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Items: 1 to 50 of 80

1.

Evaluation of ultra-low input RNA sequencing for the study of human T cell transcriptome.

Wang J, Rieder SA, Wu J, Hayes S, Halpin RA, de Los Reyes M, Shrestha Y, Kolbeck R, Raja R.

Sci Rep. 2019 Jun 11;9(1):8445. doi: 10.1038/s41598-019-44902-z.

2.

Multiple Introductions and Antigenic Mismatch with Vaccines May Contribute to Increased Predominance of G12P[8] Rotaviruses in the United States.

Ogden KM, Tan Y, Akopov A, Stewart LS, McHenry R, Fonnesbeck CJ, Piya B, Carter MH, Fedorova NB, Halpin RA, Shilts MH, Edwards KM, Payne DC, Esona MD, Mijatovic-Rustempasic S, Chappell JD, Patton JT, Halasa NB, Das SR.

J Virol. 2018 Dec 10;93(1). pii: e01476-18. doi: 10.1128/JVI.01476-18. Print 2019 Jan 1.

3.

Differing epidemiological dynamics of Chikungunya virus in the Americas during the 2014-2015 epidemic.

Tan Y, Pickett BE, Shrivastava S, Gresh L, Balmaseda A, Amedeo P, Hu L, Puri V, Fedorova NB, Halpin RA, LaPointe MP, Cone MR, Heberlein-Larson L, Kramer LD, Ciota AT, Gordon A, Shabman RS, Das SR, Harris E.

PLoS Negl Trop Dis. 2018 Jul 30;12(7):e0006670. doi: 10.1371/journal.pntd.0006670. eCollection 2018 Jul.

4.

Whole-genome sequencing and analyses identify high genetic heterogeneity, diversity and endemicity of rotavirus genotype P[6] strains circulating in Africa.

Nyaga MM, Tan Y, Seheri ML, Halpin RA, Akopov A, Stucker KM, Fedorova NB, Shrivastava S, Duncan Steele A, Mwenda JM, Pickett BE, Das SR, Jeffrey Mphahlele M.

Infect Genet Evol. 2018 Sep;63:79-88. doi: 10.1016/j.meegid.2018.05.013. Epub 2018 May 18.

5.

Avian Influenza Viruses in Wild Birds: Virus Evolution in a Multihost Ecosystem.

Venkatesh D, Poen MJ, Bestebroer TM, Scheuer RD, Vuong O, Chkhaidze M, Machablishvili A, Mamuchadze J, Ninua L, Fedorova NB, Halpin RA, Lin X, Ransier A, Stockwell TB, Wentworth DE, Kriti D, Dutta J, van Bakel H, Puranik A, Slomka MJ, Essen S, Brown IH, Fouchier RAM, Lewis NS.

J Virol. 2018 Jul 17;92(15). pii: e00433-18. doi: 10.1128/JVI.00433-18. Print 2018 Aug 1.

6.

Large-Scale Complete-Genome Sequencing and Phylodynamic Analysis of Eastern Equine Encephalitis Virus Reveals Source-Sink Transmission Dynamics in the United States.

Tan Y, Lam TT, Heberlein-Larson LA, Smole SC, Auguste AJ, Hennigan S, Halpin RA, Fedorova N, Puri V, Stockwell TB, Shilts MH, Andreadis T, Armstrong PM, Tesh RB, Weaver SC, Unnasch TR, Ciota AT, Kramer LD, Das SR.

J Virol. 2018 May 29;92(12). pii: e00074-18. doi: 10.1128/JVI.00074-18. Print 2018 Jun 15.

7.

Poor Immunogenicity, Not Vaccine Strain Egg Adaptation, May Explain the Low H3N2 Influenza Vaccine Effectiveness in 2012-2013.

Cobey S, Gouma S, Parkhouse K, Chambers BS, Ertl HC, Schmader KE, Halpin RA, Lin X, Stockwell TB, Das SR, Landon E, Tesic V, Youngster I, Pinsky BA, Wentworth DE, Hensley SE, Grad YH.

Clin Infect Dis. 2018 Jul 18;67(3):327-333. doi: 10.1093/cid/ciy097.

8.

Nasopharyngeal Lactobacillus is associated with a reduced risk of childhood wheezing illnesses following acute respiratory syncytial virus infection in infancy.

