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Karan A, Shah N, Garrigues JM, Alarcόn J, Hemarajata P, Finn LE, Poortinga K, Danza P, Kulkarni S, Kim M, Terashita D, Green NM, Balter S. Surveillance of Complicated Mpox Cases Unresponsive to Oral Tecovirimat in Los Angeles County, 2022. J Infect Dis 2024; 229:S249-S254. [PMID: 37995310 DOI: 10.1093/infdis/jiad517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/14/2023] [Accepted: 11/20/2023] [Indexed: 11/25/2023] Open
Abstract
The Los Angeles County Department of Public Health established a surveillance system to identify complicated (advanced human immunodeficiency virus [HIV] or hospitalized) mpox cases. From 1 August to 30 November 2022, we identified 1581 mpox cases, of which 134 (8.5%) were complicated. A subset of 8 cases did not recover after either initiating or completing a course of oral tecovirimat. All 8 patients were HIV positive and had advanced HIV (CD4 count <200 cells/μL). We identified 8 distinct mutations previously associated with tecovirimat resistance in specimens collected from 6 patients. Ongoing surveillance of viral evolution requires close coordination between health departments and frontline providers.
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Affiliation(s)
- Abraar Karan
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California
| | - Naman Shah
- Los Angeles County Department of Public Health, Los Angeles, California
| | - Jacob M Garrigues
- Los Angeles County Department of Public Health, Los Angeles, California
| | - Jemma Alarcόn
- Los Angeles County Department of Public Health, Los Angeles, California
| | - Peera Hemarajata
- Los Angeles County Department of Public Health, Los Angeles, California
| | - Lauren E Finn
- Los Angeles County Department of Public Health, Los Angeles, California
| | | | - Phoebe Danza
- Los Angeles County Department of Public Health, Los Angeles, California
| | - Sonali Kulkarni
- Los Angeles County Department of Public Health, Los Angeles, California
| | - Moon Kim
- Los Angeles County Department of Public Health, Los Angeles, California
| | - Dawn Terashita
- Los Angeles County Department of Public Health, Los Angeles, California
| | - Nicole M Green
- Los Angeles County Department of Public Health, Los Angeles, California
| | - Sharon Balter
- Los Angeles County Department of Public Health, Los Angeles, California
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2
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Leonard CM, Poortinga K, Nguyen E, Karan A, Kulkarni S, Cohen R, Garrigues JM, Marutani AN, Green NM, Kim, AA, Sey K, Pérez MJ. Mpox Outbreak - Los Angeles County, California, May 4-August 17, 2023. MMWR Morb Mortal Wkly Rep 2024; 73:44-48. [PMID: 38236779 PMCID: PMC10803096 DOI: 10.15585/mmwr.mm7302a4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Since May 2022, approximately 2,500 mpox cases have been reported in Los Angeles County (LAC), California. Beginning in May 2023, the LAC Department of Public Health observed a consistent increase in mpox cases after a prolonged period of low incidence. A total of 56 cases were identified during May 4-August 17, 2023. A minority of mpox patients were fully vaccinated (29%). One patient was hospitalized; no deaths were reported. Two cases of reinfection occurred, both of which were associated with mild illness. The increasing number of cases during this period was significant, as few other health departments in the United States reported an increase in mpox cases during the same period. The outbreak spread similarly to the 2022 U.S. mpox outbreak, mainly through sexual contact among gay, bisexual, and other men who have sex with men. Vaccination against mpox became available in June 2022 and has been shown to be effective at preventing mpox disease. This outbreak was substantially smaller than the 2022 mpox outbreak in LAC (2,280 cases); possible explanations for the lower case count include increased immunity provided from vaccination against mpox and population immunity from previous infections. Nonetheless, mpox continues to spread within LAC, and preventive measures, such as receipt of JYNNEOS vaccination, are recommended for persons at risk of Monkeypox virus exposure.
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Garrigues JM, Hemarajata P, Espinosa A, Hacker JK, Wynn NT, Smith TG, Gigante CM, Davidson W, Vega J, Edmondson H, Karan A, Marutani AN, Kim M, Terashita D, Balter SE, Hutson CL, Green NM. Community spread of a human monkeypox virus variant with a tecovirimat resistance-associated mutation. Antimicrob Agents Chemother 2023; 67:e0097223. [PMID: 37823631 PMCID: PMC10649028 DOI: 10.1128/aac.00972-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023] Open
Abstract
ABSTRACT
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Affiliation(s)
| | - Peera Hemarajata
- Los Angeles County Department of Public Health, Downey, California, USA
| | - Alex Espinosa
- California Department of Public Health, Richmond, California, USA
| | - Jill K. Hacker
- California Department of Public Health, Richmond, California, USA
| | - Nhien T. Wynn
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Todd G. Smith
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Whitni Davidson
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jonte Vega
- Ventura County Public Health, Oxnard, California, USA
| | | | - Abraar Karan
- Los Angeles County Department of Public Health, Downey, California, USA
- Stanford University, Stanford, California, USA
| | - Amy N. Marutani
- Los Angeles County Department of Public Health, Downey, California, USA
| | - Moon Kim
- Los Angeles County Department of Public Health, Downey, California, USA
| | - Dawn Terashita
- Los Angeles County Department of Public Health, Downey, California, USA
| | - Sharon E. Balter
- Los Angeles County Department of Public Health, Downey, California, USA
| | | | - Nicole M. Green
- Los Angeles County Department of Public Health, Downey, California, USA
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Yang S, Multani A, Garrigues JM, Oh MS, Hemarajata P, Burleson T, Green NM, Oliai C, Gaynor PT, Beaird OE, Winston DJ, Seet CS, Schaenman JM. Transient SARS-CoV-2 RNA-Dependent RNA Polymerase Mutations after Remdesivir Treatment for Chronic COVID-19 in Two Transplant Recipients: Case Report and Intra-Host Viral Genomic Investigation. Microorganisms 2023; 11:2096. [PMID: 37630656 PMCID: PMC10460003 DOI: 10.3390/microorganisms11082096] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/10/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Remdesivir is the first FDA-approved drug for treating severe SARS-CoV-2 infection and targets RNA-dependent RNA polymerase (RdRp) that is required for viral replication. To monitor for the development of mutations that may result in remdesivir resistance during prolonged treatment, we sequenced SARS-CoV-2 specimens collected at different treatment time points in two transplant patients with severe COVID-19. In the first patient, an allogeneic hematopoietic stem cell transplant recipient, a transient RdRp catalytic subunit mutation (nsp12:A449V) was observed that has not previously been associated with remdesivir resistance. As no in vitro study had been conducted to elucidate the phenotypic effect of nsp12:A449V, its clinical significance is unclear. In the second patient, two other transient RdRp mutations were detected: one in the catalytic subunit (nsp12:V166A) and the other in an accessory subunit important for processivity (nsp7:D67N). This is the first case report for a potential link between the nsp12:V166A mutation and remdesivir resistance in vivo, which had only been previously described by in vitro studies. The nsp7:D67N mutation has not previously been associated with remdesivir resistance, and whether it has a phenotypic effect is unknown. Our study revealed SARS-CoV-2 genetic dynamics during remdesivir treatment in transplant recipients that involved mutations in the RdRp complex (nsp7 and nsp12), which may be the result of selective pressure. These results suggest that close monitoring for potential resistance during the course of remdesivir treatment in highly vulnerable patient populations may be beneficial. Development and utilization of diagnostic RdRp genotyping tests may be a future direction for improving the management of chronic COVID-19.
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Affiliation(s)
- Shangxin Yang
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Ashrit Multani
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; (A.M.); (P.T.G.); (O.E.B.)
| | - Jacob M. Garrigues
- Public Health Laboratories, Los Angeles County Department of Public Health, Downey, CA 90242, USA (P.H.); (T.B.); (N.M.G.)
| | - Michael S. Oh
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; (M.S.O.); (C.O.); (D.J.W.)
| | - Peera Hemarajata
- Public Health Laboratories, Los Angeles County Department of Public Health, Downey, CA 90242, USA (P.H.); (T.B.); (N.M.G.)
| | - Taylor Burleson
- Public Health Laboratories, Los Angeles County Department of Public Health, Downey, CA 90242, USA (P.H.); (T.B.); (N.M.G.)
| | - Nicole M. Green
- Public Health Laboratories, Los Angeles County Department of Public Health, Downey, CA 90242, USA (P.H.); (T.B.); (N.M.G.)
| | - Caspian Oliai
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; (M.S.O.); (C.O.); (D.J.W.)
| | - Pryce T. Gaynor
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; (A.M.); (P.T.G.); (O.E.B.)
| | - Omer E. Beaird
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; (A.M.); (P.T.G.); (O.E.B.)
| | - Drew J. Winston
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; (M.S.O.); (C.O.); (D.J.W.)
| | - Christopher S. Seet
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; (M.S.O.); (C.O.); (D.J.W.)
| | - Joanna M. Schaenman
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; (A.M.); (P.T.G.); (O.E.B.)
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Garrigues JM, Hemarajata P, Karan A, Shah NK, Alarcón J, Marutani AN, Finn L, Smith TG, Gigante CM, Davidson W, Wynn NT, Hutson CL, Kim M, Terashita D, Balter SE, Green NM. Identification of Tecovirimat Resistance-Associated Mutations in Human Monkeypox Virus - Los Angeles County. Antimicrob Agents Chemother 2023; 67:e0056823. [PMID: 37338408 PMCID: PMC10353411 DOI: 10.1128/aac.00568-23] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023] Open
Affiliation(s)
| | - Peera Hemarajata
- Los Angeles County Department of Public Health, Downey, California, USA
| | - Abraar Karan
- Los Angeles County Department of Public Health, Downey, California, USA
- Stanford University School of Medicine, Stanford, California, USA
| | - Naman K. Shah
- Los Angeles County Department of Public Health, Downey, California, USA
| | - Jemma Alarcón
- Los Angeles County Department of Public Health, Downey, California, USA
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Amy N. Marutani
- Los Angeles County Department of Public Health, Downey, California, USA
| | - Lauren Finn
- Los Angeles County Department of Public Health, Downey, California, USA
| | - Todd G. Smith
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Whitni Davidson
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Nhien T. Wynn
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Moon Kim
- Los Angeles County Department of Public Health, Downey, California, USA
| | - Dawn Terashita
- Los Angeles County Department of Public Health, Downey, California, USA
| | - Sharon E. Balter
- Los Angeles County Department of Public Health, Downey, California, USA
| | - Nicole M. Green
- Los Angeles County Department of Public Health, Downey, California, USA
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6
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Chen NFG, Chaguza C, Gagne L, Doucette M, Smole S, Buzby E, Hall J, Ash S, Harrington R, Cofsky S, Clancy S, Kapsak CJ, Sevinsky J, Libuit K, Park DJ, Hemarajata P, Garrigues JM, Green NM, Sierra-Patev S, Carpenter-Azevedo K, Huard RC, Pearson C, Incekara K, Nishimura C, Huang JP, Gagnon E, Reever E, Razeq J, Muyombwe A, Borges V, Ferreira R, Sobral D, Duarte S, Santos D, Vieira L, Gomes JP, Aquino C, Savino IM, Felton K, Bajwa M, Hayward N, Miller H, Naumann A, Allman R, Greer N, Fall A, Mostafa HH, McHugh MP, Maloney DM, Dewar R, Kenicer J, Parker A, Mathers K, Wild J, Cotton S, Templeton KE, Churchwell G, Lee PA, Pedrosa M, McGruder B, Schmedes S, Plumb MR, Wang X, Barcellos RB, Godinho FMS, Salvato RS, Ceniseros A, Breban MI, Grubaugh ND, Gallagher GR, Vogels CBF. Development of an amplicon-based sequencing approach in response to the global emergence of mpox. PLoS Biol 2023; 21:e3002151. [PMID: 37310918 PMCID: PMC10263305 DOI: 10.1371/journal.pbio.3002151] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [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] [Received: 01/12/2023] [Accepted: 05/05/2023] [Indexed: 06/15/2023] Open
Abstract
The 2022 multicountry mpox outbreak concurrent with the ongoing Coronavirus Disease 2019 (COVID-19) pandemic further highlighted the need for genomic surveillance and rapid pathogen whole-genome sequencing. While metagenomic sequencing approaches have been used to sequence many of the early mpox infections, these methods are resource intensive and require samples with high viral DNA concentrations. Given the atypical clinical presentation of cases associated with the outbreak and uncertainty regarding viral load across both the course of infection and anatomical body sites, there was an urgent need for a more sensitive and broadly applicable sequencing approach. Highly multiplexed amplicon-based sequencing (PrimalSeq) was initially developed for sequencing of Zika virus, and later adapted as the main sequencing approach for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Here, we used PrimalScheme to develop a primer scheme for human monkeypox virus that can be used with many sequencing and bioinformatics pipelines implemented in public health laboratories during the COVID-19 pandemic. We sequenced clinical specimens that tested presumptively positive for human monkeypox virus with amplicon-based and metagenomic sequencing approaches. We found notably higher genome coverage across the virus genome, with minimal amplicon drop-outs, in using the amplicon-based sequencing approach, particularly in higher PCR cycle threshold (Ct) (lower DNA titer) samples. Further testing demonstrated that Ct value correlated with the number of sequencing reads and influenced the percent genome coverage. To maximize genome coverage when resources are limited, we recommend selecting samples with a PCR Ct below 31 Ct and generating 1 million sequencing reads per sample. To support national and international public health genomic surveillance efforts, we sent out primer pool aliquots to 10 laboratories across the United States, United Kingdom, Brazil, and Portugal. These public health laboratories successfully implemented the human monkeypox virus primer scheme in various amplicon sequencing workflows and with different sample types across a range of Ct values. Thus, we show that amplicon-based sequencing can provide a rapidly deployable, cost-effective, and flexible approach to pathogen whole-genome sequencing in response to newly emerging pathogens. Importantly, through the implementation of our primer scheme into existing SARS-CoV-2 workflows and across a range of sample types and sequencing platforms, we further demonstrate the potential of this approach for rapid outbreak response.
