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Select item 83160751.

In Vivo Generation of BK and JC Polyomavirus Defective Viral Genomes in Human Urine Samples Associated with Higher Viral Loads

Amin Addetia, Quynh Phung, Benjamin T. Bradley, Michelle J. Lin, Haiying Zhu, Hong Xie, Meei-Li Huang, Alexander L. Greninger

J Virol. 2021 Jun; 95(12): e00250-21. Prepublished online 2021 Apr 7. Published online 2021 May 24. doi: 10.1128/JVI.00250-21

PMCID:: PMC8316075

Abstract Article PDF–2.3M

Select item 67358362.

Prospective, Real-time Metagenomic Sequencing During Norovirus Outbreak Reveals Discrete Transmission Clusters

Amanda M Casto, Amanda L Adler, Negar Makhsous, Kristen Crawford, Xuan Qin, Jane M Kuypers, Meei-Li Huang, Danielle M Zerr, Alexander L Greninger

Clin Infect Dis. 2019 Sep 15; 69(6): 941–948. Published online 2018 Dec 4. doi: 10.1093/cid/ciy1020

PMCID:: PMC6735836

Abstract Article PDF–255K

Select item 64201673.

Viral Genetics Modulate Orolabial Herpes Simplex Virus Type 1 Shedding in Humans

Meena S Ramchandani, Lichen Jing, Ronnie M Russell, Tran Tran, Kerry J Laing, Amalia S Magaret, Stacy Selke, Anqi Cheng, Meei-Li Huang, Hong Xie, Eric Strachan, Alex L Greninger, Pavitra Roychoudhury, Keith R Jerome, Anna Wald, David M Koelle

J Infect Dis. 2019 Apr 1; 219(7): 1058–1066. Published online 2018 Nov 1. doi: 10.1093/infdis/jiy631

PMCID:: PMC6420167

Abstract Article PDF–670K

Select item 63555304.

Mycobacterium talmoniae, a Potential Pulmonary Pathogen Isolated from Multiple Patients with Bronchiectasis in the United States, Including the First Case of Clinical Disease in a Patient with Cystic Fibrosis

Ravikiran Vasireddy, Sruthi Vasireddy, Barbara A. Brown-Elliott, Alexander L. Greninger, Rebecca M. Davidson, Kevin L. Ard, Christine Y. Turenne, Richard J. Wallace, Jr.

J Clin Microbiol. 2019 Feb; 57(2): e00906-18. Prepublished online 2018 Nov 14. Published online 2019 Jan 30. doi: 10.1128/JCM.00906-18

PMCID:: PMC6355530

Abstract Article PDF–758K

Select item 63433355.

VAPiD: a lightweight cross-platform viral annotation pipeline and identification tool to facilitate virus genome submissions to NCBI GenBank

Ryan C. Shean, Negar Makhsous, Graham D. Stoddard, Michelle J. Lin, Alexander L. Greninger

BMC Bioinformatics. 2019; 20: 48. Published online 2019 Jan 23. doi: 10.1186/s12859-019-2606-y

PMCID:: PMC6343335

Abstract Article PDF–895K

Select item 62588396.

Limited Marginal Utility of Deep Sequencing for HIV Drug Resistance Testing in the Age of Integrase Inhibitors

Ronit R. Dalmat, Negar Makhsous, Gregory G. Pepper, Amalia Magaret, Keith R. Jerome, Anna Wald, Alexander L. Greninger

J Clin Microbiol. 2018 Dec; 56(12): e01443-18. Prepublished online 2018 Oct 10. Published online 2018 Nov 27. doi: 10.1128/JCM.01443-18

PMCID:: PMC6258839

Abstract Article PDF–373K

Select item 60305627.

Viral Entry Properties Required for Fitness in Humans Are Lost through Rapid Genomic Change during Viral Isolation

Sho Iketani, Ryan C. Shean, Marion Ferren, Negar Makhsous, Dolly B. Aquino, Amedee des Georges, Bert Rima, Cyrille Mathieu, Matteo Porotto, Anne Moscona, Alexander L. Greninger

mBio. 2018 Jul-Aug; 9(4): e00898-18. Published online 2018 Jul 3. doi: 10.1128/mBio.00898-18

PMCID:: PMC6030562

Abstract Article PDF–1.6M

Select item 60016108.

