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Bellomo CM, Alonso DO, Pérez-Sautu U, Prieto K, Kehl S, Coelho RM, Periolo N, Di Paola N, Ferressini-Gerpe N, Kuhn JH, Sanchez-Lockhart M, Palacios G, Martínez VP. Andes Virus Genome Mutations That Are Likely Associated with Animal Model Attenuation and Human Person-to-Person Transmission. mSphere 2023:e0001823. [PMID: 37097182 DOI: 10.1128/msphere.00018-23] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
We performed whole-genome sequencing with bait enrichment techniques to analyze Andes virus (ANDV), a cause of human hantavirus pulmonary syndrome. We used cryopreserved lung tissues from a naturally infected long-tailed colilargo, including early, intermediate, and late cell culture, passages of an ANDV isolate from that animal, and lung tissues from golden hamsters experimentally exposed to that ANDV isolate. The resulting complete genome sequences were subjected to detailed comparative genomic analysis against American orthohantaviruses. We identified four amino acid substitutions related to cell culture adaptation that resulted in attenuation of ANDV in the typically lethal golden hamster animal model of hantavirus pulmonary syndrome. Changes in the ANDV nucleocapsid protein, glycoprotein, and small nonstructural protein open reading frames correlated with mutations typical for ANDV strains associated with increased virulence in the small-animal model. Finally, we identified three amino acid substitutions, two in the small nonstructural protein and one in the glycoprotein, that were only present in the clade of viruses associated with efficient person-to-person transmission. Our results indicate that there are single-nucleotide polymorphisms that could be used to predict strain-specific ANDV virulence and/or transmissibility. IMPORTANCE Several orthohantaviruses cause the zoonotic disease hantavirus pulmonary syndrome (HPS) in the Americas. Among them, HPS caused by Andes virus (ANDV) is of great public health concern because it is associated with the highest case fatality rate (up to 50%). ANDV is also the only orthohantavirus associated with relatively robust evidence of person-to-person transmission. This work reveals nucleotide changes in the ANDV genome that are associated with virulence attenuation in an animal model and increased transmissibility in humans. These findings may pave the way to early severity predictions in future ANDV-caused HPS outbreaks.
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Affiliation(s)
- Carla M Bellomo
- Laboratorio Nacional de Referencia de Hantavirus, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud Dr. Carlos G. Malbran, Buenos Aires, Argentina
| | - Daniel O Alonso
- Laboratorio Nacional de Referencia de Hantavirus, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud Dr. Carlos G. Malbran, Buenos Aires, Argentina
| | - Unai Pérez-Sautu
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland, USA
| | - Karla Prieto
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland, USA
- College of Public Health, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Sebastian Kehl
- Laboratorio Nacional de Referencia de Hantavirus, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud Dr. Carlos G. Malbran, Buenos Aires, Argentina
| | - Rocio M Coelho
- Laboratorio Nacional de Referencia de Hantavirus, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud Dr. Carlos G. Malbran, Buenos Aires, Argentina
| | - Natalia Periolo
- Laboratorio Nacional de Referencia de Hantavirus, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud Dr. Carlos G. Malbran, Buenos Aires, Argentina
| | - Nicholas Di Paola
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland, USA
| | | | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA
| | - Mariano Sanchez-Lockhart
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland, USA
| | - Gustavo Palacios
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health Emerging Pathogen Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Valeria P Martínez
- Laboratorio Nacional de Referencia de Hantavirus, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud Dr. Carlos G. Malbran, Buenos Aires, Argentina
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Agbodzi B, Yousseu FBS, Simo FBN, Kumordjie S, Yeboah C, Mosore MT, Bentil RE, Prieto K, Colston SM, Attram N, Nimo-Paintsil S, Fox AT, Bonney JHK, Ampofo W, Coatsworth HG, Dinglasan RR, Wolfe DM, Wiley MR, Demanou M, Letizia AG. Chikungunya viruses containing the A226V mutation detected retrospectively in Cameroon form a new geographical subclade. Int J Infect Dis 2021; 113:65-73. [PMID: 34592442 DOI: 10.1016/j.ijid.2021.09.058] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 06/08/2021] [Revised: 08/31/2021] [Accepted: 09/22/2021] [Indexed: 10/20/2022] Open
Abstract
BACKGROUND Chikungunya virus (CHIKV) is a re-emerging arbovirus associated with sporadic outbreaks in Cameroon since 2006. Viral whole genomes were generated to analyze the origins of evolutionary lineages, the potential of emergence/re-emergence, and to infer transmission dynamics of recent Cameroon CHIKV outbreak strains. METHODS Samples collected between 2016 and 2019 during CHIKV outbreaks in Cameroon were screened for CHIKV using reverse transcription PCR (RT-PCR), followed by whole genome sequencing of positive samples. RESULTS Three coding-complete CHIKV genomes were obtained from samples, which belong to an emerging sub-lineage of the East/Central/South African genotype and formed a monophyletic taxon with previous Central African strains. This clade, which we have named the new Central African clade, appears to be evolving at 3.0 × 10-4 nucleotide substitutions per site per year (95% highest posterior density (HPD) interval of 1.94 × 10-4 to 4.1 × 10-4). Notably, mutations in the envelope proteins (E1-A226V, E2-L210Q, and E2-I211T), which are known to enhance CHIKV adaptability and infectious potential in Aedes albopictus, were present in all strains and mapped to established high-density Ae. albopictus populations. CONCLUSIONS These new CHIKV strains constitute a conserved genomic pool of an emerging sub-lineage, reflecting a putative vector host adaptation to Ae. albopictus, which has practically displaced Aedes aegypti from select regions of Cameroon.
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Affiliation(s)
- Bright Agbodzi
- US Naval Medical Research Unit - No. 3, Ghana Detachment, Accra, Ghana.
| | | | | | | | - Clara Yeboah
- US Naval Medical Research Unit - No. 3, Ghana Detachment, Accra, Ghana
| | | | - Ronald E Bentil
- US Naval Medical Research Unit - No. 3, Ghana Detachment, Accra, Ghana
| | - Karla Prieto
- Department of Environmental, Occupational, and Agricultural Health, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Sophie M Colston
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington DC, USA
| | - Naiki Attram
- US Naval Medical Research Unit - No. 3, Ghana Detachment, Accra, Ghana
| | | | - Anne T Fox
- US Naval Medical Research Unit - No. 3, Ghana Detachment, Accra, Ghana
| | - Joseph H K Bonney
- Virology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - William Ampofo
- Virology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | | | - Rhoel R Dinglasan
- University of Florida Emerging Pathogens Institute, Gainesville, Florida, USA
| | - David M Wolfe
- US Naval Medical Research Unit - No. 3, Ghana Detachment, Accra, Ghana
| | - Michael R Wiley
- Department of Environmental, Occupational, and Agricultural Health, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | | | - Andrew G Letizia
- US Naval Medical Research Unit - No. 3, Ghana Detachment, Accra, Ghana
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Pérez-Sautu U, Wiley MR, Prieto K, Chitty JA, Haddow AD, Sánchez-Lockhart M, Klein TA, Kim HC, Chong ST, Kim YJ, Choi BS, Palacios GF. Novel viruses in hard ticks collected in the Republic of Korea unveiled by metagenomic high-throughput sequencing analysis. Ticks Tick Borne Dis 2021; 12:101820. [PMID: 34555711 DOI: 10.1016/j.ttbdis.2021.101820] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 08/17/2021] [Accepted: 08/20/2021] [Indexed: 11/25/2022]
Abstract
Ticks are vectors of a wide range of zoonotic viruses of medical and veterinary importance. Recently, metagenomics studies demonstrated that they are also the source of potentially pathogenic novel viruses. During the period from 2015 to 2017, questing ticks were collected by dragging the vegetation from geographically distant locations in the Republic of Korea (ROK) and a target-independent high-throughput sequencing method was utilized to study their virome. A total of seven viruses, including six putative novel viral entities, were identified. Genomic analysis showed that the novel viruses were most closely related to members in the orders Jingchuvirales and Bunyavirales. Phylogenetic reconstruction showed that the Bunyavirales-like viruses grouped in the same clade with other viruses within the Nairovirus and Phlebovirus genera, while the novel Jingchuvirales-like virus grouped together with other viruses within the family Chuviridae. Real-time RT-PCR was used to determine the geographic distribution and prevalence of these viruses in adult ticks. These novel viruses have a wide geographic distribution in the ROK with prevalences ranging from 2% to 18%. Our study expands the knowledge about the composition of the tick virome and highlights the wide diversity of viruses they harbor in the ROK. The discovery of novel viruses associated with ticks in the ROK highlights the need for an active tick-borne disease surveillance program to identify possible reservoirs of putative novel human pathogens.
