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1
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Cooksey GLS, Morales C, Linde L, Schildhauer S, Guevara H, Chan E, Gibb K, Wong J, Lin W, Bonin BJ, Arizmendi O, Lam-Hine T, Tzvieli O, McDowell A, Kampen KM, Lopez DL, Ennis J, Lewis LS, Oren E, Hatada A, Molinar B, Frederick M, Han GS, Sanchez M, Garcia MA, McGrath A, Le NQ, Boyd E, Bertolucci RM, Corrigan J, Brodine S, Austin M, Roach WRK, Levin RM, Tyson BM, Pry JM, Cummings KJ, Wadford DA, Jain S. Severe Acute Respiratory Syndrome Coronavirus 2 and Respiratory Virus Sentinel Surveillance, California, USA, May 10, 2020-June 12, 2021. Emerg Infect Dis 2022; 28:9-19. [PMID: 34932449 PMCID: PMC8714231 DOI: 10.3201/eid2801.211682] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
State and local health departments established the California Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and Respiratory Virus Sentinel Surveillance System to conduct enhanced surveillance for SARS-CoV-2 and other respiratory pathogens at sentinel outpatient testing sites in 10 counties throughout California, USA. We describe results obtained during May 10, 2020‒June 12, 2021, and compare persons with positive and negative SARS-CoV-2 PCR results by using Poisson regression. We detected SARS-CoV-2 in 1,696 (19.6%) of 8,662 specimens. Among 7,851 specimens tested by respiratory panel, rhinovirus/enterovirus was detected in 906 (11.5%) specimens and other respiratory pathogens in 136 (1.7%) specimens. We also detected 23 co-infections with SARS-CoV-2 and another pathogen. SARS-CoV-2 positivity was associated with male participants, an age of 35-49 years, Latino race/ethnicity, obesity, and work in transportation occupations. Sentinel surveillance can provide useful virologic and epidemiologic data to supplement other disease monitoring activities and might become increasingly useful as routine testing decreases.
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2
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Ng DL, Granados AC, Santos YA, Servellita V, Goldgof GM, Meydan C, Sotomayor-Gonzalez A, Levine AG, Balcerek J, Han LM, Akagi N, Truong K, Neumann NM, Nguyen DN, Bapat SP, Cheng J, Martin CSS, Federman S, Foox J, Gopez A, Li T, Chan R, Chu CS, Wabl CA, Gliwa AS, Reyes K, Pan CY, Guevara H, Wadford D, Miller S, Mason CE, Chiu CY. A diagnostic host response biosignature for COVID-19 from RNA profiling of nasal swabs and blood. Sci Adv 2021; 7:eabe5984. [PMID: 33536218 PMCID: PMC7857687 DOI: 10.1126/sciadv.abe5984] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/15/2020] [Indexed: 05/05/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease-19 (COVID-19), has emerged as the cause of a global pandemic. We used RNA sequencing to analyze 286 nasopharyngeal (NP) swab and 53 whole-blood (WB) samples from 333 patients with COVID-19 and controls. Overall, a muted immune response was observed in COVID-19 relative to other infections (influenza, other seasonal coronaviruses, and bacterial sepsis), with paradoxical down-regulation of several key differentially expressed genes. Hospitalized patients and outpatients exhibited up-regulation of interferon-associated pathways, although heightened and more robust inflammatory responses were observed in hospitalized patients with more clinically severe illness. Two-layer machine learning-based host classifiers consisting of complete (>1000 genes), medium (<100), and small (<20) gene biomarker panels identified COVID-19 disease with 85.1-86.5% accuracy when benchmarked using an independent test set. SARS-CoV-2 infection has a distinct biosignature that differs between NP swabs and WB and can be leveraged for COVID-19 diagnosis.