Rosas-Salazar C, Shilts MH, Tovchigrechko A, Schobel S, Chappell JD, Larkin EK, Gebretsadik T, Halpin RA, Nelson KE, Moore ML, Anderson LJ, Peebles RS Jr, Das SR, Hartert TV.

J Allergy Clin Immunol. 2018 Nov;142(5):1447-1456.e9. doi: 10.1016/j.jaci.2017.10.049. Epub 2018 Jan 10.

9.

The transmission dynamics and diversity of human metapneumovirus in Peru.

Pollett S, Trovão NS, Tan Y, Eden JS, Halpin RA, Bera J, Das SR, Wentworth D, Ocaña V, Mendocilla SM, Álvarez C, Calisto ME, Garcia J, Halsey E, Ampuero JS, Nelson MI, Leguia M.

Influenza Other Respir Viruses. 2018 Jul;12(4):508-513. doi: 10.1111/irv.12537. Epub 2018 Mar 30.

10.

The emergence and evolution of influenza A (H1α) viruses in swine in Canada and the United States.

Nelson MI, Culhane MR, Trovão NS, Patnayak DP, Halpin RA, Lin X, Shilts MH, Das SR, Detmer SE.

J Gen Virol. 2017 Nov;98(11):2663-2675. doi: 10.1099/jgv.0.000924. Epub 2017 Oct 23.

11.

Multiplex Reverse Transcription-PCR for Simultaneous Surveillance of Influenza A and B Viruses.

Zhou B, Deng YM, Barnes JR, Sessions OM, Chou TW, Wilson M, Stark TJ, Volk M, Spirason N, Halpin RA, Kamaraj US, Ding T, Stockwell TB, Salvatore M, Ghedin E, Barr IG, Wentworth DE.

J Clin Microbiol. 2017 Dec;55(12):3492-3501. doi: 10.1128/JCM.00957-17. Epub 2017 Oct 4.

12.

Evolution and spread of Venezuelan equine encephalitis complex alphavirus in the Americas.

Forrester NL, Wertheim JO, Dugan VG, Auguste AJ, Lin D, Adams AP, Chen R, Gorchakov R, Leal G, Estrada-Franco JG, Pandya J, Halpin RA, Hari K, Jain R, Stockwell TB, Das SR, Wentworth DE, Smith MD, Kosakovsky Pond SL, Weaver SC.

PLoS Negl Trop Dis. 2017 Aug 3;11(8):e0005693. doi: 10.1371/journal.pntd.0005693. eCollection 2017 Aug.

13.

Reassortment of Influenza A Viruses in Wild Birds in Alaska before H5 Clade 2.3.4.4 Outbreaks.

Hill NJ, Hussein IT, Davis KR, Ma EJ, Spivey TJ, Ramey AM, Puryear WB, Das SR, Halpin RA, Lin X, Fedorova NB, Suarez DL, Boyce WM, Runstadler JA.

Emerg Infect Dis. 2017 Apr;23(4):654-657. doi: 10.3201/eid2304.161668.

14.

The effective rate of influenza reassortment is limited during human infection.

Sobel Leonard A, McClain MT, Smith GJ, Wentworth DE, Halpin RA, Lin X, Ransier A, Stockwell TB, Das SR, Gilbert AS, Lambkin-Williams R, Ginsburg GS, Woods CW, Koelle K, Illingworth CJ.

PLoS Pathog. 2017 Feb 7;13(2):e1006203. doi: 10.1371/journal.ppat.1006203. eCollection 2017 Feb.

15.

Differences in the Nasopharyngeal Microbiome During Acute Respiratory Tract Infection With Human Rhinovirus and Respiratory Syncytial Virus in Infancy.

Rosas-Salazar C, Shilts MH, Tovchigrechko A, Schobel S, Chappell JD, Larkin EK, Shankar J, Yooseph S, Nelson KE, Halpin RA, Moore ML, Anderson LJ, Peebles RS Jr, Das SR, Hartert TV.

J Infect Dis. 2016 Dec 15;214(12):1924-1928.

16.

Deep Sequencing of Influenza A Virus from a Human Challenge Study Reveals a Selective Bottleneck and Only Limited Intrahost Genetic Diversification.

