Phylogeography of the spring and fall waves of the H1N1/09 pandemic influenza virus in the United States.

Abstract:

:Spatial variation in the epidemiological patterns of successive waves of pandemic influenza virus in humans has been documented throughout the 20th century but never understood at a molecular level. However, the unprecedented intensity of sampling and whole-genome sequencing of the H1N1/09 pandemic virus now makes such an approach possible. To determine whether the spring and fall waves of the H1N1/09 influenza pandemic were associated with different epidemiological patterns, we undertook a large-scale phylogeographic analysis of viruses sampled from three localities in the United States. Analysis of genomic and epidemiological data reveals distinct spatial heterogeneities associated with the first pandemic wave, March to July 2009, in Houston, TX, Milwaukee, WI, and New York State. In Houston, no specific H1N1/09 viral lineage dominated during the spring of 2009, a period when little epidemiological activity was observed in Texas. In contrast, major pandemic outbreaks occurred at this time in Milwaukee and New York State, each dominated by a different viral lineage and resulting from strong founder effects. During the second pandemic wave, beginning in August 2009, all three U.S. localities were dominated by a single viral lineage, that which had been dominant in New York during wave 1. Hence, during this second phase of the pandemic, extensive viral migration and mixing diffused the spatially defined population structure that had characterized wave 1, amplifying the one viral lineage that had dominated early on in one of the world's largest international travel centers.

journal_name

J Virol

journal_title

Journal of virology

authors

Nelson MI,Tan Y,Ghedin E,Wentworth DE,St George K,Edelman L,Beck ET,Fan J,Lam TT,Kumar S,Spiro DJ,Simonsen L,Viboud C,Holmes EC,Henrickson KJ,Musser JM

doi

10.1128/JVI.01762-10

subject

Has Abstract

pub_date

2011-01-01 00:00:00

pages

828-34

issue

2

eissn

0022-538X

issn

1098-5514

pii

JVI.01762-10

journal_volume

85

pub_type

杂志文章
  • Herpesvirus proteins: induction of nucleoside phosphotransferase activity after herpes simplex virus infection.

    abstract::After herpes simplex virus infection of hamster kidney cells there is an induction of nucleoside phosphotransferase activity which can utilize AMP as phosphate donor. The activity is immunologically specific for the infected cell and is induced concomitantly with the virus-coded pyrimidine deoxynucleoside kinase activ...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.17.3.1056-1059.1976

    authors: Jamieson AT,Hay J,Subak-Sharpe JH

    更新日期:1976-03-01 00:00:00

  • Suppression of transcription factor early growth response 1 reduces herpes simplex virus 1-induced corneal disease in mice.

    abstract::Herpes simplex virus 1 replication initiates angiogenesis and inflammation in the cornea. This can result in herpetic stromal keratitis (HSK), which is a leading cause of infection-induced corneal blindness. Host cellular factors mediate the progression of HSK, but little is known about these cellular factors and thei...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.00505-12

    authors: Yao HW,Chen SH,Li C,Tung YY,Chen SH

    更新日期:2012-08-01 00:00:00

  • Mapping a neutralizing epitope onto the capsid of adeno-associated virus serotype 8.

    abstract::Adeno-associated viruses (AAVs) are small single-stranded DNA viruses that can package and deliver nongenomic DNA for therapeutic gene delivery. AAV8, a liver-tropic vector, has shown great promise for the treatment of hemophilia A and B. However, as with other AAV vectors, host anti-capsid immune responses are a dete...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.00218-12

    authors: Gurda BL,Raupp C,Popa-Wagner R,Naumer M,Olson NH,Ng R,McKenna R,Baker TS,Kleinschmidt JA,Agbandje-McKenna M

    更新日期:2012-08-01 00:00:00

  • High frequency of syncytium-inducing and CXCR4-tropic viruses among human immunodeficiency virus type 1 subtype C-infected patients receiving antiretroviral treatment.