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Affiliation(s)
- Nicholas F. G. Chen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Luc Gagne
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Matthew Doucette
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Sandra Smole
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Erika Buzby
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Joshua Hall
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Stephanie Ash
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Rachel Harrington
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Seana Cofsky
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Selina Clancy
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Curtis J. Kapsak
- Theiagen Genomics, Highlands Ranch, Colorado, United States of America
| | - Joel Sevinsky
- Theiagen Genomics, Highlands Ranch, Colorado, United States of America
| | - Kevin Libuit
- Theiagen Genomics, Highlands Ranch, Colorado, United States of America
| | - Daniel J. Park
- Broad Institute, Cambridge, Massachusetts, United States of America
| | - Peera Hemarajata
- Los Angeles County Public Health Laboratories, Downey, California, United States of America
| | - Jacob M. Garrigues
- Los Angeles County Public Health Laboratories, Downey, California, United States of America
| | - Nicole M. Green
- Los Angeles County Public Health Laboratories, Downey, California, United States of America
| | - Sean Sierra-Patev
- Rhode Island Department of Health, Rhode Island State Health Laboratory, Providence, Rhode Island, United States of America
| | - Kristin Carpenter-Azevedo
- Rhode Island Department of Health, Rhode Island State Health Laboratory, Providence, Rhode Island, United States of America
| | - Richard C. Huard
- Rhode Island Department of Health, Rhode Island State Health Laboratory, Providence, Rhode Island, United States of America
| | - Claire Pearson
- Connecticut Department of Public Health, Rocky Hill, Connecticut, United States of America
| | - Kutluhan Incekara
- Connecticut Department of Public Health, Rocky Hill, Connecticut, United States of America
| | - Christina Nishimura
- Connecticut Department of Public Health, Rocky Hill, Connecticut, United States of America
| | - Jian Ping Huang
- Connecticut Department of Public Health, Rocky Hill, Connecticut, United States of America
| | - Emily Gagnon
- Connecticut Department of Public Health, Rocky Hill, Connecticut, United States of America
| | - Ethan Reever
- Connecticut Department of Public Health, Rocky Hill, Connecticut, United States of America
| | - Jafar Razeq
- Connecticut Department of Public Health, Rocky Hill, Connecticut, United States of America
| | - Anthony Muyombwe
- Connecticut Department of Public Health, Rocky Hill, Connecticut, United States of America
| | - Vítor Borges
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Rita Ferreira
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Daniel Sobral
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Silvia Duarte
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Daniela Santos
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Luís Vieira
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Faculty of Veterinary Medicine, Lusófona University, Lisbon, Portugal
| | - Carly Aquino
- Delaware Public Health Laboratory, Smyrna, Delaware, United States of America
| | - Isabella M. Savino
- Delaware Public Health Laboratory, Smyrna, Delaware, United States of America
| | - Karinda Felton
- Delaware Public Health Laboratory, Smyrna, Delaware, United States of America
| | - Moneeb Bajwa
- Delaware Public Health Laboratory, Smyrna, Delaware, United States of America
| | - Nyjil Hayward
- Delaware Public Health Laboratory, Smyrna, Delaware, United States of America
| | - Holly Miller
- Delaware Public Health Laboratory, Smyrna, Delaware, United States of America
| | - Allison Naumann
- Delaware Public Health Laboratory, Smyrna, Delaware, United States of America
| | - Ria Allman
- Delaware Public Health Laboratory, Smyrna, Delaware, United States of America
| | - Neel Greer
- Delaware Public Health Laboratory, Smyrna, Delaware, United States of America
| | - Amary Fall
- Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Heba H. Mostafa
- Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Martin P. McHugh
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
- School of Medicine, University of St Andrews, St Andrews, United Kingdom
| | - Daniel M. Maloney
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Rebecca Dewar
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Juliet Kenicer
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Abby Parker
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Katharine Mathers
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Jonathan Wild
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Seb Cotton
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Kate E. Templeton
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - George Churchwell
- Florida Department of Health, Bureau of Public Health Laboratories, Jacksonville, Florida, United States of America
| | - Philip A. Lee
- Florida Department of Health, Bureau of Public Health Laboratories, Jacksonville, Florida, United States of America
| | - Maria Pedrosa
- Florida Department of Health, Bureau of Public Health Laboratories, Jacksonville, Florida, United States of America
| | - Brenna McGruder
- Florida Department of Health, Bureau of Public Health Laboratories, Jacksonville, Florida, United States of America
| | - Sarah Schmedes
- Florida Department of Health, Bureau of Public Health Laboratories, Jacksonville, Florida, United States of America
| | - Matthew R. Plumb
- Minnesota Department of Health, Public Health Laboratory, St. Paul, Minnesota, United States of America
| | - Xiong Wang
- Minnesota Department of Health, Public Health Laboratory, St. Paul, Minnesota, United States of America
| | - Regina Bones Barcellos
- Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Fernanda M. S. Godinho
- Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Richard Steiner Salvato
- Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Aimee Ceniseros
- Idaho Bureau of Laboratories, Boise, Idaho, United States of America
| | - Mallery I. Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
| | - Glen R. Gallagher
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
- Rhode Island Department of Health, Rhode Island State Health Laboratory, Providence, Rhode Island, United States of America
| | - Chantal B. F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
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Alarcón J, Kim M, Terashita D, Davar K, Garrigues JM, Guccione JP, Evans MG, Hemarajata P, Wald-Dickler N, Holtom P, Garcia Tome R, Anyanwu L, Shah NK, Miller M, Smith T, Matheny A, Davidson W, Hutson CL, Lucas J, Ukpo OC, Green NM, Balter SE. An Mpox-Related Death in the United States. N Engl J Med 2023; 388:1246-1247. [PMID: 36884032 DOI: 10.1056/nejmc2214921] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Affiliation(s)
- Jemma Alarcón
- Centers for Disease Control and Prevention, Atlanta, GA
| | - Moon Kim
- Los Angeles County Department of Public Health, Los Angeles, CA
| | - Dawn Terashita
- Los Angeles County Department of Public Health, Los Angeles, CA
| | - Kusha Davar
- Los Angeles County-University of Southern California Medical Center, Los Angeles, CA
| | | | - Jack P Guccione
- Los Angeles County Department of Medical Examiner-Coroner, Los Angeles, CA
| | | | | | - Noah Wald-Dickler
- Los Angeles County-University of Southern California Medical Center, Los Angeles, CA
| | - Paul Holtom
- Los Angeles County-University of Southern California Medical Center, Los Angeles, CA
| | - Rodrigo Garcia Tome
- Los Angeles County-University of Southern California Medical Center, Los Angeles, CA
| | - Lovelyn Anyanwu
- Los Angeles County Department of Public Health, Los Angeles, CA
| | - Naman K Shah
- Los Angeles County Department of Public Health, Los Angeles, CA
| | - Matthew Miller
- Los Angeles County Department of Medical Examiner-Coroner, Los Angeles, CA
| | - Todd Smith
- Centers for Disease Control and Prevention, Atlanta, GA
| | | | | | | | - Jonathan Lucas
- Los Angeles County Department of Medical Examiner-Coroner, Los Angeles, CA
| | - Odey C Ukpo
- Los Angeles County Department of Medical Examiner-Coroner, Los Angeles, CA
| | - Nicole M Green
- Los Angeles County Department of Public Health, Los Angeles, CA
| | - Sharon E Balter
- Los Angeles County Department of Public Health, Los Angeles, CA
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8
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Chen NF, Chaguza C, Gagne L, Doucette M, Smole S, Buzby E, Hall J, Ash S, Harrington R, Cofsky S, Clancy S, Kapsak CJ, Sevinsky J, Libuit K, Park DJ, Hemarajata P, Garrigues JM, Green NM, Sierra-Patev S, Carpenter-Azevedo K, Huard RC, Pearson C, Incekara K, Nishimura C, Huang JP, Gagnon E, Reever E, Razeq J, Muyombwe A, Borges V, Ferreira R, Sobral D, Duarte S, Santos D, Vieira L, Gomes JP, Aquino C, Savino IM, Felton K, Bajwa M, Hayward N, Miller H, Naumann A, Allman R, Greer N, Fall A, Mostafa HH, McHugh MP, Maloney DM, Dewar R, Kenicer J, Parker A, Mathers K, Wild J, Cotton S, Templeton KE, Churchwell G, Lee PA, Pedrosa M, McGruder B, Schmedes S, Plumb MR, Wang X, Barcellos RB, Godinho FM, Salvato RS, Ceniseros A, Breban MI, Grubaugh ND, Gallagher GR, Vogels CB. Development of an amplicon-based sequencing approach in response to the global emergence of human monkeypox virus. medRxiv 2023:2022.10.14.22280783. [PMID: 36299420 PMCID: PMC9603838 DOI: 10.1101/2022.10.14.22280783] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The 2022 multi-country monkeypox (mpox) outbreak concurrent with the ongoing COVID-19 pandemic has further highlighted the need for genomic surveillance and rapid pathogen whole genome sequencing. While metagenomic sequencing approaches have been used to sequence many of the early mpox infections, these methods are resource intensive and require samples with high viral DNA concentrations. Given the atypical clinical presentation of cases associated with the outbreak and uncertainty regarding viral load across both the course of infection and anatomical body sites, there was an urgent need for a more sensitive and broadly applicable sequencing approach. Highly multiplexed amplicon-based sequencing (PrimalSeq) was initially developed for sequencing of Zika virus, and later adapted as the main sequencing approach for SARS-CoV-2. Here, we used PrimalScheme to develop a primer scheme for human monkeypox virus that can be used with many sequencing and bioinformatics pipelines implemented in public health laboratories during the COVID-19 pandemic. We sequenced clinical samples that tested presumptive positive for human monkeypox virus with amplicon-based and metagenomic sequencing approaches. We found notably higher genome coverage across the virus genome, with minimal amplicon drop-outs, in using the amplicon-based sequencing approach, particularly in higher PCR cycle threshold (lower DNA titer) samples. Further testing demonstrated that Ct value correlated with the number of sequencing reads and influenced the percent genome coverage. To maximize genome coverage when resources are limited, we recommend selecting samples with a PCR cycle threshold below 31 Ct and generating 1 million sequencing reads per sample. To support national and international public health genomic surveillance efforts, we sent out primer pool aliquots to 10 laboratories across the United States, United Kingdom, Brazil, and Portugal. These public health laboratories successfully implemented the human monkeypox virus primer scheme in various amplicon sequencing workflows and with different sample types across a range of Ct values. Thus, we show that amplicon based sequencing can provide a rapidly deployable, cost-effective, and flexible approach to pathogen whole genome sequencing in response to newly emerging pathogens. Importantly, through the implementation of our primer scheme into existing SARS-CoV-2 workflows and across a range of sample types and sequencing platforms, we further demonstrate the potential of this approach for rapid outbreak response.