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Affiliation(s)
- Dianna L Ng
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Andrea C Granados
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Yale A Santos
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Gregory M Goldgof
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Alicia Sotomayor-Gonzalez
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Andrew G Levine
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Joanna Balcerek
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Lucy M Han
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Naomi Akagi
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Kent Truong
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Neil M Neumann
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - David N Nguyen
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Sagar P Bapat
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Jing Cheng
- Department of Preventive and Restorative Dental Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Claudia Sanchez-San Martin
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Scot Federman
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Allan Gopez
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Tony Li
- Department of Medicine, Division of Hematology and Oncology, University of California, San Francisco, San Francisco, CA, USA
| | - Ray Chan
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Cynthia S Chu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Chiara A Wabl
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Amelia S Gliwa
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Kevin Reyes
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Chao-Yang Pan
- Viral and Rickettsial Disease Laboratory, California Department of Health, Richmond, CA, USA
| | - Hugo Guevara
- Viral and Rickettsial Disease Laboratory, California Department of Health, Richmond, CA, USA
| | - Debra Wadford
- Viral and Rickettsial Disease Laboratory, California Department of Health, Richmond, CA, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA.
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
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3
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Deng X, Gu W, Federman S, du Plessis L, Pybus OG, Faria NR, Wang C, Yu G, Bushnell B, Pan CY, Guevara H, Sotomayor-Gonzalez A, Zorn K, Gopez A, Servellita V, Hsu E, Miller S, Bedford T, Greninger AL, Roychoudhury P, Starita LM, Famulare M, Chu HY, Shendure J, Jerome KR, Anderson C, Gangavarapu K, Zeller M, Spencer E, Andersen KG, MacCannell D, Paden CR, Li Y, Zhang J, Tong S, Armstrong G, Morrow S, Willis M, Matyas BT, Mase S, Kasirye O, Park M, Masinde G, Chan C, Yu AT, Chai SJ, Villarino E, Bonin B, Wadford DA, Chiu CY. Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California. Science 2020; 369:582-587. [PMID: 32513865 PMCID: PMC7286545 DOI: 10.1126/science.abb9263] [Citation(s) in RCA: 196] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/03/2020] [Indexed: 12/30/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread globally, with >365,000 cases in California as of 17 July 2020. We investigated the genomic epidemiology of SARS-CoV-2 in Northern California from late January to mid-March 2020, using samples from 36 patients spanning nine counties and the Grand Princess cruise ship. Phylogenetic analyses revealed the cryptic introduction of at least seven different SARS-CoV-2 lineages into California, including epidemic WA1 strains associated with Washington state, with lack of a predominant lineage and limited transmission among communities. Lineages associated with outbreak clusters in two counties were defined by a single base substitution in the viral genome. These findings support contact tracing, social distancing, and travel restrictions to contain the spread of SARS-CoV-2 in California and other states.
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Affiliation(s)
- Xianding Deng
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Wei Gu
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Scot Federman
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | | | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK
| | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, UK
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK
| | - Candace Wang
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Guixia Yu
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Brian Bushnell
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chao-Yang Pan
- California Department of Public Health, Richmond, CA, USA
| | - Hugo Guevara
- California Department of Public Health, Richmond, CA, USA
| | - Alicia Sotomayor-Gonzalez
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Kelsey Zorn
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Allan Gopez
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Elaine Hsu
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Trevor Bedford
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Alexander L Greninger
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Pavitra Roychoudhury
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Lea M Starita
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Helen Y Chu
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jay Shendure
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Keith R Jerome
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Catie Anderson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karthik Gangavarapu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emily Spencer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Clinton R Paden
- U.S. Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Yan Li
- U.S. Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jing Zhang
- U.S. Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Suxiang Tong
- U.S. Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Scott Morrow
- San Mateo County Department of Public Health, San Mateo, CA, USA
| | - Matthew Willis
- Marin County Division of Public Health, San Rafael, CA, USA
| | - Bela T Matyas
- Solano County Department of Public Health, Fairfield, CA, USA
| | - Sundari Mase
