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Miles SJ, Harrington C, Sun H, Deas A, Oberste MS, Nix WA, Vega E, Gerloff N. Validation of improved automated nucleic acid extraction methods for direct detection of polioviruses for global polio eradication. J Virol Methods 2024; 326:114914. [PMID: 38458353 DOI: 10.1016/j.jviromet.2024.114914] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 03/10/2024]
Abstract
Polioviruses (PV), the main causative agent of acute flaccid paralysis (AFP), are positive-sense single-stranded RNA viruses of the family Picornaviridae. As we approach polio eradication, accurate and timely detection of poliovirus in stool from AFP cases becomes vital to success for the eradication efforts. Direct detection of PV from clinical diagnostic samples using nucleic acid (NA) extraction and real-time reverse transcriptase polymerase chain reaction (rRT-PCR) instead of the current standard method of virus isolation in culture, eliminates the long turn-around time to diagnosis and the need for high viral titer amplification in laboratories. An essential component of direct detection of PV from AFP surveillance samples is the efficient extraction of NA. Potential supply chain issues and lack of vendor presence in certain areas of the world necessitates the validation of multiple NA extraction methods. Using retrospective PV-positive surveillance samples (n=104), two extraction kits were compared to the previously validated Zymo Research Quick-RNA™ Viral Kit. The Roche High Pure Viral RNA Kit, a column-based manual extraction method, and the MagMaX™ Pathogen RNA/DNA kit used in the automated Kingfisher Flex system were both non-inferior to the Zymo kit, with similar rates of PV detection in pivotal rRT-PCR assays, such as pan-poliovirus (PanPV), poliovirus serotype 2 (PV2), and wild poliovirus serotype 1 (WPV1). These important assays allow the identification and differentiation of PV genotypes and serotypes and are fundamental to the GPLN program. Validation of two additional kits provides feasible alternatives to the current piloted method of NA extraction for poliovirus rRT-PCR assays.
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Affiliation(s)
- Stacey Jeffries Miles
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Chelsea Harrington
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Hong Sun
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Ashley Deas
- Cherokee Nation Assurance, Contracting Agency to the Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - M Steven Oberste
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - W Allan Nix
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Everardo Vega
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Nancy Gerloff
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA.
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Ryerson AB, Lang D, Alazawi MA, Neyra M, Hill DT, St. George K, Fuschino M, Lutterloh E, Backenson B, Rulli S, Ruppert PS, Lawler J, McGraw N, Knecht A, Gelman I, Zucker JR, Omoregie E, Kidd S, Sugerman DE, Jorba J, Gerloff N, Ng TFF, Lopez A, Masters NB, Leung J, Burns CC, Routh J, Bialek SR, Oberste MS, Rosenberg ES. Wastewater Testing and Detection of Poliovirus Type 2 Genetically Linked to Virus Isolated from a Paralytic Polio Case - New York, March 9-October 11, 2022. MMWR Morb Mortal Wkly Rep 2022; 71:1418-1424. [PMID: 36327157 PMCID: PMC9639435 DOI: 10.15585/mmwr.mm7144e2] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/13/2023]
Abstract
In July 2022, a case of paralytic poliomyelitis resulting from infection with vaccine-derived poliovirus (VDPV) type 2 (VDPV2)§ was confirmed in an unvaccinated adult resident of Rockland County, New York (1). As of August 10, 2022, poliovirus type 2 (PV2)¶ genetically linked to this VDPV2 had been detected in wastewater** in Rockland County and neighboring Orange County (1). This report describes the results of additional poliovirus testing of wastewater samples collected during March 9-October 11, 2022, and tested as of October 20, 2022, from 48 sewersheds (the community area served by a wastewater collection system) serving parts of Rockland County and 12 surrounding counties. Among 1,076 wastewater samples collected, 89 (8.3%) from 10 sewersheds tested positive for PV2. As part of a broad epidemiologic investigation, wastewater testing can provide information about where poliovirus might be circulating in a community in which a paralytic case has been identified; however, the most important public health actions for preventing paralytic poliomyelitis in the United States remain ongoing case detection through national acute flaccid myelitis (AFM) surveillance†† and improving vaccination coverage in undervaccinated communities. Although most persons in the United States are sufficiently immunized, unvaccinated or undervaccinated persons living or working in Kings, Orange, Queens, Rockland, or Sullivan counties, New York should complete the polio vaccination series as soon as possible.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - 2022 U.S. Poliovirus Response Team