Ultrasensitive Capture of Human Herpes Simplex Virus Genomes Directly from Clinical Samples Reveals Extraordinarily Limited Evolution in Cell Culture

Alexander L. Greninger, Pavitra Roychoudhury, Hong Xie, Amanda Casto, Anne Cent, Gregory Pepper, David M. Koelle, Meei-Li Huang, Anna Wald, Christine Johnston, Keith R. Jerome

mSphere. 2018 May-Jun; 3(3): e00283-18. Published online 2018 Jun 13. doi: 10.1128/mSphereDirect.00283-18

PMCID:: PMC6001610

Abstract Article PDF–521K

Select item 59078539.

Rule-Out Outbreak: 24-Hour Metagenomic Next-Generation Sequencing for Characterizing Respiratory Virus Source for Infection Prevention

Alexander L. Greninger, Alpana Waghmare, Amanda Adler, Xuan Qin, Janet L. Crowley, Janet A. Englund, Jane M. Kuypers, Keith R. Jerome, Danielle M. Zerr

J Pediatric Infect Dis Soc. 2017 Jun; 6(2): 168–172. Published online 2017 Apr 4. doi: 10.1093/jpids/pix019

PMCID:: PMC5907853

Abstract Article PDF–3.6M

Select item 590559610.

The human clone ST22 SCCmec IV methicillin-resistant Staphylococcus aureus isolated from swine herds and wild primates in Nepal: is man the common source?

Marilyn C Roberts, Prabhu Raj Joshi, Alexander L Greninger, Daira Melendez, Saroj Paudel, Mahesh Acharya, Nabin Kishor Bimali, Narayan P Koju, David No, Mukesh Chalise, Randall C Kyes

FEMS Microbiol Ecol. 2018 May; 94(5): fiy052. Published online 2018 Mar 21. doi: 10.1093/femsec/fiy052

PMCID:: PMC5905596

Abstract Article PDF–367K

Select item 585949811.

Comparative genomic, transcriptomic, and proteomic reannotation of human herpesvirus 6

Alexander L. Greninger, Giselle M. Knudsen, Pavitra Roychoudhury, Derek J. Hanson, Ruth Hall Sedlak, Hong Xie, Jon Guan, Thuy Nguyen, Vikas Peddu, Michael Boeckh, Meei-Li Huang, Linda Cook, Daniel P. Depledge, Danielle M. Zerr, David M. Koelle, Soren Gantt, Tetsushi Yoshikawa, Mary Caserta, Joshua A. Hill, Keith R. Jerome

BMC Genomics. 2018; 19: 204. Published online 2018 Mar 20. doi: 10.1186/s12864-018-4604-2

PMCID:: PMC5859498

Abstract Article PDF–2.1M

Select item 585349112.

Heterogeneous Antimicrobial Susceptibility Characteristics in Pseudomonas aeruginosa Isolates from Cystic Fibrosis Patients

Xuan Qin, Chuan Zhou, Danielle M. Zerr, Amanda Adler, Amin Addetia, Shuhua Yuan, Alexander L. Greninger

mSphere. 2018 Mar-Apr; 3(2): e00615-17. Published online 2018 Mar 14. doi: 10.1128/mSphere.00615-17

PMCID:: PMC5853491

Abstract Article PDF–1.1M

Select item 585331113.

Prolonged Shedding of Human Coronavirus in Hematopoietic Cell Transplant Recipients: Risk Factors and Viral Genome Evolution

Chikara Ogimi, Alexander L Greninger, Alpana A Waghmare, Jane M Kuypers, Ryan C Shean, Hu Xie, Wendy M Leisenring, Terry L Stevens-Ayers, Keith R Jerome, Janet A Englund, Michael Boeckh

J Infect Dis. 2017 Jul 15; 216(2): 203–209. Published online 2017 May 30. doi: 10.1093/infdis/jix264

PMCID:: PMC5853311

Abstract Article PDF–209K

Select item 574491014.

