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virus evolution

Franck Maunoury, Aurore Clément, Chizoba Nwankwo, Laurie Levy-Bachelot, Armand Abergel, Vincent Di Martino, Eric Thervet, Isabelle Durand-Zaleski
OBJECTIVE: To assess the cost-effectiveness of the elbasvir/grazoprevir (EBR/GZR) regimen in patients with genotype 1 chronic hepatitis C virus (HCV) infection with severe and end-stage renal disease compared to no treatment. DESIGN: This study uses a health economic model to estimate the cost-effectiveness of treating previously untreated and treatment experienced chronic hepatitis C patients who have severe and end stage renal disease with the elbasvir-grazoprevir regimen versus no treatment in the French context...
2018: PloS One
Peng He, Patamarerk Engsontia, Guang-Lei Chen, Qian Yin, Jun Wang, Xu Lu, Ya-Nan Zhang, Zhao-Qun Li, Ming He
BACKGROUND: The white-backed planthopper (WBPH) Sogatella furcifera Horváth, the brown planthopper (BPH) Nilaparvata lugens, and the small brown planthopper (SBPH) Laodelphax striatellus (Hemiptera: Delphacidae) are rice pests that damage rice plants by sap-sucking and by transmitting viruses. Host-seeking behavior involves chemosensory receptor genes, which include odorant receptors (ORs), ionotropic receptors (IRs) and gustatory receptors (GRs). RESULTS: We used genome and transcriptome data to identify 141 ORs, 28 GRs and 25 IRs in BPH, 135 ORs, 18 GRs and 16 IRs in WBPH and 37 ORs, 14 GRs and 6 IRs in SBPH...
March 15, 2018: Pest Management Science
Xian Qi, Xiaofei An, Yongjun Jiao, Huiyan Yu, Ke Xu, Lunbiao Cui, Shenjiao Wang, Fei Deng, Xiang Huo, Haodi Huang, Qigang Dai, Changjun Bao
Five epidemic waves of human infection with influenza A (H7N9) virus have emerged in China since spring 2013. We previously described the epidemiological characterization of the fifth wave in Jiangsu province. In this study, 41 H7N9 viruses from patients and live-poultry markets were isolated and sequenced to further elucidate the genetic features of viruses of the fifth wave in Jiangsu province. Phylogenetic analysis revealed substantial genetic diversity in the internal genes, and 18 genotypes were identified from the 41 H7N9 virus strains...
March 14, 2018: Archives of Virology
Katherine S Xue, Louise H Moncla, Trevor Bedford, Jesse D Bloom
The rapid global evolution of influenza virus begins with mutations that arise de novo in individual infections, but little is known about how evolution occurs within hosts. We review recent progress in understanding how and why influenza viruses evolve within human hosts. Advances in deep sequencing make it possible to measure within-host genetic diversity in both acute and chronic influenza infections. Factors like antigenic selection, antiviral treatment, tissue specificity, spatial structure, and multiplicity of infection may affect how influenza viruses evolve within human hosts...
March 10, 2018: Trends in Microbiology
M Chen, M H Jia, Y L Ma, H B Luo, H C Chen, C J Yang, J Dai, L Yang, L J Dong, R Lu, L J Song, Y Han, J Y Lu, A K L Cheung, Z W Chen, L Lu
Multiple human immunodeficiency virus (HIV)-1 genotypes in China were first discovered in Yunnan Province before disseminating throughout the country. As the HIV-1 epidemic continues to expand in Yunnan, genetic characteristics and transmitted drug resistance (TDR) should be further investigated among the recently infected population. Among 2828 HIV-positive samples newly reported in the first quarter of 2014, 347 were identified as recent infections with BED-captured enzyme immunoassay (CEIA). Of them, 291 were successfully genotyped and identified as circulating recombinant form (CRF)08_BC (47...
March 14, 2018: Epidemiology and Infection
Katherine Lavelle, James Murphy, Brian Fitzgerald, Gabriele A Lugli, Aldert Zomer, Horst Neve, Marco Ventura, Charles M Franz, Christian Cambillau, Douwe van Sinderen, Jennifer Mahony
Phages of Streptococcus thermophilus present a major threat to the production of many fermented dairy products. To date, only a handful of studies have assessed the biodiversity of S. thermophilus phages in dairy fermentations. In order to develop strategies to limit phage predation in this important industrial environment, it is imperative that such studies are undertaken and that phage-host interactions of this species are better defined. The present study investigated the biodiversity and evolution of phages within an Irish dairy fermentation facility over an eleven year period...
March 9, 2018: Applied and Environmental Microbiology
Quang N Nguyen, David R Martinez, Jonathon E Himes, R Whitney Edwards, Qifeng Han, Amit Kumar, Riley Mangan, Nathan I Nicely, Guanhua Xie, Nathan Vandergrift, Xiaoying Shen, Justin Pollara, Sallie R Permar
BACKGROUND: The initial envelope (Env)-specific antibody response in acutely HIV-1-infected individuals and simian immunodeficiency virus (SIV)-infected rhesus monkeys (RMs) is dominated by non-neutralizing antibodies targeting Env gp41. In contrast, natural primate SIV hosts, such as African green monkeys (AGMs), develop a predominant Env gp120-specific antibody response to SIV infection. However, the fine-epitope specificity and function of SIV Env-specific plasma IgG, and their potential role on autologous virus co-evolution in SIV-infected AGMs and RMs remain unclear...
