Clinical and biological insights from viral genome sequencing

Initial sequencing and analysis of the human genome

International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216

The human microbiome project

Turnbaugh, P. J., Ley, R. E., Hamady, M., Fraser-Liggett, C. M., Knight, R., & Gordon, J. I. (2007) · Nature · doi:10.1038/nature06244 · Cited by 6,091

Whole-Genome Random Sequencing and Assembly of Haemophilus influenzae Rd

Fleischmann, R. D., Adams, M. D., White, O., Clayton, R. A., Kirkness, E. F., Kerlavage, A. R., Bult, C. J., Tomb, J.-F., Dougherty, B. A., Merrick, J. M., et al. (1995) · Science · doi:10.1126/science.7542800 · Cited by 5,654

Environmental genome shotgun sequencing of the sargasso sea

Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., Wu, D., Paulsen, I., Nelson, K. E., Nelson, W., et al. (2004) · Science · doi:10.1126/science.1093857 · Cited by 4,376

Coming of age: ten years of next-generation sequencing technologies

Goodwin, S., McPherson, J. D., & McCombie, W. R. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.49 · Cited by 4,352

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

Salter, S. J., Cox, M. J., Turek, E. M., Calus, S. T., Cookson, W. O., Moffatt, M. F., Turner, P., Parkhill, J., Loman, N. J., & Walker, A. W. (2014) · BMC Biology · doi:10.1186/s12915-014-0087-z · Cited by 3,463

Zika Virus Associated with Microcephaly

Mlakar, J., Korva, M., Tul, N., Popović, M., Poljšak-Prijatelj, M., Mraz, J., Kolenc, M., Resman Rus, K., Vesnaver Vipotnik, T., Fabjan Vodušek, V., et al. (2016) · New England Journal of Medicine · doi:10.1056/nejmoa1600651 · Cited by 2,884

The Minimal Gene Complement of Mycoplasma genitalium

Fraser, C. M., Gocayne, J. D., White, O., Adams, M. D., Clayton, R. A., Fleischmann, R. D., Bult, C. J., Kerlavage, A. R., Sutton, G., Kelley, J. M., et al. (1995) · Science · doi:10.1126/science.270.5235.397 · Cited by 2,545

Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic

Smith, G. J. D., Vijaykrishna, D., Bahl, J., Lycett, S. J., Worobey, M., Pybus, O. G., Ma, S. K., Cheung, C. L., Raghwani, J., Bhatt, S., et al. (2009) · Nature · doi:10.1038/nature08182 · Cited by 2,243

Long-Term Control of HIV by CCR5 Delta32/Delta32 Stem-Cell Transplantation

Hütter, G., Nowak, D., Mossner, M., Ganepola, S., Müßig, A., Allers, K., Schneider, T., Hofmann, J., Kücherer, C., Blau, O., et al. (2009) · New England Journal of Medicine · doi:10.1056/nejmoa0802905 · Cited by 1,837

MycoCosm portal: gearing up for 1000 fungal genomes

Grigoriev, I. V., Nikitin, R., Haridas, S., Kuo, A., Ohm, R., Otillar, R., Riley, R., Salamov, A., Zhao, X., Korzeniewski, F., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1183 · Cited by 1,498

Real-time, portable genome sequencing for Ebola surveillance

Quick, J., Loman, N. J., Duraffour, S., Simpson, J. T., Severi, E., Cowley, L., Bore, J. A., Koundouno, R., Dudas, G., Mikhail, A., et al. (2016) · Nature · doi:10.1038/nature16996 · Cited by 1,448

Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak

Gire, S. K., Goba, A., Andersen, K. G., Sealfon, R. S. G., Park, D. J., Kanneh, L., Jalloh, S., Momoh, M., Fullah, M., Dudas, G., et al. (2014) · Science · doi:10.1126/science.1259657 · Cited by 1,215

Detection and sequencing of Zika virus from amniotic fluid of fetuses with microcephaly in Brazil: a case study

Calvet, G., Aguiar, R. S., Melo, A. S. O., Sampaio, S. A., de Filippis, I., Fabri, A., Araujo, E. S. M., de Sequeira, P. C., de Mendonça, M. C. L., de Oliveira, L., et al. (2016) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(16)00095-5 · Cited by 1,165