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Affiliation(s)
- Nicholas F.G. Chen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Luc Gagne
- Massachusetts Department of Public Health, Boston, MA, USA
| | | | - Sandra Smole
- Massachusetts Department of Public Health, Boston, MA, USA
| | - Erika Buzby
- Massachusetts Department of Public Health, Boston, MA, USA
| | - Joshua Hall
- Massachusetts Department of Public Health, Boston, MA, USA
| | - Stephanie Ash
- Massachusetts Department of Public Health, Boston, MA, USA
| | | | - Seana Cofsky
- Massachusetts Department of Public Health, Boston, MA, USA
| | - Selina Clancy
- Massachusetts Department of Public Health, Boston, MA, USA
| | | | | | | | | | | | | | - Nicole M. Green
- Los Angeles County Public Health Laboratories, Downey, CA, USA
| | - Sean Sierra-Patev
- Rhode Island Department of Health, Rhode Island State Health Laboratory, Providence, RI, USA
| | | | - Richard C. Huard
- Rhode Island Department of Health, Rhode Island State Health Laboratory, Providence, RI, USA
| | - Claire Pearson
- Connecticut Department of Public Health, Rocky Hill, CT, USA
| | | | | | - Jian Ping Huang
- Connecticut Department of Public Health, Rocky Hill, CT, USA
| | - Emily Gagnon
- Connecticut Department of Public Health, Rocky Hill, CT, USA
| | - Ethan Reever
- Connecticut Department of Public Health, Rocky Hill, CT, USA
| | - Jafar Razeq
- Connecticut Department of Public Health, Rocky Hill, CT, USA
| | | | - Vítor Borges
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Rita Ferreira
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Daniel Sobral
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Silvia Duarte
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Daniela Santos
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Luís Vieira
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal,Faculty of Veterinary Medicine, Lusófona University, Lisbon, Portugal
| | - Carly Aquino
- Delaware Public Health Laboratory, Smyrna, DE, USA
| | | | | | - Moneeb Bajwa
- Delaware Public Health Laboratory, Smyrna, DE, USA
| | | | - Holly Miller
- Delaware Public Health Laboratory, Smyrna, DE, USA
| | | | - Ria Allman
- Delaware Public Health Laboratory, Smyrna, DE, USA
| | - Neel Greer
- Delaware Public Health Laboratory, Smyrna, DE, USA
| | - Amary Fall
- Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | - Martin P. McHugh
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK,School of Medicine, University of St Andrews, St Andrews, UK
| | - Daniel M. Maloney
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK,Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - Rebecca Dewar
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Juliet Kenicer
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Abby Parker
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Katharine Mathers
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Jonathan Wild
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Seb Cotton
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Kate E. Templeton
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - George Churchwell
- Florida Department of Health, Bureau of Public Health Laboratories, Jacksonville, FL, USA
| | - Philip A. Lee
- Florida Department of Health, Bureau of Public Health Laboratories, Jacksonville, FL, USA
| | - Maria Pedrosa
- Florida Department of Health, Bureau of Public Health Laboratories, Jacksonville, FL, USA
| | - Brenna McGruder
- Florida Department of Health, Bureau of Public Health Laboratories, Jacksonville, FL, USA
| | - Sarah Schmedes
- Florida Department of Health, Bureau of Public Health Laboratories, Jacksonville, FL, USA
| | - Matthew R. Plumb
- Minnesota Department of Health, Public Health Laboratory, St. Paul, MN, USA
| | - Xiong Wang
- Minnesota Department of Health, Public Health Laboratory, St. Paul, MN, USA
| | - Regina Bones Barcellos
- Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Fernanda M.S. Godinho
- Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Richard Steiner Salvato
- Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Mallery I. Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA,Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Glen R. Gallagher
- Massachusetts Department of Public Health, Boston, MA, USA,Rhode Island Department of Health, Rhode Island State Health Laboratory, Providence, RI, USA
| | - Chantal B.F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
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9
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Garrigues JM, Hemarajata P, Lucero B, Alarcón J, Ransohoff H, Marutani AN, Kim M, Marlowe EM, Realegeno SE, Kagan RM, Montero CI, Chen NFG, Grubaugh ND, Vogels CBF, Green NM. Identification of Human Monkeypox Virus Genome Deletions That Impact Diagnostic Assays. J Clin Microbiol 2022; 60:e0165522. [PMID: 36445125 PMCID: PMC9769645 DOI: 10.1128/jcm.01655-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Affiliation(s)
| | - Peera Hemarajata
- Los Angeles County Department of Public Health, Downey, California, USA
| | - Briar Lucero
- Los Angeles County Department of Public Health, Downey, California, USA
| | - Jemma Alarcón
- Los Angeles County Department of Public Health, Downey, California, USA
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Heidi Ransohoff
- Los Angeles County Department of Public Health, Downey, California, USA
| | - Amy N. Marutani
- Los Angeles County Department of Public Health, Downey, California, USA
| | - Moon Kim
- Los Angeles County Department of Public Health, Downey, California, USA
| | | | - Susan E. Realegeno
- Infectious Diseases, Quest Diagnostics, San Juan Capistrano, California, USA
| | - Ron M. Kagan
- Infectious Diseases, Quest Diagnostics, San Juan Capistrano, California, USA
| | - Clemente I. Montero
- Infectious Diseases, Quest Diagnostics, San Juan Capistrano, California, USA
| | - Nicholas F. G. Chen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Chantal B. F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Nicole M. Green
- Los Angeles County Department of Public Health, Downey, California, USA
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10
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Aden TA, Blevins P, York SW, Rager S, Balachandran D, Hutson CL, Lowe D, Mangal CN, Wolford T, Matheny A, Davidson W, Wilkins K, Cook R, Roulo RM, White MK, Berman L, Murray J, Laurance J, Francis D, Green NM, Berumen RA, Gonzalez A, Evans S, Hudziec M, Noel D, Adjei M, Hovan G, Lee P, Tate L, Gose RB, Voermans R, Crew J, Adam PR, Haydel D, Lukula S, Matluk N, Shah S, Featherston J, Ware D, Pettit D, McCutchen E, Acheampong E, Buttery E, Gorzalski A, Perry M, Fowler R, Lee RB, Nickla R, Huard R, Moore A, Jones K, Johnson R, Swaney E, Jaramillo J, Reinoso Webb C, Guin B, Yost J, Atkinson A, Griffin-Thomas L, Chenette J, Gant J, Sterkel A, Ghuman HK, Lute J, Smole SC, Arora V, Demontigny CK, Bielby M, Geeter E, Newman KAM, Glazier M, Lutkemeier W, Nelson M, Martinez R, Chaitram J, Honein MA, Villanueva JM. Rapid Diagnostic Testing for Response to the Monkeypox Outbreak - Laboratory Response Network, United States, May 17-June 30, 2022. MMWR Morb Mortal Wkly Rep 2022; 71:904-907. [PMID: 35834423 PMCID: PMC9290387 DOI: 10.15585/mmwr.mm7128e1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
As part of public health preparedness for infectious disease threats, CDC collaborates with other U.S. public health officials to ensure that the Laboratory Response Network (LRN) has diagnostic tools to detect Orthopoxviruses, the genus that includes Variola virus, the causative agent of smallpox. LRN is a network of state and local public health, federal, U.S. Department of Defense (DOD), veterinary, food, and environmental testing laboratories. CDC developed, and the Food and Drug Administration (FDA) granted 510(k) clearance* for the Non-variola Orthopoxvirus Real-time PCR Primer and Probe Set (non-variola Orthopoxvirus [NVO] assay), a polymerase chain reaction (PCR) diagnostic test to detect NVO. On May 17, 2022, CDC was contacted by the Massachusetts Department of Public Health (DPH) regarding a suspected case of monkeypox, a disease caused by the Orthopoxvirus Monkeypox virus. Specimens were collected and tested by the Massachusetts DPH public health laboratory with LRN testing capability using the NVO assay. Nationwide, 68 LRN laboratories had capacity to test approximately 8,000 NVO tests per week during June. During May 17-June 30, LRN laboratories tested 2,009 specimens from suspected monkeypox cases. Among those, 730 (36.3%) specimens from 395 patients were positive for NVO. NVO-positive specimens from 159 persons were confirmed by CDC to be monkeypox; final characterization is pending for 236. Prompt identification of persons with infection allowed rapid response to the outbreak, including isolation and treatment of patients, administration of vaccines, and other public health action. To further facilitate access to testing and increase convenience for providers and patients by using existing provider-laboratory relationships, CDC and LRN are supporting five large commercial laboratories with a national footprint (Aegis Science, LabCorp, Mayo Clinic Laboratories, Quest Diagnostics, and Sonic Healthcare) to establish NVO testing capacity of 10,000 specimens per week per laboratory. On July 6, 2022, the first commercial laboratory began accepting specimens for NVO testing based on clinician orders.
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11
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Yang S, Hemarajata P, Hilt EE, Price TK, Garner OB, Green NM. Investigation of SARS-CoV-2 Epsilon Variant and Hospitalization Status by Genomic Surveillance in a Single Large Health System During the 2020-2021 Winter Surge in Southern California. Am J Clin Pathol 2022; 157:649-652. [PMID: 34875004 PMCID: PMC8689746 DOI: 10.1093/ajcp/aqab203] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 10/27/2021] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES This study aimed to assess whether the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Epsilon variant (B.1.429/427) is more virulent, leading to more hospitalization and more severe disease requiring intensive care unit (ICU) admission. METHODS SARS-CoV-2 genomic surveillance was performed on respiratory samples from 231 unique patients, collected at a single large health system in Southern California between November 2020 and March 2021 during the winter surge. RESULTS The frequencies of the Epsilon variant among outpatients, hospitalized patients, and ICU patients were indifferent. CONCLUSIONS Our study suggests that the Epsilon variant is not associated with increased hospitalization and ICU admission.
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Affiliation(s)
- Shangxin Yang
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | | | - Evann E Hilt
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - Travis K Price
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - Omai B Garner
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - Nicole M Green
- Los Angeles Department of Public Health, Downey, CA, USA
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12
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Schrodt CA, Malenfant JH, Hunter JC, Slifka KJ, Campbell A, Stone N, Whitehouse ER, Wittry B, Christensen B, Barnes JR, Brammer L, Hemarajata P, Green NM, Civen R, Gounder PP, Rao AK. Investigation of a Suspect Severe Acute Respiratory Syndrome Coronavirus-2 and Influenza A Mixed Outbreak: Lessons Learned for Long-Term Care Facilities Nationwide. Clin Infect Dis 2021; 73:S77-S80. [PMID: 33956136 PMCID: PMC8135935 DOI: 10.1093/cid/ciab372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
A suspected outbreak of influenza A and SARS-CoV-2 at a long-term care facility in Los Angeles County was months later, determined to not involve influenza. To prevent inadvertent transmission of infections, facilities should use highly specific influenza diagnostics and follow CDC guidelines that specifically address infection control challenges.
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Affiliation(s)
- Caroline A Schrodt
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.,CDC COVID-19 Response Team, Atlanta, Georgia, USA
| | - Jason H Malenfant
- Acute Communicable Disease Control Program, Los Angeles County Department of Public Health, Los Angeles, California, USA
| | - Jennifer C Hunter
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kara Jacobs Slifka
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Angela Campbell
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Nimalie Stone
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Erin R Whitehouse
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.,CDC COVID-19 Response Team, Atlanta, Georgia, USA
| | - Beth Wittry
- CDC COVID-19 Response Team, Atlanta, Georgia, USA
| | | | - John R Barnes
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lynnette Brammer
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Peera Hemarajata
- Public Health Laboratory, Los Angeles County Department of Public Health, Downey, California, USA
| | - Nicole M Green
- Public Health Laboratory, Los Angeles County Department of Public Health, Downey, California, USA
| | - Rachel Civen
- Community Health Services Program, Los Angeles County Department of Public Health, Los Angeles, California, USA
| | - Prabhu P Gounder
- Acute Communicable Disease Control Program, Los Angeles County Department of Public Health, Los Angeles, California, USA
| | - Agam K Rao
- CDC COVID-19 Response Team, Atlanta, Georgia, USA
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13
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Deng X, Garcia-Knight MA, Khalid MM, Servellita V, Wang C, Morris MK, Sotomayor-González A, Glasner DR, Reyes KR, Gliwa AS, Reddy NP, Sanchez San Martin C, Federman S, Cheng J, Balcerek J, Taylor J, Streithorst JA, Miller S, Sreekumar B, Chen PY, Schulze-Gahmen U, Taha TY, Hayashi JM, Simoneau CR, Kumar GR, McMahon S, Lidsky PV, Xiao Y, Hemarajata P, Green NM, Espinosa A, Kath C, Haw M, Bell J, Hacker JK, Hanson C, Wadford DA, Anaya C, Ferguson D, Frankino PA, Shivram H, Lareau LF, Wyman SK, Ott M, Andino R, Chiu CY. Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant. Cell 2021; 184:3426-3437.e8. [PMID: 33991487 PMCID: PMC8057738 DOI: 10.1016/j.cell.2021.04.025] [Citation(s) in RCA: 313] [Impact Index Per Article: 104.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/02/2021] [Accepted: 04/15/2021] [Indexed: 01/07/2023]
Abstract
We identified an emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant by viral whole-genome sequencing of 2,172 nasal/nasopharyngeal swab samples from 44 counties in California, a state in the western United States. Named B.1.427/B.1.429 to denote its two lineages, the variant emerged in May 2020 and increased from 0% to >50% of sequenced cases from September 2020 to January 2021, showing 18.6%-24% increased transmissibility relative to wild-type circulating strains. The variant carries three mutations in the spike protein, including an L452R substitution. We found 2-fold increased B.1.427/B.1.429 viral shedding in vivo and increased L452R pseudovirus infection of cell cultures and lung organoids, albeit decreased relative to pseudoviruses carrying the N501Y mutation common to variants B.1.1.7, B.1.351, and P.1. Antibody neutralization assays revealed 4.0- to 6.7-fold and 2.0-fold decreases in neutralizing titers from convalescent patients and vaccine recipients, respectively. The increased prevalence of a more transmissible variant in California exhibiting decreased antibody neutralization warrants further investigation.