March 9, 2018: Retrovirology
Z Wyżewski, K P Gregorczyk, J Szczepanowska, L Szulc-Dąbrowska
Heat shock proteins (Hsps) are a family of proteins highly conserved in evolution. Members of the Hsp family are mainly responsible for proper protein folding, however they perform many other functions in living organisms. Hsp60 is a molecular chaperone that is present in mitochondria and cytosol of eukaryotic cells, as well as on their surface. It is also found in the extracellular space and in the peripheral blood. Apart from its role in assisting protein folding in cooperation with Hsp10, Hsp60 contributes to regulation of apoptosis, as well as participates in modulation of the immune system activity...
2018: Acta Virologica
Nicholas R Meyerson, Cody J Warren, Daniel A S A Vieira, Felipe Diaz-Griferro, Sara L Sawyer
HIV-1 arose as the result of spillover of simian immunodeficiency viruses (SIVs) from great apes in Africa, namely from chimpanzees and gorillas. Chimpanzees and gorillas were, themselves, infected with SIV after virus spillover from African monkeys. During spillover events, SIV is thought to require adaptation to the new host species. The host barriers that drive viral adaptation have predominantly been attributed to restriction factors, rather than cofactors (host proteins exploited to promote viral replication)...
March 2018: PLoS Pathogens
Koenraad Van Doorslaer, Simona Kraberger, Charlotte Austin, Kata Farkas, Melissa Bergeman, Emma Paunil, William Davison, Arvind Varsani
The Polyomaviridae is a diverse family of circular double-stranded DNA viruses. Polyomaviruses have been isolated from a wide array of animal hosts. An understanding of the evolutionary and ecological dynamics of these viruses is essential to understanding the pathogenicity of polyomaviruses. Using a high throughput sequencing approach, we identified a novel polyomavirus in an emerald notothen (Trematomus bernacchii) sampled in the Ross sea (Antarctica), expanding the known number of fish-associated polyomaviruses...
March 8, 2018: Journal of General Virology
Waqas Ali, Mudasser Habib, Rai Shafqat Ali Khan, Muhammad Ashir Zia, Muhammad Farooq, Sanaullah Sajid, Muhammad Salah Ud Din Shah
This study reports the molecular characterization of foot-and-mouth disease virus (FMDV) in the provinces of Punjab and Sindh, Pakistan during 2014-17. FMDV genome was detected in 42 and 41 out of 46 samples (epithelial tissue and saliva) by reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) and reverse transcriptase polymerase chain reaction (RT-PCR), respectively. Sequences of the complete VP1 coding region of the samples (n = 33) was achieved showing that 10, 4 and 19 samples belonged to serotype O, A and Asia1 respectively...
March 7, 2018: Archives of Virology
Bo Wang, Dominik Harms, C Patrick Papp, Sandra Niendorf, Sonja Jacobsen, Marc Lütgehetmann, Sven Pischke, Heiner Wedermeyer, Jörg Hofmann, C-Thomas Bock
Autochthonous Hepatitis E virus genotype 3 (HEV-3) infections in industrialized countries are more frequent than previously assumed. HEV-3 is zoonotic and the causal pathogen of chronic hepatitis E. According to the latest classification of the family Hepeviridae , 10 HEV-3 designated subtypes (HEV-3a to HEV-3j) and 7 unassigned HEV-3 subtypes are proposed. In order to identify and characterize HEV-3 variants in circulation, we developed a molecular approach combining a sensitive HEV-specific real-time RT-PCR targeting HEV ORF2/3 region and two newly designed consensus nested RT-PCRs targeting HEV ORF1 and ORF2 genes, respectively...
March 7, 2018: Journal of Clinical Microbiology
Danyil Grybchuk, Alexei Y Kostygov, Diego H Macedo, Claudia M d'Avila-Levy, Vyacheslav Yurchenko
Viruses of trypanosomatids are now being extensively studied because of their diversity and the roles they play in flagellates' biology. Among the most prominent examples are leishmaniaviruses implicated in pathogenesis of Leishmania parasites. Here, we present a historical overview of this field, starting with early reports of virus-like particles on electron microphotographs, and culminating in detailed molecular descriptions of viruses obtained using modern next generation sequencing-based techniques. Because of their diversity, different life cycle strategies and host specificity, we believe that trypanosomatids are a fertile ground for further explorations to better understand viral evolution, routes of transitions, and molecular mechanisms of adaptation to different hosts...