Dual-strain genital herpes simplex virus type 2 (HSV-2) infection in the US, Peru, and 8 countries in sub-Saharan Africa: A nested cross-sectional viral genotyping study

Christine Johnston, Amalia Magaret, Pavitra Roychoudhury, Alexander L. Greninger, Daniel Reeves, Joshua Schiffer, Keith R. Jerome, Cassandra Sather, Kurt Diem, Jairam R. Lingappa, Connie Celum, David M. Koelle, Anna Wald

PLoS Med. 2017 Dec; 14(12): e1002475. Published online 2017 Dec 27. doi: 10.1371/journal.pmed.1002475

PMCID:: PMC5744910

Abstract Article PDF–1.1M

Select item 560940915.

Conservation and Recombination in the Genome Sequence of Haemophilus influenzae Type f WAPHL1

Allen C. Bateman, Ailyn C. Perez-Osorio, Zhen Li, Michael Tran, Alexander L. Greninger

Genome Announc. 2017 Sep; 5(38): e00929-17. Published online 2017 Sep 21. doi: 10.1128/genomeA.00929-17

PMCID:: PMC5609409

Abstract Article PDF–121K

Select item 558433416.

Isolation and characterization of the fall Chinook aquareovirus

Negar Makhsous, Nicole L. Jensen, Katherine H. Haman, William N. Batts, Keith R. Jerome, James R. Winton, Alexander L. Greninger

Virol J. 2017; 14: 170. Published online 2017 Sep 5. doi: 10.1186/s12985-017-0839-9

PMCID:: PMC5584334

Abstract Article PDF–696K

Select item 556570717.

Highly conserved intragenic HSV-2 sequences: results from next-generation sequencing of HSV-2 U_L and U_S regions from genital swabs collected from 3 continents

Christine Johnston, Amalia Magaret, Pavitra Roychoudhury, Alexander L. Greninger, Anqi Cheng, Kurt Diem, Matthew P. Fitzgibbon, Meei-li Huang, Stacy Selke, Jairam R. Lingappa, Connie Celum, Keith R. Jerome, Anna Wald, David M. Koelle

Virology. Author manuscript; available in PMC 2018 Oct 1.

Published in final edited form as: Virology. 2017 Oct; 510: 90–98. Published online 2017 Jul 13. doi: 10.1016/j.virol.2017.06.031

PMCID:: PMC5565707

Abstract Article PDF–1022K

Select item 534700618.

Worldwide circulation of HSV-2 × HSV-1 recombinant strains

David M. Koelle, Peter Norberg, Matthew P. Fitzgibbon, Ronnie M. Russell, Alex L. Greninger, Meei-Li Huang, Larry Stensland, Lichen Jing, Amalia S. Magaret, Kurt Diem, Stacy Selke, Hong Xie, Connie Celum, Jairam R. Lingappa, Keith R. Jerome, Anna Wald, Christine Johnston

Sci Rep. 2017; 7: 44084. Published online 2017 Mar 13. doi: 10.1038/srep44084

PMCID:: PMC5347006

Abstract Article PDF–1.0M

Select item 533458319.

Draft Genome Sequences of Six Novel Picorna-Like Viruses from Washington State Spiders

Ryan C. Shean, Negar Makhsous, Rodney L. Crawford, Keith R. Jerome, Alexander L. Greninger

Genome Announc. 2017 Mar; 5(9): e01705-16. Published online 2017 Mar 2. doi: 10.1128/genomeA.01705-16

PMCID:: PMC5334583

Abstract Article PDF–117K

Select item 532845020.

Copy Number Heterogeneity of JC Virus Standards

Alexander L. Greninger, Allen C. Bateman, Ederlyn E. Atienza, Sharon Wendt, Negar Makhsous, Keith R. Jerome, Linda Cook

J Clin Microbiol. 2017 Mar; 55(3): 824–831. Prepublished online 2016 Dec 14. Published online 2017 Feb 22. doi: 10.1128/JCM.02337-16

PMCID:: PMC5328450

Abstract Article PDF–1.0M

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