- 2022 CDC Domestic Poliovirus Emergency Response Team; New York State Department of Health; Department of Public Health, Syracuse University, Syracuse, New York; Department of Biomedical Science, State University of New York at Albany, Albany, New York; Rockland County Department of Health, Pomona, New York; Orange County Department of Health, Goshen, New York; Sullivan County Department of Public Health, Liberty, New York; Nassau County Department of Health, Mineola, New York; New York City Department of Health and Mental Hygiene, New York, New York; Epidemic Intelligence Service, CDC; Department of Epidemiology and Biostatistics, State University of New York at Albany, Albany, New York
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Link-Gelles R, Lutterloh E, Ruppert PS, Backenson PB, St George K, Rosenberg ES, Anderson BJ, Fuschino M, Popowich M, Punjabi C, Souto M, McKay K, Rulli S, Insaf T, Hill D, Kumar J, Gelman I, Jorba J, Ng TFF, Gerloff N, Masters NB, Lopez A, Dooling K, Stokley S, Kidd S, Oberste MS, Routh J, Brister B, Bullows JE, Burns CC, Castro CJ, Cory J, Dybdahl‐Sissoko N, Emery BD, English R, Frolov AD, Getachew H, Henderson E, Hess A, Mason K, Mercante JW, Miles SJ, Liu H, Marine RL, Momin N, Pang H, Perry D, Rogers SL, Short B, Sun H, Tobolowsky F, Yee E, Hughes S, Hygiene M, Omoregie E, Hygiene M, Rosen JB, Hygiene M, Zucker JR, Hygiene M, Alazawi M, Bauer U, Godinez A, Hanson B, Heslin E, McDonald J, Mita‐Mendoza NK, Meldrum M, Neigel D, Suitor R, Larsen DA, Egan C, Faraci N, Feumba GS, Gray T, Lamson D, Laplante J, McDonough K, Migliore N, Moghe A, Ogbamikael S, Plitnick J, Ramani R, Rickerman L, Rist E, Schoultz L, Shudt M, Krauchuk J, Medina E, Lawler J, Boss H, Barca E, Ghazali DB, Goyal T, Marinelli SJ, Roberts JA, Russo GB, Thakur KT, Yang VQ. Public health response to a case of paralytic poliomyelitis in an unvaccinated person and detection of poliovirus in wastewater-New York, June-August 2022. Am J Transplant 2022; 22:2470-2474. [PMID: 36196495 DOI: 10.1111/ajt.16677] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Ruth Link-Gelles
- 2022 CDC Domestic Poliovirus Emergency Response Team, State University of New York at Albany, Albany, New York, USA
| | - Emily Lutterloh
- New York State Department of Health, State University of New York at Albany, Albany, New York, USA.,Department of Epidemiology and Biostatistics, State University of New York at Albany, Albany, New York, USA
| | | | - P Bryon Backenson
- New York State Department of Health, State University of New York at Albany, Albany, New York, USA.,Department of Epidemiology and Biostatistics, State University of New York at Albany, Albany, New York, USA
| | - Kirsten St George
- Wadsworth Center, New York State Department of Health, Albany, New York, USA.,Department of Biomedical Science, State University of New York at Albany, Albany, New York, USA
| | - Eli S Rosenberg
- New York State Department of Health, State University of New York at Albany, Albany, New York, USA.,Department of Epidemiology and Biostatistics, State University of New York at Albany, Albany, New York, USA
| | - Bridget J Anderson
- New York State Department of Health, State University of New York at Albany, Albany, New York, USA
| | - Meghan Fuschino
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Michael Popowich
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Chitra Punjabi
- Rockland County Department of Health, Pomona, New York, USA
| | - Maria Souto
- Rockland County Department of Health, Pomona, New York, USA
| | - Kevin McKay
- Rockland County Department of Health, Pomona, New York, USA
| | - Samuel Rulli
- Rockland County Department of Health, Pomona, New York, USA
| | - Tabassum Insaf
- New York State Department of Health, State University of New York at Albany, Albany, New York, USA
| | - Dustin Hill
- Department of Public Health, Syracuse University, Syracuse, New York, USA
| | - Jessica Kumar
- New York State Department of Health, State University of New York at Albany, Albany, New York, USA
| | - Irina Gelman
- Orange County Department of Health, Goshen, New York, USA
| | - Jaume Jorba
- 2022 CDC Domestic Poliovirus Emergency Response Team, State University of New York at Albany, Albany, New York, USA