- Sonoma County Department of Public Health, Santa Rosa, CA, USA
| | - Olivia Kasirye
- Sacramento County Division of Public Health, Sacramento, CA, USA
| | - Maggie Park
- San Joaquin County Department of Public Health, Stockton, CA, USA
| | - Godfred Masinde
- San Francisco County Department of Public Health, San Francisco, CA, USA
| | - Curtis Chan
- San Francisco County Department of Public Health, San Francisco, CA, USA
| | - Alexander T Yu
- California Department of Public Health, Richmond, CA, USA
| | - Shua J Chai
- California Department of Public Health, Richmond, CA, USA
- U.S. Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Elsa Villarino
- County of Santa Clara, Public Health Department, Santa Clara, CA, USA
| | - Brandon Bonin
- County of Santa Clara, Public Health Department, Santa Clara, CA, USA
| | | | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, CA, USA
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4
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Broughton JP, Deng X, Yu G, Fasching CL, Servellita V, Singh J, Miao X, Streithorst JA, Granados A, Sotomayor-Gonzalez A, Zorn K, Gopez A, Hsu E, Gu W, Miller S, Pan CY, Guevara H, Wadford DA, Chen JS, Chiu CY. CRISPR-Cas12-based detection of SARS-CoV-2. Nat Biotechnol 2020; 38:870-874. [PMID: 32300245 PMCID: PMC9107629 DOI: 10.1038/s41587-020-0513-4] [Citation(s) in RCA: 1500] [Impact Index Per Article: 375.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 04/06/2020] [Indexed: 12/26/2022]
Abstract
An outbreak of betacoronavirus severe acute respiratory syndrome (SARS)-CoV-2 began in Wuhan, China in December 2019. COVID-19, the disease associated with SARS-CoV-2 infection, rapidly spread to produce a global pandemic. We report development of a rapid (<40 min), easy-to-implement and accurate CRISPR-Cas12-based lateral flow assay for detection of SARS-CoV-2 from respiratory swab RNA extracts. We validated our method using contrived reference samples and clinical samples from patients in the United States, including 36 patients with COVID-19 infection and 42 patients with other viral respiratory infections. Our CRISPR-based DETECTR assay provides a visual and faster alternative to the US Centers for Disease Control and Prevention SARS-CoV-2 real-time RT-PCR assay, with 95% positive predictive agreement and 100% negative predictive agreement.
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Affiliation(s)
| | - Xianding Deng
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Guixia Yu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | | | - Venice Servellita
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Jasmeet Singh
- Mammoth Biosciences, Inc., South San Francisco, CA, USA
| | - Xin Miao
- Mammoth Biosciences, Inc., South San Francisco, CA, USA
| | - Jessica A Streithorst
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Andrea Granados
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Alicia Sotomayor-Gonzalez
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Kelsey Zorn
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Allan Gopez
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Elaine Hsu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Wei Gu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Chao-Yang Pan
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Hugo Guevara
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Debra A Wadford
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Janice S Chen
- Mammoth Biosciences, Inc., South San Francisco, CA, USA.
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA.
- Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA.
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5
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Broughton JP, Deng X, Yu G, Fasching CL, Servellita V, Singh J, Miao X, Streithorst JA, Granados A, Sotomayor-Gonzalez A, Zorn K, Gopez A, Hsu E, Gu W, Miller S, Pan CY, Guevara H, Wadford DA, Chen JS, Chiu CY. CRISPR-Cas12-based detection of SARS-CoV-2. Nat Biotechnol 2020; 38:870-874. [PMID: 32300245 PMCID: PMC9107629 DOI: 10.1038/s41587-020-0513-4,] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 04/06/2020] [Indexed: 02/02/2024]
Abstract
An outbreak of betacoronavirus severe acute respiratory syndrome (SARS)-CoV-2 began in Wuhan, China in December 2019. COVID-19, the disease associated with SARS-CoV-2 infection, rapidly spread to produce a global pandemic. We report development of a rapid (<40 min), easy-to-implement and accurate CRISPR-Cas12-based lateral flow assay for detection of SARS-CoV-2 from respiratory swab RNA extracts. We validated our method using contrived reference samples and clinical samples from patients in the United States, including 36 patients with COVID-19 infection and 42 patients with other viral respiratory infections. Our CRISPR-based DETECTR assay provides a visual and faster alternative to the US Centers for Disease Control and Prevention SARS-CoV-2 real-time RT-PCR assay, with 95% positive predictive agreement and 100% negative predictive agreement.
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Affiliation(s)
| | - Xianding Deng
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Guixia Yu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | | | - Venice Servellita
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Jasmeet Singh
- Mammoth Biosciences, Inc., South San Francisco, CA, USA
| | - Xin Miao
- Mammoth Biosciences, Inc., South San Francisco, CA, USA
| | - Jessica A Streithorst
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Andrea Granados
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Alicia Sotomayor-Gonzalez
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Kelsey Zorn
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Allan Gopez
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Elaine Hsu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Wei Gu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Chao-Yang Pan
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Hugo Guevara
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Debra A Wadford
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Janice S Chen
- Mammoth Biosciences, Inc., South San Francisco, CA, USA.
