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Goswami C, Sheldon M, Bixby C, Keddache M, Bogdanowicz A, Wang Y, Schultz J, McDevitt J, LaPorta J, Kwon E, Buyske S, Garbolino D, Biloholowski G, Pastuszak A, Storella M, Bhalla A, Charlier-Rodriguez F, Hager R, Grimwood R, Nahas SA. Identification of SARS-CoV-2 variants using viral sequencing for the Centers for Disease Control and Prevention genomic surveillance program. BMC Infect Dis 2022; 22:404. [PMID: 35468749 PMCID: PMC9035976 DOI: 10.1186/s12879-022-07374-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/11/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Centers for Disease Control and Prevention contracted with laboratories to sequence the SARS-CoV-2 genome from positive samples across the United States to enable public health officials to investigate the impact of variants on disease severity as well as the effectiveness of vaccines and treatment. Herein we present the initial results correlating RT-PCR quality control metrics with sample collection and sequencing methods from full SARS-CoV-2 viral genomic sequencing of 24,441 positive patient samples between April and June 2021. METHODS RT-PCR confirmed (N Gene Ct value < 30) positive patient samples, with nucleic acid extracted from saliva, nasopharyngeal and oropharyngeal swabs were selected for viral whole genome SARS-CoV-2 sequencing. Sequencing was performed using Illumina COVIDSeq™ protocol on either the NextSeq550 or NovaSeq6000 systems. Informatic variant calling, and lineage analysis were performed using DRAGEN COVID Lineage applications on Illumina's Basespace cloud analytical system. All sequence data and variant calls were uploaded to NCBI and GISAID. RESULTS An association was observed between higher sequencing coverage, quality, and samples with a lower Ct value, with < 27 being optimal, across both sequencing platforms and sample collection methods. Both nasopharyngeal swabs and saliva samples were found to be optimal samples of choice for SARS-CoV-2 surveillance sequencing studies, both in terms of strain identification and sequencing depth of coverage, with NovaSeq 6000 providing higher coverage than the NextSeq 550. The most frequent variants identified were the B.1.617.2 Delta (India) and P.1 Gamma (Brazil) variants in the samples sequenced between April 2021 and June 2021. At the time of submission, the most common variant > 99% of positives sequenced was Omicron. CONCLUSION These initial analyses highlight the importance of sequencing platform, sample collection methods, and RT-PCR Ct values in guiding surveillance efforts. These surveillance studies evaluating genetic changes of SARS-CoV-2 have been identified as critical by the CDC that can affect many aspects of public health including transmission, disease severity, diagnostics, therapeutics, and vaccines.
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Affiliation(s)
- Chirayu Goswami
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Michael Sheldon
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Christian Bixby
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | | | | | - Yihe Wang
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Jonathan Schultz
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Jessica McDevitt
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - James LaPorta
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Elaine Kwon
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Steven Buyske
- Rutgers University, 559 Hill Center, 110 Frelinghuysen Rd, Piscataway, NJ, 08854, USA
| | - Dana Garbolino
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | | | - Alex Pastuszak
- Vault Health, 115 Broadway Suite 1800, 18th Floor, Dobbs Ferry, NY, 10522, USA
| | - Mary Storella
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Amit Bhalla
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | | | - Russ Hager
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Robin Grimwood
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Shareef A Nahas
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA.