| | - Terry Fei Fan Ng
- 2022 CDC Domestic Poliovirus Emergency Response Team, State University of New York at Albany, Albany, New York, USA
| | - Nancy Gerloff
- 2022 CDC Domestic Poliovirus Emergency Response Team, State University of New York at Albany, Albany, New York, USA
| | - Nina B Masters
- 2022 CDC Domestic Poliovirus Emergency Response Team, State University of New York at Albany, Albany, New York, USA
| | - Adriana Lopez
- 2022 CDC Domestic Poliovirus Emergency Response Team, State University of New York at Albany, Albany, New York, USA
| | - Kathleen Dooling
- 2022 CDC Domestic Poliovirus Emergency Response Team, State University of New York at Albany, Albany, New York, USA
| | - Shannon Stokley
- 2022 CDC Domestic Poliovirus Emergency Response Team, State University of New York at Albany, Albany, New York, USA
| | - Sarah Kidd
- 2022 CDC Domestic Poliovirus Emergency Response Team, State University of New York at Albany, Albany, New York, USA
| | - M Steven Oberste
- 2022 CDC Domestic Poliovirus Emergency Response Team, State University of New York at Albany, Albany, New York, USA
| | - Janell Routh
- 2022 CDC Domestic Poliovirus Emergency Response Team, State University of New York at Albany, Albany, New York, USA
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Link-Gelles R, Lutterloh E, Schnabel Ruppert P, Backenson PB, St. George K, Rosenberg ES, Anderson BJ, Fuschino M, Popowich M, Punjabi C, Souto M, McKay K, Rulli S, Insaf T, Hill D, Kumar J, Gelman I, Jorba J, Ng TFF, Gerloff N, Masters NB, Lopez A, Dooling K, Stokley S, Kidd S, Oberste MS, Routh J. Public Health Response to a Case of Paralytic Poliomyelitis in an Unvaccinated Person and Detection of Poliovirus in Wastewater - New York, June-August 2022. MMWR Morb Mortal Wkly Rep 2022; 71:1065-1068. [PMID: 35980868 PMCID: PMC9400530 DOI: 10.15585/mmwr.mm7133e2] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Belgasmi H, Miles SJ, Sayyad L, Wong K, Harrington C, Gerloff N, Coulliette-Salmond AD, Guntapong R, Tacharoenmuang R, Ayutthaya AIN, Apostol LNG, Valencia MLD, Burns CC, Benito GR, Vega E. CaFÉ: A Sensitive, Low-Cost Filtration Method for Detecting Polioviruses and Other Enteroviruses in Residual Waters. Front Environ Sci 2022; 10:10.3389/fenvs.2022.914387. [PMID: 35928599 PMCID: PMC9344547 DOI: 10.3389/fenvs.2022.914387] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Acute flaccid paralysis (AFP) surveillance has been used to identify polio cases and target vaccination campaigns since the inception of the Global Poliovirus Eradication Initiative (GPEI) in 1988. To date, only Afghanistan and Pakistan have failed to interrupt wild poliovirus transmission. Circulation of vaccine-derived polioviruses (VDPV) continues to be a problem in high-risk areas of the Eastern Mediterranean, African, and Southeast Asian regions. Environmental surveillance (ES) is an important adjunct to AFP surveillance, helping to identify circulating polioviruses in problematic areas. Stools from AFP cases and contacts (>200,000 specimens/year) and ES samples (>642 sites) are referred to 146 laboratories in the Global Polio Laboratory Network (GPLN) for testing. Although most World Health Organization supported laboratories use the two-phase separation method due to its simplicity and effectiveness, alternative simple, widely available, and cost-effective methods are needed. The CAFÉ (Concentration and Filtration Elution) method was developed from existing filtration methods to handle any type of sewage or residual waters. At $10-20 US per sample for consumable materials, CAFÉ is cost effective, and all equipment and reagents are readily available from markets and suppliers globally. The report describes the results from a parallel study of CAFÉ method with the standard two-phase separation method. The study was performed with samples collected from five countries (Guatemala, Haïti, Thailand, Papua New Guinea, and the Philippines), run in three laboratories-(United States, Thailand and in the Philippines) to account for regional and sample-to-sample variability. Samples from each site were divided into two 500 ml aliquots and processed by both methods, with no other additional concentration or manipulation. The results of 338 parallel-tested samples show that the CAFÉ method is more sensitive than the two-phase separation method for detection of non-polio enteroviruses (p-value < 0.0001) and performed as well as the two-phase separation method for polioviruses detection with no significant difference (p-value > 0.05). The CAFÉ method is a robust, sensitive, and cost-effective method for isolating enteroviruses from residual waters.
