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Laird Smith M, Murrell B, Eren K, Ignacio C, Landais E, Weaver S, Phung P, Ludka C, Hepler L, Caballero G, Pollner T, Guo Y, Richman D, Poignard P, Paxinos EE, Kosakovsky Pond SL, Smith DM. Rapid Sequencing of Complete env Genes from Primary HIV-1 Samples. Virus Evol 2016; 2:vew018. [PMID: 29492273 DOI: 10.1093/ve/vew018] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The ability to study rapidly evolving viral populations has been constrained by the read length of next-generation sequencing approaches and the sampling depth of single-genome amplification methods. Here, we develop and characterize a method using Pacific Biosciences' Single Molecule, Real-Time (SMRT®) sequencing technology to sequence multiple, intact full-length human immunodeficiency virus-1 env genes amplified from viral RNA populations circulating in blood, and provide computational tools for analyzing and visualizing these data.
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Affiliation(s)
- Melissa Laird Smith
- Pacific Biosciences, Menlo Park, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Biomedical Informatics, University of California, San Diego, San Diego, CA, USA.,Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, USA.,The International Aids Vaccine Initiative, Neutralizing Antibody Center, La Jolla, CA, USA.,LabCorp, Monogram Biosciences, South San Francisco, CA, USA.,Canyon Crest Academy, San Diego, CA, USA.,Department of Pathology, University of California, San Diego, San Diego, CA, USA.,Veterans Affairs Healthcare System, San Diego, CA, USA.,Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA, USA.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Ben Murrell
- Pacific Biosciences, Menlo Park, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Biomedical Informatics, University of California, San Diego, San Diego, CA, USA.,Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, USA.,The International Aids Vaccine Initiative, Neutralizing Antibody Center, La Jolla, CA, USA.,LabCorp, Monogram Biosciences, South San Francisco, CA, USA.,Canyon Crest Academy, San Diego, CA, USA.,Department of Pathology, University of California, San Diego, San Diego, CA, USA.,Veterans Affairs Healthcare System, San Diego, CA, USA.,Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA, USA.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Kemal Eren
- Pacific Biosciences, Menlo Park, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Biomedical Informatics, University of California, San Diego, San Diego, CA, USA.,Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, USA.,The International Aids Vaccine Initiative, Neutralizing Antibody Center, La Jolla, CA, USA.,LabCorp, Monogram Biosciences, South San Francisco, CA, USA.,Canyon Crest Academy, San Diego, CA, USA.,Department of Pathology, University of California, San Diego, San Diego, CA, USA.,Veterans Affairs Healthcare System, San Diego, CA, USA.,Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA, USA.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Caroline Ignacio
- Pacific Biosciences, Menlo Park, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Biomedical Informatics, University of California, San Diego, San Diego, CA, USA.,Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, USA.,The International Aids Vaccine Initiative, Neutralizing Antibody Center, La Jolla, CA, USA.,LabCorp, Monogram Biosciences, South San Francisco, CA, USA.,Canyon Crest Academy, San Diego, CA, USA.,Department of Pathology, University of California, San Diego, San Diego, CA, USA.,Veterans Affairs Healthcare System, San Diego, CA, USA.,Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA, USA.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Elise Landais
- Pacific Biosciences, Menlo Park, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Biomedical Informatics, University of California, San Diego, San Diego, CA, USA.,Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, USA.,The International Aids Vaccine Initiative, Neutralizing Antibody Center, La Jolla, CA, USA.,LabCorp, Monogram Biosciences, South San Francisco, CA, USA.,Canyon Crest Academy, San Diego, CA, USA.,Department of Pathology, University of California, San Diego, San Diego, CA, USA.,Veterans Affairs Healthcare System, San Diego, CA, USA.,Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA, USA.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Steven Weaver
- Pacific Biosciences, Menlo Park, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Biomedical Informatics, University of California, San Diego, San Diego, CA, USA.,Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, USA.,The International Aids Vaccine Initiative, Neutralizing Antibody Center, La Jolla, CA, USA.,LabCorp, Monogram Biosciences, South San Francisco, CA, USA.,Canyon Crest Academy, San Diego, CA, USA.,Department of Pathology, University of California, San Diego, San Diego, CA, USA.,Veterans Affairs Healthcare System, San Diego, CA, USA.,Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA, USA.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Pham Phung
- Pacific Biosciences, Menlo Park, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Biomedical Informatics, University of California, San Diego, San Diego, CA, USA.,Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, USA.,The International Aids Vaccine Initiative, Neutralizing Antibody Center, La Jolla, CA, USA.,LabCorp, Monogram Biosciences, South San Francisco, CA, USA.,Canyon Crest Academy, San Diego, CA, USA.,Department of Pathology, University of California, San Diego, San Diego, CA, USA.,Veterans Affairs Healthcare System, San Diego, CA, USA.,Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA, USA.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Colleen Ludka
- Pacific Biosciences, Menlo Park, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Biomedical Informatics, University of California, San Diego, San Diego, CA, USA.,Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, USA.,The International Aids Vaccine Initiative, Neutralizing Antibody Center, La Jolla, CA, USA.,LabCorp, Monogram Biosciences, South San Francisco, CA, USA.,Canyon Crest Academy, San Diego, CA, USA.,Department of Pathology, University of California, San Diego, San Diego, CA, USA.,Veterans Affairs Healthcare System, San Diego, CA, USA.,Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA, USA.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Lance Hepler