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Radbel J, Jagpal S, Roy J, Brooks A, Tischfield J, Sheldon M, Bixby C, Witt D, Gennaro ML, Horton DB, Barrett ES, Carson JL, Panettieri RA, Blaser MJ. Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Is Comparable in Clinical Samples Preserved in Saline or Viral Transport Medium. J Mol Diagn 2020; 22:871-875. [PMID: 32405270 PMCID: PMC7219422 DOI: 10.1016/j.jmoldx.2020.04.209] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 04/28/2020] [Indexed: 12/22/2022] Open
Abstract
As the coronavirus disease 2019 (COVID-19) pandemic sweeps across the world, the availability of viral transport medium (VTM) has become severely limited, contributing to delays in diagnosis and rationing of diagnostic testing. Given that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral RNA has demonstrated stability, we posited that phosphate-buffered saline (PBS) may be a viable transport medium, as an alternative to VTM, for clinical real-time quantitative PCR (qPCR) testing. The intra-individual reliability and interindividual reliability of SARS-CoV-2 qPCR were assessed in clinical endotracheal secretion samples transported in VTM or PBS to evaluate the stability of the qPCR signal for three viral targets (N gene, ORF1ab, and S gene) when samples were stored in these media at room temperature for up to 18 hours. We report that the use of PBS as a transport medium allows high intra-individual and interindividual reliability, maintains viral stability, and compares with VTM in the detection of the three SARS-CoV-2 genes through 18 hours of storage. This study establishes PBS as a clinically useful medium that can be readily deployed for transporting and short-term preservation of specimens containing SARS-CoV-2. Use of PBS as a transport medium has the potential to increase testing capacity for SARS-CoV-2, aiding more widespread screening and early diagnosis of COVID-19.
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Affiliation(s)
- Jared Radbel
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey; Environmental and Occupational Health Sciences Institute, Rutgers University, Piscataway, New Jersey
| | - Sugeet Jagpal
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Jason Roy
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, New Jersey
| | - Andrew Brooks
- Environmental and Occupational Health Sciences Institute, Rutgers University, Piscataway, New Jersey; Rutgers University Cell and DNA Repository Infinite Biologics and Human Genetics Institute of New Jersey and Department of Genetics, Rutgers University, Piscataway, New Jersey
| | - Jay Tischfield
- Rutgers University Cell and DNA Repository Infinite Biologics and Human Genetics Institute of New Jersey and Department of Genetics, Rutgers University, Piscataway, New Jersey; Department of Pediatrics, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Michael Sheldon
- Rutgers University Cell and DNA Repository Infinite Biologics and Human Genetics Institute of New Jersey and Department of Genetics, Rutgers University, Piscataway, New Jersey
| | - Christian Bixby
- Rutgers University Cell and DNA Repository Infinite Biologics and Human Genetics Institute of New Jersey and Department of Genetics, Rutgers University, Piscataway, New Jersey
| | - Dana Witt
- Rutgers University Cell and DNA Repository Infinite Biologics and Human Genetics Institute of New Jersey and Department of Genetics, Rutgers University, Piscataway, New Jersey
| | - Maria L Gennaro
- Public Health Research Institute, Department of Medicine, New Jersey Medical School, Rutgers University, Newark, New Jersey
| | - Daniel B Horton
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, New Jersey; Department of Pediatrics, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey; Rutgers Center for Pharmacoepidemiology and Treatment Science, Institute for Health, Health Care Policy and Aging Research, New Brunswick, New Jersey
| | - Emily S Barrett
- Environmental and Occupational Health Sciences Institute, Rutgers University, Piscataway, New Jersey; Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, New Jersey
| | - Jeffrey L Carson
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Reynold A Panettieri
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey; Rutgers Institute for Translational Medicine and Science, New Brunswick, New Jersey
| | - Martin J Blaser
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey; Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey.