    abstract::Human immunodeficiency virus type 1 (HIV-1) subtype C viruses have been found to almost exclusively use the chemokine receptor CCR5 as a coreceptor for entry, even in patients with advanced AIDS. We have characterized subtype C virus isolates from 28 patients from Harare, Zimbabwe, 20 of whom were receiving antiretrov...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/jvi.77.13.7682-7688.2003

    authors: Johnston ER,Zijenah LS,Mutetwa S,Kantor R,Kittinunvorakoon C,Katzenstein DA

    更新日期:2003-07-01 00:00:00

  • Interplay between PKCδ and Sp1 on histone deacetylase inhibitor-mediated Epstein-Barr virus reactivation.

    abstract::Epstein-Barr virus (EBV) undergoes latent and lytic replication cycles, and its reactivation from latency to lytic replication is initiated by expression of the two viral immediate-early transactivators, Zta and Rta. In vitro, reactivation of EBV can be induced by anti-immunoglobulin, tetradecanoyl phorbol acetate, an...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.01602-10

    authors: Tsai PF,Lin SJ,Weng PL,Tsai SC,Lin JH,Chou YC,Tsai CH

    更新日期:2011-03-01 00:00:00

  • The leader polypeptide of Theiler's murine encephalomyelitis virus is required for the assembly of virions in mouse L cells.

    abstract::Deletion of the entire leader polypeptide of the GDVII strain of Theiler's murine encephalomyelitis virus (TMEV) results in the production of an attenuated virus that grows in baby hamster kidney (BHK) cells but cannot grow at all in mouse L-929 cells. This study examined the reasons for the failure of dl-L, the GDVII...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/jvi.74.2.875-882.2000

    authors: Badshah C,Calenoff MA,Rundell K

    更新日期:2000-01-01 00:00:00

  • The secondary structure of the human immunodeficiency virus type 1 transcript modulates viral splicing and infectivity.

    abstract::Splicing of human immunodeficiency virus type 1 (HIV-1) exon 6D is regulated by the presence of a complex splicing regulatory element (SRE) sequence that interacts with the splicing factors hnRNP H and SC35. In this work, we show that, in the context of the wild-type viral sequence, hnRNP H acts as a repressor of exon...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.00721-08

    authors: Jablonski JA,Buratti E,Stuani C,Caputi M

    更新日期:2008-08-01 00:00:00

  • O-linked glycosylation of retroviral envelope gene products.

    abstract::Treatment of [3H]glucosamine-labeled Friend mink cell focus-forming virus (FrMCF) gp70 with excess peptide:N-glycanase F (PNGase F) resulted in removal of the expected seven N-linked oligosaccharide chains; however, approximately 10% of the glucosamine label was retained in the resulting 49,000-Mr (49K) product. For [...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.62.3.1016-1021.1988

    authors: Pinter A,Honnen WJ

    更新日期:1988-03-01 00:00:00

  • Homologous recombinational repair factors are recruited and loaded onto the viral DNA genome in Epstein-Barr virus replication compartments.

    abstract::Homologous recombination is an important biological process that facilitates genome rearrangement and repair of DNA double-strand breaks (DSBs). The induction of Epstein-Barr virus (EBV) lytic replication induces ataxia telangiectasia-mutated (ATM)-dependent DNA damage checkpoint signaling, leading to the clustering o...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.00049-09

    authors: Kudoh A,Iwahori S,Sato Y,Nakayama S,Isomura H,Murata T,Tsurumi T

    更新日期:2009-07-01 00:00:00

  • Proline-rich tandem repeats of antibody complementarity-determining regions bind and neutralize human immunodeficiency virus type 1 particles.

    abstract::The proline-rich tandem repeat domain of human mucin MUC1 forms an extended structure containing large repeating loops that are crested by a turn. We show that the repeating-loop structure of MUC1 can be replaced by an antibody complementarity-determining region loop of a human immunodeficiency virus type 1 (HIV-1)-sp...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.70.10.6557-6562.1996

    authors: Fontenot JD,Zacharopoulos VR,Phillips DM

    更新日期:1996-10-01 00:00:00

  • Effects of a temperature sensitivity mutation in the J1R protein component of a complex required for vaccinia virus assembly.