Zika virus in the Americas: Early epidemiological and genetic findings

Faria, N. R., Azevedo, R. D. S. D. S., Kraemer, M. U. G., Souza, R., Cunha, M. S., Hill, S. C., Thézé, J., Bonsall, M. B., Bowden, T. A., Rissanen, I., et al. (2016) · Science · doi:10.1126/science.aaf5036 · Cited by 1,091

Actionable Diagnosis of Neuroleptospirosis by Next-Generation Sequencing

Wilson, M. R., Naccache, S. N., Samayoa, E., Biagtan, M., Bashir, H., Yu, G., Salamat, S. M., Somasekar, S., Federman, S., Miller, S., et al. (2014) · New England Journal of Medicine · doi:10.1056/nejmoa1401268 · Cited by 977

Drug-resistance genotyping in HIV-1 therapy: the VIRAD APT randomi sed controlled trial

Durant, J., Clevenbergh, P. A., Halfon, P., Delgiudice, P., Porsin, S., Simonet, P., Montagne, N., Boucher, C. A., Schapiro, J., & Dellamonica, P. (1999) · The Lancet · doi:10.1016/s0140-6736(98)12291-2 · Cited by 752

Making a definitive diagnosis: Successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease

Worthey, E. A., Mayer, A. N., Syverson, G. D., Helbling, D., Bonacci, B. B., Decker, B., Serpe, J. M., Dasu, T., Tschannen, M. R., Veith, R. L., et al. (2011) · Genetics in Medicine · doi:10.1097/gim.0b013e3182088158 · Cited by 711

Potential for Zika virus transmission through blood transfusion demonstrated during an outbreak in French Polynesia, November 2013 to February 2014

Musso, D., Nhan, T., Robin, E., Roche, C., Bierlaire, D., Zisou, K., Shan Yan, A., Cao-Lormeau, V. M., & Broult, J. (2014) · Eurosurveillance · doi:10.2807/1560-7917.es2014.19.14.20761 · Cited by 700

Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study

Bryant, J. M., Grogono, D. M., Greaves, D., Foweraker, J., Roddick, I., Inns, T., Reacher, M., Haworth, C. S., Curran, M. D., Harris, S. R., et al. (2013) · The Lancet · doi:10.1016/s0140-6736(13)60632-7 · Cited by 694

Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis

Greninger, A. L., Naccache, S. N., Federman, S., Yu, G., Mbala, P., Bres, V., Stryke, D., Bouquet, J., Somasekar, S., Linnen, J. M., et al. (2015) · Genome Medicine · doi:10.1186/s13073-015-0220-9 · Cited by 558

Routine Use of Microbial Whole Genome Sequencing in Diagnostic and Public Health Microbiology

Köser, C. U., Ellington, M. J., Cartwright, E. J. P., Gillespie, S. H., Brown, N. M., Farrington, M., Holden, M. T. G., Dougan, G., Bentley, S. D., Parkhill, J., et al. (2012) · PLoS Pathogens · doi:10.1371/journal.ppat.1002824 · Cited by 544

Hepatitis C Virus Resistance to Direct-Acting Antiviral Drugs in Interferon-Free Regimens

Pawlotsky, J.-M. (2016) · Gastroenterology · doi:10.1053/j.gastro.2016.04.003 · Cited by 519

A flexible and efficient template format for circular consensus sequencing and SNP detection

Travers, K. J., Chin, C.-S., Rank, D. R., Eid, J. S., & Turner, S. W. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq543 · Cited by 419

Rationale and Uses of a Public HIV Drug‐Resistance Database

Shafer, R. W. (2006) · The Journal of Infectious Diseases · doi:10.1086/505356 · Cited by 414

Technology: The $1,000 genome

Check Hayden, E. (2014) · Nature · doi:10.1038/507294a · Cited by 408

The complete nucleotide sequence of an infectious clone of cauliflower mosaic virus by M13mp7 shotgun sequencing

Gardner, R. C., Howarth, A. J., Hahn, P., Brown-Luedi, M., Shepherd, R. J., & Messing, J. (1981) · Nucleic Acids Research · doi:10.1093/nar/9.12.2871 · Cited by 401

Low-Abundance Drug-Resistant Viral Variants in Chronically HIV-Infected, Antiretroviral Treatment–Naive Patients Significantly Impact Treatment Outcomes

Simen, B. B., Simons, J. F., Hullsiek, K. H., Novak, R. M., MacArthur, R. D., Baxter, J. D., Huang, C., Lubeski, C., Turenchalk, G. S., Braverman, M. S., et al. (2009) · Journal of Infectious Diseases · doi:10.1086/596736 · Cited by 392