Sobel Leonard A, McClain MT, Smith GJ, Wentworth DE, Halpin RA, Lin X, Ransier A, Stockwell TB, Das SR, Gilbert AS, Lambkin-Williams R, Ginsburg GS, Woods CW, Koelle K.

J Virol. 2016 Nov 28;90(24):11247-11258. Print 2016 Dec 15.

17.

Reversion of Cold-Adapted Live Attenuated Influenza Vaccine into a Pathogenic Virus.

Zhou B, Meliopoulos VA, Wang W, Lin X, Stucker KM, Halpin RA, Stockwell TB, Schultz-Cherry S, Wentworth DE.

J Virol. 2016 Sep 12;90(19):8454-63. doi: 10.1128/JVI.00163-16. Print 2016 Oct 1.

18.

Respiratory Syncytial Virus whole-genome sequencing identifies convergent evolution of sequence duplication in the C-terminus of the G gene.

Schobel SA, Stucker KM, Moore ML, Anderson LJ, Larkin EK, Shankar J, Bera J, Puri V, Shilts MH, Rosas-Salazar C, Halpin RA, Fedorova N, Shrivastava S, Stockwell TB, Peebles RS, Hartert TV, Das SR.

Sci Rep. 2016 May 23;6:26311. doi: 10.1038/srep26311.

19.

Ecosystem Interactions Underlie the Spread of Avian Influenza A Viruses with Pandemic Potential.

Bahl J, Pham TT, Hill NJ, Hussein IT, Ma EJ, Easterday BC, Halpin RA, Stockwell TB, Wentworth DE, Kayali G, Krauss S, Schultz-Cherry S, Webster RG, Webby RJ, Swartz MD, Smith GJ, Runstadler JA.

PLoS Pathog. 2016 May 11;12(5):e1005620. doi: 10.1371/journal.ppat.1005620. eCollection 2016 May.

20.

Quantifying influenza virus diversity and transmission in humans.

Poon LL, Song T, Rosenfeld R, Lin X, Rogers MB, Zhou B, Sebra R, Halpin RA, Guan Y, Twaddle A, DePasse JV, Stockwell TB, Wentworth DE, Holmes EC, Greenbaum B, Peiris JS, Cowling BJ, Ghedin E.

Nat Genet. 2016 Feb;48(2):195-200. doi: 10.1038/ng.3479. Epub 2016 Jan 4.

21.

Molecular Evolution and Intraclade Recombination of Enterovirus D68 during the 2014 Outbreak in the United States.

Tan Y, Hassan F, Schuster JE, Simenauer A, Selvarangan R, Halpin RA, Lin X, Fedorova N, Stockwell TB, Lam TT, Chappell JD, Hartert TV, Holmes EC, Das SR.

J Virol. 2015 Dec 9;90(4):1997-2007. doi: 10.1128/JVI.02418-15. Print 2016 Feb 15.

22.

First Complete Genome Sequences of Two Keystone Viruses from Florida.

Stockwell TB, Heberlein-Larson LA, Tan Y, Halpin RA, Fedorova N, Katzel DA, Smole S, Unnasch TR, Kramer LD, Das SR.

Genome Announc. 2015 Oct 29;3(5). pii: e01255-15. doi: 10.1128/genomeA.01255-15.

23.

Comparative In Vitro and In Vivo Studies of Porcine Rotavirus G9P[13] and Human Rotavirus Wa G1P[8].

Shao L, Fischer DD, Kandasamy S, Rauf A, Langel SN, Wentworth DE, Stucker KM, Halpin RA, Lam HC, Marthaler D, Saif LJ, Vlasova AN.

J Virol. 2015 Oct 14;90(1):142-51. doi: 10.1128/JVI.02401-15. Print 2016 Jan 1.

24.

The soft palate is an important site of adaptation for transmissible influenza viruses.

Lakdawala SS, Jayaraman A, Halpin RA, Lamirande EW, Shih AR, Stockwell TB, Lin X, Simenauer A, Hanson CT, Vogel L, Paskel M, Minai M, Moore I, Orandle M, Das SR, Wentworth DE, Sasisekharan R, Subbarao K.

Nature. 2015 Oct 1;526(7571):122-5. doi: 10.1038/nature15379. Epub 2015 Sep 23.

25.

Phylogeography of Influenza A(H3N2) Virus in Peru, 2010-2012.