    abstract::Vaccinia virus J1R protein is required for virion morphogenesis (W. L. Chiu and W. Chang, J. Virol. 76:9575-9587, 2002). In this work, we further characterized the J1R protein of wild-type vaccinia virus and compared it with the protein encoded by the temperature-sensitive mutant virus Cts45. The mutant Cts45 was foun...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.79.13.8046-8056.2005

    authors: Chiu WL,Szajner P,Moss B,Chang W

    更新日期:2005-07-01 00:00:00

  • Inhibition of Japanese encephalitis virus infection by nitric oxide: antiviral effect of nitric oxide on RNA virus replication.

    abstract::The antiviral effects of nitric oxide (NO) on Japanese encephalitis virus (JEV), a member of the family Flaviviridae, were investigated in this study. In vitro, inhibition of replication of JEV in gamma interferon-activated RAW 264.7 murine macrophages was correlated to cellular NO production. When cocultured with inf...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.71.7.5227-5235.1997

    authors: Lin YL,Huang YL,Ma SH,Yeh CT,Chiou SY,Chen LK,Liao CL

    更新日期:1997-07-01 00:00:00

  • Virus-viroid interactions: Citrus Tristeza Virus enhances the accumulation of Citrus Dwarfing Viroid in Mexican lime via virus-encoded silencing suppressors.

    abstract::An assay to identify interactions between Citrus Dwarfing Viroid (CDVd) and Citrus Tristeza Virus (CTV) showed that viroid titer was enhanced by the coinfecting CTV in Mexican lime but not in etrog citron. Since CTV encodes three RNA silencing suppressors (RSSs), p23, p20 and p25, an assay using transgenic Mexican lim...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.02619-13

    authors: Serra P,Bani Hashemian SM,Fagoaga C,Romero J,Ruiz-Ruiz S,Gorris MT,Bertolini E,Duran-Vila N

    更新日期:2014-01-01 00:00:00

  • Immune-mediated thrombocytopenia in horses infected with equine infectious anemia virus.

    abstract::An adult horse infected with a virulent, cell culture-adapted strain of equine infectious anemia virus (EIAV) developed cyclical thrombocytopenia in which the nadir of platelet counts coincided with peak febrile responses. In order to investigate the mechanism of thrombocytopenia during acute febrile episodes, four ad...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.65.11.6242-6251.1991

    authors: Clabough DL,Gebhard D,Flaherty MT,Whetter LE,Perry ST,Coggins L,Fuller FJ

    更新日期:1991-11-01 00:00:00

  • Prophylactic alpha interferon treatment increases the therapeutic index of oncolytic vesicular stomatitis virus virotherapy for advanced hepatocellular carcinoma in immune-competent rats.

    abstract::Vesicular stomatitis virus (VSV) is a negative-strand RNA virus with intrinsic oncolytic specificity due to substantially attenuated antiviral responses in many tumors. We have recently reported that recombinant VSV vector can be used as an effective oncolytic agent to safely treat multifocal hepatocellular carcinoma ...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.79.21.13705-13713.2005

    authors: Shinozaki K,Ebert O,Suriawinata A,Thung SN,Woo SL

    更新日期:2005-11-01 00:00:00

  • Chromosomal localization of the Moloney sarcoma virus mouse cellular (c-mos) sequence.

    abstract::The Moloney sarcoma virus-specific onc gene, referred to as v-mos, was used as probe to hybridize to restricted DNAs from various mouse-Chinese hamster hybrid cell lines. These hybrid cells contain, in addition to all of the Chinese hamster chromosomes, various numbers (less than a full complement) of mouse chromosome...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.44.2.752-754.1982

    authors: Swan D,Oskarsson M,Keithley D,Ruddle FH,D'Eustachio P,Vande Woude GF

    更新日期:1982-11-01 00:00:00

  • Assembly Properties of Hepatitis B Virus Core Protein Mutants Correlate with Their Resistance to Assembly-Directed Antivirals.

