV infection are necessary to understand hepatitis B epidemiology in these high prevalence regions in southern Brazil...
August 6, 2018: Brazilian Journal of Infectious Diseases
Cynthia X He, Erica D Arroyo, Daniel A Cantu, Anubhuti Goel, Carlos Portera-Cailliau
The first three postnatal weeks in rodents are a time when sensory experience drives the maturation of brain circuits, an important process that is not yet well understood. Alterations in this critical period of experience-dependent circuit assembly and plasticity contribute to several neurodevelopmental disorders, such as autism, epilepsy, and schizophrenia. Therefore, techniques for recording network activity and tracing neuronal connectivity over this time period are necessary for delineating circuit refinement in typical development and how it deviates in disease...
2018: Frontiers in Neural Circuits
Jolynne Mokaya, Anna L McNaughton, Martin J Hadley, Apostolos Beloukas, Anna-Maria Geretti, Dominique Goedhals, Philippa C Matthews
International sustainable development goals for the elimination of viral hepatitis as a public health problem by 2030 highlight the pressing need to optimize strategies for prevention, diagnosis and treatment. Selected or transmitted resistance associated mutations (RAMs) and vaccine escape mutations (VEMs) in hepatitis B virus (HBV) may reduce the success of existing treatment and prevention strategies. These issues are particularly pertinent for many settings in Africa where there is high HBV prevalence and co-endemic HIV infection, but lack of robust epidemiological data and limited education, diagnostics and clinical care...
August 6, 2018: PLoS Neglected Tropical Diseases
James Lara, Mahder A Teka, Seth Sims, Guo-Liang Xia, Sumathi Ramachandran, Yury Khudyakov
Human immunodeficiency virus (HIV) infection is rising as a leading cause of morbidity and mortality among hepatitis C virus (HCV)-infected patients. Both viruses interact in co-infected hosts, which may affect their intra-host evolution, potentially leading to differing genetic composition of viral populations in co-infected (CIP) and mono-infected (MIP) patients. Here, we investigate genetic differences between intra-host variants of the HCV hypervariable region 1 (HVR1) sampled from CIP and MIP. Nucleotide (nt) sequences of intra-host HCV HVR1 variants (N = 28,622) obtained from CIP (N = 112) and MIP (n = 176) were represented using 148 physical-chemical (PhyChem) indexes of DNA nt dimers...
July 31, 2018: Infection, Genetics and Evolution
Jayashri Patil, Ashwini More, Poonam Patil, Santosh Jadhav, Priyanka Newase, Megha Agarwal, Sarika Amdekar, C G Raut, Deepti Parashar, Sarah S Cherian
During 2015-2017, chikungunya virus (CHIKV) showed a resurgence in several parts of India with Karnataka, Maharashtra and New Delhi accounting for a majority of the cases. E2-E1 gene based characterization revealed Indian subcontinent sublineage strains possessing Aedes aegypti mosquito-adaptive mutations E1: K211E and E2:V264A, with the 211 site positively selected. Novel mutational sites E1: K16E/Q, E1: K132Q/T, E1: S355T, E2: C19R and E2:S185Y could be associated with epitopes or virulence determining domains...
August 2, 2018: Archives of Virology
Agustiningsih Agustiningsih, Hidayat Trimarsanto, Restuadi Restuadi, I Made Artika, Margaret Hellard, David Handojo Muljono
Influenza viruses are by nature unstable with high levels of mutations. The sequential accumulation of mutations in the surface glycoproteins allows the virus to evade the neutralizing antibodies. The consideration of the tropics as the influenza reservoir where viral genetic and antigenic diversity are continually generated and reintroduced into temperate countries makes the study of influenza virus evolution in Indonesia essential. A total of 100 complete coding sequences (CDS) of Hemagglutinin (HA) and Neuraminidase (NA) genes of H3N2 virus were obtained from archived samples of Influenza-Like Illness (ILI) surveillance collected from 2008 to 2010...
2018: PloS One
K Tennakone, L A De Silva
Introduction: Dengue is a mosquito-borne viral infection endemic in tropical and subtropical regions, now spreading at epidemic proportions causing a major health issue in Sri Lanka and elsewhere. No effective vaccine or a curative antiviral drug is available to prevent or treat the disease. The only way of mitigating dengue at present, is through mosquito eradication and educating the public on preventive measures which can minimizing the cycle of transfer. Objectives: A theoretical model of dengue with simple mathematics is presented to gain a quantitative understanding of the pattern of dengue outbreaks in Sri Lanka and suggest control measures...
June 30, 2018: Ceylon Medical Journal
Taotao Yang, Runcheng Li, Qing Yao, Xiaofei Zhou, Huayuan Liao, Meng Ge, Xinglong Yu
Porcine teschovirus (PTV) comprises at least 13 genotypes (PTV 1-13). Here, the genotypes of field strains prevalent among pig populations in Hunan Province, China, were identified. Multiple PTV genotypes, including all genotypes except PTV 7 and 8, were found co-circulating in the pig populations, reflecting a high genetic diversity. Moreover, we identified nine novel PTV genotypes, provisionally designated as PTV 14-22. PTV 21-HuN41 and PTV 21-HuN42 were successfully isolated, and their nearly complete genomes were sequenced...
July 30, 2018: Journal of General Virology
Yongle Xu, Rui Zhang, Nannan Wang, Lanlan Cai, Yigang Tong, Qiang Sun, Feng Chen, Nianzhi Jiao
Cyanophages are thought to affect the community structure, population dynamics, metabolic activity, and evolution of picocyanobacteria and to impact the biogeochemical cycling in aquatic ecosystems. Here, we report an estuarine Synechococcus phage, S-CBWM1, which represents a novel viral lineage and exhibits interesting genetic features related to phage-host interactions and evolution. S-CBWM1 encapsidates four virion-associated proteins related to cellular metabolic regulation. Several novel auxiliary metabolic genes related to multidrug efflux, cell wall and capsule synthesis or modification were also identified...