Pollett S, Nelson MI, Kasper M, Tinoco Y, Simons M, Romero C, Silva M, Lin X, Halpin RA, Fedorova N, Stockwell TB, Wentworth D, Holmes EC, Bausch DG.

Emerg Infect Dis. 2015 Aug;21(8):1330-8. doi: 10.3201/eid2108.150084.

26.

Evolution of Influenza B Virus in Kuala Lumpur, Malaysia, between 1995 and 2008.

Sam IC, Su YC, Chan YF, Nor'E SS, Hassan A, Jafar FL, Joseph U, Halpin RA, Ghedin E, Hooi PS, Fourment M, Hassan H, AbuBakar S, Wentworth DE, Smith GJ.

J Virol. 2015 Sep;89(18):9689-92. doi: 10.1128/JVI.00708-15. Epub 2015 Jul 1.

27.

Phylodynamics of Enterovirus A71-Associated Hand, Foot, and Mouth Disease in Viet Nam.

Geoghegan JL, Tan le V, Kühnert D, Halpin RA, Lin X, Simenauer A, Akopov A, Das SR, Stockwell TB, Shrivastava S, Ngoc NM, Uyen le TT, Tuyen NT, Thanh TT, Hang VT, Qui PT, Hung NT, Khanh TH, Thinh le Q, Nhan le NT, Van HM, Viet do C, Tuan HM, Viet HL, Hien TT, Chau NV, Thwaites G, Grenfell BT, Stadler T, Wentworth DE, Holmes EC, Van Doorn HR.

J Virol. 2015 Sep;89(17):8871-9. doi: 10.1128/JVI.00706-15. Epub 2015 Jun 17.

28.

Haemagglutinin mutations and glycosylation changes shaped the 2012/13 influenza A(H3N2) epidemic, Houston, Texas.

Stucker KM, Schobel SA, Olsen RJ, Hodges HL, Lin X, Halpin RA, Fedorova N, Stockwell TB, Tovchigrechko A, Das SR, Wentworth DE, Musser JM.

Euro Surveill. 2015 May 7;20(18). pii: 21122.

29.

Influenza A virus evolution and spatio-temporal dynamics in Eurasian wild birds: a phylogenetic and phylogeographical study of whole-genome sequence data.

Lewis NS, Verhagen JH, Javakhishvili Z, Russell CA, Lexmond P, Westgeest KB, Bestebroer TM, Halpin RA, Lin X, Ransier A, Fedorova NB, Stockwell TB, Latorre-Margalef N, Olsen B, Smith G, Bahl J, Wentworth DE, Waldenström J, Fouchier RA, de Graaf M.

J Gen Virol. 2015 Aug;96(8):2050-60. doi: 10.1099/vir.0.000155. Epub 2015 Apr 22.

30.

Sequencing and analysis of globally obtained human respiratory syncytial virus A and B genomes.

Bose ME, He J, Shrivastava S, Nelson MI, Bera J, Halpin RA, Town CD, Lorenzi HA, Noyola DE, Falcone V, Gerna G, De Beenhouwer H, Videla C, Kok T, Venter M, Williams JV, Henrickson KJ.

PLoS One. 2015 Mar 20;10(3):e0120098. doi: 10.1371/journal.pone.0120098. eCollection 2015.

31.

Correction for Joseph et al., Adaptation of pandemic H2N2 influenza A viruses in humans.

Joseph U, Linster M, Suzuki Y, Krauss S, Halpin RA, Vijaykrishna D, Fabrizio TP, Bestebroer TM, Maurer-Stroh S, Webby RJ, Wentworth DE, Fouchier RA, Bahl J, Smith GJ.

J Virol. 2015 Apr;89(8):4706. doi: 10.1128/JVI.00259-15. No abstract available.

32.

Complete genomic sequence for an avian group G rotavirus from South Africa.

Stucker KM, Stockwell TB, Nyaga MM, Halpin RA, Fedorova N, Akopov A, Ngoveni H, Peenze I, Seheri ML, Mphahlele MJ, Wentworth DE.

Genome Announc. 2015 Mar 12;3(2). pii: e00107-15. doi: 10.1128/genomeA.00107-15.

33.

Spread and persistence of influenza A viruses in waterfowl hosts in the North American Mississippi migratory flyway.

