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Influenza AND phylogenetic AND NS1

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https://www.readbyqxmd.com/read/29331671/the-molecular-characteristics-of-avian-influenza-viruses-h9n2-derived-from-air-samples-in-live-poultry-markets
#1
Yanheng Wu, Jinsi Lin, Shuhuan Yang, Ying Xie, Man Wang, Xueqin Chen, Yayang Zhu, Le Luo, Wuyang Shi
OBJECTIVE: To study the molecular characteristics of H9N2-subtype avian influenza viruses (AIVs) isolated from air samples collected in live poultry markets (LPMs) and explore their sequence identities with AIVs that caused human infection. METHODS: Weekly surveillance of H9N2-subtype AIVs in the air of LPMs was conducted from 2015 to 2016. H9-positive samples were isolated from chicken embryos. Whole genome sequences of the isolated AIVs were obtained through high-throughput sequencing...
June 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29297852/predominance-of-influenza-a-h3n2-viruses-during-the-2016-2017-season-in-bulgaria
#2
Neli Korsun, Svetla Angelova, Ivelina Trifonova, Iren Tzotcheva, Sirma Mileva, Silvia Voleva, Irina Georgieva, Penka Perenovska
PURPOSE: Influenza viruses are characterised by high variability, which makes them able to cause annual epidemics. The aim of this study is to determine the antigenic and genetic characteristics of influenza viruses circulating in Bulgaria during the 2016/2017 season. METHODOLOGY: The detection and typing/subtyping of influenza viruses were performed using real time RT-PCR. Results of antigenic characterisation, phylogenetic and amino acid sequence analyses of representative influenza strains are presented herein...
February 2018: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/27489273/role-of-the-b-allele-of-influenza-a-virus-segment-8-in-setting-mammalian-host-range-and-pathogenicity
#3
Matthew L Turnbull, Helen M Wise, Marlynne Q Nicol, Nikki Smith, Rebecca L Dunfee, Philippa M Beard, Brett W Jagger, Yvonne Ligertwood, Gareth R Hardisty, Haixia Xiao, Donald J Benton, Alice M Coburn, Joao A Paulo, Steven P Gygi, John W McCauley, Jeffery K Taubenberger, Samantha J Lycett, Michael P Weekes, Bernadette M Dutia, Paul Digard
UNLABELLED: Two alleles of segment 8 (NS) circulate in nonchiropteran influenza A viruses. The A allele is found in avian and mammalian viruses, but the B allele is viewed as being almost exclusively found in avian viruses. This might reflect the fact that one or both of its encoded proteins (NS1 and NEP) are maladapted for replication in mammalian hosts. To test this, a number of clade A and B avian virus-derived NS segments were introduced into human H1N1 and H3N2 viruses. In no case was the peak virus titer substantially reduced following infection of various mammalian cell types...
October 15, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27369428/genetic-characterization-of-highly-pathogenic-avian-influenza-h5n1-viruses-isolated-from-naturally-infected-pigeons-in-egypt
#4
Emad Mohamed Elgendy, Yohei Watanabe, Tomo Daidoji, Yasuha Arai, Kazuyoshi Ikuta, Madiha Salah Ibrahim, Takaaki Nakaya
Avian influenza viruses impose serious public health burdens with significant mortality and morbidity not only in poultry but also in humans. While poultry susceptibility to avian influenza virus infection is well characterized, pigeons have been thought to have low susceptibility to these viruses. However, recent studies reported natural pigeon infections with highly pathogenic avian influenza H5N1 viruses. In Egypt, which is one of the H5N1 endemic areas for birds, pigeons are raised in towers built on farms in backyards and on house roofs, providing a potential risk for virus transmission from pigeons to humans...
December 2016: Virus Genes
https://www.readbyqxmd.com/read/27169600/genomic-characterization-of-influenza-a-h7n9-viruses-isolated-in-shenzhen-southern-china-during-the-second-epidemic-wave
#5
Shisong Fang, Xin Wang, Fangyuan Dong, Tao Jin, Guang Liu, Xing Lu, Bo Peng, Weihua Wu, Hui Liu, Dongfeng Kong, Xiujuan Tang, Yanmin Qin, Shujiang Mei, Xu Xie, Jianfan He, Hanwu Ma, Renli Zhang, Jinquan Cheng
There were three epidemic waves of human infection with avian influenza A (H7N9) virus in 2013-2014. While many analyses of the genomic origin, evolution, and molecular characteristics of the influenza A (H7N9) virus have been performed using sequences from the first epidemic wave, genomic characterization of the virus from the second epidemic wave has been comparatively less reported. In this study, an in-depth analysis was performed with respect to the genomic characteristics of 11 H7N9 virus strains isolated from confirmed cases and four H7N9 virus strains isolated from environmental samples in Shenzhen during the second epidemic wave...