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Affiliation(s)
- Hanen Belgasmi
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Stacey Jeffries Miles
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | | | | | - Chelsea Harrington
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Nancy Gerloff
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Angela D Coulliette-Salmond
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
- U.S Public Health Service, Rockville, MD, United States
| | - Ratigorn Guntapong
- Department of Medical Science, Enteric Viruses Section, National Institute of Health, Nonthaburi, Thailand
| | - Ratana Tacharoenmuang
- Department of Medical Science, Enteric Viruses Section, National Institute of Health, Nonthaburi, Thailand
| | | | | | | | - Cara C. Burns
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Gloria-Rey Benito
- Pan American Health Organization, World Health Organization, Washington, DC, United States
| | - Everardo Vega
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
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Gerloff N, Mandelbaum M, Pang H, Collins N, Brown B, Sun H, Harrington C, Hecker J, Agha C, Burns CC, Vega E. Direct detection of polioviruses using a recombinant poliovirus receptor. PLoS One 2021; 16:e0259099. [PMID: 34727100 PMCID: PMC8562806 DOI: 10.1371/journal.pone.0259099] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 10/12/2021] [Indexed: 11/28/2022] Open
Abstract
Polioviruses are positive-sense, single-stranded RNA picornaviruses and the principal cause of poliomyelitis. Global poliovirus surveillance has relied on poliovirus isolation in cells, which may take a minimum of 10 days, involves maintaining two cell lines, and propagates virus in high titers. With eradication underway, a major objective of the Global Polio Eradication Initiative (GPEI) is to develop culture-independent detection of polioviruses as an alternative method to complement the current virus isolation technique. A culture-independent method on poliovirus-positive stool suspensions was assessed with commercially available recombinant soluble poliovirus receptor (PVR) coupled to Histidine (His) tags. Viral RNA was screened by quantitative real-time reverse transcription PCR using the poliovirus intratypic differentiation kit. Poliovirus recovery was optimized with PVR-His-tagged protein and buffers supplemented with polyethylene glycol. To validate the poliovirus-PVR-His tag purification assay, 182 poliovirus-positive stools of programmatic importance were parallel tested against the GPLN-accepted virus isolation method. The PVR-His tag enrichment method detected poliovirus in 164 of 171 poliovirus-positive stools, whereas the virus isolation method misidentified 38 stools as poliovirus-negative (McNemar χ2 p<0.0001). Using this method in combination with RNA extraction, viral RNA recovery increased and showed similar (WPV1) or higher (Sabin 1) sensitivity than the World Health Organization accredited variation of the virus isolation method. The PVR-His enrichment method could be a viable addition to poliovirus surveillance; similar methods have the potential to capture other human pathogens such as EV71 using an appropriate soluble His tag receptor.