A novel outbreak enterovirus D68 strain associated with acute flaccid myelitis cases in the USA (2012–14): a retrospective cohort study

Greninger, A. L., Naccache, S. N., Messacar, K., Clayton, A., Yu, G., Somasekar, S., Federman, S., Stryke, D., Anderson, C., Yagi, S., et al. (2015) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(15)70093-9 · Cited by 390

Virome Capture Sequencing Enables Sensitive Viral Diagnosis and Comprehensive Virome Analysis

Briese, T., Kapoor, A., Mishra, N., Jain, K., Kumar, A., Jabado, O. J., & Lipkin, W. I. (2015) · mBio · doi:10.1128/mbio.01491-15 · Cited by 383

The Los Alamos hepatitis C sequence database

Kuiken, C., Yusim, K., Boykin, L., & Richardson, R. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bth485 · Cited by 374

Extremely High Mutation Rate of HIV-1 In Vivo

Cuevas, J. M., Geller, R., Garijo, R., López-Aldeguer, J., & Sanjuán, R. (2015) · PLOS Biology · doi:10.1371/journal.pbio.1002251 · Cited by 371

Twenty years of bacterial genome sequencing

Loman, N. J., & Pallen, M. J. (2015) · Nature Reviews Microbiology · doi:10.1038/nrmicro3565 · Cited by 344

Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing

Schmidt, K., Mwaigwisya, S., Crossman, L. C., Doumith, M., Munroe, D., Pires, C., Khan, A. M., Woodford, N., Saunders, N. J., Wain, J., et al. (2017) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkw397 · Cited by 301

Diagnosis of Neuroinvasive Astrovirus Infection in an Immunocompromised Adult With Encephalitis by Unbiased Next-Generation Sequencing

Naccache, S. N., Peggs, K. S., Mattes, F. M., Phadke, R., Garson, J. A., Grant, P., Samayoa, E., Federman, S., Miller, S., Lunn, M. P., et al. (2015) · Clinical Infectious Diseases · doi:10.1093/cid/ciu912 · Cited by 294

Human Coronavirus OC43 Associated with Fatal Encephalitis

Morfopoulou, S., Brown, J. R., Davies, E. G., Anderson, G., Virasami, A., Qasim, W., Chong, W. K., Hubank, M., Plagnol, V., Desforges, M., et al. (2016) · New England Journal of Medicine · doi:10.1056/nejmc1509458 · Cited by 276

Enhanced virome sequencing using targeted sequence capture

Wylie, T. N., Wylie, K. M., Herter, B. N., & Storch, G. A. (2015) · Genome Research · doi:10.1101/gr.191049.115 · Cited by 263

A Variegated Squirrel Bornavirus Associated with Fatal Human Encephalitis

Hoffmann, B., Tappe, D., Höper, D., Herden, C., Boldt, A., Mawrin, C., Niederstraßer, O., Müller, T., Jenckel, M., van der Grinten, E., et al. (2015) · New England Journal of Medicine · doi:10.1056/nejmoa1415627 · Cited by 260

Genome Diversity of Epstein-Barr Virus from Multiple Tumor Types and Normal Infection

Palser, A. L., Grayson, N. E., White, R. E., Corton, C., Correia, S., Ba abdullah, M. M., Watson, S. J., Cotten, M., Arrand, J. R., Murray, P. G., et al. (2015) · Journal of Virology · doi:10.1128/jvi.03614-14 · Cited by 260

The Perils of Pathogen Discovery: Origin of a Novel Parvovirus-Like Hybrid Genome Traced to Nucleic Acid Extraction Spin Columns

Naccache, S. N., Greninger, A. L., Lee, D., Coffey, L. L., Phan, T., Rein-Weston, A., Aronsohn, A., Hackett, J., Delwart, E. L., & Chiu, C. Y. (2013) · Journal of Virology · doi:10.1128/jvi.02323-13 · Cited by 255

Human IFNAR2 deficiency: Lessons for antiviral immunity

Duncan, C. J. A., Mohamad, S. M. B., Young, D. F., Skelton, A. J., Leahy, T. R., Munday, D. C., Butler, K. M., Morfopoulou, S., Brown, J. R., Hubank, M., et al. (2015) · Science Translational Medicine · doi:10.1126/scitranslmed.aac4227 · Cited by 237