August 2016: Archives of Virology
https://www.readbyqxmd.com/read/26711034/ns-gene-based-phylogenetic-analysis-of-equine-influenza-viruses-isolated-in-poland
#6
Malgorzata Kwasnik, Ilona M Gora, Jerzy Rola, Jan F Zmudzinski, Wojciech Rozek
The phylogenetic analysis of influenza virus is based mainly on the variable hemagglutinin or neuraminidase genes. However, some discrete evolutionary trends might be revealed when more conservative genes are considered. We compared all available in GenBank database full length NS sequences of equine influenza virus including Polish isolates. Four nucleotides at positions A202, A237, T672 and A714 and three amino acids at positions H59, K71 and S216 which are also present in A/eq/Pulawy/2006 and A/eq/Pulawy/2008 may be discriminating for the Florida sublineage...
2016: Veterinary Microbiology
https://www.readbyqxmd.com/read/25962145/pathogenicity-of-highly-pathogenic-avian-influenza-virus-h5n1-in-naturally-infected-poultry-in-egypt
#7
Ibrahim Thabet Hagag, Shimaa M G Mansour, Zerui Zhang, Ahmed A H Ali, El-Bakry M Ismaiel, Ali A Salama, Carol J Cardona, James Collins, Zheng Xing
Highly pathogenic avian influenza virus (HPAIV) H5N1 has been endemic in Egypt since 2006, and there is increasing concern for its potential to become highly transmissible among humans. Infection by HPAIV H5N1 has been described in experimentally challenged birds. However, the pathogenicity of the H5N1 isolated in Egypt has never been reported in naturally infected chickens and ducks. Here we report a 2013 outbreak of HPAIV H5N1 in commercial poultry farms and backyards in Sharkia Province, Egypt. The main symptoms were ecchymosis on the shanks and feet, cyanosis of the comb and wattles, subcutaneous edema of the head and neck for chickens, and nervous signs (torticollis) for ducks...
2015: PloS One
https://www.readbyqxmd.com/read/25435177/genetic-characterisation-of-influenza-b-viruses-detected-in-singapore-2004-to-2009
#8
Muhammad Raihan Jumat, Richard J Sugrue, Boon-Huan Tan
BACKGROUND: Influenza B viruses are classified into two main lineages: Yamagata-like and Victoria-like, which differ antigenically and phylogenetically. To understand the evolution of influenza B viruses in South East Asia as well as to determine the vaccine efficacy, we genetically characterised gene segments 4, 6 and 8 from non-tissue culture adapted influenza B viruses detected in Singapore from 2004 to 2009. METHODS: vRNA were extracted from the nasopharyngeal swabs or nasal washes of SAF servicemen displaying febrile and respiratory symptoms, and subjected to PCR assay to test for the presence of influenza B virus...
2014: BMC Research Notes
https://www.readbyqxmd.com/read/25210166/accumulation-of-human-adapting-mutations-during-circulation-of-a-h1n1-pdm09-influenza-virus-in-humans-in-the-united-kingdom
#9
Ruth A Elderfield, Simon J Watson, Alexandra Godlee, Walt E Adamson, Catherine I Thompson, Jake Dunning, Mirian Fernandez-Alonso, Deena Blumenkrantz, Tracy Hussell, Maria Zambon, Peter Openshaw, Paul Kellam, Wendy S Barclay
UNLABELLED: The influenza pandemic that emerged in 2009 provided an unprecedented opportunity to study adaptation of a virus recently acquired from an animal source during human transmission. In the United Kingdom, the novel virus spread in three temporally distinct waves between 2009 and 2011. Phylogenetic analysis of complete viral genomes showed that mutations accumulated over time. Second- and third-wave viruses replicated more rapidly in human airway epithelial (HAE) cells than did the first-wave virus...
November 2014: Journal of Virology
https://www.readbyqxmd.com/read/25100840/influenza-a-virus-acquires-enhanced-pathogenicity-and-transmissibility-after-serial-passages-in-swine
#10
Kai Wei, Honglei Sun, Zhenhong Sun, Yipeng Sun, Weili Kong, Juan Pu, Guangpeng Ma, Yanbo Yin, Hanchun Yang, Xin Guo, Kin-Chow Chang, Jinhua Liu
Genetic and phylogenetic analyses suggest that the pandemic H1N1/2009 virus was derived from well-established swine influenza lineages; however, there is no convincing evidence that the pandemic virus was generated from a direct precursor in pigs. Furthermore, the evolutionary dynamics of influenza virus in pigs have not been well documented. Here, we subjected a recombinant virus (rH1N1) with the same constellation makeup as the pandemic H1N1/2009 virus to nine serial passages in pigs. The severity of infection sequentially increased with each passage...