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Affiliation(s)
- Unai Pérez-Sautu
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, 21702, Maryland, USA.
| | - Michael R Wiley
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, 21702, Maryland, USA; College of Public Health, University of Nebraska Medical Center, Omaha, 68198, Nebraska, USA
| | - Karla Prieto
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, 21702, Maryland, USA; College of Public Health, University of Nebraska Medical Center, Omaha, 68198, Nebraska, USA
| | - Joseph A Chitty
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, 21702, Maryland, USA
| | - Andrew D Haddow
- Virology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, 21702, Maryland, USA; Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, 30144, Georgia, USA
| | - Mariano Sánchez-Lockhart
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, 21702, Maryland, USA; Department of Pathology & Microbiology, University of Nebraska Medical Centre, Omaha, 68198, Nebraska, USA
| | - Terry A Klein
- Force Health Protection and Preventive Medicine, Medical Department Activity-Korea /65(th) Medical Brigade, Unit 15281, APO AP 96271, USA
| | - Heung-Chul Kim
- Force Health Protection and Preventive Medicine, Medical Department Activity-Korea /65(th) Medical Brigade, Unit 15281, APO AP 96271, USA
| | - Sung-Tae Chong
- Force Health Protection and Preventive Medicine, Medical Department Activity-Korea /65(th) Medical Brigade, Unit 15281, APO AP 96271, USA
| | - Yu-Jin Kim
- Army Headquarters, Gyeryong-si, 32800, Republic of Korea
| | | | - Gustavo F Palacios
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, 21702, Maryland, USA
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Alonso DO, Pérez-Sautu U, Bellomo CM, Prieto K, Iglesias A, Coelho R, Periolo N, Domenech I, Talmon G, Hansen R, Palacios G, Martinez VP. Person-to-Person Transmission of Andes Virus in Hantavirus Pulmonary Syndrome, Argentina, 2014. Emerg Infect Dis 2021; 26:756-759. [PMID: 32186494 PMCID: PMC7101103 DOI: 10.3201/eid2604.190799] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Andes virus is unique among hantaviruses because it can be transmitted from person to person. This mechanism was previously supported by epidemiologic data and genetic evidence based only on partial sequences. We used full-length virus sequencing to confirm person-to-person transmission of this virus in a cluster of 3 cases in Argentina in 2014.
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Maljkovic Berry I, Rutvisuttinunt W, Voegtly LJ, Prieto K, Pollett S, Cer RZ, Kugelman JR, Bishop-Lilly KA, Morton L, Waitumbi J, Jarman RG. A Department of Defense Laboratory Consortium Approach to Next Generation Sequencing and Bioinformatics Training for Infectious Disease Surveillance in Kenya. Front Genet 2020; 11:577563. [PMID: 33101395 PMCID: PMC7546821 DOI: 10.3389/fgene.2020.577563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/31/2020] [Indexed: 11/30/2022] Open
Abstract
Epidemics of emerging and re-emerging infectious diseases are a danger to civilian and military populations worldwide. Health security and mitigation of infectious disease threats is a priority of the United States Government and the Department of Defense (DoD). Next generation sequencing (NGS) and Bioinformatics (BI) enhances traditional biosurveillance by providing additional data to understand transmission, identify resistance and virulence factors, make predictions, and update risk assessments. As more and more laboratories adopt NGS and BI technologies they encounter challenges in building local capacity. In addition to choosing the right sequencing platform and approach, considerations must also be made for the complexity of bioinformatics analyses, data storage, as well as personnel and computational requirements. To address these needs, a comprehensive training program was developed covering wet lab and bioinformatics approaches to NGS. The program is meant to be modular and adaptive to meet both common and individualized needs of medical research and public health laboratories across the DoD. The training program was first deployed internationally to the Basic Science Laboratory of the US Army Medical Research Directorate-Africa in Kisumu, Kenya, which is an overseas Lab of the Walter Reed Army Institute of Research (WRAIR). A week-long workshop with intensive focus on targeted sequencing and the bioinformatics of genome assembly (n = 24 participants) was held. Post-workshop self-assessment (completed by 21 participants) noted significant median gains in knowledge domains related to NGS targeted sequencing, bioinformatics for genome assembly, and sequence quality assessment. The participants also reported that the information on study design, sample preparation, sequencing quality control, data quality assessment, reporting, and basic and advanced bioinformatics analysis were the most useful information presented in the training. While longer-term evaluations are planned, the training resulted in significant short-term improvement of a laboratory’s self-reported wet lab and bioinformatics capabilities. This framework can be used for future DoD laboratory development in the area of NGS and BI for infectious disease surveillance, ultimately enhancing this global DoD capability.
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Affiliation(s)
- Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Wiriya Rutvisuttinunt
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States.,Office of Genomics and Advanced Technologies National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
| | - Logan J Voegtly
- Genomics & Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, MD, United States.,Leidos, Reston, VA, United States
| | - Karla Prieto
- College of Public Health, University of Nebraska Medical Center, Omaha, NE, United States.,Center for Genomic Studies, United States Army Medical Research Institute for Infectious Diseases, Frederick, MD, United States
| | - Simon Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Regina Z Cer
- Genomics & Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, MD, United States.,Leidos, Reston, VA, United States
| | - Jeffrey R Kugelman
- Center for Genomic Studies, United States Army Medical Research Institute for Infectious Diseases, Frederick, MD, United States
| | - Kimberly A Bishop-Lilly
- Genomics & Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, MD, United States
| | - Lindsay Morton
- Global Emerging Infections Surveillance, Armed Forces Health Surveillance Branch, Silver Spring, MD, United States
| | - John Waitumbi
- Basic Science Laboratory, US Army Medical Research Directorate-Africa/Kenya Medical Research Institute, Kisumu, Kenya
| | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States
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Padilla SL, Prieto K, Dohm DJ, Turell MJ, Klein TA, Fernández R, Watts DM, Lowen RG, Palacios GF, Pitt ML, Wiley MR, Nasar F. Complete genomic sequences of Venezuelan equine encephalitis virus subtype IIID isolates from mosquitoes. Arch Virol 2020; 165:1715-1717. [PMID: 32417973 DOI: 10.1007/s00705-020-04647-x] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 04/07/2020] [Indexed: 10/24/2022]
Abstract
Venezuelan equine encephalitis virus (VEEV) is an important pathogen of medical and veterinary importance in the Americas. In this report, we present the complete genome sequences of five VEEV isolates obtained from pools of Culex (Melanoconion) gnomatos (4) or Culex (Melanoconion) pedroi (1) from Iquitos, Peru. Genetic and phylogenetic analyses showed that all five isolates grouped within the VEEV complex sister to VEEV IIIC and are members of subtype IIID. This is the first report of full-length genomic sequences of VEEV IIID.
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Affiliation(s)
- Susana L Padilla
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, MD, 21702, USA
- Public Health Command-Pacific, Honolulu, Hawaii, USA
| | - Karla Prieto
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
- College of Public Health, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - David J Dohm
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, MD, 21702, USA
| | - Michael J Turell
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, MD, 21702, USA
- VectorID LLC, Frederick, MD, USA
| | - Terry A Klein
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, MD, 21702, USA
- 65th Medical Brigade/Medical Department Activity-Korea, Unit 15281, Pyeongtaek, Republic of Korea
| | - Roberto Fernández
- Department of Entomology, U.S. Naval Medical Research Unit No. 6, Callao, Peru
| | - Douglas M Watts
- Department of Entomology, U.S. Naval Medical Research Unit No. 6, Callao, Peru
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA
| | - Robert G Lowen
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, MD, 21702, USA
- Public Health Command-Atlantic, Fort George G. Meade, MD, USA
| | - Gustavo F Palacios
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
| | - Margaret L Pitt
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, MD, 21702, USA
| | - Michael R Wiley
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
- College of Public Health, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Farooq Nasar
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, MD, 21702, USA.
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Pérez-Sautu U, Wiley MR, Iglesias-Caballero M, Pozo F, Prieto K, Chitty JA, García-García ML, Calvo C, Casas I, Palacios G. Target-independent high-throughput sequencing methods provide evidence that already known human viral pathogens play a main role in respiratory infections with unexplained etiology. Emerg Microbes Infect 2019; 8:1054-1065. [PMID: 31335277 PMCID: PMC6691886 DOI: 10.1080/22221751.2019.1640587] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Despite the advanced PCR-based assays available, a fraction of the pediatric respiratory infections remain unexplained every epidemic season, and there is a perception that novel viruses might be present in these specimens. We systematically collected samples from a prospective cohort of pediatric patients with respiratory infections, that returned negative results by validated molecular RT–PCR assays, and studied them with a target-independent, high-throughput sequencing-based approach. We also included a matched cohort of children with no symptoms of respiratory infection, as a contrast study population. More than fifty percent of the specimens from the group of patients with unexplained respiratory infections were resolved. However, the higher rate of detection was not due to the presence of novel viruses, but to the identification of well-known viral respiratory pathogens. Our results show that already known viral pathogens are responsible for the majority of cases that remain unexplained after the epidemic season. High-throughput sequencing approaches that use pathogen-specific probes are easier to standardize because they ensure reproducible library enrichment and sequencing. In consequence, these techniques might be desirable from a regulatory standpoint for diagnostic laboratories seeking to benefit from the many advantages of these sequencing technologies.