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Affiliation(s)
- Xianding Deng
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA
| | - Miguel A Garcia-Knight
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mir M Khalid
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA
| | - Candace Wang
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA
| | | | - Alicia Sotomayor-González
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA
| | - Dustin R Glasner
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA
| | - Kevin R Reyes
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA
| | - Amelia S Gliwa
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA
| | - Nikitha P Reddy
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA
| | - Claudia Sanchez San Martin
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA
| | - Scot Federman
- Laboratory for Genomics Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jing Cheng
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Joanna Balcerek
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jordan Taylor
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jessica A Streithorst
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Bharath Sreekumar
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA
| | - Pei-Yi Chen
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA
| | - Ursula Schulze-Gahmen
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA
| | - Taha Y Taha
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA
| | - Jennifer M Hayashi
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA
| | - Camille R Simoneau
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA
| | - G Renuka Kumar
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA
| | - Sarah McMahon
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA
| | - Peter V Lidsky
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yinghong Xiao
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Peera Hemarajata
- Los Angeles County Public Health Laboratories, Downey, CA 90242, USA
| | - Nicole M Green
- Los Angeles County Public Health Laboratories, Downey, CA 90242, USA
| | - Alex Espinosa
- California Department of Public Health, Richmond, CA 94804, USA
| | - Chantha Kath
- California Department of Public Health, Richmond, CA 94804, USA
| | - Monica Haw
- California Department of Public Health, Richmond, CA 94804, USA
| | - John Bell
- California Department of Public Health, Richmond, CA 94804, USA
| | - Jill K Hacker
- California Department of Public Health, Richmond, CA 94804, USA
| | - Carl Hanson
- California Department of Public Health, Richmond, CA 94804, USA
| | - Debra A Wadford
- California Department of Public Health, Richmond, CA 94804, USA
| | - Carlos Anaya
- Monterey County Department of Public Health, Monterey, CA 93906, USA
| | - Donna Ferguson
- Monterey County Department of Public Health, Monterey, CA 93906, USA
| | - Phillip A Frankino
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Haridha Shivram
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Liana F Lareau
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Stacia K Wyman
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Melanie Ott
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
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14
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Deng X, Garcia-Knight MA, Khalid MM, Servellita V, Wang C, Morris MK, Sotomayor-González A, Glasner DR, Reyes KR, Gliwa AS, Reddy NP, Martin CSS, Federman S, Cheng J, Balcerek J, Taylor J, Streithorst JA, Miller S, Kumar GR, Sreekumar B, Chen PY, Schulze-Gahmen U, Taha TY, Hayashi J, Simoneau CR, McMahon S, Lidsky PV, Xiao Y, Hemarajata P, Green NM, Espinosa A, Kath C, Haw M, Bell J, Hacker JK, Hanson C, Wadford DA, Anaya C, Ferguson D, Lareau LF, Frankino PA, Shivram H, Wyman SK, Ott M, Andino R, Chiu CY. Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. medRxiv 2021:2021.03.07.21252647. [PMID: 33758899 PMCID: PMC7987058 DOI: 10.1101/2021.03.07.21252647] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [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: 12/17/2022]
Abstract
We identified a novel SARS-CoV-2 variant by viral whole-genome sequencing of 2,172 nasal/nasopharyngeal swab samples from 44 counties in California. Named B.1.427/B.1.429 to denote its 2 lineages, the variant emerged around May 2020 and increased from 0% to >50% of sequenced cases from September 1, 2020 to January 29, 2021, exhibiting an 18.6-24% increase in transmissibility relative to wild-type circulating strains. The variant carries 3 mutations in the spike protein, including an L452R substitution. Our analyses revealed 2-fold increased B.1.427/B.1.429 viral shedding in vivo and increased L452R pseudovirus infection of cell cultures and lung organoids, albeit decreased relative to pseudoviruses carrying the N501Y mutation found in the B.1.1.7, B.1.351, and P.1 variants. Antibody neutralization assays showed 4.0 to 6.7-fold and 2.0-fold decreases in neutralizing titers from convalescent patients and vaccine recipients, respectively. The increased prevalence of a more transmissible variant in California associated with decreased antibody neutralization warrants further investigation.
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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
| | - Miguel A Garcia-Knight
- Department of Microbiology and Immunology, University of California San Francisco, California, USA
| | - Mir M Khalid
- Department of Medicine, University of California San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Candace Wang
- Department of Laboratory Medicine, University of California San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Mary Kate Morris
- California Department of Public Health, Richmond, California, USA
| | - Alicia Sotomayor-González
- Department of Laboratory Medicine, University of California San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Dustin R Glasner
- Department of Laboratory Medicine, University of California San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Kevin R Reyes
- Department of Laboratory Medicine, University of California San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Amelia S Gliwa
- Department of Laboratory Medicine, University of California San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Nikitha P Reddy
- Department of Laboratory Medicine, University of California San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Claudia Sanchez San Martin
- Department of Laboratory Medicine, University of California San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Scot Federman
- Laboratory for Genomics Research, University of California San Francisco, California, USA
| | - Jing Cheng
- Department of Medicine, University of California San Francisco, California, USA
| | - Joanna Balcerek
- Department of Laboratory Medicine, University of California San Francisco, California, USA
| | - Jordan Taylor
- Department of Laboratory Medicine, University of California San Francisco, California, USA
| | - Jessica A Streithorst
- Department of Laboratory Medicine, University of California San Francisco, California, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California San Francisco, California, USA
| | - G Renuka Kumar
- Department of Medicine, University of California San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
| | - Bharath Sreekumar
- Department of Medicine, University of California San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
| | - Pei-Yi Chen
- Department of Medicine, University of California San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
| | - Ursula Schulze-Gahmen
- Department of Medicine, University of California San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
| | - Taha Y Taha
- Department of Medicine, University of California San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
| | - Jennifer Hayashi
- Department of Medicine, University of California San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
| | - Camille R Simoneau
- Department of Medicine, University of California San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
| | - Sarah McMahon
- Department of Medicine, University of California San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
| | - Peter V Lidsky
- Department of Microbiology and Immunology, University of California San Francisco, California, USA
| | - Yinghong Xiao
- Department of Microbiology and Immunology, University of California San Francisco, California, USA
| | - Peera Hemarajata
- Los Angeles County Department of Public Health, Los Angeles, California, USA
| | - Nicole M Green
- Los Angeles County Department of Public Health, Los Angeles, California, USA
| | - Alex Espinosa
- California Department of Public Health, Richmond, California, USA
| | - Chantha Kath
- California Department of Public Health, Richmond, California, USA
| | - Monica Haw
- California Department of Public Health, Richmond, California, USA
| | - John Bell
- California Department of Public Health, Richmond, California, USA
| | - Jill K Hacker
- California Department of Public Health, Richmond, California, USA
| | - Carl Hanson
- California Department of Public Health, Richmond, California, USA
| | - Debra A Wadford
- California Department of Public Health, Richmond, California, USA
| | - Carlos Anaya
- Monterey County Department of Public Health, Monterey, California, USA
| | - Donna Ferguson
- Monterey County Department of Public Health, Monterey, California, USA
| | - Liana F Lareau
- Department of Bioengineering, University of California Berkeley, Berkeley, California, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, California, USA
| | - Phillip A Frankino
- Innovative Genomics Institute, University of California Berkeley, Berkeley, California, USA
| | - Haridha Shivram
- Innovative Genomics Institute, University of California Berkeley, Berkeley, California, USA
| | - Stacia K Wyman
- Innovative Genomics Institute, University of California Berkeley, Berkeley, California, USA
| | - Melanie Ott
- Department of Medicine, University of California San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, California, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California 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, University of California San Francisco, California, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, California, USA
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15
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OYong K, Killerby M, Pan CY, Huynh T, Green NM, Wadford DA, Terashita D. Outbreak of Epidemic Keratoconjunctivitis Caused by Human Adenovirus Type D53 in an Eye Care Clinic - Los Angeles County, 2017. MMWR Morb Mortal Wkly Rep 2018; 67:1347-1349. [PMID: 30521501 PMCID: PMC6329482 DOI: 10.15585/mmwr.mm6748a4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
On June 22, 2017, the Los Angeles County Department of Public Health (LAC DPH) was notified of seven patients who were seen at an eye care clinic on June 8, 2017, and later developed symptoms of epidemic keratoconjunctivitis (EKC). EKC is a contagious, severe form of viral conjunctivitis that can cause pain and blurred vision for up to 4 weeks (1). LAC DPH conducted an investigation, which identified 17 patients with EKC, including 15 who had visited the optometry clinic and two who were household contacts of clinic patients. Observations in the clinic found deficiencies in disinfection of tonometers (an instrument connected to a slit lamp and used to test for glaucoma by measuring intraocular pressure) and multiuse eye drop administration. Staff member education and revision of disinfection practices interrupted further transmission. Patient specimens tested positive for human adenovirus (HAdV) type D53 (HAdV-53). As the first documented EKC outbreak associated with HAdV-D53 in the United States, this outbreak highlights the need for rigorous implementation of recommended infection prevention practices in eye care settings.
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16
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Abstract
Introduction: Clinical management and identification of respiratory diseases has become more rapid and increasingly specific due to widespread use of PCR(polymerase chain reaction) multiplex technologies. Although significantly improving clinical diagnosis, multiplexed PCR assays could have a greater impact on local and global disease surveillance. The authors wish to propose methods of evaluating respiratory multiplex assays to maximize diagnostic yields specifically for surveillance efforts. Areas covered: The authors review multiplexed assays and critically assess what barriers have limited these assays for disease surveillance and how these barriers might be addressed. The manuscript focuses specifically on the case study of using multiplexed assays for surveillance of respiratory pathogens. The authors also provide a method of validation of specific surveillance measures. Expert commentary: Current commercially available respiratory multiplex PCR assays are widely used for clinical diagnosis; however, specific barriers have limited their use for surveillance. Key barriers include differences in testing phase requirements and diagnostic performance evaluation. In this work the authors clarify phase testing requirements and introduce unique diagnostic performance measures that simplify the use of these assays on a per target basis for disease surveillance.
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Affiliation(s)
- John D Diaz-Decaro
- a Los Angeles County Public Health Laboratories , Research & Training Unit , Downey , CA , USA.,b UCLA Fielding School of Public Health , Environmental Health Sciences , Los Angeles , CA , USA
| | - Nicole M Green
- a Los Angeles County Public Health Laboratories , Research & Training Unit , Downey , CA , USA
| | - Hilary A Godwin
- b UCLA Fielding School of Public Health , Environmental Health Sciences , Los Angeles , CA , USA
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17
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Tovar Padua L, Kamali A, Kim H, Green NM, Civen R, Schwartz B, Krogstad P, Deville J, Yeganeh N, Lugo D, Baker A, Soni P, Cho C, Svircic N, Dry S, Seeger L, Lloyd J, Deukmedjian G, Bowen R, Hale G, Zaki SR, Mead P, Nielsen-Saines K. Unique Case of Disseminated Plague With Multifocal Osteomyelitis. J Pediatric Infect Dis Soc 2017; 6:e165-e168. [PMID: 28379405 DOI: 10.1093/jpids/pix007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 01/13/2017] [Indexed: 11/12/2022]
Abstract
Plague is a disease caused by Yersinia pestis. Septicemic and pneumonic plague have a high mortality rate if untreated. Here we describe the challenges of accurately diagnosing a nonfatal pediatric case of septicemic plague with involvement of multiple organs; to our knowledge, the first documented case of multifocal plague osteomyelitis.