October 2014: Journal of Virology
https://www.readbyqxmd.com/read/25003973/genetic-dynamic-analysis-of-the-influenza-a-h5n1-ns1-gene-in-china
#11
Kaifa Wei, Yanhui Chen, Yina Lin, Yutian Pan
The direct precursors of the A/Goose/Guangdong/1/1996 (GS/GD) virus lineage and its reassortants have been established geographically and ecologically. To investigate the variation and evolutionary dynamics of H5N1 viruses, whole-genome viral sequences (n = 164) were retrieved from the NCBI Influenza Virus Resource. Here, we present phylogenetic evidence for intrasubtype reassortments among H5N1 viruses isolated from China during 1996-2012. On the basis of phylogenetic analysis, we identified four major groups and further classified the reassortant viruses into three subgroups...
2014: PloS One
https://www.readbyqxmd.com/read/24758106/characterization-of-a-low-pathogenic-avian-influenza-h5n2-virus-isolated-from-a-turkey-breeder-flock-in-manitoba-canada
#12
Y Berhane, T Joseph, H Kehler, T Hisanaga, C Embury-Hyatt, S Diederich, K Hooper McGreevy, K Handel, C Cottam-Birt, J Pasick
In November 2010, an outbreak of avian influenza (AI) due to the H5N2 subtype virus occurred in a turkey breeder farm in northern Manitoba, Canada. The only clinical signs observed were depression, decrease in food consumption, and loss of egg production. The hemagglutinin (HA) cleavage (HA(0)) site of the isolated H5N2 virus was PQRETR/GLF, consistent with low pathogenic AI viruses. The intravenous pathogenicity index of this virus was zero. Whole-genome sequencing of two isolates that originated from two different barns was performed, and both isolates had 100% identical protein sequence in PB2, HA, NP, M1, M2, NS1, and NS2...
March 2014: Avian Diseases
https://www.readbyqxmd.com/read/24574395/an-unbiased-genetic-screen-reveals-the-polygenic-nature-of-the-influenza-virus-anti-interferon-response
#13
Maite Pérez-Cidoncha, Marian J Killip, Juan C Oliveros, Víctor J Asensio, Yolanda Fernández, José A Bengoechea, Richard E Randall, Juan Ortín
UNLABELLED: Influenza A viruses counteract the cellular innate immune response at several steps, including blocking RIG I-dependent activation of interferon (IFN) transcription, interferon (IFN)-dependent upregulation of IFN-stimulated genes (ISGs), and the activity of various ISG products; the multifunctional NS1 protein is responsible for most of these activities. To determine the importance of other viral genes in the interplay between the virus and the host IFN response, we characterized populations and selected mutants of wild-type viruses selected by passage through non-IFN-responsive cells...
May 2014: Journal of Virology
https://www.readbyqxmd.com/read/24415946/intrasubtype-reassortments-cause-adaptive-amino-acid-replacements-in-h3n2-influenza-genes
#14
Alexey D Neverov, Ksenia V Lezhnina, Alexey S Kondrashov, Georgii A Bazykin
Reassortments and point mutations are two major contributors to diversity of Influenza A virus; however, the link between these two processes is unclear. It has been suggested that reassortments provoke a temporary increase in the rate of amino acid changes as the viral proteins adapt to new genetic environment, but this phenomenon has not been studied systematically. Here, we use a phylogenetic approach to infer the reassortment events between the 8 segments of influenza A H3N2 virus since its emergence in humans in 1968...
January 2014: PLoS Genetics
https://www.readbyqxmd.com/read/24161299/molecular-phylogeny-and-evolutionary-dynamics-of-influenza-a-nonstructural-ns-gene
#15
Jianpeng Xu, Haizhen A Zhong, Alex Madrahimov, Tomáš Helikar, Guoqing Lu
While the nonstructural gene (NS) of the influenza A virus plays a crucial role in viral virulence and replication, the complete understanding of its molecular phylogeny and evolutionary dynamics remains lacking. In this study, the phylogenetic analysis of 7581 NS sequences revealed ten distinct lineages within alleles A and B: three host-specific (human, classical swine and equine), two reassortment-originated (A(H1N1)pdm09 and triple reassortment swine), one transmission-originated (Eurasian swine), and two geographically isolated avian (Eurasian/Oceanian and North American) for allele A and two geographically isolated avian (Eurasian/Oceanian and North American) for allele B...