Fries AC, Nolting JM, Bowman AS, Lin X, Halpin RA, Wester E, Fedorova N, Stockwell TB, Das SR, Dugan VG, Wentworth DE, Gibbs HL, Slemons RD.

J Virol. 2015 May;89(10):5371-81. doi: 10.1128/JVI.03249-14. Epub 2015 Mar 4.

34.

Whole genome detection of rotavirus mixed infections in human, porcine and bovine samples co-infected with various rotavirus strains collected from sub-Saharan Africa.

Nyaga MM, Jere KC, Esona MD, Seheri ML, Stucker KM, Halpin RA, Akopov A, Stockwell TB, Peenze I, Diop A, Ndiaye K, Boula A, Maphalala G, Berejena C, Mwenda JM, Steele AD, Wentworth DE, Mphahlele MJ.

Infect Genet Evol. 2015 Apr;31:321-34. doi: 10.1016/j.meegid.2015.02.011. Epub 2015 Feb 17.

35.

Adaptation of pandemic H2N2 influenza A viruses in humans.

Joseph U, Linster M, Suzuki Y, Krauss S, Halpin RA, Vijaykrishna D, Fabrizio TP, Bestebroer TM, Maurer-Stroh S, Webby RJ, Wentworth DE, Fouchier RA, Bahl J, Smith GJ; CEIRS H2N2 Working Group.

J Virol. 2015 Feb;89(4):2442-7. doi: 10.1128/JVI.02590-14. Epub 2014 Dec 10. Erratum in: J Virol. 2015 Apr;89(8):4706.

36.

Equine influenza A(H3N8) virus isolated from Bactrian camel, Mongolia.

Yondon M, Zayat B, Nelson MI, Heil GL, Anderson BD, Lin X, Halpin RA, McKenzie PP, White SK, Wentworth DE, Gray GC.

Emerg Infect Dis. 2014 Dec;20(12):2144-7. doi: 10.3201/eid2012.140435.

37.

H7N9 influenza A virus in turkeys in Minnesota.

Lebarbenchon C, Pedersen JC, Sreevatsan S, Ramey AM, Dugan VG, Halpin RA, Ferro PJ, Lupiani B, Enomoto S, Poulson RL, Smeltzer M, Cardona CJ, Tompkins SM, Wentworth DE, Stallknecht DE, Brown JD.

J Gen Virol. 2015 Feb;96(Pt 2):269-76. doi: 10.1099/vir.0.067504-0. Epub 2014 Oct 28.

38.

The evolutionary dynamics of influenza A and B viruses in the tropical city of Managua, Nicaragua.

Nelson MI, Balmaseda A, Kuan G, Saborio S, Lin X, Halpin RA, Stockwell TB, Wentworth DE, Harris E, Gordon A.

Virology. 2014 Aug;462-463:81-90. doi: 10.1016/j.virol.2014.05.025. Epub 2014 Jun 22.

39.

Whole-genome analyses of DS-1-like human G2P[4] and G8P[4] rotavirus strains from Eastern, Western and Southern Africa.

Nyaga MM, Stucker KM, Esona MD, Jere KC, Mwinyi B, Shonhai A, Tsolenyanu E, Mulindwa A, Chibumbya JN, Adolfine H, Halpin RA, Roy S, Stockwell TB, Berejena C, Seheri ML, Mwenda JM, Steele AD, Wentworth DE, Mphahlele MJ.

Virus Genes. 2014 Oct;49(2):196-207. doi: 10.1007/s11262-014-1091-7. Epub 2014 Jun 22.

40.

Whole genome analyses of G1P[8] rotavirus strains from vaccinated and non-vaccinated South African children presenting with diarrhea.

Magagula NB, Esona MD, Nyaga MM, Stucker KM, Halpin RA, Stockwell TB, Seheri ML, Steele AD, Wentworth DE, Mphahlele MJ.

J Med Virol. 2015 Jan;87(1):79-101. doi: 10.1002/jmv.23971. Epub 2014 May 20.

41.

Analysis of recombinant H7N9 wild-type and mutant viruses in pigs shows that the Q226L mutation in HA is important for transmission.

Liu Q, Zhou B, Ma W, Bawa B, Ma J, Wang W, Lang Y, Lyoo Y, Halpin RA, Lin X, Stockwell TB, Webby R, Wentworth DE, Richt JA.