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Affiliation(s)
| | - Amanda Kamali
- Epidemic Intelligence Service, Division of Scientific Education and Professional Development.,Acute Communicable Disease Control, Los Angeles County Department of Public Health, Los Angeles
| | | | - Nicole M Green
- Public Health Laboratory, Los Angeles County Department of Public Health, Downey
| | - Rachel Civen
- Acute Communicable Disease Control, Los Angeles County Department of Public Health, Los Angeles
| | - Benjamin Schwartz
- Acute Communicable Disease Control, Los Angeles County Department of Public Health, Los Angeles
| | | | | | | | - Debra Lugo
- Division of Pediatric Infectious Diseases
| | | | - Priya Soni
- Division of Pediatric Infectious Diseases
| | - Catherine Cho
- Department of Family Medicine, Northridge Hospital Medical Center, California
| | - Natalia Svircic
- Department of Family Medicine, Northridge Hospital Medical Center, California
| | | | | | | | | | - Richard Bowen
- Orthopedic Surgery, David Geffen UCLA School of Medicine, Los Angeles, California
| | - Gillian Hale
- Infectious Diseases Pathology Branch, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Sherif R Zaki
- Infectious Diseases Pathology Branch, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Paul Mead
- Bacterial Diseases Branch, Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado
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18
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Buono SA, Godwin HA, Green NM. Comparing three treponemal tests for syphilis screening. Diagn Microbiol Infect Dis 2017; 89:173-177. [PMID: 28844341 DOI: 10.1016/j.diagmicrobio.2017.07.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 03/16/2017] [Revised: 06/18/2017] [Accepted: 07/20/2017] [Indexed: 10/19/2022]
Abstract
We compared the performance and ease of use for three high-throughput treponemal immunoassays: Phoenix Biotech Trep-Sure Total Antibody EIA, Siemens ADVIA® Centaur Syphilis Assay, and DiaSorin LIAISON® Treponema Assay. One thousand serum samples submitted for routine screening were used in this study. Each assay demonstrated comparable sensitivity, specificity, and percent agreement (98-100%) compared with Treponema pallidum particle agglutination (TP-PA). Thus, treponemal immunoassays are an acceptable alternative for syphilis screening or confirmatory testing. Batch sizes and technologist active time varied between each treponemal immunoassay; the chemiluminescence platforms offered significantly greater ability to batch (random access vs. fixed batch sizes) in less time. When we compared the results obtained using a reverse algorithm approach to those obtained using a traditional algorithm, we found that the reverse algorithm identified 38 additional seropositive individuals that were not detected using the traditional algorithm. Clinical evaluation was useful for resolving cases with discordant serology.
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Affiliation(s)
- Sean A Buono
- Department of Environmental Health Sciences, Fielding School of Public Health, University of California, Los Angeles, CA 90095; Los Angeles County Public Health Laboratories, Los Angeles County, Department of Public Health, Downey, CA 90242.
| | - Hilary A Godwin
- Department of Environmental Health Sciences, Fielding School of Public Health, University of California, Los Angeles, CA 90095; Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095
| | - Nicole M Green
- Department of Environmental Health Sciences, Fielding School of Public Health, University of California, Los Angeles, CA 90095; Los Angeles County Public Health Laboratories, Los Angeles County, Department of Public Health, Downey, CA 90242
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19
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Kamali A, Jamieson DJ, Kpaduwa J, Schrier S, Kim M, Green NM, Ströher U, Muehlenbachs A, Bell M, Rollin PE, Mascola L. Pregnancy, Labor, and Delivery after Ebola Virus Disease and Implications for Infection Control in Obstetric Services, United States. Emerg Infect Dis 2016; 22. [PMID: 27191253 PMCID: PMC4918171 DOI: 10.3201/eid2207.160269] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Women who become pregnant after recovery pose little risk for transmitting the virus to the baby or others. Many of the survivors of the 2014–2015 epidemic of Ebola virus disease (EVD) in West Africa were women of childbearing age. Limited clinical and laboratory data exist that describe these women’s pregnancies and outcomes. We report the case of an EVD survivor who became pregnant and delivered her child in the United States, and we discuss implications of this case for infection control practices in obstetric services. Hospitals in the United States must be prepared to care for EVD survivors.
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20
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Green NM, Matthews JJ. The management of acute hip pain in the military: femoral neck stress fractures and tears of the acetabular labrum. J R Nav Med Serv 2016; 102:124-129. [PMID: 29896943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Acute hip pain is a common presenting complaint amongst the military population. It can present in a variety of ways, with a broad range of differential diagnoses to consider. Most cases of acute hip pain in military patients tend to be traumatic in origin. Pathology within the hip can be a diagnostic challenge, as symptoms often overlap between differential diagnoses and examination findings are not always sensitive or specific. Any hip injury will potentially downgrade a military patient and can also be a significant cause of long-term morbidity. Being able to manage the patient with acute hip pain effectively will ensure that patients spend less time in the diagnostic chain and reach the definitive treatment they require to continue to carry out their primary role. This paper describes how best to manage military patients who present with acute hip pain. It covers the diagnostic challenges faced by clinicians, the differential diagnoses of acute hip pain and describes the management of some common injuries of the hip: tears of the acetabular labrum and femoral neck stress fractures.
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21
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Yang S, Hemarajata P, Hindler J, Ward K, Adisetiyo H, Li F, Aldrovandi GM, Green NM, Russell D, Rubin Z, Humphries RM. Investigation of a suspected nosocomial transmission of blaKPC3-mediated carbapenem-resistant Klebsiella pneumoniae by whole genome sequencing. Diagn Microbiol Infect Dis 2015; 84:337-42. [PMID: 26867964 DOI: 10.1016/j.diagmicrobio.2015.12.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [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: 10/14/2015] [Revised: 11/25/2015] [Accepted: 12/24/2015] [Indexed: 10/22/2022]
Abstract
Whole genome sequencing (WGS) was compared to pulse-field gel electrophoresis (PFGE) of XbaI-digested genomic DNA, as methods by which to evaluate a potential transmission of carbapenem-resistant Klebsiella pneumoniae between 2 hospital inpatients. PFGE result demonstrated only 1-band difference between the isolates, suggesting probable relatedness. In contrast, while WGS data demonstrated the same sequence type and very similar chromosomal sequences, over 20 single nucleotide variants were identified between the isolates, bringing into question whether there was a transmission event. WGS also identified an additional plasmid, with an XbaI restriction site in the isolates of the second patient that was not identified by PFGE. While WGS provided additional information that was not available by PFGE, in this study, neither method could definitively conclude the relatedness between the isolates.
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Affiliation(s)
- Shangxin Yang
- Pathology & Laboratory Medicine, UCLA, Los Angeles, CA, USA
| | | | - Janet Hindler
- Pathology & Laboratory Medicine, UCLA, Los Angeles, CA, USA
| | - Kevin Ward
- Pathology & Laboratory Medicine, UCLA, Los Angeles, CA, USA
| | - Helty Adisetiyo
- Mi Next Generation Science (MiNGS) Core Laboratory, Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Fan Li
- Mi Next Generation Science (MiNGS) Core Laboratory, Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Grace M Aldrovandi
- Mi Next Generation Science (MiNGS) Core Laboratory, Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Nicole M Green
- Los Angeles County Public Health Laboratory, Downey, CA, USA
| | - Dana Russell
- Division of Infectious Diseases, UCLA, Los Angeles, CA, USA
| | - Zachary Rubin
- Division of Infectious Diseases, UCLA, Los Angeles, CA, USA
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22
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Millman AJ, Kornylo Duong K, Lafond K, Green NM, Lippold SA, Jhung MA. Influenza Outbreaks Among Passengers and Crew on Two Cruise Ships: A Recent Account of Preparedness and Response to an Ever-Present Challenge. J Travel Med 2015; 22:306-11. [PMID: 26031322 PMCID: PMC4869710 DOI: 10.1111/jtm.12215] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND During spring 2014, two large influenza outbreaks occurred among cruise ship passengers and crew on trans-hemispheric itineraries. METHODS Passenger and crew information for both ships was obtained from components of the ship medical records. Data included demographics, diagnosis of influenza-like illness (ILI) or acute respiratory illness (ARI), illness onset date, passenger cabin number, crew occupation, influenza vaccination history, and rapid influenza diagnostic test (RIDT) result, if performed. RESULTS In total, 3.7% of passengers and 3.1% of crew on Ship A had medically attended acute respiratory illness (MAARI). On Ship B, 6.2% of passengers and 4.7% of crew had MAARI. In both outbreaks, passengers reported illness prior to the ship's departure. Influenza activity was low in the places of origin of the majority of passengers and both ships' ports of call. The median age of affected passengers on both ships was 70 years. Diagnostic testing revealed three different co-circulating influenza viruses [influenza A(H1N1)pdm09, influenza A(H3N2), and influenza B] on Ship A and one circulating influenza virus (influenza B) on Ship B. Both ships voluntarily reported the outbreaks to the Centers for Disease Control and Prevention (CDC) and implemented outbreak response plans including isolation of sick individuals and antiviral treatment and prophylaxis. CONCLUSIONS Influenza activity can become widespread during cruise ship outbreaks and can occur outside of traditional influenza seasons. Comprehensive outbreak prevention and control plans, including prompt antiviral treatment and prophylaxis, may mitigate the impact of influenza outbreaks on cruise ships.
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Affiliation(s)
- Alexander J Millman
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Krista Kornylo Duong
- Division of Global Migration and Quarantine, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Kathryn Lafond
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Nicole M Green
- Los Angeles County Public Health Laboratory, Downey, CA, USA
| | - Susan A Lippold
- Division of Global Migration and Quarantine, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Michael A Jhung
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
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23
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Sitkiewicz I, Green NM, Guo N, Mereghetti L, Musser JM. Lateral gene transfer of streptococcal ICE element RD2 (region of difference 2) encoding secreted proteins. BMC Microbiol 2011; 11:65. [PMID: 21457552 PMCID: PMC3083328 DOI: 10.1186/1471-2180-11-65] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [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: 10/15/2010] [Accepted: 04/01/2011] [Indexed: 11/10/2022] Open
Abstract
Background The genome of serotype M28 group A Streptococcus (GAS) strain MGAS6180 contains a novel genetic element named Region of Difference 2 (RD2) that encodes seven putative secreted extracellular proteins. RD2 is present in all serotype M28 strains and strains of several other GAS serotypes associated with female urogenital infections. We show here that the GAS RD2 element is present in strain MGAS6180 both as an integrative chromosomal form and a circular extrachromosomal element. RD2-like regions were identified in publicly available genome sequences of strains representing three of the five major group B streptococcal serotypes causing human disease. Ten RD2-encoded proteins have significant similarity to proteins involved in conjugative transfer of Streptococcus thermophilus integrative chromosomal elements (ICEs). Results We transferred RD2 from GAS strain MGAS6180 (serotype M28) to serotype M1 and M4 GAS strains by filter mating. The copy number of the RD2 element was rapidly and significantly increased following treatment of strain MGAS6180 with mitomycin C, a DNA damaging agent. Using a PCR-based method, we also identified RD2-like regions in multiple group C and G strains of Streptococcus dysgalactiae subsp.equisimilis cultured from invasive human infections. Conclusions Taken together, the data indicate that the RD2 element has disseminated by lateral gene transfer to genetically diverse strains of human-pathogenic streptococci.
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Affiliation(s)
- Izabela Sitkiewicz
- Department of Pathology, The Methodist Hospital, Houston, TX 77030, USA.
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24
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Abstract
1. The reaction between avidin and biotin was found to be exothermic, DeltaH being -20.3kcal./mole of biotin bound. The corresponding value of DeltaH for streptavidin was -23kcal./mole. 2. The heat evolved was independent of the pH (between 5 and 9), of the buffer (borate or ammonia) and of the fractional saturation of the avidin with biotin. 3. The entropy change for the reaction was zero, and it is suggested that the entropy increase to be expected from hydrophobic interactions was counterbalanced by a decrease in entropy accompanying the formation of buried hydrogen bonds. 4. Modification of the potential hydrogen-bonding sites of the imidazolidone ring led to a decreased heat output and a positive entropy of reaction.