    abstract::The hepatitis B virus (HBV) capsid or core protein (Cp) can self-assemble to form an icosahedral capsid. It is now being pursued as a target for small-molecule antivirals that enhance the rate and extent of its assembly to yield empty and/or aberrant capsids. These small molecules are thus called core protein alloster...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.01082-18

    authors: Ruan L,Hadden JA,Zlotnick A

    更新日期:2018-09-26 00:00:00

  • Dendritic cells transduced with an adenovirus vector encoding Epstein-Barr virus latent membrane protein 2B: a new modality for vaccination.

    abstract::Epstein-Barr virus (EBV) is a herpesvirus commonly associated with several malignancies, particularly in immunocompromised hosts. As a strategy for stimulating immunity against EBV for the treatment of EBV-associated tumors, we have genetically engineered dendritic cells (DC) to express EBV antigens, such as latent me...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.73.12.10416-10425.1999

    authors: Ranieri E,Herr W,Gambotto A,Olson W,Rowe D,Robbins PD,Kierstead LS,Watkins SC,Gesualdo L,Storkus WJ

    更新日期:1999-12-01 00:00:00

  • Protein synthesis in Newcastle disease virus-infected chicken embryo cells.

    abstract::A double-isotopic label difference analysis of polyacrylamide gels has been used to distinguish between cellular and viral protein accumulation in infected cells and to quantify the kinetics of accumulation of viral polypeptides. This technique, coupled with the determination of total radioactive amino acid incorporat...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.13.4.788-800.1974

    authors: Hightower LE,Bratt MA

    更新日期:1974-04-01 00:00:00

  • Role of the varicella-zoster virus gB cytoplasmic domain in gB transport and viral egress.

    abstract::To study the function of the varicella-zoster virus (VZV) gB cytoplasmic domain during viral infection, we produced a VZV recombinant virus that expresses a truncated form of gB lacking the C-terminal 36 amino acids of its cytoplasmic domain (VZV gB-36). VZV gB-36 replicates in noncomplementing cells and grows at a ra...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/jvi.76.2.591-599.2002

    authors: Heineman TC,Hall SL

    更新日期:2002-01-01 00:00:00

  • The Genome of a Tortoise Herpesvirus (Testudinid Herpesvirus 3) Has a Novel Structure and Contains a Large Region That Is Not Required for Replication In Vitro or Virulence In Vivo.

    abstract:UNLABELLED:Testudinid herpesvirus 3 (TeHV-3) is the causative agent of a lethal disease affecting several tortoise species. The threat that this virus poses to endangered animals is focusing efforts on characterizing its properties, in order to enable the development of prophylactic methods. We have sequenced the genom...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.01794-15

    authors: Gandar F,Wilkie GS,Gatherer D,Kerr K,Marlier D,Diez M,Marschang RE,Mast J,Dewals BG,Davison AJ,Vanderplasschen AF

    更新日期:2015-11-01 00:00:00

  • Disulfide bond configuration of human cytomegalovirus glycoprotein B.

    abstract::Glycoprotein B (gB) is the most highly conserved of the envelope glycoproteins of human herpesviruses. The gB protein of human cytomegalovirus (CMV) serves multiple roles in the life cycle of the virus. To investigate structural properties of gB that give rise to its function, we sought to determine the disulfide bond...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/jvi.76.12.6073-6082.2002

    authors: Lopper M,Compton T

    更新日期:2002-06-01 00:00:00

  • Sequences between the enhancer and promoter in the long terminal repeat affect murine leukemia virus pathogenicity and replication in the thymus.

    abstract::We previously showed that the 93-bp region between the enhancer and promoter (named DEN for downstream of enhancer) of the long terminal repeat (LTR) of the MCF13 murine leukemia virus is an important determinant of the ability of this virus to induce thymic lymphoma. In this study we observed that DEN plays a role in...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.73.6.4890-4898.1999

    authors: Yoshimura FK,Wang T,Cankovic M

    更新日期:1999-06-01 00:00:00

  • Functional domains of delta antigens and viral RNA required for RNA packaging of hepatitis delta virus.