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA.
- Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA.
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6
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Deng X, Gu W, Federman S, du Plessis L, Pybus OG, Faria N, Wang C, Yu G, Pan CY, Guevara H, Sotomayor-Gonzalez A, Zorn K, Gopez A, Servellita V, Hsu E, Miller S, Bedford T, Greninger AL, Roychoudhury P, Starita LM, Famulare M, Chu HY, Shendure J, Jerome KR, Anderson C, Gangavarapu K, Zeller M, Spencer E, Andersen KG, MacCannell D, Paden CR, Li Y, Zhang J, Tong S, Armstrong G, Morrow S, Willis M, Matyas BT, Mase S, Kasirye O, Park M, Chan C, Yu AT, Chai SJ, Villarino E, Bonin B, Wadford DA, Chiu CY. A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage. medRxiv 2020. [PMID: 32511579 PMCID: PMC7276006 DOI: 10.1101/2020.03.27.20044925] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has spread globally, resulting in >300,000 reported cases worldwide as of March 21st, 2020. Here we investigate the genetic diversity and genomic epidemiology of SARS-CoV-2 in Northern California using samples from returning travelers, cruise ship passengers, and cases of community transmission with unclear infection sources. Virus genomes were sampled from 29 patients diagnosed with COVID-19 infection from Feb 3rd through Mar 15th. Phylogenetic analyses revealed at least 8 different SARS-CoV-2 lineages, suggesting multiple independent introductions of the virus into the state. Virus genomes from passengers on two consecutive excursions of the Grand Princess cruise ship clustered with those from an established epidemic in Washington State, including the WA1 genome representing the first reported case in the United States on January 19th. We also detected evidence for presumptive transmission of SARS-CoV-2 lineages from one community to another. These findings suggest that cryptic transmission of SARS-CoV-2 in Northern California to date is characterized by multiple transmission chains that originate via distinct introductions from international and interstate travel, rather than widespread community transmission of a single predominant lineage. Rapid testing and contact tracing, social distancing, and travel restrictions are measures that will help to slow SARS-CoV-2 spread in California and other regions of the USA.
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Affiliation(s)
- Xianding Deng
- Department of Laboratory Medicine, University of California, San Francisco, California, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Wei Gu
- Department of Laboratory Medicine, University of California, San Francisco, California, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Scot Federman
- Department of Laboratory Medicine, University of California, San Francisco, California, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | | | | | - Nuno Faria
- Department of Zoology, University of Oxford, Oxford, UK
| | - Candace Wang
- Department of Laboratory Medicine, University of California, San Francisco, California, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Guixia Yu
- Department of Laboratory Medicine, University of California, San Francisco, California, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Chao-Yang Pan
- California Department of Public Health, Richmond, California, USA
| | - Hugo Guevara
- California Department of Public Health, Richmond, California, USA
| | - Alicia Sotomayor-Gonzalez
- Department of Laboratory Medicine, University of California, San Francisco, California, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Kelsey Zorn
- Department of Biochemistry and Biophysics, San Francisco, California, USA
| | - Allan Gopez
- Department of Laboratory Medicine, University of California, San Francisco, California, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, California, USA
| | - Elaine Hsu
- Department of Laboratory Medicine, University of California, San Francisco, California, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, California, USA
| | - Trevor Bedford
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Alexander L Greninger
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Pavitra Roychoudhury
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Lea M Starita
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA.,Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Helen Y Chu
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA.,Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jay Shendure
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA.,Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.,Howards Hughes Medical Institute, Seattle, WA, USA
| | - Keith R Jerome
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Catie Anderson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karthik Gangavarapu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emily Spencer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Duncan MacCannell