Efficient de novo assembly of single-cell bacterial genomes from short-read data sets

Chitsaz, H., Yee-Greenbaum, J. L., Tesler, G., Lombardo, M.-J., Dupont, C. L., Badger, J. H., Novotny, M., Rusch, D. B., Fraser, L. J., Gormley, N. A., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1966 · Cited by 236

Clusters of Antibiotic Resistance Genes Enriched Together Stay Together in Swine Agriculture

Johnson, T. A., Stedtfeld, R. D., Wang, Q., Cole, J. R., Hashsham, S. A., Looft, T., Zhu, Y.-G., & Tiedje, J. M. (2016) · mBio · doi:10.1128/mbio.02214-15 · Cited by 231

Specific Capture and Whole-Genome Sequencing of Viruses from Clinical Samples

Depledge, D. P., Palser, A. L., Watson, S. J., Lai, I. Y.-C., Gray, E. R., Grant, P., Kanda, R. K., Leproust, E., Kellam, P., & Breuer, J. (2011) · PLoS ONE · doi:10.1371/journal.pone.0027805 · Cited by 229

Probable transfusion‐transmitted Zika virus in Brazil

Barjas‐Castro, M. L., Angerami, R. N., Cunha, M. S., Suzuki, A., Nogueira, J. S., Rocco, I. M., Maeda, A. Y., Vasami, F. G. S., Katz, G., Boin, I. F. S. F., et al. (2016) · Transfusion · doi:10.1111/trf.13681 · Cited by 216

Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe

Aanensen, D. M., Feil, E. J., Holden, M. T. G., Dordel, J., Yeats, C. A., Fedosejev, A., Goater, R., Castillo-Ramírez, S., Corander, J., Colijn, C., et al. (2016) · mBio · doi:10.1128/mbio.00444-16 · Cited by 213

A Method for Selectively Enriching Microbial DNA from Contaminating Vertebrate Host DNA

Feehery, G. R., Yigit, E., Oyola, S. O., Langhorst, B. W., Schmidt, V. T., Stewart, F. J., Dimalanta, E. T., Amaral-Zettler, L. A., Davis, T., Quail, M. A., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0076096 · Cited by 212

Astrovirus VA1/HMO-C: An Increasingly Recognized Neurotropic Pathogen in Immunocompromised Patients

Brown, J. R., Morfopoulou, S., Hubb, J., Emmett, W. A., Ip, W., Shah, D., Brooks, T., Paine, S. M. L., Anderson, G., Virasami, A., et al. (2015) · Clinical Infectious Diseases · doi:10.1093/cid/ciu940 · Cited by 209

Extensive Genome-Wide Variability of Human Cytomegalovirus in Congenitally Infected Infants

Renzette, N., Bhattacharjee, B., Jensen, J. D., Gibson, L., & Kowalik, T. F. (2011) · PLoS Pathogens · doi:10.1371/journal.ppat.1001344 · Cited by 199

A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control

Bartha, I., Carlson, J. M., Brumme, C. J., McLaren, P. J., Brumme, Z. L., John, M., Haas, D. W., Martinez-Picado, J., Dalmau, J., López-Galíndez, C., et al. (2013) · eLife · doi:10.7554/elife.01123 · Cited by 196

Mobile real-time surveillance of Zika virus in Brazil

Faria, N. R., Sabino, E. C., Nunes, M. R. T., Alcantara, L. C. J., Loman, N. J., & Pybus, O. G. (2016) · Genome Medicine · doi:10.1186/s13073-016-0356-2 · Cited by 195

Molecular Epidemiology and Evolution of Influenza Viruses Circulating within European Swine between 2009 and 2013

Watson, S. J., Langat, P., Reid, S. M., Lam, T. T., Cotten, M. L., Kelly, M., Reeth, K. V., Qiu, Y., Simon, G., Bonin, E., et al. (2015) · Journal of Virology · doi:10.1128/jvi.00840-15 · Cited by 195

Wide Spectra of Quality Control

Akyar, I. (2011) · InTech eBooks · doi:10.5772/1142 · Cited by 178

Shift of HIV Tropism in Stem-Cell Transplantation with CCR5 Delta32 Mutation

Kordelas, L., Verheyen, J., & Esser, S. (2014) · New England Journal of Medicine · doi:10.1056/nejmc1405805 · Cited by 166