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Affiliation(s)
- Unai Pérez-Sautu
- a Influenza and Respiratory Viruses Unit, National Center for Microbiology, Instituto de Salud Carlos III (ISCIII) , Madrid , Spain.,b Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID) , Frederick , MD , USA
| | - Michael Ross Wiley
- b Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID) , Frederick , MD , USA.,c College of Public Health, University of Nebraska Medical Center , Omaha , NE , USA
| | - María Iglesias-Caballero
- a Influenza and Respiratory Viruses Unit, National Center for Microbiology, Instituto de Salud Carlos III (ISCIII) , Madrid , Spain
| | - Francisco Pozo
- a Influenza and Respiratory Viruses Unit, National Center for Microbiology, Instituto de Salud Carlos III (ISCIII) , Madrid , Spain
| | - Karla Prieto
- b Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID) , Frederick , MD , USA.,c College of Public Health, University of Nebraska Medical Center , Omaha , NE , USA
| | - Joseph Alex Chitty
- b Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID) , Frederick , MD , USA
| | | | | | - Inmaculada Casas
- a Influenza and Respiratory Viruses Unit, National Center for Microbiology, Instituto de Salud Carlos III (ISCIII) , Madrid , Spain
| | - Gustavo Palacios
- b Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID) , Frederick , MD , USA
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Wiley MR, Fakoli L, Letizia AG, Welch SR, Ladner JT, Prieto K, Reyes D, Espy N, Chitty JA, Pratt CB, Di Paola N, Taweh F, Williams D, Saindon J, Davis WG, Patel K, Holland M, Negrón D, Ströher U, Nichol ST, Sozhamannan S, Rollin PE, Dogba J, Nyenswah T, Bolay F, Albariño CG, Fallah M, Palacios G. Lassa virus circulating in Liberia: a retrospective genomic characterisation. Lancet Infect Dis 2019; 19:1371-1378. [PMID: 31588039 DOI: 10.1016/s1473-3099(19)30486-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/28/2019] [Accepted: 07/18/2019] [Indexed: 01/10/2023]
Abstract
BACKGROUND An alarming rise in reported Lassa fever cases continues in west Africa. Liberia has the largest reported per capita incidence of Lassa fever cases in the region, but genomic information on the circulating strains is scarce. The aim of this study was to substantially increase the available pool of data to help foster the generation of targeted diagnostics and therapeutics. METHODS Clinical serum samples collected from 17 positive Lassa fever cases originating from Liberia (16 cases) and Guinea (one case) within the past decade were processed at the Liberian Institute for Biomedical Research using a targeted-enrichment sequencing approach, producing 17 near-complete genomes. An additional 17 Lassa virus sequences (two from Guinea, seven from Liberia, four from Nigeria, and four from Sierra Leone) were generated from viral stocks at the US Centers for Disease Control and Prevention (Atlanta, GA) from samples originating from the Mano River Union (Guinea, Liberia, and Sierra Leone) region and Nigeria. Sequences were compared with existing Lassa virus genomes and published Lassa virus assays. FINDINGS The 23 new Liberian Lassa virus genomes grouped within two clades (IV.A and IV.B) and were genetically divergent from those circulating elsewhere in west Africa. A time-calibrated phylogeographic analysis incorporating the new genomes suggests Liberia was the entry point of Lassa virus into the Mano River Union region and estimates the introduction to have occurred between 300-350 years ago. A high level of diversity exists between the Liberian Lassa virus genomes. Nucleotide percent difference between Liberian Lassa virus genomes ranged up to 27% in the L segment and 18% in the S segment. The commonly used Lassa Josiah-MGB assay was up to 25% divergent across the target sites when aligned to the Liberian Lassa virus genomes. INTERPRETATION The large amount of novel genomic diversity of Lassa virus observed in the Liberian cases emphasises the need to match deployed diagnostic capabilities with locally circulating strains and underscores the importance of evaluating cross-lineage protection in the development of vaccines and therapeutics. FUNDING Defense Biological Product Assurance Office of the US Department of Defense and the Armed Forces Health Surveillance Branch and its Global Emerging Infections Surveillance and Response Section.
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Affiliation(s)
- Michael R Wiley
- Department of Environmental, Agricultural and Occupational Health, College of Public Health, University of Nebraska Medical Center, Omaha, NE, USA; Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Lawrence Fakoli
- National Public Health Institute of Liberia, Monrovia, Liberia
| | - Andrew G Letizia
- Naval Medical Research Unit Three Ghana Detachment, Accra, Ghana
| | - Stephen R Welch
- US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jason T Ladner
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA; Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Karla Prieto
- Department of Environmental, Agricultural and Occupational Health, College of Public Health, University of Nebraska Medical Center, Omaha, NE, USA; Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Daniel Reyes
- Department of Environmental, Agricultural and Occupational Health, College of Public Health, University of Nebraska Medical Center, Omaha, NE, USA; Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Nicole Espy
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Joseph A Chitty
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Catherine B Pratt
- Department of Environmental, Agricultural and Occupational Health, College of Public Health, University of Nebraska Medical Center, Omaha, NE, USA; Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Nicholas Di Paola
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Fahn Taweh
- National Public Health Institute of Liberia, Monrovia, Liberia
| | - Desmond Williams
- US Centers for Disease Control and Prevention, Atlanta, GA, USA; US Centers for Disease Control and Prevention, Monrovia, Liberia
| | - Jon Saindon
- US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - William G Davis
- US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ketan Patel
- US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | | | - Ute Ströher
- US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Stuart T Nichol
- US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Shanmuga Sozhamannan
- Defense Biological Product Assurance Office, Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (CBRND)-Joint Project Lead, CBRND Enabling Biotechnologies, Frederick, MD, USA; Logistics Management Institute, Tysons, VA, USA
| | - Pierre E Rollin
- US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - John Dogba
- National Public Health Institute of Liberia, Monrovia, Liberia
| | | | - Fatorma Bolay
- National Public Health Institute of Liberia, Monrovia, Liberia
| | | | - Mosoka Fallah
- National Public Health Institute of Liberia, Monrovia, Liberia
| | - Gustavo Palacios
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA.
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9
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Whitmer SLM, Ladner JT, Wiley MR, Patel K, Dudas G, Rambaut A, Sahr F, Prieto K, Shepard SS, Carmody E, Knust B, Naidoo D, Deen G, Formenty P, Nichol ST, Palacios G, Ströher U. Active Ebola Virus Replication and Heterogeneous Evolutionary Rates in EVD Survivors. Cell Rep 2019; 22:1159-1168. [PMID: 29386105 PMCID: PMC5809616 DOI: 10.1016/j.celrep.2018.01.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 11/20/2017] [Accepted: 01/02/2018] [Indexed: 11/18/2022] Open
Abstract
Following cessation of continuous Ebola virus (EBOV) transmission within Western Africa, sporadic EBOV disease (EVD) cases continued to re-emerge beyond the viral incubation period. Epidemiological and genomic evidence strongly suggests that this represented transmission from EVD survivors. To investigate whether persistent infections are characterized by ongoing viral replication, we sequenced EBOV from the semen of nine EVD survivors and a subset of corresponding acute specimens. EBOV evolutionary rates during persistence were either similar to or reduced relative to acute infection rates. Active EBOV replication/transcription continued during convalescence, but decreased over time, consistent with viral persistence rather than viral latency. Patterns of genetic divergence suggest a moderate relaxation of selective constraints within the sGP carboxy-terminal tail during persistent infections, but do not support widespread diversifying selection. Altogether, our data illustrate that EBOV persistence in semen, urine, and aqueous humor is not a quiescent or latent infection. During persistence, EBOV exhibits heterogeneous evolutionary rates Active EBOV transcription and replication occurs during persistence RNA hyper-editing observed during viral persistence No evidence for significant selective pressure during persistence
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Affiliation(s)
- Shannon L M Whitmer
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Jason T Ladner
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Michael R Wiley
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Ketan Patel
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Gytis Dudas
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, King's Buildings, Edinburgh, UK; Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Foday Sahr
- Sierra Leone Armed Forces, Freetown, Sierra Leone
| | - Karla Prieto
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Samuel S Shepard
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ellie Carmody
- Division of Infectious Diseases, NYU School of Medicine, Bellevue Hospital Center, New York, NY, USA
| | - Barbara Knust
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Dhamari Naidoo
- Health Emergency Programme, World Health Organization, Geneva, Switzerland
| | - Gibrilla Deen
- Sierra Leone Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Pierre Formenty
- Health Emergency Programme, World Health Organization, Geneva, Switzerland
| | - Stuart T Nichol
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Gustavo Palacios
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Ute Ströher
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA.
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10
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Haston JC, Rostad CA, Jerris RC, Milla SS, McCracken C, Pratt C, Wiley M, Prieto K, Palacios G, Shane AL, McElroy AK. Prospective Cohort Study of Next-Generation Sequencing as a Diagnostic Modality for Unexplained Encephalitis in Children. J Pediatric Infect Dis Soc 2019; 9:326-333. [PMID: 31107955 PMCID: PMC7457329 DOI: 10.1093/jpids/piz032] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [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: 01/14/2019] [Accepted: 04/25/2019] [Indexed: 11/12/2022]
Abstract
BACKGROUND Encephalitis is an inflammatory condition of the brain associated with long-term neurologic sequelae and even death in children. Although viruses are often implicated, an etiology is not identified in the majority of cases. Metagenomics-based next-generation sequencing (mNGS) is a high-throughput sequencing technique that can enhance the detection of novel or low-frequency pathogens. METHODS Hospitalized immunocompetent children aged 6 months to 18 years with encephalitis of unidentified etiology were eligible for enrollment. Demographic, historical, and clinical information was obtained, and residual blood and cerebrospinal fluid (CSF) samples were subjected to mNGS. Pathogens were identified by querying the sequence data against the NCBI GenBank database. RESULTS Twenty children were enrolled prospectively between 2013 and 2017. mNGS of CSF identified 7 nonhuman nucleic acid sequences of significant frequency in 6 patients, including that of Mycoplasma bovis, parvovirus B19, Neisseria meningitidis, and Balamuthia mandrillaris. mNGS also detected Cladophialophora species, tobacco mosaic virus, and human bocavirus, which were presumed to be contaminants or nonpathogenic organisms. One patient was found to have positive serology results for California encephalitis virus, but mNGS did not detect it. Patients for whom mNGS identified a diagnosis had a significantly higher CSF white blood cell count, a higher CSF protein concentration, and a lower CSF glucose level than patients for whom mNGS did not identify a diagnosis. CONCLUSION We describe here the results of a prospective cohort analysis to evaluate mNGS as a diagnostic tool for children with unexplained encephalitis. Although mNGS detected multiple nonpathogenic organisms, it also identified multiple pathogens successfully and was most useful in patients with a CSF abnormality.
