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Viral evolution

Xian Lin, Shiman Yu, Kelei Guo, Xin Sun, Haiming Yi, Meilin Jin
Reassortment is a key driving force of the evolution and host adaptation of the influenza virus. A(H1N1)pdm2009 (pdm09), a novel H1N1 influenza viral subtype, caused a pandemic in 2009. The strain was established in pig herds and cocirculated with the highly pathogenic H5N1 avian influenza virus. The coexistence of pdm09 with H5N1 raises concerns that reassortment may cause the development of novel viral strains with unpredictable virulence. Given that the viral polymerase subunit PB2 is a determinant of host range and pathogenicity, and that the substantial amino acid differences in PB2 between pdm09 and H5N1, including positions 590/591 and 271, which are shown to play key roles in enhanced polymerase activity in mammalian host cells, we generated a reassortant virus containing PB2 derived from a pdm09 (A/Liaoning/1/2009, LN/09) to investigate if pdm09-derived PB2 can function in a heterologous avian virus isolate as an adaptive strategy, with H5N1 (A/duck/Hubei/hangmei01/2006, HM/06) as the backbone...
2018: Frontiers in Microbiology
Pablo Lopez, Omayra De Jesus, Yasuhiro Yamamura, Nayra Rodriguez, Andrea Arias, Raphael Sanchez, Yadira Rodriguez, Vivian Tamayo-Agrait, Wilfredo Cuevas, Vanessa Rivera-Amill
Human immunodeficiency virus-1 (HIV-1) subtype B virus is the most prevalent subtype in Puerto Rico (PR), accounting for about 90% of infection in the island. Recently, other subtypes and circulating recombinant forms (CRF) including F (12_BF), A (01_BF), and CRF-39 BF-like have been identified. The purpose of this study is to assess the distribution of drug resistance mutations and subtypes in PR. A total of 846 nucleotide sequences from the period comprising 2013 through 2017 were obtained from our "HIV Genotyping" test file...
April 15, 2018: AIDS Research and Human Retroviruses
Silvia Pagliarini, Andrei Korobeinikov
To explore how particularities of a host cell-virus system, and in particular host cell replication, affect viral evolution, in this paper we formulate a mathematical model of marine bacteriophage evolution. The intrinsic simplicity of real-life phage-bacteria systems, and in particular aquatic systems, for which the assumption of homogeneous mixing is well justified, allows for a reasonably simple model. The model constructed in this paper is based upon the Beretta-Kuang model of bacteria-phage interaction in an aquatic environment (Beretta & Kuang 1998 Math...
March 2018: Royal Society Open Science
Patrick T Dolan, Zachary J Whitfield, Raul Andino
The deterministic force of natural selection and stochastic influence of drift shape RNA virus evolution. New deep-sequencing and microfluidics technologies allow us to quantify the effect of mutations and trace the evolution of viral populations with single-genome and single-nucleotide resolution. Such experiments can reveal the topography of the genotype-fitness landscapes that shape the path of viral evolution. By combining historical analyses, like phylogenetic approaches, with high-throughput and high-resolution evolutionary experiments, we can observe parallel patterns of evolution that drive important phenotypic transitions...
April 11, 2018: Cell Host & Microbe
Juan Pasquau, Carmen Hidalgo-Tenorio, María Luisa Montes, Alberto Romero-Palacios, Jorge Vergas, Isabel Sanjoaquín, José Hernández-Quero, Koldo Aguirrebengoa, Francisco Orihuela, Arkaitz Imaz, María José Ríos-Villegas, Juan Flores, María Carmen Fariñas, Pilar Vázquez, María José Galindo, Isabel García-Mercé, Fernando Lozano, Ignacio de Los Santos, Samantha Elizabeth de Jesus, Coral García-Vallecillos
TRIAL DESIGN: The QoLKAMON study evaluated quality of life, efficacy and treatment safety in HIV patients receiving lopinavir/ritonavir in monotherapy (MT) versus continuing combined antiretroviral triple treatment with a boosted protease inhibitor (TT). METHODS: This was a 24-week, open-label, multicentre study in virologically-suppressed HIV-infected participants (N = 225) with a 2:1 randomization: 146 patients who switched to MT were compared with 79 patients who remained on a TT regimen...
2018: PloS One
Ben Longdon, Jonathan P Day, Joel M Alves, Sophia C L Smith, Thomas M Houslay, John E McGonigle, Lucia Tagliaferri, Francis M Jiggins
Host shifts, where a pathogen invades and establishes in a new host species, are a major source of emerging infectious diseases. They frequently occur between related host species and often rely on the pathogen evolving adaptations that increase their fitness in the novel host species. To investigate genetic changes in novel hosts, we experimentally evolved replicate lineages of an RNA virus (Drosophila C Virus) in 19 different species of Drosophilidae and deep sequenced the viral genomes. We found a strong pattern of parallel evolution, where viral lineages from the same host were genetically more similar to each other than to lineages from other host species...