July 26, 2018: Environmental Microbiology
Patrick T Dolan, Zachary J Whitfield, Raul Andino
RNA viruses are unique in their evolutionary capacity, exhibiting high mutation rates and frequent recombination. They rapidly adapt to environmental changes, such as shifts in immune pressure or pharmacological challenge. The evolution of RNA viruses has been brought into new focus with the recent developments of genetic and experimental tools to explore and manipulate the evolutionary dynamics of viral populations. These studies have uncovered new mechanisms that enable viruses to overcome evolutionary challenges in the environment and have emphasized the intimate relationship of viral populations with evolution...
July 26, 2018: Annual Review of Virology
Nagarjun Kasaraneni, Ana M Chamoun-Emanuelli, Gus A Wright, Zhilei Chen
Despite recent improvements in the engineering of viral envelope proteins, it remains a significant challenge to create lentiviral vectors that allow targeted transduction to specific cell populations of interest. In this study, we developed a simple 'plug and play' strategy to retarget lentiviral vectors to any desired cell types through in vitro covalent modification of the virions with specific cell-targeting proteins (CTPs). This strategy exploits a disulfide bond-forming protein-peptide pair PDZ1 and its pentapeptide ligand (ThrGluPheCysAla, TEFCA)...
July 20, 2018: Scientific Reports
Isaac Makundi, Yushi Koshida, Yasuyuki Endo, Kazuo Nishigaki
Felis catus gammaherpesvirus 1 (FcaGHV1) is a widely endemic infection of domestic cats. Current epidemiological data identify domestic cats as the sole natural host for FcaGHV1. The Tsushima leopard cat (TLC; Prionailurus bengalensis euptilurus) is a critically endangered species that lives only on Tsushima Island, Nagasaki, Japan. Nested PCR was used to test the blood or spleen of 89 TLCs for FcaGHV1 DNA; three (3.37%; 95% CI, 0.70⁻9.54) were positive. For TLC management purposes, we also screened domestic cats and the virus was detected in 13...
July 19, 2018: Viruses
Alicja E Grzegorzewska
Genetic polymorphisms within the interferon λ (IFN-λ) chromosomal region, mainly rs12979860 of IFN-λ4 gene (IFNL4), are known as associated with spontaneous hepatitis C virus (HCV) resolution and sustained viral response to therapy with pegylated interferon-α and ribavirin. Strong linkage disequilibrium of IFNL4 rs12979860 with IFNL4 rs368234815, which is casually associated with HCV spontaneous and therapeutical eradication, at least partially explains favorable HCV outcomes attributed to major homozygosity in rs12979860...
July 19, 2018: Current Medicinal Chemistry
Sudip Kumar Dutta, Tamanash Bhattacharya, Anusri Tripathi
This is the first study reporting whole genome sequences of two CHIKV strains (KJ679577 and KJ679578) isolated from Eastern Indian patients sera during 2010-2011 outbreak, both of which were of ECSA genotype, but from different subgroups: Indian Ocean outbreak and ECSA subtypes. Furthermore, viral sequences were analyzed using different in-silico approaches to identify potential genetic variations that might have functional implications on various aspects of virus replication, viral protein functionality, immunogenicity and transmission...
July 2018: 3 Biotech
Yusuke Ito, Alexandra Tauzin, Azaria Remion, Keisuke Ejima, Fabrizio Mammano, Shingo Iwami
HIV-1 mutations rapidly accumulate through genetic recombination events, which require the infection of a single cell by two virions (coinfection). Accumulation of mutations in the viral population may lead to immune escape and high-level drug resistance. The existence of cell subpopulations characterized by different susceptibility to HIV-1 infection has been proposed as an important parameter driving coinfection (Dang et al., 2004). While the mechanism and the quantification of HIV-1 coinfection have been recently investigated by mathematical models, the detailed dynamics of this process during cell-free infection remains elusive...
July 7, 2018: Journal of Theoretical Biology
Daniele Ramazzotti, Alex Graudenzi, Giulio Caravagna, Marco Antoniotti
Several diseases related to cell proliferation are characterized by the accumulation of somatic DNA changes, with respect to wild-type conditions. Cancer and HIV are 2 common examples of such diseases, where the mutational load in the cancerous/viral population increases over time. In these cases, selective pressures are often observed along with competition, co-operation, and parasitism among distinct cellular clones. Recently, we presented a mathematical framework to model these phenomena, based on a combination of Bayesian inference and Suppes' theory of probabilistic causation, depicted in graphical structures dubbed Suppes-Bayes Causal Networks (SBCNs)...
2018: Evolutionary Bioinformatics Online
Cristiane Pinheiro Pestana, Rafael Lawson-Ferreira, Carolina Lessa-Aquino, Maria da Luz Fernandes Leal, Marcos da Silva Freire, Akira Homma, Marco Alberto Medeiros
Yellow Fever (YF) is an acute viral hemorrhagic disease prevalent mainly in Africa and Americas, with 20-60% fatality rate in severe forms. Currently, antiviral drugs for the infection are not available, reinforcing the importance of vaccination in resident populations and travelers. Manufactured in 7 different countries, the YF vaccine was first created in 1937 and two substrains are used for production, 17DD and 17D-204. The vaccine produced in Bio-Manguinhos/Brazil uses 17DD substrain and more than 160 million doses have been exported to over 74 countries...
October 2018: Journal of Virological Methods
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