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Affiliation(s)
- Julia C Haston
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia,Children’s Healthcare of Atlanta, Georgia
| | - Christina A Rostad
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia,Children’s Healthcare of Atlanta, Georgia
| | | | - Sarah S Milla
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia,Children’s Healthcare of Atlanta, Georgia
| | - Courtney McCracken
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia,Children’s Healthcare of Atlanta, Georgia
| | - Catherine Pratt
- US Army Medical Research Institute of Infectious Diseases (USAMRIID), Frederick, Maryland,College of Public Health, University of Nebraska Medical Center, Omaha
| | - Michael Wiley
- US Army Medical Research Institute of Infectious Diseases (USAMRIID), Frederick, Maryland,College of Public Health, University of Nebraska Medical Center, Omaha
| | - Karla Prieto
- US Army Medical Research Institute of Infectious Diseases (USAMRIID), Frederick, Maryland,College of Public Health, University of Nebraska Medical Center, Omaha
| | - Gustavo Palacios
- US Army Medical Research Institute of Infectious Diseases (USAMRIID), Frederick, Maryland
| | - Andi L Shane
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia,Children’s Healthcare of Atlanta, Georgia
| | - Anita K McElroy
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia,Children’s Healthcare of Atlanta, Georgia,Department of Pediatrics, University of Pittsburgh, Pennsylvania,Correspondence: A. K. McElroy, MD, PhD, University of Pittsburgh, Department of Pediatrics, 3501 Fifth Ave, Pittsburgh, PA 15261 ()
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11
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Mbala-Kingebeni P, Aziza A, Di Paola N, Wiley MR, Makiala-Mandanda S, Caviness K, Pratt CB, Ladner JT, Kugelman JR, Prieto K, Chitty JA, Larson PA, Beitzel B, Ayouba A, Vidal N, Karhemere S, Diop M, Diagne MM, Faye M, Faye O, Aruna A, Nsio J, Mulangu F, Mukadi D, Mukadi P, Kombe J, Mulumba A, Villabona-Arenas CJ, Pukuta E, Gonzalez J, Bartlett ML, Sozhamannan S, Gross SM, Schroth GP, Tim R, Zhao JJ, Kuhn JH, Diallo B, Yao M, Fall IS, Ndjoloko B, Mossoko M, Lacroix A, Delaporte E, Sanchez-Lockhart M, Sall AA, Muyembe-Tamfum JJ, Peeters M, Palacios G, Ahuka-Mundeke S. Medical countermeasures during the 2018 Ebola virus disease outbreak in the North Kivu and Ituri Provinces of the Democratic Republic of the Congo: a rapid genomic assessment. Lancet Infect Dis 2019; 19:648-657. [PMID: 31000464 DOI: 10.1016/s1473-3099(19)30118-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/21/2019] [Accepted: 03/06/2019] [Indexed: 11/30/2022]
Abstract
BACKGROUND The real-time generation of information about pathogen genomes has become a vital goal for transmission analysis and characterisation in rapid outbreak responses. In response to the recently established genomic capacity in the Democratic Republic of the Congo, we explored the real-time generation of genomic information at the start of the 2018 Ebola virus disease (EVD) outbreak in North Kivu Province. METHODS We used targeted-enrichment sequencing to produce two coding-complete Ebola virus genomes 5 days after declaration of the EVD outbreak in North Kivu. Subsequent sequencing efforts yielded an additional 46 genomes. Genomic information was used to assess early transmission, medical countermeasures, and evolution of Ebola virus. FINDINGS The genomic information demonstrated that the EVD outbreak in the North Kivu and Ituri Provinces was distinct from the 2018 EVD outbreak in Équateur Province of the Democratic Republic of the Congo. Primer and probe mismatches to Ebola virus were identified in silico for all deployed diagnostic PCR assays, with the exception of the Cepheid GeneXpert GP assay. INTERPRETATION The first two coding-complete genomes provided actionable information in real-time for the deployment of the rVSVΔG-ZEBOV-GP Ebola virus envelope glycoprotein vaccine, available therapeutics, and sequence-based diagnostic assays. Based on the mutations identified in the Ebola virus surface glycoprotein (GP12) observed in all 48 genomes, deployed monoclonal antibody therapeutics (mAb114 and ZMapp) should be efficacious against the circulating Ebola virus variant. Rapid Ebola virus genomic characterisation should be included in routine EVD outbreak response procedures to ascertain efficacy of medical countermeasures. FUNDING Defense Biological Product Assurance Office.
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Affiliation(s)
- Placide Mbala-Kingebeni
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France; Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Amuri Aziza
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Nicholas Di Paola
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Michael R Wiley
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA; College of Public Health, Northern Arizona University, Flagstaff, AZ, USA
| | - Sheila Makiala-Mandanda
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Katie Caviness
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Catherine B Pratt
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA; College of Public Health, Northern Arizona University, Flagstaff, AZ, USA
| | - Jason T Ladner
- University of Nebraska Medical Center, Omaha, NE, USA; The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | | | - Karla Prieto
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA; College of Public Health, Northern Arizona University, Flagstaff, AZ, USA
| | - Joseph A Chitty
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Peter A Larson
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Brett Beitzel
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Ahidjo Ayouba
- TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France
| | - Nicole Vidal
- TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France
| | - Stomy Karhemere
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | | | | | | | | | - Aaron Aruna
- Direction Générale de Lutte contre la Maladie, Kinshasa, Democratic Republic of the Congo
| | - Justus Nsio
- Direction Générale de Lutte contre la Maladie, Kinshasa, Democratic Republic of the Congo
| | - Felix Mulangu
- Direction Générale de Lutte contre la Maladie, Kinshasa, Democratic Republic of the Congo
| | - Daniel Mukadi
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Patrick Mukadi
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - John Kombe
- Direction Générale de Lutte contre la Maladie, Kinshasa, Democratic Republic of the Congo
| | - Anastasie Mulumba
- l'Organisation Mondiale de la Santé, Kinshasa, Democratic Republic of the Congo
| | | | - Elisabeth Pukuta
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Jeanette Gonzalez
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Maggie L Bartlett
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA; Department of Pathology and Microbiology, Northern Arizona University, Flagstaff, AZ, USA
| | - Shanmuga Sozhamannan
- Defense Biological Product Assurance Office, Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense-Joint Project Management Office for Guardian, Frederick, MA, USA; The Tauri Group, Alexandria, VA, USA
| | | | | | | | | | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | | | - Michel Yao
- World Health Organization, Geneva, Switzerland
| | | | - Bathe Ndjoloko
- Direction Générale de Lutte contre la Maladie, Kinshasa, Democratic Republic of the Congo
| | - Mathias Mossoko
- Direction Générale de Lutte contre la Maladie, Kinshasa, Democratic Republic of the Congo
| | - Audrey Lacroix
- TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France
| | - Eric Delaporte
- TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France
| | - Mariano Sanchez-Lockhart
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA; Department of Pathology and Microbiology, Northern Arizona University, Flagstaff, AZ, USA
| | | | - Jean-Jacques Muyembe-Tamfum
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Martine Peeters
- TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France
| | - Gustavo Palacios
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA.
| | - Steve Ahuka-Mundeke
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of the Congo
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12
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Oliveira DBL, Durigon GS, Mendes ÉA, Ladner JT, Andreata-Santos R, Araujo DB, Botosso VF, Paola ND, Neto DFL, Cunha MP, Braconi CT, Alves RPS, Jesus MR, Pereira LR, Melo SR, Mesquita FS, Silveira VB, Thomazelli LM, Favoretto SR, Almonfrey FB, Abdulkader RCRM, Gabrili JM, Tambourgi DV, Oliveira SF, Prieto K, Wiley MR, Ferreira LCS, Silva MV, Palacios GF, Zanotto PMA, Durigon EL. Persistence and Intra-Host Genetic Evolution of Zika Virus Infection in Symptomatic Adults: A Special View in the Male Reproductive System. Viruses 2018; 10:v10110615. [PMID: 30405055 PMCID: PMC6267439 DOI: 10.3390/v10110615] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 10/04/2018] [Accepted: 10/20/2018] [Indexed: 01/27/2023] Open
Abstract
We followed the presence of Zika virus (ZIKV) in four healthy adults (two men and two women), for periods ranging from 78 to 298 days post symptom onset. The patients were evaluated regarding the presence of the virus in different body fluids (blood, saliva, urine and semen), development of immune responses (including antibodies, cytokines and chemokines), and virus genetic variation within samples collected from semen and urine during the infection course. The analysis was focused primarily on the two male patients who shed the virus for up to 158 days after the initial symptoms. ZIKV particles were detected in the spermatozoa cytoplasm and flagella, in immature sperm cells and could also be isolated from semen in cell culture, confirming that the virus is able to preserve integrity and infectivity during replication in the male reproductive system (MRS). Despite the damage caused by ZIKV infection within the MRS, our data showed that ZIKV infection did not result in infertility at least in one of the male patients. This patient was able to conceive a child after the infection. We also detected alterations in the male genital cytokine milieu, which could play an important role in the replication and transmission of the virus which could considerably increase the risk of ZIKV sexual spread. In addition, full genome ZIKV sequences were obtained from several samples (mainly semen), which allowed us to monitor the evolution of the virus within a patient during the infection course. We observed genetic changes over time in consensus sequences and lower frequency intra-host single nucleotide variants (iSNV), that suggested independent compartmentalization of ZIKV populations in the reproductive and urinary systems. Altogether, the present observations confirm the risks associated with the long-term replication and shedding of ZIKV in the MRS and help to elucidate patterns of intra-host genetic evolution during long term replication of the virus.