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Affiliation(s)
- N M Green
- Laboratory of Chemistry, National Institute for Arthritis and Metabolic Diseases, National Institutes of Health, Bethesda 14, U.S.A
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25
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Affiliation(s)
- N M Green
- National Institute for Medical Research, Mill Hill, London NW7 1AA, U.K
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26
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Sitkiewicz I, Green NM, Guo N, Bongiovanni AM, Witkin SS, Musser JM. Transcriptome adaptation of group B Streptococcus to growth in human amniotic fluid. PLoS One 2009; 4:e6114. [PMID: 19568429 PMCID: PMC2700258 DOI: 10.1371/journal.pone.0006114] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Accepted: 05/25/2009] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Streptococcus agalactiae (group B Streptococcus) is a bacterial pathogen that causes severe intrauterine infections leading to fetal morbidity and mortality. The pathogenesis of GBS infection in this environment is poorly understood, in part because we lack a detailed understanding of the adaptation of this pathogen to growth in amniotic fluid. To address this knowledge deficit, we characterized the transcriptome of GBS grown in human amniotic fluid (AF) and compared it with the transcriptome in rich laboratory medium. METHODS GBS was grown in Todd Hewitt-yeast extract medium and human AF. Bacteria were collected at mid-logarithmic, late-logarithmic and stationary growth phase. We performed global expression microarray analysis using a custom-made Affymetrix GeneChip. The normalized hybridization values derived from three biological replicates at each growth point were obtained. AF/THY transcript ratios representing greater than a 2-fold change and P-value exceeding 0.05 were considered to be statistically significant. PRINCIPAL FINDINGS We have discovered that GBS significantly remodels its transcriptome in response to exposure to human amniotic fluid. GBS grew rapidly in human AF and did not exhibit a global stress response. The majority of changes in GBS transcripts in AF compared to THY medium were related to genes mediating metabolism of amino acids, carbohydrates, and nucleotides. The majority of the observed changes in transcripts affects genes involved in basic bacterial metabolism and is connected to AF composition and nutritional requirements of the bacterium. Importantly, the response to growth in human AF included significant changes in transcripts of multiple virulence genes such as adhesins, capsule, and hemolysin and IL-8 proteinase what might have consequences for the outcome of host-pathogen interactions. CONCLUSIONS/SIGNIFICANCE Our work provides extensive new information about how the transcriptome of GBS responds to growth in AF, and thus new leads for pathogenesis research.
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Affiliation(s)
- Izabela Sitkiewicz
- Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, and Department of Pathology, The Methodist Hospital, Houston, Texas, United States of America
| | - Nicole M. Green
- Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, and Department of Pathology, The Methodist Hospital, Houston, Texas, United States of America
| | - Nina Guo
- Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, and Department of Pathology, The Methodist Hospital, Houston, Texas, United States of America
| | - Ann Marie Bongiovanni
- Weill Medical College of Cornell University, New York, New York, United States of America
| | - Steven S. Witkin
- Weill Medical College of Cornell University, New York, New York, United States of America
| | - James M. Musser
- Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, and Department of Pathology, The Methodist Hospital, Houston, Texas, United States of America
- Weill Medical College of Cornell University, New York, New York, United States of America
- * E-mail:
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Mereghetti L, Sitkiewicz I, Green NM, Musser JM. Extensive adaptive changes occur in the transcriptome of Streptococcus agalactiae (group B streptococcus) in response to incubation with human blood. PLoS One 2008; 3:e3143. [PMID: 18769548 PMCID: PMC2519835 DOI: 10.1371/journal.pone.0003143] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Accepted: 08/14/2008] [Indexed: 11/19/2022] Open
Abstract
To enhance understanding of how Streptococcus agalactiae (group B streptococcus, GBS) adapts during invasive infection, we performed a whole-genome transcriptome analysis after incubation with whole human blood. Global changes occurred in the GBS transcriptome rapidly in response to blood contact following shift from growth in a rich laboratory medium. Most (83%) of the significantly altered transcripts were down-regulated after 30 minutes of incubation in blood, and all functional categories of genes were abundantly represented. We observed complex dynamic changes in the expression of transcriptional regulators and stress response genes that allow GBS to rapidly adapt to blood. The transcripts of relatively few proven virulence genes were up-regulated during the first 90 minutes. However, a key discovery was that genes encoding proteins involved in interaction with the host coagulation/fibrinolysis system and bacterial-host interactions were rapidly up-regulated. Extensive transcript changes also occurred for genes involved in carbohydrate metabolism, including multi-functional proteins and regulators putatively involved in pathogenesis. Finally, we discovered that an incubation temperature closer to that occurring in patients with severe infection and high fever (40°C) induced additional differences in the GBS transcriptome relative to normal body temperature (37°C). Taken together, the data provide extensive new information about transcriptional adaptation of GBS exposed to human blood, a crucial step during GBS pathogenesis in invasive diseases, and identify many new leads for molecular pathogenesis research.
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Affiliation(s)
- Laurent Mereghetti
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology, The Methodist Hospital Research Institute, Houston, Texas, United States of America
- Université François-Rabelais, Faculté de Médecine, EA3854 “Bactéries et risque materno-foetal”, et Centre Hospitalier Universitaire, Tours, France
| | - Izabela Sitkiewicz
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology, The Methodist Hospital Research Institute, Houston, Texas, United States of America
| | - Nicole M. Green
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology, The Methodist Hospital Research Institute, Houston, Texas, United States of America
| | - James M. Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology, The Methodist Hospital Research Institute, Houston, Texas, United States of America
- * E-mail:
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Mereghetti L, Sitkiewicz I, Green NM, Musser JM. Remodeling of the Streptococcus agalactiae transcriptome in response to growth temperature. PLoS One 2008; 3:e2785. [PMID: 18665215 PMCID: PMC2464734 DOI: 10.1371/journal.pone.0002785] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2008] [Accepted: 06/25/2008] [Indexed: 01/22/2023] Open
Abstract
Background To act as a commensal bacterium and a pathogen in humans and animals, Streptococcus agalactiae (group B streptococcus, GBS) must be able to monitor and adapt to different environmental conditions. Temperature variation is a one of the most commonly encountered variables. Methodology/Principal Findings To understand the extent to which GBS modify gene expression in response to temperatures encountered in the various hosts, we conducted a whole genome transcriptome analysis of organisms grown at 30°C and 40°C. We identified extensive transcriptome remodeling at various stages of growth, especially in the stationary phase (significant transcript changes occurred for 25% of the genes). A large proportion of genes involved in metabolism was up-regulated at 30°C in stationary phase. Conversely, genes up-regulated at 40°C relative to 30°C include those encoding virulence factors such as hemolysins and extracellular secreted proteins with LPXTG motifs. Over-expression of hemolysins was linked to larger zones of hemolysis and enhanced hemolytic activity at 40°C. A key theme identified by our study was that genes involved in purine metabolism and iron acquisition were significantly up-regulated at 40°C. Conclusion/Significance Growth of GBS in vitro at different temperatures resulted in extensive remodeling of the transcriptome, including genes encoding proven and putative virulence genes. The data provide extensive new leads for molecular pathogenesis research.
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Affiliation(s)
- Laurent Mereghetti
- Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, Houston, Texas, United States of America
- Université François-Rabelais, Faculté de Médecine, EA3854 “Bactéries et risque materno-foetal” and Centre Hospitalier Universitaire, Tours, France
| | - Izabela Sitkiewicz
- Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, Houston, Texas, United States of America
| | - Nicole M. Green
- Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, Houston, Texas, United States of America
| | - James M. Musser
- Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, Houston, Texas, United States of America
- * E-mail:
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Green NM, Taylor WR, Brandl C, Korczak B, MacLennan DH. Structural and mechanistic implications of the amino acid sequence of calcium-transporting ATPases. Ciba Found Symp 2007; 122:93-114. [PMID: 2947788 DOI: 10.1002/9780470513347.ch7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Work is reviewed in which the amino acid sequences of two Ca2+-transporting ATPases of sarcoplasmic reticulum (SR) from slow (or cardiac) and fast skeletal muscle were determined from the nucleotide sequences of cloned cDNAs. Analysis of hydrophobicity and secondary structure, combined with the known shape derived from electron micrographs, leads to a model of five domains with functional implications. The major globular part of the molecule is in the cytoplasm and consists of one antiparallel and two parallel beta-sheet domains. One of the latter binds ATP, which, in the presence of Ca2+, phosphorylates an aspartic acid on the other domain. It is proposed that subsequent kinase-like movements are transmitted to the SR membrane via a penta-helical, calcium-binding stalk. The Ca2+ is first trapped and then translocated via the ten helices which constitute the transmembrane (channel) region. The difference in requirements for counter ions between the Ca2+- and Na+/K+-ATPases can be explained in terms of differing charge distributions in this channel.
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Zhang S, Green NM, Sitkiewicz I, Lefebvre RB, Musser JM. Identification and characterization of an antigen I/II family protein produced by group A Streptococcus. Infect Immun 2006; 74:4200-13. [PMID: 16790795 PMCID: PMC1489706 DOI: 10.1128/iai.00493-06] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Group A Streptococcus (GAS) is a gram-positive human bacterial pathogen that causes infections ranging in severity from pharyngitis to life-threatening invasive disease, such as necrotizing fasciitis. Serotype M28 strains are consistently isolated from invasive infections, particularly puerperal sepsis, a severe infection that occurs during or after childbirth. We recently sequenced the genome of a serotype M28 GAS strain and discovered a novel 37.4-kb foreign genetic element designated region of difference 2 (RD2). RD2 is similar in gene content and organization to genomic islands found in group B streptococci (GBS), the major cause of neonatal infections. RD2 encodes seven proteins with conventional gram-positive secretion signal sequences, six of which have not been characterized. Herein, we report that one of these six proteins (M28_Spy1325; Spy1325) is a member of the antigen I/II family of cell surface-anchored molecules produced by oral streptococci. PCR and DNA sequence analysis found that Spy1325 is very well conserved in GAS strains of distinct M protein serotypes. As assessed by real-time TaqMan quantitative PCR, the Spy1325 gene was expressed in vitro, and Spy1325 protein was present in culture supernatants and on the GAS cell surface. Western immunoblotting and enzyme-linked immunosorbent assays indicated that Spy1325 was produced by GAS in infected mice and humans. Importantly, the immunization of mice with recombinant Spy1325 fragments conferred protection against GAS-mediated mortality. Similar to other antigen I/II proteins, recombinant Spy1325 bound purified human salivary agglutinin glycoprotein. Spy1325 may represent a shared virulence factor among GAS, GBS, and oral streptococci.
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Affiliation(s)
- Shizhen Zhang
- Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, The Methodist Hospital, B154, 6565 Fannin St., Houston, TX 77030, USA
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Green NM, Beres SB, Graviss EA, Allison JE, McGeer AJ, Vuopio-Varkila J, LeFebvre RB, Musser JM. Genetic diversity among type emm28 group A Streptococcus strains causing invasive infections and pharyngitis. J Clin Microbiol 2005; 43:4083-91. [PMID: 16081955 PMCID: PMC1233891 DOI: 10.1128/jcm.43.8.4083-4091.2005] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [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: 11/20/2022] Open
Abstract
Genome sequencing of group A Streptococcus (GAS) has revealed that prophages account for the vast majority of gene content differences between strains. Serotype M28 strains are a leading cause of pharyngitis and invasive infections, but little is known about genetic diversity present in natural populations of these organisms. To study this issue, population-based samples of 568 strains from Ontario, Canada; Finland; and Houston, Texas, were analyzed. Special attention was given to analysis of variation in prophage-encoded virulence gene content by a PCR-based method. Thirty and 29 distinct prophage-encoded virulence gene profiles were identified among pharyngitis and invasive infection isolates. Thirteen profiles, representing the majority of the strains, were shared between these two classes of isolates. Significant differences were observed in the frequency of occurrence of certain prophage toxin gene profiles and infection type. M28 strains are highly diverse in prophage-encoded virulence gene content and integration site, supporting the key concept that prophages are critical contributors to GAS genetic diversity and population biology. Nucleotide sequence variation in the emm gene (encodes M protein) was also examined. Only three allelic variants were identified in the hypervariable portion of the emm28 gene. All but one strain had the same inferred amino acid sequence in the first 100 amino acids of the mature M28 protein. In contrast, size differences in the emm28 gene and inferred protein due to variable numbers of C-terminal repeats were common. The presence of macrolide resistance genes (mefA, ermB, and ermTR) was analyzed by PCR, and less than 2% of the strains were positive.