- United States Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Clinton R Paden
- United States Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Yan Li
- United States Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jing Zhang
- United States Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Suxiang Tong
- United States Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Gregory Armstrong
- United States Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Scott Morrow
- San Mateo County Department of Public Health, San Mateo, California, USA
| | - Matthew Willis
- Marin County Division of Public Health, San Rafael, California, USA
| | - Bela T Matyas
- Solano County Department of Public Health, Fairfield, California, USA
| | - Sundari Mase
- Sonoma County Department of Public Health, Santa Rosa, California, USA
| | - Olivia Kasirye
- Sacramento County Division of Public Health, Sacramento, California, USA
| | - Maggie Park
- San Joaquin County Department of Public Health, Stockton, California, USA
| | - Curtis Chan
- San Francisco County Department of Public Health, San Francisco, California, USA
| | - Alexander T Yu
- California Department of Public Health, Richmond, California, USA
| | - Shua J Chai
- California Department of Public Health, Richmond, California, USA.,United States Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Elsa Villarino
- Santa Clara County Department of Public Health, Santa Clara, California, USA
| | - Brandon Bonin
- Santa Clara County Department of Public Health, Santa Clara, California, USA
| | - Debra A Wadford
- California Department of Public Health, Richmond, California, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, California, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA.,Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, California, USA
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7
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Broughton JP, Deng X, Yu G, Fasching CL, Singh J, Streithorst J, Granados A, Sotomayor-Gonzalez A, Zorn K, Gopez A, Hsu E, Gu W, Miller S, Pan CY, Guevara H, Wadford DA, Chen JS, Chiu CY. Rapid Detection of 2019 Novel Coronavirus SARS-CoV-2 Using a CRISPR-based DETECTR Lateral Flow Assay. medRxiv 2020:2020.03.06.20032334. [PMID: 32511449 PMCID: PMC7239074 DOI: 10.1101/2020.03.06.20032334] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
An outbreak of novel betacoronavirus, SARS-CoV-2 (formerly named 2019-nCoV), began in Wuhan, China in December 2019 and the COVID-19 disease associated with infection has since spread rapidly to multiple countries. Here we report the development of SARS-CoV-2 DETECTR, a rapid (~30 min), low-cost, and accurate CRISPR-Cas12 based lateral flow assay for detection of SARS-CoV-2 from respiratory swab RNA extracts. We validated this method using contrived reference samples and clinical samples from infected US patients and demonstrated comparable performance to the US CDC SARS-CoV-2 real-time RT-PCR assay.
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Affiliation(s)
| | - Xianding Deng
- Department of Laboratory Medicine, University of California, San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Guixia Yu
- Department of Laboratory Medicine, University of California, San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | | | - Jasmeet Singh
- Mammoth Biosciences, Inc., San Francisco, California, USA
| | - Jessica Streithorst
- Department of Laboratory Medicine, University of California, San Francisco, California, USA
| | - Andrea Granados
- Department of Laboratory Medicine, University of California, San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Alicia Sotomayor-Gonzalez
- Department of Laboratory Medicine, University of California, San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Kelsey Zorn
- Department of Biochemistry and Biophysics, San Francisco, California, USA
| | - Allan Gopez
- Department of Laboratory Medicine, University of California, San Francisco, California, USA
| | - Elaine Hsu
- Department of Laboratory Medicine, University of California, San Francisco, California, USA
| | - Wei Gu
- Department of Laboratory Medicine, University of California, San Francisco, California, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, California, USA
| | - Chao-Yang Pan
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Hugo Guevara
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Debra A. Wadford
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Janice S. Chen
- Mammoth Biosciences, Inc., San Francisco, California, USA
| | - Charles Y. Chiu
- Department of Laboratory Medicine, University of California, San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, California, USA
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8