April 2018: PLoS Pathogens
Anna A Schönherz, Roald Forsberg, Bernt Guldbrandtsen, Albert J Buitenhuis, Katja Einer-Jensen
Viral haemorrhagic septicaemia virus (VHSV), a rhabdovirus infecting teleost fish, has repeatedly crossed the boundary from marine fish species to freshwater cultured rainbow trout. These naturally replicated cross-species transmission events permit the study of general and repeatable evolutionary events occurring in connection with viral emergence into a novel host species.The purpose of this study was to investigate adaptive molecular evolution of the VHSV glycoprotein, one of the key virus proteins involved in viral emergence, following emergence from marine species into freshwater cultured rainbow trout...
April 11, 2018: Journal of Virology
Junna Kawasaki, Kazuo Nishigaki
An endogenous retrovirus (ERV) is a remnant of an ancient retroviral infection in the host genome. Although most ERVs have lost their viral productivity, a few ERVs retain their replication capacity. In addition, partially inactivated ERVs can present a potential risk to the host via their encoded virulence factors or the generation of novel viruses by viral recombination. ERVs can also eventually acquire a biological function, and this ability has been a driving force of host evolution. Therefore, the presence of an ERV can be harmful or beneficial to the host...
April 6, 2018: Viruses
Xing-Ye Wang, Cheng-Jie Ji, Xue Zhang, De-Peng Xu, De-Li Zhang
From September 2015 to May 2016, epidemic outbreaks of a diarrheal disease caused severe economic losses to the swine industry in northwest China. Typical clinical symptoms of the disease included severe diarrhea, vomiting, dehydration and death. In order to identify the pathogen, 27 intestinal samples were collected from dead piglets in Shaanxi, Gansu and Qinghai provinces and from Ningxia Hui Autonomous Region. All samples were tested using RT-PCR to detect rotavirus (RV), porcine epidemic diarrhea virus (PEDV) and transmissible gastroenteritis virus (TGEV)...
April 3, 2018: Infection, Genetics and Evolution
Isabel Pagani, Andrea Di Pietro, Alexandra Oteiza, Michela Ghitti, Nadir Mechti, Nadia Naffakh, Elisa Vicenzi
Influenza A viruses (IAVs) can cause zoonotic infections with pandemic potential when most of the human population is immunologically naive. After a pandemic, IAVs evolve to become seasonal in the human host by acquiring adaptive mutations. We have previously reported that the interferon (IFN)-inducible tripartite motif 22 (TRIM22) protein restricts the replication of seasonal IAVs by direct interaction with the viral nucleoprotein (NP), leading to its polyubiquitination and proteasomal degradation. Here we show that, in contrast to seasonal H1N1 IAVs, the 2009 pandemic H1N1 strain as well as H1N1 strains from the 1930s are resistant to TRIM22 restriction...
April 25, 2018: MSphere
Hervé Seligmann
Genetic codes mainly evolve by reassigning punctuation codons, starts and stops. Previous analyses assuming that undefined amino acids translate stops showed greater divergence between nuclear and mitochondrial genetic codes. Here, three independent methods converge on which amino acids translated stops at split between nuclear and mitochondrial genetic codes: (a) alignment-free genetic code comparisons inserting different amino acids at stops; (b) alignment-based blast analyses of hypothetical peptides translated from non-coding mitochondrial sequences, inserting different amino acids at stops; (c) biases in amino acid insertions at stops in proteomic data...
April 2, 2018: Bio Systems
Jiayi Wang, Nadine M Shaban, Allison M Land, William L Brown, Reuben S Harris
Several members of the APOBEC3 DNA cytosine deaminase family can potently inhibit Vif-deficient HIV-1 by catalyzing cytosine deamination in viral cDNA and impeding reverse transcription. HIV-1 counteracts restriction with the virally encoded Vif protein, which targets relevant APOBEC3 proteins for proteasomal degradation. HIV-1 Vif is optimized for degrading the restrictive human APOBEC3 repertoire and, in general, lentiviral Vif proteins specifically target the restricting APOBEC3 enzymes of each host species...
April 4, 2018: Journal of Virology
Yong-Chao Li, Jian-Guo Shen, Guo-Huan Zhao, Qin Yao, Wei-Min Li
We report the recovery of a 7068-nt viral sequence from the "viral fossils" embedded in the genome of Alhagi sparsifolia, a typical desert plant. Although the full viral genome remains to be completed, the putative genome structure, the deduced amino acids and phylogenetic analysis unambiguously demonstrate that this viral sequence represents a novel species of the genus Badnavirus. The putative virus is tentatively termed Alhagi bacilliform virus (ABV). Southern blotting and inverse polymerase chain reaction (PCR) data indicate that the ABV-related sequence is integrated into the A...