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Affiliation(s)
- Danielle B L Oliveira
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Giuliana S Durigon
- Medical School Clinic Hospital, University of São Paulo, São Paulo, SP 05403-000, Brazil.
| | - Érica A Mendes
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Jason T Ladner
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA.
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011-4073, USA.
| | - Robert Andreata-Santos
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Danielle B Araujo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Viviane F Botosso
- Virology Laboratory, Butantan Institute, São Paulo, SP 05503-900, Brazil.
| | - Nicholas D Paola
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Daniel F L Neto
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Marielton P Cunha
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Carla T Braconi
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Rúbens P S Alves
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Monica R Jesus
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Lennon R Pereira
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Stella R Melo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Flávio S Mesquita
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Vanessa B Silveira
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Luciano M Thomazelli
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | | | - Franciane B Almonfrey
- Medical School Clinic Hospital, University of São Paulo, São Paulo, SP 05403-000, Brazil.
| | | | - Joel M Gabrili
- Virology Laboratory, Butantan Institute, São Paulo, SP 05503-900, Brazil.
- Immunochemistry Laboratory, Butantan Institute, São Paulo, SP 05503-900, Brazil.
| | - Denise V Tambourgi
- Virology Laboratory, Butantan Institute, São Paulo, SP 05503-900, Brazil.
| | - Sérgio F Oliveira
- Department of Cellular and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Karla Prieto
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA.
- Department of Environmental, Agricultural and Occupational Health, University of Nebraska Medical Center, Omaha, NE 68198-4388, USA.
| | - Michael R Wiley
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA.
- Department of Environmental, Agricultural and Occupational Health, University of Nebraska Medical Center, Omaha, NE 68198-4388, USA.
| | - Luís C S Ferreira
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Marcos V Silva
- Institute of Infectology Emílio Ribas e Pontifícia Universidade Católica (PUC-SP), São Paulo, SP 01246-900, Brazil.
| | - Gustavo F Palacios
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA.
| | - Paolo M A Zanotto
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Edison L Durigon
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil.
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13
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Amarasinghe GK, Aréchiga Ceballos NG, Banyard AC, Basler CF, Bavari S, Bennett AJ, Blasdell KR, Briese T, Bukreyev A, Caì Y, Calisher CH, Campos Lawson C, Chandran K, Chapman CA, Chiu CY, Choi KS, Collins PL, Dietzgen RG, Dolja VV, Dolnik O, Domier LL, Dürrwald R, Dye JM, Easton AJ, Ebihara H, Echevarría JE, Fooks AR, Formenty PBH, Fouchier RAM, Freuling CM, Ghedin E, Goldberg TL, Hewson R, Horie M, Hyndman TH, Jiāng D, Kityo R, Kobinger GP, Kondō H, Koonin EV, Krupovic M, Kurath G, Lamb RA, Lee B, Leroy EM, Maes P, Maisner A, Marston DA, Mor SK, Müller T, Mühlberger E, Ramírez VMN, Netesov SV, Ng TFF, Nowotny N, Palacios G, Patterson JL, Pawęska JT, Payne SL, Prieto K, Rima BK, Rota P, Rubbenstroth D, Schwemmle M, Siddell S, Smither SJ, Song Q, Song T, Stenglein MD, Stone DM, Takada A, Tesh RB, Thomazelli LM, Tomonaga K, Tordo N, Towner JS, Vasilakis N, Vázquez-Morón S, Verdugo C, Volchkov VE, Wahl V, Walker PJ, Wang D, Wang LF, Wellehan JFX, Wiley MR, Whitfield AE, Wolf YI, Yè G, Zhāng YZ, Kuhn JH. Taxonomy of the order Mononegavirales: update 2018. Arch Virol 2018; 163:2283-2294. [PMID: 29637429 DOI: 10.1007/s00705-018-3814-x] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 03/12/2018] [Indexed: 11/27/2022]
Abstract
In 2018, the order Mononegavirales was expanded by inclusion of 1 new genus and 12 novel species. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV) and summarizes additional taxonomic proposals that may affect the order in the near future.
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Affiliation(s)
- Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | | | | | - Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Sina Bavari
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Andrew J Bennett
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Kim R Blasdell
- Australian Animal Health Laboratory, CSIRO Health and Biosecurity, Geelong, VIC, Australia
| | - Thomas Briese
- Department of Epidemiology, Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | | | - Yíngyún Caì
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA
| | - Charles H Calisher
- Arthropod-Borne and Infectious Diseases Laboratory, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Cristine Campos Lawson
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Colin A Chapman
- Department of Anthropology and McGill School of Environment, McGill University, Montreal, QC, Canada.,Wildlife Conservation Society, Bronx, NY, USA.,Section of Social Systems Evolution, Primate Research Institute, Kyoto University, Kyoto, Japan
| | | | - Kang-Seuk Choi
- Avian Disease Research Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Peter L Collins
- Respiratory Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MA, USA
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Valerian V Dolja
- Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, USA
| | - Olga Dolnik
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Leslie L Domier
- Department of Crop Sciences, University of Illinois, Chicago, IL, USA
| | | | - John M Dye
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Andrew J Easton
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Hideki Ebihara
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Juan E Echevarría
- National Center of Microbiology, Carlos III Institute of Health, Majadahonda, Madrid, Spain
| | | | | | - Ron A M Fouchier
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Conrad M Freuling
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institute, WHO Collaborating Centre for Rabies Surveillance and Research, Greifswald-Insel Riems, Germany
| | - Elodie Ghedin
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Tony L Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Roger Hewson
- Public Health England, Porton Down, Salisbury, Wiltshire, UK
| | - Masayuki Horie
- Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
| | - Timothy H Hyndman
- College of Veterinary Medicine, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
| | - Dàohóng Jiāng
- State Key Laboratory of Agricultural Microbiology, The Provincial Key Lab of Plant Pathology of Húběi Province, College of Plant Science and Technology, Huázhōng Agricultural University, Wuhan, China
| | - Robert Kityo
- Department of Zoology, Makerere University, Kampala, Uganda
| | - Gary P Kobinger
- Department of Microbiology, Immunology and Infectious Diseases, Université Laval, Quebec City, Canada
| | - Hideki Kondō
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Mart Krupovic
- Department of Microbiology, Institut Pasteur, Paris, France
| | - Gael Kurath
- US Geological Survey Western Fisheries Research Center, Seattle, WA, USA
| | - Robert A Lamb
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.,Howard Hughes Medical Institute, Northwestern University, Evanston, IL, USA
| | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric M Leroy
- Centre International de Recherches Médicales de Franceville, Institut de Recherche pour le Développement, Franceville, Gabon
| | - Piet Maes
- Zoonotic Infectious Diseases Unit, KU Leuven, Leuven, Belgium
| | - Andrea Maisner
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | | | - Sunil Kumar Mor
- Department of Veterinary Population Medicine and Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - Thomas Müller
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institute, WHO Collaborating Centre for Rabies Surveillance and Research, Greifswald-Insel Riems, Germany
| | - Elke Mühlberger
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
| | | | - Sergey V Netesov
- Novosibirsk State University, Novosibirsk, Novosibirsk Oblast, Russia
| | - Terry Fei Fan Ng
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Norbert Nowotny
- Institute of Virology, University of Veterinary Medicine, Vienna, Austria.,Department of Basic Medical Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Gustavo Palacios
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Jean L Patterson
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Janusz T Pawęska
- Center for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham, Johannesburg, Gauteng, South Africa
| | - Susan L Payne
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Karla Prieto
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Bertus K Rima
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, The Queen's University of Belfast, Belfast, Northern Ireland, UK
| | - Paul Rota
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Dennis Rubbenstroth
- Institute of Virology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Martin Schwemmle
- Institute of Virology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Stuart Siddell
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | | | - Qisheng Song
- Division of Plant Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, MO, USA
| | - Timothy Song
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Mark D Stenglein
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - David M Stone
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, UK
| | - Ayato Takada
- Division of Global Epidemiology, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Robert B Tesh
- Department of Pathology and Center for Biodefense and Emerging Infectious Diseases, Center for Tropical Diseases and Institute for Human Infections and Immunity, The University of Texas Medical Branch, Galveston, TX, USA
| | | | - Keizō Tomonaga
- Institute for Frontier Life and Medical Sciences (inFront), Kyoto University, Kyoto, Japan
| | - Noël Tordo
- Institut Pasteur, Unité des Stratégies Antivirales, WHO Collaborative Centre for Viral Haemorrhagic Fevers and Arboviruses, OIE Reference Laboratory for RVFV and CCHFV, Paris, France.,Institut Pasteur de Guinée, Conakry, Guinea
| | - Jonathan S Towner
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Nikos Vasilakis
- Department of Pathology and Center for Biodefense and Emerging Infectious Diseases, Center for Tropical Diseases and Institute for Human Infections and Immunity, The University of Texas Medical Branch, Galveston, TX, USA
| | - Sonia Vázquez-Morón
- National Center of Microbiology, Carlos III Institute of Health, Majadahonda, Madrid, Spain
| | - Claudio Verdugo
- Universidad Austral de Chile Facultad de Ciencias Veterinarias, Valdivia, Chile
| | - Viktor E Volchkov
- Molecular Basis of Viral Pathogenicity, CIRI, INSERM U1111-CNRS, UMR5308, Université de Lyon, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Victoria Wahl
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD, USA
| | - Peter J Walker
- School of Biological Sciences, University of Queensland, St. Lucia, QLD, Australia
| | - David Wang
- Departments of Molecular Microbiology and Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - James F X Wellehan
- College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Michael R Wiley
- The University of Texas Medical Branch, Galveston, TX, USA.,University of Nebraska Medical Center, Omaha, NE, USA
| | - Anna E Whitfield
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Gōngyín Yè
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yǒng-Zhèn Zhāng
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA.