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Affiliation(s)
- Nancy Gerloff
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Mark Mandelbaum
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Hong Pang
- Cherokee Nation Assurance, Contracting Agency to the Division of Viral Diseases, Atlanta, Georgia, United States of America
| | - Nikail Collins
- IHRC, Contracting agency to the Division of Viral Diseases, Atlanta, Georgia, United States of America
| | - Brittani Brown
- IHRC, Contracting agency to the Division of Viral Diseases, Atlanta, Georgia, United States of America
| | - Hong Sun
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Chelsea Harrington
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Jessica Hecker
- Cherokee Nation Assurance, Contracting Agency to the Division of Viral Diseases, Atlanta, Georgia, United States of America
| | - Chadi Agha
- IHRC, Contracting agency to the Division of Viral Diseases, Atlanta, Georgia, United States of America
| | - Cara C. Burns
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Everardo Vega
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
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Chakraborty A, Rahman M, Hossain MJ, Khan SU, Haider MS, Sultana R, Ali Rimi N, Islam MS, Haider N, Islam A, Sultana Shanta I, Sultana T, Al Mamun A, Homaira N, Goswami D, Nahar K, Alamgir ASM, Rahman M, Mahbuba Jamil K, Azziz-Baumgartner E, Simpson N, Shu B, Lindstrom S, Gerloff N, Davis CT, Katz JM, Mikolon A, Uyeki TM, Luby SP, Sturm-Ramirez K. Mild Respiratory Illness Among Young Children Caused by Highly Pathogenic Avian Influenza A (H5N1) Virus Infection in Dhaka, Bangladesh, 2011. J Infect Dis 2017; 216:S520-S528. [PMID: 28934459 DOI: 10.1093/infdis/jix019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Background In March 2011, a multidisciplinary team investigated 2 human cases of highly pathogenic avian influenza A(H5N1) virus infection, detected through population-based active surveillance for influenza in Bangladesh, to assess transmission and contain further spread. Methods We collected clinical and exposure history of the case patients and monitored persons coming within 1 m of a case patient during their infectious period. Nasopharyngeal wash specimens from case patients and contacts were tested with real-time reverse-transcription polymerase chain reaction, and virus culture and isolates were characterized. Serum samples were tested with microneutralization and hemagglutination inhibition assays. We tested poultry, wild bird, and environmental samples from case patient households and surrounding areas for influenza viruses. Results Two previously healthy case patients, aged 13 and 31 months, had influenzalike illness and fully recovered. They had contact with poultry 7 and 10 days before illness onset, respectively. None of their 57 contacts were subsequently ill. Clade 2.2.2.1 highly pathogenic avian influenza H5N1 viruses were isolated from the case patients and from chicken fecal samples collected at the live bird markets near the patients' dwellings. Conclusion Identification of H5N1 cases through population-based surveillance suggests possible additional undetected cases throughout Bangladesh and highlights the importance of surveillance for mild respiratory illness among populations frequently exposed to infected poultry.
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Affiliation(s)
- Apurba Chakraborty
- Institute of Epidemiology, Disease Control and Research.,International Centre for Diarrhoeal Diseases Research (icddr,b)
| | | | - M Jahangir Hossain
- International Centre for Diarrhoeal Diseases Research (icddr,b).,Medical Research Council Unit, The Gambia
| | | | | | - Rebeca Sultana
- International Centre for Diarrhoeal Diseases Research (icddr,b)
| | - Nadia Ali Rimi
- International Centre for Diarrhoeal Diseases Research (icddr,b)
| | - M Saiful Islam
- International Centre for Diarrhoeal Diseases Research (icddr,b)
| | - Najmul Haider
- International Centre for Diarrhoeal Diseases Research (icddr,b)
| | - Ausraful Islam
- International Centre for Diarrhoeal Diseases Research (icddr,b)
| | | | - Tahmina Sultana
- International Centre for Diarrhoeal Diseases Research (icddr,b)
| | | | - Nusrat Homaira
- International Centre for Diarrhoeal Diseases Research (icddr,b).,UNSW, Sydney, Australia
| | - Doli Goswami
- International Centre for Diarrhoeal Diseases Research (icddr,b)
| | - Kamrun Nahar
- International Centre for Diarrhoeal Diseases Research (icddr,b)