Antiviral drug resistance in herpesviruses other than cytomegalovirus

Piret, J., & Boivin, G. (2014) · Reviews in Medical Virology · doi:10.1002/rmv.1787 · Cited by 159

Use of Massively Parallel Ultradeep Pyrosequencing To Characterize the Genetic Diversity of Hepatitis B Virus in Drug-Resistant and Drug-Naive Patients and To Detect Minor Variants in Reverse Transcriptase and Hepatitis B S Antigen

Solmone, M., Vincenti, D., Prosperi, M. C. F., Bruselles, A., Ippolito, G., & Capobianchi, M. R. (2009) · Journal of Virology · doi:10.1128/jvi.02011-08 · Cited by 158

Dynamic regulation of HIV-1 mRNA populations analyzed by single-molecule enrichment and long-read sequencing

Ocwieja, K. E., Sherrill-Mix, S. A., Mukherjee, R., Custers-Allen, R., David, P. H., Brown, M., Wang, S., Link, D. R., Olson, J., Travers, K. J., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks753 · Cited by 156

Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer

Kilianski, A., Haas, J., Corriveau, E. J., Liem, A. T., Willis, K. L., Kadavy, D. R., Rosenzweig, C. N., & Minot, S. S. (2015) · GigaScience · doi:10.1186/s13742-015-0051-z · Cited by 152

Disease-associated XMRV sequences are consistent with laboratory contamination

Hué, S., Gray, E. R., Gall, A., Katzourakis, A., Tan, C. P., Houldcroft, C. J., McLaren, S., Pillay, D., Futreal, P. A., Garson, J. A., et al. (2010) · Retrovirology · doi:10.1186/1742-4690-7-111 · Cited by 150

Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples

Matranga, C. B., Andersen, K. G., Winnicki, S., Busby, M., Gladden, A. D., Tewhey, R., Stremlau, M. H., Berlin, A. M., Gire, S., England, E. M., et al. (2014) · Genome biology · doi:10.1186/s13059-014-0519-7 · Cited by 147

INC-Seq: accurate single molecule reads using nanopore sequencing

Li, C., Chng, K. R., Boey, E. J. H., Ng, A. H. Q., Wilm, A., & Nagarajan, N. (2016) · GigaScience · doi:10.1186/s13742-016-0140-7 · Cited by 137

Comparison of Next-Generation Sequencing Technologies for Comprehensive Assessment of Full-Length Hepatitis C Viral Genomes

Thomson, E. C., Ip, C. L. C., Badhan, A., Christiansen, M. T., Adamson, W. E., Ansari, M. A., Bibby, D., Breuer, J., Brown, A., Bowden, R. J., et al. (2016) · Journal of Clinical Microbiology · doi:10.1128/jcm.00330-16 · Cited by 135

Detection of virus in CSF from the cases with meningoencephalitis by next-generation sequencing

Guan, H., Shen, A., Lv, X., Yang, X., Ren, H., Zhao, Y., Zhang, Y., Gong, Y., Ni, P., Wu, H., et al. (2015) · Journal of NeuroVirology · doi:10.1007/s13365-015-0390-7 · Cited by 134

Next-Generation Sequencing for Diagnosis and Tailored Therapy: A Case Report of Astrovirus-Associated Progressive Encephalitis

Frémond, M., Pérot, P., Muth, E., Cros, G., Dumarest, M., Mahlaoui, N., Seilhean, D., Desguerre, I., Hébert, C., Corre-Catelin, N., et al. (2015) · Journal of the Pediatric Infectious Diseases Society · doi:10.1093/jpids/piv040 · Cited by 130

Bias in Whole Genome Amplification: Causes and Considerations

Sabina, J., & Leamon, J. H. (2015) · Methods in molecular biology · doi:10.1007/978-1-4939-2990-0_2 · Cited by 130

The diagnosis of infectious diseases by whole genome next generation sequencing: a new era is opening

Lecuit, M., & Éloit, M. (2014) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2014.00025 · Cited by 128

Clinical management of HIV-1 resistance

Paredes, R., & Clotet, B. (2009) · Antiviral Research · doi:10.1016/j.antiviral.2009.09.015 · Cited by 127

Direct Sequencing and Characterization of a Clinical Isolate of Epstein-Barr Virus from Nasopharyngeal Carcinoma Tissue by Using Next-Generation Sequencing Technology