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Labidi-Galy S, deLa Motte Rouge T, Derbel O, Wolfer A, Kalbacher E, Olivier T, Combes JD, Hu-Heimgartner K, Tredan O, Guevara H, Heinzelmann-Schwarz V, Fehr M, de Castelbajac V, Vaflard P, Crivelli L, Bonadona V, Viassolo V, Bazan F, Rodrigues M, Ray-Coquard I. Clinical factors associated with prolonged response and survival under olaparib as maintenance therapy in BRCA mutated ovarian cancers. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz250.011] [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: 11/13/2022] Open
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9
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Okomo-Adhiambo M, Mishin VP, Sleeman K, Saguar E, Guevara H, Reisdorf E, Griesser RH, Spackman KJ, Mendenhall M, Carlos MP, Healey B, St George K, Laplante J, Aden T, Chester S, Xu X, Gubareva LV. Standardizing the influenza neuraminidase inhibition assay among United States public health laboratories conducting virological surveillance. Antiviral Res 2016; 128:28-35. [PMID: 26808479 DOI: 10.1016/j.antiviral.2016.01.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 01/11/2016] [Accepted: 01/15/2016] [Indexed: 01/15/2023]
Abstract
BACKGROUND Monitoring influenza virus susceptibility to neuraminidase (NA) inhibitors (NAIs) is vital for detecting drug-resistant variants, and is primarily assessed using NA inhibition (NI) assays, supplemented by NA sequence analysis. However, differences in NI testing methodologies between surveillance laboratories results in variability of 50% inhibitory concentration (IC50) values, which impacts data sharing, reporting and interpretation. In 2011, the Centers for Disease Control and Prevention (CDC), in collaboration with the Association for Public Health Laboratories (APHL) spearheaded efforts to standardize fluorescence-based NI assay testing in the United States (U.S.), with the goal of achieving consistency of IC50 data. METHODS For the standardization process, three participating state public health laboratories (PHLs), designated as National Surveillance Reference Centers for Influenza (NSRC-Is), assessed the NAI susceptibility of the 2011-12 CDC reference virus panel using stepwise procedures, with support from the CDC reference laboratory. Next, the NSRC-Is assessed the NAI susceptibility of season 2011-12 U.S. influenza surveillance isolates (n = 940), with a large subset (n = 742) tested in parallel by CDC. Subsequently, U.S. influenza surveillance isolates (n = 9629) circulating during the next three influenza seasons (2012-15), were independently tested by the three NSRC-Is (n = 7331) and CDC (n = 2298). RESULTS The NI assay IC50s generated by respective NSRC-Is using viruses and drugs prepared by CDC were similar to those obtained with viruses and drugs prepared in-house, and were uniform between laboratories. IC50s for U.S. surveillance isolates tested during four consecutive influenza seasons (2011-15) were consistent from season to season, within and between laboratories. CONCLUSION These results show that the NI assay is robust enough to be standardized, marking the first time IC50 data have been normalized across multiple laboratories, and used for U.S. national NAI susceptibility surveillance.
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Affiliation(s)
- M Okomo-Adhiambo
- Influenza Division, NCIRD, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - V P Mishin
- Influenza Division, NCIRD, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - K Sleeman
- Influenza Division, NCIRD, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - E Saguar
- California Department of Public Health (CDPH), Richmond, CA, USA
| | - H Guevara
- California Department of Public Health (CDPH), Richmond, CA, USA
| | - E Reisdorf
- Wisconsin State Laboratory of Hygiene (WSLH), Madison, WI, USA
| | - R H Griesser
- Wisconsin State Laboratory of Hygiene (WSLH), Madison, WI, USA
| | - K J Spackman
- Unified State Laboratories: Public Health (USLPH), Taylorsville, UT, USA
| | - M Mendenhall
- Unified State Laboratories: Public Health (USLPH), Taylorsville, UT, USA
| | - M P Carlos
- Maryland Department of Health and Mental Hygiene (MD DHMH) Laboratories Administration, Baltimore, MD, USA
| | - B Healey
- Maryland Department of Health and Mental Hygiene (MD DHMH) Laboratories Administration, Baltimore, MD, USA
| | - K St George
- Wadsworth Center, New York State Department of Health (NYSDOH), Albany, NY, USA
| | - J Laplante
- Wadsworth Center, New York State Department of Health (NYSDOH), Albany, NY, USA
| | - T Aden
- Association of Public Health Laboratories (APHL), Silver Spring, MD, USA
| | - S Chester
- Association of Public Health Laboratories (APHL), Silver Spring, MD, USA
| | - X Xu
- Influenza Division, NCIRD, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - L V Gubareva
- Influenza Division, NCIRD, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA.