March 2014: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/24016442/-genetic-evolution-of-non-structural-gene-among-avian-influenza-h5n1-viruses-isolated-from-the-boundary-of-yunnan-province
#16
Xue Xiao, Wen-dong Zhang, Bo-fang Duan, Huan-yun Zhao, Qing-liang Liu, Ting-song Hu, Wei Qiu, Zi-liang Feng, Ying Zheng, Quan-shui Fan, Ying-guo Zhang, Fu-qiang Zhang
OBJECTIVE: To elucidate the characteristics of variation and the genetic evolution of non-structural protein (NS1, NS2) genes related to avian influenza subtype H5N1 viruses isolated from the boundary region of Yunnan province. METHODS: Swab samples were collected from foreign poultry and wild birds in the boundary regions of Yunnan province and screened by H5/N1 subtype-specific multiplex RT-PCR. The NS segment of H5N1 virus from the positive samples were amplified by RT-PCR and cloned into pMD18-T vectors for sequencing...
May 2013: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
https://www.readbyqxmd.com/read/23959028/the-non-structural-ns-gene-segment-of-h9n2-influenza-virus-isolated-from-backyard-poultry-in-pakistan-reveals-strong-genetic-and-functional-similarities-to-the-ns-gene-of-highly-pathogenic-h5n1
#17
Muhammad Munir, Siamak Zohari, Munir Iqbal, Muhammad Abbas, Daniel Roberto Perez, Mikael Berg
Apart from natural reassortment, co-circulation of different avian influenza virus strains in poultry populations can lead to generation of novel variants and reassortant viruses. In this report, we studied the genetics and functions of a reassorted non-structural gene (NS) of H9N2 influenza virus collected from back yard poultry (BYP) flock. Phylogenetic reconstruction based on hemagglutinin and neuraminidase genes indicates that an isolate from BYP belongs to H9N2. However, the NS gene-segment of this isolate cluster into genotype Z, clade 2...
October 1, 2013: Virulence
https://www.readbyqxmd.com/read/23667580/protein-clustering-and-rna-phylogenetic-reconstruction-of-the-influenza-a-corrected-virus-ns1-protein-allow-an-update-in-classification-and-identification-of-motif-conservation
#18
Edgar E Sevilla-Reyes, David A Chavaro-Pérez, Elvira Piten-Isidro, Luis H Gutiérrez-González, Teresa Santos-Mendoza
The non-structural protein 1 (NS1) of influenza A virus (IAV), coded by its third most diverse gene, interacts with multiple molecules within infected cells. NS1 is involved in host immune response regulation and is a potential contributor to the virus host range. Early phylogenetic analyses using 50 sequences led to the classification of NS1 gene variants into groups (alleles) A and B. We reanalyzed NS1 diversity using 14,716 complete NS IAV sequences, downloaded from public databases, without host bias. Removal of sequence redundancy and further structured clustering at 96...
2013: PloS One
https://www.readbyqxmd.com/read/23408626/synergistic-effect-of-the-pdz-and-p85%C3%AE-binding-domains-of-the-ns1-protein-on-virulence-of-an-avian-h5n1-influenza-a-virus
#19
Shufang Fan, Catherine A Macken, Chengjun Li, Makoto Ozawa, Hideo Goto, N F N Iswahyudi, Chairul A Nidom, Hualan Chen, Gabriele Neumann, Yoshihiro Kawaoka
The influenza A virus NS1 protein affects virulence through several mechanisms, including the host's innate immune response and various signaling pathways. Highly pathogenic avian influenza (HPAI) viruses of the H5N1 subtype continue to evolve through reassortment and mutations. Our recent phylogenetic analysis identified a group of HPAI H5N1 viruses with two characteristic mutations in NS1: the avian virus-type PDZ domain-binding motif ESEV (which affects virulence) was replaced with ESKV, and NS1-138F (which is highly conserved among all influenza A viruses and may affect the activation of the phosphatidylinositol 3-kinase [PI3K]/Akt signaling pathway) was replaced with NS1-138Y...
May 2013: Journal of Virology
https://www.readbyqxmd.com/read/23055004/molecular-characterization-of-avian-like-h1n1-swine-influenza-a-viruses-isolated-in-eastern-china-2011
#20
Xian Qi, Yuning Pan, Yuanfang Qin, Rongqiang Zu, Fengyang Tang, Minghao Zhou, Hua Wang, Yongchun Song
Currently, three predominant subtypes of influenza virus are prevalent in pig populations worldwide: H1N1, H3N2, and H1N2. European avian-like H1N1 viruses, which were initially detected in European pig populations in 1979, have been circulating in pigs in eastern China since 2007. In this study, six influenza A viruses were isolated from 60 swine lung samples collected from January to April 2011 in eastern China. Based on whole genome sequencing, molecular characteristics of two isolates were determined. Phylogenetic analysis showed the eight genes of the two isolates were closely related to those of the avian-like H1N1 viruses circulating in pig populations, especially similar to those found in China...
October 2012: Virologica Sinica
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