Liu, P., Fang, X., Feng, Z., Guo, Y., Peng, R., Liu, T., Huang, Z., Feng, Y., Sun, X., Xiong, Z., et al. (2011) · Journal of Virology · doi:10.1128/jvi.00823-11 · Cited by 125

Protocol for Metagenomic Virus Detection in Clinical Specimens1

Kohl, C., Brinkmann, A., Dąbrowski, P. W., Radonić, A., Nitsche, A., & Kurth, A. A. (2014) · Emerging infectious diseases · doi:10.3201/eid2101.140766 · Cited by 110

Deep Sequencing of Viral Genomes Provides Insight into the Evolution and Pathogenesis of Varicella Zoster Virus and Its Vaccine in Humans

Depledge, D. P., Kundu, S., Jensen, N. J., Gray, E. R., Jones, M., Steinberg, S., Gershon, A. A., Kinchington, P. R., Schmid, D. S., Balloux, F., et al. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst210 · Cited by 106

Deep Sequencing of Norovirus Genomes Defines Evolutionary Patterns in an Urban Tropical Setting

Cotten, M. L., Petrova, V. N., Phan, M. V. T., Rabaa, M. A., Watson, S. J., Ong, S. H., Kellam, P., & Baker, S. G. (2014) · Journal of Virology · doi:10.1128/jvi.01333-14 · Cited by 103

Local Evolutionary Patterns of Human Respiratory Syncytial Virus Derived from Whole-Genome Sequencing

Agoti, C. N., Otieno, J. R., Munywoki, P. K., Mwihuri, A. G., Cane, P. A., Nokes, D. J., Kellam, P., & Cotten, M. L. (2015) · Journal of Virology · doi:10.1128/jvi.03391-14 · Cited by 92

Genome-Wide Patterns of Intrahuman Dengue Virus Diversity Reveal Associations with Viral Phylogenetic Clade and Interhost Diversity

Parameswaran, P., Charlebois, P., Téllez, Y., Nunez, A. C., Ryan, E. M., Malboeuf, C. M., Levin, J. Z., Lennon, N. J., Balmaseda, Á., Harris, E., et al. (2012) · Journal of Virology · doi:10.1128/jvi.00736-12 · Cited by 90

Detection of Low Frequency Multi-Drug Resistance and Novel Putative Maribavir Resistance in Immunocompromised Pediatric Patients with Cytomegalovirus

Houldcroft, C. J., Bryant, J. M., Depledge, D. P., et al. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.01317 · Cited by 87

Next-Generation Whole Genome Sequencing Identifies the Direction of Norovirus Transmission in Linked Patients

Kundu, S., Lockwood, J., Depledge, D. P., Chaudhry, Y., Aston, A., Rao, K., Hartley, J. C., Goodfellow, I., & Breuer, J. (2013) · Clinical Infectious Diseases · doi:10.1093/cid/cit287 · Cited by 86

Norovirus Whole-Genome Sequencing by SureSelect Target Enrichment: a Robust and Sensitive Method

Brown, J. R., Roy, S., Ruis, C., Romero, E. Y., Shah, D., Williams, R. J., & Breuer, J. (2016) · Journal of Clinical Microbiology · doi:10.1128/jcm.01052-16 · Cited by 85

Islands of linkage in an ocean of pervasive recombination reveals two-speed evolution of human cytomegalovirus genomes

Lassalle, F., Depledge, D. P., Reeves, M. B., Brown, A. C., Christiansen, M. T., Tutill, H. J., Williams, R. J., Einer-Jensen, K., Holdstock, J., Atkinson, C. E., et al. (2016) · Virus Evolution · doi:10.1093/ve/vew017 · Cited by 81

Whole-Genome Sequencing of Measles Virus Genotypes H1 and D8 During Outbreaks of Infection Following the 2010 Olympic Winter Games Reveals Viral Transmission Routes

Gardy, J. L., Naus, M., Amlani, A., Chung, W., Kim, H., Tan, M., Severini, A., Krajden, M., Puddicombe, D., Sahni, V., et al. (2015) · The Journal of Infectious Diseases · doi:10.1093/infdis/jiv271 · Cited by 79

DNA Extraction Columns Contaminated with Murine Sequences

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ve-SEQ: Robust, unbiased enrichment for streamlined detection and whole-genome sequencing of HCV and other highly diverse pathogens

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