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10
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Louie JK, Yang S, Acosta M, Yen C, Samuel MC, Schechter R, Guevara H, Uyeki TM. Treatment with neuraminidase inhibitors for critically ill patients with influenza A (H1N1)pdm09. Clin Infect Dis 2012; 55:1198-204. [PMID: 22843781 DOI: 10.1093/cid/cis636] [Citation(s) in RCA: 167] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Neuraminidase inhibitor (NAI) antiviral drugs can shorten the duration of uncomplicated influenza when administered early (<48 hours after illness onset) to otherwise healthy outpatients, but the optimal timing of effective therapy for critically ill patients is not well established. METHODS We analyzed California surveillance data to characterize the outcomes of patients in intensive care units (ICUs) treated with NAIs for influenza A(H1N1)pdm09 (pH1N1). Demographic and clinical data were abstracted from medical records, using standardized case report forms. RESULTS From 3 April 2009 through 10 August 2010, 1950 pH1N1 cases hospitalized in ICUs were reported. Of 1859 (95%) with information available, 1676 (90%) received NAI treatment, and 183 (10%) did not. The median age was 37 years (range, 1 week-93 years), 1473 (79%) had ≥1 comorbidity, and 492 (26%) died. The median time from symptom onset to starting NAI treatment was 4 days (range, 0-52 days). NAI treatment was associated with survival: 107 of 183 untreated case patients (58%) survived, compared with 1260 of 1676 treated case patients (75%; P ≤ .0001). There was a trend toward improved survival for those treated earliest (P < .0001). Treatment initiated within 5 days after symptom onset was associated with improved survival compared to those never treated (P < .05). CONCLUSIONS NAI treatment of critically ill pH1N1 patients improves survival. While earlier treatment conveyed the most benefit, patients who started treatment up to 5 days after symptom onset also were more likely to survive. Further research is needed about whether starting NAI treatment >5 days after symptom onset may also convey benefit.
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Affiliation(s)
- Janice K Louie
- California Department of Public Health, 850 Marina Bay Pkwy., Richmond, CA 94804, USA.
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11
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Louie JK, Guevara H, Boston E, Dahlke M, Nevarez M, Kong T, Schechter R, Glaser CA, Schnurr DP. Rapid influenza antigen test for diagnosis of pandemic (H1N1) 2009. Emerg Infect Dis 2010; 16:824-6. [PMID: 20409373 DOI: 10.3201/eid1605.091797] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We compared the QuickVue Influenza test with PCR for diagnosing pandemic (H1N1) 2009 in 404 persons with influenza-like illness. Overall sensitivity, specificity, and positive and negative predictive values were 66%, 84%, 84%, and 64%, respectively. Rapid test results should be interpreted cautiously when pandemic (H1N1) 2009 virus is suspected.
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Affiliation(s)
- Janice K Louie
- California Department of Public Health, Richmond, California 94804, USA.
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12
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Louie JK, Guevara H, Boston E, Dahlke M, Nevarez M, Kong T, Schechter R, Glaser CA, Schnurr DP. Rapid influenza antigen test for diagnosis of pandemic (H1N1) 2009. Emerg Infect Dis 2010. [PMID: 20409373 PMCID: PMC2954007 DOI: 10.3201/eid1605.091794] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
We compared the QuickVue Influenza test with PCR for diagnosing pandemic (H1N1) 2009 in 404 persons with influenza-like illness. Overall sensitivity, specificity, and positive and negative predictive values were 66%, 84%, 84%, and 64%, respectively. Rapid test results should be interpreted cautiously when pandemic (H1N1) 2009 virus is suspected.
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Affiliation(s)
- Janice K Louie
- California Department of Public Health, Richmond, California 94804, USA.
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13
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Guevara H, Casseb J, Zijenah LS, Mbizvo M, Oceguera LF, Hanson CV, Katzenstein DA, Hendry RM. Maternal HIV-1 antibody and vertical transmission in subtype C virus infection. J Acquir Immune Defic Syndr 2002; 29:435-40. [PMID: 11981358 DOI: 10.1097/00126334-200204150-00002] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The role of maternal humoral immune response and viral load was analyzed in relation to the incidence of mother-to-child transmission (MTCT) of infants born to HIV-1 subtype C infected mothers. High levels of viral RNA in the serum correlated with MTCT as did high titers of subtype C consensus V3 peptide binding antibodies (BA) and neutralizing antibody (NA) to subtype B HIV-1MN. Logistic regression analysis showed that maternal viral load and V3 peptide subtype C BA were independent predictors for MTCT, odds ratio (OR) = 2.22 and OR = 2.52, respectively. No correlation between NA to homologous HIV-1 subtype C virus and MTCT was found. BA to V3 peptides may provide a rapid inexpensive method that can be used to determine the risk of HIV-1 MTCT.