| | - A S M Alamgir
- Institute of Epidemiology, Disease Control and Research.,World Health Organization, Dhaka, Bangladesh
| | | | | | | | - Natosha Simpson
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Bo Shu
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Nancy Gerloff
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - C Todd Davis
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Andrea Mikolon
- International Centre for Diarrhoeal Diseases Research (icddr,b).,Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Timothy M Uyeki
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Stephen P Luby
- International Centre for Diarrhoeal Diseases Research (icddr,b).,Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Katharine Sturm-Ramirez
- International Centre for Diarrhoeal Diseases Research (icddr,b).,Centers for Disease Control and Prevention, Atlanta, Georgia
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8
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Nguyen DT, Jang Y, Nguyen TD, Jones J, Shepard SS, Yang H, Gerloff N, Fabrizio T, Nguyen LV, Inui K, Yang G, Creanga A, Wang L, Mai DT, Thor S, Stevens J, To TL, Wentworth DE, Nguyen T, Pham DV, Bryant JE, Davis CT. Shifting Clade Distribution, Reassortment, and Emergence of New Subtypes of Highly Pathogenic Avian Influenza A(H5) Viruses Collected from Vietnamese Poultry from 2012 to 2015. J Virol 2017; 91:e01708-16. [PMID: 28003481 PMCID: PMC5309939 DOI: 10.1128/jvi.01708-16] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [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] [Received: 09/02/2016] [Accepted: 11/28/2016] [Indexed: 11/20/2022] Open
Abstract
Whole-genome sequences of representative highly pathogenic avian influenza A(H5) viruses from Vietnam were generated, comprising samples from poultry outbreaks and active market surveillance collected from January 2012 to August 2015. Six hemagglutinin gene clades were characterized. Clade 1.1.2 was predominant in southern Mekong provinces throughout 2012 and 2013 but gradually disappeared and was not detected after April 2014. Clade 2.3.2.1c viruses spread rapidly during 2012 and were detected in the south and center of the country. A number of clade 1.1.2 and 2.3.2.1c interclade reassortant viruses were detected with different combinations of internal genes derived from 2.3.2.1a and 2.3.2.1b viruses, indicating extensive cocirculation. Although reassortment generated genetic diversity at the genotype level, there was relatively little genetic drift within the individual gene segments, suggesting genetic stasis over recent years. Antigenically, clade 1.1.2, 2.3.2.1a, 2.3.2.1b, and 2.3.2.1c viruses remained related to earlier viruses and WHO-recommended prepandemic vaccine strains representing these clades. Clade 7.2 viruses, although detected in only low numbers, were the exception, as indicated by introduction of a genetically and antigenically diverse strain in 2013. Clade 2.3.4.4 viruses (H5N1 and H5N6) were likely introduced in April 2014 and appeared to gain dominance across northern and central regions. Antigenic analyses of clade 2.3.4.4 viruses compared to existing clade 2.3.4 candidate vaccine viruses (CVV) indicated the need for an updated vaccine virus. A/Sichuan/26221/2014 (H5N6) virus was developed, and ferret antisera generated against this virus were demonstrated to inhibit some but not all clade 2.3.4.4 viruses, suggesting consideration of alternative clade 2.3.4.4 CVVs.IMPORTANCE Highly pathogenic avian influenza (HPAI) A(H5) viruses have circulated continuously in Vietnam since 2003, resulting in hundreds of poultry outbreaks and sporadic human infections. Despite a significant reduction in the number of human infections in recent years, poultry outbreaks continue to occur and the virus continues to diversify. Vaccination of poultry has been used as a means to control the spread and impact of the virus, but due to the diversity and changing distribution of antigenically distinct viruses, the utility of vaccines in the face of mismatched circulating strains remains questionable. This study assessed the putative amino acid changes in viruses leading to antigenic variability, underscoring the complexity of vaccine selection for both veterinary and public health purposes. Given the overlapping geographic distributions of multiple, antigenically distinct clades of HPAI A(H5) viruses in Vietnam, the vaccine efficacy of bivalent poultry vaccine formulations should be tested in the future.