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Affiliation(s)
- Nicole M. Green
- Center for Human Bacterial Pathogenesis Research, Department of Pathology, Baylor College of Medicine, Houston, Texas 77030, Laboratory of Human Bacterial Pathogenesis, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana 59840, Department of Pathology, Microbiology, and Immunology, University of California—Davis, Davis, California 95616, Pediatric Medical Group, Houston, Texas 77098, Mount Sinai Hospital, Department of Microbiology, University of Toronto, Toronto, Ontario M5G 1X5, Canada, National Public Health Institute, Helsinki, Finland
| | - Stephen B. Beres
- Center for Human Bacterial Pathogenesis Research, Department of Pathology, Baylor College of Medicine, Houston, Texas 77030, Laboratory of Human Bacterial Pathogenesis, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana 59840, Department of Pathology, Microbiology, and Immunology, University of California—Davis, Davis, California 95616, Pediatric Medical Group, Houston, Texas 77098, Mount Sinai Hospital, Department of Microbiology, University of Toronto, Toronto, Ontario M5G 1X5, Canada, National Public Health Institute, Helsinki, Finland
| | - Edward A. Graviss
- Center for Human Bacterial Pathogenesis Research, Department of Pathology, Baylor College of Medicine, Houston, Texas 77030, Laboratory of Human Bacterial Pathogenesis, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana 59840, Department of Pathology, Microbiology, and Immunology, University of California—Davis, Davis, California 95616, Pediatric Medical Group, Houston, Texas 77098, Mount Sinai Hospital, Department of Microbiology, University of Toronto, Toronto, Ontario M5G 1X5, Canada, National Public Health Institute, Helsinki, Finland
| | - James E. Allison
- Center for Human Bacterial Pathogenesis Research, Department of Pathology, Baylor College of Medicine, Houston, Texas 77030, Laboratory of Human Bacterial Pathogenesis, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana 59840, Department of Pathology, Microbiology, and Immunology, University of California—Davis, Davis, California 95616, Pediatric Medical Group, Houston, Texas 77098, Mount Sinai Hospital, Department of Microbiology, University of Toronto, Toronto, Ontario M5G 1X5, Canada, National Public Health Institute, Helsinki, Finland
| | - Allison J. McGeer
- Center for Human Bacterial Pathogenesis Research, Department of Pathology, Baylor College of Medicine, Houston, Texas 77030, Laboratory of Human Bacterial Pathogenesis, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana 59840, Department of Pathology, Microbiology, and Immunology, University of California—Davis, Davis, California 95616, Pediatric Medical Group, Houston, Texas 77098, Mount Sinai Hospital, Department of Microbiology, University of Toronto, Toronto, Ontario M5G 1X5, Canada, National Public Health Institute, Helsinki, Finland
| | - Jaana Vuopio-Varkila
- Center for Human Bacterial Pathogenesis Research, Department of Pathology, Baylor College of Medicine, Houston, Texas 77030, Laboratory of Human Bacterial Pathogenesis, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana 59840, Department of Pathology, Microbiology, and Immunology, University of California—Davis, Davis, California 95616, Pediatric Medical Group, Houston, Texas 77098, Mount Sinai Hospital, Department of Microbiology, University of Toronto, Toronto, Ontario M5G 1X5, Canada, National Public Health Institute, Helsinki, Finland
| | - Rance B. LeFebvre
- Center for Human Bacterial Pathogenesis Research, Department of Pathology, Baylor College of Medicine, Houston, Texas 77030, Laboratory of Human Bacterial Pathogenesis, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana 59840, Department of Pathology, Microbiology, and Immunology, University of California—Davis, Davis, California 95616, Pediatric Medical Group, Houston, Texas 77098, Mount Sinai Hospital, Department of Microbiology, University of Toronto, Toronto, Ontario M5G 1X5, Canada, National Public Health Institute, Helsinki, Finland
| | - James M. Musser
- Center for Human Bacterial Pathogenesis Research, Department of Pathology, Baylor College of Medicine, Houston, Texas 77030, Laboratory of Human Bacterial Pathogenesis, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana 59840, Department of Pathology, Microbiology, and Immunology, University of California—Davis, Davis, California 95616, Pediatric Medical Group, Houston, Texas 77098, Mount Sinai Hospital, Department of Microbiology, University of Toronto, Toronto, Ontario M5G 1X5, Canada, National Public Health Institute, Helsinki, Finland
- Corresponding author. Mailing address: Department of Pathology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030. Phone: (713) 798-3823. Fax: (713) 798-4595. E-mail:
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Green NM, Zhang S, Porcella SF, Nagiec MJ, Barbian KD, Beres SB, LeFebvre RB, Musser JM. Genome Sequence of a Serotype M28 Strain of Group AStreptococcus:Potential New Insights into Puerperal Sepsis and Bacterial Disease Specificity. J Infect Dis 2005; 192:760-70. [PMID: 16088825 DOI: 10.1086/430618] [Citation(s) in RCA: 189] [Impact Index Per Article: 9.9] [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] [Received: 10/29/2004] [Accepted: 01/26/2005] [Indexed: 11/03/2022] Open
Abstract
Puerperal sepsis, a major cause of death of young women in Europe in the 1800s, was due predominantly to the gram-positive pathogen group A Streptococcus. Studies conducted during past decades have shown that serotype M28 strains are the major group A Streptococcus organisms responsible for many of these infections. To begin to increase our understanding of their enrichment in puerperal sepsis, we sequenced the genome of a genetically representative strain. This strain has genes encoding a novel array of prophage virulence factors, cell-surface proteins, and other molecules likely to contribute to host-pathogen interactions. Importantly, genes for 7 inferred extracellular proteins are encoded by a 37.4-kb foreign DNA element that is shared with group B Streptococcus and is present in all serotype M28 strains. Proteins encoded by the 37.4-kb element were expressed extracellularly and in human infections. Acquisition of foreign genes has helped create a disease-specialist clone of this pathogen.
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Affiliation(s)
- Nicole M Green
- Laboratory of Human Bacterial Pathogenesis, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Disease, National Institutes of Health, Hamilton, Montana, USA
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Reid SD, Montgomery AG, Voyich JM, DeLeo FR, Lei B, Ireland RM, Green NM, Liu M, Lukomski S, Musser JM. Characterization of an extracellular virulence factor made by group A Streptococcus with homology to the Listeria monocytogenes internalin family of proteins. Infect Immun 2003; 71:7043-52. [PMID: 14638794 PMCID: PMC308899 DOI: 10.1128/iai.71.12.7043-7052.2003] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2003] [Revised: 06/12/2003] [Accepted: 08/12/2003] [Indexed: 11/20/2022] Open
Abstract
Leucine-rich repeats (LRR) characterize a diverse array of proteins and function to provide a versatile framework for protein-protein interactions. Importantly, each of the bacterial LRR proteins that have been well described, including those of Listeria monocytogenes, Yersinia pestis, and Shigella flexneri, have been implicated in virulence. Here we describe an 87.4-kDa group A Streptococcus (GAS) protein (designated Slr, for streptococcal leucine-rich) containing 10 1/2 sequential units of a 22-amino-acid C-terminal LRR homologous to the LRR of the L. monocytogenes internalin family of proteins. In addition to the LRR domain, slr encodes a gram-positive signal secretion sequence characteristic of a lipoprotein and a putative N-terminal domain with a repeated histidine triad motif (HxxHxH). Real-time reverse transcriptase PCR assays indicated that slr is transcribed abundantly in vitro in the exponential phase of growth. Flow cytometry confirmed that Slr was attached to the GAS cell surface. Western immunoblot analysis of sera obtained from 80 patients with invasive infections, noninvasive soft tissue infections, pharyngitis, and rheumatic fever indicated that Slr is produced in vivo. An isogenic mutant strain lacking slr was significantly less virulent in an intraperitoneal mouse model of GAS infection and was significantly more susceptible to phagocytosis by human polymorphonuclear leukocytes. These studies characterize the first GAS LRR protein as an extracellular virulence factor that contributes to pathogenesis and may participate in evasion of the innate host defense.
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Affiliation(s)
- Sean D Reid
- Laboratory of Human Bacterial Pathogenesis, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana 59840, USA.
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Reid SD, Green NM, Sylva GL, Voyich JM, Stenseth ET, DeLeo FR, Palzkill T, Low DE, Hill HR, Musser JM. Postgenomic analysis of four novel antigens of group a streptococcus: growth phase-dependent gene transcription and human serologic response. J Bacteriol 2002; 184:6316-24. [PMID: 12399501 PMCID: PMC151937 DOI: 10.1128/jb.184.22.6316-6324.2002] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Analysis of three group A Streptococcus genomes (serotypes M1, M3, and M18) recently identified four previously undescribed genes that encode extracellular proteins. Each of these genes encode proteins with an LPXTG amino acid motif that covalently links many virulence factors produced by gram-positive bacteria to the cell surface. Western immunoblot analysis of serum samples obtained from 80 patients with invasive infections, noninvasive soft tissue infections, pharyngitis, and rheumatic fever indicated that these four proteins are expressed in vivo. However, the level of gene transcript and the time of maximal gene transcription varied in representative serotype M1, M3, and M18 strains. Surface expression of two proteins was confirmed by flow cytometry. Studies using a mouse infection model suggest that antibodies specific for one of the proteins (Spy0843) may contribute to a protective host immune response against a serotype M1 infection. These results are additional evidence that postgenomic strategies provide new ways to identify and investigate novel bacterial proteins that may participate in host-pathogen interactions or serve as targets for therapeutics research.
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Affiliation(s)
- Sean D Reid
- Laboratory of Human Bacterial Pathogenesis, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana 59840, USA
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Asahi M, Green NM, Kurzydlowski K, Tada M, MacLennan DH. Phospholamban domain IB forms an interaction site with the loop between transmembrane helices M6 and M7 of sarco(endo)plasmic reticulum Ca2+ ATPases. Proc Natl Acad Sci U S A 2001; 98:10061-6. [PMID: 11526231 PMCID: PMC56915 DOI: 10.1073/pnas.181348298] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2001] [Indexed: 12/20/2022] Open
Abstract
Transmembrane helix M6 of the sarco(endo)plasmic reticulum Ca2+ ATPase (SERCA) has been shown to form a site of interaction with phospholamban (PLN). Site-directed mutagenesis was carried out in the cytoplasmic loop (L67) between M6 and M7 in SERCA1a to detect other SERCA-PLN binding sites. Mutants N810A, D813A, and R822A had diminished ability to interact functionally with PLN, but only D813A and R822A had reduced physical interaction with PLN. PLN mutants R25A, Q26A, N27A, L28A, Q29A, and N30A had enhanced physical interaction with wild-type (wt) SERCA1a, but physical interaction of these PLN mutants with SERCA1a mutants D813A and R822A was reduced about 2.5 fold (range 1.44-2.82). Exceptions were the interactions of PLN N27A and N30A with SERCA1a D813A, which were reduced by 7.3- and 5.8-fold, respectively. A superinhibitory PLN deletion mutant, PLNDelta21-29, had strong physical interactions with SERCA1a and with SERCA1a mutant D813A. Physical interactions with SERCA1a and mutant D813A were sharply diminished, however, for the PLN deletion mutant, PLNDelta21-30, lacking PLN N30. Physical interactions between SERCA1a and a PLN-cytochrome b(5) chimera containing PLN residues 1-29 were much stronger than those between a PLN-cytochrome b(5) chimera containing PLN residues 1-21 and lacking N27. These results suggest that a SERCA1-PLN interaction site occurs between L67 of SERCA1a and domain IB of PLN, which involves SERCA1a D813 and PLN N27 and N30.
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Affiliation(s)
- M Asahi
- Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada
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Reid SD, Green NM, Buss JK, Lei B, Musser JM. Multilocus analysis of extracellular putative virulence proteins made by group A Streptococcus: population genetics, human serologic response, and gene transcription. Proc Natl Acad Sci U S A 2001; 98:7552-7. [PMID: 11416223 PMCID: PMC34706 DOI: 10.1073/pnas.121188598] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Species of pathogenic microbes are composed of an array of evolutionarily distinct chromosomal genotypes characterized by diversity in gene content and sequence (allelic variation). The occurrence of substantial genetic diversity has hindered progress in developing a comprehensive understanding of the molecular basis of virulence and new therapeutics such as vaccines. To provide new information that bears on these issues, 11 genes encoding extracellular proteins in the human bacterial pathogen group A Streptococcus identified by analysis of four genomes were studied. Eight of the 11 genes encode proteins with a LPXTG(L) motif that covalently links Gram-positive virulence factors to the bacterial cell surface. Sequence analysis of the 11 genes in 37 geographically and phylogenetically diverse group A Streptococcus strains cultured from patients with different infection types found that recent horizontal gene transfer has contributed substantially to chromosomal diversity. Regions of the inferred proteins likely to interact with the host were identified by molecular population genetic analysis, and Western immunoblot analysis with sera from infected patients confirmed that they were antigenic. Real-time reverse transcriptase-PCR (TaqMan) assays found that transcription of six of the 11 genes was substantially up-regulated in the stationary phase. In addition, transcription of many genes was influenced by the covR and mga trans-acting gene regulatory loci. Multilocus investigation of putative virulence genes by the integrated approach described herein provides an important strategy to aid microbial pathogenesis research and rapidly identify new targets for therapeutics research.