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Affiliation(s)
- Hugo Guevara
- Viral and Rickettsial Disease Laboratory, California Department of Health Services, Richmond, CA, U.S.A
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14
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Guevara H, Johnston E, Zijenah L, Tobaiwa O, Mason P, Contag C, Mahomed K, Hendry M, Katzenstein D. Prenatal transmission of subtype C HIV-1 in Zimbabwe: HIV-1 RNA and DNA in maternal and cord blood. J Acquir Immune Defic Syndr 2000; 25:390-7. [PMID: 11141238 DOI: 10.1097/00042560-200012150-00002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Maternal and cord samples from HIV-seropositive women and their infants in Zimbabwe, where subtype C is the predominant strain of HIV, were analyzed to determine the frequency of detection of HIV RNA and DNA. HIV RNA was detected in 90% of maternal and in 38% of cord plasma at levels at least 25% of maternal plasma. Heteroduplex mobility assays and sequencing of virus envelope (C2-V5) demonstrated closely related, but unique, subtype C viruses in maternal and cord RNA, and a significantly greater frequency of cord viremia among women with homogenous, compared with heterogeneous viral envelope RNA. Quantification of RNA, measures of envelope viral diversity, and phylogenetic analysis of maternal and cord plasma RNA provide evidence for the frequent exposure and potential transmission of HIV from mother to infant before birth.
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Affiliation(s)
- H Guevara
- Viral and Rickettsial Disease Laboratory, California Department of Health Services, Berkeley, USA
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15
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Guevara H, Johnston E, Zijenah L, Tobaiwa O, Mason P, Contag C, Mahomed K, Hendry M, Katzenstein D. Prenatal Transmission of Subtype C HIV-1 in Zimbabwe: HIV-1 RNA and DNA in Maternal and Cord Blood. J Acquir Immune Defic Syndr 2000. [DOI: 10.1097/00126334-200012150-00002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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16
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Rojas M, Guevara H, Rincón R, Rodríguez M, Olivet C. [Occupational exposure and health effects of metallic mercury among dentists and dental assistants: a preliminary study. Valencia, Venezuela; 1998]. Acta Cient Venez 2000; 51:32-8. [PMID: 10974705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
The aim of this investigation was to establish mercury (Hg) health effects on dentists and dental assistants, its relationship with exposure conditions and the potential renal damage Hg-related. The total population was 66 people, with a sample of 37 (56%), 22 dentists (59.5%, 19 male, 3 female) and 15 dental assistants (40.5%, all female). This was accomplished by an interview, Hg in urine (Hg-U) and N-acetyl-B-D-glucosaminidase activity in urine (NAG-U). Average values of Hg-U for dentists were 22.4 +/- 6.4 micrograms/g creatinine and 22.2 +/- 6.1 micrograms/g creatinine for dental assistants NAG-U average values were 2.9 +/- 3 U/L and 5.2 +/- 8.1 U/L respectively. There were no statistically significant differences between these averages (p > 0.05). There was no correlation between the quantity of amalgam prepared and working hours with Hg-U and NAG-U. Most frequent symptoms referred by dentists were: irritability (54.5%), cephalalgia (45.4%), arthralgias (40.9%), and the ones more referred by assistants were arthralgias (53.3%), irritability (46.7%) and cephalalgia (46.7%). It was not found a significative risk of having them among these groups. There is a need for further investigations including environmental monitoring of Hg, clinical evaluation and neurobehavioural tests to detect early effects. It is important to enforce personal safety measures to control the exposure.
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Affiliation(s)
- M Rojas
- Centro de Investigaciones Toxicológicas, Universidad de Carabobo (CITUC), Valencia, Venezuela
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17
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18
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Sánchez F, Gómez JA, Guevara H, Santamaría A. [Diagnostic value examination of the eye fundus in pregnant patients with arterial hypertension]. Rev Colomb Obstet Ginecol 1970; 21:105-9. [PMID: 5450669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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