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Affiliation(s)
- Diep T Nguyen
- National Center for Veterinary Diagnostics, Department of Animal Health, Hanoi, Vietnam
- Department of Animal Health, Ministry of Agriculture and Rural Development of Vietnam, Hanoi, Vietnam
- Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Hanoi, Vietnam
- Center for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Yunho Jang
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Tho D Nguyen
- National Center for Veterinary Diagnostics, Department of Animal Health, Hanoi, Vietnam
| | - Joyce Jones
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Samuel S Shepard
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Hua Yang
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Nancy Gerloff
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Thomas Fabrizio
- St. Jude's Center for Excellence in Influenza Research and Surveillance, Memphis, Tennessee, USA
| | - Long V Nguyen
- Department of Animal Health, Ministry of Agriculture and Rural Development of Vietnam, Hanoi, Vietnam
| | - Ken Inui
- Food and Agriculture Organization of the United Nations, Hanoi, Vietnam
| | - Genyan Yang
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Adrian Creanga
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Li Wang
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Duong T Mai
- National Center for Veterinary Diagnostics, Department of Animal Health, Hanoi, Vietnam
| | - Sharmi Thor
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - James Stevens
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Thanh L To
- National Center for Veterinary Diagnostics, Department of Animal Health, Hanoi, Vietnam
| | - David E Wentworth
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Tung Nguyen
- Department of Animal Health, Ministry of Agriculture and Rural Development of Vietnam, Hanoi, Vietnam
| | - Dong V Pham
- Department of Animal Health, Ministry of Agriculture and Rural Development of Vietnam, Hanoi, Vietnam
| | - Juliet E Bryant
- Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Hanoi, Vietnam
- Center for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - C Todd Davis
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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9
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Kis Z, Jones J, Creanga A, Ferdinand K, Inui K, Gerloff N, Davis CT, Nguyen T, Donis RO. Real-time RT-PCR assay to differentiate clades of H5N1 avian influenza viruses circulating in Vietnam. J Virol Methods 2013; 193:452-8. [PMID: 23850699 DOI: 10.1016/j.jviromet.2013.06.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 06/09/2013] [Accepted: 06/14/2013] [Indexed: 11/25/2022]
Abstract
Continued circulation and geographical expansion of highly pathogenic avian influenza H5N1 virus have led to the emergence of numerous clades in Vietnam. Although viral RNA sequencing and phylogenetic analysis are the gold standard for H5N1 HA clade designation, limited sequencing capacity in many laboratories precludes rapid H5N1 clade identification and detection of novel viruses. Therefore, a Taqman real-time RT-PCR assay for rapid differentiation of the four major H5N1 clades detected in Vietnam was developed. Using HA sequence alignments of clades 1.1, 2.3.2.1, 2.3.4, and 7 viruses, primers and FAM-labeled probes were designed to target conserved regions characteristic of each clade. The assay was optimized and evaluated using circulating clades of H5N1 collected in Vietnam from 2007 to 2012 and shown to be both sensitive and specific for the differentiation of the four H5N1 clades. The assay provides a useful tool for screening of large specimen collections for HA gene sequencing and phylogenetic analysis and for the rapid identification of molecular clade signatures to support outbreak investigations and surveillance activities. Finally, this assay may be useful to monitor for the emergence of novel or variant clades of H5N1 in Vietnam in the future or in other countries where these particular clades may circulate.
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Affiliation(s)
- Z Kis
- Influenza Division, CDC, USA; National Center for Epidemiology, Budapest, Hungary
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10
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Mossong J, Opp M, Gerloff N, Hau P, Kremer J, Lackenby A, Gregory V, Even J, Huberty-Krau P, Muller CP. Emergence of oseltamivir-resistant influenza A H1N1 virus during the 2007–2008 winter season in Luxembourg: Clinical characteristics and epidemiology. Antiviral Res 2009; 84:91-4. [DOI: 10.1016/j.antiviral.2009.08.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Revised: 06/12/2009] [Accepted: 08/04/2009] [Indexed: 10/20/2022]
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11
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Muller C, Gerloff N, Snoeck C, Kremer J, Owoade A, Taiwo J, Ouedraogo JB, Sow A, Manu S, Dodman T, Ottossen U. OP3-2 Spread and evolution of avian influenza virus in poultry and wild-birds in Africa. J Clin Virol 2009. [PMCID: PMC7129415 DOI: 10.1016/s1386-6532(09)70048-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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