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Affiliation(s)
- S D Reid
- Laboratory of Human Bacterial Pathogenesis, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
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Abstract
Members of the large family of P-type pumps use active transport to maintain gradients of a wide variety of cations across cellular membranes. Recent structures of two P-type pumps at 8-A resolution have revealed the arrangement of transmembrane helices but were insufficient to reveal the architecture of the cytoplasmic domains. However, recent proposals of a structural homology with a superfamily of hydrolases offer a new basis for modeling these domains. In the current work, we have extended the sequence comparison for the superfamily and delineated domains in the 8-A density map of Ca(2+)-ATPase. The homology suggests a new domain structure for Ca(2+)-ATPase and, specifically, that the phosphorylation domain adopts a Rossman fold. Accordingly, the atomic structure of L-2 haloacid dehalogenase has been fitted into the relevant domain of Ca(2+)-ATPase. The resulting model suggests the existence of two ATP sites at the interface between two domains. Based on this new model, we are able to reconcile numerous results of mutagenesis and chemical cross-linking within the catalytic domains. Furthermore, we have used the model to predict the configuration of Mg.ATP at its binding site. Based on this prediction, we propose a mechanism, involving a change in Mg(2+) liganding, for initiating the domain movements that couple sites of ion transport to ATP hydrolysis.
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Affiliation(s)
- D L Stokes
- Skirball Institute of Biomolecular Research, Department of Cell Biology, New York University School of Medicine, New York, New York 10016, USA.
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39
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MacLennan DH, Rice WJ, Odermatt A, Green NM. Structure-function relationships in the Ca(2+)-binding and translocation domain of SERCA1: physiological correlates in Brody disease. Acta Physiol Scand Suppl 1998; 643:55-67. [PMID: 9789547] [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: 02/09/2023]
Abstract
Alanine-scanning mutagenesis of all amino acids in transmembrane helices M4, M5, M6 and M8, which contain known Ca2+ binding residues in the Ca(2+)-ATPase of skeletal muscle sarcoplasmic reticulum, revealed patches of mutation-sensitivity in M4, M5 and M6, but in M8. A six-residue motif, (E/D)GLPA(T/V), in M4 and M6 and its counterpart in M5 were highlighted by mutagenesis. Site-directed disulfide mapping of helices M4 and M6 demonstrated that these transmembrane helices associate as a right-handed coiled-coil. This structural information, combined with the earlier analysis of the association of each Ca2+ binding residue with either Ca2+ binding site I or site II, permitted the development of a "side-by-side" model for the two Ca2+ binding sites in the Ca(2+)-ATPase. In about half of Brody disease families, mutations create stop codons which delete all or part of the Ca2+ binding and translocation domain, resulting in loss of SERCA1 function and muscle disease.
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Affiliation(s)
- D H MacLennan
- Banting and Best Department of Medical Research, University of Toronto, Ontario, Canada
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40
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Abstract
The calcium pump from sarcoplasmic reticulum (Ca2+-ATPase) is typical of the large family of P-type cation pumps. These couple ATP hydrolysis with cation transport, generating cation gradients across membranes. Ca2+-ATPase specifically maintains the low cytoplasmic calcium concentration of resting muscle by pumping calcium into the sarcoplasmic reticulum; subsequent release is used to initiate contraction. No high-resolution structure of a P-type pump has yet been determined, although a 14-A structure of Ca2+-ATPase, obtained by electron microscopy of frozen-hydrated, tubular crystals, showed a large cytoplasmic head connected to the transmembrane domain by a narrow stalk. We have now improved the resolution to 8A and can discern ten transmembrane alpha-helices, four of which continue into the stalk On the basis of constraints from transmembrane topology, site-directed mutagenesis and disulphide crosslinking, we have made tentative assignments for these alpha-helices within the amino-acid sequence. A distinct cavity leads to the putative calcium-binding site, providing a plausible path for calcium release to the lumen of the sarcoplasmic reticulum.
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Affiliation(s)
- P Zhang
- Skirball Institute of Biomolecular Medicine, New York University Medical Center, New York 10016, USA
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41
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Rice WJ, Green NM, MacLennan DH. Site-directed disulfide mapping of helices M4 and M6 in the Ca2+ binding domain of SERCA1a, the Ca2+ ATPase of fast twitch skeletal muscle sarcoplasmic reticulum. J Biol Chem 1997; 272:31412-9. [PMID: 9395473 DOI: 10.1074/jbc.272.50.31412] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [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: 02/05/2023] Open
Abstract
In an attempt to define the spatial relationships among SERCA1a transmembrane helices M4, M5, M6, and M8, involved in Ca2+ binding, all six cysteine residues were removed from predicted transmembrane sequences by substitution with Ser or Ala. The cysteine-depleted protein retained 44% of wild type Ca2+ transport activity. Pairs of cysteine residues were then reintroduced to determine whether their juxtaposition would result in the formation of disulfide cross-links between transmembrane helices. In initial studies designed to map the juxtaposition of Ca2+ binding residues, Cys was substituted for Glu309 or Gly310 in transmembrane sequence M4, in combination with the substitution of Cys for Glu771 in M5; for Asn796, Thr799, or Asp800 in M6; or for Glu908 in M8. These double mutants all retained the capacity to form a phosphoenzyme intermediate from Pi (but not from ATP in the presence of Ca2+), and in all but mutants E309C/N796C and G310C/N796C, phosphoenzyme formation was insensitive to 100 microM Ca2+. These results support the view that both Glu309 and Asn796 contribute to Ca2+ binding site II, which is not required for conversion of E2, the substrate for Pi phosphorylation, to E1. Cross-linking in mutants E309C/N796C and G310C/D800C established reference points for the orientation of M4 and M6 relative to each other and provided the basis for the prediction of potential additional cross-links. Strong links were formed with the pairs T317C/A804C and T317C/L807C near the cytoplasmic ends of the two helices and with A305C/L792C and A305C/L793C near the lumenal ends. These combined results support the conclusion that M4 and M6 form a right-handed coiled-coil structure that forms part of the pathway of Ca2+ translocation. In addition to providing a possible explanation for the mutation sensitivity of several pairs of residues in these helices, the proposed association of M4 and M6 supports a new model for the orientation of the two Ca2+ binding sites among transmembrane helices M4, M5, and M6.
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Affiliation(s)
- W J Rice
- Banting and Best Department of Medical Research, University of Toronto, Charles H. Best Institute, 112 College St., Toronto, Ontario M5G 1L6 Canada
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Affiliation(s)
- D H MacLennan
- Banting and Best Department of Medical Research, C. H. Best Institute, University of Toronto, Toronto, Ontario M5G 1L6, Canada.
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43
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Abstract
Electron microscopy has recently provided improved structures for P-type ion pumps. In the case of Ca(2+)-ATPase, the use of unstained specimens revealed the structure of the transmembrane domain. The composition of this domain has been controversial due to the variety of methods used to study the number and exact locations of transmembrane crossings within the sequence. After reviewing the results from several members of the family, we found a consensus for 10 transmembrane segments, and also that 10 helices fitted well into the structure of Ca(2+)-ATPase. Thus, we present the most detailed model for transmembrane structure so far, in the hope of stimulating more precise experimental strategies.
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Affiliation(s)
- D L Stokes
- Department of Molecular Physiology and Biological Physics, University of Virginia Health Sciences Center, Charlottesville 22908
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44
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Abstract
Integral membrane proteins (of the alpha-helical class) are of central importance in a wide variety of vital cellular functions. Despite considerable effort on methods to predict the location of the helices, little attention has been directed toward developing an automatic method to pack the helices together. In principle, the prediction of membrane proteins should be easier than the prediction of globular proteins: there is only one type of secondary structure and all helices pack with a common alignment across the membrane. This allows all possible structures to be represented on a simple lattice and exhaustively enumerated. Prediction success lies not in generating many possible folds but in recognizing which corresponds to the native. Our evaluation of each fold is based on how well the exposed surface predicted from a multiple sequence alignment fits its allocated position. Just as exposure to solvent in globular proteins can be predicted from sequence variation, so exposure to lipid can be recognized by variable-hydrophobic (variphobic) positions. Application to both bacteriorhodopsin and the eukaryotic rhodopsin/opsin families revealed that the angular size of the lipid-exposed faces must be predicted accurately to allow selection of the correct fold. With the inherent uncertainties in helix prediction and parameter choice, this accuracy could not be guaranteed but the correct fold was typically found in the top six candidates. Our method provides the first completely automatic method that can proceed from a scan of the protein sequence databanks to a predicted three-dimensional structure with no intervention required from the investigator. Within the limited domain of the seven helix bundle proteins, a good chance can be given of selecting the correct structure. However, the limited number of sequences available with a corresponding known structure makes further characterization of the method difficult.
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Affiliation(s)
- W R Taylor
- Laboratory of Mathematical Biology, National Institute for Medical Research, London, U.K
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Affiliation(s)
- N M Green
- National Institute for Medical Research, London, UK
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Lacapère JJ, Garin J, Trinnaman B, Green NM. Identification of amino acid residues photolabeled with 8-azidoadenosine 5'-diphosphate in the catalytic site of sarcoplasmic reticulum Ca-ATPase. Biochemistry 1993; 32:3414-21. [PMID: 8384881 DOI: 10.1021/bi00064a027] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The photoreactive ADP analogue 8-N3-ADP binds in the dark to the catalytic site of the sarcoplasmic reticulum Ca-ATPase. An apparent Kd value of 30 microM has been deduced from competition with ADP in the presence of EGTA. Photoirradiation of Ca-ATPase with 8-N3-[3H]ADP in the presence of calcium results in irreversible inhibition of ATPase activity with corresponding stoichiometries of covalently and specifically photolabeled Ca-ATPase. The site of photolabeling of the Ca-ATPase in the presence of calcium has been explored. Controlled trypsin digestion of the labeled protein shows that 8-azido-ADP is incorporated in the B subfragment. Extensive trypsin digestion of the labeled protein releases a small peptide as revealed by gel filtration chromatography (Sephadex G-50). Further HPLC purification on a reverse-phase column (C8) eluted with a water/acetonitrile gradient buffered at pH 6 or at pH 2 gives a single labeled peptide. Edman degradation of that isolated peptide, as well as the amino acid composition, shows that it contains five amino acid residues (Val-530-Arg-534) with the radioactivity localized on Thr-532 and Thr-533.
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Affiliation(s)
- J J Lacapère
- Section de Biophysique des Proteines et des Membranes (URA 1290 CNRS), Departement de Biologie Moleculaire et Cellulaire, CEN Saclay, Gif sur Yvette, France
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47
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Affiliation(s)
- N M Green
- National Institute for Medical Research, Mill Hill, London, England
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49
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Abstract
The sequences of the peptide binding domains of 33 70 kd heat shock proteins (hsp70) have been aligned and a consensus secondary structure has been deduced. Individual members showed no significant deviation from the consensus, which showed a beta 4 alpha motif repeated twice, followed by two further helices and a terminus rich in Pro and Gly. The repeated motif could be aligned with the secondary structure of the functionally equivalent peptide binding domain of human leucocyte antigen (HLA) class I maintaining equivalent residues in structurally important positions in the two families and a model was built based on this alignment. The interaction of this domain with the ATP domain is considered. The overall model is shown to be consistent with the properties of products of chymotryptic cleavage.
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Affiliation(s)
- F Rippmann
- National Institute for Medical Research, Mill Hill, London, UK
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Treves S, De Mattei M, Landfredi M, Villa A, Green NM, MacLennan DH, Meldolesi J, Pozzan T. Calreticulin is a candidate for a calsequestrin-like function in Ca2(+)-storage compartments (calciosomes) of liver and brain. Biochem J 1990; 271:473-80. [PMID: 2241926 PMCID: PMC1149579 DOI: 10.1042/bj2710473] [Citation(s) in RCA: 106] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In a search for the non-muscle equivalent of calsequestrin (the low-affinity high-capacity Ca2(+)-binding protein responsible for Ca2+ storage within the terminal cisternae of the sarcoplasmic reticulum), acidic proteins were extracted from rat liver and brain microsomal preparations and purified by column chromatography. No calsequestrin was observed in these extracts, but the N-terminal amino acid sequence of the major Ca2(+)-binding protein of the liver microsomal fraction was determined and found to correspond to that of calreticulin. This protein was found to bind approx. 50 mol of Ca2+/mol of protein, with low affinity (average Kd approx. 1.0 mM). A monoclonal antibody, C6, raised against skeletal-muscle calsequestrin cross-reacted with calreticulin in SDS/PAGE immunoblots, but polyclonal antibodies reacted with native calreticulin only weakly, or not at all, after SDS denaturation. Immuno-gold decoration of liver ultrathin cryosections with affinity-purified antibodies against liver calreticulin revealed luminal labelling of vacuolar profiles indistinguishable from calciosomes, the subcellular structures previously identified by the use of anti-calsequestrin antibodies. We conclude that calreticulin is the Ca2(+)-binding protein segregated within the calciosome lumen, previously described as being calsequestrin-like. Because of its properties and intraluminal location, calreticulin might play a critical role in Ca2+ storage and release in non-muscle cells, similar to that played by calsequestrin in the muscle sarcoplasmic reticulum.
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Affiliation(s)
- S Treves
- Institute of General Pathology, University of Padova, Italy
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