2018: Journal of Zhejiang University. Science. B
Rafaela S Fontenele, Rayane A Abreu, Natalia S Lamas, Dione M T Alves-Freitas, Andreza H Vidal, Raul R Poppiel, Fernando L Melo, Cristiano Lacorte, Darren P Martin, Magnolia A Campos, Arvind Varsani, Simone G Ribeiro
Brazil is one of the major passion fruit producers worldwide. Viral diseases are among the most important constraints for passion fruit production. Here we identify and characterize a new passion fruit infecting-virus belonging to the family Geminiviridae : passion fruit chlorotic mottle virus (PCMoV). PCMoV is a divergent geminivirus unlike previously characterized passion fruit-infecting geminiviruses that belonged to the genus Begomovirus . Among the presently known geminiviruses, it is most closely related to, and shares ~62% genome-wide identity with citrus chlorotic dwarf associated virus (CCDaV) and camelia chlorotic dwarf associated virus (CaCDaV)...
April 2, 2018: Viruses
Ornpreya Suptawiwat, Alita Kongchanagul, Chompunuch Boonarkart, Prasert Auewarakul
It was previously shown that the seasonal H1N1 influenza virus antigenic drift occurred at a slower rate than the seasonal H3N2 virus during the first decade of the 21 t h century. It was hypothesized that the slower antigenic evolution led to a decrease in average ages of infection, which in turn resulted in lower level of global viral circulation. It is unclear what caused the difference between the two viruses, but a plausible explanation may be related to the fact that the H1N1 virus had been in human population for much longer than the H3N2 virus...
March 30, 2018: Virus Research
Diego Forni, Chiara Pontremoli, Uberto Pozzoli, Mario Clerici, Rachele Cagliani, Manuela Sironi
The Mammarenavirus genus includes several pathogenic species of rodent-borne viruses. Old World (OW) mammarenaviruses infect rodents in the Murinae subfamily and are mainly transmitted in Africa and Asia; New World (NW) mammarenaviruses are found in rodents of the Cricetidae subfamily in the Americas. We applied a selection-informed method to estimate that OW and NW mammarenaviruses diverged less than ∼45,000 years ago (ya). By incorporating phylogeographic inference, we show that NW mammarenaviruses emerged in the Latin America-Caribbean region ∼41,400-3,300 ya, whereas OW mammarenaviruses originated ∼23,100-1,880 ya, most likely in Southern Africa...
March 1, 2018: Genome Biology and Evolution
Patrique Praest, A Manuel Liaci, Friedrich Förster, Emmanuel J H J Wiertz
Several hundred million years of co-evolution of vertebrates and invading pathogens have shaped the adaptive immune system to fight back the unwanted invaders through highly sophisticated defense mechanisms. Herpesviruses manage to dodge this immune response by hampering one of the central hinges of human adaptive immunity, the major histocompatibility complex (MHC) class I antigen presentation pathway. One of the bottlenecks of this pathway is the loading of pathogen-derived peptides onto MHC-I molecules in the endoplasmic reticulum (ER)...
March 29, 2018: Molecular Immunology
Jing Li, Ting Zhang, Kun Cai, Yongzhogn Jiang, Xuhua Guan, Jianbo Zhan, Wenjing Zou, Zhaohui Yang, Xuesen Xing, Yang Wu, Yi Song, Xuejie Yu, Junqiang Xu
Norovirus (NoV) is a major pathogenic agent of human acute viral gastroenteritis that occurs worldwide. In March 2017, a series of acute NoV-associated gastroenteritis outbreaks occurred in Hubei Province in central China. Here, we sought to better understand the main genotypes and potential evolutionary advantages of circulating NoV strains underlying these outbreaks. During the outbreak, 111 fecal swabs and stool samples were collected from outpatients with acute NoV-associated gastroenteritis in Hubei Province...
March 28, 2018: Virus Research
Elnaz Shadabi, Binhua Liang, Francis A Plummer, Ma Luo
BACKGROUND: Human immunodeficiency virus-1 (HIV-1) mutates rapidly to escape host immune pressure. This results in the generation of positively selected mutations (PSM) throughout the viral genome. Escape mutations in Nef, one of the accessory proteins of HIV-1, which plays an important role in viral pathogenicity have previously been identified in several large cohort studies, but the evolution of PSMs overtime in various HIV-1 subtypes remains unknown. METHODS: 161 clade A1, 3093 clade B, 647 clade C and 115 clade D HIV-1 nef sequences were obtained from the HIV Database of Los Alamos National Laboratory and aligned using MEGA 6...
March 30, 2018: Current HIV Research
Myriam Dao, Adrien Pécriaux, Thomas Bessede, Antoine Dürrbach, Charlotte Mussini, Catherine Guettier, Sophie Ferlicot
BK polyomavirus (BKV) nephropathy is a major concern in renal transplantation. Its main consequence is graft loss, which occurs in more than 50% of the cases. De novo renal cell carcinoma in renal allograft is a very rare event. Most of these tumors are papillary or clear cell carcinomas. We report herein the first case of collecting duct carcinoma of the renal allograft in a kidney-pancreas allograft adult recipient. Collecting duct carcinoma occurs long after the cure of a BKV nephropathy. At this time, BKV viremia and viruria were negative as well as the immunostaining for SV40 in the non-tumor kidney...
March 13, 2018: Oncotarget
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