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Barnas D, Koontz D, Bazmi H, Bixby C, Jemsek J, Mellors JW. Clonal resistance analyses of HIV type-1 after failure of therapy with didanosine, lamivudine and tenofovir. Antivir Ther 2010; 15:437-41. [PMID: 20516563 DOI: 10.3851/imp1539] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND The rapid failure of initial therapy with combinations of nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs) that exclude zidovudine has not been fully explained by standard virus population analyses of HIV type-1 (HIV-1) drug resistance. We therefore investigated HIV-1 genotype and phenotype at the single genome level in samples from patients on a failing regimen of tenofovir (TNV), didanosine (ddI) and lamivudine (3TC). METHODS Single genome sequencing was performed on 9 failure samples containing both K65R and M184V mutations by standard genotype, either as wild-type/mutant mixtures (6/9) or as mutant only (3/9). Recombinant clones with different combinations of observed mutations were generated and tested for NRTI susceptibility. RESULTS Of the 204 single genome sequences analysed, 50% were K65R/M184V double mutants, 38% were M184V single mutants, 10% were M184I single mutants and only 1% (2 sequences) were K65R single mutants. Phenotypic testing of recombinant clones showed a significant increase in resistance for double mutants: mean fold resistance to abacavir, ddI and TNV was 6.5, 4.3 and 1.6 for K65R/M184V double mutants versus 2.5, 1.9 and 0.6 for M184V single mutants, respectively (P<0.001). CONCLUSIONS Mutants with K65R and M184V linked on the same genome were the most common HIV-1 variants in samples analysed from patients failing TNV, ddI and 3TC with both mutations detected by standard genotype. The double mutant exhibited reduced susceptibility to all three NRTIs in the regimen. This resistant phenotype, resulting from just two linked point mutations, likely contributes to rapid failure of NRTI combinations that exclude zidovudine.
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Affiliation(s)
- Douglas Barnas
- Department of Medicine, Division Infectious Diseases, University of Pittsburgh, Pittsburgh, PA, USA
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Bixby C, Ibe B, Abdullah M, Zhou W, Longo L, Raj J. Platelet Activating Factor Plays a Significant Role in Pulmonary Vascular Remodeling Associated with Chronic High-Altitude Hypoxia in Ovine Fetal Lambs. J Investig Med 2006. [DOI: 10.1177/108155890605401s44] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- C. Bixby
- Division of Neonatology, Harbor-UCLA Medical Center, Los Angeles Biomedical Research Institute, Torrance, CA
- Center for Perinatal Biology, Department of Physiology and Pharmacology and Department of Obstetrics and Gynecology, Loma Linda University School of Medicine, Loma Linda, CA
| | - B.O. Ibe
- Division of Neonatology, Harbor-UCLA Medical Center, Los Angeles Biomedical Research Institute, Torrance, CA
- Center for Perinatal Biology, Department of Physiology and Pharmacology and Department of Obstetrics and Gynecology, Loma Linda University School of Medicine, Loma Linda, CA
| | - M. Abdullah
- Division of Neonatology, Harbor-UCLA Medical Center, Los Angeles Biomedical Research Institute, Torrance, CA
- Center for Perinatal Biology, Department of Physiology and Pharmacology and Department of Obstetrics and Gynecology, Loma Linda University School of Medicine, Loma Linda, CA
| | - W. Zhou
- Division of Neonatology, Harbor-UCLA Medical Center, Los Angeles Biomedical Research Institute, Torrance, CA
- Center for Perinatal Biology, Department of Physiology and Pharmacology and Department of Obstetrics and Gynecology, Loma Linda University School of Medicine, Loma Linda, CA
| | - L.D. Longo
- Division of Neonatology, Harbor-UCLA Medical Center, Los Angeles Biomedical Research Institute, Torrance, CA
- Center for Perinatal Biology, Department of Physiology and Pharmacology and Department of Obstetrics and Gynecology, Loma Linda University School of Medicine, Loma Linda, CA
| | - J.U. Raj
- Division of Neonatology, Harbor-UCLA Medical Center, Los Angeles Biomedical Research Institute, Torrance, CA
- Center for Perinatal Biology, Department of Physiology and Pharmacology and Department of Obstetrics and Gynecology, Loma Linda University School of Medicine, Loma Linda, CA
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Bixby C, Ibe BO, Abdullah M, Zhou W, Longo LD, Raj JU. 160 PLATELET ACTIVATING FACTOR PLAYS A SIGNIFICANT ROLE IN PULMONARY VASCULAR REMODELING ASSOCIATED WITH CHRONIC HIGH-ALTITUDE HYPOXIA IN OVINE FETAL LAMBS. J Investig Med 2006. [DOI: 10.2310/6650.2005.x0004.159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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