February 19, 2018: Memórias do Instituto Oswaldo Cruz
Sebastián Duchêne, Edward C Holmes
Pithovirus sibericum is a giant (610 Kpb) double-stranded DNA virus discovered in a purportedly 30,000-year-old permafrost sample. A closely related virus, Pithovirus massiliensis , was recently isolated from a sewer in southern France. An initial comparison of these two virus genomes assumed that P. sibericum was directly ancestral to P. massiliensis and gave a maximum evolutionary rate of 2.60 × 10-5 nucleotide substitutions per site per year (subs/site/year). If correct, this would make pithoviruses among the fastest-evolving DNA viruses, with rates close to those seen in some RNA viruses...
January 2018: Virus Evolution
Xue-Lian Luo, Shan Lu, Dong Jin, Jing Yang, Shu-Sheng Wu, Jianguo Xu
Wildlife has been considered the main source of novel viruses causing emerging infectious diseases. Marmota himalayana is endemic to the Qinghai-Tibetan Plateau, China. Here, based on a high-throughput method using Illumina RNA sequencing, we studied the RNA virome of M. himalayana and discovered multiple novel viruses, especially picobirnaviruses (PBVs), which have a bi-segmented genome and belong to the family Picobirnaviridae. A total of 63% of the viral contigs corresponded to PBVs, comprising 274 segment 1 and 56 segment 2 sequences...
March 7, 2018: Emerging Microbes & Infections
Haiyun Jin, Wan Wang, Xueqin Yang, Hailong Su, Jiawen Fan, Rui Zhu, Shifeng Wang, Huoying Shi, Xiufan Liu
BACKGROUND: Vaccines constitute a unique selective pressure, different from natural selection, drives the evolution of influenza virus. In this study, A/Chicken/Shanghai/F/1998 (H9N2) was continually passaged in specific pathogen-free embryonated chicken eggs with or without selective pressures from antibodies induced by homologous maternal antibodies. Genetic mutations, antigenic drift, replication, and pathogenicity of the passaged virus were evaluated. RESULTS: Antigenic drift of the passaged viruses occurred in the 47th generation (vF47) under selective pressure on antibodies and in the 52nd generation (nF52) without selective pressure from antibodies...
March 6, 2018: BMC Veterinary Research
Clément Gilbert, Cédric Feschotte
It is becoming clear that most eukaryotic transposable elements (TEs) owe their evolutionary success in part to horizontal transfer events, which enable them to invade new species. Recent large-scale studies are beginning to unravel the mechanisms and ecological factors underlying this mode of transmission. Viruses are increasingly recognized as vectors in the process but also as a direct source of genetic material horizontally acquired by eukaryotic organisms. Because TEs and endogenous viruses are major catalysts of variation and innovation in genomes, we argue that horizontal inheritance has had a more profound impact in eukaryotic evolution than is commonly appreciated...
March 2, 2018: Current Opinion in Genetics & Development
Alessandra Mendelski Pereira, Denise Leite Maia Monteiro, Heron Werner, Pedro Daltro, Tatiana Fazecas, Bianca Guedes, Gabriele Tonni, Alberto Borges Peixoto, Edward Araujo Júnior
The recent epidemic of Zika virus (ZIKV) infection in Central and South America is one of the most serious global public health emergencies since the Ebola outbreak in West Africa. In Brazil, especially in the north, northeast, and southeast parts of the country, the ZIKV outbreak is a cause of concern for pregnant women because ZIKV intrauterine infection has been found to be associated with multiple brain malformations and microcephaly. In Brazil, the number of newborns with confirmed microcephaly per year recorded during the ZIKV outbreak, has been approximately 15 times greater than previously reported...
March 1, 2018: Journal of the Turkish German Gynecological Association
Fırat Dogan, Selvi Deniz Dorttas, Seval Bilge Dagalp, Veysel Soydal Ataseven, Feray Alkan
Papillomaviruses (PVs) are epitheliotropic viruses that cause benign proliferative lesions in the skin (warts or papillomas) and mucous membranes of their natural hosts. Recently, new PVs have been found in many animal species. The most common current approach for identifying novel PV types is based on PCR, using various consensus or degenerated primer (broad-range primers), designed on the basis of the multiple alignment of nucleotide or amino acid sequences of a large number of different human papillomaviruses (HPV)...
March 3, 2018: Archives of Virology
Bo Wang, Wen Li, Ji-Hua Zhou, Bei Li, Wei Zhang, Wei-Hong Yang, Hong Pan, Li-Xia Wang, C Thomas Bock, Zheng-Li Shi, Yun-Zhi Zhang, Xing-Lou Yang
Hepatitis E virus (HEV) is the prototype of the family Hepeviridae and the causative agent of common acute viral hepatitis. Genetically diverse HEV-related viruses have been detected in a variety of mammals and some of them may have zoonotic potential. In this study, we tested 278 specimens collected from seven wild small mammal species in Yunnan province, China, for the presence and prevalence of orthohepevirus by broad-spectrum reverse transcription (RT)-PCR. HEV-related sequences were detected in two rodent species, including Chevrier's field mouse (Apodemus chevrieri, family Muridae) and Père David's vole (Eothenomys melanogaster, family Cricetidae), with the infection rates of 29...
March 2, 2018: Virologica Sinica
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