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14
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Grubaugh ND, Ladner JT, Kraemer MUG, Dudas G, Tan AL, Gangavarapu K, Wiley MR, White S, Thézé J, Magnani DM, Prieto K, Reyes D, Bingham AM, Paul LM, Robles-Sikisaka R, Oliveira G, Pronty D, Barcellona CM, Metsky HC, Baniecki ML, Barnes KG, Chak B, Freije CA, Gladden-Young A, Gnirke A, Luo C, MacInnis B, Matranga CB, Park DJ, Qu J, Schaffner SF, Tomkins-Tinch C, West KL, Winnicki SM, Wohl S, Yozwiak NL, Quick J, Fauver JR, Khan K, Brent SE, Reiner RC, Lichtenberger PN, Ricciardi MJ, Bailey VK, Watkins DI, Cone MR, Kopp EW, Hogan KN, Cannons AC, Jean R, Monaghan AJ, Garry RF, Loman NJ, Faria NR, Porcelli MC, Vasquez C, Nagle ER, Cummings DAT, Stanek D, Rambaut A, Sanchez-Lockhart M, Sabeti PC, Gillis LD, Michael SF, Bedford T, Pybus OG, Isern S, Palacios G, Andersen KG. Genomic epidemiology reveals multiple introductions of Zika virus into the United States. Nature 2017; 546:401-405. [PMID: 28538723 PMCID: PMC5536180 DOI: 10.1038/nature22400] [Citation(s) in RCA: 232] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/28/2017] [Indexed: 12/23/2022]
Abstract
Zika virus (ZIKV) is causing an unprecedented epidemic linked to severe congenital abnormalities. In July 2016, mosquito-borne ZIKV transmission was reported in the continental United States; since then, hundreds of locally acquired infections have been reported in Florida. To gain insights into the timing, source, and likely route(s) of ZIKV introduction, we tracked the virus from its first detection in Florida by sequencing ZIKV genomes from infected patients and Aedes aegypti mosquitoes. We show that at least 4 introductions, but potentially as many as 40, contributed to the outbreak in Florida and that local transmission is likely to have started in the spring of 2016-several months before its initial detection. By analysing surveillance and genetic data, we show that ZIKV moved among transmission zones in Miami. Our analyses show that most introductions were linked to the Caribbean, a finding corroborated by the high incidence rates and traffic volumes from the region into the Miami area. Our study provides an understanding of how ZIKV initiates transmission in new regions.
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Affiliation(s)
- Nathan D Grubaugh
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Jason T Ladner
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland 21702, USA
| | - Moritz U G Kraemer
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
- Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Gytis Dudas
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Amanda L Tan
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida 33965, USA
| | - Karthik Gangavarapu
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Michael R Wiley
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland 21702, USA
- College of Public Health, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA
| | - Stephen White
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Miami, Florida 33125, USA
| | - Julien Thézé
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
| | - Diogo M Magnani
- Department of Pathology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Karla Prieto
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland 21702, USA
- College of Public Health, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA
| | - Daniel Reyes
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland 21702, USA
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA
| | - Andrea M Bingham
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, Florida 32399, USA
| | - Lauren M Paul
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida 33965, USA
| | - Refugio Robles-Sikisaka
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Glenn Oliveira
- Scripps Translational Science Institute, La Jolla, California 92037, USA
| | - Darryl Pronty
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Miami, Florida 33125, USA
| | - Carolyn M Barcellona
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida 33965, USA
| | - Hayden C Metsky
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Mary Lynn Baniecki
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Kayla G Barnes
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Bridget Chak
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Catherine A Freije
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | | | - Andreas Gnirke
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Cynthia Luo
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Bronwyn MacInnis
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | | | - Daniel J Park
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - James Qu
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | | | | | - Kendra L West
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Sarah M Winnicki
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Shirlee Wohl
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Nathan L Yozwiak
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Joshua Quick
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Joseph R Fauver
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Kamran Khan
- Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, Ontario M5B 1T8, Canada
- Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Shannon E Brent
- Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, Ontario M5B 1T8, Canada
| | - Robert C Reiner
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, Washington 98121, USA
| | - Paola N Lichtenberger
- Division of Infectious Diseases, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Michael J Ricciardi
- Department of Pathology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Varian K Bailey
- Department of Pathology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - David I Watkins
- Department of Pathology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Marshall R Cone
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida 33612, USA
| | - Edgar W Kopp
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida 33612, USA
| | - Kelly N Hogan
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida 33612, USA
| | - Andrew C Cannons
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida 33612, USA
| | - Reynald Jean
- Florida Department of Health in Miami-Dade County, Miami, Florida 33125, USA
| | - Andrew J Monaghan
- National Center for Atmospheric Research, Boulder, Colorado 80307, USA
| | - Robert F Garry
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana 70112, USA
| | - Nicholas J Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
| | | | | | - Elyse R Nagle
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland 21702, USA
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA
| | - Derek A T Cummings
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida 32610, USA
| | - Danielle Stanek
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, Florida 32399, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Mariano Sanchez-Lockhart
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland 21702, USA
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA
| | - Pardis C Sabeti
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Leah D Gillis
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Miami, Florida 33125, USA
| | - Scott F Michael
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida 33965, USA
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
| | - Sharon Isern
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida 33965, USA
| | - Gustavo Palacios
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland 21702, USA
| | - Kristian G Andersen
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037, USA
- Scripps Translational Science Institute, La Jolla, California 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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15
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Costa-da-Silva AL, Ioshino RS, Petersen V, Lima AF, Cunha MDP, Wiley MR, Ladner JT, Prieto K, Palacios G, Costa DD, Suesdek L, Zanotto PMDA, Capurro ML. First report of naturally infected Aedes aegypti with chikungunya virus genotype ECSA in the Americas. PLoS Negl Trop Dis 2017; 11:e0005630. [PMID: 28614394 PMCID: PMC5470658 DOI: 10.1371/journal.pntd.0005630] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 05/09/2017] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The worldwide expansion of new emergent arboviruses such as Chikungunya and Zika reinforces the importance in understanding the role of mosquito species in spreading these pathogens in affected regions. This knowledge is essential for developing effective programs based on species specificity to avoid the establishment of endemic transmission cycles sustained by the identified local vectors. Although the first autochthonous transmission of Chikungunya virus was described in 2014 in the north of Brazil, the main outbreaks were reported in 2015 and 2016 in the northeast of Brazil. METHODOLOGY/PRINCIPAL FINDINGS During 5 days of February 2016, we collected mosquitoes in homes of 6 neighborhoods of Aracaju city, the capital of Sergipe state. Four mosquito species were identified but Culex quinquefasciatus and Aedes aegypti were the most abundant. Field-caught mosquitoes were tested for Chikungunya (CHIKV), Zika (ZIKV) and Dengue viruses (DENV) by qRT-PCR and one CHIKV-infected Ae. aegypti female was detected. The complete sequence of CHIKV genome was obtained from this sample and phylogenetic analysis revealed that this isolate belongs to the East-Central-South-African (ECSA) genotype. CONCLUSIONS Our study describes the first identification of a naturally CHIKV-infected Ae. aegypti in Brazil and the first report of a CHIKV from ECSA genotype identified in this species in the Americas. These findings support the notion of Ae. aegypti being a vector involved in CHIKV outbreaks in northeast of Brazil.