    abstract::The functions of delta antigens (HDAgs) in the morphogenesis of hepatitis delta virus (HDV) have been studied previously. The C terminus of large HDAg has been shown to complex with the small surface antigen (HBsAg) of helper hepatitis B virus, whereas the assembly of small HDAg requires interaction with the N terminu...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.69.4.2508-2514.1995

    authors: Chang MF,Chen CH,Lin SL,Chen CJ,Chang SC

    更新日期:1995-04-01 00:00:00

  • The S RNA segment of lymphocytic choriomeningitis virus codes for the nucleoprotein and glycoproteins 1 and 2.

    abstract::The lymphocytic choriomeningitis virus (LCMV) genome consists of a large RNA segment and a small RNA segment. The three major structural proteins of this virus are an internal nucleoprotein and two surface glycoproteins. Intertypic reassortants between the Armstrong and WE strains of LCMV were made to map proteins enc...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.53.3.966-968.1985

    authors: Riviere Y,Ahmed R,Southern PJ,Buchmeier MJ,Dutko FJ,Oldstone MB

    更新日期:1985-03-01 00:00:00

  • Nucleocytoplasmic traffic disorder induced by cardioviruses.

    abstract::Some picornaviruses, for example, poliovirus, increase bidirectional permeability of the nuclear envelope and suppress active nucleocytoplasmic transport. These activities require the viral protease 2A(pro). Here, we studied nucleocytoplasmic traffic in cells infected with encephalomyocarditis virus (EMCV; a cardiovir...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.80.6.2705-2717.2006

    authors: Lidsky PV,Hato S,Bardina MV,Aminev AG,Palmenberg AC,Sheval EV,Polyakov VY,van Kuppeveld FJ,Agol VI

    更新日期:2006-03-01 00:00:00

  • Identification and Characterization of a Novel Broad-Spectrum Virus Entry Inhibitor.

    abstract:UNLABELLED:Virus entry into cells is a multistep process that often requires the subversion of subcellular machineries. A more complete understanding of these steps is necessary to develop new antiviral strategies. While studying the potential role of the actin network and one of its master regulators, the small GTPase...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.00103-16

    authors: Chou YY,Cuevas C,Carocci M,Stubbs SH,Ma M,Cureton DK,Chao L,Evesson F,He K,Yang PL,Whelan SP,Ross SR,Kirchhausen T,Gaudin R

    更新日期:2016-04-14 00:00:00

  • Presence of a retroviral encapsidation sequence in nonretroviral RNA increases the efficiency of formation of cDNA genes.

    abstract::We showed previously that retrovirus vector particles can encapsidate RNAs without retroviral cis-acting sequences, that such RNAs are reverse transcribed in infected target cells, and that the cDNA copies are inserted into the host genome resulting in cDNA genes (R. Dornburg and H. M. Temin, Mol. Cell. Biol. 8:2328-2...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.64.2.886-889.1990

    authors: Dornburg R,Temin HM

    更新日期:1990-02-01 00:00:00

  • Treatment with anti-LFA-1 delays the CD8+ cytotoxic-T-lymphocyte response and viral clearance in mice with primary respiratory syncytial virus infection.

    abstract::Cytotoxic T lymphocytes (CTLs) play an important role in the immune response against respiratory syncytial virus (RSV) infection. The cell surface molecule lymphocyte function-associated antigen 1 (LFA-1) is an important contributor to CTL activation, CTL-mediated direct cell lysis, and lymphocyte migration. In an att...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/jvi.78.6.3014-3023.2004

    authors: Rutigliano JA,Johnson TR,Hollinger TN,Fischer JE,Aung S,Graham BS

    更新日期:2004-03-01 00:00:00

  • Vectorial entry and release of hepatitis A virus in polarized human hepatocytes.

    abstract::Hepatitis A virus (HAV) is an enterically transmitted virus that replicates predominantly in hepatocytes within the liver before excretion via bile through feces. Hepatocytes are polarized epithelial cells, and it has been assumed that the virus load in bile results from direct export of HAV via the apical domain of p...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.00219-08

    authors: Snooks MJ,Bhat P,Mackenzie J,Counihan NA,Vaughan N,Anderson DA

    更新日期:2008-09-01 00:00:00