- Pacific Biosciences, Menlo Park, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Biomedical Informatics, University of California, San Diego, San Diego, CA, USA.,Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, USA.,The International Aids Vaccine Initiative, Neutralizing Antibody Center, La Jolla, CA, USA.,LabCorp, Monogram Biosciences, South San Francisco, CA, USA.,Canyon Crest Academy, San Diego, CA, USA.,Department of Pathology, University of California, San Diego, San Diego, CA, USA.,Veterans Affairs Healthcare System, San Diego, CA, USA.,Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA, USA.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Gemma Caballero
- Pacific Biosciences, Menlo Park, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Biomedical Informatics, University of California, San Diego, San Diego, CA, USA.,Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, USA.,The International Aids Vaccine Initiative, Neutralizing Antibody Center, La Jolla, CA, USA.,LabCorp, Monogram Biosciences, South San Francisco, CA, USA.,Canyon Crest Academy, San Diego, CA, USA.,Department of Pathology, University of California, San Diego, San Diego, CA, USA.,Veterans Affairs Healthcare System, San Diego, CA, USA.,Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA, USA.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Tristan Pollner
- Pacific Biosciences, Menlo Park, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Biomedical Informatics, University of California, San Diego, San Diego, CA, USA.,Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, USA.,The International Aids Vaccine Initiative, Neutralizing Antibody Center, La Jolla, CA, USA.,LabCorp, Monogram Biosciences, South San Francisco, CA, USA.,Canyon Crest Academy, San Diego, CA, USA.,Department of Pathology, University of California, San Diego, San Diego, CA, USA.,Veterans Affairs Healthcare System, San Diego, CA, USA.,Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA, USA.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Yan Guo
- Pacific Biosciences, Menlo Park, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Biomedical Informatics, University of California, San Diego, San Diego, CA, USA.,Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, USA.,The International Aids Vaccine Initiative, Neutralizing Antibody Center, La Jolla, CA, USA.,LabCorp, Monogram Biosciences, South San Francisco, CA, USA.,Canyon Crest Academy, San Diego, CA, USA.,Department of Pathology, University of California, San Diego, San Diego, CA, USA.,Veterans Affairs Healthcare System, San Diego, CA, USA.,Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA, USA.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Douglas Richman
- Pacific Biosciences, Menlo Park, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Biomedical Informatics, University of California, San Diego, San Diego, CA, USA.,Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, USA.,The International Aids Vaccine Initiative, Neutralizing Antibody Center, La Jolla, CA, USA.,LabCorp, Monogram Biosciences, South San Francisco, CA, USA.,Canyon Crest Academy, San Diego, CA, USA.,Department of Pathology, University of California, San Diego, San Diego, CA, USA.,Veterans Affairs Healthcare System, San Diego, CA, USA.,Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA, USA.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | | | - Pascal Poignard
- Pacific Biosciences, Menlo Park, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Biomedical Informatics, University of California, San Diego, San Diego, CA, USA.,Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, USA.,The International Aids Vaccine Initiative, Neutralizing Antibody Center, La Jolla, CA, USA.,LabCorp, Monogram Biosciences, South San Francisco, CA, USA.,Canyon Crest Academy, San Diego, CA, USA.,Department of Pathology, University of California, San Diego, San Diego, CA, USA.,Veterans Affairs Healthcare System, San Diego, CA, USA.,Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA, USA.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Ellen E Paxinos
- Pacific Biosciences, Menlo Park, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Biomedical Informatics, University of California, San Diego, San Diego, CA, USA.,Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, USA.,The International Aids Vaccine Initiative, Neutralizing Antibody Center, La Jolla, CA, USA.,LabCorp, Monogram Biosciences, South San Francisco, CA, USA.,Canyon Crest Academy, San Diego, CA, USA.,Department of Pathology, University of California, San Diego, San Diego, CA, USA.,Veterans Affairs Healthcare System, San Diego, CA, USA.,Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA, USA.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Sergei L Kosakovsky Pond
- Pacific Biosciences, Menlo Park, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Biomedical Informatics, University of California, San Diego, San Diego, CA, USA.,Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, USA.,The International Aids Vaccine Initiative, Neutralizing Antibody Center, La Jolla, CA, USA.,LabCorp, Monogram Biosciences, South San Francisco, CA, USA.,Canyon Crest Academy, San Diego, CA, USA.,Department of Pathology, University of California, San Diego, San Diego, CA, USA.,Veterans Affairs Healthcare System, San Diego, CA, USA.,Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA, USA.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Davey M Smith
- Pacific Biosciences, Menlo Park, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Biomedical Informatics, University of California, San Diego, San Diego, CA, USA.,Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, USA.,The International Aids Vaccine Initiative, Neutralizing Antibody Center, La Jolla, CA, USA.,LabCorp, Monogram Biosciences, South San Francisco, CA, USA.,Canyon Crest Academy, San Diego, CA, USA.,Department of Pathology, University of California, San Diego, San Diego, CA, USA.,Veterans Affairs Healthcare System, San Diego, CA, USA.,Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA, USA.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
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