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Affiliation(s)
- André Luis Costa-da-Silva
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brasil
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, INCT-EM, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rafaella Sayuri Ioshino
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brasil
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, INCT-EM, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Vivian Petersen
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brasil
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, Brazil
| | | | | | - Michael R. Wiley
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Jason T. Ladner
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Karla Prieto
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Gustavo Palacios
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | | | - Lincoln Suesdek
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, Brazil
- Programa de Pós-graduação do Instituto de Medicina Tropical, Universidade de São Paulo, SP, Brasil
| | | | - Margareth Lara Capurro
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brasil
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, INCT-EM, Rio de Janeiro, Rio de Janeiro, Brazil
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16
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Ladner JT, Wiley MR, Beitzel B, Auguste AJ, Dupuis AP, Lindquist ME, Sibley SD, Kota KP, Fetterer D, Eastwood G, Kimmel D, Prieto K, Guzman H, Aliota MT, Reyes D, Brueggemann EE, St John L, Hyeroba D, Lauck M, Friedrich TC, O'Connor DH, Gestole MC, Cazares LH, Popov VL, Castro-Llanos F, Kochel TJ, Kenny T, White B, Ward MD, Loaiza JR, Goldberg TL, Weaver SC, Kramer LD, Tesh RB, Palacios G. A Multicomponent Animal Virus Isolated from Mosquitoes. Cell Host Microbe 2016; 20:357-367. [PMID: 27569558 DOI: 10.1016/j.chom.2016.07.011] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 06/09/2016] [Accepted: 07/26/2016] [Indexed: 11/24/2022]
Abstract
RNA viruses exhibit a variety of genome organization strategies, including multicomponent genomes in which each segment is packaged separately. Although multicomponent genomes are common among viruses infecting plants and fungi, their prevalence among those infecting animals remains unclear. We characterize a multicomponent RNA virus isolated from mosquitoes, designated Guaico Culex virus (GCXV). GCXV belongs to a diverse clade of segmented viruses (Jingmenvirus) related to the prototypically unsegmented Flaviviridae. The GCXV genome comprises five segments, each of which appears to be separately packaged. The smallest segment is not required for replication, and its presence is variable in natural infections. We also describe a variant of Jingmen tick virus, another Jingmenvirus, sequenced from a Ugandan red colobus monkey, thus expanding the host range of this segmented and likely multicomponent virus group. Collectively, this study provides evidence for the existence of multicomponent animal viruses and their potential relevance for animal and human health.
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Affiliation(s)
- Jason T Ladner
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA.
| | - Michael R Wiley
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Brett Beitzel
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Albert J Auguste
- Institute for Human Infections and Immunity, Departments of Pathology, Microbiology & Immunology, and Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Alan P Dupuis
- Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY 12159, USA
| | - Michael E Lindquist
- Virology Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Samuel D Sibley
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Krishna P Kota
- Molecular and Translational Sciences Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - David Fetterer
- Research Support Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Gillian Eastwood
- Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY 12159, USA
| | - David Kimmel
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Karla Prieto
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Hilda Guzman
- Institute for Human Infections and Immunity, Departments of Pathology, Microbiology & Immunology, and Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Matthew T Aliota
- Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY 12159, USA
| | - Daniel Reyes
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Ernst E Brueggemann
- Molecular and Translational Sciences Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Lena St John
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | | | - Michael Lauck
- Wisconsin National Primate Research Center, Madison, WI 53715, USA; Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA; Wisconsin National Primate Research Center, Madison, WI 53715, USA
| | - David H O'Connor
- Wisconsin National Primate Research Center, Madison, WI 53715, USA; Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Marie C Gestole
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Lisa H Cazares
- Molecular and Translational Sciences Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA; Henry M. Jackson Foundation, Bethesda, MD 20817, USA; DoD Biotechnology High Performance Computing Software Applications Institute, Frederick, MD 21702, USA; Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD 21702, USA
| | - Vsevolod L Popov
- Institute for Human Infections and Immunity, Departments of Pathology, Microbiology & Immunology, and Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA
| | | | | | - Tara Kenny
- Molecular and Translational Sciences Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Bailey White
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Michael D Ward
- Molecular and Translational Sciences Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Jose R Loaiza
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología, Ciudad de Panamá, Panamá
| | - Tony L Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA; Makerere University, Kampala, Uganda; Wisconsin National Primate Research Center, Madison, WI 53715, USA
| | - Scott C Weaver
- Institute for Human Infections and Immunity, Departments of Pathology, Microbiology & Immunology, and Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Laura D Kramer
- Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY 12159, USA; School of Public Health, State University of New York at Albany, One University Place Rensselaer, East Greenbush, NY 12144, USA
| | - Robert B Tesh
- Institute for Human Infections and Immunity, Departments of Pathology, Microbiology & Immunology, and Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Gustavo Palacios
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA.
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17
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Kuhn JH, Wiley MR, Rodriguez SE, Bào Y, Prieto K, Travassos da Rosa APA, Guzman H, Savji N, Ladner JT, Tesh RB, Wada J, Jahrling PB, Bente DA, Palacios G. Genomic Characterization of the Genus Nairovirus (Family Bunyaviridae). Viruses 2016; 8:E164. [PMID: 27294949 PMCID: PMC4926184 DOI: 10.3390/v8060164] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [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: 04/02/2016] [Revised: 05/25/2016] [Accepted: 05/26/2016] [Indexed: 12/21/2022] Open
Abstract
Nairovirus, one of five bunyaviral genera, includes seven species. Genomic sequence information is limited for members of the Dera Ghazi Khan, Hughes, Qalyub, Sakhalin, and Thiafora nairovirus species. We used next-generation sequencing and historical virus-culture samples to determine 14 complete and nine coding-complete nairoviral genome sequences to further characterize these species. Previously unsequenced viruses include Abu Mina, Clo Mor, Great Saltee, Hughes, Raza, Sakhalin, Soldado, and Tillamook viruses. In addition, we present genomic sequence information on additional isolates of previously sequenced Avalon, Dugbe, Sapphire II, and Zirqa viruses. Finally, we identify Tunis virus, previously thought to be a phlebovirus, as an isolate of Abu Hammad virus. Phylogenetic analyses indicate the need for reassignment of Sapphire II virus to Dera Ghazi Khan nairovirus and reassignment of Hazara, Tofla, and Nairobi sheep disease viruses to novel species. We also propose new species for the Kasokero group (Kasokero, Leopards Hill, Yogue viruses), the Ketarah group (Gossas, Issyk-kul, Keterah/soft tick viruses) and the Burana group (Wēnzhōu tick virus, Huángpí tick virus 1, Tǎchéng tick virus 1). Our analyses emphasize the sister relationship of nairoviruses and arenaviruses, and indicate that several nairo-like viruses (Shāyáng spider virus 1, Xīnzhōu spider virus, Sānxiá water strider virus 1, South Bay virus, Wǔhàn millipede virus 2) require establishment of novel genera in a larger nairovirus-arenavirus supergroup.
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Affiliation(s)
- Jens H Kuhn
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA.
| | - Michael R Wiley
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA.
| | - Sergio E Rodriguez
- Galveston National Laboratory, Institute for Human Infection and Immunity, Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Yīmíng Bào
- Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Karla Prieto
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA.
| | - Amelia P A Travassos da Rosa
- Galveston National Laboratory, Institute for Human Infection and Immunity, Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Hilda Guzman
- Galveston National Laboratory, Institute for Human Infection and Immunity, Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Nazir Savji
- School of Medicine, New York University, New York, NY 10016, USA.
| | - Jason T Ladner
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA.
| | - Robert B Tesh
- Galveston National Laboratory, Institute for Human Infection and Immunity, Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Jiro Wada
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA.
| | - Peter B Jahrling
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA.
| | - Dennis A Bente
- Galveston National Laboratory, Institute for Human Infection and Immunity, Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Gustavo Palacios
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA.
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18
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Blackley DJ, Wiley MR, Ladner JT, Fallah M, Lo T, Gilbert ML, Gregory C, D’ambrozio J, Coulter S, Mate S, Balogun Z, Kugelman J, Nwachukwu W, Prieto K, Yeiah A, Amegashie F, Kearney B, Wisniewski M, Saindon J, Schroth G, Fakoli L, Diclaro JW, Kuhn JH, Hensley LE, Jahrling PB, Ströher U, Nichol ST, Massaquoi M, Kateh F, Clement P, Gasasira A, Bolay F, Monroe SS, Rambaut A, Sanchez-Lockhart M, Scott Laney A, Nyenswah T, Christie A, Palacios G. Reduced evolutionary rate in reemerged Ebola virus transmission chains. Sci Adv 2016; 2:e1600378. [PMID: 27386513 PMCID: PMC4928956 DOI: 10.1126/sciadv.1600378] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [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] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 04/11/2016] [Indexed: 06/06/2023]
Abstract
On 29 June 2015, Liberia's respite from Ebola virus disease (EVD) was interrupted for the second time by a renewed outbreak ("flare-up") of seven confirmed cases. We demonstrate that, similar to the March 2015 flare-up associated with sexual transmission, this new flare-up was a reemergence of a Liberian transmission chain originating from a persistently infected source rather than a reintroduction from a reservoir or a neighboring country with active transmission. Although distinct, Ebola virus (EBOV) genomes from both flare-ups exhibit significantly low genetic divergence, indicating a reduced rate of EBOV evolution during persistent infection. Using this rate of change as a signature, we identified two additional EVD clusters that possibly arose from persistently infected sources. These findings highlight the risk of EVD flare-ups even after an outbreak is declared over.