J Virol. 2014 Jul;88(14):8153-65. doi: 10.1128/JVI.00894-14. Epub 2014 May 7.

42.

North Atlantic migratory bird flyways provide routes for intercontinental movement of avian influenza viruses.

Dusek RJ, Hallgrimsson GT, Ip HS, Jónsson JE, Sreevatsan S, Nashold SW, TeSlaa JL, Enomoto S, Halpin RA, Lin X, Fedorova N, Stockwell TB, Dugan VG, Wentworth DE, Hall JS.

PLoS One. 2014 Mar 19;9(3):e92075. doi: 10.1371/journal.pone.0092075. eCollection 2014.

43.

Universal influenza B virus genomic amplification facilitates sequencing, diagnostics, and reverse genetics.

Zhou B, Lin X, Wang W, Halpin RA, Bera J, Stockwell TB, Barr IG, Wentworth DE.

J Clin Microbiol. 2014 May;52(5):1330-7. doi: 10.1128/JCM.03265-13. Epub 2014 Feb 5.

44.

Isolation, propagation, genome analysis and epidemiology of HKU1 betacoronaviruses.

Dominguez SR, Shrivastava S, Berglund A, Qian Z, Góes LG, Halpin RA, Fedorova N, Ransier A, Weston PA, Durigon EL, Jerez JA, Robinson CC, Town CD, Holmes KV.

J Gen Virol. 2014 Apr;95(Pt 4):836-48. doi: 10.1099/vir.0.059832-0. Epub 2014 Jan 6.

45.

Genomewide analysis of reassortment and evolution of human influenza A(H3N2) viruses circulating between 1968 and 2011.

Westgeest KB, Russell CA, Lin X, Spronken MI, Bestebroer TM, Bahl J, van Beek R, Skepner E, Halpin RA, de Jong JC, Rimmelzwaan GF, Osterhaus AD, Smith DJ, Wentworth DE, Fouchier RA, de Graaf M.

J Virol. 2014 Mar;88(5):2844-57. doi: 10.1128/JVI.02163-13. Epub 2013 Dec 26.

46.

Migration and persistence of human influenza A viruses, Vietnam, 2001-2008.

Le MQ, Lam HM, Cuong VD, Lam TT, Halpin RA, Wentworth DE, Hien NT, Thanh le T, Phuong HV, Horby P, Boni MF.

Emerg Infect Dis. 2013 Nov;19(11):1756-65. doi: 10.3201/eid1911.130349.

47.

Genomic analysis of pandemic and post-pandemic influenza A pH1N1 viruses isolated in Rio Grande do Sul, Brazil.

Sant'Anna FH, Borges LG, Fallavena PR, Gregianini TS, Matias F, Halpin RA, Wentworth D, d'Azevedo PA, Veiga AB.

Arch Virol. 2014 Apr;159(4):621-30. doi: 10.1007/s00705-013-1855-8. Epub 2013 Oct 10.

PMID:
24114147
48.

Influenza a virus migration and persistence in North American wild birds.

Bahl J, Krauss S, Kühnert D, Fourment M, Raven G, Pryor SP, Niles LJ, Danner A, Walker D, Mendenhall IH, Su YC, Dugan VG, Halpin RA, Stockwell TB, Webby RJ, Wentworth DE, Drummond AJ, Smith GJ, Webster RG.

PLoS Pathog. 2013;9(8):e1003570. doi: 10.1371/journal.ppat.1003570. Epub 2013 Aug 29.

49.

Evolution of a reassortant North American gull influenza virus lineage: drift, shift and stability.

Hall JS, Teslaa JL, Nashold SW, Halpin RA, Stockwell T, Wentworth DE, Dugan V, Ip HS.

Virol J. 2013 Jun 6;10:179. doi: 10.1186/1743-422X-10-179.

50.

Rapid research response to the 2009 A(H1N1)pdm09 influenza pandemic (Revised).

Keitel WA, Piedra PA, Atmar RL, Demmler G, El Sahly HM, Barrett J, Halpin RA, Lagos R, Fisher-Hoch S, Munoz F.

BMC Res Notes. 2013 May 3;6:177. doi: 10.1186/1756-0500-6-177.

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