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Affiliation(s)
| | - Michael R. Wiley
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
| | - Jason T. Ladner
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
| | | | - Terrence Lo
- Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Merle L. Gilbert
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
| | | | - Jonathan D’ambrozio
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
| | - Stewart Coulter
- Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Suzanne Mate
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
| | | | - Jeffrey Kugelman
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
| | | | - Karla Prieto
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
| | | | | | - Brian Kearney
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
| | - Meagan Wisniewski
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
| | - John Saindon
- Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | | | - Lawrence Fakoli
- Liberian Institute for Biomedical Research, Charlesville, Liberia
| | | | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - Lisa E. Hensley
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - Peter B. Jahrling
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - Ute Ströher
- Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Stuart T. Nichol
- Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | | | | | - Peter Clement
- World Health Organization, CH-1211 Geneva 27, Switzerland
| | - Alex Gasasira
- World Health Organization, CH-1211 Geneva 27, Switzerland
| | - Fatorma Bolay
- Liberian Institute for Biomedical Research, Charlesville, Liberia
| | | | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA
- Centre for Immunology, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Mariano Sanchez-Lockhart
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
| | - A. Scott Laney
- Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | | | - Athalia Christie
- Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Gustavo Palacios
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
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19
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Kugelman JR, Rossi CA, Wiley MR, Ladner JT, Nagle ER, Pfeffer BP, Garcia K, Prieto K, Wada J, Kuhn JH, Palacios G. Informing the Historical Record of Experimental Nonhuman Primate Infections with Ebola Virus: Genomic Characterization of USAMRIID Ebola Virus/H.sapiens-tc/COD/1995/Kikwit-9510621 Challenge Stock "R4368" and Its Replacement "R4415". PLoS One 2016; 11:e0150919. [PMID: 27002733 PMCID: PMC4803331 DOI: 10.1371/journal.pone.0150919] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/14/2016] [Indexed: 11/19/2022] Open
Abstract
The creation of licensed medical countermeasures against Select Agents such as Ebola virus (EBOV) is critically dependent on the use of standardized reagents, assays, and animal models. We performed full genome reconstruction, population genomics, contaminant analysis, and characterization of the glycoprotein gene editing site of historical United States Army Medical Research Institute of Infectious Diseases (USAMRIID) nonhuman-primate challenge stock Ebola virus Kikwit “R4368” and its 2014 replacement “R4415.” We also provide characterization of the master stock used to create “R4415.” The obtained data are essential to understanding the quality of the seed stock reagents used in pivotal animal studies that have been used to inform medical countermeasure development. Furthermore, these data might add to the understanding of the influence of EBOV variant populations on pathogenesis and disease outcome and inform attempts to avoid the evolution of EBOV escape mutants in response to current therapeutics. Finally, as the primary challenge stocks have changed over time, these data will provide a baseline for understanding and correlating past and future animal study results.
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Affiliation(s)
- Jeffrey R. Kugelman
- United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, Maryland, United States of America
| | - Cynthia A. Rossi
- United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, Maryland, United States of America
| | - Michael R. Wiley
- United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, Maryland, United States of America
| | - Jason T. Ladner
- United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, Maryland, United States of America
| | - Elyse R. Nagle
- United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, Maryland, United States of America
| | - Bradley P. Pfeffer
- United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, Maryland, United States of America
| | - Karla Garcia
- United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, Maryland, United States of America
| | - Karla Prieto
- United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, Maryland, United States of America
| | - Jiro Wada
- Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, United States of America
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, United States of America
| | - Gustavo Palacios
- United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, Maryland, United States of America
- * E-mail:
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20
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Mate SE, Kugelman JR, Nyenswah TG, Ladner JT, Wiley MR, Cordier-Lassalle T, Christie A, Schroth GP, Gross SM, Davies-Wayne GJ, Shinde SA, Murugan R, Sieh SB, Badio M, Fakoli L, Taweh F, de Wit E, van Doremalen N, Munster VJ, Pettitt J, Prieto K, Humrighouse BW, Ströher U, DiClaro JW, Hensley LE, Schoepp RJ, Safronetz D, Fair J, Kuhn JH, Blackley DJ, Laney AS, Williams DE, Lo T, Gasasira A, Nichol ST, Formenty P, Kateh FN, De Cock KM, Bolay F, Sanchez-Lockhart M, Palacios G. Molecular Evidence of Sexual Transmission of Ebola Virus. N Engl J Med 2015; 373:2448-54. [PMID: 26465384 PMCID: PMC4711355 DOI: 10.1056/nejmoa1509773] [Citation(s) in RCA: 304] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A suspected case of sexual transmission from a male survivor of Ebola virus disease (EVD) to his female partner (the patient in this report) occurred in Liberia in March 2015. Ebola virus (EBOV) genomes assembled from blood samples from the patient and a semen sample from the survivor were consistent with direct transmission. The genomes shared three substitutions that were absent from all other Western African EBOV sequences and that were distinct from the last documented transmission chain in Liberia before this case. Combined with epidemiologic data, the genomic analysis provides evidence of sexual transmission of EBOV and evidence of the persistence of infective EBOV in semen for 179 days or more after the onset of EVD. (Funded by the Defense Threat Reduction Agency and others.).
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Affiliation(s)
- Suzanne E Mate
- From the Center for Genome Sciences (S.E.M., J.R.K., J.T.L., M.R.W., K.P., M.S.-L., G.P.) and Diagnostic Systems Division (R.J.S.), U.S. Army Medical Research Institute of Infectious Diseases, and the Division of Clinical Research, Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH) (J.P., L.E.H., J.H.K.) - all in Frederick, MD; the Ministry of Health and Social Welfare (T.G.N., S.B.S., M.B., F.N.K.) and the World Health Organization (WHO) (G.J.D.-W., R.M.), Monrovia, and the Liberian Institute for Biomedical Research, Charlesville (L.F., F.T., F.B.) - all in Liberia; WHO, Geneva (T.C.-L., A.G., P.F.); the Centers for Disease Control and Prevention, Atlanta (A.C., B.W.H., U.S., D.J.B., A.S.L., D.E.W., T.L., S.T.N., K.M.D.C.); Illumina, San Diego, CA (G.P.S., S.M.G.); WHO, New Delhi, India (S.A.S); Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT (E.W., N.D., V.J.M., D.S.); Naval Medical Research Unit 3, Cairo (J.W.D.); and the Foundation Mérieux, Washington, DC (J.F.)
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21
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Leguia M, Loyola S, Rios J, Juarez D, Guevara C, Silva M, Prieto K, Wiley M, Kasper MR, Palacios G, Bausch DG. Full Genomic Characterization of a Saffold Virus Isolated in Peru. Pathogens 2015; 4:816-25. [PMID: 26610576 PMCID: PMC4693166 DOI: 10.3390/pathogens4040816] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 11/17/2015] [Indexed: 11/16/2022] Open
Abstract
While studying respiratory infections of unknown etiology we detected Saffold virus in an oropharyngeal swab collected from a two-year-old female suffering from diarrhea and respiratory illness. The full viral genome recovered by deep sequencing showed 98% identity to a previously described Saffold strain isolated in Japan. Phylogenetic analysis confirmed the Peruvian Saffold strain belongs to genotype 3 and is most closely related to strains that have circulated in Asia. This is the first documented case report of Saffold virus in Peru and the only complete genomic characterization of a Saffold-3 isolate from the Americas.
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Affiliation(s)
- Mariana Leguia
- Naval Medical Research Unit No. 6 (NAMRU-6), Callao 2, Peru.
| | - Steev Loyola
- Naval Medical Research Unit No. 6 (NAMRU-6), Callao 2, Peru.
| | - Jane Rios
- Naval Medical Research Unit No. 6 (NAMRU-6), Callao 2, Peru.
| | - Diana Juarez
- Naval Medical Research Unit No. 6 (NAMRU-6), Callao 2, Peru.
| | | | - Maria Silva
- Naval Medical Research Unit No. 6 (NAMRU-6), Callao 2, Peru.
| | - Karla Prieto
- Center for Genome Sciences, United States Army Medical Research Institute for Infectious Diseases (USAMRIID), Frederick, MD 21702, USA.
| | - Michael Wiley
- Center for Genome Sciences, United States Army Medical Research Institute for Infectious Diseases (USAMRIID), Frederick, MD 21702, USA.
| | | | - Gustavo Palacios
- Center for Genome Sciences, United States Army Medical Research Institute for Infectious Diseases (USAMRIID), Frederick, MD 21702, USA.
| | - Daniel G Bausch
- Naval Medical Research Unit No. 6 (NAMRU-6), Callao 2, Peru.
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22
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Kugelman JR, Wiley MR, Mate S, Ladner JT, Beitzel B, Fakoli L, Taweh F, Prieto K, Diclaro JW, Minogue T, Schoepp RJ, Schaecher KE, Pettitt J, Bateman S, Fair J, Kuhn JH, Hensley L, Park DJ, Sabeti PC, Sanchez-Lockhart M, Bolay FK, Palacios G. Monitoring of Ebola Virus Makona Evolution through Establishment of Advanced Genomic Capability in Liberia. Emerg Infect Dis 2015; 21:1135-43. [PMID: 26079255 PMCID: PMC4816332 DOI: 10.3201/eid2107.150522] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
To support Liberia's response to the ongoing Ebola virus (EBOV) disease epidemic in Western Africa, we established in-country advanced genomic capabilities to monitor EBOV evolution. Twenty-five EBOV genomes were sequenced at the Liberian Institute for Biomedical Research, which provided an in-depth view of EBOV diversity in Liberia during September 2014-February 2015. These sequences were consistent with a single virus introduction to Liberia; however, shared ancestry with isolates from Mali indicated at least 1 additional instance of movement into or out of Liberia. The pace of change is generally consistent with previous estimates of mutation rate. We observed 23 nonsynonymous mutations and 1 nonsense mutation. Six of these changes are within known binding sites for sequence-based EBOV medical countermeasures; however, the diagnostic and therapeutic impact of EBOV evolution within Liberia appears to be low.
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